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Source code for tool_shed.test.functional.test_0300_reset_all_metadata
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
column_maker_repository_long_description = "A flexible aligner and methylation caller for Bisulfite-Seq applications."
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"
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)
self.login(email=common.admin_email, username=common.admin_username)
[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=category_0000,
)
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=category_0010,
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 column_maker_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="column_maker_0020",
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category=category_0020,
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_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=category_0020,
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)
column_maker_repository = self.get_or_create_repository(
name="column_maker_0030",
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category=category_0030,
strings_displayed=[],
)
self.upload_file(
column_maker_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_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=category_0030,
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=category_0030,
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=category_0030,
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:
column_maker_repository = self._get_repository_by_name_and_owner(
"column_maker_0030", common.test_user_1_name
)
emboss_repository = self._get_repository_by_name_and_owner("emboss_0030", common.test_user_1_name)
emboss_5_repository = self._get_repository_by_name_and_owner("emboss_5_0030", common.test_user_1_name)
emboss_6_repository = self._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"])
column_maker_tuple = (
self.url,
column_maker_repository.name,
column_maker_repository.owner,
self.get_repository_tip(column_maker_repository),
)
emboss_5_tuple = (
self.url,
emboss_5_repository.name,
emboss_5_repository.owner,
self.get_repository_tip(emboss_5_repository),
)
emboss_6_tuple = (
self.url,
emboss_6_repository.name,
emboss_6_repository.owner,
self.get_repository_tip(emboss_6_repository),
)
self.create_repository_dependency(
repository=emboss_5_repository,
repository_tuples=[column_maker_tuple],
filepath=repository_dependencies_path,
)
self.create_repository_dependency(
repository=emboss_6_repository,
repository_tuples=[column_maker_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=category_0040,
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=category_0040,
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._get_repository_by_name_and_owner("freebayes_0040", common.test_user_1_name)
filtering_repository = self._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.owner,
self.get_repository_tip(freebayes_repository),
)
filtering_tuple = (
self.url,
filtering_repository.name,
filtering_repository.owner,
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=category,
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=category,
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_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=category,
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=category,
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=category,
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=category,
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._get_repository_by_name_and_owner(column_repository_name, common.test_user_1_name)
convert_repository = self._get_repository_by_name_and_owner(
convert_repository_name, common.test_user_1_name
)
emboss_repository = self._get_repository_by_name_and_owner(emboss_repository_name, common.test_user_1_name)
filtering_repository = self._get_repository_by_name_and_owner(
filtering_repository_name, common.test_user_1_name
)
freebayes_repository = self._get_repository_by_name_and_owner(
freebayes_repository_name, common.test_user_1_name
)
bismark_repository = self._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.owner,
self.get_repository_tip(column_repository),
)
convert_tuple = (
self.url,
convert_repository.name,
convert_repository.owner,
self.get_repository_tip(convert_repository),
)
freebayes_tuple = (
self.url,
freebayes_repository.name,
freebayes_repository.owner,
self.get_repository_tip(freebayes_repository),
)
emboss_tuple = (
self.url,
emboss_repository.name,
emboss_repository.owner,
self.get_repository_tip(emboss_repository),
)
bismark_tuple = (
self.url,
bismark_repository.name,
bismark_repository.owner,
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=emboss_repository, repository_tuples=[bismark_tuple], filepath=dependency_xml_path
)
self.create_repository_dependency(
repository=freebayes_repository,
repository_tuples=[freebayes_tuple, bismark_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_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_for_db_object(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_for_db_object(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}.")