diff --git a/lib/galaxy_test/driver/driver_util.py b/lib/galaxy_test/driver/driver_util.py
index a3d471c2ab6..7c95fd1c452 100644
--- a/lib/galaxy_test/driver/driver_util.py
+++ b/lib/galaxy_test/driver/driver_util.py
@@ -79,7 +79,6 @@ log = logging.getLogger("test_driver")
# Global variables to pass database contexts around - only needed for older
# Tool Shed twill tests that didn't utilize the API for such interactions.
-galaxy_context = None
tool_shed_context = None
install_context = None
@@ -633,9 +632,7 @@ def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:
app = GalaxyUniverseApplication(**simple_kwargs)
log.info("Embedded Galaxy application started")
- global galaxy_context
global install_context
- galaxy_context = app.model.context
install_context = app.install_model.context
# Toolbox indexing happens via the work queue out of band recently, and,
diff --git a/lib/tool_shed/test/base/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..28b432030b8 100644
--- a/lib/tool_shed/test/base/test_db_util.py
+++ b/lib/tool_shed/test/base/test_db_util.py
@@ -10,7 +10,6 @@ import galaxy.model
import galaxy.model.tool_shed_install
import tool_shed.webapp.model as model
from galaxy_test.driver.driver_util import (
- galaxy_context as ga_session,
install_context as install_session,
tool_shed_context as sa_session,
)
@@ -56,26 +55,6 @@ 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)
- .filter(model.DefaultUserPermissions.table.c.role_id == role.id)
- .all()
- )
-
-
-def get_default_user_permissions_by_user(user):
- return (
- sa_session.query(model.DefaultUserPermissions)
- .filter(model.DefaultUserPermissions.table.c.user_id == user.id)
- .all()
- )
-
-
def get_galaxy_repository_by_name_owner_changeset_revision(repository_name, owner, changeset_revision):
return (
install_session.query(galaxy.model.tool_shed_install.ToolShedRepository)
@@ -110,13 +89,6 @@ def get_installed_repository_by_name_owner(repository_name, owner, return_multip
return query.first()
-def get_private_role(user):
- for role in user.all_roles():
- if role.name == user.email and role.description == f"Private Role for {user.email}":
- return role
- raise AssertionError(f"Private role not found for user '{user.email}'")
-
-
def get_role(user, role_name):
for role in user.all_roles():
if role.name == role_name:
@@ -196,17 +168,6 @@ def ga_refresh(obj):
install_session.refresh(obj)
-def get_galaxy_private_role(user):
- for role in user.all_roles():
- if role.name == user.email and role.description == f"Private Role for {user.email}":
- return role
- raise AssertionError(f"Private role not found for user '{user.email}'")
-
-
-def get_galaxy_user(email):
- return ga_session.query(galaxy.model.User).filter(galaxy.model.User.table.c.email == email).first()
-
-
def get_repository_by_name_and_owner(name, owner_username, return_multiple=False):
owner = get_user_by_name(owner_username)
repository = (
diff --git a/lib/tool_shed/test/base/twilltestcase.py b/lib/tool_shed/test/base/twilltestcase.py
index 05b01f38ea6..65e1717045b 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,
@@ -248,20 +250,15 @@ 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)
- def browse_custom_datatypes(self, strings_displayed=None, strings_not_displayed=None):
- url = "/repository/browse_datatypes"
- self.visit_url(url)
- self.check_for_strings(strings_displayed, strings_not_displayed)
-
def browse_repository(self, repository, strings_displayed=None, strings_not_displayed=None):
params = {"id": self.security.encode_id(repository.id)}
self.visit_url("/repository/browse_repository", params=params)
@@ -451,13 +448,14 @@ 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 +813,17 @@ 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 +831,11 @@ 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
@@ -854,13 +858,6 @@ class ShedTwillTestCase(ShedBaseTestCase):
changelog_tuples.append((ctx.rev(), ctx))
return changelog_tuples
- def get_repository_datatypes_count(self, repository):
- metadata = self.get_repository_metadata(repository)[0].metadata
- if "datatypes" not in metadata:
- return 0
- else:
- return len(metadata["datatypes"])
-
def get_repository_file_list(self, repository, base_path, current_path=None):
"""Recursively load repository folder contents and append them to a list. Similar to os.walk but via /repository/open_folder."""
