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Cleanup random tool_shed imports in Galaxy.

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This commit is contained in:
John Chilton
2019-11-11 00:28:49 -05:00
parent 3278d1df89
commit 8a537d6c65
11 changed files with 61 additions and 57 deletions
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lib/galaxy/config/__init__.py
+3 -3
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@@ -1100,13 +1100,13 @@ class ConfiguresGalaxyMixin(object):
self.security = idencoding.IdEncodingHelper(id_secret=self.config.id_secret)
def _configure_tool_shed_registry(self):
import tool_shed.tool_shed_registry
import galaxy.tool_shed.tool_shed_registry
# Set up the tool sheds registry
if os.path.isfile(self.config.tool_sheds_config_file):
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry(self.config.tool_sheds_config_file)
else:
self.tool_shed_registry = tool_shed.tool_shed_registry.Registry()
self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry()
def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
"""
lib/galaxy/tool_shed/util/tool_dependency_util.py
+1 -1
View File
@@ -5,9 +5,9 @@ import shutil
from sqlalchemy import and_
from galaxy import util
from galaxy.web.form_builder import SelectField
from galaxy.tool_shed.util.hg_util import get_config_from_disk
from galaxy.util.tool_shed.xml_util import parse_xml
from galaxy.web.form_builder import SelectField
log = logging.getLogger(__name__)
lib/galaxy/tools/__init__.py
+16 -13
View File
@@ -24,8 +24,6 @@ from six import itervalues, string_types
from six.moves.urllib.parse import unquote_plus
from webob.compat import cgi_FieldStorage
import tool_shed.util.repository_util as repository_util
import tool_shed.util.shed_util_common
from galaxy import (
exceptions,
model
@@ -34,6 +32,8 @@ from galaxy.job_execution import output_collect
from galaxy.managers.jobs import JobSearch
from galaxy.metadata import get_metadata_compute_strategy
from galaxy.model.tags import GalaxyTagHandler
from galaxy.tool_shed.util.repository_util import get_installed_repository
from galaxy.tool_shed.util.shed_util_common import set_image_paths
from galaxy.tool_util.deps import (
CachedDependencyManager,
)
@@ -102,9 +102,12 @@ from galaxy.util.template import (
fill_template,
refactoring_tool,
)
from galaxy.util.tool_shed.common_util import (
get_tool_shed_repository_url,
get_tool_shed_url_from_tool_shed_registry,
)
from galaxy.version import VERSION_MAJOR
from galaxy.work.context import WorkRequestContext
from tool_shed.util import common_util
from .execute import (
execute as execute_job,
MappingParameters,
@@ -333,7 +336,7 @@ class ToolBox(BaseGalaxyToolBox):
# Abstract toolbox doesn't have a dependency on the database, so
# override _get_tool_shed_repository here to provide this information.
return repository_util.get_installed_repository(
return get_installed_repository(
self.app,
tool_shed=tool_shed,
name=name,
@@ -521,12 +524,12 @@ class Tool(Dictifiable):
def tool_shed_repository(self):
