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<|file_name|>setup.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
from distutils.core import setup
setup(name='django-modeltranslation',
version='0.4.0-alpha1',
description='Translates Django models using a registration approach.',
long_description='The modeltranslation application can be used to '
'translate dynamic content of existing models to an '
'arbitrary number of languages without having to '
'change the original model classes. It uses a '
'registration approach (comparable to Django\'s admin '
'app) to be able to add translations to existing or '
'new projects and is fully integrated into the Django '
'admin backend.',
author='Peter Eschler',
author_email='p.eschler@nmy.de',
maintainer='Dirk Eschler',
maintainer_email='d.eschler@nmy.de',<｜fim▁hole｜> packages=['modeltranslation', 'modeltranslation.management',
'modeltranslation.management.commands'],
package_data={'modeltranslation': ['static/modeltranslation/css/*.css',
'static/modeltranslation/js/*.js']},
include_package_data = True,
requires=['django(>=1.0)'],
download_url='http://django-modeltranslation.googlecode.com/files/django-modeltranslation-0.4.0-alpha1.tar.gz',
classifiers=['Framework :: Django',
'Intended Audience :: Developers',
'License :: OSI Approved :: BSD License'],
license='New BSD')<｜fim▁end｜> | url='http://code.google.com/p/django-modeltranslation/', |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
def doReplacements(self, txt):
d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt
def run(self):
query8 = self.getQuery()<｜fim▁hole｜> #pylint:disable=E6601
query8.open() #there will be missing tables here<｜fim▁end｜> | query8.sql = self.doReplacements(query8.sql) |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
<|fim_middle|>
<｜fim▁end｜> | def doReplacements(self, txt):
d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt
def run(self):
query8 = self.getQuery()
query8.sql = self.doReplacements(query8.sql)
#pylint:disable=E6601
query8.open() #there will be missing tables here |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
def doReplacements(self, txt):
<|fim_middle|>
def run(self):
query8 = self.getQuery()
query8.sql = self.doReplacements(query8.sql)
#pylint:disable=E6601
query8.open() #there will be missing tables here
<｜fim▁end｜> | d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
def doReplacements(self, txt):
d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt
def run(self):
<|fim_middle|>
<｜fim▁end｜> | query8 = self.getQuery()
query8.sql = self.doReplacements(query8.sql)
#pylint:disable=E6601
query8.open() #there will be missing tables here |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
def <|fim_middle|>(self, txt):
d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt
def run(self):
query8 = self.getQuery()
query8.sql = self.doReplacements(query8.sql)
#pylint:disable=E6601
query8.open() #there will be missing tables here
<｜fim▁end｜> | doReplacements |
<|file_name|>func_noerror_query_heir.py<|end_file_name|><｜fim▁begin｜># pylint:disable=R0201
from OpenOrange import *
from User import User
from RetroactiveAccounts import RetroactiveAccounts
class HeirFinder(RetroactiveAccounts):
def doReplacements(self, txt):
d = {1:"ONE", 2:"TWO"}
us = User.bring("USER")
txt = txt.replace(":1", us.Name + d[1])
return txt
def <|fim_middle|>(self):
query8 = self.getQuery()
query8.sql = self.doReplacements(query8.sql)
#pylint:disable=E6601
query8.open() #there will be missing tables here
<｜fim▁end｜> | run |
<|file_name|>DataTypeMapIntFloat.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import sys
import hyperdex.client
from hyperdex.client import LessEqual, GreaterEqual, Range, Regex, LengthEquals, LengthLessEqual, LengthGreaterEqual
c = hyperdex.client.Client(sys.argv[1], int(sys.argv[2]))<｜fim▁hole｜>assert c.put('kv', 'k', {}) == True
assert c.get('kv', 'k') == {'v': {}}
assert c.put('kv', 'k', {'v': {1: 3.14, 2: 0.25, 3: 1.0}}) == True
assert c.get('kv', 'k') == {'v': {1: 3.14, 2: 0.25, 3: 1.0}}
assert c.put('kv', 'k', {'v': {}}) == True
assert c.get('kv', 'k') == {'v': {}}<｜fim▁end｜> | def to_objectset(xs):
return set([frozenset(x.items()) for x in xs]) |
<|file_name|>DataTypeMapIntFloat.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import sys
import hyperdex.client
from hyperdex.client import LessEqual, GreaterEqual, Range, Regex, LengthEquals, LengthLessEqual, LengthGreaterEqual
c = hyperdex.client.Client(sys.argv[1], int(sys.argv[2]))
def to_objectset(xs):
<|fim_middle|>
assert c.put('kv', 'k', {}) == True
assert c.get('kv', 'k') == {'v': {}}
assert c.put('kv', 'k', {'v': {1: 3.14, 2: 0.25, 3: 1.0}}) == True
assert c.get('kv', 'k') == {'v': {1: 3.14, 2: 0.25, 3: 1.0}}
assert c.put('kv', 'k', {'v': {}}) == True
assert c.get('kv', 'k') == {'v': {}}
<｜fim▁end｜> | return set([frozenset(x.items()) for x in xs]) |
<|file_name|>DataTypeMapIntFloat.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
import sys
import hyperdex.client
from hyperdex.client import LessEqual, GreaterEqual, Range, Regex, LengthEquals, LengthLessEqual, LengthGreaterEqual
c = hyperdex.client.Client(sys.argv[1], int(sys.argv[2]))
def <|fim_middle|>(xs):
return set([frozenset(x.items()) for x in xs])
assert c.put('kv', 'k', {}) == True
assert c.get('kv', 'k') == {'v': {}}
assert c.put('kv', 'k', {'v': {1: 3.14, 2: 0.25, 3: 1.0}}) == True
assert c.get('kv', 'k') == {'v': {1: 3.14, 2: 0.25, 3: 1.0}}
