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Use API in lieu of direct db access in shed functional tests for categories.

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This commit is contained in:
John Chilton
2022-09-20 18:25:47 -04:00
parent fcbaf62e05
commit cec8c1ac9f
57 changed files with 269 additions and 231 deletions
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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
-4
View File
@@ -56,10 +56,6 @@ def get_all_installed_repositories(actually_installed=False):
return install_session.query(galaxy.model.tool_shed_install.ToolShedRepository).all()
def get_category_by_name(name):
return sa_session.query(model.Category).filter(model.Category.table.c.name == name).first()
def get_default_user_permissions_by_role(role):
return (
sa_session.query(model.DefaultUserPermissions)
lib/tool_shed/test/base/twilltestcase.py
+19 -10
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,
@@ -248,11 +250,11 @@ class ShedTwillTestCase(ShedBaseTestCase):
self.visit_url("/repository/manage_repository_admins", params=params)
self.check_for_strings(strings_displayed=["Role", "has been associated"])
def browse_category(self, category, strings_displayed=None, strings_not_displayed=None):
def browse_category(self, category: Category, strings_displayed=None, strings_not_displayed=None):
params = {
"sort": "name",
"operation": "valid_repositories_by_category",
"id": self.security.encode_id(category.id),
"id": category.id,
}
self.visit_url("/repository/browse_valid_categories", params=params)
self.check_for_strings(strings_displayed, strings_not_displayed)
@@ -451,13 +453,14 @@ class ShedTwillTestCase(ShedBaseTestCase):
return True
raise
def create_category(self, **kwd):
category = test_db_util.get_category_by_name(kwd["name"])
def create_category(self, **kwd) -> Category:
category = self.populator.get_category_with_name(kwd["name"])
if category is None:
params = {"operation": "create"}
self.visit_url("/admin/manage_categories", params=params)
self.submit_form(button="create_category_button", **kwd)
category = test_db_util.get_category_by_name(kwd["name"])
category = self.populator.get_category_with_name(kwd["name"])
assert category
return category
def create_repository_dependency(
@@ -815,13 +818,17 @@ class ShedTwillTestCase(ShedBaseTestCase):
def get_hg_repo(self, path):
return hg.repository(ui.ui(), path.encode("utf-8"))
def get_repositories_category_api(self, categories, strings_displayed=None, strings_not_displayed=None):
def get_repositories_category_api(
self, categories: List[Category], strings_displayed=None, strings_not_displayed=None
):
for category in categories:
url = f"/api/categories/{self.security.encode_id(category.id)}/repositories"
url = f"/api/categories/{category.id}/repositories"
self.visit_url(url)
self.check_for_strings(strings_displayed, strings_not_displayed)
def get_or_create_repository(self, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd):
def get_or_create_repository(
self, category: Category, owner=None, strings_displayed=None, strings_not_displayed=None, **kwd
):
# If not checking for a specific string, it should be safe to assume that
# we expect repository creation to be successful.
if strings_displayed is None:
@@ -829,9 +836,11 @@ class ShedTwillTestCase(ShedBaseTestCase):
if strings_not_displayed is None:
strings_not_displayed = []
repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner)
category_id = category.id
assert category_id
if repository is None:
self.visit_url("/repository/create_repository")
self.submit_form(button="create_repository_button", **kwd)
self.submit_form(button="create_repository_button", category_id=category_id, **kwd)
self.check_for_strings(strings_displayed, strings_not_displayed)
repository = test_db_util.get_repository_by_name_and_owner(kwd["name"], owner)
return repository
@@ -1051,7 +1060,7 @@ class ShedTwillTestCase(ShedBaseTestCase):
**kwd,
):
self.browse_tool_shed(url=self.url)
self.browse_category(test_db_util.get_category_by_name(category_name))
self.browse_category(self.populator.get_category_with_name(category_name))
self.preview_repository_in_tool_shed(name, owner, strings_displayed=preview_strings_displayed)
repository = test_db_util.get_repository_by_name_and_owner(name, owner)
repository_id = self.security.encode_id(repository.id)
lib/tool_shed/test/functional/test_0000_basic_repository_features.py
+6 -6
View File
@@ -52,14 +52,14 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
def test_0015_create_repository(self):
"""Create the filtering repository"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")
strings_displayed = self.expect_repo_created_strings(repository_name)
self.get_or_create_repository(
name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
@@ -305,7 +305,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
def test_0095_verify_reserved_repository_name_handling(self):
"""Check that reserved repository names are handled correctly."""
category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")
error_message = (
"The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a repository name."