# If this tool is included in an installed tool shed repository, return it.
if self.tool_shed:
return repository_util.get_installed_repository(self.app,
tool_shed=self.tool_shed,
name=self.repository_name,
owner=self.repository_owner,
installed_changeset_revision=self.installed_changeset_revision,
from_cache=True)
return get_installed_repository(self.app,
tool_shed=self.tool_shed,
name=self.repository_name,
owner=self.repository_owner,
installed_changeset_revision=self.installed_changeset_revision,
from_cache=True)
@property
def produces_collections_with_unknown_structure(self):
@@ -1244,7 +1247,7 @@ class Tool(Dictifiable):
self.repository_owner = tool_shed_repository.owner
self.changeset_revision = tool_shed_repository.changeset_revision
self.installed_changeset_revision = tool_shed_repository.installed_changeset_revision
self.sharable_url = common_util.get_tool_shed_repository_url(
self.sharable_url = get_tool_shed_repository_url(
self.app, self.tool_shed, self.repository_owner, self.repository_name
)
@@ -1281,7 +1284,7 @@ class Tool(Dictifiable):
if help_text is not None:
try:
if help_text.find('.. image:: ') >= 0 and (self.tool_shed_repository or self.repository_id):
help_text = tool_shed.util.shed_util_common.set_image_paths(
help_text = set_image_paths(
self.app, help_text, encoded_repository_id=self.repository_id, tool_shed_repository=self.tool_shed_repository, tool_id=self.old_id, tool_version=self.version
)
except Exception:
@@ -2174,7 +2177,7 @@ class Tool(Dictifiable):
message += 'You can re-run the job with this tool version, which is a different version of the original tool. '
else:
new_tool_shed_url = '%s/%s/' % (tool.sharable_url, tool.changeset_revision)
old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split('/repos/')[0])
old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(self.app, tool_id.split('/repos/')[0])
old_tool_shed_url = '%s/view/%s/%s/' % (old_tool_shed_url, tool.repository_owner, tool.repository_name)
message = 'This job was run with <a href=\"%s\" target=\"_blank\">tool id \"%s\"</a>, version "%s", which is not available. ' % (old_tool_shed_url, tool_id, tool_version)
if len(tools) > 1:
lib/galaxy/util/tool_shed/common_util.py
+1 -1
View File
@@ -15,7 +15,7 @@ log = logging.getLogger(__name__)
REPOSITORY_OWNER = 'devteam'
# not valid for installed Galaxy, fix
MIGRATE_DIR = os.path.abspath(os.path.join(
os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'tool_shed', 'galaxy_install', 'migrate'))
os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'galaxy', 'tool_shed', 'galaxy_install', 'migrate'))
TOOL_MIGRATION_SCRIPTS_DIR = os.path.join(MIGRATE_DIR, 'scripts')
TOOL_MIGRATION_VERSIONS_DIR = os.path.join(MIGRATE_DIR, 'versions')
lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
+24 -20
View File
@@ -8,7 +8,6 @@ from paste.httpexceptions import (
)
from sqlalchemy import and_
import tool_shed.util.shed_util_common as suc
from galaxy import (
exceptions,
util
@@ -16,12 +15,17 @@ from galaxy import (
from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
from galaxy.tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
from galaxy.tool_shed.util.repository_util import (
check_for_updates,
get_installed_repository,
get_installed_tool_shed_repository,
get_tool_shed_repository_by_id,
)
from galaxy.tool_shed.util.shed_util_common import have_shed_tool_conf_for_install
from galaxy.tool_shed.util.tool_util import generate_message_for_invalid_tools
from galaxy.web import expose_api, require_admin, url_for
from galaxy.webapps.base.controller import BaseAPIController
from tool_shed.util import (
repository_util,
tool_util
)
log = logging.getLogger(__name__)
@@ -41,7 +45,7 @@ class ToolShedRepositoriesController(BaseAPIController):
def __ensure_can_install_repos(self, trans):
# Make sure this Galaxy instance is configured with a shed-related tool panel configuration file.
if not suc.have_shed_tool_conf_for_install(self.app):
if not have_shed_tool_conf_for_install(self.app):
message = get_message_for_no_shed_tool_config()
log.debug(message)
return dict(status='error', error=message)
@@ -238,7 +242,7 @@ class ToolShedRepositoriesController(BaseAPIController):
"""
if id:
try:
repository = repository_util.get_tool_shed_repository_by_id(self.app, id)
repository = get_tool_shed_repository_by_id(self.app, id)
except ValueError:
raise HTTPBadRequest(detail="No repository with id '%s' found" % id)
else:
@@ -247,11 +251,11 @@ class ToolShedRepositoriesController(BaseAPIController):
tsr_arguments = {key: kwd[key] for key in tsr_arguments}
except KeyError as e:
raise HTTPBadRequest(detail="Missing required parameter '%s'" % e.args[0])
repository = repository_util.get_installed_repository(app=self.app,
tool_shed=tsr_arguments['tool_shed_url'],
name=tsr_arguments['name'],
owner=tsr_arguments['owner'],
changeset_revision=tsr_arguments['changeset_revision'])
repository = get_installed_repository(app=self.app,
tool_shed=tsr_arguments['tool_shed_url'],
name=tsr_arguments['name'],
owner=tsr_arguments['owner'],
changeset_revision=tsr_arguments['changeset_revision'])
if not repository:
raise HTTPBadRequest(detail="Repository not found")
irm = InstalledRepositoryManager(app=self.app)
@@ -292,7 +296,7 @@ class ToolShedRepositoriesController(BaseAPIController):
:param id: the encoded repository id
'''
repository_id = kwd.get('id', None)
message, status = repository_util.check_for_updates(self.app, trans.install_model, repository_id)
message, status = check_for_updates(self.app, trans.install_model, repository_id)
return {'status': status, 'message': message}
@expose_api
@@ -305,7 +309,7 @@ class ToolShedRepositoriesController(BaseAPIController):
successful = []
for repository_id in repository_ids:
try:
repository = repository_util.get_installed_tool_shed_repository(self.app, repository_id)
repository = get_installed_tool_shed_repository(self.app, repository_id)
irmm.set_repository(repository)
irmm.reset_all_metadata_on_installed_repository()
if irmm.invalid_file_tups:
@@ -350,11 +354,11 @@ class ToolShedRepositoriesController(BaseAPIController):
irmm.reset_all_metadata_on_installed_repository()
irmm_invalid_file_tups = irmm.get_invalid_file_tups()
if irmm_invalid_file_tups:
message = tool_util.generate_message_for_invalid_tools(self.app,
irmm_invalid_file_tups,
repository,
None,
as_html=False)
message = generate_message_for_invalid_tools(self.app,
irmm_invalid_file_tups,
repository,
None,
as_html=False)
results['unsuccessful_count'] += 1
else:
message = "Successfully reset metadata on repository %s owned by %s" % \
@@ -378,7 +382,7 @@ class ToolShedRepositoriesController(BaseAPIController):
:param id: the encoded id of the ToolShedRepository object
"""
# Example URL: http://localhost:8763/api/tool_shed_repositories/df7a1f0c02a5b08e
tool_shed_repository = repository_util.get_tool_shed_repository_by_id(self.app, id)
tool_shed_repository = get_tool_shed_repository_by_id(self.app, id)
if tool_shed_repository is None:
log.debug("Unable to locate tool_shed_repository record for id %s." % (str(id)))
return {}
lib/galaxy/webapps/galaxy/controllers/admin.py
+5 -8
View File
@@ -16,21 +16,18 @@ from galaxy import (
from galaxy.actions.admin import AdminActions
from galaxy.exceptions import ActionInputError, MessageException
from galaxy.model import tool_shed_install as install_model
from galaxy.tool_shed.util.repository_util import get_ids_of_tool_shed_repositories_being_installed
from galaxy.util import (
nice_size,
sanitize_text,
url_get
)
from galaxy.util.tool_shed import common_util, encoding_util
from galaxy.web import url_for
from galaxy.web.framework.helpers import grids, time_ago
from galaxy.web.params import QuotaParamParser
from galaxy.webapps.base import controller
from galaxy.webapps.base.controller import UsesQuotaMixin
from tool_shed.util import (
common_util,
encoding_util,
repository_util
)
from tool_shed.util.web_util import escape
@@ -550,7 +547,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
status = kwd.get('status', 'done')
settings = {
'is_repo_installed': trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None,
'installing_repository_ids': repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