if current_path is None:
@@ -912,13 +909,6 @@ class ShedTwillTestCase(ShedBaseTestCase):
repo = self.get_hg_repo(self.get_repo_path(repository))
return str(repo[repo.changelog.tip()])
- def get_sniffers_count(self):
- url = "/api/datatypes/sniffers"
- self.visit_galaxy_url(url)
- html = self.last_page()
- sniffers = loads(html)
- return len(sniffers)
-
def get_tools_from_repository_metadata(self, repository, include_invalid=False):
"""Get a list of valid and (optionally) invalid tool dicts from the repository metadata."""
valid_tools = []
@@ -1051,7 +1041,7 @@ 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)
@@ -1178,11 +1168,6 @@ class ShedTwillTestCase(ShedBaseTestCase):
self.visit_url("/repository/load_invalid_tool", params=params)
self.check_for_strings(strings_displayed, strings_not_displayed)
- def load_page_for_installed_tool(self, tool_guid, strings_displayed=None, strings_not_displayed=None):
- params = {"tool_id": tool_guid}
- self.visit_galaxy_url("/tool_runner", params=params)
- self.check_for_strings(strings_displayed, strings_not_displayed)
-
def preview_repository_in_tool_shed(
self, name, owner, changeset_revision=None, strings_displayed=None, strings_not_displayed=None
):
diff --git a/lib/tool_shed/test/functional/api_notes.md b/lib/tool_shed/test/functional/api_notes.md
new file mode 100644
index 00000000000..18174ff96a9
--- /dev/null
+++ b/lib/tool_shed/test/functional/api_notes.md
@@ -0,0 +1,42 @@
+# Tool Shed Migration Notes
+
+The Galaxy developer community has different intentions and ideas for the tool shed going forward including:
+
+- a complete rewrite (https://github.com/hexylena/shed)
+- merge the existing functionality that is needed into DockStore (https://dockstore.org/)
+- a rewrite of Galaxy to just use GitHub directly (the Anton approach)
+- spinning the codebase off as is (duplicating and freezing the Galaxy half) (https://github.com/galaxyproject/galaxy/pull/8830)
+- spinning the code base while continuing reuse via Python packaging
+
+There is largely agreement that the tool shed code is aging and if the UI should continue
+to exist it should be rewritten. The ecosystem has evolved such that I think all parties would
+also agree that all server access (by Galaxy or a new UI) should be via a tool shed API and should
+be typed and well modelled.
+
+This chart is meant to track what API endpoints are used where and how they are used to gauage
+how conservative we should be in breaking backward compatiblity. This chart doesn't guarentee
+endpoints will remain, will stay consistent, or even that a tool shed API will continue to exist.
+It is just meant to track information and allow us to make clear choices. Nothing is scared here.
+
+Things seemingly *NOT* used by Galaxy, Planemo, or Ephemeris. These are easy candidates for
+for deletion instead of writing new tests and modernizing the API.
+
+- reset_metadata_on_repositories
+- remove_repository_registry_entry
+- get_repository_revision_install_info
+- get_installable_revisions
+- The whole Groups API.
+- The whole Repository Revisions API.
