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