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Merge pull request #21953 from jmchilton/toolshed_cleanup_iteration

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Shed Cleanup - Eliminate Twill
This commit is contained in:
Marius van den Beek
2026-03-02 10:54:49 +01:00
committed by GitHub
parent 96184ef0d3 272a5b826a
commit 8bb0116006
67 changed files with 161 additions and 363 deletions
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lib/galaxy/dependencies/dev-requirements.txt
-1
View File
@@ -210,7 +210,6 @@ total-perspective-vortex==3.1.3
trio==0.33.0
trio-websocket==0.12.2
tuspy==1.1.0
twill==3.3.1
twine==6.2.0
types-cachetools==6.2.0.20251022
types-requests==2.32.4.20260107
lib/galaxy/dependencies/pinned-test-requirements.txt
-1
View File
@@ -162,7 +162,6 @@ total-perspective-vortex==3.1.3
trio==0.33.0
trio-websocket==0.12.2
tuspy==1.1.0
twill==3.3.1
types-cachetools==6.2.0.20251022
types-requests==2.32.4.20260107
typing-extensions==4.15.0
lib/galaxy/tool_util/verify/interactor.py
+1 -2
View File
@@ -1779,8 +1779,7 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
output_data = data_list[name]
except (TypeError, KeyError):
# Legacy - fall back on ordered data list access if data_list is
# just a list (case with twill variant or if output changes its
# name).
# just a list (e.g. if output changes its name).
try:
if hasattr(data_list, "values"):
output_data = list(data_list.values())[output_index]
lib/galaxy/tools/parameters/basic.py
-1
View File
@@ -1392,7 +1392,6 @@ class ColumnListParameter(SelectToolParameter):
those columns that contain numerical values in the associated DataToolParameter.
# TODO: we need better testing here, but not sure how to associate a DatatoolParameter with a ColumnListParameter
# from a twill perspective...
>>> # Mock up a history (not connected to database)
>>> from galaxy.model import History, HistoryDatasetAssociation
lib/tool_shed/test/README.md
+2 -2
View File
@@ -52,9 +52,9 @@ Modern Playwright/API tests:
### API Tests (ShedApiTestCase)
```python
from tool_shed.test.base.twilltestcase import ShedTwillTestCase
from tool_shed.test.base.testcase import ShedTestCase
class TestMyFeature(ShedTwillTestCase):
class TestMyFeature(ShedTestCase):
def test_create_repo(self):
category = self.create_category(name="Test")
repo = self.get_or_create_repository(
lib/tool_shed/test/base/README.md
+12 -14
View File
@@ -6,26 +6,25 @@ Base classes and utilities for Tool Shed functional tests.
```
base/
├── driver.py # ToolShedTestDriver - embedded server setup
├── twilltestcase.py # ShedTwillTestCase - main test base class
├── driver.py # ToolShedTestDriver - embedded server setup
├── testcase.py # ShedTestCase - main test base class
├── playwrighttestcase.py # PlaywrightTestCase - browser test base
├── playwrightbrowser.py # PlaywrightShedBrowser - browser abstraction
├── twillbrowser.py # TwillShedBrowser - legacy browser
├── browser.py # ShedBrowser protocol
├── populators.py # ToolShedPopulator - API fixture creation
├── api.py # ShedApiTestCase - API test base
├── api_util.py # API interaction utilities
└── test_db_util.py # Direct database access
├── browser.py # ShedBrowser protocol
├── populators.py # ToolShedPopulator - API fixture creation
├── api.py # ShedApiTestCase - API test base
├── api_util.py # API interaction utilities
└── test_db_util.py # Direct database access
```
## Base Classes
### ShedTwillTestCase
### ShedTestCase
Main test base class with repository/category management:
```python
class TestFeature(ShedTwillTestCase):
class TestFeature(ShedTestCase):
def test_repo_creation(self):
category = self.create_category(name="Tools")
repo = self.get_or_create_repository(
@@ -37,6 +36,7 @@ class TestFeature(ShedTwillTestCase):
```
Key methods:
- `create_category()` - Create test category
- `get_or_create_repository()` - Create repository with category
- `upload_file()` / `commit_tar_to_repository()` - Upload content
@@ -57,6 +57,7 @@ class TestUI(PlaywrightTestCase):
```
Properties:
- `_page` - Playwright Page instance
- `_playwright_browser` - PlaywrightShedBrowser wrapper
@@ -129,14 +130,11 @@ browser.expect_logged_in()
```
Locators available via `Locators` class:
- `Locators.toolbar_login`
- `Locators.login_submit_button`
- `Locators.register_link`
### TwillShedBrowser
Legacy browser using Twill library (deprecated, use Playwright).
## Test Driver
`ToolShedTestDriver` sets up embedded shed server:
lib/tool_shed/test/base/browser.py
-5
View File
@@ -35,11 +35,6 @@ class ShedBrowser(metaclass=abc.ABCMeta):
def submit_form_with_name(self, form_name: str, button="runtool_btn", **kwd):
"""Submit the target button."""
@property
@abc.abstractmethod
def is_twill(self) -> bool:
"""Return whether this is a twill browser."""
@abc.abstractmethod
def edit_repository_categories(self, categories_to_add: list[str], categories_to_remove: list[str]) -> None:
"""Select some new categories and then restore the component."""
lib/tool_shed/test/base/driver.py
+1 -1
View File
@@ -157,7 +157,7 @@ class ToolShedTestDriver(driver_util.TestDriver):
tool_shed_test_port = tool_shed_server_wrapper.port
log.info(f"Functional tests will be run against {tool_shed_test_host}:{tool_shed_test_port}")
# Used by get_filename in tool shed's twilltestcase
# Used by get_filename in tool shed's testcase
if "TOOL_SHED_TEST_FILE_DIR" not in os.environ:
os.environ["TOOL_SHED_TEST_FILE_DIR"] = driver_util.TOOL_SHED_TEST_DATA
lib/tool_shed/test/base/playwrightbrowser.py
+1 -5
View File
@@ -76,7 +76,7 @@ class PlaywrightShedBrowser(ShedBrowser):
from galaxy.util import smart_str
with tempfile.NamedTemporaryFile(suffix=suffix, prefix="twilltestcase-", delete=False) as fh:
with tempfile.NamedTemporaryFile(suffix=suffix, prefix="testcase-", delete=False) as fh:
fh.write(smart_str(content))
return fh.name
@@ -163,10 +163,6 @@ class PlaywrightShedBrowser(ShedBrowser):
select_locator.select_option(label=usernames)
self.submit_form_with_name("user_access", "user_access_button")
@property
def is_twill(self) -> bool:
return False
def logout_if_logged_in(self, assert_logged_out=True):
self._page.wait_for_selector(f"{Locators.toolbar_login}, {Locators.toolbar_logout}")
logout_locator = self._page.locator(Locators.toolbar_logout)
lib/tool_shed/test/base/playwrighttestcase.py
+2 -2
View File
@@ -5,12 +5,12 @@ from pathlib import Path
from playwright.sync_api import Page
from .playwrightbrowser import PlaywrightShedBrowser
from .twilltestcase import ShedTwillTestCase
from .testcase import ShedTestCase
SCREENSHOT_DIR_ENV = "TOOL_SHED_TEST_SCREENSHOTS"
class PlaywrightTestCase(ShedTwillTestCase):
class PlaywrightTestCase(ShedTestCase):
"""Base class for Playwright-based frontend tests."""
@property
lib/tool_shed/test/base/twilltestcase.py → lib/tool_shed/test/base/testcase.py
+30 -33
View File
@@ -77,10 +77,6 @@ from . import (
from .api import ShedApiTestCase
from .browser import ShedBrowser
from .playwrightbrowser import PlaywrightShedBrowser
from .twillbrowser import (
page_content,
visit_url,
)
if TYPE_CHECKING:
from galaxy.model.scoped_session import install_model_scoped_session
@@ -196,8 +192,10 @@ class ToolShedInstallationClient(metaclass=abc.ABCMeta):
class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
"""A Galaxy API + Database as a installation target for the tool shed."""
def __init__(self, testcase: "ShedTwillTestCase"):
def __init__(self, testcase: "ShedTestCase"):
self.testcase = testcase
self._session = requests.Session()
self._last_page_content = ""
def setup(self):
self._galaxy_login()
@@ -247,7 +245,7 @@ class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
for data_manager_name in data_manager_names:
params = {"id": data_managers[data_manager_name]["guid"]}
self._visit_galaxy_url("/data_manager/jobs_list", params=params)
content = page_content()
content = self._last_page_content
for expected in strings_displayed:
if content.find(expected) == -1:
raise AssertionError(f"Failed to find pattern {expected} in {content}")
@@ -257,7 +255,7 @@ class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
) -> dict[str, Any]:
params = {"id": self.testcase.security.encode_id(installed_repository.id)}
self._visit_galaxy_url("/admin_toolshed/manage_repository_json", params=params)
json = page_content()
json = self._last_page_content
return loads(json)
def install_repository(
@@ -413,7 +411,7 @@ class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
def _galaxy_token(self):
self._visit_galaxy_url("/")
html = page_content()
html = self._last_page_content
token_def_index = html.find("session_csrf_token")
token_sep_index = html.find("=", token_def_index)
token_quote_start_index = html.find('"', token_sep_index)
@@ -426,7 +424,7 @@ class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
tool_guid = quote_plus(tool_metadata[0]["guid"], safe="")
api_url = f"/api/tools/{tool_guid}"
self._visit_galaxy_url(api_url)
tool_dict = loads(page_content())
tool_dict = loads(self._last_page_content)
tool_panel_section = tool_dict["panel_section_name"]
return tool_panel_section
@@ -445,11 +443,17 @@ class GalaxyInteractorToolShedInstallationClient(ToolShedInstallationClient):
allowed_codes = [200]
url = f"{self.testcase.galaxy_url}{url}"
url = self.testcase.join_url_and_params(url, params)
return visit_url(url, allowed_codes)
response = self._session.get(url, timeout=DEFAULT_SOCKET_TIMEOUT)
assert response.status_code in allowed_codes, "Invalid HTTP return code {}, allowed codes: {}".format(
response.status_code,
", ".join(str(code) for code in allowed_codes),
)
self._last_page_content = response.text
return url
class StandaloneToolShedInstallationClient(ToolShedInstallationClient):
def __init__(self, testcase: "ShedTwillTestCase"):
def __init__(self, testcase: "ShedTestCase"):
self.testcase = testcase
self.temp_directory = Path(tempfile.mkdtemp(prefix="toolshedtestinstalltarget"))
tool_shed_target = ToolShedTarget(
@@ -612,13 +616,11 @@ class StandaloneToolShedInstallationClient(ToolShedInstallationClient):
@pytest.mark.usefixtures("shed_browser")
class ShedTwillTestCase(ShedApiTestCase):
class ShedTestCase(ShedApiTestCase):
"""Class of FunctionalTestCase geared toward HTML interactions using the Twill library."""
requires_galaxy: bool = False
_installation_client: Optional[
Union[StandaloneToolShedInstallationClient, GalaxyInteractorToolShedInstallationClient]
] = None
_installation_client: Optional[ToolShedInstallationClient] = None
__browser: Optional[ShedBrowser] = None
def setUp(self):
@@ -629,14 +631,16 @@ class ShedTwillTestCase(ShedApiTestCase):
self.hgweb_config_dir = os.environ.get("TEST_HG_WEB_CONFIG_DIR")
self.hgweb_config_manager = hgweb_config.hgweb_config_manager
self.hgweb_config_manager.hgweb_config_dir = self.hgweb_config_dir
self.tool_shed_test_tmp_dir = os.environ.get("TOOL_SHED_TEST_TMP_DIR", None)
self.file_dir = os.environ.get("TOOL_SHED_TEST_FILE_DIR", None)
self.tool_shed_test_tmp_dir: str = os.environ.get("TOOL_SHED_TEST_TMP_DIR", "")
self.file_dir: str = os.environ.get("TOOL_SHED_TEST_FILE_DIR", "")
self.shed_tool_conf = os.environ.get("GALAXY_TEST_SHED_TOOL_CONF")
self.test_db_util = test_db_util
if os.environ.get("TOOL_SHED_TEST_INSTALL_CLIENT") == "standalone":