+
+| api | Galaxy | Planemo | Ephemeris | Pydantic or API tests | Used for TS Functional Testing | Notes |
+| --- | ------ | ------- | --------- | --------------------- | ------------------------------ | ----- |
+| GET categories | ? | ? | ? | YES | NO | Easy to maintain/migrate |
+| POST categories | NO | NO | NO | YES | YES | Easy to maintain/migrate |
+| get_repository_revision_install_info | YES | | | | | NO | Used by install code. |
+| get_ordered_installable_revisions | NO | NO | YES | YES | NO | used by complete_repo_information in ephemeris for shed_tools |
+| reset_metadata_on_repository | NO | NO | NO | YES | NO | Bjoern said it was a thing that is done via the UI still |
+| GET repositories/{repository_id}/metadata| Yes (getRepository in client?) | NO? | NO? | YES | NO | |
+| tool search | NO | NO | NO | YES | NO | Community contributed - used by tool dog or something? |
+| repo search | YES | NO | NO | YES | NO | Used by the Vue tool shed install interface. |
+| repositories/{repository_id}/changeset_revision | NO | YES | NO | YES | NO | |
+| POST repositories | NO | YES | NO | YES | NO | |
diff --git a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
index 3525f9684e6..9b632b11fc7 100644
--- a/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
+++ b/lib/tool_shed/test/functional/test_0000_basic_repository_features.py
@@ -18,21 +18,8 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_repository_without_categories(self):
"""Verify that a repository cannot be created unless at least one category has been defined."""
@@ -52,14 +39,14 @@ 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 +292,7 @@ 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 +301,7 @@ 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 +420,8 @@ 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..f0c7c820df8 100644
--- a/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
@@ -26,15 +26,7 @@ class TestFreebayesRepository(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
@@ -51,13 +43,13 @@ 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..769d2704cf4 100644
--- a/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
@@ -18,15 +18,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
@@ -36,14 +28,14 @@ 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 +52,13 @@ 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..6389b4c3c20 100644
--- a/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
@@ -20,15 +20,7 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
@@ -39,13 +31,13 @@ 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 +54,13 @@ 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 +77,13 @@ 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 +101,13 @@ 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..7f47b7ee754 100644
--- a/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
@@ -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."""
@@ -18,32 +21,25 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
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 +57,13 @@ 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..1ec35851ba0 100644
--- a/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
+++ b/lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
@@ -37,15 +37,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0050."""
@@ -56,7 +48,7 @@ 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 +71,7 @@ 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 +98,7 @@ 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 +121,7 @@ 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 +144,7 @@ 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 +167,7 @@ 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..547433099d2 100644
--- a/lib/tool_shed/test/functional/test_0070_invalid_tool.py
+++ b/lib/tool_shed/test/functional/test_0070_invalid_tool.py
@@ -16,15 +16,7 @@ class TestBismarkRepository(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category_and_repository(self):
"""Create a category for this test suite, then create and populate a bismark repository. It should contain at least one each valid and invalid tool."""
@@ -35,7 +27,7 @@ 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..5c2674f0936 100644
--- a/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
@@ -21,15 +21,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_column_repository(self):
"""Create and populate the column_maker repository."""
@@ -40,7 +32,7 @@ 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 +57,7 @@ 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..1d9a9221c26 100644
--- a/lib/tool_shed/test/functional/test_0090_tool_search.py
+++ b/lib/tool_shed/test/functional/test_0090_tool_search.py
@@ -33,15 +33,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_bwa_base_repository(self):
"""Create and populate bwa_base_0090."""
@@ -52,7 +44,7 @@ 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 +68,7 @@ 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 +91,7 @@ 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 +114,7 @@ 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 +137,7 @@ 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..2723595c5c1 100644
--- a/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
@@ -28,15 +28,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_bwa_package_repository(self):
"""Create and populate package_bwa_0_5_9_0100."""
@@ -48,7 +40,7 @@ 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 +69,7 @@ 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..44165cfe410 100644
--- a/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
@@ -21,15 +21,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
@@ -38,13 +30,13 @@ 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 +53,13 @@ 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..8daa7050143 100644
--- a/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
+++ b/lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
@@ -22,9 +22,6 @@ Tool shed side:
3a) Check for appropriate strings.
"""
-base_datatypes_count = 0
-repository_datatypes_count = 0
-
class TestRepositoryMultipleOwners(ShedTwillTestCase):
def test_0000_initiate_users(self):
@@ -34,21 +31,8 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_datatypes_repository(self):
"""Create and populate the blast_datatypes_0120 repository
@@ -64,7 +48,7 @@ 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(
@@ -86,7 +70,6 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb,
the datatypes that are defined in datatypes_conf.xml.
