From fcbaf62e05ec5fcf1ae8fd4b3b2226904c414e41 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 09:34:08 -0400 Subject: [PATCH 01/11] API migration notes... --- lib/tool_shed/test/functional/api_notes.md | 42 +++++++++++++++++++ .../test/functional/test_shed_repositories.py | 11 ----- 2 files changed, 42 insertions(+), 11 deletions(-) create mode 100644 lib/tool_shed/test/functional/api_notes.md diff --git a/lib/tool_shed/test/functional/api_notes.md b/lib/tool_shed/test/functional/api_notes.md new file mode 100644 index 00000000000..18174ff96a9 --- /dev/null +++ b/lib/tool_shed/test/functional/api_notes.md @@ -0,0 +1,42 @@ +# Tool Shed Migration Notes + +The Galaxy developer community has different intentions and ideas for the tool shed going forward including: + +- a complete rewrite (https://github.com/hexylena/shed) +- merge the existing functionality that is needed into DockStore (https://dockstore.org/) +- a rewrite of Galaxy to just use GitHub directly (the Anton approach) +- spinning the codebase off as is (duplicating and freezing the Galaxy half) (https://github.com/galaxyproject/galaxy/pull/8830) +- spinning the code base while continuing reuse via Python packaging + +There is largely agreement that the tool shed code is aging and if the UI should continue +to exist it should be rewritten. The ecosystem has evolved such that I think all parties would +also agree that all server access (by Galaxy or a new UI) should be via a tool shed API and should +be typed and well modelled. + +This chart is meant to track what API endpoints are used where and how they are used to gauage +how conservative we should be in breaking backward compatiblity. This chart doesn't guarentee +endpoints will remain, will stay consistent, or even that a tool shed API will continue to exist. +It is just meant to track information and allow us to make clear choices. Nothing is scared here. + +Things seemingly *NOT* used by Galaxy, Planemo, or Ephemeris. These are easy candidates for +for deletion instead of writing new tests and modernizing the API. + +- reset_metadata_on_repositories +- remove_repository_registry_entry +- get_repository_revision_install_info +- get_installable_revisions +- The whole Groups API. +- The whole Repository Revisions API. + +| api | Galaxy | Planemo | Ephemeris | Pydantic or API tests | Used for TS Functional Testing | Notes | +| --- | ------ | ------- | --------- | --------------------- | ------------------------------ | ----- | +| GET categories | ? | ? | ? | YES | NO | Easy to maintain/migrate | +| POST categories | NO | NO | NO | YES | YES | Easy to maintain/migrate | +| get_repository_revision_install_info | YES | | | | | NO | Used by install code. | +| get_ordered_installable_revisions | NO | NO | YES | YES | NO | used by complete_repo_information in ephemeris for shed_tools | +| reset_metadata_on_repository | NO | NO | NO | YES | NO | Bjoern said it was a thing that is done via the UI still | +| GET repositories/{repository_id}/metadata| Yes (getRepository in client?) | NO? | NO? | YES | NO | | +| tool search | NO | NO | NO | YES | NO | Community contributed - used by tool dog or something? | +| repo search | YES | NO | NO | YES | NO | Used by the Vue tool shed install interface. | +| repositories/{repository_id}/changeset_revision | NO | YES | NO | YES | NO | | +| POST repositories | NO | YES | NO | YES | NO | | diff --git a/lib/tool_shed/test/functional/test_shed_repositories.py b/lib/tool_shed/test/functional/test_shed_repositories.py index e5cb021242e..0f0fee3be3a 100644 --- a/lib/tool_shed/test/functional/test_shed_repositories.py +++ b/lib/tool_shed/test/functional/test_shed_repositories.py @@ -5,17 +5,6 @@ from ..base.api import ShedApiTestCase COLUMN_MAKER_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar") -# Things seemingly *NOT* used by Galaxy, Planemo, or Ephemeris... -# (perhaps we can delete instead of test?)... -# - reset_metadata_on_repository -# - reset_metadata_on_repositories -# - remove_repository_registry_entry -# - get_repository_revision_install_info -# - get_installable_revisions - -# Non repositories API seemingly unused and seemingly better rewritten if wanted. -# - The whole Groups API. -# - The whole Repository Revisions API. class ShedRepositoriesApiTestCase(ShedApiTestCase): def test_create(self): populator = self.populator From cec8c1ac9f2bcae63acde474591e8c3e947a0cdd Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 14:52:25 -0400 Subject: [PATCH 02/11] Use API in lieu of direct db access in shed functional tests for categories. --- lib/tool_shed/test/base/api.py | 61 ++++++++++--------- lib/tool_shed/test/base/populators.py | 32 ++++++++-- lib/tool_shed/test/base/test_db_util.py | 4 -- lib/tool_shed/test/base/twilltestcase.py | 29 ++++++--- .../test_0000_basic_repository_features.py | 12 ++-- ..._0010_repository_with_tool_dependencies.py | 4 +- ...test_0020_basic_repository_dependencies.py | 8 +-- ...st_0030_repository_dependency_revisions.py | 16 ++--- ...t_0040_repository_circular_dependencies.py | 13 ++-- ...est_0050_circular_dependencies_4_levels.py | 12 ++-- .../test/functional/test_0070_invalid_tool.py | 2 +- ...est_0080_advanced_circular_dependencies.py | 4 +- .../test/functional/test_0090_tool_search.py | 10 +-- ...st_0100_complex_repository_dependencies.py | 4 +- ..._invalid_simple_repository_dependencies.py | 8 +-- ...e_repository_dependency_multiple_owners.py | 4 +- .../functional/test_0140_tool_help_images.py | 2 +- .../test_0150_prior_installation_required.py | 4 +- ...60_circular_prior_installation_required.py | 6 +- ...170_complex_prior_installation_required.py | 4 +- .../test_0300_reset_all_metadata.py | 32 +++++----- .../functional/test_0310_hg_api_features.py | 2 +- ...test_0420_citable_urls_for_repositories.py | 2 +- .../functional/test_0430_browse_utilities.py | 4 +- ...st_0440_deleting_dependency_definitions.py | 18 +++--- .../test_0460_upload_to_repository.py | 24 ++++---- ...st_0470_tool_dependency_repository_type.py | 12 ++-- ...t_0480_tool_dependency_xml_verification.py | 4 +- .../test_0530_repository_admin_feature.py | 2 +- .../test_0540_get_all_metadata_from_api.py | 6 +- ...test_0550_metadata_updated_dependencies.py | 6 +- .../test_1000_install_basic_repository.py | 4 +- ...stall_repository_with_tool_dependencies.py | 4 +- ...repository_with_repository_dependencies.py | 6 +- ...ll_repository_with_dependency_revisions.py | 10 +-- ..._repository_basic_circular_dependencies.py | 4 +- ...est_1050_circular_dependencies_4_levels.py | 12 ++-- .../test/functional/test_1070_invalid_tool.py | 6 +- ...vanced_circular_dependency_installation.py | 4 +- ...est_1090_repository_dependency_handling.py | 4 +- ...install_updated_repository_dependencies.py | 4 +- ...ll_repository_with_complex_dependencies.py | 4 +- ...tory_with_invalid_repository_dependency.py | 8 +-- ...e_repository_dependency_multiple_owners.py | 4 +- .../functional/test_1160_tool_help_images.py | 2 +- .../test_1170_prior_installation_required.py | 4 +- ...80_circular_prior_installation_required.py | 6 +- ...190_complex_prior_installation_required.py | 4 +- ...ninstall_and_reinstall_basic_repository.py | 2 +- ...stall_repository_with_tool_dependencies.py | 2 +- ...ll_repository_with_dependency_revisions.py | 8 +-- .../test_1300_reset_all_metadata.py | 26 ++++---- .../functional/test_1410_update_manager.py | 2 +- .../test_1430_repair_installed_repository.py | 8 +-- .../functional/test_1460_data_managers.py | 4 +- ...st_1470_updating_installed_repositories.py | 2 +- lib/tool_shed_client/schema/__init__.py | 5 ++ 57 files changed, 269 insertions(+), 231 deletions(-) diff --git a/lib/tool_shed/test/base/api.py b/lib/tool_shed/test/base/api.py index d69674f4d4d..41af69afe05 100644 --- a/lib/tool_shed/test/base/api.py +++ b/lib/tool_shed/test/base/api.py @@ -28,6 +28,37 @@ from .populators import ToolShedPopulator class ShedBaseTestCase(DrivenFunctionalTestCase): + _populator: Optional[ToolShedPopulator] = None + + @property + def populator(self) -> ToolShedPopulator: + if self._populator is None: + self._populator = ToolShedPopulator(self.admin_api_interactor, self.api_interactor) + return self._populator + + @property + def admin_api_interactor(self) -> ShedApiInteractor: + return ShedApiInteractor(self.url, get_admin_api_key()) + + @property + def api_interactor(self) -> ShedApiInteractor: + user_api_key = get_user_api_key() + if user_api_key is None: + email = TEST_USER + password = "testpassword" + ensure_user_with_email(self.admin_api_interactor, email, password) + user_api_key = self._api_key(email, password) + return ShedApiInteractor(self.url, user_api_key) + + def _api_key(self, email: str, password: str) -> str: + headers = baseauth_headers(email, password) + url = urljoin(self.url, "api/authenticate/baseauth") + auth_response = requests.get(url, headers=headers) + api_asserts.assert_status_code_is(auth_response, 200) + auth_dict = auth_response.json() + api_asserts.assert_has_keys(auth_dict, "api_key") + return auth_dict["api_key"] + def setUp(self): host = os.environ.get("TOOL_SHED_TEST_HOST") assert host @@ -78,40 +109,10 @@ class ShedGalaxyInteractorApi(GalaxyInteractorApi): class ShedApiTestCase(ShedBaseTestCase, UsesShedApi): - _populator: Optional[ToolShedPopulator] = None _galaxy_interactor: Optional[GalaxyInteractorApi] = None - @property - def populator(self) -> ToolShedPopulator: - if self._populator is None: - self._populator = ToolShedPopulator(self.admin_api_interactor, self.api_interactor) - return self._populator - @property def galaxy_interactor(self) -> GalaxyInteractorApi: if self._galaxy_interactor is None: self._galaxy_interactor = ShedGalaxyInteractorApi(self.galaxy_url) return self._galaxy_interactor - - @property - def admin_api_interactor(self) -> ShedApiInteractor: - return ShedApiInteractor(self.url, get_admin_api_key()) - - @property - def api_interactor(self) -> ShedApiInteractor: - user_api_key = get_user_api_key() - if user_api_key is None: - email = TEST_USER - password = "testpassword" - ensure_user_with_email(self.admin_api_interactor, email, password) - user_api_key = self._api_key(email, password) - return ShedApiInteractor(self.url, user_api_key) - - def _api_key(self, email: str, password: str) -> str: - headers = baseauth_headers(email, password) - url = urljoin(self.url, "api/authenticate/baseauth") - auth_response = requests.get(url, headers=headers) - api_asserts.assert_status_code_is(auth_response, 200) - auth_dict = auth_response.json() - api_asserts.assert_has_keys(auth_dict, "api_key") - return auth_dict["api_key"] diff --git a/lib/tool_shed/test/base/populators.py b/lib/tool_shed/test/base/populators.py index 964f0c083ac..deb025d4e8a 100644 --- a/lib/tool_shed/test/base/populators.py +++ b/lib/tool_shed/test/base/populators.py @@ -1,4 +1,8 @@ -from typing import Union +from typing import ( + List, + Optional, + Union, +) import requests @@ -10,6 +14,7 @@ from galaxy_test.base import api_asserts from galaxy_test.base.api_util import random_name from tool_shed_client.schema import ( Category, + CreateCategoryRequest, GetOrderedInstallableRevisionsRequest, OrderedInstallableRevisions, Repository, @@ -109,13 +114,30 @@ class ToolShedPopulator: index_response = self._admin_api_interactor.put("tools/build_search_index") index_response.raise_for_status() - def new_category(self, prefix=DEFAULT_PREFIX) -> Category: - name = random_name(prefix=prefix) - body = {"name": name, "description": "testcreaterepo"} - response = self._admin_api_interactor.post("categories", json=body) + def new_category( + self, name: Optional[str] = None, description: Optional[str] = None, prefix=DEFAULT_PREFIX + ) -> Category: + category_name = name or random_name(prefix=prefix) + category_description = description or "testcreaterepo" + request = CreateCategoryRequest(name=category_name, description=category_description) + response = self._admin_api_interactor.post("categories", json=request.dict()) response.raise_for_status() return Category(**response.json()) + def get_categories(self) -> List[Category]: + response = self._api_interactor.get("categories") + response.raise_for_status() + return [Category(**c) for c in response.json()] + + def get_category_with_name(self, name: str) -> Optional[Category]: + response = self._api_interactor.get("categories") + response.raise_for_status() + categories = [c for c in self.get_categories() if c.name == name] + return categories[0] if categories else None + + def has_category_with_name(self, name: str) -> bool: + return self.get_category_with_name(name) is not None + def get_ordered_installable_revisions(self, owner: str, name: str) -> OrderedInstallableRevisions: request = GetOrderedInstallableRevisionsRequest(owner=owner, name=name) revisions_response = self._api_interactor.get( diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index 7c02906476b..bb758d56d3b 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -56,10 +56,6 @@ def get_all_installed_repositories(actually_installed=False): return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).all() -def get_category_by_name(name): - return sa_session.query(model.Category).filter(model.Category.table.c.name == name).first() - - def get_default_user_permissions_by_role(role): return ( sa_session.query(model.DefaultUserPermissions) diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index 05b01f38ea6..14665b9cb59 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -5,6 +5,7 @@ import string import tempfile import time from json import loads +from typing import List from urllib.parse import ( quote_plus, urlencode, @@ -34,6 +35,7 @@ from tool_shed.util import ( hgweb_config, xml_util, ) +from tool_shed_client.schema import Category from . import ( common, test_db_util, @@ -248,11 +250,11 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url("/repository/manage_repository_admins", params=params) self.check_for_strings(strings_displayed=["Role", "has been associated"]) - def browse_category(self, category, strings_displayed=None, strings_not_displayed=None): + def browse_category(self, category: Category, strings_displayed=None, strings_not_displayed=None): params = { "sort": "name", "operation": "valid_repositories_by_category", - "id": self.security.encode_id(category.id), + "id": category.id, } self.visit_url("/repository/browse_valid_categories", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) @@ -451,13 +453,14 @@ class ShedTwillTestCase(ShedBaseTestCase): return True raise - def create_category(self, **kwd): - category = test_db_util.get_category_by_name(kwd["name"]) + def create_category(self, **kwd) -> Category: + category = self.populator.get_category_with_name(kwd["name"]) if category is None: params = {"operation": "create"} self.visit_url("/admin/manage_categories", params=params) self.submit_form(button="create_category_button", **kwd) - category = test_db_util.get_category_by_name(kwd["name"]) + category = self.populator.get_category_with_name(kwd["name"]) + assert category return category def create_repository_dependency( @@ -815,13 +818,17 @@ class ShedTwillTestCase(ShedBaseTestCase): def get_hg_repo(self, path): return hg.repository(ui.ui(), path.encode("utf-8")) - def get_repositories_category_api(self, categories, strings_displayed=None, strings_not_displayed=None): + def get_repositories_category_api( + self, categories: List[Category], strings_displayed=None, strings_not_displayed=None + ): for category in categories: - url = f"/api/categories/{self.security.encode_id(category.id)}/repositories" + url = f"/api/categories/{category.id}/repositories" self.visit_url(url) self.check_for_strings(strings_displayed, strings_not_displayed) - def get_or_create_repository(self, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd): + def get_or_create_repository( + self, category: Category, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd + ): # If not checking for a specific string, it should be safe to assume that # we expect repository creation to be successful. if strings_displayed is None: @@ -829,9 +836,11 @@ class ShedTwillTestCase(ShedBaseTestCase): if strings_not_displayed is None: strings_not_displayed = [] repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner) + category_id = category.id + assert category_id if repository is None: self.visit_url("/repository/create_repository") - self.submit_form(button="create_repository_button", **kwd) + self.submit_form(button="create_repository_button", category_id=category_id, **kwd) self.check_for_strings(strings_displayed, strings_not_displayed) repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner) return repository @@ -1051,7 +1060,7 @@ class ShedTwillTestCase(ShedBaseTestCase): **kwd, ): self.browse_tool_shed(url=self.url) - self.browse_category(test_db_util.get_category_by_name(category_name)) + self.browse_category(self.populator.get_category_with_name(category_name)) self.preview_repository_in_tool_shed(name, owner, strings_displayed=preview_strings_displayed) repository = test_db_util.get_repository_by_name_and_owner(name, owner) repository_id = self.security.encode_id(repository.id) diff --git a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py index 3525f9684e6..dbb5552c7a1 100644 --- a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py +++ b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py @@ -52,14 +52,14 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): def test_0015_create_repository(self): """Create the filtering repository""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1") + category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1") strings_displayed = self.expect_repo_created_strings(repository_name) self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) @@ -305,7 +305,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): def test_0095_verify_reserved_repository_name_handling(self): """Check that reserved repository names are handled correctly.""" - category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1") + category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1") error_message = ( "The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name." ) @@ -314,7 +314,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[error_message], ) @@ -433,8 +433,8 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): def test_0135_api_get_repositories_in_category(self): """Load the api endpoint for repositories in a category.""" categories = [] - categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")) - categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 2")) + categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")) + categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 2")) self.get_repositories_category_api(categories) def test_0140_view_invalid_changeset(self): diff --git a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py index 3c767f1bb2a..ab62120ceb5 100644 --- a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py @@ -51,13 +51,13 @@ class TestFreebayesRepository(ShedTwillTestCase): upload, as well as on the manage repository page. """ self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0010 Repository With Tool Dependencies") + category = self.populator.get_category_with_name("Test 0010 Repository With Tool Dependencies") repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py index 7da246743a1..4d32c6955ab 100644 --- a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py @@ -36,14 +36,14 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0010_create_column_maker_repository(self): """Create and populate column_maker_0020.""" - category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies") + category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies") 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_repository_name, description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -60,13 +60,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0020_create_emboss_5_repository_and_upload_files(self): """Create and populate the emboss_5_0020 repository.""" - category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies") + category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies") 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), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py index d7b457891f9..4c6df862180 100644 --- a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py @@ -39,13 +39,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase): def test_0010_create_emboss_5_repository(self): """Create and populate the emboss_5_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") + category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions") repository = self.get_or_create_repository( name=emboss_5_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), + category=category, ) self.upload_file( repository, @@ -62,13 +62,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase): def test_0015_create_emboss_6_repository(self): """Create and populate the emboss_6_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") + category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions") repository = self.get_or_create_repository( name=emboss_6_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), + category=category, ) self.upload_file( repository, @@ -85,13 +85,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase): def test_0020_create_dependent_repository(self): """Create and populate the emboss_datatypes_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") + category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions") repository = self.get_or_create_repository( name=column_maker_repository_name, description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, ) if self.repository_is_new(repository): self.upload_file( @@ -109,13 +109,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase): def test_0025_create_emboss_repository(self): """Create and populate the emboss_0030 repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") + category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions") 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), + category=category, ) self.upload_file( repository, diff --git a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py index 2fd8f324897..b846ce5e77b 100644 --- a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py @@ -11,6 +11,9 @@ filtering_repository_name = "filtering_0040" filtering_repository_description = "Galaxy's filtering tool for test 0040" filtering_repository_long_description = "Long description of Galaxy's filtering tool for test 0040" +CATEGORY_NAME = "test_0040_repository_circular_dependencies" +CATEGORY_DESC = "Testing handling of circular repository dependencies." + class TestRepositoryCircularDependencies(ShedTwillTestCase): """Verify that the code correctly displays repositories with circular repository dependencies.""" @@ -31,19 +34,20 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): def test_0005_create_category(self): """Create a category for this test suite""" self.create_category( - name="test_0040_repository_circular_dependencies", - description="Testing handling of circular repository dependencies.", + name=CATEGORY_NAME, + description=CATEGORY_DESC, ) def test_0010_create_freebayes_repository(self): """Create and populate freebayes_0040.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) + category = self.populator.get_category_with_name(CATEGORY_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, - categories=["test_0040_repository_circular_dependencies"], + category=category, strings_displayed=[], ) self.upload_file( @@ -61,12 +65,13 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): def test_0015_create_filtering_repository(self): """Create and populate filtering_0040.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) + category = self.populator.get_category_with_name(CATEGORY_NAME) 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, - categories=["test_0040_repository_circular_dependencies"], + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py index cae45959577..3edca69132a 100644 --- a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py +++ b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py @@ -56,7 +56,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -79,7 +79,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -106,7 +106,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -129,7 +129,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -152,7 +152,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -175,7 +175,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): description=bismark_repository_description, long_description=bismark_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0070_invalid_tool.py b/lib/tool_shed/test/functional/test_0070_invalid_tool.py index dba482a7b92..b8e6f6621a7 100644 --- a/lib/tool_shed/test/functional/test_0070_invalid_tool.py +++ b/lib/tool_shed/test/functional/test_0070_invalid_tool.py @@ -35,7 +35,7 @@ class TestBismarkRepository(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py index 4710b4fd8e4..e20de949cec 100644 --- a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py @@ -40,7 +40,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -65,7 +65,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0090_tool_search.py b/lib/tool_shed/test/functional/test_0090_tool_search.py index 886d022f2a5..90869bd82af 100644 --- a/lib/tool_shed/test/functional/test_0090_tool_search.py +++ b/lib/tool_shed/test/functional/test_0090_tool_search.py @@ -52,7 +52,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): 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), + category=category, strings_displayed=[], ) self.upload_file( @@ -76,7 +76,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): 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), + category=category, strings_displayed=[], ) self.upload_file( @@ -99,7 +99,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -122,7 +122,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -145,7 +145,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py index 06e6e59c99d..5a660317a33 100644 --- a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py @@ -48,7 +48,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase): description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -77,7 +77,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase): 