Warning
This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for tool_shed.test.functional.test_0300_reset_all_metadata
import os
from ..base.twilltestcase import common, ShedTwillTestCase
datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This repository contains no tools."
emboss_repository_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
emboss_repository_long_description = 'Galaxy wrappers for Emboss version 5.0.0 tools'
workflow_filename = 'Workflow_for_0060_filter_workflow_repository.ga'
workflow_name = 'Workflow for 0060_filter_workflow_repository'
emboss_datatypes_repository_name = 'emboss_datatypes_0050'
emboss_datatypes_repository_description = "Datatypes for emboss"
emboss_repository_name = 'emboss_0050'
emboss_5_repository_name = 'emboss_5_0050'
emboss_6_repository_name = 'emboss_6_0050'
filtering_repository_name = 'filtering_0050'
filtering_repository_description = "Galaxy's filtering tool"
filtering_repository_long_description = "Long description of Galaxy's filtering tool"
freebayes_repository_name = 'freebayes_0050'
freebayes_repository_description = "Galaxy's freebayes tool"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
column_repository_name = 'column_maker_0050'
column_repository_description = "Add column"
column_repository_long_description = "Compute an expression on every row"
convert_repository_name = 'convert_chars_0050'
convert_repository_description = "Convert delimiters"
convert_repository_long_description = "Convert delimiters to tab"
bismark_repository_name = 'bismark_0050'
bismark_repository_description = "A flexible aligner."
bismark_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."
category_0050_name = 'Test 0050 Circular Dependencies 5 Levels'
category_0050_description = 'Test circular dependency features'
running_standalone = False
[docs]class TestResetAllRepositoryMetadata(ShedTwillTestCase):
'''Verify that the "Reset selected metadata" feature works.'''
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
assert test_user_1 is not None, 'Problem retrieving user with email %s from the database' % common.test_user_1_email
self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
admin_user = self.test_db_util.get_user(common.admin_email)
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % common.admin_email
self.test_db_util.get_private_role(admin_user)
[docs] def test_0005_create_filtering_repository(self):
'''Create and populate the filtering_0000 repository.'''
global running_standalone
self.login(email=common.admin_email, username=common.admin_username)
category_0000 = self.create_category(name='Test 0000 Basic Repository Features 1', description='Test 0000 Basic Repository Features 1')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='filtering_0000',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id))
if self.repository_is_new(repository):
running_standalone = True
self.upload_file(repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0010_create_freebayes_repository(self):
'''Create and populate the freebayes_0010 repository.'''
global running_standalone
self.login(email=common.admin_email, username=common.admin_username)
category_0010 = self.create_category(name='Test 0010 Repository With Tool Dependencies', description='Tests for a repository with tool dependencies.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='freebayes_0010',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
strings_displayed=[])
if running_standalone:
self.upload_file(repository,
filename='freebayes/freebayes.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes.xml.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(repository,
filename='freebayes/tool_data_table_conf.xml.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_data_table_conf.xml.sample',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(repository,
filename='freebayes/sam_fa_indices.loc.sample',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded sam_fa_indices.loc.sample',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(repository,
filename='freebayes/tool_dependencies.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded tool_dependencies.xml',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0015_create_datatypes_0020_repository(self):
'''Create and populate the emboss_datatypes_0020 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0020 = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='emboss_datatypes_0020',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
strings_displayed=[])
self.upload_file(repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0020_create_emboss_0020_repository(self):
'''Create and populate the emboss_0020 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0020 = self.create_category(name='Test 0020 Basic Repository Dependencies', description='Testing basic repository dependency features.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='emboss_0020',
description=emboss_repository_long_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
strings_displayed=[])
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0025_create_emboss_datatypes_0030_repository(self):
'''Create and populate the emboss_0030 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
datatypes_repository = self.get_or_create_repository(name='emboss_datatypes_0030',
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(datatypes_repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0030_create_emboss_5_repository(self):
'''Create and populate the emboss_5_0030 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
emboss_5_repository = self.get_or_create_repository(name='emboss_5_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_5_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0035_create_emboss_6_repository(self):
'''Create and populate the emboss_6_0030 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
emboss_6_repository = self.get_or_create_repository(name='emboss_6_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_6_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0040_create_emboss_0030_repository(self):
'''Create and populate the emboss_0030 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0030 = self.create_category(name='Test 0030 Repository Dependency Revisions', description='Testing repository dependencies by revision.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
emboss_repository = self.get_or_create_repository(name='emboss_0030',
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
strings_displayed=[])
self.upload_file(emboss_repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss.tar',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0045_create_repository_dependencies_for_0030(self):
'''Create the dependency structure for test 0030.'''
