Fix SA2.0 (query->select) in galaxy.tools

lib/galaxy/tools/__init__.py

@@ -30,6 +30,11 @@
 from lxml import etree
 from mako.template import Template
 from packaging.version import Version
+from sqlalchemy import (
+    delete,
+    func,
+    select,
+)
 
 from galaxy import (
     exceptions,
@@ -39,6 +44,8 @@
 from galaxy.job_execution import output_collect
 from galaxy.metadata import get_metadata_compute_strategy
 from galaxy.model.base import transaction
+from galaxy.model.repositories.job import JobRepository
+from galaxy.model.repositories.stored_workflow import StoredWorkflowRepository
 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 (
@@ -346,9 +353,9 @@ def __init__(self, app):
 
     def reset_tags(self):
         log.info(
-            f"removing all tool tag associations ({str(self.sa_session.query(self.app.model.ToolTagAssociation).count())})"
+            f"removing all tool tag associations ({str(self.sa_session.scalar(select(func.count(self.app.model.ToolTagAssociation))))})"
         )
-        self.sa_session.query(self.app.model.ToolTagAssociation).delete()
+        self.sa_session.execute(delete(self.app.model.ToolTagAssociation))
         with transaction(self.sa_session):
             self.sa_session.commit()
 
@@ -359,7 +366,8 @@ def handle_tags(self, tool_id, tool_definition_source):
             for tag_name in tag_names:
                 if tag_name == "":
                     continue
-                tag = self.sa_session.query(self.app.model.Tag).filter_by(name=tag_name).first()
+                stmt = select(self.app.model.Tag).filter_by(name=tag_name).limit(1)
+                tag = self.sa_session.scalars(stmt).first()
                 if not tag:
                     tag = self.app.model.Tag(name=tag_name)
                     self.sa_session.add(tag)
@@ -618,7 +626,7 @@ def _load_workflow(self, workflow_id):
         which is encoded in the tool panel.
         """
         id = self.app.security.decode_id(workflow_id)
-        stored = self.app.model.context.query(self.app.model.StoredWorkflow).get(id)
+        stored = StoredWorkflowRepository(self.app.model.context).get(id)
         return stored.latest_workflow
 
     def __build_tool_version_select_field(self, tools, tool_id, set_selected):
@@ -3121,7 +3129,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                 self.sa_session.commit()
 
     def job_failed(self, job_wrapper, message, exception=False):
-        job = job_wrapper.sa_session.query(model.Job).get(job_wrapper.job_id)
+        job = JobRepository(job_wrapper.sa_session).get(job_wrapper.job_id)
         if job:
             inp_data = {}
             for dataset_assoc in job.input_datasets:
@@ -3168,7 +3176,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
 
     def job_failed(self, job_wrapper, message, exception=False):
         super().job_failed(job_wrapper, message, exception=exception)
-        job = job_wrapper.sa_session.query(model.Job).get(job_wrapper.job_id)
+        job = JobRepository(job_wrapper.sa_session).get(job_wrapper.job_id)
         self.__remove_interactivetool_by_job(job)
 
 

lib/galaxy/tools/actions/__init__.py

@@ -24,6 +24,8 @@
 from galaxy.model.base import transaction
 from galaxy.model.dataset_collections.builder import CollectionBuilder
 from galaxy.model.none_like import NoneDataset
+from galaxy.model.repositories.hda import HistoryDatasetAssociationRepository as hda_repo
+from galaxy.model.repositories.job import JobRepository
 from galaxy.objectstore import ObjectStorePopulator
 from galaxy.tools.parameters import update_dataset_ids
 from galaxy.tools.parameters.basic import (
@@ -481,7 +483,7 @@ def handle_output(name, output, hidden=None):
             if async_tool and name in incoming:
                 # HACK: output data has already been created as a result of the async controller
                 dataid = incoming[name]
-                data = trans.sa_session.query(app.model.HistoryDatasetAssociation).get(dataid)
+                data = hda_repo(trans.sa_session).get(dataid)
                 assert data is not None
                 out_data[name] = data
             else:
@@ -745,7 +747,7 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current
         input datasets to be those of the job that is being rerun.
         """
         try:
-            old_job = trans.sa_session.query(trans.app.model.Job).get(rerun_remap_job_id)
+            old_job = JobRepository(trans.sa_session).get(rerun_remap_job_id)
             assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid"
             assert (
                 old_job.tool_id == current_job.tool_id

lib/galaxy/tools/actions/upload_common.py

@@ -13,6 +13,7 @@
     Optional,
 )
 
