Loading lib/galaxy/managers/jobs.py +12 −0 Original line number Diff line number Diff line import json import logging import typing from pathlib import Path from datetime import ( date, datetime, Loading Loading @@ -236,6 +237,17 @@ class JobManager: if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user): raise ItemAccessibilityException("You are not allowed to rerun this job.") trans.sa_session.refresh(job) if job.state == job.states.RUNNING: try: stdout_path = Path(".").parent.parent.parent.parent.parent / "database/jobs_directory/000" / str( job.id) / "outputs/tool_stdout" stdout_file = open(stdout_path, "r") # stderr_file = open("../../../../../database/jobs_directory/000/" + str(job.id) + "/outputs/tool_stderr") job.job_stdout = stdout_file.read() job.tool_stdout = job.job_stdout # job.stderr = stderr_file.read() except: log.error("Could not load std out") return job def stop(self, job, message=None): Loading Loading
lib/galaxy/managers/jobs.py +12 −0 Original line number Diff line number Diff line import json import logging import typing from pathlib import Path from datetime import ( date, datetime, Loading Loading @@ -236,6 +237,17 @@ class JobManager: if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user): raise ItemAccessibilityException("You are not allowed to rerun this job.") trans.sa_session.refresh(job) if job.state == job.states.RUNNING: try: stdout_path = Path(".").parent.parent.parent.parent.parent / "database/jobs_directory/000" / str( job.id) / "outputs/tool_stdout" stdout_file = open(stdout_path, "r") # stderr_file = open("../../../../../database/jobs_directory/000/" + str(job.id) + "/outputs/tool_stderr") job.job_stdout = stdout_file.read() job.tool_stdout = job.job_stdout # job.stderr = stderr_file.read() except: log.error("Could not load std out") return job def stop(self, job, message=None): Loading