# TODO: once nose is out of the way - try to get away without
# instantiating the unused Galaxy server here.
installation_client_class = StandaloneToolShedInstallationClient
installation_client_class: Union[
type[StandaloneToolShedInstallationClient], type[GalaxyInteractorToolShedInstallationClient]
] = StandaloneToolShedInstallationClient
full_stack_galaxy = False
else:
installation_client_class = GalaxyInteractorToolShedInstallationClient
@@ -656,12 +660,6 @@ class ShedTwillTestCase(ShedApiTestCase):
assert self.__browser
return self.__browser
def _escape_page_content_if_needed(self, content: str) -> str:
# if twill browser is being used - replace spaces with " "
if self._browser.is_twill:
content = content.replace(" ", " ")
return content
def check_for_strings(self, strings_displayed=None, strings_not_displayed=None):
strings_displayed = strings_displayed or []
strings_not_displayed = strings_not_displayed or []
@@ -837,7 +835,7 @@ class ShedTwillTestCase(ShedApiTestCase):
return self._browser.visit_url(url, allowed_codes=allowed_codes)
def write_temp_file(self, content, suffix=".html"):
with tempfile.NamedTemporaryFile(suffix=suffix, prefix="twilltestcase-", delete=False) as fh:
with tempfile.NamedTemporaryFile(suffix=suffix, prefix="testcase-", delete=False) as fh:
fh.write(smart_str(content))
return fh.name
@@ -1260,10 +1258,6 @@ class ShedTwillTestCase(ShedApiTestCase):
self._browser.fill_form_value("edit_repository", input_elem_name, kwd[input_elem_name])
strings_displayed.append(self.escape_html(kwd[input_elem_name]))
self._browser.submit_form_with_name("edit_repository", "edit_repository_button")
# TODO: come back to this (and similar conditional below), the problem is check
# for strings isn't working with with textboxes I think?
if self._browser.is_twill:
self.check_for_strings(strings_displayed)
if revert:
strings_displayed = []
# assert original_information[input_elem_name]
@@ -1273,8 +1267,6 @@ class ShedTwillTestCase(ShedApiTestCase):
)
strings_displayed.append(self.escape_html(original_information[input_elem_name]))
self._browser.submit_form_with_name("edit_repository", "edit_repository_button")
if self._browser.is_twill:
self.check_for_strings(strings_displayed)
def enable_email_alerts(self, repository: Repository, strings_displayed=None, strings_not_displayed=None) -> None:
repository_id = repository.id
@@ -1534,7 +1526,7 @@ class ShedTwillTestCase(ShedApiTestCase):
def grant_role_to_user(self, user, role):
strings_displayed = [self.security.encode_id(role.id), role.name]
strings_not_displayed = []
strings_not_displayed: list[str] = []
self.visit_url("/admin/roles")
self.check_for_strings(strings_displayed, strings_not_displayed)
params = dict(operation="manage users and groups", id=self.security.encode_id(role.id))
@@ -1692,6 +1684,7 @@ class ShedTwillTestCase(ShedApiTestCase):
self.check_for_strings(strings_displayed, strings_not_displayed)
def reactivate_repository(self, installed_repository):
assert self._installation_client
self._installation_client.reactivate_repository(installed_repository)
def reinstall_repository_api(
@@ -1703,6 +1696,7 @@ class ShedTwillTestCase(ShedApiTestCase):
):
name = installed_repository.name
owner = installed_repository.owner
assert self._installation_client
self._installation_client.install_repository(
name,
owner,
@@ -1816,10 +1810,12 @@ class ShedTwillTestCase(ShedApiTestCase):
@property
def shed_tool_data_table_conf(self):
assert self._installation_client
return self._installation_client.shed_tool_data_table_conf
@property
def tool_data_path(self):
assert self._installation_client
return self._installation_client.tool_data_path
def _refresh_tool_shed_repository(self, repo: galaxy_model.ToolShedRepository) -> None:
@@ -1855,6 +1851,7 @@ class ShedTwillTestCase(ShedApiTestCase):
# </table>
# </tables>
required_data_table_entry = None
assert data_tables is not None
for table_elem in data_tables.findall("table"):
# The value of table_elem will be something like: <table comment_char="#" name="sam_fa_indexes">
for required_data_table_entry in required_data_table_entries:
@@ -1867,7 +1864,7 @@ class ShedTwillTestCase(ShedApiTestCase):
# The "path" attribute of the "file" tag is the location that Galaxy always uses because the
# Galaxy ToolDataTableManager was implemented in such a way that the hard-coded path is used
# rather than allowing the location to be a configurable setting like the tool shed requires.
file_path = file_elem.get("path", None)
file_path = file_elem.get("path", None) if file_elem is not None else None
# The value of file_path will be something like: "tool-data/all_fasta.loc"
assert (
file_path is not None
lib/tool_shed/test/base/twillbrowser.py
-148
View File
@@ -1,148 +0,0 @@
import tempfile
import twill.commands as tc
from twill.browser import FormElement # type: ignore[attr-defined, unused-ignore]
from galaxy.util import smart_str
from .browser import (
FormValueType,
ShedBrowser,
)
tc.options["equiv_refresh_interval"] = 0
# Resetting all repository metadata can take a really long time
tc.timeout(240)
def visit_url(url: str, allowed_codes: list[int]) -> str:
tc.go(url)
return_code = tc.browser.code
assert return_code in allowed_codes, "Invalid HTTP return code {}, allowed codes: {}".format(
return_code,
", ".join(str(code) for code in allowed_codes),
)
return url
def page_content() -> str:
return tc.browser.html
class TwillShedBrowser(ShedBrowser):
def visit_url(self, url: str, allowed_codes: list[int]) -> str:
return visit_url(url, allowed_codes=allowed_codes)
def page_content(self) -> str:
"""
Return the last visited page (usually HTML, but can binary data as
well).
