Merge branch 'release_23.1' into dev

lib/galaxy/jobs/handler.py

@@ -269,55 +269,55 @@ def job_pair_for_id(self, id):
     def __check_jobs_at_startup(self):
         """
         Checks all jobs that are in the 'new', 'queued', 'running', or 'stopped' state in
-        the database and requeues or cleans up as necessary.  Only run as the
-        job handler starts.
+        the database and requeues or cleans up as necessary. Only run as the job handler starts.
         In case the activation is enforced it will filter out the jobs of inactive users.
         """
         stmt = self._build_check_jobs_at_startup_statement()
         with self.sa_session() as session, session.begin():
-            jobs_at_startup = session.scalars(stmt)
-            for job in jobs_at_startup:
-                if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
-                    log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to recover job")
-                    self.job_wrapper(job).fail(
-                        "This tool was disabled before the job completed.  Please contact your Galaxy administrator."
-                    )
-                elif job.job_runner_name is not None and job.job_runner_external_id is None:
-                    # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
-                    log.debug(
-                        f"({job.id}) Job runner assigned but no external ID recorded, adding to the job handler queue"
-                    )
-                    job.job_runner_name = None
-                    if self.track_jobs_in_database:
-                        job.set_state(model.Job.states.NEW)
-                    else:
-                        self.queue.put((job.id, job.tool_id))
-                elif (
-                    job.job_runner_name is not None
-                    and job.job_runner_external_id is not None
-                    and job.destination_id is None
-                ):
-                    # This is the first start after upgrading from URLs to destinations, convert the URL to a destination and persist
-                    job_wrapper = self.job_wrapper(job)
-                    job_destination = self.dispatcher.url_to_destination(job.job_runner_name)
-                    if job_destination.id is None:
-                        job_destination.id = "legacy_url"
-                    job_wrapper.set_job_destination(job_destination, job.job_runner_external_id)
-                    self.dispatcher.recover(job, job_wrapper)
-                    log.info(f"({job.id}) Converted job from a URL to a destination and recovered")
-                elif job.job_runner_name is None:
-                    # Never (fully) dispatched
-                    log.debug(
-                        f"({job.id}) No job runner assigned and job still in '{job.state}' state, adding to the job handler queue"
-                    )
-                    if self.track_jobs_in_database:
-                        job.set_state(model.Job.states.NEW)
-                    else:
-                        self.queue.put((job.id, job.tool_id))
-                else:
-                    # Already dispatched and running
-                    job_wrapper = self.__recover_job_wrapper(job)
-                    self.dispatcher.recover(job, job_wrapper)
+            try:
+                for job in session.scalars(stmt):
+                    with session.begin_nested():
+                        self._check_job_at_startup(job)
+            finally:
+                session.commit()
+
+    def _check_job_at_startup(self, job):
+        if not self.app.toolbox.has_tool(job.tool_id, job.tool_version, exact=True):
+            log.warning(f"({job.id}) Tool '{job.tool_id}' removed from tool config, unable to recover job")
+            self.job_wrapper(job).fail(
+                "This tool was disabled before the job completed.  Please contact your Galaxy administrator."
+            )
+        elif job.job_runner_name is not None and job.job_runner_external_id is None:
+            # This could happen during certain revisions of Galaxy where a runner URL was persisted before the job was dispatched to a runner.
+            log.debug(f"({job.id}) Job runner assigned but no external ID recorded, adding to the job handler queue")
+            job.job_runner_name = None
+            if self.track_jobs_in_database:
+                job.set_state(model.Job.states.NEW)
+            else:
+                self.queue.put((job.id, job.tool_id))
+        elif job.job_runner_name is not None and job.job_runner_external_id is not None and job.destination_id is None:
+            # This is the first start after upgrading from URLs to destinations, convert the URL to a destination and persist
+            job_wrapper = self.job_wrapper(job)
+            job_destination = self.dispatcher.url_to_destination(job.job_runner_name)
+            if job_destination.id is None:
+                job_destination.id = "legacy_url"
+            job_wrapper.set_job_destination(job_destination, job.job_runner_external_id)
+            self.dispatcher.recover(job, job_wrapper)
+            log.info(f"({job.id}) Converted job from a URL to a destination and recovered")
+        elif job.job_runner_name is None:
+            # Never (fully) dispatched
+            log.debug(
+                f"({job.id}) No job runner assigned and job still in '{job.state}' state, adding to the job handler queue"
+            )
+            if self.track_jobs_in_database:
+                job.set_state(model.Job.states.NEW)
+            else:
+                self.queue.put((job.id, job.tool_id))
+        else:
+            # Already dispatched and running
+            job_wrapper = self.__recover_job_wrapper(job)
+            self.dispatcher.recover(job, job_wrapper)
+        pass
 
     def _build_check_jobs_at_startup_statement(self):
         if self.track_jobs_in_database:

lib/galaxy/webapps/galaxy/services/datasets.py

@@ -545,15 +545,16 @@ def extra_files(
         Generate list of extra files.
         """
         hda = self.hda_manager.get_accessible(history_content_id, trans.user)
-        extra_files_path = hda.extra_files_path
         rval = []
-        for root, directories, files in safe_walk(extra_files_path):
-            for directory in directories:
-                rval.append(
-                    {"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)}
-                )
-            for file in files:
-                rval.append({"class": "File", "path": os.path.relpath(os.path.join(root, file), extra_files_path)})
+        if not hda.is_pending and hda.extra_files_path_exists():
+            extra_files_path = hda.extra_files_path
+            for root, directories, files in safe_walk(extra_files_path):
+                for directory in directories:
+                    rval.append(
+                        {"class": "Directory", "path": os.path.relpath(os.path.join(root, directory), extra_files_path)}
+                    )
+                for file in files:
+                    rval.append({"class": "File", "path": os.path.relpath(os.path.join(root, file), extra_files_path)})
 
         return rval
 

tools/filters/convert_characters.py

@@ -22,7 +22,7 @@ def __main__():
         from_ch += "+"
 
     skipped = 0
-    with open(args[0], "rU") as fin:
+    with open(args[0]) as fin:
         with open(args[2], "w") as fout:
             for line in fin:
                 if options.strip: