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Source code for tool_shed.test.functional.test_0000_basic_repository_features
import logging
import pytest
from ..base import common
from ..base.api import skip_if_api_v2
from ..base.twilltestcase import ShedTwillTestCase
repository_name = "filtering_0000"
repository_description = "Galaxy's filtering tool for test 0000"
repository_long_description = "Long description of Galaxy's filtering tool for test 0000"
log = logging.getLogger(__name__)
[docs]class TestBasicRepositoryFeatures(ShedTwillTestCase):
"""Test core repository features."""
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts and login as an admin user."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
self.login(email=common.admin_email, username=common.admin_username)
[docs] @skip_if_api_v2
# no replicating the functionality in tool shed 2.0, use Planemo
# to create repositories.
def test_0005_create_repository_without_categories(self):
"""Verify that a repository cannot be created unless at least one category has been defined."""
strings_displayed = ["No categories have been configured in this instance of the Galaxy Tool Shed"]
self.visit_url("/repository/create_repository")
self.check_for_strings(strings_displayed=strings_displayed, strings_not_displayed=[])
[docs] def test_0010_create_categories(self):
"""Create categories for this test suite"""
self.create_category(
name="Test 0000 Basic Repository Features 1", description="Test 0000 Basic Repository Features 1"
)
self.create_category(
name="Test 0000 Basic Repository Features 2", description="Test 0000 Basic Repository Features 2"
)
[docs] 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.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=category,
strings_displayed=strings_displayed,
)
[docs] def test_0020_edit_repository(self):
"""Edit the repository name, description, and long description"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
new_name = "renamed_filtering"
new_description = "Edited filtering tool"
new_long_description = "Edited long description"
self.edit_repository_information(
repository, repo_name=new_name, description=new_description, long_description=new_long_description
)
[docs] def test_0025_change_repository_category(self):
"""Change the categories associated with the filtering repository"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.edit_repository_categories(
repository,
categories_to_add=["Test 0000 Basic Repository Features 2"],
categories_to_remove=["Test 0000 Basic Repository Features 1"],
)
[docs] @skip_if_api_v2
def test_0030_grant_write_access(self):
"""Grant write access to another user"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.grant_write_access(repository, usernames=[common.test_user_2_name])
self.revoke_write_access(repository, common.test_user_2_name)
[docs] def test_0035_upload_filtering_1_1_0(self):
"""Upload filtering_1.1.0.tar to the repository"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.commit_tar_to_repository(
repository, "filtering/filtering_1.1.0.tar", commit_message="Uploaded filtering 1.1.0"
)
[docs] 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)
tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/filtering_0000/Filter1/1.1.0"
tool_metadata_strings_displayed = [
tool_guid,
"1.1.0", # The tool version.
"Filter1", # The tool ID.
"Filter", # The tool name.
"data on any column using simple expressions",
] # The tool description.
tool_page_strings_displayed = ["Filter (version 1.1.0)"]
self.check_repository_tools_for_changeset_revision(
repository,
tip,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed,
)
self.check_repository_metadata(repository, tip_only=False)
self.browse_repository(
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,
strings_displayed=strings,
)
[docs] @skip_if_api_v2
def test_0045_alter_repository_states(self):
"""Test toggling the malicious and deprecated repository flags."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.login(email=common.admin_email, username=common.admin_username)
self.set_repository_malicious(
repository, set_malicious=True, strings_displayed=["The repository tip has been defined as malicious."]