"""
return page_content()
def check_page_for_string(self, patt: str) -> None:
page = self.page_content()
if page.find(patt) == -1:
fname = self.write_temp_file(page)
errmsg = f"no match to '{patt}'\npage content written to '{fname}'\npage: [[{page}]]"
raise AssertionError(errmsg)
def check_string_not_in_page(self, patt: str) -> None:
page = self.page_content()
if page.find(patt) != -1:
fname = self.write_temp_file(page)
errmsg = f"string ({patt}) incorrectly displayed in page.\npage content written to '{fname}'"
raise AssertionError(errmsg)
def write_temp_file(self, content, suffix=".html"):
with tempfile.NamedTemporaryFile(suffix=suffix, prefix="twilltestcase-", delete=False) as fh:
fh.write(smart_str(content))
return fh.name
def submit_form_with_name(self, form_name: str, button="runtool_btn", **kwd):
forms_by_name: dict[str, FormElement] = {f.get("name"): f for f in self._show_forms()}
form = forms_by_name[form_name]
self._submit_form(form, button, **kwd)
def _show_forms(self) -> list[FormElement]:
"""Shows form, helpful for debugging new tests"""
return tc.browser.forms
def submit_form(self, form_no=-1, button="runtool_btn", form=None, **kwd):
if form is None:
try:
form = self._show_forms()[form_no]
except IndexError:
raise ValueError("No form to submit found")
self._submit_form(form, button, **kwd)
def _submit_form(self, form, button, **kwd):
controls = {c.name: c for c in form.inputs}
form_name = form.get("name")
for control_name, control_value in kwd.items():
if control_name not in controls:
continue # these cannot be handled safely - cause the test to barf out
if not isinstance(control_value, list):
control_value = [str(control_value)]
control = controls[control_name]
control_type = getattr(control, "type", None)
if control_type in (
"text",
"textfield",
"submit",
"password",
"TextareaElement",
"checkbox",
"radio",
None,
):
for cv in control_value:
tc.fv(form_name, control.name, cv)
else:
# Add conditions for other control types here when necessary.
pass
tc.submit(button)
def fill_form_value(self, form_name: str, control_name: str, value: FormValueType):
value = str(value)
tc.fv(form_name, control_name, value)
def edit_repository_categories(self, categories_to_add: list[str], categories_to_remove: list[str]) -> None:
"""Select some new categories and then restore the component."""
strings_displayed = []
strings_not_displayed = []
for category in categories_to_add:
self.fill_form_value("categories", "category_id", f"+{category}")
strings_displayed.append(f"selected>{category}")
for category in categories_to_remove:
self.fill_form_value("categories", "category_id", f"-{category}")
strings_not_displayed.append(f"selected>{category}")
self.submit_form_with_name("categories", "manage_categories_button")
self._check_for_strings(strings_displayed, strings_not_displayed)
strings_displayed = []
strings_not_displayed = []
for category in categories_to_remove:
self.fill_form_value("categories", "category_id", f"+{category}")
strings_displayed.append(f"selected>{category}")
for category in categories_to_add:
self.fill_form_value("categories", "category_id", f"-{category}")
strings_not_displayed.append(f"selected>{category}")
self.submit_form_with_name("categories", "manage_categories_button")
self._check_for_strings(strings_displayed, strings_not_displayed)
def grant_users_access(self, usernames: list[str]):
for username in usernames:
self.fill_form_value("user_access", "allow_push", f"+{username}")
self.submit_form_with_name("user_access", "user_access_button")
@property
def is_twill(self) -> bool:
return True
def _check_for_strings(self, strings_displayed: list[str], strings_not_displayed: list[str]):
if strings_displayed:
for check_str in strings_displayed:
self.check_page_for_string(check_str)
if strings_not_displayed:
for check_str in strings_not_displayed:
self.check_string_not_in_page(check_str)
lib/tool_shed/test/functional/test_0000_basic_repository_features.py
+8 -27
View File
@@ -3,7 +3,7 @@ import logging
import pytest
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repository_name = "filtering_0000"
repository_description = "Galaxy's filtering tool for test 0000"
@@ -12,7 +12,7 @@ repository_long_description = "Long description of Galaxy's filtering tool for t
log = logging.getLogger(__name__)
class TestBasicRepositoryFeatures(ShedTwillTestCase):
class TestBasicRepositoryFeatures(ShedTestCase):
"""Test core repository features."""
def test_0000_initiate_users(self):
@@ -73,7 +73,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
def test_0040_verify_repository(self):
"""Display basic repository pages"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
latest_changeset_revision = self.get_repository_tip(repository)
self.check_for_valid_tools(repository, strings_displayed=["Filter1"])
self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=1)
tip = self.get_repository_tip(repository)
@@ -97,11 +96,6 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
repository, strings_displayed=[f"Repository '{repository.name}' revision", "(repository tip)"]
)
strings = ["Uploaded filtering 1.1.0"]
if self._browser.is_twill:
# this appears in a link - it isn't how one would check this
# in playwright. But also we're testing the mercurial page
# here so this is probably a questionable check overall.
strings += [latest_changeset_revision]
self.display_repository_clone_page(
common.test_user_1_name,
repository_name,
@@ -112,23 +106,13 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
"""Upload filtering.txt file associated with tool version 1.1.0."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.add_file_to_repository(repository, "filtering/filtering_0000.txt")
expected = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
expected = "Readme file for filtering 1.1.0"
self.display_manage_repository_page(repository, strings_displayed=[expected])
def test_0060_upload_filtering_test_data(self):
"""Upload filtering test data."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.add_tar_to_repository(repository, "filtering/filtering_test_data.tar")
if self._browser.is_twill:
# probably not porting this functionality - just test
# with Twill for older UI and drop when that is all dropped
self.display_repository_file_contents(
repository=repository,
filename="1.bed",
filepath="test-data",
strings_displayed=[],
strings_not_displayed=[],
)
self.check_repository_metadata(repository, tip_only=True)
def test_0065_upload_filtering_2_2_0(self):
@@ -165,10 +149,10 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
"""Upload readme.txt file associated with tool version 2.2.0."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.add_file_to_repository(repository, "readme.txt")
content = self._escape_page_content_if_needed("This is a readme file.")
content = "This is a readme file."
