Unverified Commit 1d7a5548 authored by John Chilton's avatar John Chilton Committed by GitHub
Browse files

Merge pull request #12696 from jmchilton/unit_testing_fixes_2 

Assorted random typing fixes.
parents e7c12347 78da479d

lib/galaxy/tool_util/unittest_utils/__init__.py

+3 −3
Original line number Diff line number Diff line 
from galaxy.util.bunch import Bunch

from unittest.mock import Mock





def mock_trans(has_user=True, is_admin=False):

    """A mock ``trans`` object for exposing user info to toolbox filter unit tests."""

    trans = Bunch(user_is_admin=is_admin)

    trans = Mock(user_is_admin=is_admin)

    if has_user:

        trans.user = Bunch(preferences={})

        trans.user = Mock(preferences={})

    else:

        trans.user = None

    return trans

lib/galaxy/util/lazy_process.py

+1 −0
Original line number Diff line number Diff line
@@ -30,6 +30,7 @@ class LazyProcess: 
        with self.thread_lock:

            self.allow_process_request = False

        if self.running:

            assert self.process  # tell type checker it can not be None if self.running

            self.process.terminate()

            time.sleep(.01)

            if self.running:

lib/galaxy/webapps/galaxy/api/extended_metadata.py

+16 −23
Original line number Diff line number Diff line
@@ -2,13 +2,14 @@ 
API operations on annotations.

"""

import logging

from typing import Generic, Optional, TypeVar



from galaxy import (

    managers,

    web

    model,

    web,

)

from galaxy.webapps.base.controller import (

    HTTPNotImplemented,

    UsesExtendedMetadataMixin,

    UsesLibraryMixinItems,

    UsesStoredWorkflowMixin
@@ -17,10 +18,16 @@ from . import BaseGalaxyAPIController, depends 


log = logging.getLogger(__name__)



T = TypeVar('T')



class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin):



    @web.legacy_expose_api

class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetadataMixin, UsesLibraryMixinItems, UsesStoredWorkflowMixin, Generic[T]):

    exmeta_item_id: str



    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[T]:

        ...



    @web.expose_api

    def index(self, trans, **kwd):

        idnum = kwd[self.exmeta_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=False)
@@ -29,7 +36,7 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada 
            if ex_meta is not None:

                return ex_meta.data



    @web.legacy_expose_api

    @web.expose_api

    def create(self, trans, payload, **kwd):

        idnum = kwd[self.exmeta_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=True)
@@ -41,26 +48,12 @@ class BaseExtendedMetadataController(BaseGalaxyAPIController, UsesExtendedMetada 
            ex_obj = self.create_extended_metadata(trans, payload)

            self.set_item_extended_metadata_obj(trans, item, ex_obj)



    @web.legacy_expose_api

    def delete(self, trans, **kwd):

        idnum = kwd[self.tagged_item_id]

        item = self._get_item_from_id(trans, idnum, check_writable=True)

        if item is not None:

            ex_obj = self.get_item_extended_metadata_obj(trans, item)

            if ex_obj is not None:

                self.unset_item_extended_metadata_obj(trans, item)

                self.delete_extended_metadata(trans, ex_obj)



    @web.legacy_expose_api

    def undelete(self, trans, **kwd):

        raise HTTPNotImplemented()





class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController):

class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController[model.LibraryDatasetDatasetAssociation]):

    controller_name = "library_dataset_extended_metadata"

    exmeta_item_id = "library_content_id"



    def _get_item_from_id(self, trans, idstr, check_writable=True):

    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.LibraryDatasetDatasetAssociation]:

        if check_writable:

            item = self.get_library_dataset_dataset_association(trans, idstr)

            if trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item):
@@ -72,12 +65,12 @@ class LibraryDatasetExtendMetadataController(BaseExtendedMetadataController): 
        return None





class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController):

class HistoryDatasetExtendMetadataController(BaseExtendedMetadataController[model.HistoryDatasetAssociation]):

    controller_name = "history_dataset_extended_metadata"

    exmeta_item_id = "history_content_id"

    hda_manager: managers.hdas.HDAManager = depends(managers.hdas.HDAManager)



    def _get_item_from_id(self, trans, idstr, check_writable=True):

    def _get_item_from_id(self, trans, idstr, check_writable=True) -> Optional[model.HistoryDatasetAssociation]:

        decoded_idstr = self.decode_id(idstr)

        if check_writable:

            return self.hda_manager.get_owned(decoded_idstr, trans.user, current_history=trans.history)

lib/galaxy/webapps/galaxy/api/library_datasets.py

+3 −2
Original line number Diff line number Diff line
@@ -456,8 +456,9 @@ class LibraryDatasetsController(BaseGalaxyAPIController, UsesVisualizationMixin, 
            path = os.path.join(full_dir, path)

            if unsafe_walk(path, allowlist=[full_dir] + trans.app.config.user_library_import_symlink_allowlist, username=username):

                # the path is a dir and contains files that symlink outside the user dir

                error = 'User attempted to import a path that resolves to a path outside of their import dir: %s -> %s', \

                error = 'User attempted to import a path that resolves to a path outside of their import dir: %s -> %s' % (

                    path, os.path.realpath(path)

                )

                if trans.app.config.user_library_import_check_permissions:

                    error += ' or is not readable for them.'

                log.error(error)

lib/galaxy_test/driver/driver_util.py

+1 −1
Original line number Diff line number Diff line
@@ -621,7 +621,7 @@ def setup_shed_tools_for_test(app, tmpdir, testing_migrated_tools, testing_insta 
        app.toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)





def build_galaxy_app(simple_kwargs):

def build_galaxy_app(simple_kwargs) -> GalaxyUniverseApplication:

    """Build a Galaxy app object from a simple keyword arguments.



    Construct paste style complex dictionary and use load_app_properties so