)
self.set_repository_malicious(
repository,
set_malicious=False,
strings_displayed=["The repository tip has been defined as <b>not</b> malicious."],
)
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
self.set_repository_deprecated(repository, strings_displayed=["has been marked as deprecated"])
strings_displayed = ["This repository has been marked as deprecated", "Mark repository as not deprecated"]
self.display_manage_repository_page(
repository,
strings_displayed=strings_displayed,
strings_not_displayed=["Reset all repository metadata"],
)
self.browse_repository(repository)
self.set_repository_deprecated(
repository, strings_displayed=["has been marked as not deprecated"], set_deprecated=False
)
strings_displayed = ["Mark repository as deprecated", "Reset all repository metadata"]
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
[docs] @skip_if_api_v2
# probably not porting this functionality - just test
# with Twill for older UI and drop when that is all dropped
def test_0050_display_repository_tip_file(self):
"""Display the contents of filtering.xml in the repository tip revision"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
if self._browser.is_twill:
self.display_repository_file_contents(
repository=repository,
filename="filtering.xml",
filepath=None,
strings_displayed=["1.1.0"],
strings_not_displayed=[],
)
[docs] def test_0055_upload_filtering_txt_file(self):
"""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")
self.display_manage_repository_page(repository, strings_displayed=[expected])
[docs] 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)
[docs] def test_0065_upload_filtering_2_2_0(self):
"""Upload filtering version 2.2.0"""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.add_tar_to_repository(repository, "filtering/filtering_2.2.0.tar")
[docs] def test_0070_verify_filtering_repository(self):
"""Verify the new tool versions and repository metadata."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
tip = self.get_repository_tip(repository)
self.check_for_valid_tools(repository)
if self.is_v2:
strings_displayed = []
else:
strings_displayed = ["Select a revision"]
self.display_manage_repository_page(repository, strings_displayed=strings_displayed)
self.check_count_of_metadata_revisions_associated_with_repository(repository, metadata_count=2)
tool_guid = f"{self.url.replace('http://', '').rstrip('/')}/repos/user1/filtering_0000/Filter1/2.2.0"
tool_metadata_strings_displayed = [
tool_guid,
"2.2.0", # The tool version.
"Filter1", # The tool ID.
"Filter", # The tool name.
"data on any column using simple expressions",
] # The tool description.
tool_page_strings_displayed = ["Filter (version 2.2.0)"]
self.check_repository_tools_for_changeset_revision(
repository,
tip,
tool_metadata_strings_displayed=tool_metadata_strings_displayed,
tool_page_strings_displayed=tool_page_strings_displayed,
)
self.check_repository_metadata(repository, tip_only=False)
[docs] def test_0075_upload_readme_txt_file(self):
"""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.")
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")
self.display_manage_repository_page(
repository,
strings_displayed=[
readme_content,
content,
],
)
[docs] def test_0080_delete_readme_txt_file(self):
"""Delete the readme.txt file."""
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")
self.display_manage_repository_page(repository, strings_displayed=[readme_content])
[docs] @skip_if_api_v2 # not re-implemented in the UI, there are API tests though
def test_0085_search_for_valid_filter_tool(self):
"""Search for the filtering tool by tool ID, name, and version."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
tip_changeset = self.get_repository_tip(repository)
search_fields = dict(tool_id="Filter1", tool_name="filter", tool_version="2.2.0")
self.search_for_valid_tools(
search_fields=search_fields, strings_displayed=[tip_changeset], strings_not_displayed=[]
)
[docs] def test_0090_verify_repository_metadata(self):
"""Verify that resetting the metadata does not change it."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.verify_unchanged_repository_metadata(repository)
[docs] def test_0095_verify_reserved_repository_name_handling(self):
"""Check that reserved repository names are handled correctly."""
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."
)
with pytest.raises(AssertionError):
self.get_or_create_repository(
name="repos",
description=repository_description,
long_description=repository_long_description,
owner=common.test_user_1_name,
category=category,
strings_displayed=[error_message],
)
[docs] def test_0100_verify_reserved_username_handling(self):
"""Check that reserved usernames are handled correctly."""
self.login(email="baduser@bx.psu.edu", username="repos")
test_user_1 = self.test_db_util.get_user("baduser@bx.psu.edu")
assert test_user_1 is None, 'Creating user with public name "repos" succeeded.'
if not self.is_v2:
# no longer use this terminology but the above test case ensures
# the important thing and caught a bug in v2
error_message = (
"The term 'repos' is a reserved word in the Tool Shed, so it cannot be used as a public user name."