self.display_manage_repository_page(repository, strings_displayed=[content])
# Verify that there is a different readme file for each metadata revision.
readme_content = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
readme_content = "Readme file for filtering 1.1.0"
self.display_manage_repository_page(
repository,
strings_displayed=[
@@ -182,7 +166,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.delete_files_from_repository(repository, filenames=["readme.txt"])
self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
readme_content = self._escape_page_content_if_needed("Readme file for filtering 1.1.0")
readme_content = "Readme file for filtering 1.1.0"
self.display_manage_repository_page(repository, strings_displayed=[readme_content])
def test_0090_verify_repository_metadata(self):
@@ -223,7 +207,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
# Upload readme.txt to the filtering_0000 repository and verify that it is now displayed.
self.add_file_to_repository(repository, "filtering/readme.txt")
content = self._escape_page_content_if_needed("These characters should not")
content = "These characters should not"
self.display_manage_repository_page(repository, strings_displayed=[content])
def test_0130_verify_handling_of_invalid_characters(self):
@@ -241,7 +225,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
break
# Check for the changeset revision, repository name, owner username, 'repos' in the clone url, and the captured
# unicode decoding error message.
content = self._escape_page_content_if_needed("These characters should not")
content = "These characters should not"
strings_displayed = [
f"{revision_number}:{revision_hash}",
"filtering_0000",
@@ -265,10 +249,7 @@ class TestBasicRepositoryFeatures(ShedTwillTestCase):
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
encoded_repository_id = repository.id
assert encoded_repository_id
strings_displayed = ["Invalid+changeset+revision"]
view_repo_url = (
f"/repository/view_repository?id={encoded_repository_id}&changeset_revision=nonsensical_changeset"
)
self.visit_url(view_repo_url)
if self._browser.is_twill:
self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=[])
lib/tool_shed/test/functional/test_0010_repository_with_tool_dependencies.py
+2 -2
View File
@@ -1,7 +1,7 @@
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repository_name = "freebayes_0010"
repository_description = "Galaxy's freebayes tool"
@@ -18,7 +18,7 @@ repository_long_description = "Long description of Galaxy's freebayes tool"
"""
class TestFreebayesRepository(ShedTwillTestCase):
class TestFreebayesRepository(ShedTestCase):
"""Testing freebayes with tool data table entries, .loc files, and tool dependencies."""
def test_0000_create_or_login_admin_user(self):
lib/tool_shed/test/functional/test_0020_basic_repository_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
@@ -10,7 +10,7 @@ emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
class TestBasicRepositoryDependencies(ShedTwillTestCase):
class TestBasicRepositoryDependencies(ShedTestCase):
"""Testing emboss 5 with repository dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0030_repository_dependency_revisions.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0030"
column_maker_repository_description = "Add column"
@@ -12,7 +12,7 @@ emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0030"
class TestRepositoryDependencyRevisions(ShedTwillTestCase):
class TestRepositoryDependencyRevisions(ShedTestCase):
"""Test dependencies on different revisions of a repository."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0040_repository_circular_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
freebayes_repository_name = "freebayes_0040"
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
@@ -13,7 +13,7 @@ CATEGORY_NAME = "test_0040_repository_circular_dependencies"
CATEGORY_DESC = "Testing handling of circular repository dependencies."
class TestRepositoryCircularDependencies(ShedTwillTestCase):
class TestRepositoryCircularDependencies(ShedTestCase):
"""Verify that the code correctly displays repositories with circular repository dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0050_circular_dependencies_4_levels.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
emboss_repository_name = "emboss_0050"
emboss_repository_description = "Galaxy's emboss tool"
@@ -29,7 +29,7 @@ category_name = "Test 0050 Circular Dependencies 5 Levels"
category_description = "Test circular dependency features"
class TestRepositoryCircularDependenciesToNLevels(ShedTwillTestCase):
class TestRepositoryCircularDependenciesToNLevels(ShedTestCase):
"""Verify that the code correctly handles circular dependencies down to n levels."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0070_invalid_tool.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repository_name = "bismark_0070"
repository_description = "Galaxy's bismark wrapper"
@@ -8,7 +8,7 @@ category_name = "Test 0070 Invalid Tool Revisions"
category_description = "Tests for a repository with invalid tool revisions."
class TestBismarkRepository(ShedTwillTestCase):
class TestBismarkRepository(ShedTestCase):
"""Testing bismark with valid and invalid tool entries."""
def test_0000_create_or_login_admin_user(self):
lib/tool_shed/test/functional/test_0080_advanced_circular_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_0080"
column_repository_description = "Add column"
@@ -13,7 +13,7 @@ category_name = "Test 0080 Advanced Circular Dependencies"
category_description = "Test circular dependency features"
class TestRepositoryCircularDependencies(ShedTwillTestCase):
class TestRepositoryCircularDependencies(ShedTestCase):
"""Verify that the code correctly handles circular dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0090_tool_search.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
emboss_repository_name = "emboss_0090"
emboss_repository_description = "Galaxy's emboss tool"
@@ -25,7 +25,7 @@ category_name = "Test 0090 Tool Search And Installation"
category_description = "Test 0090 Tool Search And Installation"
class TestRepositoryCircularDependenciesAgain(ShedTwillTestCase):
class TestRepositoryCircularDependenciesAgain(ShedTestCase):
"""Test more features related to repository dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0100_complex_repository_dependencies.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -19,7 +19,7 @@ category_name = "Test 0100 Complex Repository Dependencies"
category_description = "Test 0100 Complex Repository Dependencies"
class TestComplexRepositoryDependencies(ShedTwillTestCase):
class TestComplexRepositoryDependencies(ShedTestCase):
"""Test features related to complex repository dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0110_invalid_simple_repository_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0110"
column_maker_repository_description = "A flexible aligner."