assert c.put('kv', 'k', {'v': {}}) == True
assert c.get('kv', 'k') == {'v': {}}
<｜fim▁end｜> | to_objectset |
<|file_name|>test_issue_064.py<|end_file_name|><｜fim▁begin｜><｜fim▁hole｜><｜fim▁end｜> | def test_is_generator_alias():
from nose.util import is_generator, isgenerator |
<|file_name|>test_issue_064.py<|end_file_name|><｜fim▁begin｜>def test_is_generator_alias():
<|fim_middle|>
<｜fim▁end｜> | from nose.util import is_generator, isgenerator |
<|file_name|>test_issue_064.py<|end_file_name|><｜fim▁begin｜>def <|fim_middle|>():
from nose.util import is_generator, isgenerator
<｜fim▁end｜> | test_is_generator_alias |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted<｜fim▁hole｜> a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}<｜fim▁end｜> | :status 404: Bot was not found
""" |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
<|fim_middle|>
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | """Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]} |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
<|fim_middle|>
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | """Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize() |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
<|fim_middle|>
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | """Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)} |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
<|fim_middle|>
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | return NotImplemented |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
<|fim_middle|>
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | """Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'} |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
<|fim_middle|>
<｜fim▁end｜> | """Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'} |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
<|fim_middle|>
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | return {'message': 'No such bot'}, 404 |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def <|fim_middle|>():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | get_abusehelper |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def <|fim_middle|>(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | get_got |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def <|fim_middle|>():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | add_bot |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def <|fim_middle|>(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | update_bot |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def <|fim_middle|>(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def delete_abusehelper():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | delete_bot |
<|file_name|>abusehelper.py<|end_file_name|><｜fim▁begin｜>from flask import request, current_app, url_for
from flask_jsonschema import validate
from .. import db
from ..models import AHBot as Bot
from .decorators import json_response
from . import api
@api.route('/abusehelper', methods=['GET'])
@json_response
def get_abusehelper():
"""Return a list of available abusehelper
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"abusehelper": [
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
]
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json array abusehelper: List of available bots
:>jsonobj integer id: Bot ID
:>jsonobj integer name: Bot name
:status 200: Deliverable endpoint found, response may be empty
:status 404: Not found
"""
bots = Bot.query.filter().all()
return {'abusehelper': [a.serialize() for a in bots]}
@api.route('/abusehelper/<int:bot_id>', methods=['GET'])
@json_response
def get_got(bot_id):
"""Get bot from database
**Example request**:
.. sourcecode:: http
GET /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
}
:param bot_id: Bot unique ID
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json integer id: Bot unique ID
:>json integer name: Bot name
:status 200: ASN found
:status 404: Resource not found
"""
a = Bot.query.get_or_404(bot_id)
return a.serialize()
@api.route('/abusehelper', methods=['POST', 'PUT'])
@validate('abusehelper', 'add_bot')
@json_response
def add_bot():
"""Add new bot entry
**Example request**:
.. sourcecode:: http
POST /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
Content-Type: application/json
{
"name": "ShadowServerBot",
"url": "http://sample.com/path.html"
}
**Example response**:
.. sourcecode:: http
HTTP/1.0 201 CREATED
Content-Type: application/json
{
"bot": {
"name": "ShadowServerBot",
"url": "http://sample.com/path.html",
"id": 1
},
'message': "Bot added"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:<json integer name: Bot name
:>jsonobj integer id: Unique ID of new bot
:>jsonobj integer name: bot name
:>json string message: Status message
:status 201: ASN successfully saved
:status 400: Bad request
"""
a = Bot.fromdict(request.json)
db.session.add(a)
db.session.commit()
return {'bot': a.serialize(), 'message': 'Bot added'}, 201, \
{'Location': url_for('api.get_bot', bot_id=a.id)}
@api.route('/abusehelper/<int:bot_id>', methods=['PUT'])
@validate('abusehelper', 'update_bot')
@json_response
def update_bot(bot_id):
return NotImplemented
@api.route('/abusehelper/<int:bot_id>', methods=['DELETE'])
@json_response
def delete_bot(bot_id):
"""Delete bot
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper/1 HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bot deleted"
}
