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Refactor TagManager (back) to TagHandler.

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The original TagHandler used trans and app and was what I think we convinced of as a "Manager" - something that provides business logic and ties app and trans to the model (and other lower layers of Galaxy). Since 7c86c5480b the tag manager has not needed app or trans to do any of its work. It is a clean model manipulation utility. It also doesn't use or check security, it isn't a "Manager" in our sense. It is a model utility and so it belongs in galaxy.model I believe.

This also "fixes" the problem of galaxy.managers dependending on galaxy.model and then galaxy.model depending back on galaxy.managers. Hopefully it is clear the dependency chain should be one direction and that is galaxy.managers depends on galaxy.model and not vice versa.

In addition to allowing us to properly create a package out the models, this also fixes something needling me in the history import/export and model store branch - the tag manager is/was the only manager I needed to import/export histories and such - that was good evidence I think that it wasn't a manager and should have been in models all along.
This commit is contained in:
John Chilton
2019-03-14 10:34:11 -04:00
parent d566ed9b8b
commit dfd016a7a4
12 changed files with 52 additions and 53 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/app.py
+2 -2
View File
@@ -16,7 +16,7 @@ from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.folders import FolderManager
from galaxy.managers.histories import HistoryManager
from galaxy.managers.libraries import LibraryManager
from galaxy.managers.tags import GalaxyTagManager
from galaxy.model.tags import GalaxyTagHandler
from galaxy.queue_worker import GalaxyQueueWorker
from galaxy.tools.cache import (
ToolCache,
@@ -94,7 +94,7 @@ class UniverseApplication(config.ConfiguresGalaxyMixin):
# Security helper
self._configure_security()
# Tag handler
self.tag_handler = GalaxyTagManager(self.model.context)
self.tag_handler = GalaxyTagHandler(self.model.context)
self.dataset_collections_service = DatasetCollectionManager(self)
self.history_manager = HistoryManager(self)
self.dependency_resolvers_view = DependencyResolversView(self)
lib/galaxy/managers/collections.py
+8 -8
View File
@@ -14,9 +14,9 @@ from galaxy.managers import (
hdas,
histories,
lddas,
tags
)
from galaxy.managers.collections_util import validate_input_element_identifiers
from galaxy.model import tags
from galaxy.util import (
odict,
validation
@@ -43,7 +43,7 @@ class DatasetCollectionManager(object):
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.tag_manager = tags.GalaxyTagManager(app.model.context)
self.tag_handler = tags.GalaxyTagHandler(app.model.context)
self.ldda_manager = lddas.LDDAManager(app)
def precreate_dataset_collection_instance(self, trans, parent, name, structure, implicit_inputs=None, implicit_output_name=None, tags=None):
@@ -154,7 +154,7 @@ class DatasetCollectionManager(object):
# values.
if isinstance(tags, list):
assert implicit_inputs is None, implicit_inputs
tags = self.tag_manager.add_tags_from_list(trans.user, dataset_collection_instance, tags)
tags = self.tag_handler.add_tags_from_list(trans.user, dataset_collection_instance, tags)
else:
tags = self._append_tags(dataset_collection_instance, implicit_inputs, tags)
return self.__persist(dataset_collection_instance, flush=flush)
@@ -284,8 +284,8 @@ class DatasetCollectionManager(object):
if copy_elements:
copy_kwds["element_destination"] = parent
new_hdca = source_hdca.copy(**copy_kwds)
tags_str = self.tag_manager.get_tags_str(source_hdca.tags)
self.tag_manager.apply_item_tags(trans.get_user(), new_hdca, tags_str)
tags_str = self.tag_handler.get_tags_str(source_hdca.tags)
self.tag_handler.apply_item_tags(trans.get_user(), new_hdca, tags_str)
parent.add_dataset_collection(new_hdca)
trans.sa_session.add(new_hdca)
trans.sa_session.flush()
@@ -300,7 +300,7 @@ class DatasetCollectionManager(object):
changed['annotation'] = new_data['annotation']
if 'tags' in new_data.keys() and trans.get_user():
# set_tags_from_list will flush on its own, no need to add to 'changed' here and incur a second flush.
self.tag_manager.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
self.tag_handler.set_tags_from_list(trans.get_user(), dataset_collection_instance, new_data['tags'])
if changed.keys():
trans.sa_session.flush()
@@ -431,11 +431,11 @@ class DatasetCollectionManager(object):
element = hda
if hide_source_items and self.hda_manager.get_owned(hda.id, user=trans.user, current_history=trans.history):
hda.visible = False
self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
elif src_type == 'ldda':
element = self.ldda_manager.get(trans, encoded_id, check_accessible=True)
element = element.to_history_dataset_association(trans.history, add_to_history=True)
self.tag_manager.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
self.tag_handler.apply_item_tags(user=trans.user, item=element, tags_str=tag_str)
elif src_type == 'hdca':
# TODO: Option to copy? Force copy? Copy or allow if not owned?
element = self.__get_history_collection_instance(trans, encoded_id).collection
lib/galaxy/managers/library_datasets.py
+3 -3
View File
@@ -10,8 +10,8 @@ from galaxy.exceptions import (
)
from galaxy.managers import (
datasets,
tags
)
from galaxy.model import tags
from galaxy.util import validation
log = logging.getLogger(__name__)
@@ -22,7 +22,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
def __init__(self, app):
self.app = app
self.tag_manager = tags.GalaxyTagManager(app.model.context)
self.tag_handler = tags.GalaxyTagHandler(app.model.context)
def get(self, trans, decoded_library_dataset_id, check_accessible=True):
"""
@@ -219,7 +219,7 @@ class LibraryDatasetsManager(datasets.DatasetAssociationManager):
rval['date_uploaded'] = ldda.create_time.strftime("%Y-%m-%d %I:%M %p")
rval['can_user_modify'] = trans.user_is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, ld)
rval['is_unrestricted'] = trans.app.security_agent.dataset_is_public(ldda.dataset)
rval['tags'] = self.tag_manager.get_tags_str(ldda.tags)
rval['tags'] = self.tag_handler.get_tags_str(ldda.tags)
# Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency
rval['can_user_manage'] = trans.user_is_admin or trans.app.security_agent.can_manage_dataset(current_user_roles, ldda.dataset)
lib/galaxy/managers/taggable.py
+2 -2
View File
@@ -45,7 +45,7 @@ class TaggableManagerMixin(object):
#: class of TagAssociation (e.g. HistoryTagAssociation)
tag_assoc = None
# TODO: most of this can be done by delegating to the TagManager?
# TODO: most of this can be done by delegating to the GalaxyTagHandler?
def get_tags(self, item):
"""
Return a list of tag strings.
@@ -59,7 +59,7 @@ class TaggableManagerMixin(object):
return _tags_from_strings(item, self.app.tag_handler, new_tags, user=user)
# def tags_by_user( self, user, **kwargs ):
# TODO: here or TagManager
# TODO: here or GalaxyTagHandler
# pass
lib/galaxy/model/__init__.py
+3 -3
View File
@@ -43,9 +43,9 @@ from sqlalchemy.schema import UniqueConstraint
import galaxy.model.metadata
import galaxy.model.orm.now
import galaxy.model.tags
import galaxy.security.passwords
import galaxy.util
from galaxy.managers import tags
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.model.util import pgcalc
from galaxy.security import get_permitted_actions
@@ -3145,7 +3145,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, RepresentById):
copied_from_library_dataset_dataset_association=self,
history=target_history)
tag_manager = tags.GalaxyTagManager(sa_session)
tag_manager = galaxy.model.tags.GalaxyTagHandler(sa_session)
src_ldda_tags = tag_manager.get_tags_str(self.tags)
tag_manager.apply_item_tags(user=self.user, item=hda, tags_str=src_ldda_tags)
@@ -3175,7 +3175,7 @@ class LibraryDatasetDatasetAssociation(DatasetInstance, HasName, RepresentById):
copied_from_library_dataset_dataset_association=self,
folder=target_folder)
tag_manager = tags.GalaxyTagManager(sa_session)
tag_manager = galaxy.model.tags.GalaxyTagHandler(sa_session)
src_ldda_tags = tag_manager.get_tags_str(self.tags)
tag_manager.apply_item_tags(user=self.user, item=ldda, tags_str=src_ldda_tags)
lib/galaxy/managers/tags.py → lib/galaxy/model/tags.py
+5 -5
View File
@@ -22,7 +22,7 @@ class ItemTagAssocInfo(object):
self.item_id_col = item_id_col
class TagManager(object):
class TagHandler(object):
"""
Manages CRUD operations related to tagging objects.