"""
- global repository_datatypes_count
repository = self.test_db_util.get_repository_by_name_and_owner(
datatypes_repository_name, common.test_user_2_name
)
@@ -101,7 +84,6 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
"blastdbp",
]
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
- repository_datatypes_count = int(self.get_repository_datatypes_count(repository))
def test_0015_create_tool_repository(self):
"""Create and populate the blastxml_to_top_descr_0120 repository
@@ -117,7 +99,7 @@ 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..62ad565119a 100644
--- a/lib/tool_shed/test/functional/test_0140_tool_help_images.py
+++ b/lib/tool_shed/test/functional/test_0140_tool_help_images.py
@@ -30,15 +30,7 @@ class TestToolHelpImages(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_htseq_count_repository(self):
"""Create and populate htseq_count_0140.
@@ -54,7 +46,7 @@ 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..7b9869c65cd 100644
--- a/lib/tool_shed/test/functional/test_0150_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0150_prior_installation_required.py
@@ -35,15 +35,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0150."""
@@ -54,7 +46,7 @@ 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 +69,7 @@ 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..6b7a0e58592 100644
--- a/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
@@ -34,15 +34,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0160."""
@@ -53,7 +45,7 @@ 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 +68,7 @@ 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 +91,7 @@ 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..f63d54fc55d 100644
--- a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
@@ -35,15 +35,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_matplotlib_repository(self):
"""Create and populate the package_matplotlib_1_2_0170 repository.
@@ -57,7 +49,7 @@ 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 +76,7 @@ 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..6bdc4fab6f3 100644
--- a/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
@@ -46,15 +46,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_filtering_repository(self):
"""Create and populate the filtering_0000 repository."""
@@ -69,7 +61,7 @@ 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 +102,7 @@ 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 +166,7 @@ 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 +196,7 @@ 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 +226,7 @@ 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 +256,7 @@ 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 +286,7 @@ 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 +316,7 @@ 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 +397,7 @@ 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 +428,7 @@ 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 +489,7 @@ 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 +516,7 @@ 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 +546,7 @@ 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 +573,7 @@ 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 +600,7 @@ 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 +627,7 @@ 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..7c8873c3605 100644
--- a/lib/tool_shed/test/functional/test_0310_hg_api_features.py
+++ b/lib/tool_shed/test/functional/test_0310_hg_api_features.py
@@ -27,21 +27,8 @@ class TestHgWebFeatures(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_filtering_repository(self):
"""Create and populate the filtering_0310 repository.
@@ -56,7 +43,7 @@ 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..014eb031d05 100644
--- a/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+++ b/lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
@@ -37,15 +37,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_repository(self):
"""Create and populate the filtering_0420 repository
@@ -64,7 +56,7 @@ 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..e897ca6c38f 100644
--- a/lib/tool_shed/test/functional/test_0430_browse_utilities.py
+++ b/lib/tool_shed/test/functional/test_0430_browse_utilities.py
@@ -33,15 +33,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0010_create_emboss_repository(self):
"""Create and populate the emboss_0430 repository
@@ -59,7 +51,7 @@ 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 +82,7 @@ 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..b70f63f3ce9 100644
--- a/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+++ b/lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
@@ -61,15 +61,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_column_maker_repository(self):
"""Create and populate a repository named column_maker_0440.
@@ -87,7 +79,7 @@ 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 +99,7 @@ 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 +107,7 @@ 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 +211,7 @@ 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 +219,7 @@ 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 +240,7 @@ 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 +248,7 @@ 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 +346,7 @@ 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 +354,7 @@ 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..c27ede6ff3d 100644
--- a/lib/tool_shed/test/functional/test_0460_upload_to_repository.py
+++ b/lib/tool_shed/test/functional/test_0460_upload_to_repository.py
@@ -62,21 +62,8 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_datatypes_repository(self):
"""Create and populate the emboss_datatypes_0460 repository
@@ -91,13 +78,13 @@ 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 +112,7 @@ 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 +122,7 @@ 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 +221,13 @@ 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 +246,7 @@ 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 +334,7 @@ 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 +344,7 @@ 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 +446,13 @@ 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 +471,7 @@ 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..7fcaf6f3a99 100644
--- a/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
+++ b/lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
@@ -68,22 +68,9 @@ class TestEnvironmentInheritance(ShedTwillTestCase):
def test_0000_initiate_users_and_category(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
def test_0005_create_libx11_repository(self):
"""Create and populate package_x11_client_1_5_proto_7_0_0470.