)
@@ -314,7 +314,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[error_message],
)
@@ -433,8 +433,8 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
def test_0135_api_get_repositories_in_category(self):
"""Load the api endpoint for repositories in a category."""
categories = []
categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1"))
categories.append(self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 2"))
categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 1"))
categories.append(self.populator.get_category_with_name("Test 0000 Basic Repository Features 2"))
self.get_repositories_category_api(categories)
def test_0140_view_invalid_changeset(self):
lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
+2 -2
View File
@@ -51,13 +51,13 @@ class TestFreebayesRepository(ShedTwillTestCase):
upload, as well as on the manage repository page.
"""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0010 Repository With Tool Dependencies")
category = self.populator.get_category_with_name("Test 0010 Repository With Tool Dependencies")
repository = self.get_or_create_repository(
name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
+4 -4
View File
@@ -36,14 +36,14 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0010_create_column_maker_repository(self):
"""Create and populate column_maker_0020."""
category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
column_maker_repository = self.get_or_create_repository(
name=column_maker_repository_name,
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -60,13 +60,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0020_create_emboss_5_repository_and_upload_files(self):
"""Create and populate the emboss_5_0020 repository."""
category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
repository = self.get_or_create_repository(
name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
+8 -8
View File
@@ -39,13 +39,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
def test_0010_create_emboss_5_repository(self):
"""Create and populate the emboss_5_0030 repository."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
repository = self.get_or_create_repository(
name=emboss_5_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
self.upload_file(
repository,
@@ -62,13 +62,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
def test_0015_create_emboss_6_repository(self):
"""Create and populate the emboss_6_0030 repository."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
repository = self.get_or_create_repository(
name=emboss_6_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
self.upload_file(
repository,
@@ -85,13 +85,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
def test_0020_create_dependent_repository(self):
"""Create and populate the emboss_datatypes_0030 repository."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
repository = self.get_or_create_repository(
name=column_maker_repository_name,
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
self.upload_file(
@@ -109,13 +109,13 @@ class TestRepositoryDependencyRevisions(ShedTwillTestCase):
def test_0025_create_emboss_repository(self):
"""Create and populate the emboss_0030 repository."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
repository = self.get_or_create_repository(
name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
self.upload_file(
repository,
lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
+9 -4
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."""
@@ -31,19 +34,20 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
def test_0005_create_category(self):
"""Create a category for this test suite"""
self.create_category(
name="test_0040_repository_circular_dependencies",
description="Testing handling of circular repository dependencies.",
name=CATEGORY_NAME,
description=CATEGORY_DESC,
)
def test_0010_create_freebayes_repository(self):
"""Create and populate freebayes_0040."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(CATEGORY_NAME)
repository = self.get_or_create_repository(
name=freebayes_repository_name,
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
categories=["test_0040_repository_circular_dependencies"],
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -61,12 +65,13 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
def test_0015_create_filtering_repository(self):
"""Create and populate filtering_0040."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.populator.get_category_with_name(CATEGORY_NAME)
repository = self.get_or_create_repository(
name=filtering_repository_name,
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
categories=["test_0040_repository_circular_dependencies"],
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
+6 -6
View File
@@ -56,7 +56,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -79,7 +79,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -106,7 +106,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -129,7 +129,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -152,7 +152,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -175,7 +175,7 @@ class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
description=bismark_repository_description,
long_description=bismark_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0070_invalid_tool.py
+1 -1
View File
@@ -35,7 +35,7 @@ class TestBismarkRepository(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
+2 -2
View File
@@ -40,7 +40,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -65,7 +65,7 @@ class TestRepositoryCircularDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0090_tool_search.py
+5 -5
View File
@@ -52,7 +52,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -76,7 +76,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
description=bwa_color_repository_description,
long_description=bwa_color_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -99,7 +99,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -122,7 +122,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -145,7 +145,7 @@ class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
+2 -2
View File
@@ -48,7 +48,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase):
description=bwa_package_repository_description,
long_description=bwa_package_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -77,7 +77,7 @@ class TestComplexRepositoryDependencies(ShedTwillTestCase):
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Populate the repository named bwa_base_repository_0100 with a bwa_base tool archive.
lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
+4 -4
View File
@@ -38,13 +38,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0010_create_emboss_datatypes_repository_and_upload_tarball(self):
"""Create and populate the emboss_datatypes repository."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
column_maker_repository = self.get_or_create_repository(
name=column_maker_repository_name,
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -61,13 +61,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
def test_0020_create_emboss_5_repository_and_upload_files(self):
"""Create and populate the emboss_5_0110 repository."""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
+2 -2
View File
@@ -64,7 +64,7 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_2_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -117,7 +117,7 @@ class TestRepositoryMultipleOwners(ShedTwillTestCase):
description=tool_repository_description,
long_description=tool_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
lib/tool_shed/test/functional/test_0140_tool_help_images.py
+1 -1
View File
@@ -54,7 +54,7 @@ class TestToolHelpImages(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Upload htseq_count.tar to the repository.
lib/tool_shed/test/functional/test_0150_prior_installation_required.py
+2 -2
View File
@@ -54,7 +54,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -77,7 +77,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
+3 -3
View File
@@ -53,7 +53,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -76,7 +76,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -99,7 +99,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=filter_repository_description,
long_description=filter_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+2 -2
View File
@@ -57,7 +57,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
description=matplotlib_repository_description,
long_description=matplotlib_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -84,7 +84,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
description=numpy_repository_description,
long_description=numpy_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+16 -16
View File
@@ -69,7 +69,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0000.id),
category=category_0000,
)
if self.repository_is_new(repository):
running_standalone = True
@@ -110,7 +110,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0010.id),
category=category_0010,
strings_displayed=[],
)
if running_standalone:
@@ -174,7 +174,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
category=category_0020,
strings_displayed=[],
)
self.upload_file(
@@ -204,7 +204,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_long_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0020.id),
category=category_0020,
strings_displayed=[],
)
self.upload_file(
@@ -234,7 +234,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
category=category_0030,
strings_displayed=[],
)
self.upload_file(
@@ -264,7 +264,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
category=category_0030,
strings_displayed=[],
)
self.upload_file(
@@ -294,7 +294,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
category=category_0030,
strings_displayed=[],
)
self.upload_file(
@@ -324,7 +324,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0030.id),
category=category_0030,
strings_displayed=[],
)
self.upload_file(
@@ -405,7 +405,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
category=category_0040,
strings_displayed=[],
)
if running_standalone:
@@ -436,7 +436,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category_0040.id),
category=category_0040,
strings_displayed=[],
)
self.upload_file(
@@ -497,7 +497,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -524,7 +524,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -554,7 +554,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -581,7 +581,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -608,7 +608,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -635,7 +635,7 @@ class TestResetAllRepositoryMetadata(ShedTwillTestCase):
description=bismark_repository_description,
long_description=bismark_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0310_hg_api_features.py
+1 -1
View File
@@ -56,7 +56,7 @@ class TestHgWebFeatures(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+1 -1
View File
@@ -64,7 +64,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
lib/tool_shed/test/functional/test_0430_browse_utilities.py
+2 -2
View File
@@ -59,7 +59,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -90,7 +90,7 @@ class TestToolShedBrowseUtilities(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+9 -9
View File
@@ -87,7 +87,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -107,7 +107,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
We are at simple repository dependencies, step 2 - Create and populate convert_chars_0440 so that it has an installable revision 0.
