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Source code for tool_shed.test.functional.test_1450_installing_datatypes_sniffers
from ..base.twilltestcase import (
common,
ShedTwillTestCase,
)
repository_name = "proteomics_datatypes_1450"
repository_description = "Proteomics datatypes"
repository_long_description = "Datatypes used in proteomics"
category_name = "Test 1450 Datatype Sniffers"
category_description = "Test 1450 - Installing Datatype Sniffers"
"""
1. Get a count of datatypes and sniffers.
2. Install proteomics_datatypes_1450.
3. Verify the count of datatypes and sniffers is the previous count + the datatypes contained within proteomics_datatypes_1450.
4. Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1.
5. Reactivate proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
6. Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to the count determined in step 1.
7. Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been increased by the contents of the repository.
"""
base_datatypes_count = 0
repository_datatypes_count = 0
base_sniffers_count = 0
[docs]class TestInstallDatatypesSniffers(ShedTwillTestCase):
"""Test installing a repository that defines datatypes and datatype sniffers."""
[docs] def test_0000_initiate_users(self):
"""Create necessary user accounts."""
self.login(email=common.test_user_1_email, username=common.test_user_1_name)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
assert (
test_user_1 is not None
), f"Problem retrieving user with email {common.test_user_1_email} from the database"
self.test_db_util.get_private_role(test_user_1)
self.login(email=common.admin_email, username=common.admin_username)
admin_user = self.test_db_util.get_user(common.admin_email)
assert admin_user is not None, f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_private_role(admin_user)
self.galaxy_login(email=common.admin_email, username=common.admin_username)
galaxy_admin_user = self.test_db_util.get_galaxy_user(common.admin_email)
assert (
galaxy_admin_user is not None
), f"Problem retrieving user with email {common.admin_email} from the database"
self.test_db_util.get_galaxy_private_role(galaxy_admin_user)
[docs] def test_0005_ensure_repositories_and_categories_exist(self):
"""Create the 1450 category and proteomics_datatypes_1450 repository."""
global repository_datatypes_count
self.login(email=common.admin_email, username=common.admin_username)
category = self.create_category(name=category_name, description=category_description)
self.login(email=common.test_user_1_email, username=common.test_user_1_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),
strings_displayed=[],
)
if self.repository_is_new(repository):
self.upload_file(
repository,
filename="proteomics_datatypes/proteomics_datatypes.tar",
filepath=None,
valid_tools_only=True,
uncompress_file=False,
remove_repo_files_not_in_tar=False,
commit_message="Uploaded datatype and sniffer definitions.",
strings_displayed=[],
strings_not_displayed=[],
)
repository_datatypes_count = self.get_repository_datatypes_count(repository)
[docs] def test_0010_install_datatypes_repository(self):
"""Install the proteomics_datatypes_1450 repository into the Galaxy instance.
This includes steps 1 and 2 - Get a count of datatypes and sniffers.
Store a count of the current datatypes registry and sniffers in global variables, to compare with the updated count
after changing the installation status of the proteomics_datatypes_1450 repository.
"""
global base_datatypes_count
global base_sniffers_count
base_datatypes_count = self.get_datatypes_count()
base_sniffers_count = self.get_sniffers_count()
self.galaxy_login(email=common.admin_email, username=common.admin_username)
strings_displayed = ["proteomics"]
self.install_repository(
"proteomics_datatypes_1450",
common.test_user_1_name,
category_name,
strings_displayed=strings_displayed,
new_tool_panel_section_label="test_1450",
)
installed_repository = self.test_db_util.get_installed_repository_by_name_owner(
"proteomics_datatypes_1450", common.test_user_1_name
)
strings_displayed = [
"user1",
self.url.replace("http://", ""),
installed_repository.installed_changeset_revision,
]
self.display_galaxy_browse_repositories_page(strings_displayed=strings_displayed)
[docs] def test_0015_verify_datatypes_count(self):
"""Verify that datatypes were added in the previous step.
