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Merge pull request #14662 from jmchilton/cleanup_ts_tests

Browse Source 
Cleanup Tool Shed Tests
This commit is contained in:
John Chilton
2022-09-21 15:49:43 -04:00
committed by GitHub
parent d5c9cc647f 5bf5a3d85e
commit 5059ec02f0
61 changed files with 311 additions and 965 deletions
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lib/galaxy_test/driver/driver_util.py
-3
View File
@@ -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,
lib/tool_shed/test/base/api.py
+31 -30
View File
@@ -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"]
lib/tool_shed/test/base/populators.py
+27 -5
View File
@@ -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(
lib/tool_shed/test/base/test_db_util.py
-39
View File
@@ -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 = (
lib/tool_shed/test/base/twilltestcase.py
+19 -34
View File
@@ -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
):
lib/tool_shed/test/functional/api_notes.md
+42
View File
@@ -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 | |
lib/tool_shed/test/functional/test_0000_basic_repository_features.py
+6 -19
View File
@@ -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):
lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
+4 -12
View File
@@ -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(
lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
+8 -16
View File
@@ -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,
lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
+9 -12
View File
@@ -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(
lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
+6 -14
View File
@@ -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(
lib/tool_shed/test/functional/test_0070_invalid_tool.py
+1 -9
View File
@@ -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(
lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_0090_tool_search.py
+5 -13
View File
@@ -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(
lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
+2 -10
View File
@@ -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.
lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
+4 -12
View File
@@ -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(
lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
+2 -20
View File
@@ -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(
lib/tool_shed/test/functional/test_0140_tool_help_images.py
+1 -9
View File
@@ -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.
lib/tool_shed/test/functional/test_0150_prior_installation_required.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
+3 -11
View File
@@ -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(
lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+16 -24
View File
@@ -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(
lib/tool_shed/test/functional/test_0310_hg_api_features.py
+1 -14
View File
@@ -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(
lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+1 -9
View File
@@ -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(
lib/tool_shed/test/functional/test_0430_browse_utilities.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+9 -17
View File
@@ -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 <b>convert_chars_0440</b> 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 <b>bwa_package_0440</b> 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 <b>bwa_base_0440</b> 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 <b>bwa_tool_dependency_0440</b> 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(
lib/tool_shed/test/functional/test_0460_upload_to_repository.py
+12 -25
View File
@@ -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(
lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
+6 -19
View File
@@ -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.
lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
+2 -15
View File
@@ -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(
lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
+1 -14
View File
@@ -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(
lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
+3 -11
View File
@@ -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']}"
lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
+3 -11
View File
@@ -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']}"
lib/tool_shed/test/functional/test_1000_install_basic_repository.py
+2 -15
View File
@@ -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):
lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
+2 -13
View File
@@ -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(
lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
+3 -16
View File
@@ -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"]
lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
+5 -18
View File
@@ -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"]
lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
+2 -10
View File
@@ -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):
lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
+6 -14
View File
@@ -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):
lib/tool_shed/test/functional/test_1070_invalid_tool.py
+3 -16
View File
@@ -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]
lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
+2 -15
View File
@@ -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):
lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
+2 -15
View File
@@ -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):
lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
+2 -15
View File
@@ -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):
lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
+2 -10
View File
@@ -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)
lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+4 -12
View File
@@ -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(
lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
+2 -31
View File
@@ -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]
lib/tool_shed/test/functional/test_1160_tool_help_images.py
+1 -9
View File
@@ -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):
lib/tool_shed/test/functional/test_1170_prior_installation_required.py
+2 -15
View File
@@ -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:
lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
+3 -16
View File
@@ -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:
lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+2 -10
View File
@@ -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(
lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+1 -14
View File
@@ -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(
lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+1 -12
View File
@@ -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(
lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+4 -15
View File
@@ -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(
lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+13 -21
View File
@@ -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(
lib/tool_shed/test/functional/test_1410_update_manager.py
+1 -14
View File
@@ -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,
lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
+4 -17
View File
@@ -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(
lib/tool_shed/test/functional/test_1460_data_managers.py
+2 -15
View File
@@ -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.
lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
+1 -9
View File
@@ -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(
lib/tool_shed/test/functional/test_shed_repositories.py
-11
View File
@@ -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
lib/tool_shed_client/schema/__init__.py
+5
View File
@@ -31,6 +31,11 @@ class Category(BaseModel):
name: str
class CreateCategoryRequest(BaseModel):
name: str
description: str
class ValidRepostiroyUpdateMessage(BaseModel):
message: str
mypy.ini
-110
View File
@@ -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]