"""
category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions")
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
strings_displayed = ["Repository <b>convert_chars_0440</b> has been created"]
repository = self.get_or_create_repository(
@@ -115,7 +115,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -219,7 +219,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
We are at complex repository dependencies, step 1 - Create and populate bwa_package_0440 so that it has a valid
tool dependency definition and an installable revision 0.
"""
category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions")
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
strings_displayed = ["Repository <b>bwa_package_0440</b> has been created"]
repository = self.get_or_create_repository(
@@ -227,7 +227,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
description=bwa_package_repository_description,
long_description=bwa_package_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -248,7 +248,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
We are at complex repository dependencies, step 2 - Create and populate bwa_base_0440 so that it has an installable revision 0.
This repository should contain a tool with a defined dependency that will be satisfied by the tool dependency defined in bwa_package_0440.
"""
category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions")
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
strings_displayed = ["Repository <b>bwa_base_0440</b> has been created"]
repository = self.get_or_create_repository(
@@ -256,7 +256,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
@@ -354,7 +354,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
We are at tool dependencies, step 1 - Create and populate bwa_tool_dependency_0440 so that it has a valid tool
dependency definition and an installable revision 0.
"""
category = self.test_db_util.get_category_by_name("Test 0440 Deleted Dependency Definitions")
category = self.populator.get_category_with_name("Test 0440 Deleted Dependency Definitions")
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
strings_displayed = ["Repository <b>bwa_tool_dependency_0440</b> has been created"]
repository = self.get_or_create_repository(
@@ -362,7 +362,7 @@ class TestDeletedDependencies(ShedTwillTestCase):
description=bwa_tool_dependency_repository_description,
long_description=bwa_tool_dependency_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
self.upload_file(
lib/tool_shed/test/functional/test_0460_upload_to_repository.py
+12 -12
View File
@@ -91,13 +91,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
This is step 2 - Create and populate package_bwa_0_5_9_0460.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=bwa_repository_name,
description=bwa_repository_description,
long_description=bwa_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -125,7 +125,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
- Upload via url, with the tool_dependencies.xml in the root of another repository.
- Upload via url, with the tool_dependencies.xml in a subfolder within another repository.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository_base_name = "complex_dependency_test_%d_0460"
repository_base_description = "Test #%d for complex repository dependency definitions."
repository_base_long_description = "Test #%d for complex repository dependency definitions."
@@ -135,7 +135,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
description=repository_base_description % number,
long_description=repository_base_long_description % number,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
@@ -234,13 +234,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
This is step 7 - Create hg_tool_dependency_0460 and hg_subfolder_tool_dependency_0460 and populate with tool dependencies.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name="hg_tool_dependency_0460",
description=bwa_repository_description,
long_description=bwa_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -259,7 +259,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
description=bwa_repository_description,
long_description=bwa_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -347,7 +347,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
- Upload via url, with the repository_dependencies.xml in the root of another repository.
- Upload via url, with the repository_dependencies.xml in a subfolder within another repository.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository_base_name = "repository_dependency_test_%d_0460"
repository_base_description = "Test #%d for repository dependency definitions."
repository_base_long_description = "Test #%d for repository dependency definitions."
@@ -357,7 +357,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
description=repository_base_description % number,
long_description=repository_base_long_description % number,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
@@ -459,13 +459,13 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
This is step 14 - Create hg_repository_dependency_0460 and hg_subfolder_repository_dependency_0460 and populate
with repository dependencies.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name="hg_repository_dependency_0460",
description=bwa_repository_description,
long_description=bwa_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -484,7 +484,7 @@ class TestAutomaticDependencyRevision(ShedTwillTestCase):
description=bwa_repository_description,
long_description=bwa_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
+6 -6
View File
@@ -93,13 +93,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase):
Create and populate a repository named package_x11_client_1_5_proto_7_0 that contains only a single file named tool_dependencies.xml.
