16 Jun 2021 02:01:59,888 INFO : Starting to run task 'org.labkey.study.pipeline.StudyReloadSourceTask' at location 'webserver'
16 Jun 2021 02:01:59,895 INFO : Starting REDCap export
16 Jun 2021 02:02:00,923 INFO : Creating study archive
16 Jun 2021 02:02:00,956 INFO : Writing dataset metadata
16 Jun 2021 02:02:01,089 INFO : Creating column lookups
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: demographics row ignored.
16 Jun 2021 02:02:01,829 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: emergency_contact_info row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,830 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: baseline_lab_data row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,831 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: visit_blood_workup row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_data row ignored.
16 Jun 2021 02:02:01,832 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,833 WARN : Unable to locate subject id field: first_name for dataset: completion_project_questionnaire row ignored.
16 Jun 2021 02:02:01,835 INFO : Finished creating study archive
16 Jun 2021 02:02:01,835 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyReloadSourceTask'
16 Jun 2021 02:02:01,893 INFO : Starting to run task 'org.labkey.study.importer.StudyImportInitialTask' at location 'webserver'
16 Jun 2021 02:02:01,910 INFO : Reloading study from study.xml
16 Jun 2021 02:02:01,921 INFO : Loading top-level study properties (label, start/end date, description, etc.)
16 Jun 2021 02:02:02,323 INFO : Done importing top-level study properties (label, start/end date, description, etc.)
16 Jun 2021 02:02:02,356 INFO : Loading datasets manifest from datasets_manifest.xml
16 Jun 2021 02:02:02,360 INFO : Loading dataset schema from datasets_metadata.xml
16 Jun 2021 02:02:03,119 INFO : Successfully completed task 'org.labkey.study.importer.StudyImportInitialTask'
16 Jun 2021 02:02:03,166 INFO : Starting to run task 'org.labkey.study.pipeline.StudyImportDatasetTask' at location 'webserver'
16 Jun 2021 02:02:03,174 INFO : Start batch RedCap Integration.dataset
16 Jun 2021 02:02:03,216 INFO : demographics: Starting import from dataset001.tsv
16 Jun 2021 02:02:03,707 INFO : demographics: Processed 5 rows from dataset001.tsv
16 Jun 2021 02:02:03,708 INFO : demographics: Deleted 5 rows
16 Jun 2021 02:02:03,708 INFO : demographics: Merged 5 rows
16 Jun 2021 02:02:03,752 INFO : emergency_contact_info: Starting import from dataset002.tsv
16 Jun 2021 02:02:03,993 INFO : emergency_contact_info: Processed 5 rows from dataset002.tsv
16 Jun 2021 02:02:03,994 INFO : emergency_contact_info: Deleted 5 rows
16 Jun 2021 02:02:03,994 INFO : emergency_contact_info: Merged 5 rows
16 Jun 2021 02:02:04,021 INFO : baseline_lab_data: Starting import from dataset003.tsv
16 Jun 2021 02:02:04,220 INFO : baseline_lab_data: Processed 5 rows from dataset003.tsv
16 Jun 2021 02:02:04,220 INFO : baseline_lab_data: Deleted 5 rows
16 Jun 2021 02:02:04,220 INFO : baseline_lab_data: Merged 5 rows
16 Jun 2021 02:02:04,252 INFO : visit_blood_workup: Starting import from dataset004.tsv
16 Jun 2021 02:02:04,340 INFO : completion_data: Starting import from dataset005.tsv
16 Jun 2021 02:02:04,407 INFO : completion_project_questionnaire: Starting import from dataset006.tsv
16 Jun 2021 02:02:04,459 INFO : Finish batch RedCap Integration.dataset