"""
@@ -319,10 +319,10 @@ class TagManager(object):
return name_value_pair
class GalaxyTagManager(TagManager):
class GalaxyTagHandler(TagHandler):
def __init__(self, sa_session):
from galaxy import model
TagManager.__init__(self, sa_session)
TagHandler.__init__(self, sa_session)
self.item_tag_assoc_info["History"] = ItemTagAssocInfo(model.History,
model.HistoryTagAssociation,
model.HistoryTagAssociation.table.c.history_id)
@@ -349,6 +349,6 @@ class GalaxyTagManager(TagManager):
model.VisualizationTagAssociation.table.c.visualization_id)
class CommunityTagManager(TagManager):
class CommunityTagHandler(TagHandler):
def __init__(self, sa_session):
TagManager.__init__(self, sa_session)
TagHandler.__init__(self, sa_session)
lib/galaxy/tools/__init__.py
+2 -2
View File
@@ -26,8 +26,8 @@ from galaxy import (
model
)
from galaxy.managers.jobs import JobSearch
from galaxy.managers.tags import GalaxyTagManager
from galaxy.metadata import get_metadata_compute_strategy
from galaxy.model.tags import GalaxyTagHandler
from galaxy.queue_worker import send_control_task
from galaxy.tools.actions import DefaultToolAction
from galaxy.tools.actions.data_manager import DataManagerToolAction
@@ -2824,7 +2824,7 @@ class TagFromFileTool(DatabaseOperationTool):
how = incoming['how']
new_tags_dataset_assoc = incoming["tags"]
new_elements = odict()
tags_manager = GalaxyTagManager(trans.app.model.context)
tags_manager = GalaxyTagHandler(trans.app.model.context)
new_datasets = []
def add_copied_value_to_new_elements(new_tags_dict, dce):
lib/galaxy/tools/actions/upload_common.py
+2 -2
View File
@@ -14,7 +14,7 @@ from webob.compat import cgi_FieldStorage
from galaxy import datatypes, util
from galaxy.exceptions import ConfigDoesNotAllowException, ObjectInvalid
from galaxy.managers import tags
from galaxy.model import tags
from galaxy.util import unicodify
from galaxy.util.odict import odict
@@ -220,7 +220,7 @@ def __new_library_upload(trans, cntrller, uploaded_dataset, library_bunch, state
sa_session=trans.sa_session)
if uploaded_dataset.get('tag_using_filenames', False):
tag_from_filename = os.path.splitext(os.path.basename(uploaded_dataset.name))[0]
tag_manager = tags.GalaxyTagManager(trans.sa_session)
tag_manager = tags.GalaxyTagHandler(trans.sa_session)
tag_manager.apply_item_tag(item=ldda, user=trans.user, name='name', value=tag_from_filename)
trans.sa_session.add(ldda)
lib/galaxy/web/base/controller.py
+4 -4
View File
@@ -24,7 +24,6 @@ from galaxy.managers import (
api_keys,
base as managers_base,
configuration,
tags,
users,
workflows
)
@@ -32,7 +31,8 @@ from galaxy.model import (
ExtendedMetadata,
ExtendedMetadataIndex,
HistoryDatasetAssociation,
LibraryDatasetDatasetAssociation
LibraryDatasetDatasetAssociation,
tags,
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.dictifiable import Dictifiable
@@ -1551,8 +1551,8 @@ class UsesTagsMixin(SharableItemSecurityMixin):
return self.get_tag_handler(trans)._get_item_tag_assoc(user, tagged_item, tag_name)
def set_tags_from_list(self, trans, item, new_tags_list, user=None):
tags_manager = tags.GalaxyTagManager(trans.app.model.context)
return tags_manager.set_tags_from_list(user, item, new_tags_list)
tag_handler = tags.GalaxyTagHandler(trans.app.model.context)
return tag_handler.set_tags_from_list(user, item, new_tags_list)
def get_user_tags_used(self, trans, user=None):
"""
lib/galaxy/webapps/tool_shed/app.py
+2 -2
View File
@@ -10,7 +10,7 @@ import tool_shed.repository_registry
import tool_shed.repository_types.registry
from galaxy import tools
from galaxy.config import configure_logging
from galaxy.managers.tags import CommunityTagManager
from galaxy.model.tags import CommunityTagHandler
from galaxy.util.dbkeys import GenomeBuilds
from galaxy.web import security
from galaxy.web.stack import application_stack_instance
@@ -54,7 +54,7 @@ class UniverseApplication(object):
# Initialize the Tool Shed security helper.
self.security = security.SecurityHelper(id_secret=self.config.id_secret)
# initialize the Tool Shed tag handler.
self.tag_handler = CommunityTagManager(self)
self.tag_handler = CommunityTagHandler(self)