Keep the repository type as the default "Unrestricted".
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=package_libx11_repository_name,
description=package_libx11_repository_description,
long_description=package_libx11_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Upload the tool dependency definition to the package_x11_client_1_5_proto_7_0_0470 repository.
@@ -124,13 +124,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase):
above package_x11_client_1_5_proto_7_0 repository. Upload the tool_dependencues.xml file such that it does not have a changeset_revision
defined so it will get automatically populated.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=package_emboss_repository_name,
description=package_emboss_repository_description,
long_description=package_emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Upload the edited tool dependency definition to the package_emboss_5_0_0 repository.
@@ -155,13 +155,13 @@ class TestEnvironmentInheritance(ShedTwillTestCase):
on the package_emboss_5_0_0 repository above. Upload the tool_dependencies.xml file such that it does not have a change set_revision defined
so it will get automatically populated.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Populate emboss_5 with tool and dependency definitions.
lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
+2 -2
View File
@@ -52,13 +52,13 @@ class TestDependencyDefinitionValidation(ShedTwillTestCase):
Create a repository named package_invalid_tool_dependency_xml_1_0_0 that will contain only a single file named tool_dependencies.xml.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
+1 -1
View File
@@ -67,7 +67,7 @@ class TestRepositoryAdminRole(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_0540_get_all_metadata_from_api.py
+3 -3
View File
@@ -67,7 +67,7 @@ class TestGetAllMetadata(ShedTwillTestCase):
description=repositories["bwa"]["description"],
long_description=repositories["bwa"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert repository is not None, f"Error creating repository {repositories['bwa']['name']}"
@@ -95,7 +95,7 @@ class TestGetAllMetadata(ShedTwillTestCase):
description=repositories["convert"]["description"],
long_description=repositories["convert"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert repository is not None, f"Error creating repository {repositories['convert']['name']}"
@@ -133,7 +133,7 @@ class TestGetAllMetadata(ShedTwillTestCase):
description=repositories["column"]["description"],
long_description=repositories["column"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert repository is not None, f"Error creating repository {repositories['column']['name']}"
lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
+3 -3
View File
@@ -71,7 +71,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
description=repositories["freebayes"]["description"],
long_description=repositories["freebayes"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert freebayes is not None, f"Error creating freebayes {repositories['freebayes']['name']}"
@@ -99,7 +99,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
description=repositories["samtools"]["description"],
long_description=repositories["samtools"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert samtools is not None, f"Error creating samtools {repositories['samtools']['name']}"
@@ -123,7 +123,7 @@ class TestGetUpdatedMetadata(ShedTwillTestCase):
description=repositories["filtering"]["description"],
long_description=repositories["filtering"]["long_description"],
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
assert repository is not None, f"Error creating repository {repositories['filtering']['name']}"
lib/tool_shed/test/functional/test_1000_install_basic_repository.py
+2 -2
View File
@@ -43,7 +43,7 @@ class BasicToolShedFeatures(ShedTwillTestCase):
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
self.upload_file(
@@ -101,7 +101,7 @@ class BasicToolShedFeatures(ShedTwillTestCase):
def test_0015_browse_test_0000_category(self):
"""Browse the category created in test 0000. It should contain the filtering_0000 repository also created in that test."""