:param bot_id: Bot unique ID.
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.filter_by(id == bot_id).delete()
if not a:
return {'message': 'No such bot'}, 404
db.session.commit()
return {'message': 'Bot deleted'}
@api.route('/abusehelper', methods=['DELETE'])
@json_response
def <|fim_middle|>():
"""Clear abusehelper table
**Example request**:
.. sourcecode:: http
DELETE /api/1.0/abusehelper HTTP/1.1
Host: do.cert.europa.eu
Accept: application/json
**Example response**:
.. sourcecode:: http
HTTP/1.0 200 OK
Content-Type: application/json
{
"message": "Bots deleted"
}
:reqheader Accept: Content type(s) accepted by the client
:resheader Content-Type: this depends on `Accept` header or request
:>json string message: Action status status
:status 200: Bot was deleted
:status 404: Bot was not found
"""
a = Bot.query.all().delete()
db.session.commit()
current_app.log.debug('Deleted {} abusehelper'.format(a))
return {'message': 'Bots deleted'}
<｜fim▁end｜> | delete_abusehelper |
<|file_name|>EasyDialogs_AskYesNoCancel.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# encoding: utf-8
#
# Copyright (c) 2008 Doug Hellmann All rights reserved.
#
"""
"""
__version__ = "$Id$"
#end_pymotw_header
import EasyDialogs
valid_responses = { 1:'yes',
0:'no',
-1:'cancel',
}
response = EasyDialogs.AskYesNoCancel('Select an option')<｜fim▁hole｜><｜fim▁end｜> | print 'You selected:', valid_responses[response] |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))<｜fim▁hole｜>
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()<｜fim▁end｜> | except OSError:
pass
|
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
<|fim_middle|>
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role)) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
<|fim_middle|>
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {} |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
<|fim_middle|>
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | """Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
<|fim_middle|>
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
<|fim_middle|>
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | """Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
<|fim_middle|>
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return [] |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
<|fim_middle|>
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | """Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
<|fim_middle|>
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
<|fim_middle|>
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
<|fim_middle|>
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
<|fim_middle|>
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | create_role(into)
for role in roles:
move(role, target_role=into, copy=copy) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
<|fim_middle|>
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
<|fim_middle|>
if __name__ == '__main__':
main()
<｜fim▁end｜> | roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3]) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
<|fim_middle|>
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | raise Exception('could not create role "{}"'.format(role)) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
<|fim_middle|>
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | return os.path.join(for_destination, 'roles', dep) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
<|fim_middle|>
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | return dep |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
<|fim_middle|>
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | os.chdir(roles_path) |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
<|fim_middle|>
<｜fim▁end｜> | main() |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def <|fim_middle|>(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | create_role |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def <|fim_middle|>(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | get_metadata |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def <|fim_middle|>(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | ensure_meta |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def <|fim_middle|>(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | set_metadata |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def <|fim_middle|>(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | add_dependency |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def <|fim_middle|>(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | sub_roles |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def <|fim_middle|>(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | fix_dependency |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def <|fim_middle|>(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | f |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def <|fim_middle|>(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | fix_dependencies |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def <|fim_middle|>(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | move |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def <|fim_middle|>(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | concat |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def <|fim_middle|>():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def main():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | test |
