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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, f'Problem retrieving user with email {common.test_user_1_email} from the database'
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, f'Problem retrieving user with email {common.admin_email} from the database'
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(f'Metadata changed after reset for repository {repository.name}.')