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Source code for tool_shed.test.functional.test_0050_circular_dependencies_4_levels
from ..base.twilltestcase import common, ShedTwillTestCase
emboss_datatypes_repository_name = 'emboss_datatypes_0050'
emboss_datatypes_repository_description = "Datatypes for emboss"
emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
emboss_repository_name = 'emboss_0050'
emboss_repository_description = "Galaxy's emboss tool"
emboss_repository_long_description = "Long description of Galaxy's emboss tool"
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_name = 'Test 0050 Circular Dependencies 5 Levels'
category_description = 'Test circular dependency features'
[docs]class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
'''Verify that the code correctly handles circular dependencies down to n levels.'''
[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_convert_repository(self):
'''Create and populate convert_chars_0050.'''
category = self.create_category(name=category_name, description=category_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_0010_create_column_repository(self):
'''Create and populate convert_chars_0050.'''
category = self.create_category(name=category_name, description=category_description)
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_0015_create_emboss_datatypes_repository(self):
'''Create and populate emboss_datatypes_0050.'''
category = self.create_category(name=category_name, description=category_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=emboss_datatypes_repository_description,
long_description=emboss_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_0020_create_emboss_repository(self):
'''Create and populate emboss_0050.'''
category = self.create_category(name=category_name, description=category_description)
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_0025_create_filtering_repository(self):
'''Create and populate filtering_0050.'''
category = self.create_category(name=category_name, description=category_description)
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_0030_create_freebayes_repository(self):
'''Create and populate freebayes_0050.'''
category = self.create_category(name=category_name, description=category_description)
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_0035_create_bismark_repository(self):
'''Create and populate bismark_0050.'''
category = self.create_category(name=category_name, description=category_description)
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_0040_create_and_upload_dependency_definitions(self):
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_0045_verify_repository_dependencies(self):
'''Verify that the generated dependency circle does not cause an infinite loop.
Expected structure:
id: 2 key: http://toolshed.local:10001__ESEP__filtering__ESEP__test__ESEP__871602b4276b
['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04']
id: 3 key: http://toolshed.local:10001__ESEP__emboss_datatypes__ESEP__test__ESEP__dbd4f68bf507
['http://toolshed.local:10001', 'freebayes', 'test', 'f40028114098']
id: 4 key: http://toolshed.local:10001__ESEP__freebayes__ESEP__test__ESEP__f40028114098
['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507']
['http://toolshed.local:10001', 'emboss_5', 'test', '8de5fe0d7b04']
['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0']
id: 5 key: http://toolshed.local:10001__ESEP__column_maker__ESEP__test__ESEP__83e956bdbac0
['http://toolshed.local:10001', 'convert_chars', 'test', 'b28134220c8a']
id: 6 key: http://toolshed.local:10001__ESEP__convert_chars__ESEP__test__ESEP__b28134220c8a
['http://toolshed.local:10001', 'column_maker', 'test', '83e956bdbac0']
id: 7 key: http://toolshed.local:10001__ESEP__emboss_5__ESEP__test__ESEP__8de5fe0d7b04
['http://toolshed.local:10001', 'emboss_datatypes', 'test', 'dbd4f68bf507']
'''
emboss_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)
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)
bismark_repository = self.test_db_util.get_repository_by_name_and_owner(bismark_repository_name, common.test_user_1_name)
self.check_repository_dependency(convert_repository, column_repository)
self.check_repository_dependency(column_repository, convert_repository)
self.check_repository_dependency(emboss_datatypes_repository, bismark_repository)
self.check_repository_dependency(emboss_repository, emboss_datatypes_repository)
self.check_repository_dependency(filtering_repository, emboss_repository)
for repository in [emboss_datatypes_repository, emboss_repository, column_repository]:
self.check_repository_dependency(freebayes_repository, repository)
strings_displayed = ['freebayes_0050 depends on freebayes_0050, emboss_datatypes_0050, emboss_0050, column_maker_0050.']
self.display_manage_repository_page(freebayes_repository,
strings_displayed=strings_displayed)
[docs] def test_0050_verify_tool_dependencies(self):
'''Check that freebayes and emboss display tool dependencies.'''
freebayes_repository = self.test_db_util.get_repository_by_name_and_owner(freebayes_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)
self.display_manage_repository_page(freebayes_repository,
strings_displayed=['freebayes', '0.9.4_9696d0ce8a9', 'samtools', '0.1.18', 'Tool dependencies', 'package'])
self.display_manage_repository_page(emboss_repository, strings_displayed=['Tool dependencies', 'emboss', '5.0.0', 'package'])
[docs] def test_0055_verify_repository_metadata(self):
'''Verify that resetting the metadata does not change it.'''
emboss_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)
for repository in [emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository]:
self.verify_unchanged_repository_metadata(repository)