16 Jun 2021 02:02:04,463 INFO : Updating participant visits
16 Jun 2021 02:02:04,463 INFO : Updating participants
16 Jun 2021 02:02:04,468 INFO : Updating participant visit table
16 Jun 2021 02:02:04,537 INFO : Updating visit table
16 Jun 2021 02:02:04,540 INFO : Updating cohorts
16 Jun 2021 02:02:04,540 INFO : Clearing participant visit caches
16 Jun 2021 02:02:04,542 INFO : Finished updating participants
16 Jun 2021 02:02:04,544 INFO : Successfully completed task 'org.labkey.study.pipeline.StudyImportDatasetTask'
16 Jun 2021 02:02:04,583 INFO : Starting to run task 'org.labkey.api.specimen.pipeline.StudyImportSpecimenTask' at location 'webserver'
16 Jun 2021 02:02:04,585 INFO : Successfully completed task 'org.labkey.api.specimen.pipeline.StudyImportSpecimenTask'
16 Jun 2021 02:02:04,638 INFO : Starting to run task 'org.labkey.study.importer.StudyImportFinalTask' at location 'webserver'
16 Jun 2021 02:02:04,665 INFO : Loading dataset cohort assignments
16 Jun 2021 02:02:04,666 INFO : Done importing dataset cohort assignments
16 Jun 2021 02:02:04,704 INFO : Loading lists
16 Jun 2021 02:02:04,714 INFO : Truncating list: vbw8
16 Jun 2021 02:26:42,040 INFO : Recreating list: vbw8
16 Jun 2021 02:26:42,308 INFO : Truncating list: cpq13
16 Jun 2021 02:26:42,453 INFO : Recreating list: cpq13
16 Jun 2021 02:26:42,571 INFO : Truncating list: sex
16 Jun 2021 02:26:42,665 INFO : Recreating list: sex
16 Jun 2021 02:26:42,747 INFO : Truncating list: withdraw_reason
16 Jun 2021 02:26:42,865 INFO : Recreating list: withdraw_reason
16 Jun 2021 02:26:42,947 INFO : Truncating list: cpq6
16 Jun 2021 02:26:43,040 INFO : Recreating list: cpq6
16 Jun 2021 02:26:43,124 INFO : Truncating list: vbw9
16 Jun 2021 02:26:43,217 INFO : Recreating list: vbw9
16 Jun 2021 02:26:43,300 INFO : Truncating list: cpq8
16 Jun 2021 02:26:43,384 INFO : Recreating list: cpq8
16 Jun 2021 02:26:43,464 INFO : Truncating list: cpq10
16 Jun 2021 02:26:43,552 INFO : Recreating list: cpq10
16 Jun 2021 02:26:43,635 INFO : Truncating list: vbw6
16 Jun 2021 02:26:43,739 INFO : Recreating list: vbw6
16 Jun 2021 02:26:43,846 INFO : Truncating list: cpq11
16 Jun 2021 02:26:43,955 INFO : Recreating list: cpq11
16 Jun 2021 02:26:44,044 INFO : Truncating list: vbw7
16 Jun 2021 02:26:44,138 INFO : Recreating list: vbw7
16 Jun 2021 02:26:44,275 INFO : Merged 5 row(s) into list: withdraw_reason
16 Jun 2021 02:26:44,320 INFO : Merged 3 row(s) into list: cpq13
16 Jun 2021 02:26:44,363 INFO : Merged 6 row(s) into list: cpq11
16 Jun 2021 02:26:44,404 INFO : Merged 4 row(s) into list: cpq10
16 Jun 2021 02:26:44,445 INFO : Merged 2 row(s) into list: sex
16 Jun 2021 02:26:44,485 INFO : Merged 2 row(s) into list: vbw9
16 Jun 2021 02:26:44,528 INFO : Merged 3 row(s) into list: cpq8
16 Jun 2021 02:26:44,569 INFO : Merged 3 row(s) into list: vbw8
16 Jun 2021 02:26:44,612 INFO : Merged 4 row(s) into list: vbw7
16 Jun 2021 02:26:44,654 INFO : Merged 5 row(s) into list: cpq6
16 Jun 2021 02:26:44,694 INFO : Merged 2 row(s) into list: vbw6
16 Jun 2021 02:26:44,698 INFO : 11 lists imported successfully
16 Jun 2021 02:26:44,698 INFO : Done importing lists
16 Jun 2021 02:26:44,711 INFO : Post-processing queries
16 Jun 2021 02:26:44,711 INFO : Skipping query validation.
16 Jun 2021 02:26:44,711 INFO : Done post-processing queries
16 Jun 2021 02:26:44,730 INFO : Successfully completed task 'org.labkey.study.importer.StudyImportFinalTask'