)
self.check_for_strings(strings_displayed=[error_message])
[docs] @skip_if_api_v2 # v2 doesn't implement repository deleting repositories
def test_0110_delete_filtering_repository(self):
"""Delete the filtering_0000 repository and verify that it no longer has any downloadable revisions."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.login(email=common.admin_email, username=common.admin_username)
self.delete_repository(repository)
metadata = self.populator.get_metadata(repository, downloadable_only=False)
for _, value in metadata.__root__.items():
assert not value.downloadable
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
# for metadata_revision in repository.metadata_revisions:
# self.test_db_util.refresh(metadata_revision)
# Marking a repository as deleted should result in no metadata revisions being downloadable.
# assert True not in [metadata.downloadable for metadata in self._db_repository(repository).metadata_revisions]
[docs] @skip_if_api_v2 # v2 doesn't implement repository deleting repositories
def test_0115_undelete_filtering_repository(self):
"""Undelete the filtering_0000 repository and verify that it now has two downloadable revisions."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
self.login(email=common.admin_email, username=common.admin_username)
self.undelete_repository(repository)
# Explicitly reload all metadata revisions from the database, to ensure that we have the current status of the downloadable flag.
# for metadata_revision in repository.metadata_revisions:
# self.test_db_util.refresh(metadata_revision)
# Marking a repository as undeleted should result in all previously downloadable metadata revisions being downloadable again.
# In this case, there should be two downloadable revisions, one for filtering 1.1.0 and one for filtering 2.2.0.
assert True in [metadata.downloadable for metadata in self._db_repository(repository).metadata_revisions]
assert len(self._db_repository(repository).downloadable_revisions) == 2
[docs] @skip_if_api_v2 # not re-implementing in tool shed 2.0
def test_0120_enable_email_notifications(self):
"""Enable email notifications for test user 2 on filtering_0000."""
# Log in as test_user_2
self.login(email=common.test_user_2_email, username=common.test_user_2_name)
# Get the repository, so we can pass the encoded repository id and browse_repositories method to the set_email_alerts method.
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
strings_displayed = ["Total alerts added: 1, total alerts removed: 0"]
self.enable_email_alerts(repository, strings_displayed=strings_displayed)
[docs] def test_0125_upload_new_readme_file(self):
"""Upload a new readme file to the filtering_0000 repository and verify that there is no error."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
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")
self.display_manage_repository_page(repository, strings_displayed=[content])
[docs] def test_0130_verify_handling_of_invalid_characters(self):
"""Load the above changeset in the change log and confirm that there is no server error displayed."""
repository = self._get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
changeset_revision = self.get_repository_tip(repository)
repository_id = repository.id
changelog_tuples = self.get_repository_changelog_tuples(repository)
revision_number = -1
revision_hash = "000000000000"
for numeric_changeset, changeset_hash in changelog_tuples:
if str(changeset_hash) == str(changeset_revision):
revision_number = numeric_changeset
revision_hash = changeset_hash
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")
strings_displayed = [
"%d:%s" % (revision_number, revision_hash),
"filtering_0000",
"user1",
"repos",
"added:",
f"+{content}",
]
self.load_changeset_in_tool_shed(repository_id, changeset_revision, strings_displayed=strings_displayed)
[docs] def test_0135_api_get_repositories_in_category(self):
"""Load the api endpoint for repositories in a category."""
categories = [
self.populator.get_category_with_name(name)
for name in ("Test 0000 Basic Repository Features 1", "Test 0000 Basic Repository Features 2")
]
self.get_repositories_category_api(categories)
[docs] def test_0140_view_invalid_changeset(self):
"""View repository using an invalid changeset"""
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=[])