@@ -93,13 +80,13 @@ 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 +111,13 @@ 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 +142,13 @@ 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..7cafb988070 100644
--- a/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
+++ b/lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
@@ -28,22 +28,9 @@ class TestDependencyDefinitionValidation(ShedTwillTestCase):
def test_0000_initiate_users_and_category(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
def test_0005_create_tool_dependency_repository(self):
"""Create and populate package_invalid_tool_dependency_xml_1_0_0.
@@ -52,13 +39,13 @@ 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..823a69bc4ee 100644
--- a/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
+++ b/lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
@@ -39,21 +39,8 @@ class TestRepositoryAdminRole(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_filtering_repository(self):
"""Create and populate the filtering_0530 repository.
@@ -67,7 +54,7 @@ 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..277a6c05371 100644
--- a/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
+++ b/lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
@@ -47,15 +47,7 @@ class TestGetAllMetadata(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_bwa_package_repository(self):
"""Create and populate package_bwa_0_5_9_0540."""
@@ -67,7 +59,7 @@ 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 +87,7 @@ 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 +125,7 @@ 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..17c8b0ded21 100644
--- a/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
+++ b/lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
@@ -51,15 +51,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_freebayes_repository(self):
"""Create and populate package_freebayes_0550."""
@@ -71,7 +63,7 @@ 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 +91,7 @@ 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 +115,7 @@ 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..c6d08d0bbb7 100644
--- a/lib/tool_shed/test/functional/test_1000_install_basic_repository.py
+++ b/lib/tool_shed/test/functional/test_1000_install_basic_repository.py
@@ -10,21 +10,8 @@ class BasicToolShedFeatures(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0000 category and upload the filtering repository to it, if necessary."""
@@ -43,7 +30,7 @@ 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 +88,7 @@ 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..3eb2154526a 100644
--- a/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
@@ -19,19 +19,8 @@ class ToolWithToolDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0010 category and upload the freebayes repository to it, if necessary."""
@@ -44,7 +33,7 @@ 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 +113,7 @@ 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..8bad1742afe 100644
--- a/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
@@ -18,21 +18,8 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0020 category and any missing repositories."""
@@ -45,7 +32,7 @@ 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 +52,7 @@ 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 +83,7 @@ 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..ec269e6b44d 100644
--- a/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
@@ -22,21 +22,8 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0030 category and add repositories to it, if necessary."""
@@ -50,7 +37,7 @@ 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 +58,7 @@ 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 +89,7 @@ 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 +120,7 @@ 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 +162,7 @@ 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..165bddcfe05 100644
--- a/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
@@ -22,15 +22,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_freebayes_repository(self):
"""Create and populate freebayes_0040."""
@@ -44,7 +36,7 @@ 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 +65,7 @@ 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..60154e18d95 100644
--- a/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
+++ b/lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
@@ -39,15 +39,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0050."""
@@ -59,7 +51,7 @@ 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 +76,7 @@ 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 +104,7 @@ 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 +128,7 @@ 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 +152,7 @@ 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 +176,7 @@ 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..00d9b0bf4f0 100644
--- a/lib/tool_shed/test/functional/test_1070_invalid_tool.py
+++ b/lib/tool_shed/test/functional/test_1070_invalid_tool.py
@@ -16,33 +16,20 @@ class TestFreebayesRepository(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_ensure_existence_of_repository_and_category(self):
"""Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool."""
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 +60,7 @@ 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..12d1e7f51cb 100644
--- a/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
+++ b/lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
@@ -27,21 +27,8 @@ class TestRepositoryDependencies(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_and_populate_column_repository(self):
"""Create the category for this test suite, then create and populate column_maker."""