global running_standalone
if running_standalone:
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_datatypes_0030', common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_0030', common.test_user_1_name)
emboss_5_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_5_0030', common.test_user_1_name)
emboss_6_repository = self.test_db_util.get_repository_by_name_and_owner('emboss_6_0030', common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0330', additional_paths=['emboss'])
datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
emboss_5_tuple = (self.url, emboss_5_repository.name, emboss_5_repository.user.username, self.get_repository_tip(emboss_5_repository))
emboss_6_tuple = (self.url, emboss_6_repository.name, emboss_6_repository.user.username, self.get_repository_tip(emboss_6_repository))
self.create_repository_dependency(repository=emboss_5_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
self.create_repository_dependency(repository=emboss_6_repository, repository_tuples=[datatypes_tuple], filepath=repository_dependencies_path)
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_5_tuple], filepath=repository_dependencies_path)
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[emboss_6_tuple], filepath=repository_dependencies_path)
[docs] def test_0050_create_freebayes_repository(self):
'''Create and populate the freebayes_0040 repository.'''
global running_standalone
self.login(email=common.admin_email, username=common.admin_username)
category_0040 = self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='freebayes_0040',
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
if running_standalone:
self.upload_file(repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0055_create_filtering_repository(self):
'''Create and populate the filtering_0040 repository.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category_0040 = self.create_category(name='test_0040_repository_circular_dependencies', description='Testing handling of circular repository dependencies.')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name='filtering_0040',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
strings_displayed=[])
self.upload_file(repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0060_create_dependency_structure(self):
'''Create the dependency structure for test 0040.'''
global running_standalone
if running_standalone:
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner('freebayes_0040', common.test_user_1_name)
filtering_repository = self.test_db_util.get_repository_by_name_and_owner('filtering_0040', common.test_user_1_name)
repository_dependencies_path = self.generate_temp_path('test_0340', additional_paths=['dependencies'])
freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
filtering_tuple = (self.url, filtering_repository.name, filtering_repository.user.username, self.get_repository_tip(filtering_repository))
self.create_repository_dependency(repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=repository_dependencies_path)
self.create_repository_dependency(repository=freebayes_repository, repository_tuples=[filtering_tuple], filepath=repository_dependencies_path)
[docs] def test_0065_create_convert_repository(self):
'''Create and populate convert_chars_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=convert_repository_name,
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='convert_chars/convert_chars.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded convert_chars tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0070_create_column_repository(self):
'''Create and populate convert_chars_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=column_repository_name,
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='column_maker/column_maker.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded column_maker tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0075_create_emboss_datatypes_repository(self):
'''Create and populate emboss_datatypes_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=emboss_datatypes_repository_name,
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='emboss/datatypes/datatypes_conf.xml',
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded datatypes_conf.xml.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0080_create_emboss_repository(self):
'''Create and populate emboss_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='emboss/emboss.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded emboss tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0085_create_filtering_repository(self):
'''Create and populate filtering_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
filtering_repository = self.get_or_create_repository(name=filtering_repository_name,
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(filtering_repository,
filename='filtering/filtering_1.1.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 1.1.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0090_create_freebayes_repository(self):
'''Create and populate freebayes_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=freebayes_repository_name,
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='freebayes/freebayes.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded freebayes tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0095_create_bismark_repository(self):
'''Create and populate bismark_0050.'''
global running_standalone
if running_standalone:
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_0050_name, description=category_0050_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
repository = self.get_or_create_repository(name=bismark_repository_name,
description=bismark_repository_description,
long_description=bismark_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[])
self.upload_file(repository,
filename='bismark/bismark.tar',
filepath=None,
valid_tools_only=False,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded bismark tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0100_create_and_upload_dependency_definitions(self):
'''Create the dependency structure for test 0050.'''
