Unverified Commit 0f670d72 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #16175 from mvdbeek/startup_fix_when_tool_removed_between_reboot 

[23.0] Startup fix when tool removed between reboot
parents e14c2d16 2088717d

lib/galaxy/jobs/__init__.py

+17 −13
Original line number Diff line number Diff line
@@ -1047,7 +1047,7 @@ class MinimalJobWrapper(HasResourceParameters): 
        )



    def tool_directory(self):

        tool_dir = self.tool.tool_dir

        tool_dir = self.tool and self.tool.tool_dir

        if tool_dir is not None:

            tool_dir = os.path.abspath(tool_dir)

        return tool_dir
@@ -1058,6 +1058,7 @@ class MinimalJobWrapper(HasResourceParameters): 
            job = self.get_job()

            work_request = WorkRequestContext(self.app, user=job.user)

            user_context = ProvidesUserFileSourcesUserContext(work_request)

            tool_source = self.tool and self.tool.tool_source.to_string()

            self._job_io = JobIO(

                sa_session=self.sa_session,

                job=job,
@@ -1079,9 +1080,9 @@ class MinimalJobWrapper(HasResourceParameters): 
                check_job_script_integrity=self.app.config.check_job_script_integrity,

                check_job_script_integrity_count=self.app.config.check_job_script_integrity_count,

                check_job_script_integrity_sleep=self.app.config.check_job_script_integrity_sleep,

                tool_source=self.tool.tool_source.to_string(),

                tool_source_class=type(self.tool.tool_source).__name__,

                tool_dir=self.tool.tool_dir,

                tool_source=tool_source,

                tool_source_class=type(self.tool.tool_source).__name__ if self.tool else None,

                tool_dir=self.tool and self.tool.tool_dir,

                is_task=self.is_task,

            )

        return self._job_io
@@ -1412,6 +1413,7 @@ class MinimalJobWrapper(HasResourceParameters): 
                # a better message

                etype, evalue, tb = sys.exc_info()



            try:

                if self.outputs_to_working_directory and not self.__link_file_check() and working_directory_exists:

                    for dataset_path in self.job_io.get_output_fnames():

                        try:
@@ -1419,6 +1421,8 @@ class MinimalJobWrapper(HasResourceParameters): 
                            log.debug("fail(): Moved %s to %s", dataset_path.false_path, dataset_path.real_path)

                        except OSError as e:

                            log.error("fail(): Missing output file in working directory: %s", unicodify(e))

            except Exception as e:

                log.exception(str(e))

            for dataset_assoc in job.output_datasets + job.output_library_datasets:

                dataset = dataset_assoc.dataset

                self.sa_session.refresh(dataset)
@@ -1563,12 +1567,12 @@ class MinimalJobWrapper(HasResourceParameters): 


    @property

    def home_target(self):

        home_target = self.tool.home_target

        home_target = self.tool and self.tool.home_target

        return home_target



    @property

    def tmp_target(self):

        return self.tool.tmp_target

        return self.tool and self.tool.tmp_target



    def get_destination_configuration(self, key, default=None):

        """Get a destination parameter that can be defaulted back