'installing_repository_ids': get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True),
'is_tool_shed_installed': bool(trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds)
}
return self._bootstrapped_client(trans, app_name='admin', settings=settings, message=message, status=status)
@@ -886,7 +883,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
status = util.restore_text(kwd.get('status', 'done'))
migration_stages_dict = OrderedDict()
# FIXME: this isn't valid in an installed context
migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions'))
migration_scripts_dir = os.path.abspath(os.path.join(trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'galaxy_install', 'migrate', 'versions'))
modules = os.listdir(migration_scripts_dir)
modules.sort()
modules.reverse()
@@ -912,7 +909,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
is_repo_installed = trans.install_model.context.query(trans.install_model.ToolShedRepository).first() is not None
installing_repository_ids = repository_util.get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True)
installing_repository_ids = get_ids_of_tool_shed_repositories_being_installed(trans.app, as_string=True)
return trans.fill_template('/webapps/galaxy/admin/center.mako',
is_repo_installed=is_repo_installed,
installing_repository_ids=installing_repository_ids,
lib/galaxy/workflow/modules.py
+2 -2
View File
@@ -53,7 +53,7 @@ from galaxy.util.bunch import Bunch
from galaxy.util.json import safe_loads
from galaxy.util.rules_dsl import RuleSet
from galaxy.util.template import fill_template
from tool_shed.util import common_util
from galaxy.util.tool_shed.common_util import get_tool_shed_url_from_tool_shed_registry
log = logging.getLogger(__name__)
@@ -848,7 +848,7 @@ class ToolModule(WorkflowModule):
if step.tool_id and step.tool_id != module.tool_id: # This means the exact version of the tool is not installed. We inform the user.
old_tool_shed = step.tool_id.split("/repos/")[0]
if old_tool_shed not in tool_id: # Only display the following warning if the tool comes from a different tool shed
old_tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
old_tool_shed_url = get_tool_shed_url_from_tool_shed_registry(trans.app, old_tool_shed)
if not old_tool_shed_url: # a tool from a different tool_shed has been found, but the original tool shed has been deactivated
old_tool_shed_url = "http://" + old_tool_shed # let's just assume it's either http, or a http is forwarded to https.
old_url = old_tool_shed_url + "/view/%s/%s/" % (module.tool.repository_owner, module.tool.repository_name)
test/unit/shed_unit/test_fabric_util.py
+1 -1
View File
@@ -1,6 +1,6 @@
from contextlib import contextmanager
from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
def test_env_file_builder():
test/unit/shed_unit/test_installed_repository_manager.py
+5 -5
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@@ -2,14 +2,14 @@ import os
from mock import MagicMock
from tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
from tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
from tool_shed.util import (
common_util,
from galaxy.tool_shed.galaxy_install.install_manager import InstallRepositoryManager
from galaxy.tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager
from galaxy.tool_shed.galaxy_install.update_repository_manager import UpdateRepositoryManager
from galaxy.tool_shed.util import (
hg_util,
repository_util,
)
from galaxy.util.tool_shed import common_util
from ..tools.test_toolbox import (
BaseToolBoxTestCase,
DEFAULT_TEST_REPO
test/unit/shed_unit/test_td_common_util.py
+2 -2
View File
@@ -1,9 +1,9 @@
from contextlib import contextmanager
from os.path import join
from galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
from galaxy.util import parse_xml_string
from tool_shed.galaxy_install.tool_dependencies.env_manager import EnvManager
from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder
TEST_DEPENDENCIES_DIR = "/opt/galaxy/dependencies"
TEST_INSTALL_DIR = "%s/test_install_dir" % TEST_DEPENDENCIES_DIR
test/unit/shed_unit/test_tool_panel_manager.py
+1 -1
View File
@@ -1,7 +1,7 @@
import os
from galaxy.tool_shed.galaxy_install.tools import tool_panel_manager
from galaxy.util import parse_xml
from tool_shed.galaxy_install.tools import tool_panel_manager
from tool_shed.tools import tool_version_manager
from ..tools.test_toolbox import (
BaseToolBoxTestCase,