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), + category=category, strings_displayed=[], ) # Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive. diff --git a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py index 3cb9dddb3c5..47a6feaa251 100644 --- a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py @@ -38,13 +38,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self): """Create and populate the emboss_datatypes repository.""" self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) column_maker_repository = self.get_or_create_repository( name=column_maker_repository_name, description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -61,13 +61,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0020_create_emboss_5_repository_and_upload_files(self): """Create and populate the emboss_5_0110 repository.""" - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_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), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py index d173222fe72..f3cab1689a7 100644 --- a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -64,7 +64,7 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase): description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_2_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -117,7 +117,7 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase): description=tool_repository_description, long_description=tool_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0140_tool_help_images.py b/lib/tool_shed/test/functional/test_0140_tool_help_images.py index 01115a70a64..9e634194813 100644 --- a/lib/tool_shed/test/functional/test_0140_tool_help_images.py +++ b/lib/tool_shed/test/functional/test_0140_tool_help_images.py @@ -54,7 +54,7 @@ class TestToolHelpImages(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) # Upload htseq_count.tar to the repository. diff --git a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py index d5c32174faa..c5dea295a88 100644 --- a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py @@ -54,7 +54,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -77,7 +77,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py index 9b230f5b273..b8c9c47dbc1 100644 --- a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py @@ -53,7 +53,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -76,7 +76,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -99,7 +99,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=filter_repository_description, long_description=filter_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py index 4e6403d8fb8..8b64a2ff8b6 100644 --- a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py @@ -57,7 +57,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): description=matplotlib_repository_description, long_description=matplotlib_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -84,7 +84,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): description=numpy_repository_description, long_description=numpy_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py index bd3f7ae86e9..61c083f51bf 100644 --- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py +++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py @@ -69,7 +69,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0000, ) if self.repository_is_new(repository): running_standalone = True @@ -110,7 +110,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0010, strings_displayed=[], ) if running_standalone: @@ -174,7 +174,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category_0020.id), + category=category_0020, strings_displayed=[], ) self.upload_file( @@ -204,7 +204,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0020, strings_displayed=[], ) self.upload_file( @@ -234,7 +234,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category_0030.id), + category=category_0030, strings_displayed=[], ) self.upload_file( @@ -264,7 +264,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0030, strings_displayed=[], ) self.upload_file( @@ -294,7 +294,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0030, strings_displayed=[], ) self.upload_file( @@ -324,7 +324,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0030, strings_displayed=[], ) self.upload_file( @@ -405,7 +405,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0040, strings_displayed=[], ) if running_standalone: @@ -436,7 +436,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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), + category=category_0040, strings_displayed=[], ) self.upload_file( @@ -497,7 +497,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -524,7 +524,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -554,7 +554,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -581,7 +581,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -608,7 +608,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -635,7 +635,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): description=bismark_repository_description, long_description=bismark_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0310_hg_api_features.py b/lib/tool_shed/test/functional/test_0310_hg_api_features.py index b41e4c6bcde..f3f47b1f98c 100644 --- a/lib/tool_shed/test/functional/test_0310_hg_api_features.py +++ b/lib/tool_shed/test/functional/test_0310_hg_api_features.py @@ -56,7 +56,7 @@ class TestHgWebFeatures(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py index ea8fb6cc9f3..13720b7b562 100644 --- a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py +++ b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py @@ -64,7 +64,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0430_browse_utilities.py b/lib/tool_shed/test/functional/test_0430_browse_utilities.py index 0fd5f39b7f6..38c0c325cc2 100644 --- a/lib/tool_shed/test/functional/test_0430_browse_utilities.py +++ b/lib/tool_shed/test/functional/test_0430_browse_utilities.py @@ -59,7 +59,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -90,7 +90,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py index 9221ca08d79..dcedf318fc7 100644 --- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py +++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py @@ -87,7 +87,7 @@ class TestDeletedDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -107,7 +107,7 @@ class TestDeletedDependencies(ShedTwillTestCase): We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0. """ - category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions") + category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions") self.login(email=common.test_user_1_email, username=common.test_user_1_name) strings_displayed = ["Repository convert_chars_0440 has been created"] repository = self.get_or_create_repository( @@ -115,7 +115,7 @@ class TestDeletedDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -219,7 +219,7 @@ class TestDeletedDependencies(ShedTwillTestCase): We are at complex repository dependencies, step 1 - Create and populate bwa_package_0440 so that it has a valid tool dependency definition and an installable revision 0. """ - category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions") + category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions") self.login(email=common.test_user_1_email, username=common.test_user_1_name) strings_displayed = ["Repository bwa_package_0440 has been created"] repository = self.get_or_create_repository( @@ -227,7 +227,7 @@ class TestDeletedDependencies(ShedTwillTestCase): description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -248,7 +248,7 @@ class TestDeletedDependencies(ShedTwillTestCase): We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0. This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440. """ - category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions") + category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions") self.login(email=common.test_user_1_email, username=common.test_user_1_name) strings_displayed = ["Repository bwa_base_0440 has been created"] repository = self.get_or_create_repository( @@ -256,7 +256,7 @@ class TestDeletedDependencies(ShedTwillTestCase): 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), + category=category, strings_displayed=strings_displayed, ) self.upload_file( @@ -354,7 +354,7 @@ class TestDeletedDependencies(ShedTwillTestCase): We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid tool dependency definition and an installable revision 0. """ - category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions") + category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions") self.login(email=common.test_user_1_email, username=common.test_user_1_name) strings_displayed = ["Repository bwa_tool_dependency_0440 has been created"] repository = self.get_or_create_repository( @@ -362,7 +362,7 @@ class TestDeletedDependencies(ShedTwillTestCase): description=bwa_tool_dependency_repository_description, long_description=bwa_tool_dependency_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py index 2bb38dde80f..80da7c5dd85 100644 --- a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py +++ b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py @@ -91,13 +91,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): This is step 2 - Create and populate package_bwa_0_5_9_0460. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=bwa_repository_name, description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -125,7 +125,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): - Upload via url, with the tool_dependencies.xml in the root of another repository. - Upload via url, with the tool_dependencies.xml in a subfolder within another repository. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository_base_name = "complex_dependency_test_%d_0460" repository_base_description = "Test #%d for complex repository dependency definitions." repository_base_long_description = "Test #%d for complex repository dependency definitions." @@ -135,7 +135,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): description=repository_base_description % number, long_description=repository_base_long_description % number, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) @@ -234,13 +234,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): This is step 7 - Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with tool dependencies. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name="hg_tool_dependency_0460", description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -259,7 +259,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -347,7 +347,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): - Upload via url, with the repository_dependencies.xml in the root of another repository. - Upload via url, with the repository_dependencies.xml in a subfolder within another repository. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository_base_name = "repository_dependency_test_%d_0460" repository_base_description = "Test #%d for repository dependency definitions." repository_base_long_description = "Test #%d for repository dependency definitions." @@ -357,7 +357,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): description=repository_base_description % number, long_description=repository_base_long_description % number, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) @@ -459,13 +459,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate with repository dependencies. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name="hg_repository_dependency_0460", description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -484,7 +484,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): description=bwa_repository_description, long_description=bwa_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py index fce719e6b77..7b2f0461287 100644 --- a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py +++ b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py @@ -93,13 +93,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase): Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml. Keep the repository type as the default "Unrestricted". """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=package_libx11_repository_name, description=package_libx11_repository_description, long_description=package_libx11_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) # Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository. @@ -124,13 +124,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase): above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision defined so it will get automatically populated. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=package_emboss_repository_name, description=package_emboss_repository_description, long_description=package_emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) # Upload the edited tool dependency definition to the package_emboss_5_0_0 repository. @@ -155,13 +155,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase): on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined so it will get automatically populated. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_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), + category=category, strings_displayed=[], ) # Populate emboss_5 with tool and dependency definitions. diff --git a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py index b51e1944efc..29126a54881 100644 --- a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py +++ b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py @@ -52,13 +52,13 @@ class TestDependencyDefinitionValidation(ShedTwillTestCase): Create a repository named package_invalid_tool_dependency_xml_1_0_0 that will contain only a single file named tool_dependencies.xml. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py index a19b6f77b77..4045ff5295e 100644 --- a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py +++ b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py @@ -67,7 +67,7 @@ class TestRepositoryAdminRole(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py index 78578ca186e..803c27eeb52 100644 --- a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py +++ b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py @@ -67,7 +67,7 @@ class TestGetAllMetadata(ShedTwillTestCase): description=repositories["bwa"]["description"], long_description=repositories["bwa"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['bwa']['name']}" @@ -95,7 +95,7 @@ class TestGetAllMetadata(ShedTwillTestCase): description=repositories["convert"]["description"], long_description=repositories["convert"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['convert']['name']}" @@ -133,7 +133,7 @@ class TestGetAllMetadata(ShedTwillTestCase): description=repositories["column"]["description"], long_description=repositories["column"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['column']['name']}" diff --git a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py index 62481139eed..8c322ccc665 100644 --- a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py +++ b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py @@ -71,7 +71,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): description=repositories["freebayes"]["description"], long_description=repositories["freebayes"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert freebayes is not None, f"Error creating freebayes {repositories['freebayes']['name']}" @@ -99,7 +99,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): description=repositories["samtools"]["description"], long_description=repositories["samtools"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert samtools is not None, f"Error creating samtools {repositories['samtools']['name']}" @@ -123,7 +123,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): description=repositories["filtering"]["description"], long_description=repositories["filtering"]["long_description"], owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) assert repository is not None, f"Error creating repository {repositories['filtering']['name']}" diff --git a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py index 38bc1a6268e..2fd978971e0 100644 --- a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py @@ -43,7 +43,7 @@ class BasicToolShedFeatures(ShedTwillTestCase): 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.id), + category=category, ) if self.repository_is_new(repository): self.upload_file( @@ -101,7 +101,7 @@ class BasicToolShedFeatures(ShedTwillTestCase): def test_0015_browse_test_0000_category(self): """Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test.""" - category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1") + category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1") self.browse_category(category, strings_displayed=["filtering_0000"]) def test_0020_preview_filtering_repository(self): diff --git a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py index 1296376a286..c7796fbafd3 100644 --- a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py @@ -44,7 +44,7 @@ class ToolWithToolDependencies(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, ) if self.repository_is_new(repository): self.upload_file( @@ -124,7 +124,7 @@ class ToolWithToolDependencies(ShedTwillTestCase): """Browse the available tool sheds in this Galaxy instance and preview the freebayes tool.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=[category_name]) - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) self.browse_category(category, strings_displayed=[repository_name]) strings_displayed = [repository_name, "Valid tools", "Tool dependencies"] self.preview_repository_in_tool_shed( diff --git a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py index 61b811e50f6..69dfd9beb21 100644 --- a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py @@ -45,7 +45,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -65,7 +65,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -96,7 +96,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase): """Browse the available tool sheds in this Galaxy instance and preview the emboss tool.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=["Test 0020 Basic Repository Dependencies"]) - category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies") + category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies") self.browse_category(category, strings_displayed=["emboss_0020"]) self.preview_repository_in_tool_shed( "emboss_0020", common.test_user_1_name, strings_displayed=["emboss_0020", "Valid tools"] diff --git a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py index 9a5555d7b21..99bd0db4e28 100644 --- a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py @@ -50,7 +50,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -71,7 +71,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -102,7 +102,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -133,7 +133,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -175,7 +175,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): """Browse the available tool sheds in this Galaxy instance and preview the emboss tool.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"]) - category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions") + category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions") self.browse_category(category, strings_displayed=["emboss_0030"]) self.preview_repository_in_tool_shed( "emboss_0030", common.test_user_1_name, strings_displayed=["emboss_0030", "Valid tools"] diff --git a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py index 80da1e0f5c3..8a7ba644c2d 100644 --- a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -44,7 +44,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -73,7 +73,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py index 1290eab7d9b..7b29da1f40f 100644 --- a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py +++ b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py @@ -59,7 +59,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -84,7 +84,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -112,7 +112,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -136,7 +136,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -160,7 +160,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=freebayes_repository_description, long_description=freebayes_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -184,7 +184,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): description=bismark_repository_description, long_description=bismark_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1070_invalid_tool.py b/lib/tool_shed/test/functional/test_1070_invalid_tool.py index 47d9f944c99..0059ac752d8 100644 --- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py +++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py @@ -36,13 +36,13 @@ class TestFreebayesRepository(ShedTwillTestCase): """Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.""" self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=repository_name, description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -73,7 +73,7 @@ class TestFreebayesRepository(ShedTwillTestCase): """Browse the available tool sheds in this Galaxy instance and preview the bismark repository.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) self.browse_tool_shed(url=self.url, strings_displayed=[category_name]) - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) self.browse_category(category, strings_displayed=[repository_name]) self.preview_repository_in_tool_shed( repository_name, common.test_user_1_name, strings_displayed=[repository_name] diff --git a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py index 23e9c64627e..de559348e5c 100644 --- a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py +++ b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py @@ -53,7 +53,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -81,7 +81,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py index e8c0a23f45b..71ed5b316e6 100644 --- a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py +++ b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py @@ -50,7 +50,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -75,7 +75,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py index 62970273c76..c35e25fdca8 100644 --- a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py @@ -46,7 +46,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -72,7 +72,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py index 3b230f3ecd0..d97b9534655 100644 --- a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py +++ b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py @@ -48,7 +48,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase): description=bwa_package_repository_description, long_description=bwa_package_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -87,7 +87,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase): 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), + category=category, strings_displayed=[], ) self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name) diff --git a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py index 40dae7fddbe..a1f56f391da 100644 --- a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py +++ b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py @@ -40,13 +40,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): """Create and populate the column_maker repository.""" global running_standalone self.login(email=common.test_user_1_email, username=common.test_user_1_name) - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) column_maker_repository = self.get_or_create_repository( name=column_maker_repository_name, description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -67,13 +67,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): """Create and populate the emboss_5_0110 repository.""" global running_standalone if running_standalone: - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_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), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py index 89d7681e379..734c966039a 100644 --- a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py @@ -69,7 +69,7 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): description=datatypes_repository_description, long_description=datatypes_repository_long_description, owner=common.test_user_2_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) if self.repository_is_new(repository): @@ -124,7 +124,7 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): description=tool_repository_description, long_description=tool_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=strings_displayed, ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1160_tool_help_images.py b/lib/tool_shed/test/functional/test_1160_tool_help_images.py index 4881a4fa4ca..718a955761f 100644 --- a/lib/tool_shed/test/functional/test_1160_tool_help_images.py +++ b/lib/tool_shed/test/functional/test_1160_tool_help_images.py @@ -50,7 +50,7 @@ class TestToolHelpImages(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): diff --git a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py index a06e32bac48..fd884346197 100644 --- a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py @@ -67,7 +67,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -93,7 +93,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if running_standalone: diff --git a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py index affea075c83..43d77d148b8 100644 --- a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py @@ -80,7 +80,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=convert_repository_description, long_description=convert_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -106,7 +106,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if running_standalone: @@ -131,7 +131,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): description=filter_repository_description, long_description=filter_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if running_standalone: diff --git a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py index 28daca73f48..e24ebfdab00 100644 --- a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py @@ -62,7 +62,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): description=matplotlib_repository_description, long_description=matplotlib_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -95,7 +95,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): description=numpy_repository_description, long_description=numpy_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py