@@ -53,7 +40,7 @@ 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 +68,7 @@ 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..8fe92e3cbbc 100644
--- a/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
+++ b/lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
@@ -25,21 +25,8 @@ class TestRepositoryDependencies(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_and_populate_column_repository(self):
"""Create a category for this test suite and add repositories to it."""
@@ -50,7 +37,7 @@ 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 +62,7 @@ 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..02972015f67 100644
--- a/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
@@ -21,21 +21,8 @@ class TestRepositoryDependencies(ShedTwillTestCase):
def test_0000_create_or_login_admin_user(self):
"""Create necessary user accounts and login as an admin user."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_and_populate_column_repository(self):
"""Create a category for this test suite and add repositories to it."""
@@ -46,7 +33,7 @@ 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 +59,7 @@ 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..91c23eafb26 100644
--- a/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
@@ -28,15 +28,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_bwa_package_repository(self):
"""Create and populate package_bwa_0_5_9_0100."""
@@ -48,7 +40,7 @@ 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 +79,7 @@ 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..cc63e9e54d1 100644
--- a/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+++ b/lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
@@ -22,15 +22,7 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_category(self):
"""Create a category for this test suite"""
@@ -40,13 +32,13 @@ 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 +59,13 @@ 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..affccd8c3fb 100644
--- a/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
+++ b/lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
@@ -26,8 +26,6 @@ Galaxy side:
1a) Check for appropriate strings in the installed blastxml_to_top_descr_0120 and blast_datatypes_0120 repositories.
"""
-base_datatypes_count = 0
-repository_datatypes_count = 0
running_standalone = False
@@ -39,21 +37,8 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_datatypes_repository(self):
"""Create and populate the blast_datatypes_0120 repository
@@ -69,7 +54,7 @@ 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):
@@ -92,7 +77,6 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
Check for appropriate strings, most importantly BlastXml, BlastNucDb, and BlastProtDb,
the datatypes that are defined in datatypes_conf.xml.
"""
- global repository_datatypes_count
repository = self.test_db_util.get_repository_by_name_and_owner(
datatypes_repository_name, common.test_user_2_name
)
@@ -107,7 +91,6 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
"blastdbp",
]
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
- repository_datatypes_count = int(self.get_repository_datatypes_count(repository))
def test_0015_create_tool_repository(self):
"""Create and populate the blastxml_to_top_descr_0120 repository
@@ -124,7 +107,7 @@ 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):
@@ -218,24 +201,12 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
are now new datatypes in the registry matching the ones defined in blast_datatypes_0120. Also check that
blast_datatypes_0120 is labeled as an installed repository dependency of blastxml_to_top_descr_0120.
"""
- global repository_datatypes_count
- global base_datatypes_count
tool_repository = self.test_db_util.get_installed_repository_by_name_owner(
tool_repository_name, common.test_user_1_name
)
datatypes_repository = self.test_db_util.get_installed_repository_by_name_owner(
datatypes_repository_name, common.test_user_2_name
)
- current_datatypes = int(self.get_datatypes_count())
- expected_count = base_datatypes_count + repository_datatypes_count
- # Once the BLAST datatypes have been included in Galaxy itself, the count won't change
- assert (
- current_datatypes == base_datatypes_count or current_datatypes == expected_count
- ), "Installing %s did not add new datatypes. Expected: %d. Found: %d" % (
- "blastxml_to_top_descr_0120",
- expected_count,
- current_datatypes,
- )
strings_displayed = ["Installed repository dependencies", "user1", "blast_datatypes_0120"]
strings_displayed.extend(
["Valid tools", "BLAST top hit", "Make a table", datatypes_repository.installed_changeset_revision]
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..5d6f33cdbaf 100644
--- a/lib/tool_shed/test/functional/test_1160_tool_help_images.py
+++ b/lib/tool_shed/test/functional/test_1160_tool_help_images.py
@@ -26,15 +26,7 @@ class TestToolHelpImages(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_htseq_count_repository(self):
"""Create and populate htseq_count_0140.