<|file_name|>concat_roles.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/python
import glob
import os
import shutil
import subprocess
import sys
import yaml
def create_role(role):
ret = subprocess.check_output(
'ansible-galaxy init {}'.format(role).split())
if not ret.strip().endswith('created successfully'):
raise Exception('could not create role "{}"'.format(role))
def get_metadata(role):
try:
main = open(os.path.join(role, 'meta/main.yml'))
return yaml.load(main)
except IOError:
return {}
def ensure_meta(role):
"""Ensure the role has a meta directory"""
try:
os.makedirs(os.path.join(role, 'meta'))
except OSError:
pass
def set_metadata(role, metadata):
ensure_meta(role)
new_main = os.path.join(role, 'meta/main.yml.new')
orig_main = os.path.join(role, 'meta/main.yml')
with open(new_main, 'w') as out:
yaml.dump(metadata, out, default_flow_style=False, explicit_start=True)
os.rename(new_main, orig_main)
def add_dependency(src_role, target_role):
"""Add metadata saying that 'target_role' depends on 'src_role'"""
md = get_metadata(target_role)
deps = md.setdefault('dependencies', [])
deps.append(os.path.join(target_role, 'roles', src_role))
set_metadata(target_role, md)
def sub_roles(role):
try:
return glob.glob(os.path.join(role, 'roles/*'))
except OSError:
return []
def fix_dependency(role, for_destination):
"""Fix the sub-role dependency.
Dependency on a sub-role has to be changed once we move the base
role.
"""
metadata = get_metadata(role)
deps = metadata.setdefault('dependencies', [])
def f(dep):
if dep.startswith(role):
return os.path.join(for_destination, 'roles', dep)
else:
return dep
metadata['dependencies'] = [f(dep) for dep in deps]
set_metadata(role, metadata)
def fix_dependencies(src_role, for_destination):
for role in sub_roles(src_role):
fix_dependencies(role, for_destination)
fix_dependency(src_role, for_destination)
def move(src_role, target_role, copy=False):
op = shutil.copytree if copy else shutil.move
try:
os.makedirs(os.path.join(target_role, 'roles'))
except OSError:
pass
fix_dependencies(src_role, for_destination=target_role)
op(src_role, os.path.join(target_role, 'roles', src_role))
add_dependency(src_role, target_role)
def concat(roles, into, copy=False):
create_role(into)
for role in roles:
move(role, target_role=into, copy=copy)
def test():
roles = ['foo', 'bar', 'spam']
try:
for role in roles:
create_role(role)
move('foo', 'bar')
assert get_metadata('bar')['dependencies'] == ['bar/roles/foo']
move('bar', 'spam')
assert get_metadata('spam')['dependencies'] == ['spam/roles/bar']
assert get_metadata('spam/roles/bar')['dependencies'] == ['spam/roles/bar/roles/foo']
finally:
for role in roles:
shutil.rmtree(role, ignore_errors=True)
def <|fim_middle|>():
roles_path = None
if roles_path is not None:
os.chdir(roles_path)
concat([sys.argv[1], sys.argv[2]], into=sys.argv[3])
if __name__ == '__main__':
main()
<｜fim▁end｜> | main |
<|file_name|>0005_auto_20170521_0103.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('maposmatic', '0004_maprenderingjob_track'),
]
operations = [
migrations.AlterField(<｜fim▁hole｜> ]<｜fim▁end｜> | model_name='maprenderingjob',
name='track',
field=models.FileField(null=True, upload_to=b'upload/tracks/', blank=True),
), |
<|file_name|>0005_auto_20170521_0103.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
<|fim_middle|>
<｜fim▁end｜> | dependencies = [
('maposmatic', '0004_maprenderingjob_track'),
]
operations = [
migrations.AlterField(
model_name='maprenderingjob',
name='track',
field=models.FileField(null=True, upload_to=b'upload/tracks/', blank=True),
),
] |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
<｜fim▁hole｜> ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)<｜fim▁end｜> | for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
|
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
<|fim_middle|>
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
<|fim_middle|>
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output)) |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
<|fim_middle|>
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
<|fim_middle|>
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html' |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
<|fim_middle|>
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | template_name = 'admin/attachment/widgets/preview_image_input_vertical.html' |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
<|fim_middle|>
<｜fim▁end｜> | def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None) |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
<|fim_middle|>
<｜fim▁end｜> | for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None) |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
<|fim_middle|>
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
<|fim_middle|>
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | ext = u"." + filename.rpartition('.')[2] |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
<|fim_middle|>
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
<|fim_middle|>
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | return FILE_INPUT_CONTRADICTION |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
<|fim_middle|>
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | ext = u"." + filename.rpartition('.')[2] |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def <|fim_middle|>(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | render |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def <|fim_middle|>(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | value_from_datadict |