@@ -13,7 +13,7 @@ category_name = "Test 0110 Invalid Repository Dependencies"
category_desc = "Test 0110 Invalid Repository Dependencies"
class TestBasicRepositoryDependencies(ShedTwillTestCase):
class TestBasicRepositoryDependencies(ShedTestCase):
"""Testing emboss 5 with repository dependencies."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0120_simple_repository_dependency_multiple_owners.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
datatypes_repository_name = "blast_datatypes_0120"
datatypes_repository_description = "Galaxy applicable datatypes for BLAST"
@@ -21,7 +21,7 @@ Tool shed side:
"""
class TestRepositoryMultipleOwners(ShedTwillTestCase):
class TestRepositoryMultipleOwners(ShedTestCase):
def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user.
lib/tool_shed/test/functional/test_0140_tool_help_images.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -22,7 +22,7 @@ src="/repository/static/images/<id>/count_modes.png"
"""
class TestToolHelpImages(ShedTwillTestCase):
class TestToolHelpImages(ShedTestCase):
"""Test features related to tool help images."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0150_prior_installation_required.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_0150"
column_repository_description = "Add column"
@@ -27,7 +27,7 @@ Verify that convert_chars was installed first, contrary to the ordering that wou
"""
class TestSimplePriorInstallation(ShedTwillTestCase):
class TestSimplePriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0160_circular_prior_installation_required.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
filter_repository_name = "filtering_0160"
filter_repository_description = "Galaxy's filtering tool for test 0160"
@@ -26,7 +26,7 @@ Verify display.
"""
class TestSimplePriorInstallation(ShedTwillTestCase):
class TestSimplePriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+2 -2
View File
@@ -1,7 +1,7 @@
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
matplotlib_repository_name = "package_matplotlib_1_2_0170"
matplotlib_repository_description = (
@@ -29,7 +29,7 @@ category_description = "Test 0170 Prior Installation Complex Dependencies"
"""
class TestComplexPriorInstallation(ShedTwillTestCase):
class TestComplexPriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0300_reset_all_metadata.py
+2 -2
View File
@@ -1,7 +1,7 @@
import pytest
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
@@ -40,7 +40,7 @@ category_0050_description = "Test circular dependency features"
running_standalone = False
class TestResetAllRepositoryMetadata(ShedTwillTestCase):
class TestResetAllRepositoryMetadata(ShedTestCase):
"""Verify that the "Reset selected metadata" feature works."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0310_hg_api_features.py
+2 -2
View File
@@ -2,7 +2,7 @@ import logging
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -19,7 +19,7 @@ category_description = "Test 0310 for verifying the tool shed http interface to
"""
class TestHgWebFeatures(ShedTwillTestCase):
class TestHgWebFeatures(ShedTestCase):
"""Test http mercurial interface."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+4 -16
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -25,7 +25,7 @@ first_changeset_hash = ""
"""
class TestRepositoryCitableURLs(ShedTwillTestCase):
class TestRepositoryCitableURLs(ShedTestCase):
"""Test repository citable url features."""
def test_0000_initiate_users(self):
@@ -83,9 +83,6 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
"""
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
encoded_user_id = self.security.encode_id(test_user_1.id)
# Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
# then directly load the url that the iframe should be loading and check for the expected strings.
# The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
strings_displayed: list[str] = []
strings_displayed_in_iframe = ["user1", "filtering_0420", repository_description]
self.load_citable_url(
@@ -109,14 +106,11 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
encoded_user_id = self.security.encode_id(test_user_1.id)
encoded_repository_id = repository.id
# Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
# then directly load the url that the iframe should be loading and check for the expected strings.
# The iframe should point to /repository/bview_repository?id=<encoded repository ID>
strings_displayed: list[str] = []
strings_displayed_in_iframe = [
"user1",
"filtering_0420",
self._escape_page_content_if_needed(repository_long_description),
repository_long_description,
]
strings_displayed_in_iframe.append(self.get_repository_tip(repository))
self.load_citable_url(
@@ -140,14 +134,11 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
encoded_user_id = self.security.encode_id(test_user_1.id)
encoded_repository_id = repository.id
# Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
# then directly load the url that the iframe should be loading and check for the expected strings.
# The iframe should point to /repository/view_repository?id=<encoded repository ID>
strings_displayed: list[str] = []
strings_displayed_in_iframe = [
"user1",
"filtering_0420",
self._escape_page_content_if_needed(repository_long_description),
repository_long_description,
first_changeset_hash,
]
self.load_citable_url(
@@ -185,9 +176,6 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
"""
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
encoded_user_id = self.security.encode_id(test_user_1.id)
# Since twill does not load the contents of an iframe, we need to check that the iframe has been generated correctly,
# then directly load the url that the iframe should be loading and check for the expected strings.
# The iframe should point to /repository/browse_repositories?user_id=<encoded user ID>&operation=repositories_by_user
strings_displayed = ["Repository user1/!!invalid!! is not found"]
strings_displayed_in_iframe: list[str] = []
self.load_citable_url(
lib/tool_shed/test/functional/test_0430_browse_utilities.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -21,7 +21,7 @@ freebayes_repository_long_description = "Long description of Freebayes tool for
"""
class TestToolShedBrowseUtilities(ShedTwillTestCase):
class TestToolShedBrowseUtilities(ShedTestCase):
"""Test browsing for Galaxy utilities."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0440_deleting_dependency_definitions.py
+2 -2
View File
@@ -1,6 +1,6 @@
from tool_shed_client.schema import Repository
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_0440"
column_repository_description = "Add column"
@@ -50,7 +50,7 @@ Tool dependencies:
"""
class TestDeletedDependencies(ShedTwillTestCase):
class TestDeletedDependencies(ShedTestCase):
"""Test metadata setting when dependency definitions are deleted."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0460_upload_to_repository.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -54,7 +54,7 @@ For all steps, verify that the generated dependency points to the tip of the spe
"""
class TestAutomaticDependencyRevision(ShedTwillTestCase):
class TestAutomaticDependencyRevision(ShedTestCase):
"""Test defining repository dependencies without specifying the changeset revision."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0470_tool_dependency_repository_type.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -60,7 +60,7 @@ emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 t
"""
class TestEnvironmentInheritance(ShedTwillTestCase):
class TestEnvironmentInheritance(ShedTestCase):
"""Test referencing environment variables that were defined in a separate tool dependency."""
def test_0000_initiate_users_and_category(self):
lib/tool_shed/test/functional/test_0480_tool_dependency_xml_verification.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -20,7 +20,7 @@ repository_long_description = "This repository is in the test suite 0480"
"""
class TestDependencyDefinitionValidation(ShedTwillTestCase):
class TestDependencyDefinitionValidation(ShedTestCase):
"""Test the tool shed's tool dependency XML validation."""
def test_0000_initiate_users_and_category(self):
lib/tool_shed/test/functional/test_0530_repository_admin_feature.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -31,7 +31,7 @@ category_description = "Verify the functionality of the code that handles the re
"""
class TestRepositoryAdminRole(ShedTwillTestCase):
class TestRepositoryAdminRole(ShedTestCase):
"""Verify that the code correctly handles the repository admin role."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_0550_metadata_updated_dependencies.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -43,7 +43,7 @@ category_description = "Verify metadata updates"
"""
class TestGetUpdatedMetadata(ShedTwillTestCase):
class TestGetUpdatedMetadata(ShedTestCase):
"""Verify that updated repositories still have correct dependency links."""