This is step 3 - Verify the count of datatypes and sniffers is the
previous count + the datatypes contained within proteomics_datatypes_1450.
Compare the current datatypes registry and sniffers with the values that were retrieved in the previous step.
"""
current_datatypes = self.get_datatypes_count()
assert (
current_datatypes == base_datatypes_count + repository_datatypes_count
), "Found %d datatypes, expected %d." % (current_datatypes, base_datatypes_count + repository_datatypes_count)
current_sniffers = self.get_sniffers_count()
assert (
current_sniffers > base_sniffers_count
), "Sniffer count after installing proteomics_datatypes_1450 is %d, which is not greater than %d" % (
current_sniffers,
base_sniffers_count,
)
[docs] def test_0020_deactivate_datatypes_repository(self):
"""Deactivate the installed proteomics_datatypes_1450 repository.
This is step 4 - Deactivate proteomics_datatypes_1450, verify the count
of datatypes and sniffers is equal to the count determined in step 1.
Deactivate proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
determined in the first step.
"""
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global base_datatypes_count
global base_sniffers_count
self.deactivate_repository(repository)
new_datatypes_count = self.get_datatypes_count()
assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % (
base_datatypes_count,
new_datatypes_count,
)
current_sniffers = self.get_sniffers_count()
assert (
current_sniffers == base_sniffers_count
), "Sniffer count after deactivating proteomics_datatypes_1450 is %d, expected %d" % (
current_sniffers,
base_sniffers_count,
)
[docs] def test_0025_reactivate_datatypes_repository(self):
"""Reactivate the deactivated proteomics_datatypes_1450 repository.
This is step 5 - Reactivate proteomics_datatypes, verify that the count
of datatypes and sniffers has been increased by the contents of the repository.
"""
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global repository_datatypes_count
global base_datatypes_count
global base_sniffers_count
self.reactivate_repository(repository)
new_datatypes_count = self.get_datatypes_count()
assert (
new_datatypes_count == base_datatypes_count + repository_datatypes_count
), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
current_sniffers = self.get_sniffers_count()
assert (
current_sniffers > base_sniffers_count
), "Sniffer count after reactivating proteomics_datatypes_1450 is %d, which is not greater than %d" % (
current_sniffers,
base_sniffers_count,
)
[docs] def test_0030_uninstall_datatypes_repository(self):
"""Uninstall the installed proteomics_datatypes_1450 repository.
This is step 6 - Uninstall proteomics_datatypes_1450, verify the count
of datatypes and sniffers is equal to the count determined in step 1.
Uninstall proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
determined in the first step.
"""
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global base_datatypes_count
self.uninstall_repository(repository)
new_datatypes_count = self.get_datatypes_count()
assert new_datatypes_count == base_datatypes_count, "Expected %d datatypes, got %d" % (
base_datatypes_count,
new_datatypes_count,
)
current_sniffers = self.get_sniffers_count()
assert (
current_sniffers == base_sniffers_count
), "Sniffer count after uninstalling proteomics_datatypes_1450 is %d, expected %d" % (
current_sniffers,
base_sniffers_count,
)
[docs] def test_0035_reinstall_datatypes_repository(self):
"""Reinstall the uninstalled proteomics_datatypes_1450 repository.
This is step 7 - Reinstall proteomics_datatypes_1450, verify that the
count of datatypes and sniffers has been increased by the contents of
the repository.
"""
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global repository_datatypes_count
global base_datatypes_count
self.reinstall_repository(repository)
new_datatypes_count = self.get_datatypes_count()
assert (
new_datatypes_count == base_datatypes_count + repository_datatypes_count
), "Found %d datatypes, expected %d." % (new_datatypes_count, base_datatypes_count + repository_datatypes_count)
current_sniffers = self.get_sniffers_count()
assert (
current_sniffers > base_sniffers_count
), "Sniffer count after reinstalling proteomics_datatypes_1450 is %d, which is not greater than %d" % (
current_sniffers,
base_sniffers_count,
)