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Source code for tool_shed.test.functional.test_0090_tool_search
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
emboss_datatypes_repository_name = "emboss_datatypes_0090"
emboss_datatypes_repository_description = "Datatypes for emboss"
emboss_datatypes_repository_long_description = "Long description of Emboss' datatypes"
emboss_repository_name = "emboss_0090"
emboss_repository_description = "Galaxy's emboss tool"
emboss_repository_long_description = "Long description of Galaxy's emboss tool"
filtering_repository_name = "filtering_0090"
filtering_repository_description = "Galaxy's filtering tool"
filtering_repository_long_description = "Long description of Galaxy's filtering tool"
freebayes_repository_name = "freebayes_0090"
freebayes_repository_description = "Galaxy's freebayes tool"
freebayes_repository_long_description = "Long description of Galaxy's freebayes tool"
bwa_base_repository_name = "bwa_base_0090"
bwa_base_repository_description = "BWA Base"
bwa_base_repository_long_description = "NT space mapping with BWA"
bwa_color_repository_name = "bwa_color_0090"
bwa_color_repository_description = "BWA Color"
bwa_color_repository_long_description = "Color space mapping with BWA"
category_name = "Test 0090 Tool Search And Installation"
category_description = "Test 0090 Tool Search And Installation"
[docs]class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
"""Test more features related to repository dependencies."""
[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_bwa_base_repository(self):
"""Create and populate bwa_base_0090."""
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=bwa_base_repository_name,
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
self.upload_file(
repository,
filename="bwa/bwa_base.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded BWA tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0010_create_bwa_color_repository(self):
"""Create and populate bwa_color_0090."""
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=bwa_color_repository_name,
description=bwa_color_repository_description,
long_description=bwa_color_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
strings_displayed=[],
)
self.upload_file(
repository,
filename="bwa/bwa_color.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=True,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded BWA color tarball.",
strings_displayed=[],
strings_not_displayed=[],
)
[docs] def test_0015_create_emboss_datatypes_repository(self):
"""Create and populate emboss_datatypes_0090."""
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_0090."""
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=False,
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_0090."""
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_0090."""
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_and_upload_dependency_definitions(self):
"""Create and upload repository dependency definitions."""
bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_color_repository_name, common.test_user_1_name
)
bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_base_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
)
dependency_xml_path = self.generate_temp_path("test_0090", additional_paths=["freebayes"])
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),
)
filtering_tuple = (
self.url,
filtering_repository.name,
filtering_repository.user.username,
self.get_repository_tip(filtering_repository),
)
self.create_repository_dependency(
repository=emboss_repository, repository_tuples=[datatypes_tuple], filepath=dependency_xml_path
)
self.create_repository_dependency(
repository=filtering_repository, repository_tuples=[freebayes_tuple], filepath=dependency_xml_path
)
self.create_repository_dependency(
repository=bwa_base_repository, repository_tuples=[emboss_tuple], filepath=dependency_xml_path
)
self.create_repository_dependency(
repository=bwa_color_repository, repository_tuples=[filtering_tuple], filepath=dependency_xml_path
)
[docs] def test_0040_verify_repository_dependencies(self):
"""Verify the generated dependency structure."""
bwa_color_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_color_repository_name, common.test_user_1_name
)
bwa_base_repository = self.test_db_util.get_repository_by_name_and_owner(
bwa_base_repository_name, common.test_user_1_name
)
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
)
self.check_repository_dependency(emboss_repository, emboss_datatypes_repository)
self.check_repository_dependency(filtering_repository, freebayes_repository)
self.check_repository_dependency(bwa_base_repository, emboss_repository)
self.check_repository_dependency(bwa_color_repository, filtering_repository)