index 71756223560..4f0c450ab0b 100644 --- a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -40,7 +40,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): description="Galaxy's filtering tool for test 0000", long_description="Long description of Galaxy's filtering tool for test 0000", owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, ) if self.repository_is_new(repository): self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py index c5119012405..7676db9eb55 100644 --- a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -38,7 +38,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): 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.id), + category=category, ) if self.repository_is_new(repository): self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py index 2984d95f880..037fda8ff5d 100644 --- a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -49,7 +49,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -59,7 +59,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -90,7 +90,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -121,7 +121,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py index b7d0f6646ba..038b032cc36 100644 --- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py +++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py @@ -83,7 +83,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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.id), + category=category, ) if self.repository_is_new(repository): running_standalone = True @@ -118,7 +118,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -175,7 +175,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=column_maker_repository_description, long_description=column_maker_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -195,7 +195,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description="Galaxy wrappers for Emboss version 5.0.0 tools", long_description="Galaxy wrappers for Emboss version 5.0.0 tools", owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -219,7 +219,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=column_repository_description, long_description=column_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(column_maker_repository): @@ -239,7 +239,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -270,7 +270,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -301,7 +301,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=emboss_repository_description, long_description=emboss_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -347,7 +347,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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.id), + category=category, strings_displayed=[], ) if self.repository_is_new(repository): @@ -367,7 +367,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description=filtering_repository_description, long_description=filtering_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -422,7 +422,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): description="Galaxy's emboss tool", long_description="Long description of Galaxy's emboss tool", owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) if self.repository_is_new(emboss_repository): @@ -431,7 +431,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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.id), + category=category, strings_displayed=[], ) freebayes_repository = self.get_or_create_repository( @@ -439,7 +439,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1410_update_manager.py b/lib/tool_shed/test/functional/test_1410_update_manager.py index e75198762a3..b64d8b9044b 100644 --- a/lib/tool_shed/test/functional/test_1410_update_manager.py +++ b/lib/tool_shed/test/functional/test_1410_update_manager.py @@ -63,7 +63,7 @@ class TestUpdateManager(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, ) self.upload_file( repository, diff --git a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py index 6f3258a46b9..5eb9e9566a3 100644 --- a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py +++ b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py @@ -64,13 +64,13 @@ class TestRepairRepository(ShedTwillTestCase): This repository will be depended on by the column_1430 repository. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=filter_repository_name, description=filter_repository_description, long_description=filter_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( @@ -92,13 +92,13 @@ class TestRepairRepository(ShedTwillTestCase): This repository will depend on the filter_1430 repository. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_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), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed/test/functional/test_1460_data_managers.py b/lib/tool_shed/test/functional/test_1460_data_managers.py index f93d03bffbc..95c097d34eb 100644 --- a/lib/tool_shed/test/functional/test_1460_data_managers.py +++ b/lib/tool_shed/test/functional/test_1460_data_managers.py @@ -57,13 +57,13 @@ class TestDataManagers(ShedTwillTestCase): Create and populate a repository that contains a Data manager. """ - category = self.test_db_util.get_category_by_name(category_name) + category = self.populator.get_category_with_name(category_name) repository = self.get_or_create_repository( name=data_manager_repository_name, description=data_manager_repository_description, long_description=data_manager_repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) # Upload the data manager files to the repository. diff --git a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py index 862a6d27030..544291abdae 100644 --- a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py +++ b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py @@ -51,7 +51,7 @@ class TestUpdateInstalledRepository(ShedTwillTestCase): description=repository_description, long_description=repository_long_description, owner=common.test_user_1_name, - category_id=self.security.encode_id(category.id), + category=category, strings_displayed=[], ) self.upload_file( diff --git a/lib/tool_shed_client/schema/__init__.py b/lib/tool_shed_client/schema/__init__.py index 6dcafd0605d..d404086539a 100644 --- a/lib/tool_shed_client/schema/__init__.py +++ b/lib/tool_shed_client/schema/__init__.py @@ -31,6 +31,11 @@ class Category(BaseModel): name: str +class CreateCategoryRequest(BaseModel): + name: str + description: str + + class ValidRepostiroyUpdateMessage(BaseModel): message: str From 8134c58f35ac856e2a638038410d98a3829f8ea3 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 15:28:55 -0400 Subject: [PATCH 03/11] Remove some datatypes cruft in tool shed tests. --- lib/tool_shed/test/base/twilltestcase.py | 7 ------- ...mple_repository_dependency_multiple_owners.py | 5 ----- ...mple_repository_dependency_multiple_owners.py | 16 ---------------- 3 files changed, 28 deletions(-) diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index 14665b9cb59..9e26479a8c2 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -863,13 +863,6 @@ class ShedTwillTestCase(ShedBaseTestCase): changelog_tuples.append((ctx.rev(), ctx)) return changelog_tuples - def get_repository_datatypes_count(self, repository): - metadata = self.get_repository_metadata(repository)[0].metadata - if "datatypes" not in metadata: - return 0 - else: - return len(metadata["datatypes"]) - def get_repository_file_list(self, repository, base_path, current_path=None): """Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder.""" if current_path is None: diff --git a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py index f3cab1689a7..f135b8f1f75 100644 --- a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -22,9 +22,6 @@ Tool shed side: 3a) Check for appropriate strings. """ -base_datatypes_count = 0 -repository_datatypes_count = 0 - class TestRepositoryMultipleOwners(ShedTwillTestCase): def test_0000_initiate_users(self): @@ -86,7 +83,6 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase): Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb, the datatypes that are defined in datatypes_conf.xml. """ - global repository_datatypes_count repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) @@ -101,7 +97,6 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase): "blastdbp", ] self.display_manage_repository_page(repository, strings_displayed=strings_displayed) - repository_datatypes_count = int(self.get_repository_datatypes_count(repository)) def test_0015_create_tool_repository(self): """Create and populate the blastxml_to_top_descr_0120 repository diff --git a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py index 734c966039a..1a9c4c08921 100644 --- a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py @@ -26,8 +26,6 @@ Galaxy side: 1a) Check for appropriate strings in the installed blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories. """ -base_datatypes_count = 0 -repository_datatypes_count = 0 running_standalone = False @@ -92,7 +90,6 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb, the datatypes that are defined in datatypes_conf.xml. """ - global repository_datatypes_count repository = self.test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_2_name ) @@ -107,7 +104,6 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): "blastdbp", ] self.display_manage_repository_page(repository, strings_displayed=strings_displayed) - repository_datatypes_count = int(self.get_repository_datatypes_count(repository)) def test_0015_create_tool_repository(self): """Create and populate the blastxml_to_top_descr_0120 repository @@ -218,24 +214,12 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): are now new datatypes in the registry matching the ones defined in blast_datatypes_0120. Also check that blast_datatypes_0120 is labeled as an installed repository dependency of blastxml_to_top_descr_0120. """ - global repository_datatypes_count - global base_datatypes_count tool_repository = self.test_db_util.get_installed_repository_by_name_owner( tool_repository_name, common.test_user_1_name ) datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner( datatypes_repository_name, common.test_user_2_name ) - current_datatypes = int(self.get_datatypes_count()) - expected_count = base_datatypes_count + repository_datatypes_count - # Once the BLAST datatypes have been included in Galaxy itself, the count won't change - assert ( - current_datatypes == base_datatypes_count or current_datatypes == expected_count - ), "Installing %s did not add new datatypes. Expected: %d. Found: %d" % ( - "blastxml_to_top_descr_0120", - expected_count, - current_datatypes, - ) strings_displayed = ["Installed repository dependencies", "user1", "blast_datatypes_0120"] strings_displayed.extend( ["Valid tools", "BLAST top hit", "Make a table", datatypes_repository.installed_changeset_revision] From 860ab797a8bad2e5770627511815d4ef9cc706e4 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 18:34:19 -0400 Subject: [PATCH 04/11] Remove a couple functions from test_db_util that talk to the Galaxy database directly. These functions were just effectively ensuring a Galaxy user was created properly - but the framework does that and the UI login double does that. --- lib/tool_shed/test/base/test_db_util.py | 11 ----------- .../functional/test_1000_install_basic_repository.py | 5 ----- ..._1010_install_repository_with_tool_dependencies.py | 3 --- ...install_repository_with_repository_dependencies.py | 5 ----- ...30_install_repository_with_dependency_revisions.py | 5 ----- .../test/functional/test_1070_invalid_tool.py | 5 ----- ..._1080_advanced_circular_dependency_installation.py | 5 ----- .../test_1090_repository_dependency_handling.py | 5 ----- ...st_1100_install_updated_repository_dependencies.py | 5 ----- .../test_1170_prior_installation_required.py | 5 ----- .../test_1180_circular_prior_installation_required.py | 5 ----- ...t_1200_uninstall_and_reinstall_basic_repository.py | 5 ----- ...all_reinstall_repository_with_tool_dependencies.py | 3 --- ..._reinstall_repository_with_dependency_revisions.py | 3 --- .../test/functional/test_1410_update_manager.py | 5 ----- 15 files changed, 75 deletions(-) diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index bb758d56d3b..3bd2ec9b56a 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -192,17 +192,6 @@ def ga_refresh(obj): install_session.refresh(obj) -def get_galaxy_private_role(user): - for role in user.all_roles(): - if role.name == user.email and role.description == f"Private Role for {user.email}": - return role - raise AssertionError(f"Private role not found for user '{user.email}'") - - -def get_galaxy_user(email): - return ga_session.query(galaxy.model.User).filter(galaxy.model.User.table.c.email == email).first() - - def get_repository_by_name_and_owner(name, owner_username, return_multiple=False): owner = get_user_by_name(owner_username) repository = ( diff --git a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py index 2fd978971e0..6eb044e84ec 100644 --- a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py @@ -20,11 +20,6 @@ class BasicToolShedFeatures(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0000 category and upload the filtering repository to it, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py index c7796fbafd3..6fa71b3c4e7 100644 --- a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py @@ -19,9 +19,6 @@ class ToolWithToolDependencies(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py index 69dfd9beb21..3ffbbcbdb5c 100644 --- a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py @@ -28,11 +28,6 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0020 category and any missing repositories.""" diff --git a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py index 99bd0db4e28..96ce478c2fc 100644 --- a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py @@ -32,11 +32,6 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0030 category and add repositories to it, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1070_invalid_tool.py b/lib/tool_shed/test/functional/test_1070_invalid_tool.py index 0059ac752d8..524047b499f 100644 --- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py +++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py @@ -16,11 +16,6 @@ class TestFreebayesRepository(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py index de559348e5c..5842e81ff88 100644 --- a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py +++ b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py @@ -27,11 +27,6 @@ class TestRepositoryDependencies(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py index 71ed5b316e6..70ac52b6a03 100644 --- a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py +++ b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py @@ -25,11 +25,6 @@ class TestRepositoryDependencies(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py index c35e25fdca8..7eac46d5e7b 100644 --- a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py @@ -21,11 +21,6 @@ class TestRepositoryDependencies(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py index fd884346197..266c59ddcda 100644 --- a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py @@ -41,11 +41,6 @@ class TestSimplePriorInstallation(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py index 43d77d148b8..20f92c9227a 100644 --- a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py @@ -54,11 +54,6 @@ class TestSimplePriorInstallation(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py index 4f0c450ab0b..c9866871627 100644 --- a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -20,11 +20,6 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0000 category and upload the filtering repository to the tool shed, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py index 7676db9eb55..52b1670a1e0 100644 --- a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -12,9 +12,6 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py index 037fda8ff5d..0ba69beee96 100644 --- a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -22,9 +22,6 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) - admin_user = self.test_db_util.get_galaxy_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_galaxy_private_role(admin_user) 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 ( diff --git a/lib/tool_shed/test/functional/test_1410_update_manager.py b/lib/tool_shed/test/functional/test_1410_update_manager.py index b64d8b9044b..af6f2b8bbfa 100644 --- a/lib/tool_shed/test/functional/test_1410_update_manager.py +++ b/lib/tool_shed/test/functional/test_1410_update_manager.py @@ -43,11 +43,6 @@ class TestUpdateManager(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) - galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email) - assert ( - galaxy_admin_user is not None - ), f"Problem retrieving user with email {common.admin_email} from the database" - self.test_db_util.get_galaxy_private_role(galaxy_admin_user) def test_0005_create_filtering_repository(self): """Create and populate the filtering_1410 repository. From f24c720fc029a73791db2778628532bdb9c78ae7 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 18:39:20 -0400 Subject: [PATCH 05/11] Remove unused functions in test_db_util. --- lib/tool_shed/test/base/test_db_util.py | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index 3bd2ec9b56a..01eaac9663e 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -56,22 +56,6 @@ def get_all_installed_repositories(actually_installed=False): return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).all() -def get_default_user_permissions_by_role(role): - return ( - sa_session.query(model.DefaultUserPermissions) - .filter(model.DefaultUserPermissions.table.c.role_id == role.id) - .all() - ) - - -def get_default_user_permissions_by_user(user): - return ( - sa_session.query(model.DefaultUserPermissions) - .filter(model.DefaultUserPermissions.table.c.user_id == user.id) - .all() - ) - - def get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision): return ( install_session.query(galaxy.model.tool_shed_install.ToolShedRepository) From 678d702fbd24ea3c97047097d4437acbec33265e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 18:36:45 -0400 Subject: [PATCH 06/11] Remove unused mypy entry. --- mypy.ini | 2 -- 1 file changed, 2 deletions(-) diff --git a/mypy.ini b/mypy.ini index 933d9e160eb..01518052989 100644 --- a/mypy.ini +++ b/mypy.ini @@ -610,8 +610,6 @@ check_untyped_defs = False check_untyped_defs = False [mypy-test.functional.test_toolbox] check_untyped_defs = False -[mypy-tool_shed.test.functional_tests] -check_untyped_defs = False [mypy-tool_shed.test.base.test_db_util] check_untyped_defs = False [mypy-integration.test_save_job_id_on_datasets] From 797db736fec402f9765f1308a77d1acc50af62fb Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 19 Sep 2022 18:42:30 -0400 Subject: [PATCH 07/11] Remove typing exceptions for tool shed tests. The testing seems fixed. --- mypy.ini | 108 ------------------------------------------------------- 1 file changed, 108 deletions(-) diff --git a/mypy.ini b/mypy.ini index 01518052989..1ab424fc315 100644 --- a/mypy.ini +++ b/mypy.ini @@ -662,114 +662,6 @@ check_untyped_defs = False check_untyped_defs = False [mypy-test.functional.conftest] check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1470_updating_installed_repositories] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1460_data_managers] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1430_repair_installed_repository] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1410_update_manager] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1300_reset_all_metadata] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1190_complex_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1180_circular_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1170_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1160_tool_help_images] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1100_install_updated_repository_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1090_repository_dependency_handling] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1080_advanced_circular_dependency_installation] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1070_invalid_tool] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1050_circular_dependencies_4_levels] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_1000_install_basic_repository] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0550_metadata_updated_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0540_get_all_metadata_from_api] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0530_repository_admin_feature] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0480_tool_dependency_xml_verification] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0470_tool_dependency_repository_type] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0460_upload_to_repository] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0440_deleting_dependency_definitions] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0430_browse_utilities] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0420_citable_urls_for_repositories] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0410_repository_component_review_access_control] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0400_repository_component_reviews] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0310_hg_api_features] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0300_reset_all_metadata] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0170_complex_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0160_circular_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0150_prior_installation_required] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0140_tool_help_images] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0100_complex_repository_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0090_tool_search] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0080_advanced_circular_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0070_invalid_tool] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0050_circular_dependencies_4_levels] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0040_repository_circular_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0030_repository_dependency_revisions] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0020_basic_repository_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0010_repository_with_tool_dependencies] -check_untyped_defs = False -[mypy-tool_shed.test.functional.test_0000_basic_repository_features] -check_untyped_defs = False [mypy-integration.test_containerized_jobs] check_untyped_defs = False [mypy-integration.test_chained_dynamic_destinations] From 4ec76afaac3c72b22304f87b57e63189403fa602 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 20 Sep 2022 09:35:05 -0400 Subject: [PATCH 08/11] Eliminate more unneeded role checks in tool shed functional tests. --- lib/tool_shed/test/base/test_db_util.py | 7 ------- .../test_0000_basic_repository_features.py | 13 ------------- .../test_0010_repository_with_tool_dependencies.py | 8 -------- .../test_0020_basic_repository_dependencies.py | 8 -------- .../test_0030_repository_dependency_revisions.py | 8 -------- .../test_0040_repository_circular_dependencies.py | 8 -------- .../test_0050_circular_dependencies_4_levels.py | 8 -------- .../test/functional/test_0070_invalid_tool.py | 8 -------- .../test_0080_advanced_circular_dependencies.py | 8 -------- .../test/functional/test_0090_tool_search.py | 8 -------- .../test_0100_complex_repository_dependencies.py | 8 -------- ...t_0110_invalid_simple_repository_dependencies.py | 8 -------- ..._simple_repository_dependency_multiple_owners.py | 13 ------------- .../test/functional/test_0140_tool_help_images.py | 8 -------- .../test_0150_prior_installation_required.py | 8 -------- ...est_0160_circular_prior_installation_required.py | 8 -------- ...test_0170_complex_prior_installation_required.py | 8 -------- .../test/functional/test_0300_reset_all_metadata.py | 8 -------- .../test/functional/test_0310_hg_api_features.py | 13 ------------- .../test_0420_citable_urls_for_repositories.py | 8 -------- .../test/functional/test_0430_browse_utilities.py | 8 -------- .../test_0440_deleting_dependency_definitions.py | 8 -------- .../functional/test_0460_upload_to_repository.py | 13 ------------- .../test_0470_tool_dependency_repository_type.py | 13 ------------- .../test_0480_tool_dependency_xml_verification.py | 13 ------------- .../test_0530_repository_admin_feature.py | 13 ------------- .../test_0540_get_all_metadata_from_api.py | 8 -------- .../test_0550_metadata_updated_dependencies.py | 8 -------- .../test_1000_install_basic_repository.py | 8 -------- ...010_install_repository_with_tool_dependencies.py | 8 -------- ...stall_repository_with_repository_dependencies.py | 8 -------- ..._install_repository_with_dependency_revisions.py | 8 -------- ...nstall_repository_basic_circular_dependencies.py | 8 -------- .../test_1050_circular_dependencies_4_levels.py | 8 -------- .../test/functional/test_1070_invalid_tool.py | 8 -------- ...080_advanced_circular_dependency_installation.py | 8 -------- .../test_1090_repository_dependency_handling.py | 8 -------- ..._1100_install_updated_repository_dependencies.py | 8 -------- ..._install_repository_with_complex_dependencies.py | 8 -------- ...repository_with_invalid_repository_dependency.py | 8 -------- ..._simple_repository_dependency_multiple_owners.py | 13 ------------- .../test/functional/test_1160_tool_help_images.py | 8 -------- .../test_1170_prior_installation_required.py | 8 -------- ...est_1180_circular_prior_installation_required.py | 8 -------- ...test_1190_complex_prior_installation_required.py | 8 -------- ...1200_uninstall_and_reinstall_basic_repository.py | 8 -------- ...l_reinstall_repository_with_tool_dependencies.py | 8 -------- ...einstall_repository_with_dependency_revisions.py | 8 -------- .../test/functional/test_1300_reset_all_metadata.py | 8 -------- .../test/functional/test_1410_update_manager.py | 8 -------- .../test_1430_repair_installed_repository.py | 13 ------------- .../test/functional/test_1460_data_managers.py | 13 ------------- .../test_1470_updating_installed_repositories.py | 8 -------- 53 files changed, 473 deletions(-) diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index 