category = self.test_db_util.get_category_by_name("Test 0000 Basic Repository Features 1")
category = self.populator.get_category_with_name("Test 0000 Basic Repository Features 1")
self.browse_category(category, strings_displayed=["filtering_0000"])
def test_0020_preview_filtering_repository(self):
lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
+2 -2
View File
@@ -44,7 +44,7 @@ class ToolWithToolDependencies(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
self.upload_file(
@@ -124,7 +124,7 @@ class ToolWithToolDependencies(ShedTwillTestCase):
"""Browse the available tool sheds in this Galaxy instance and preview the freebayes tool."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
self.browse_category(category, strings_displayed=[repository_name])
strings_displayed = [repository_name, "Valid tools", "Tool dependencies"]
self.preview_repository_in_tool_shed(
lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
+3 -3
View File
@@ -45,7 +45,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -65,7 +65,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -96,7 +96,7 @@ class ToolWithRepositoryDependencies(ShedTwillTestCase):
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.browse_tool_shed(url=self.url, strings_displayed=["Test 0020 Basic Repository Dependencies"])
category = self.test_db_util.get_category_by_name("Test 0020 Basic Repository Dependencies")
category = self.populator.get_category_with_name("Test 0020 Basic Repository Dependencies")
self.browse_category(category, strings_displayed=["emboss_0020"])
self.preview_repository_in_tool_shed(
"emboss_0020", common.test_user_1_name, strings_displayed=["emboss_0020", "Valid tools"]
lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
+5 -5
View File
@@ -50,7 +50,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -71,7 +71,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -102,7 +102,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -133,7 +133,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -175,7 +175,7 @@ class RepositoryWithDependencyRevisions(ShedTwillTestCase):
"""Browse the available tool sheds in this Galaxy instance and preview the emboss tool."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.browse_tool_shed(url=self.url, strings_displayed=["Test 0030 Repository Dependency Revisions"])
category = self.test_db_util.get_category_by_name("Test 0030 Repository Dependency Revisions")
category = self.populator.get_category_with_name("Test 0030 Repository Dependency Revisions")
self.browse_category(category, strings_displayed=["emboss_0030"])
self.preview_repository_in_tool_shed(
"emboss_0030", common.test_user_1_name, strings_displayed=["emboss_0030", "Valid tools"]
lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
+2 -2
View File
@@ -44,7 +44,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -73,7 +73,7 @@ class TestInstallingCircularDependencies(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
+6 -6
View File
@@ -59,7 +59,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -84,7 +84,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -112,7 +112,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -136,7 +136,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -160,7 +160,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=freebayes_repository_description,
long_description=freebayes_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -184,7 +184,7 @@ class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
description=bismark_repository_description,
long_description=bismark_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1070_invalid_tool.py
+3 -3
View File
@@ -36,13 +36,13 @@ class TestFreebayesRepository(ShedTwillTestCase):
"""Create freebayes repository and upload only freebayes.xml. This should result in an error message and invalid tool."""
self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=repository_name,
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -73,7 +73,7 @@ class TestFreebayesRepository(ShedTwillTestCase):
"""Browse the available tool sheds in this Galaxy instance and preview the bismark repository."""
self.galaxy_login(email=common.admin_email, username=common.admin_username)
self.browse_tool_shed(url=self.url, strings_displayed=[category_name])
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
self.browse_category(category, strings_displayed=[repository_name])
self.preview_repository_in_tool_shed(
repository_name, common.test_user_1_name, strings_displayed=[repository_name]
lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
+2 -2
View File
@@ -53,7 +53,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -81,7 +81,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
+2 -2
View File
@@ -50,7 +50,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -75,7 +75,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
+2 -2
View File
@@ -46,7 +46,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -72,7 +72,7 @@ class TestRepositoryDependencies(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
+2 -2
View File
@@ -48,7 +48,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
description=bwa_package_repository_description,
long_description=bwa_package_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -87,7 +87,7 @@ class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
description=bwa_base_repository_description,
long_description=bwa_base_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.test_db_util.get_repository_by_name_and_owner(bwa_package_repository_name, common.test_user_1_name)
lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+4 -4
View File
@@ -40,13 +40,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
"""Create and populate the column_maker repository."""
global running_standalone
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
column_maker_repository = self.get_or_create_repository(
name=column_maker_repository_name,
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -67,13 +67,13 @@ class TestBasicRepositoryDependencies(ShedTwillTestCase):
"""Create and populate the emboss_5_0110 repository."""