<|file_name|>widgets.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
import re
from django.utils.safestring import mark_safe
from django.contrib.admin.widgets import AdminFileWidget
from django.template.defaultfilters import slugify
from django.utils.encoding import smart_text
from unidecode import unidecode
from django.forms.widgets import FILE_INPUT_CONTRADICTION, CheckboxInput, ClearableFileInput
class ImagePreviewWidget(AdminFileWidget):
template_name = 'admin/attachment/widgets/preview_image_input.html'
def render(self, name, value, attrs=None, renderer=None):
output = []
output.append(super(AdminFileWidget, self).render(name, value, attrs)) # really for AdminFileWidget
instance = getattr(value, 'instance', None)
if instance is not None and value:
output = ['<a target="_blank" href="%s"><img src="%s" alt="%s"/></a>' % \
(instance.image.url, instance.thumb.url, instance.image)] + output
return mark_safe(u''.join(output))
def value_from_datadict(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
upload = super(ImagePreviewWidget, self).value_from_datadict(data, files, name)
if not self.is_required and CheckboxInput().value_from_datadict(
data, files, self.clear_checkbox_name(name)):
if upload:
# If the user contradicts themselves (uploads a new file AND
# checks the "clear" checkbox), we return a unique marker
# object that FileField will turn into a ValidationError.
return FILE_INPUT_CONTRADICTION
# False signals to clear any existing value, as opposed to just None
return False
return upload
class ImagePreviewWidgetHorizontal(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_horizontal.html'
class ImagePreviewWidgetVertical(ImagePreviewWidget):
template_name = 'admin/attachment/widgets/preview_image_input_vertical.html'
class FileWidget(ClearableFileInput):
def <|fim_middle|>(self, data, files, name):
for key, file in files.items():
filename = file._get_name()
ext = u""
if '.' in filename:
ext = u"." + filename.rpartition('.')[2]
filename = filename.rpartition('.')[0]
filename = re.sub(r'[_.,:;@#$%^&?*|()\[\]]', '-', filename)
filename = slugify(unidecode(smart_text(filename))) + ext
files[key]._set_name(filename)
return files.get(name, None)
<｜fim▁end｜> | value_from_datadict |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
<｜fim▁hole｜> fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)<｜fim▁end｜> | return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs, |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
<|fim_middle|>
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
<|fim_middle|>
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.') |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
<|fim_middle|>
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
<|fim_middle|>
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
<|fim_middle|>
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label])) |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
<|fim_middle|>
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | """ Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n') |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
<|fim_middle|>
<｜fim▁end｜> | """ Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order) |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
<|fim_middle|>
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.') |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
<|fim_middle|>
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.') |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
<|fim_middle|>
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.') |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
<|fim_middle|>
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | output_dir += '/' |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def <|fim_middle|>(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | parse_fasta_file |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def <|fim_middle|>(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | verify_equivalency |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def <|fim_middle|>(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | truncate_seqs |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def <|fim_middle|>(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | get_output_filepaths |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def <|fim_middle|>(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | write_trunc_fasta |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def <|fim_middle|>(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def truncate_fasta_qual(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | write_trunc_qual |
<|file_name|>truncate_fasta_qual_files.py<|end_file_name|><｜fim▁begin｜>#!/usr/bin/env python
# File created Sept 29, 2010
from __future__ import division
__author__ = "William Walters"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["William Walters", "Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@colorado.edu"
from os.path import basename
from skbio.parse.sequences import parse_fasta
from qiime.parse import parse_qual_score
def parse_fasta_file(fasta_lines):
""" Parses fasta file, generates dict of label:seq, list of seqs order
fasta_lines: list of lines from fasta file.