@@ -50,7 +42,7 @@ 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..ada5e3acb45 100644
--- a/lib/tool_shed/test/functional/test_1170_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1170_prior_installation_required.py
@@ -41,21 +41,8 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0150."""
@@ -67,7 +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=[],
)
if self.repository_is_new(repository):
@@ -93,7 +80,7 @@ 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..d78b0dae319 100644
--- a/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
@@ -54,21 +54,8 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_convert_repository(self):
"""Create and populate convert_chars_0160."""
@@ -80,7 +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):
@@ -106,7 +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:
@@ -131,7 +118,7 @@ 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..aa697481767 100644
--- a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+++ b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
@@ -39,15 +39,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_matplotlib_repository(self):
"""Create and populate the package_matplotlib_1_2_0170 repository.
@@ -62,7 +54,7 @@ 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 +87,7 @@ 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..aea8956ed9f 100644
--- a/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+++ b/lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
@@ -10,21 +10,8 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0000 category and upload the filtering repository to the tool shed, if necessary."""
@@ -40,7 +27,7 @@ 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..a1a95a18e56 100644
--- a/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+++ b/lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
@@ -12,19 +12,8 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0010 category and upload the freebayes repository to the tool shed, if necessary."""
@@ -38,7 +27,7 @@ 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..32513136e7d 100644
--- a/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+++ b/lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
@@ -22,19 +22,8 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(admin_user)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 0030 category and upload the emboss repository to the tool shed, if necessary."""
@@ -49,7 +38,7 @@ 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 +48,7 @@ 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 +79,7 @@ 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 +110,7 @@ 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..68b45dfdcc3 100644
--- a/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+++ b/lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
@@ -47,15 +47,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_categories(self):
"""Create the categories for the repositories in this test script."""
@@ -83,7 +75,7 @@ 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 +110,7 @@ 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 +167,7 @@ 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 +187,7 @@ 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 +211,7 @@ 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 +231,7 @@ 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 +262,7 @@ 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 +293,7 @@ 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 +339,7 @@ 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 +359,7 @@ 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 +414,7 @@ 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 +423,7 @@ 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 +431,7 @@ 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..fa95795a7f0 100644
--- a/lib/tool_shed/test/functional/test_1410_update_manager.py
+++ b/lib/tool_shed/test/functional/test_1410_update_manager.py
@@ -33,21 +33,8 @@ class TestUpdateManager(ShedTwillTestCase):
Previously created accounts will not be re-created.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
- galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
- assert (
- galaxy_admin_user is not None
- ), f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
def test_0005_create_filtering_repository(self):
"""Create and populate the filtering_1410 repository.
@@ -63,7 +50,7 @@ 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..9d71d177f7d 100644
--- a/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
+++ b/lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
@@ -40,22 +40,9 @@ class TestRepairRepository(ShedTwillTestCase):
def test_0000_initiate_users_and_category(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
def test_0005_create_filter_repository(self):
"""Create and populate the filter_1430 repository.
@@ -64,13 +51,13 @@ 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 +79,13 @@ 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..267edfd6ca3 100644
--- a/lib/tool_shed/test/functional/test_1460_data_managers.py
+++ b/lib/tool_shed/test/functional/test_1460_data_managers.py
@@ -33,22 +33,9 @@ class TestDataManagers(ShedTwillTestCase):
def test_0000_initiate_users_and_category(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
- test_user_2 = self.test_db_util.get_user(common.test_user_2_email)
- assert (
- test_user_2 is not None
- ), f"Problem retrieving user with email {common.test_user_2_email} from the database"
- self.test_db_util.get_private_role(test_user_2)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
def test_0010_create_data_manager_repository(self):
"""Create and populate data_manager_1460.
@@ -57,13 +44,13 @@ 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..44c7542afbc 100644
--- a/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
+++ b/lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
@@ -32,15 +32,7 @@ class TestUpdateInstalledRepository(ShedTwillTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
- test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
- assert (
- test_user_1 is not None
- ), f"Problem retrieving user with email {common.test_user_1_email} from the database"
- self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
- admin_user = self.test_db_util.get_user(common.admin_email)
- assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
- self.test_db_util.get_private_role(admin_user)
def test_0005_create_filtering_repository(self):
"""Create and populate the filtering_0530 repository."""