global running_standalone
if running_standalone:
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=emboss_repository_name,
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
+2 -2
View File
@@ -69,7 +69,7 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
description=datatypes_repository_description,
long_description=datatypes_repository_long_description,
owner=common.test_user_2_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
if self.repository_is_new(repository):
@@ -124,7 +124,7 @@ class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
description=tool_repository_description,
long_description=tool_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=strings_displayed,
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1160_tool_help_images.py
+1 -1
View File
@@ -50,7 +50,7 @@ class TestToolHelpImages(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
lib/tool_shed/test/functional/test_1170_prior_installation_required.py
+2 -2
View File
@@ -67,7 +67,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -93,7 +93,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if running_standalone:
lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
+3 -3
View File
@@ -80,7 +80,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=convert_repository_description,
long_description=convert_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -106,7 +106,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if running_standalone:
@@ -131,7 +131,7 @@ class TestSimplePriorInstallation(ShedTwillTestCase):
description=filter_repository_description,
long_description=filter_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if running_standalone:
lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+2 -2
View File
@@ -62,7 +62,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
description=matplotlib_repository_description,
long_description=matplotlib_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -95,7 +95,7 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
description=numpy_repository_description,
long_description=numpy_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+1 -1
View File
@@ -40,7 +40,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description="Galaxy's filtering tool for test 0000",
long_description="Long description of Galaxy's filtering tool for test 0000",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
self.upload_file(
lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+1 -1
View File
@@ -38,7 +38,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
self.upload_file(
lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+4 -4
View File
@@ -49,7 +49,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -59,7 +59,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -90,7 +90,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -121,7 +121,7 @@ class UninstallingAndReinstallingRepositories(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+13 -13
View File
@@ -83,7 +83,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
if self.repository_is_new(repository):
running_standalone = True
@@ -118,7 +118,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -175,7 +175,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=column_maker_repository_description,
long_description=column_maker_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -195,7 +195,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy wrappers for Emboss version 5.0.0 tools",
long_description="Galaxy wrappers for Emboss version 5.0.0 tools",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -219,7 +219,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(column_maker_repository):
@@ -239,7 +239,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -270,7 +270,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -301,7 +301,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=emboss_repository_description,
long_description=emboss_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -347,7 +347,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(repository):
@@ -367,7 +367,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description=filtering_repository_description,
long_description=filtering_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -422,7 +422,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's emboss tool",
long_description="Long description of Galaxy's emboss tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
if self.repository_is_new(emboss_repository):
@@ -431,7 +431,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's filtering tool",
long_description="Long description of Galaxy's filtering tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
freebayes_repository = self.get_or_create_repository(
@@ -439,7 +439,7 @@ class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
description="Galaxy's freebayes tool",
long_description="Long description of Galaxy's freebayes tool",
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_1410_update_manager.py
+1 -1
View File
@@ -63,7 +63,7 @@ class TestUpdateManager(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
)
self.upload_file(
repository,
lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
+4 -4
View File
@@ -64,13 +64,13 @@ class TestRepairRepository(ShedTwillTestCase):
This repository will be depended on by the column_1430 repository.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=filter_repository_name,
description=filter_repository_description,
long_description=filter_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
@@ -92,13 +92,13 @@ class TestRepairRepository(ShedTwillTestCase):
This repository will depend on the filter_1430 repository.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=column_repository_name,
description=column_repository_description,
long_description=column_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
lib/tool_shed/test/functional/test_1460_data_managers.py
+2 -2
View File
@@ -57,13 +57,13 @@ class TestDataManagers(ShedTwillTestCase):
Create and populate a repository that contains a Data manager.
"""
category = self.test_db_util.get_category_by_name(category_name)
category = self.populator.get_category_with_name(category_name)
repository = self.get_or_create_repository(
name=data_manager_repository_name,
description=data_manager_repository_description,
long_description=data_manager_repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
# Upload the data manager files to the repository.
lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
+1 -1
View File
@@ -51,7 +51,7 @@ class TestUpdateInstalledRepository(ShedTwillTestCase):
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category_id=self.security.encode_id(category.id),
category=category,
strings_displayed=[],
)
self.upload_file(
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