06 Jan 2020 10:53:48,393 INFO : Running LINCS pipeline on PSP for: LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32 06 Jan 2020 10:53:48,393 INFO : ======================================= 06 Jan 2020 10:53:49,214 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority' 06 Jan 2020 10:53:49,214 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32 06 Jan 2020 10:53:49,214 INFO : Submitting job for runId: 80575, name: LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32 06 Jan 2020 10:53:49,215 INFO : Looking for existing job with name LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32 06 Jan 2020 10:53:49,584 INFO : PSP job name: LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32 06 Jan 2020 10:53:49,584 INFO : Sending JSON: 06 Jan 2020 10:53:49,584 INFO : { "level 4": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32_LVL4.gct" }}, "assay": "GCP", "name": "LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32", "config": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32.cfg" }}, "level 2": {"panorama": { "method": "GET", "url": "https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=80575&remote=true&reportName=GCT%20File%20GCP" }}, "level 3": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32_LVL3.gct" }} } 06 Jan 2020 10:53:49,585 INFO : Sending POST request to https://api.clue.io/api/psp 06 Jan 2020 10:53:49,819 INFO : Response code - 200 06 Jan 2020 10:53:49,819 INFO : Response from server: {"name":"LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32","assay":"GCP","status":"Waiting_To_Download","id":"5e13823d5beec6001388e35b","created":"2020-01-06T18:53:49.667Z","last_modified":"2020-01-06T18:53:49.667Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=80575&remote=true&reportName=GCT%20File%20GCP"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate83_annotated_minimized_2020-01-06_13-51-32.cfg"}}} 06 Jan 2020 10:53:49,820 INFO : Sent POST request to https://api.clue.io/api/psp 06 Jan 2020 10:53:49,822 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:53:49,944 INFO : Status: Waiting_To_Download 06 Jan 2020 10:54:09,944 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:54:10,217 INFO : Status: Waiting_To_Download 06 Jan 2020 10:54:30,218 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:54:30,500 INFO : Status: Waiting_To_Download 06 Jan 2020 10:54:50,500 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:54:50,769 INFO : Status: Waiting_To_Download 06 Jan 2020 10:55:10,770 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:55:11,121 INFO : Status: Waiting_To_Download 06 Jan 2020 10:55:31,121 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:55:31,402 INFO : Status: Waiting_To_Download 06 Jan 2020 10:55:51,402 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:55:51,681 INFO : Status: Waiting_To_Download 06 Jan 2020 10:56:11,682 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:56:11,961 INFO : Status: Waiting_To_Download 06 Jan 2020 10:56:31,961 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:56:32,309 INFO : Status: Waiting_To_Download 06 Jan 2020 10:56:52,310 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:56:52,592 INFO : Status: Waiting_To_Download 06 Jan 2020 10:57:12,592 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:57:12,872 INFO : Status: Waiting_To_Download 06 Jan 2020 10:57:32,872 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:57:33,154 INFO : Status: Waiting_To_Download 06 Jan 2020 10:57:53,155 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:57:53,505 INFO : Status: Waiting_To_Download 06 Jan 2020 10:58:13,506 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:58:13,782 INFO : Status: Waiting_To_Download 06 Jan 2020 10:58:33,782 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:58:34,055 INFO : Status: Waiting_To_Download 06 Jan 2020 10:58:54,055 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:58:54,333 INFO : Status: Waiting_To_Download 06 Jan 2020 10:59:14,334 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:59:14,608 INFO : Status: Waiting_To_Download 06 Jan 2020 10:59:34,608 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:59:34,895 INFO : Status: Waiting_To_Download 06 Jan 2020 10:59:54,896 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 10:59:55,244 INFO : Status: Waiting_To_Download 06 Jan 2020 11:00:15,244 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:00:15,515 INFO : Status: Waiting_To_Download 06 Jan 2020 11:00:35,515 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:00:35,785 INFO : Status: Waiting_To_Download 06 Jan 2020 11:00:55,786 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:00:56,070 INFO : Status: Waiting_To_Download 06 Jan 2020 11:01:16,071 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:01:16,360 INFO : Status: Waiting_To_Download 06 Jan 2020 11:01:36,360 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:01:36,630 INFO : Status: Waiting_To_Download 06 Jan 2020 11:01:56,630 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:01:56,908 INFO : Status: Waiting_To_Download 06 Jan 2020 11:02:16,908 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:02:17,181 INFO : Status: Waiting_To_Download 06 Jan 2020 11:02:37,181 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:02:37,545 INFO : Status: Waiting_To_Download 06 Jan 2020 11:02:57,545 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:02:57,814 INFO : Status: Waiting_To_Download 06 Jan 2020 11:03:17,814 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:03:18,085 INFO : Status: Waiting_To_Download 06 Jan 2020 11:03:21,335 INFO : Attempting to cancel job as requested by karen@broadinstitute.org. 06 Jan 2020 11:03:38,085 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:03:38,365 INFO : Status: Waiting_To_Download 06 Jan 2020 11:03:58,366 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:03:58,717 INFO : Status: Waiting_To_Download 06 Jan 2020 11:04:18,717 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:04:19,000 INFO : Status: Waiting_To_Download 06 Jan 2020 11:04:39,000 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:04:39,268 INFO : Status: Waiting_To_Download 06 Jan 2020 11:04:59,268 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:04:59,538 