+from sqlalchemy import select
 from sqlalchemy.orm import joinedload
 from webob.compat import cgi_FieldStorage
 
@@ -30,6 +31,9 @@
     Role,
 )
 from galaxy.model.base import transaction
+from galaxy.model.repositories.form_definition import FormDefinitionRepository
+from galaxy.model.repositories.library_folder import LibraryFolderRepository
+from galaxy.model.repositories.role import RoleRepository
 from galaxy.util import is_url
 from galaxy.util.path import external_chown
 
@@ -94,21 +98,22 @@ def handle_library_params(
     # See if we have any template field contents
     template_field_contents = {}
     template_id = params.get("template_id", None)
-    folder = trans.sa_session.query(LibraryFolder).get(folder_id)
+    folder = LibraryFolderRepository(trans.sa_session).get(folder_id)
     # We are inheriting the folder's info_association, so we may have received inherited contents or we may have redirected
     # here after the user entered template contents ( due to errors ).
     template: Optional[FormDefinition] = None
     if template_id not in [None, "None"]:
-        template = trans.sa_session.query(FormDefinition).get(template_id)
+        template = FormDefinitionRepository(trans.sa_session).get(template_id)
         assert template
         for field in template.fields:
             field_name = field["name"]
             if params.get(field_name, False):
                 field_value = util.restore_text(params.get(field_name, ""))
                 template_field_contents[field_name] = field_value
     roles: List[Role] = []
+    role_repo = RoleRepository(trans.sa_session)
     for role_id in util.listify(params.get("roles", [])):
-        role = trans.sa_session.query(Role).get(role_id)
+        role = role_repo.get(role_id)
         roles.append(role)
     tags = params.get("tags", None)
     return LibraryParams(
@@ -436,10 +441,11 @@ def active_folders(trans, folder):
     # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
     # Much faster way of retrieving all active sub-folders within a given folder than the
     # performance of the mapper.  This query also eagerloads the permissions on each folder.
-    return (
-        trans.sa_session.query(LibraryFolder)
+    stmt = (
+        select(LibraryFolder)
         .filter_by(parent=folder, deleted=False)
         .options(joinedload(LibraryFolder.actions))
-        .order_by(LibraryFolder.table.c.name)
-        .all()
+        .unique()
+        .order_by(LibraryFolder.name)
     )
+    return trans.sa_session.scalars(stmt).all()

lib/galaxy/tools/errors.py

@@ -10,6 +10,7 @@
     util,
     web,
 )
+from galaxy.model.repositories.hda import HistoryDatasetAssociationRepository as hda_repo
 from galaxy.security.validate_user_input import validate_email_str
 from galaxy.util import unicodify
 
@@ -135,12 +136,13 @@ def __init__(self, hda, app):
         # Get the dataset
         sa_session = app.model.context
         if not isinstance(hda, model.HistoryDatasetAssociation):
+            _hda_repo = hda_repo(sa_session)
             hda_id = hda
             try:
-                hda = sa_session.query(model.HistoryDatasetAssociation).get(hda_id)
+                hda = _hda_repo.get(hda_id)
                 assert hda is not None, ValueError("No HDA yet")
             except Exception:
-                hda = sa_session.query(model.HistoryDatasetAssociation).get(app.security.decode_id(hda_id))
+                hda = _hda_repo.get(app.security.decode_id(hda_id))
         assert isinstance(hda, model.HistoryDatasetAssociation), ValueError(f"Bad value provided for HDA ({hda}).")
         self.hda = hda
         # Get the associated job

lib/galaxy/tools/imp_exp/__init__.py

@@ -4,6 +4,8 @@
 import shutil
 from typing import Optional
 
+from sqlalchemy import select
+
 from galaxy import model
 from galaxy.model import store
 from galaxy.model.base import transaction
@@ -49,7 +51,8 @@ def cleanup_after_job(self):
         # Import history.
         #
 
-        jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).first()
+        stmt = select(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).limit(1)
+        jiha = self.sa_session.scalars(stmt).first()
         if not jiha:
             return None
         user = jiha.job.user