01eaac9663e..e219f2c5939 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -90,13 +90,6 @@ def get_installed_repository_by_name_owner(repository_name, owner, return_multip return query.first() -def get_private_role(user): - for role in user.all_roles(): - if role.name == user.email and role.description == f"Private Role for {user.email}": - return role - raise AssertionError(f"Private role not found for user '{user.email}'") - - def get_role(user, role_name): for role in user.all_roles(): if role.name == role_name: diff --git a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py index dbb5552c7a1..9b632b11fc7 100644 --- a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py +++ b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py @@ -18,21 +18,8 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_repository_without_categories(self): """Verify that a repository cannot be created unless at least one category has been defined.""" diff --git a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py index ab62120ceb5..f0c7c820df8 100644 --- a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py @@ -26,15 +26,7 @@ class TestFreebayesRepository(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py index 4d32c6955ab..769d2704cf4 100644 --- a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py @@ -18,15 +18,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py index 4c6df862180..6389b4c3c20 100644 --- a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py @@ -20,15 +20,7 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase): 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py index b846ce5e77b..7f47b7ee754 100644 --- a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py @@ -21,15 +21,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py index 3edca69132a..1ec35851ba0 100644 --- a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py +++ b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py @@ -37,15 +37,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase): 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0050.""" diff --git a/lib/tool_shed/test/functional/test_0070_invalid_tool.py b/lib/tool_shed/test/functional/test_0070_invalid_tool.py index b8e6f6621a7..547433099d2 100644 --- a/lib/tool_shed/test/functional/test_0070_invalid_tool.py +++ b/lib/tool_shed/test/functional/test_0070_invalid_tool.py @@ -16,15 +16,7 @@ class TestBismarkRepository(ShedTwillTestCase): def test_0000_create_or_login_admin_user(self): """Create necessary user accounts and login as an admin user.""" 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) def test_0005_create_category_and_repository(self): """Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool.""" diff --git a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py index e20de949cec..5c2674f0936 100644 --- a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py @@ -21,15 +21,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase): 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) def test_0005_create_column_repository(self): """Create and populate the column_maker repository.""" diff --git a/lib/tool_shed/test/functional/test_0090_tool_search.py b/lib/tool_shed/test/functional/test_0090_tool_search.py index 90869bd82af..1d9a9221c26 100644 --- a/lib/tool_shed/test/functional/test_0090_tool_search.py +++ b/lib/tool_shed/test/functional/test_0090_tool_search.py @@ -33,15 +33,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase): 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) def test_0005_create_bwa_base_repository(self): """Create and populate bwa_base_0090.""" diff --git a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py index 5a660317a33..2723595c5c1 100644 --- a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py @@ -28,15 +28,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase): 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) def test_0005_create_bwa_package_repository(self): """Create and populate package_bwa_0_5_9_0100.""" diff --git a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py index 47a6feaa251..44165cfe410 100644 --- a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py @@ -21,15 +21,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py index f135b8f1f75..8daa7050143 100644 --- a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py @@ -31,21 +31,8 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_1_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_datatypes_repository(self): """Create and populate the blast_datatypes_0120 repository diff --git a/lib/tool_shed/test/functional/test_0140_tool_help_images.py b/lib/tool_shed/test/functional/test_0140_tool_help_images.py index 9e634194813..62ad565119a 100644 --- a/lib/tool_shed/test/functional/test_0140_tool_help_images.py +++ b/lib/tool_shed/test/functional/test_0140_tool_help_images.py @@ -30,15 +30,7 @@ class TestToolHelpImages(ShedTwillTestCase): 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) def test_0005_create_htseq_count_repository(self): """Create and populate htseq_count_0140. diff --git a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py index c5dea295a88..7b9869c65cd 100644 --- a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py @@ -35,15 +35,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0150.""" diff --git a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py index b8c9c47dbc1..6b7a0e58592 100644 --- a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py @@ -34,15 +34,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0160.""" diff --git a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py index 8b64a2ff8b6..f63d54fc55d 100644 --- a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py @@ -35,15 +35,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): 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) def test_0005_create_matplotlib_repository(self): """Create and populate the package_matplotlib_1_2_0170 repository. diff --git a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py index 61c083f51bf..6bdc4fab6f3 100644 --- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py +++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py @@ -46,15 +46,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase): 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) def test_0005_create_filtering_repository(self): """Create and populate the filtering_0000 repository.""" diff --git a/lib/tool_shed/test/functional/test_0310_hg_api_features.py b/lib/tool_shed/test/functional/test_0310_hg_api_features.py index f3f47b1f98c..7c8873c3605 100644 --- a/lib/tool_shed/test/functional/test_0310_hg_api_features.py +++ b/lib/tool_shed/test/functional/test_0310_hg_api_features.py @@ -27,21 +27,8 @@ class TestHgWebFeatures(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_filtering_repository(self): """Create and populate the filtering_0310 repository. diff --git a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py index 13720b7b562..014eb031d05 100644 --- a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py +++ b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py @@ -37,15 +37,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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) def test_0005_create_repository(self): """Create and populate the filtering_0420 repository diff --git a/lib/tool_shed/test/functional/test_0430_browse_utilities.py b/lib/tool_shed/test/functional/test_0430_browse_utilities.py index 38c0c325cc2..e897ca6c38f 100644 --- a/lib/tool_shed/test/functional/test_0430_browse_utilities.py +++ b/lib/tool_shed/test/functional/test_0430_browse_utilities.py @@ -33,15 +33,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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) def test_0010_create_emboss_repository(self): """Create and populate the emboss_0430 repository diff --git a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py index dcedf318fc7..b70f63f3ce9 100644 --- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py +++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py @@ -61,15 +61,7 @@ class TestDeletedDependencies(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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) def test_0005_create_column_maker_repository(self): """Create and populate a repository named column_maker_0440. diff --git a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py index 80da7c5dd85..c27ede6ff3d 100644 --- a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py +++ b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py @@ -62,21 +62,8 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_datatypes_repository(self): """Create and populate the emboss_datatypes_0460 repository diff --git a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py index 7b2f0461287..7fcaf6f3a99 100644 --- a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py +++ b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py @@ -68,22 +68,9 @@ class TestEnvironmentInheritance(ShedTwillTestCase): def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" 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) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_libx11_repository(self): """Create and populate package_x11_client_1_5_proto_7_0_0470. diff --git a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py index 29126a54881..7cafb988070 100644 --- a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py +++ b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py @@ -28,22 +28,9 @@ class TestDependencyDefinitionValidation(ShedTwillTestCase): def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" 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) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_tool_dependency_repository(self): """Create and populate package_invalid_tool_dependency_xml_1_0_0. diff --git a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py index 4045ff5295e..823a69bc4ee 100644 --- a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py +++ b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py @@ -39,21 +39,8 @@ class TestRepositoryAdminRole(ShedTwillTestCase): 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_filtering_repository(self): """Create and populate the filtering_0530 repository. diff --git a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py index 803c27eeb52..277a6c05371 100644 --- a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py +++ b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py @@ -47,15 +47,7 @@ class TestGetAllMetadata(ShedTwillTestCase): 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) def test_0005_create_bwa_package_repository(self): """Create and populate package_bwa_0_5_9_0540.""" diff --git a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py index 8c322ccc665..17c8b0ded21 100644 --- a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py +++ b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py @@ -51,15 +51,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase): 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) def test_0005_freebayes_repository(self): """Create and populate package_freebayes_0550.""" diff --git a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py index 6eb044e84ec..c6d08d0bbb7 100644 --- a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py @@ -10,15 +10,7 @@ class BasicToolShedFeatures(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) def test_0005_ensure_repositories_and_categories_exist(self): diff --git a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py index 6fa71b3c4e7..3eb2154526a 100644 --- a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py @@ -20,15 +20,7 @@ class ToolWithToolDependencies(ShedTwillTestCase): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0010 category and upload the freebayes repository to it, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py index 3ffbbcbdb5c..8bad1742afe 100644 --- a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py @@ -18,15 +18,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) def test_0005_ensure_repositories_and_categories_exist(self): diff --git a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py index 96ce478c2fc..ec269e6b44d 100644 --- a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py @@ -22,15 +22,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) def test_0005_ensure_repositories_and_categories_exist(self): diff --git a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py index 8a7ba644c2d..165bddcfe05 100644 --- a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -22,15 +22,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase): 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) def test_0005_create_freebayes_repository(self): """Create and populate freebayes_0040.""" diff --git a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py index 7b29da1f40f..60154e18d95 100644 --- a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py +++ b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py @@ -39,15 +39,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase): 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0050.""" diff --git a/lib/tool_shed/test/functional/test_1070_invalid_tool.py b/lib/tool_shed/test/functional/test_1070_invalid_tool.py index 524047b499f..00d9b0bf4f0 100644 --- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py +++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py @@ -17,15 +17,7 @@ class TestFreebayesRepository(ShedTwillTestCase): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_ensure_existence_of_repository_and_category(self): """Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool.""" diff --git a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py index 5842e81ff88..12d1e7f51cb 100644 --- a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py +++ b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py @@ -28,15 +28,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_create_and_populate_column_repository(self): """Create the category for this test suite, then create and populate column_maker.""" diff --git a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py index 70ac52b6a03..8fe92e3cbbc 100644 --- a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py +++ b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py @@ -26,15 +26,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_create_and_populate_column_repository(self): """Create a category for this test suite and add repositories to it.""" diff --git a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py index 7eac46d5e7b..02972015f67 100644 --- a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py +++ b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py @@ -22,15 +22,7 @@ class TestRepositoryDependencies(ShedTwillTestCase): """Create necessary user accounts and login as an admin user.