global running_standalone
if running_standalone:
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
column_repository = self.test_db_util.get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
convert_repository = self.test_db_util.get_repository_by_name_and_owner(convert_repository_name, common.test_user_1_name)
datatypes_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_datatypes_repository_name, common.test_user_1_name)
emboss_repository = self.test_db_util.get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
filtering_repository = self.test_db_util.get_repository_by_name_and_owner(filtering_repository_name, common.test_user_1_name)
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_repository_name, common.test_user_1_name)
bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
dependency_xml_path = self.generate_temp_path('test_0050', additional_paths=['freebayes'])
# convert_chars depends on column_maker
# column_maker depends on convert_chars
# emboss depends on emboss_datatypes
# emboss_datatypes depends on bismark
# freebayes depends on freebayes, emboss, emboss_datatypes, and column_maker
# filtering depends on emboss
column_tuple = (self.url, column_repository.name, column_repository.user.username, self.get_repository_tip(column_repository))
convert_tuple = (self.url, convert_repository.name, convert_repository.user.username, self.get_repository_tip(convert_repository))
freebayes_tuple = (self.url, freebayes_repository.name, freebayes_repository.user.username, self.get_repository_tip(freebayes_repository))
emboss_tuple = (self.url, emboss_repository.name, emboss_repository.user.username, self.get_repository_tip(emboss_repository))
datatypes_tuple = (self.url, datatypes_repository.name, datatypes_repository.user.username, self.get_repository_tip(datatypes_repository))
bismark_tuple = (self.url, bismark_repository.name, bismark_repository.user.username, self.get_repository_tip(bismark_repository))
self.create_repository_dependency(repository=convert_repository, repository_tuples=[column_tuple], filepath=dependency_xml_path)
self.create_repository_dependency(repository=column_repository, repository_tuples=[convert_tuple], filepath=dependency_xml_path)
self.create_repository_dependency(repository=datatypes_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path)
self.create_repository_dependency(repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path)
self.create_repository_dependency(repository=freebayes_repository,
repository_tuples=[freebayes_tuple, datatypes_tuple, emboss_tuple, column_tuple],
filepath=dependency_xml_path)
self.create_repository_dependency(repository=filtering_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path)
[docs] def test_0105_create_filtering_repository(self):
'''Create and populate the filtering_0060 repository.'''
self.login(email=common.admin_email, username=common.admin_username)
category_0060 = self.create_category(name='Test 0060 Workflow Features', description='Test 0060 - Workflow Features')
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
workflow_repository = self.get_or_create_repository(name='filtering_0060',
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0060.id),
strings_displayed=[])
if self.repository_is_new(workflow_repository):
workflow = open(self.get_filename('filtering_workflow/Workflow_for_0060_filter_workflow_repository.ga')).read()
workflow = workflow.replace('__TEST_TOOL_SHED_URL__', self.url.replace('http://', ''))
workflow_filepath = self.generate_temp_path('test_0360', additional_paths=['filtering_workflow'])
if not os.path.exists(workflow_filepath):
os.makedirs(workflow_filepath)
open(os.path.join(workflow_filepath, workflow_filename), 'w+').write(workflow)
self.upload_file(workflow_repository,
filename=workflow_filename,
filepath=workflow_filepath,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering workflow.',
strings_displayed=[],
strings_not_displayed=[])
self.upload_file(workflow_repository,
filename='filtering/filtering_2.2.0.tar',
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message='Uploaded filtering 2.2.0 tarball.',
strings_displayed=[],
strings_not_displayed=[])
[docs] def test_0110_reset_metadata_on_all_repositories(self):
'''Reset metadata on all repositories, then verify that it has not changed.'''
self.login(email=common.admin_email, username=common.admin_username)
old_metadata = dict()
new_metadata = dict()
repositories = self.test_db_util.get_all_repositories()
for repository in repositories:
old_metadata[self.security.encode_id(repository.id)] = dict()
for metadata in self.get_repository_metadata(repository):
old_metadata[self.security.encode_id(repository.id)][metadata.changeset_revision] = metadata.metadata
self.reset_metadata_on_selected_repositories(list(old_metadata.keys()))
for repository in repositories:
new_metadata[self.security.encode_id(repository.id)] = dict()
for metadata in self.get_repository_metadata(repository):
new_metadata[self.security.encode_id(repository.id)][metadata.changeset_revision] = metadata.metadata
if old_metadata[self.security.encode_id(repository.id)] != new_metadata[self.security.encode_id(repository.id)]:
raise AssertionError('Metadata changed after reset for repository %s.' % repository.name)