from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
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"
running_standalone = False
[docs]class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
"""Verify that the code correctly handles circular dependencies down to n levels."""
requires_galaxy = True
[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_convert_repository(self):
"""Create and populate convert_chars_0050."""
category = self.create_category(name=category_name, description=category_description)
global running_standalone
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=[],
)
if self.repository_is_new(repository):
running_standalone = True
self.commit_tar_to_repository(
repository,
"convert_chars/convert_chars.tar",
commit_message="Uploaded convert_chars tarball.",
)
[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=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
self.commit_tar_to_repository(
repository,
"column_maker/column_maker.tar",
commit_message="Uploaded column_maker tarball.",
)
[docs] def test_0015_create_emboss_datatypes_repository(self):
"""noop now..."""
pass
[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=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
self.commit_tar_to_repository(
repository,
"emboss/emboss.tar",
commit_message="Uploaded emboss tarball.",
)
[docs] def test_0025_create_filtering_repository(self):
"""Create and populate filtering_0050."""
category = self.create_category(name=category_name, description=category_description)
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=[],
)
if self.repository_is_new(repository):
self.commit_tar_to_repository(
repository,
"filtering/filtering_1.1.0.tar",
commit_message="Uploaded filtering 1.1.0 tarball.",
)
[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=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
self.commit_tar_to_repository(
repository,
"freebayes/freebayes.tar",
commit_message="Uploaded freebayes tarball.",
)
[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=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
self.user_populator().setup_bismark_repo(repository, end=1)
[docs] def test_0040_create_and_upload_dependency_definitions(self):
"""Set up the dependency structure."""
global running_standalone
if running_standalone:
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_1050", additional_paths=["dependencies"])
# convert_chars depends on column_maker
# column_maker depends on convert_chars
# emboss depends on bismark
# freebayes depends on freebayes, emboss, bismark, 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, 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_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
)
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)
bismark_repository = self._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_repository, bismark_repository)
self.check_repository_dependency(filtering_repository, emboss_repository)
for repository in [bismark_repository, emboss_repository, column_repository]:
self.check_repository_dependency(freebayes_repository, repository)
freebayes_dependencies = [
freebayes_repository,
emboss_repository,
column_repository,
]
strings_displayed = [
f"{freebayes_repository.name} depends on {', '.join(repo.name for repo in freebayes_dependencies)}."
]
if not self.is_v2:
self.display_manage_repository_page(freebayes_repository, strings_displayed=strings_displayed)
[docs] def test_0055_install_column_repository(self):
"""Install column_maker with repository dependencies."""
self._install_repository(
column_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section_label="column_maker",
)
# This should result in column_maker and convert_chars being installed, and the rest never installed.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
]
strings_displayed = ["column_maker_0050", "convert_chars_0050"]
strings_not_displayed = [
"emboss_0050",
"filtering_0050",
"freebayes_0050",
"bismark_0050",
]
self._assert_has_installed_repos_with_names(*strings_displayed)
self._assert_has_no_installed_repos_with_names(*strings_not_displayed)
self.verify_installed_repositories(installed_repositories=installed_repositories)
[docs] def test_0060_install_emboss_repository(self):
"""Install emboss_5 with repository dependencies."""
global running_standalone
self._install_repository(
emboss_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section_label="emboss_5_0050",
)
# Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name),
]
strings_displayed = [
"emboss_0050",
"column_maker_0050",
"convert_chars_0050",
"bismark_0050",
]
strings_not_displayed = ["filtering_0050", "freebayes_0050"]
self._assert_has_installed_repos_with_names(*strings_displayed)
self._assert_has_no_installed_repos_with_names(*strings_not_displayed)
self.verify_installed_repositories(installed_repositories)
[docs] def test_0065_deactivate_bismark_repository(self):
"""Deactivate bismark and verify things are okay."""
repository = self._get_installed_repository_by_name_owner(bismark_repository_name, common.test_user_1_name)
self.deactivate_repository(repository)
# Now we have emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
]
strings_displayed = ["emboss_0050", "column_maker_0050", "convert_chars_0050"]
strings_not_displayed = ["bismark", "filtering_0050", "freebayes_0050"]
self._assert_has_installed_repos_with_names(*strings_displayed)
self._assert_has_no_installed_repos_with_names(*strings_not_displayed)
self.verify_installed_repositories(installed_repositories)
[docs] def test_0070_uninstall_emboss_repository(self):
"""Uninstall the emboss_5 repository."""
repository = self._get_installed_repository_by_name_owner(emboss_repository_name, common.test_user_1_name)
self._uninstall_repository(repository)
self._assert_has_no_installed_repos_with_names(repository.name)
self._refresh_tool_shed_repository(repository)
self.check_galaxy_repository_tool_panel_section(repository, "emboss_5_0050")
# Now we have bismark, column_maker, and convert_chars installed, filtering and freebayes never installed,
# and emboss uninstalled.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
]
strings_displayed = ["column_maker_0050", "convert_chars_0050"]
strings_not_displayed = ["emboss_0050", "filtering_0050", "freebayes_0050"]
self._assert_has_installed_repos_with_names(*strings_displayed)
self._assert_has_no_installed_repos_with_names(*strings_not_displayed)
self.verify_installed_repositories(installed_repositories)
[docs] def test_0075_install_freebayes_repository(self):
"""Install freebayes with repository dependencies. This should also automatically reactivate bismark and reinstall emboss_5."""
strings_displayed = ["Handle", "tool dependencies", "freebayes", "0.9.4_9696d0ce8a9", "samtools", "0.1.18"]
self._install_repository(
freebayes_repository_name,
common.test_user_1_name,
category_name,
install_tool_dependencies=False,
install_repository_dependencies=True,
new_tool_panel_section_label="freebayes",
)
self._assert_has_installed_repos_with_names("emboss_0050")
# Installing freebayes should automatically reinstall emboss and reactivate bismark.
# Now column_maker, convert_chars, emboss, freebayes, and bismark should be installed.
installed_repositories = [
(column_repository_name, common.test_user_1_name),
(emboss_repository_name, common.test_user_1_name),
(freebayes_repository_name, common.test_user_1_name),
(convert_repository_name, common.test_user_1_name),
(bismark_repository_name, common.test_user_1_name),
]
strings_displayed = [
"emboss_0050",
"column_maker_0050",
"convert_chars_0050",
"bismark_0050",
"freebayes_0050",
]
strings_not_displayed = ["filtering_0050"]
self._assert_has_installed_repos_with_names(*strings_displayed)
self._assert_has_no_installed_repos_with_names(*strings_not_displayed)
self.verify_installed_repositories(installed_repositories)