[WIP] Fix SA2.0 (query->select) in galaxy.jobs

lib/galaxy/jobs/__init__.py

@@ -25,6 +25,7 @@
 import yaml
 from packaging.version import Version
 from pulsar.client.staging import COMMAND_VERSION_FILENAME
+from sqlalchemy import select
 
 from galaxy import (
     model,
@@ -1042,11 +1043,8 @@ def metadata_strategy(self):
     def remote_command_line(self):
         use_remote = self.get_destination_configuration("tool_evaluation_strategy") == "remote"
         # It wouldn't be hard to support history export, but we want to do this in task queue workers anyway ...
-        return (
-            use_remote
-            and self.external_output_metadata.extended
-            and not self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=self.get_job()).first()
-        )
+        stmt = select(model.JobExportHistoryArchive).filter_by(job=self.get_job()).limit(1)
+        return use_remote and self.external_output_metadata.extended and not self.sa_session.scalars(stmt).first()
 
     def tool_directory(self):
         tool_dir = self.tool and self.tool.tool_dir
@@ -1181,7 +1179,7 @@ def galaxy_url(self):
         return self.get_destination_configuration("galaxy_infrastructure_url")
 
     def get_job(self) -> model.Job:
-        return self.sa_session.query(model.Job).get(self.job_id)
+        return self.sa_session.get(model.Job, self.job_id)
 
     def get_id_tag(self):
         # For compatibility with drmaa, which uses job_id right now, and TaskWrapper
@@ -1232,10 +1230,12 @@ def prepare(self, compute_environment=None):
         job = self._load_job()
 
         def get_special():
-            jeha = self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=job).first()
+            stmt = select(model.JobExportHistoryArchive).filter_by(job=job).limit(1)
+            jeha = self.sa_session.scalars(stmt).first()
             if jeha:
                 return jeha.fda
-            return self.sa_session.query(model.GenomeIndexToolData).filter_by(job=job).first()
+            stmt = select(model.GenomeIndexToolData).filter_by(job=job).limit(1)
+            return self.sa_session.scalars(stmt).first()
 
         # TODO: The upload tool actions that create the paramfile can probably be turned in to a configfile to remove this special casing
         if job.tool_id == "upload1":
@@ -2579,12 +2579,12 @@ def can_split(self):
 
     def get_job(self):
         if self.job_id:
-            return self.sa_session.query(model.Job).get(self.job_id)
+            return self.sa_session.get(model.Job, self.job_id)
         else:
             return None
 
     def get_task(self):
-        return self.sa_session.query(model.Task).get(self.task_id)
+        return self.sa_session.get(model.Task, self.task_id)
 
     def get_id_tag(self):
         # For compatibility with drmaa job runner and TaskWrapper, instead of using job_id directly

lib/galaxy/jobs/runners/__init__.py

@@ -15,6 +15,8 @@
     Queue,
 )
 
+from sqlalchemy import select
+
 import galaxy.jobs
 from galaxy import model
 from galaxy.exceptions import ConfigurationError
@@ -379,11 +381,12 @@ def _walk_dataset_outputs(self, job: model.Job):
                 dataset_assoc.dataset.dataset.history_associations + dataset_assoc.dataset.dataset.library_associations
             ):
                 if isinstance(dataset, self.app.model.HistoryDatasetAssociation):
-                    joda = (
-                        self.sa_session.query(self.app.model.JobToOutputDatasetAssociation)
+                    stmt = (
+                        select(self.app.model.JobToOutputDatasetAssociation)
                         .filter_by(job=job, dataset=dataset)
-                        .first()
+                        .limit(1)
                     )
+                    joda = self.sa_session.scalars(stmt).first()
                     yield (joda, dataset)
         # TODO: why is this not just something easy like:
         # for dataset_assoc in job.output_datasets + job.output_library_datasets:

lib/galaxy/jobs/runners/godocker.py

@@ -236,7 +236,7 @@ def check_watched_item(self, job_state):
     def stop_job(self, job_wrapper):
         """Attempts to delete a dispatched executing Job in GoDocker"""
         # This function is called by fail_job() where
-        # param job = self.sa_session.query(self.app.model.Job).get(job_state.job_wrapper.job_id)
+        # param job = self.sa_session.get(self.app.model.Job, job_state.job_wrapper.job_id)
         # No Return data expected
         job_id = job_wrapper.job_id
         log.debug(f"STOP JOB EXECUTION OF JOB ID: {str(job_id)}")

lib/galaxy/jobs/runners/pulsar.py

@@ -35,6 +35,7 @@
 
 # TODO: Perform pulsar release with this included in the client package
 from pulsar.client.staging import DEFAULT_DYNAMIC_COLLECTION_PATTERN
+from sqlalchemy import select
 
 from galaxy import model
 from galaxy.job_execution.compute_environment import ComputeEnvironment
@@ -949,10 +950,8 @@ def __async_update(self, full_status):
             remote_job_id = full_status["job_id"]
             if len(remote_job_id) == 32:
                 # It is a UUID - assign_ids = uuid in destination params...
-                sa_session = self.app.model.session
-                galaxy_job_id = (
-                    sa_session.query(model.Job).filter(model.Job.job_runner_external_id == remote_job_id).one().id
-                )
+                stmt = select(model.Job).filter(model.Job.job_runner_external_id == remote_job_id)
+                galaxy_job_id = self.app.model.session.execute(stmt).scalar_one().id
             else:
                 galaxy_job_id = remote_job_id
             job, job_wrapper = self.app.job_manager.job_handler.job_queue.job_pair_for_id(galaxy_job_id)