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_create_and_populate_column_repository(self): """Create a category for this test suite and add repositories to it.""" diff --git a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py index d97b9534655..91c23eafb26 100644 --- a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py +++ b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py @@ -28,15 +28,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase): 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) def test_0005_create_bwa_package_repository(self): """Create and populate package_bwa_0_5_9_0100.""" diff --git a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py index a1f56f391da..cc63e9e54d1 100644 --- a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py +++ b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py @@ -22,15 +22,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase): def test_0000_initiate_users(self): """Create necessary user accounts and login as an admin user.""" 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) def test_0005_create_category(self): """Create a category for this test suite""" diff --git a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py index 1a9c4c08921..affccd8c3fb 100644 --- a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py +++ b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py @@ -37,21 +37,8 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_1_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_datatypes_repository(self): """Create and populate the blast_datatypes_0120 repository diff --git a/lib/tool_shed/test/functional/test_1160_tool_help_images.py b/lib/tool_shed/test/functional/test_1160_tool_help_images.py index 718a955761f..5d6f33cdbaf 100644 --- a/lib/tool_shed/test/functional/test_1160_tool_help_images.py +++ b/lib/tool_shed/test/functional/test_1160_tool_help_images.py @@ -26,15 +26,7 @@ class TestToolHelpImages(ShedTwillTestCase): 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) def test_0005_create_htseq_count_repository(self): """Create and populate htseq_count_0140. diff --git a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py index 266c59ddcda..ada5e3acb45 100644 --- a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py @@ -42,15 +42,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0150.""" diff --git a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py index 20f92c9227a..d78b0dae319 100644 --- a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py @@ -55,15 +55,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_create_convert_repository(self): """Create and populate convert_chars_0160.""" diff --git a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py index e24ebfdab00..aa697481767 100644 --- a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py +++ b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py @@ -39,15 +39,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase): 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) def test_0005_create_matplotlib_repository(self): """Create and populate the package_matplotlib_1_2_0170 repository. diff --git a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py index c9866871627..aea8956ed9f 100644 --- a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -10,15 +10,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) def test_0005_ensure_repositories_and_categories_exist(self): diff --git a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py index 52b1670a1e0..a1a95a18e56 100644 --- a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -13,15 +13,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0010 category and upload the freebayes repository to the tool shed, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py index 0ba69beee96..32513136e7d 100644 --- a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -23,15 +23,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase): """Create necessary user accounts.""" self.galaxy_login(email=common.admin_email, username=common.admin_username) 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) def test_0005_ensure_repositories_and_categories_exist(self): """Create the 0030 category and upload the emboss repository to the tool shed, if necessary.""" diff --git a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py index 038b032cc36..68b45dfdcc3 100644 --- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py +++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py @@ -47,15 +47,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase): 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) def test_0005_create_categories(self): """Create the categories for the repositories in this test script.""" diff --git a/lib/tool_shed/test/functional/test_1410_update_manager.py b/lib/tool_shed/test/functional/test_1410_update_manager.py index af6f2b8bbfa..fa95795a7f0 100644 --- a/lib/tool_shed/test/functional/test_1410_update_manager.py +++ b/lib/tool_shed/test/functional/test_1410_update_manager.py @@ -33,15 +33,7 @@ class TestUpdateManager(ShedTwillTestCase): Previously created accounts will not be re-created. """ 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) self.galaxy_login(email=common.admin_email, username=common.admin_username) def test_0005_create_filtering_repository(self): diff --git a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py index 5eb9e9566a3..9d71d177f7d 100644 --- a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py +++ b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py @@ -40,22 +40,9 @@ class TestRepairRepository(ShedTwillTestCase): def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" 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) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0005_create_filter_repository(self): """Create and populate the filter_1430 repository. diff --git a/lib/tool_shed/test/functional/test_1460_data_managers.py b/lib/tool_shed/test/functional/test_1460_data_managers.py index 95c097d34eb..267edfd6ca3 100644 --- a/lib/tool_shed/test/functional/test_1460_data_managers.py +++ b/lib/tool_shed/test/functional/test_1460_data_managers.py @@ -33,22 +33,9 @@ class TestDataManagers(ShedTwillTestCase): def test_0000_initiate_users_and_category(self): """Create necessary user accounts and login as an admin user.""" 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) self.create_category(name=category_name, description=category_description) self.login(email=common.test_user_2_email, username=common.test_user_2_name) - test_user_2 = self.test_db_util.get_user(common.test_user_2_email) - assert ( - test_user_2 is not None - ), f"Problem retrieving user with email {common.test_user_2_email} from the database" - self.test_db_util.get_private_role(test_user_2) 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) def test_0010_create_data_manager_repository(self): """Create and populate data_manager_1460. diff --git a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py index 544291abdae..44c7542afbc 100644 --- a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py +++ b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py @@ -32,15 +32,7 @@ class TestUpdateInstalledRepository(ShedTwillTestCase): 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) def test_0005_create_filtering_repository(self): """Create and populate the filtering_0530 repository.""" From 68fc220a7779fe5578438ad388b1d5fc4c71ef50 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 20 Sep 2022 11:40:19 -0400 Subject: [PATCH 09/11] Remove unused twilltestcase method. --- lib/tool_shed/test/base/twilltestcase.py | 7 ------- 1 file changed, 7 deletions(-) diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index 9e26479a8c2..a560e840f52 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -914,13 +914,6 @@ class ShedTwillTestCase(ShedBaseTestCase): repo = self.get_hg_repo(self.get_repo_path(repository)) return str(repo[repo.changelog.tip()]) - def get_sniffers_count(self): - url = "/api/datatypes/sniffers" - self.visit_galaxy_url(url) - html = self.last_page() - sniffers = loads(html) - return len(sniffers) - def get_tools_from_repository_metadata(self, repository, include_invalid=False): """Get a list of valid and (optionally) invalid tool dicts from the repository metadata.""" valid_tools = [] From ee33f082e6f7f41603c998f70102f72e305c80e1 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 20 Sep 2022 11:43:36 -0400 Subject: [PATCH 10/11] Remove more unused code from tool shed tests. --- lib/tool_shed/test/base/twilltestcase.py | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py index a560e840f52..65e1717045b 100644 --- a/lib/tool_shed/test/base/twilltestcase.py +++ b/lib/tool_shed/test/base/twilltestcase.py @@ -259,11 +259,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url("/repository/browse_valid_categories", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def browse_custom_datatypes(self, strings_displayed=None, strings_not_displayed=None): - url = "/repository/browse_datatypes" - self.visit_url(url) - self.check_for_strings(strings_displayed, strings_not_displayed) - def browse_repository(self, repository, strings_displayed=None, strings_not_displayed=None): params = {"id": self.security.encode_id(repository.id)} self.visit_url("/repository/browse_repository", params=params) @@ -1173,11 +1168,6 @@ class ShedTwillTestCase(ShedBaseTestCase): self.visit_url("/repository/load_invalid_tool", params=params) self.check_for_strings(strings_displayed, strings_not_displayed) - def load_page_for_installed_tool(self, tool_guid, strings_displayed=None, strings_not_displayed=None): - params = {"tool_id": tool_guid} - self.visit_galaxy_url("/tool_runner", params=params) - self.check_for_strings(strings_displayed, strings_not_displayed) - def preview_repository_in_tool_shed( self, name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None ): From 5bf5a3d85e91fee7438e3201cbed8f5e44192198 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 20 Sep 2022 18:30:34 -0400 Subject: [PATCH 11/11] Cleanup galaxy context no longer needed for tool shed tests. --- lib/galaxy_test/driver/driver_util.py | 3 --- lib/tool_shed/test/base/test_db_util.py | 1 - 2 files changed, 4 deletions(-) diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py index a3d471c2ab6..7c95fd1c452 100644 --- a/lib/galaxy_test/driver/driver_util.py +++ b/lib/galaxy_test/driver/driver_util.py @@ -79,7 +79,6 @@ log = logging.getLogger("test_driver") # Global variables to pass database contexts around - only needed for older # Tool Shed twill tests that didn't utilize the API for such interactions. -galaxy_context = None tool_shed_context = None install_context = None @@ -633,9 +632,7 @@ def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication: app = GalaxyUniverseApplication(**simple_kwargs) log.info("Embedded Galaxy application started") - global galaxy_context global install_context - galaxy_context = app.model.context install_context = app.install_model.context # Toolbox indexing happens via the work queue out of band recently, and, diff --git a/lib/tool_shed/test/base/test_db_util.py b/lib/tool_shed/test/base/test_db_util.py index e219f2c5939..28b432030b8 100644 --- a/lib/tool_shed/test/base/test_db_util.py +++ b/lib/tool_shed/test/base/test_db_util.py @@ -10,7 +10,6 @@ import galaxy.model import galaxy.model.tool_shed_install import tool_shed.webapp.model as model from galaxy_test.driver.driver_util import ( - galaxy_context as ga_session, install_context as install_session, tool_shed_context as sa_session, )