# Initialize the Tool Shed tool data tables. Never pass a configuration file here
# because the Tool Shed should always have an empty dictionary!
self.tool_data_tables = galaxy.tools.data.ToolDataTableManager(self.config.tool_data_path)
test/unit/managers/test_TagManager.py → test/unit/managers/test_TagHandler.py
+18 -18
View File
@@ -2,7 +2,7 @@
from galaxy.managers import hdas
from galaxy.managers.datasets import DatasetManager
from galaxy.managers.histories import HistoryManager
from galaxy.managers.tags import GalaxyTagManager
from galaxy.model.tags import GalaxyTagHandler
from galaxy.util import unicodify
from .base import BaseTestCase
@@ -12,14 +12,14 @@ user2_data = dict(email='user2@user2.user2', username='user2', password=default_
# =============================================================================
class TagManagerTestCase(BaseTestCase):
class TagHandlerTestCase(BaseTestCase):
def set_up_managers(self):
super(TagManagerTestCase, self).set_up_managers()
super(TagHandlerTestCase, self).set_up_managers()
self.hda_manager = hdas.HDAManager(self.app)
self.history_manager = HistoryManager(self.app)
self.dataset_manager = DatasetManager(self.app)
self.tag_manager = GalaxyTagManager(self.trans.sa_session)
self.tag_handler = GalaxyTagHandler(self.trans.sa_session)
self.user = self.user_manager.create(**user2_data)
def _create_vanilla_hda(self, user=None):
@@ -59,49 +59,49 @@ class TagManagerTestCase(BaseTestCase):
]
for tag_string, expected_tag in zip(tag_strings, expected_tags):
hda = self._create_vanilla_hda()
self.tag_manager.apply_item_tags(user=self.user, item=hda, tags_str=tag_string)
self.tag_handler.apply_item_tags(user=self.user, item=hda, tags_str=tag_string)
self._check_tag_list(hda.tags, expected_tag)
def test_set_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2']
self.tag_manager.set_tags_from_list(self.user, hda, tags)
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self._check_tag_list(hda.tags, tags)
# Setting tags should erase previous tags
self.tag_manager.set_tags_from_list(self.user, hda, ['tag1'])
self.tag_handler.set_tags_from_list(self.user, hda, ['tag1'])
self._check_tag_list(hda.tags, expected_tags=['tag1'])
def test_add_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2']
self.tag_manager.add_tags_from_list(self.user, hda, tags)
self.tag_handler.add_tags_from_list(self.user, hda, tags)
self._check_tag_list(tags=hda.tags, expected_tags=tags)
# Adding tags should keep previous tags
self.tag_manager.add_tags_from_list(self.user, hda, ['tag3'])
self.tag_handler.add_tags_from_list(self.user, hda, ['tag3'])
self._check_tag_list(hda.tags, expected_tags=['tag1', 'tag2', 'tag3'])
def test_remove_tag_from_list(self):
hda = self._create_vanilla_hda()
tags = ['tag1', 'tag2']
self.tag_manager.set_tags_from_list(self.user, hda, tags)
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self._check_tag_list(hda.tags, tags)
self.tag_manager.remove_tags_from_list(self.user, hda, ['tag1'])
self.tag_handler.remove_tags_from_list(self.user, hda, ['tag1'])
self._check_tag_list(hda.tags, ['tag2'])
def test_delete_item_tags(self):
hda = self._create_vanilla_hda()
tags = ['tag1']
self.tag_manager.set_tags_from_list(self.user, hda, tags)
self.tag_manager.delete_item_tags(user=self.user, item=hda)
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self.tag_handler.delete_item_tags(user=self.user, item=hda)
self.assertEqual(hda.tags, [])
def test_item_has_tag(self):
hda = self._create_vanilla_hda()
tags = ['tag1']
self.tag_manager.set_tags_from_list(self.user, hda, tags)
self.assertTrue(self.tag_manager.item_has_tag(self.user, item=hda, tag='tag1'))
self.tag_handler.set_tags_from_list(self.user, hda, tags)
self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag='tag1'))
# ItemTagAssociation
self.assertTrue(self.tag_manager.item_has_tag(self.user, item=hda, tag=hda.tags[0]))
self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag=hda.tags[0]))
# Tag
self.assertTrue(self.tag_manager.item_has_tag(self.user, item=hda, tag=hda.tags[0].tag))
self.assertFalse(self.tag_manager.item_has_tag(self.user, item=hda, tag='tag2'))
self.assertTrue(self.tag_handler.item_has_tag(self.user, item=hda, tag=hda.tags[0].tag))
self.assertFalse(self.tag_handler.item_has_tag(self.user, item=hda, tag='tag2'))
test/unit/unittest_utils/galaxy_mock.py
+1 -2
View File
@@ -13,8 +13,7 @@ from galaxy import (
from galaxy.auth import AuthManager
from galaxy.datatypes import registry
from galaxy.jobs.manager import NoopManager
from galaxy.managers import tags
from galaxy.model import mapping
from galaxy.model import mapping, tags
from galaxy.tools.deps.containers import NullContainerFinder
from galaxy.util.bunch import Bunch
from galaxy.util.dbkeys import GenomeBuilds