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_1000_install_basic_repository.py
+2 -2
View File
@@ -1,11 +1,11 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repo_name = "filtering_0000"
repo_description = "Galaxy's filtering tool"
class TestBasicToolShedFeatures(ShedTwillTestCase):
class TestBasicToolShedFeatures(ShedTestCase):
"""Test installing a basic repository."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1010_install_repository_with_tool_dependencies.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repository_name = "freebayes_0010"
repository_description = "Galaxy's freebayes tool"
@@ -10,7 +10,7 @@ category_name = "Test 0010 Repository With Tool Dependencies"
log = logging.getLogger(__name__)
class TestToolWithToolDependencies(ShedTwillTestCase):
class TestToolWithToolDependencies(ShedTestCase):
"""Test installing a repository with tool dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1020_install_repository_with_repository_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
@@ -10,7 +10,7 @@ emboss_repository_description = "Galaxy wrappers for Emboss version 5.0.0 tools
emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 tools for test 0020"
class TestToolWithRepositoryDependencies(ShedTwillTestCase):
class TestToolWithRepositoryDependencies(ShedTestCase):
"""Test installing a repository with repository dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1030_install_repository_with_dependency_revisions.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0030"
column_maker_repository_description = "A flexible aligner."
@@ -14,7 +14,7 @@ emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 t
running_standalone = False
class TestRepositoryWithDependencyRevisions(ShedTwillTestCase):
class TestRepositoryWithDependencyRevisions(ShedTestCase):
"""Test installing a repository with dependency revisions."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1040_install_repository_basic_circular_dependencies.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
freebayes_repository_name = "freebayes_0040"
freebayes_repository_description = "Galaxy's freebayes tool for test 0040"
@@ -14,7 +14,7 @@ category_name = "test_0040_repository_circular_dependencies"
running_standalone = False
class TestInstallingCircularDependencies(ShedTwillTestCase):
class TestInstallingCircularDependencies(ShedTestCase):
"""Verify that the code correctly handles installing repositories with circular dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1050_circular_dependencies_4_levels.py
+2 -2
View File
@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
emboss_repository_name = "emboss_0050"
emboss_repository_description = "Galaxy's emboss tool"
@@ -31,7 +31,7 @@ category_description = "Test circular dependency features"
running_standalone = False
class TestInstallRepositoryCircularDependencies(ShedTwillTestCase):
class TestInstallRepositoryCircularDependencies(ShedTestCase):
"""Verify that the code correctly handles circular dependencies down to n levels."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1070_invalid_tool.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
repository_name = "bismark_0070"
repository_description = "Galaxy's bismark wrapper"
@@ -8,7 +8,7 @@ category_name = "Test 0070 Invalid Tool Revisions"
category_description = "Test 1070 for a repository with an invalid tool."
class TestFreebayesRepository(ShedTwillTestCase):
class TestFreebayesRepository(ShedTestCase):
"""Test repository with multiple revisions with invalid tools."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1080_advanced_circular_dependency_installation.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_0080"
column_repository_description = "Add column"
@@ -19,7 +19,7 @@ log = logging.getLogger(__name__)
running_standalone = False
class TestRepositoryDependencies(ShedTwillTestCase):
class TestRepositoryDependencies(ShedTestCase):
"""Testing uninstalling and reinstalling repository dependencies, and setting tool panel sections."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1090_repository_dependency_handling.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_1085"
column_repository_description = "Add column"
@@ -17,7 +17,7 @@ category_description = "Test circular dependency features"
log = logging.getLogger(__name__)
class TestRepositoryDependencies(ShedTwillTestCase):
class TestRepositoryDependencies(ShedTestCase):
"""Testing the behavior of repository dependencies with tool panel sections."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1100_install_updated_repository_dependencies.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_repository_name = "column_maker_1087"
column_repository_description = "Add column"
@@ -13,7 +13,7 @@ category_name = "Test 1087 Advanced Circular Dependencies"
category_description = "Test circular dependency features"
class TestRepositoryDependencies(ShedTwillTestCase):
class TestRepositoryDependencies(ShedTestCase):
"""Test installing a repository, then updating it to include repository dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1120_install_repository_with_complex_dependencies.py
+2 -2
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@@ -1,7 +1,7 @@
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
bwa_base_repository_name = "bwa_base_repository_0100"
bwa_base_repository_description = "BWA Base"
@@ -20,7 +20,7 @@ category_description = "Test 0100 Complex Repository Dependencies"
running_standalone = False
class TestInstallingComplexRepositoryDependencies(ShedTwillTestCase):
class TestInstallingComplexRepositoryDependencies(ShedTestCase):
"""Test features related to installing repositories with complex repository dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1130_install_repository_with_invalid_repository_dependency.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0110"
column_maker_repository_description = "A flexible aligner."
@@ -14,7 +14,7 @@ category_desc = "Test 0110 Invalid Repository Dependencies"
running_standalone = False
class TestBasicRepositoryDependencies(ShedTwillTestCase):
class TestBasicRepositoryDependencies(ShedTestCase):
"""Testing emboss 5 with repository dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1140_simple_repository_dependency_multiple_owners.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
datatypes_repository_name = "blast_datatypes_0120"
datatypes_repository_description = "Galaxy applicable datatypes for BLAST"
@@ -27,7 +27,7 @@ Galaxy side:
running_standalone = False
class TestInstallRepositoryMultipleOwners(ShedTwillTestCase):
class TestInstallRepositoryMultipleOwners(ShedTestCase):
requires_galaxy = True
def test_0000_initiate_users(self):
lib/tool_shed/test/functional/test_1160_tool_help_images.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -18,7 +18,7 @@ category_description = "Test 0140 Tool Help Images"
# src="/repository/static/images/<id>/count_modes.png"
class TestToolHelpImages(ShedTwillTestCase):
class TestToolHelpImages(ShedTestCase):
"""Test features related to tool help images."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1170_prior_installation_required.py
+2 -2
View File
@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -33,7 +33,7 @@ Verify that convert_chars was installed first, contrary to the ordering that wou
running_standalone = False
class TestSimplePriorInstallation(ShedTwillTestCase):
class TestSimplePriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1180_circular_prior_installation_required.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -46,7 +46,7 @@ Verify that convert_chars was installed first, contrary to the ordering that wou
running_standalone = False
class TestSimplePriorInstallation(ShedTwillTestCase):
class TestSimplePriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+2 -2
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@@ -1,7 +1,7 @@
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
matplotlib_repository_name = "package_matplotlib_1_2_0170"
matplotlib_repository_description = (
@@ -33,7 +33,7 @@ category_description = "Test 0170 Prior Installation Complex Dependencies"
running_standalone = False
class TestComplexPriorInstallation(ShedTwillTestCase):
class TestComplexPriorInstallation(ShedTestCase):
"""Test features related to datatype converters."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1200_uninstall_and_reinstall_basic_repository.py
+2 -2
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@@ -1,8 +1,8 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
class TestUninstallingAndReinstallingRepositories(ShedTwillTestCase):
class TestUninstallingAndReinstallingRepositories(ShedTestCase):
"""Test uninstalling and reinstalling a basic repository."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py
+2 -2
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@@ -1,10 +1,10 @@
import os
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
class TestUninstallingAndReinstallingRepositories(ShedTwillTestCase):
class TestUninstallingAndReinstallingRepositories(ShedTestCase):
"""Test uninstalling and reinstalling a repository with tool dependencies."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0030"
column_maker_repository_description = "Add column"
@@ -14,7 +14,7 @@ emboss_repository_long_description = "Galaxy wrappers for Emboss version 5.0.0 t
running_standalone = False
class TestUninstallingAndReinstallingRepositories(ShedTwillTestCase):
class TestUninstallingAndReinstallingRepositories(ShedTestCase):
"""Test uninstalling and reinstalling a repository with repository dependency revisions."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1300_reset_all_metadata.py
+2 -2
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@@ -1,5 +1,5 @@
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
column_maker_repository_name = "column_maker_0020"
column_maker_repository_description = "A flexible aligner."
@@ -39,7 +39,7 @@ repository_datatypes_count = 0
running_standalone = False
class TestResetInstalledRepositoryMetadata(ShedTwillTestCase):
class TestResetInstalledRepositoryMetadata(ShedTestCase):
"""Verify that the "Reset selected metadata" feature works."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1410_update_manager.py
+2 -2
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@@ -2,7 +2,7 @@ import logging
import time
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -21,7 +21,7 @@ category_description = "Functional test suite to test the update manager."
"""
class TestUpdateManager(ShedTwillTestCase):
class TestUpdateManager(ShedTestCase):
"""Test the Galaxy update manager."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1430_repair_installed_repository.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -32,7 +32,7 @@ In Galaxy:
"""
class TestRepairRepository(ShedTwillTestCase):
class TestRepairRepository(ShedTestCase):
"""Test repairing an installed repository."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1460_data_managers.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -25,7 +25,7 @@ data_manager_tar_file = "1460_files/data_manager_files/test_data_manager.tar"
# TODO: Allow testing actual Execution of installed Data Manager Tool.
class TestDataManagers(ShedTwillTestCase):
class TestDataManagers(ShedTestCase):
"""Test installing a repository containing a Data Manager."""
requires_galaxy = True
lib/tool_shed/test/functional/test_1470_updating_installed_repositories.py
+2 -2
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@@ -1,7 +1,7 @@
import logging
from ..base import common
from ..base.twilltestcase import ShedTwillTestCase
from ..base.testcase import ShedTestCase
log = logging.getLogger(__name__)
@@ -24,7 +24,7 @@ category_description = (
"""
class TestUpdateInstalledRepository(ShedTwillTestCase):
class TestUpdateInstalledRepository(ShedTestCase):
"""Verify that the code correctly handles updating an installed repository, then uninstalling and reinstalling."""
requires_galaxy = True
mypy.ini
-2
View File
@@ -710,8 +710,6 @@ check_untyped_defs = False
check_untyped_defs = False
[mypy-test.functional.test_toolbox_pytest]
check_untyped_defs = False
[mypy-tool_shed.test.base.twilltestcase]
check_untyped_defs = False
[mypy-galaxy_test.selenium.test_histories_published]
check_untyped_defs = False
[mypy-galaxy_test.selenium.test_histories_list]
packages/tool_shed/setup.cfg
+1 -2
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@@ -57,7 +57,6 @@ install_requires =
slowapi
starlette
starlette-context
twill
typing-extensions
WebOb
Whoosh
@@ -65,7 +64,7 @@ packages = find:
python_requires = >=3.10
[options.extras_require]
test =
test =
pytest
[options.packages.find]
pyproject.toml
-1
View File
@@ -152,7 +152,6 @@ test = [
"testfixtures",
"total-perspective-vortex>=3.1.1,<4", # https://github.com/galaxyproject/total-perspective-vortex/pull/173
"tuspy",
"twill>=3.2.5", # Python 3.13 support
"watchdog",
"Werkzeug",
]
run_tests.sh
+1 -2
View File
@@ -46,8 +46,7 @@ The main test types are as follows:
quickly test just a component or a few components of Galaxy's backend code.
- Selenium: These are full stack tests meant to test the Galaxy UI with real
browsers and are located in lib/galaxy_test/selenium.
- ToolShed: These are web tests that use the older Python web testing
framework twill to test ToolShed related functionality. These are
- ToolShed: These are tests that test ToolShed related functionality. These are
located in lib/tool_shed/test.
Python testing is done via pytest. Specific tests can be selected