@@ -51,7 +43,7 @@ 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/test/functional/test_shed_repositories.py b/lib/tool_shed/test/functional/test_shed_repositories.py
index e5cb021242e..0f0fee3be3a 100644
--- a/lib/tool_shed/test/functional/test_shed_repositories.py
+++ b/lib/tool_shed/test/functional/test_shed_repositories.py
@@ -5,17 +5,6 @@ from ..base.api import ShedApiTestCase
COLUMN_MAKER_PATH = resource_path(__package__, "../test_data/column_maker/column_maker.tar")
-# Things seemingly *NOT* used by Galaxy, Planemo, or Ephemeris...
-# (perhaps we can delete instead of test?)...
-# - reset_metadata_on_repository
-# - reset_metadata_on_repositories
-# - remove_repository_registry_entry
-# - get_repository_revision_install_info
-# - get_installable_revisions
-
-# Non repositories API seemingly unused and seemingly better rewritten if wanted.
-# - The whole Groups API.
-# - The whole Repository Revisions API.
class ShedRepositoriesApiTestCase(ShedApiTestCase):
def test_create(self):
populator = self.populator
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
diff --git a/mypy.ini b/mypy.ini
index 933d9e160eb..1ab424fc315 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -610,8 +610,6 @@ check_untyped_defs = False
check_untyped_defs = False
[mypy-test.functional.test_toolbox]
check_untyped_defs = False
-[mypy-tool_shed.test.functional_tests]
-check_untyped_defs = False
[mypy-tool_shed.test.base.test_db_util]
check_untyped_defs = False
[mypy-integration.test_save_job_id_on_datasets]
@@ -664,114 +662,6 @@ check_untyped_defs = False
check_untyped_defs = False
[mypy-test.functional.conftest]
check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1470_updating_installed_repositories]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1460_data_managers]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1430_repair_installed_repository]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1410_update_manager]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1300_reset_all_metadata]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1230_uninstall_reinstall_repository_with_dependency_revisions]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1210_uninstall_reinstall_repository_with_tool_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1200_uninstall_and_reinstall_basic_repository]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1190_complex_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1180_circular_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1170_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1160_tool_help_images]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1140_simple_repository_dependency_multiple_owners]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1130_install_repository_with_invalid_repository_dependency]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1120_install_repository_with_complex_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1100_install_updated_repository_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1090_repository_dependency_handling]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1080_advanced_circular_dependency_installation]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1070_invalid_tool]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1050_circular_dependencies_4_levels]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1040_install_repository_basic_circular_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1030_install_repository_with_dependency_revisions]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1020_install_repository_with_repository_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1010_install_repository_with_tool_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_1000_install_basic_repository]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0550_metadata_updated_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0540_get_all_metadata_from_api]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0530_repository_admin_feature]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0480_tool_dependency_xml_verification]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0470_tool_dependency_repository_type]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0460_upload_to_repository]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0440_deleting_dependency_definitions]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0430_browse_utilities]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0420_citable_urls_for_repositories]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0410_repository_component_review_access_control]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0400_repository_component_reviews]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0310_hg_api_features]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0300_reset_all_metadata]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0170_complex_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0160_circular_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0150_prior_installation_required]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0140_tool_help_images]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0120_simple_repository_dependency_multiple_owners]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0110_invalid_simple_repository_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0100_complex_repository_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0090_tool_search]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0080_advanced_circular_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0070_invalid_tool]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0050_circular_dependencies_4_levels]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0040_repository_circular_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0030_repository_dependency_revisions]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0020_basic_repository_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0010_repository_with_tool_dependencies]
-check_untyped_defs = False
-[mypy-tool_shed.test.functional.test_0000_basic_repository_features]
-check_untyped_defs = False
[mypy-integration.test_containerized_jobs]
check_untyped_defs = False
[mypy-integration.test_chained_dynamic_destinations]