"""
fasta_seqs = {}
seq_order = []
for label, seq in parse_fasta(fasta_lines):
fasta_seqs[label.split()[0].strip()] = seq
seq_order.append(label)
return fasta_seqs, seq_order
def verify_equivalency(fasta_seqs,
qual_scores):
""" Tests for equivalent labels, base positions between fasta and qual file
fasta_seqs: dict of label:seq from fasta file
qual_scores: dict of label: qual scores
"""
if len(fasta_seqs) != len(qual_scores):
raise ValueError('Number of sequences not equal in input fasta ' +
'and qual file.')
qual_scores_labels = set(qual_scores.keys())
for label in fasta_seqs.keys():
# Should have equivalent labels
if label not in qual_scores_labels:
raise ValueError('Fasta label %s not found in quality score ' %
label + 'file.')
# should have equivalent lengths
if len(fasta_seqs[label]) != len(qual_scores[label]):
raise ValueError('Sequence %s does not have equivalent ' %
label + 'base positions between fasta and quality score file.')
def truncate_seqs(fasta_seqs,
qual_scores,
base_pos):
""" Truncates sequences to base position specified with base_pos
fasta_seqs: dict of seq label: seq string
qual_scores: dict of seq label: numpy array of int scores
base_pos: index in sequence to truncate at
"""
trunc_fasta_seqs = {}
trunc_qual_scores = {}
for seq in fasta_seqs:
trunc_fasta_seqs[seq] = fasta_seqs[seq][:base_pos]
trunc_qual_scores[seq] = qual_scores[seq][:base_pos]
return trunc_fasta_seqs, trunc_qual_scores
def get_output_filepaths(output_dir,
fasta_fp,
qual_fp):
""" Returns output filepaths for filtered fasta and quality files
output_dir: output directory
fasta_fp: input fasta filepath
qual_fp: input quality scores filepath
"""
if not output_dir.endswith('/'):
output_dir += '/'
fasta_out_fp = output_dir + basename(fasta_fp).split('.')[0] +\
"_filtered.fasta"
qual_out_fp = output_dir + basename(qual_fp).split('.')[0] +\
"_filtered.qual"
return fasta_out_fp, qual_out_fp
def write_trunc_fasta(trunc_fasta_seqs,
fasta_out_fp,
seq_order):
""" Writes truncated fasta seqs in order specified with seq_order
trunc_fasta_seqs: dict of fasta label: truncated sequence string
fasta_out_fp: output filepath to write to
seq_order: list of fasta labels in the order of the original input fasta
"""
fasta_out = open(fasta_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
fasta_out.write(">%s\n%s\n" % (label, trunc_fasta_seqs[trunc_label]))
def write_trunc_qual(trunc_qual_scores,
qual_out_fp,
seq_order):
""" Writes truncated quality score files out in proper format
trunc_qual_scores: dict of seq label: numpy array of scores as ints
qual_out_fp: output filepath to write truncated quality scores to
seq_order: List of full fasta labels to write to output filepath and
maintain the same order as input quality file.
"""
qual_line_size = 60
qual_out = open(qual_out_fp, "w")
for label in seq_order:
trunc_label = label.split()[0].strip()
current_trunc_qual_scores = trunc_qual_scores[trunc_label]
qual_out.write(">%s\n" % label)
current_qual_scores_lines = []
# Quality score format is a string of 60 base calls, followed by a
# newline, until the last N bases are written
for slice in range(0, len(trunc_qual_scores[trunc_label]),
qual_line_size):
# current_segment = map(str,
# current_trunc_qual_scores[slice:slice + qual_line_size])
current_segment = current_trunc_qual_scores[
slice:slice +
qual_line_size]
current_qual_scores_lines.append(" ".join(current_segment))
qual_out.write('\n'.join(current_qual_scores_lines))
qual_out.write('\n')
def <|fim_middle|>(fasta_fp,
qual_fp,
output_dir,
base_pos):
""" Main program function for generating quality score histogram
fasta_fp: fasta filepath
qual_fp: quality score filepath
output_dir: output directory
base_pos: Nucleotide position to truncate the fasta and quality score at.