INFO : Status: Waiting_To_Download 06 Jan 2020 11:05:19,538 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:05:19,832 INFO : Status: Waiting_To_Download 06 Jan 2020 11:05:39,832 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:05:40,108 INFO : Status: Waiting_To_Download 06 Jan 2020 11:06:00,109 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:06:00,458 INFO : Status: Waiting_To_Download 06 Jan 2020 11:06:20,459 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:06:20,737 INFO : Status: Waiting_To_Download 06 Jan 2020 11:06:40,738 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:06:41,011 INFO : Status: Waiting_To_Download 06 Jan 2020 11:07:01,011 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:07:01,294 INFO : Status: Waiting_To_Download 06 Jan 2020 11:07:21,294 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:07:21,659 INFO : Status: Waiting_To_Download 06 Jan 2020 11:07:41,659 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:07:41,930 INFO : Status: Waiting_To_Download 06 Jan 2020 11:08:01,930 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:08:02,202 INFO : Status: Waiting_To_Download 06 Jan 2020 11:08:22,203 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:08:22,480 INFO : Status: Waiting_To_Download 06 Jan 2020 11:08:42,481 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:08:42,844 INFO : Status: Waiting_To_Download 06 Jan 2020 11:09:02,844 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:09:03,121 INFO : Status: Waiting_To_Download 06 Jan 2020 11:09:23,122 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:09:23,404 INFO : Status: Waiting_To_Download 06 Jan 2020 11:09:43,404 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:09:43,683 INFO : Status: Waiting_To_Download 06 Jan 2020 11:10:03,683 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:10:04,034 INFO : Status: Waiting_To_Download 06 Jan 2020 11:10:24,035 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:10:24,305 INFO : Status: Waiting_To_Download 06 Jan 2020 11:10:44,306 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:10:44,583 INFO : Status: Waiting_To_Download 06 Jan 2020 11:11:04,583 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:11:04,853 INFO : Status: Waiting_To_Download 06 Jan 2020 11:11:24,853 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:11:25,201 INFO : Status: Waiting_To_Download 06 Jan 2020 11:11:45,202 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:11:45,472 INFO : Status: Waiting_To_Download 06 Jan 2020 11:12:05,473 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:12:05,744 INFO : Status: Waiting_To_Download 06 Jan 2020 11:12:25,744 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:12:26,027 INFO : Status: Waiting_To_Download 06 Jan 2020 11:12:46,027 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:12:46,384 INFO : Status: Waiting_To_Download 06 Jan 2020 11:13:06,385 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:13:06,656 INFO : Status: Waiting_To_Download 06 Jan 2020 11:13:26,656 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:13:26,934 INFO : Status: Waiting_To_Download 06 Jan 2020 11:13:46,934 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:13:47,271 INFO : Status: Waiting_To_Download 06 Jan 2020 11:14:07,271 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:14:07,625 INFO : Status: Waiting_To_Download 06 Jan 2020 11:14:27,625 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:14:27,900 INFO : Status: Waiting_To_Download 06 Jan 2020 11:14:47,901 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:14:48,174 INFO : Status: Waiting_To_Download 06 Jan 2020 11:15:08,174 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:15:08,447 INFO : Status: Waiting_To_Download 06 Jan 2020 11:15:28,447 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:15:28,716 INFO : Status: Waiting_To_Download 06 Jan 2020 11:15:48,717 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:15:49,000 INFO : Status: Waiting_To_Download 06 Jan 2020 11:16:09,000 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:16:09,349 INFO : Status: Waiting_To_Download 06 Jan 2020 11:16:29,349 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:16:29,620 INFO : Status: Waiting_To_Download 06 Jan 2020 11:16:49,620 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:16:49,895 INFO : Status: Waiting_To_Download 06 Jan 2020 11:17:09,895 INFO : Checking status of job 5e13823d5beec6001388e35b 06 Jan 2020 11:17:10,211 INFO : Failed to complete task 'org.labkey.lincs.psp.LincsPspTask' 06 Jan 2020 11:17:10,212 ERROR: Optimistic concurrency exception: Row deleted java.sql.SQLException: Optimistic concurrency exception: Row deleted at org.labkey.api.exceptions.OptimisticConflictException.(OptimisticConflictException.java:34) at org.labkey.api.exceptions.OptimisticConflictException.create(OptimisticConflictException.java:49) at org.labkey.api.data.Table.update(Table.java:950) at org.labkey.api.data.Table.update(Table.java:801) at org.labkey.api.data.Table.update(Table.java:793) at org.labkey.lincs.LincsManager.updateLincsPspJob(LincsManager.java:157) at org.labkey.lincs.psp.LincsPspUtil.updateJobStatus(LincsPspUtil.java:291) at org.labkey.lincs.psp.LincsPspTask.postToPsp(LincsPspTask.java:109) at org.labkey.lincs.psp.LincsPspTask.run(LincsPspTask.java:37) at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:795) at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1026) at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:567) at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312) at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259) at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193) at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47) at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470) at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865) at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39) at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277) at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244) at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483) at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675) at java.base/java.lang.Thread.run(Thread.java:835)