"""
qual_lines = open(qual_fp, "U")
fasta_lines = open(fasta_fp, "U")
qual_scores = parse_qual_score(qual_lines, value_cast_f=str)
# Get dict of fasta label:seq, and the sequence order (so output can
# be in the same order as the input sequences.
fasta_seqs, seq_order = parse_fasta_file(fasta_lines)
# Make sure the quality scores and fasta sequences have corresponding
# labels and base numbers
verify_equivalency(fasta_seqs, qual_scores)
# Truncate seqs to base_pos index
trunc_fasta_seqs, trunc_qual_scores = truncate_seqs(fasta_seqs,
qual_scores, base_pos)
# Get output filepaths
fasta_out_fp, qual_out_fp = get_output_filepaths(output_dir, fasta_fp,
qual_fp)
# Write truncated sequences out
write_trunc_fasta(trunc_fasta_seqs, fasta_out_fp, seq_order)
write_trunc_qual(trunc_qual_scores, qual_out_fp, seq_order)
<｜fim▁end｜> | truncate_fasta_qual |
<|file_name|>0013_show2.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('setlist', '0012_remove_show_leg'),
]
operations = [
migrations.CreateModel(
name='Show2',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('venue', models.ForeignKey(to='setlist.Venue', to_field='id')),
('tour', models.ForeignKey(to='setlist.Tour', to_field='id')),
('date', models.DateField(db_index=True)),
('setlist', models.TextField(default=b'', blank=True)),
('notes', models.TextField(default=b'', blank=True)),
('source', models.TextField(default=b'', blank=True)),
],
options={<｜fim▁hole｜> bases=(models.Model,),
),
]<｜fim▁end｜> | }, |
<|file_name|>0013_show2.py<|end_file_name|><｜fim▁begin｜># -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
<|fim_middle|>
<｜fim▁end｜> | dependencies = [
('setlist', '0012_remove_show_leg'),
]
operations = [
migrations.CreateModel(
name='Show2',
fields=[
('id', models.AutoField(verbose_name='ID', serialize=False, auto_created=True, primary_key=True)),
('venue', models.ForeignKey(to='setlist.Venue', to_field='id')),
('tour', models.ForeignKey(to='setlist.Tour', to_field='id')),
('date', models.DateField(db_index=True)),
('setlist', models.TextField(default=b'', blank=True)),
('notes', models.TextField(default=b'', blank=True)),
('source', models.TextField(default=b'', blank=True)),
],
options={
},
bases=(models.Model,),
),
] |
<|file_name|>test_attachment.py<|end_file_name|><｜fim▁begin｜>from O365 import attachment
import unittest
import json
import base64
from random import randint
att_rep = open('attachment.json','r').read()
att_j = json.loads(att_rep)
class TestAttachment (unittest.TestCase):
def setUp(self):
self.att = attachment.Attachment(att_j['value'][0])<｜fim▁hole｜> self.assertTrue(self.att.isType('txt'))
def test_getType(self):
self.assertEqual(self.att.getType(),'.txt')
def test_save(self):
name = self.att.json['Name']
name1 = self.newFileName(name)
self.att.json['Name'] = name1
self.assertTrue(self.att.save('/tmp'))
with open('/tmp/'+name1,'r') as ins:
f = ins.read()
self.assertEqual('testing w00t!',f)
name2 = self.newFileName(name)
self.att.json['Name'] = name2
self.assertTrue(self.att.save('/tmp/'))
with open('/tmp/'+name2,'r') as ins:
f = ins.read()
self.assertEqual('testing w00t!',f)
def newFileName(self,val):
for i in range(4):
val = str(randint(0,9)) + val
return val
def test_getByteString(self):
self.assertEqual(self.att.getByteString(),b'testing w00t!')
def test_getBase64(self):
self.assertEqual(self.att.getBase64(),'dGVzdGluZyB3MDB0IQ==\n')
def test_setByteString(self):
test_string = b'testing testie test'
self.att.setByteString(test_string)
enc = base64.encodebytes(test_string)
self.assertEqual(self.att.json['ContentBytes'],enc)
def setBase64(self):
wrong_test_string = 'I am sooooo not base64 encoded.'
right_test_string = 'Base64 <3 all around!'
enc = base64.encodestring(right_test_string)
self.assertRaises(self.att.setBase64(wrong_test_string))
self.assertEqual(self.att.json['ContentBytes'],'dGVzdGluZyB3MDB0IQ==\n')
self.att.setBase64(enc)
self.assertEqual(self.att.json['ContentBytes'],enc)
if __name__ == '__main__':
unittest.main()<｜fim▁end｜> |
def test_isType(self): |