29 Feb 2024 16:04:05,950 DEBUG: Resetting Job ID: d423ce63-b98c-103c-bde6-b73401f77cb0
29 Feb 2024 16:04:06,074 INFO : Starting to run task 'org.labkey.pipeline.importer.FolderImportTask' at location 'webserver'
29 Feb 2024 16:04:06,334 DEBUG: [/home/Demos/HIV Study Tutorial] Importing folder properties from: /labkey/labkey/files/home/Demos/HIV Study Tutorial/@files/.unzip
29 Feb 2024 16:04:06,340 DEBUG: [/home/Demos/HIV Study Tutorial] Default date format: yyyy-MM-dd
29 Feb 2024 16:04:06,357 DEBUG: [/home/Demos/HIV Study Tutorial] Default date-time format: yyyy-MM-dd
29 Feb 2024 16:04:06,391 INFO : Loading missing value indicators
29 Feb 2024 16:04:06,429 INFO : Done importing missing value indicators
29 Feb 2024 16:04:06,448 INFO : Loading queries
29 Feb 2024 16:04:06,627 WARN : Importing: metadata "StudyData.query.xml" for "study.StudyData": Creating metadata xml override for table that doesn't exist
29 Feb 2024 16:04:06,644 INFO : 5 queries imported
29 Feb 2024 16:04:06,658 INFO : Done importing queries
29 Feb 2024 16:04:06,669 INFO : Loading grid views
29 Feb 2024 16:04:06,816 INFO : 9 custom views imported
29 Feb 2024 16:04:06,824 INFO : Done importing grid views
29 Feb 2024 16:04:06,874 INFO : Loading view categories
29 Feb 2024 16:04:06,980 INFO : Done importing view categories
29 Feb 2024 16:04:06,992 INFO : Loading etl definitions
29 Feb 2024 16:04:07,009 INFO : Starting Data Class Importer
29 Feb 2024 16:04:07,021 INFO : No types XAR file to process.
29 Feb 2024 16:04:07,027 INFO : Finished Data Class Importer
29 Feb 2024 16:04:07,034 INFO : Starting to copy files
29 Feb 2024 16:04:07,224 INFO : Copied 9 files
29 Feb 2024 16:04:07,231 INFO : Ensuring exp.data rows exist for imported files
29 Feb 2024 16:04:09,248 INFO : Loading lists
29 Feb 2024 16:04:09,304 INFO : Recreating list: Instruments
29 Feb 2024 16:04:10,100 INFO : Recreating list: Countries
29 Feb 2024 16:04:10,365 INFO : Recreating list: ARVType
29 Feb 2024 16:04:10,628 INFO : Recreating list: Languages
29 Feb 2024 16:04:11,115 INFO : Merged 5 row(s) into list: Countries
29 Feb 2024 16:04:11,186 INFO : Merged 6 row(s) into list: ARVType
29 Feb 2024 16:04:11,232 INFO : Merged 6 row(s) into list: Languages
29 Feb 2024 16:04:11,243 INFO : 4 lists imported successfully
29 Feb 2024 16:04:11,250 INFO : Done importing lists
29 Feb 2024 16:04:11,262 INFO : Loading study
29 Feb 2024 16:04:11,341 INFO : Loading study from study.xml
29 Feb 2024 16:04:11,348 INFO : Creating study
29 Feb 2024 16:04:15,961 INFO : Loading top-level study properties (label, start/end date, description, etc.)
29 Feb 2024 16:04:16,096 INFO : Done importing top-level study properties (label, start/end date, description, etc.)
29 Feb 2024 16:04:16,334 INFO : Loading visit map from visit_map.xml
29 Feb 2024 16:04:16,618 INFO : Done importing visit map
29 Feb 2024 16:04:16,651 INFO : Loading assay schedule tables
29 Feb 2024 16:04:16,803 INFO : Done importing assay schedule tables
29 Feb 2024 16:04:16,834 INFO : Loading datasets manifest from datasets_manifest.xml
29 Feb 2024 16:04:16,866 INFO : Loading dataset schema from datasets_metadata.xml
29 Feb 2024 16:04:21,653 INFO : Start batch Example.dataset
29 Feb 2024 16:04:21,698 INFO : Demographics: Starting import from dataset5001.tsv
29 Feb 2024 16:04:21,837 INFO : Demographics: Processed 12 rows from dataset5001.tsv
29 Feb 2024 16:04:21,843 INFO : Demographics: Merged 12 rows
29 Feb 2024 16:04:21,875 INFO : MedicalHistory: Starting import from dataset5002.tsv
29 Feb 2024 16:04:21,937 INFO : MedicalHistory: Processed 12 rows from dataset5002.tsv
29 Feb 2024 16:04:21,943 INFO : MedicalHistory: Merged 12 rows
29 Feb 2024 16:04:21,981 INFO : PhysicalExam: Starting import from dataset5003.tsv
29 Feb 2024 16:04:22,248 INFO : PhysicalExam: Processed 300 rows from dataset5003.tsv
29 Feb 2024 16:04:22,254 INFO : PhysicalExam: Merged 300 rows
29 Feb 2024 16:04:22,282 INFO : LabResults: Starting import from dataset5004.tsv
29 Feb 2024 16:04:22,533 INFO : LabResults: Processed 300 rows from dataset5004.tsv
29 Feb 2024 16:04:22,540 INFO : LabResults: Merged 300 rows
29 Feb 2024 16:04:22,596 INFO : ViralLoad_PCR: Starting import from dataset5005.tsv
29 Feb 2024 16:04:22,804 INFO : ViralLoad_PCR: Processed 300 rows from dataset5005.tsv
29 Feb 2024 16:04:22,810 INFO : ViralLoad_PCR: Merged 300 rows
29 Feb 2024 16:04:22,839 INFO : ViralLoad_NASBA: Starting import from dataset5006.tsv
29 Feb 2024 16:04:23,048 INFO : ViralLoad_NASBA: Processed 300 rows from dataset5006.tsv
29 Feb 2024 16:04:23,056 INFO : ViralLoad_NASBA: Merged 300 rows
29 Feb 2024 16:04:23,063 INFO : Finish batch Example.dataset
29 Feb 2024 16:04:23,080 INFO : Updating study-wide subject/visit information...
29 Feb 2024 16:04:23,086 INFO : Updating participants
29 Feb 2024 16:04:23,128 INFO : Updating participant visit table
29 Feb 2024 16:04:23,245 INFO : Update visit row IDs
29 Feb 2024 16:04:23,294 INFO : Updating visit table
29 Feb 2024 16:04:23,300 INFO : Select distinct sequence numbers from participant visit table
29 Feb 2024 16:04:23,314 INFO : Updating cohorts
29 Feb 2024 16:04:23,320 INFO : Clearing participant visit caches
29 Feb 2024 16:04:23,330 INFO : Subject/visit update complete.
29 Feb 2024 16:04:23,369 INFO : Loading cohort settings
29 Feb 2024 16:04:23,382 INFO : Importing cohort settings from /cohorts.xml
29 Feb 2024 16:04:23,499 INFO : Applying automatic cohort settings
29 Feb 2024 16:04:23,596 INFO : Done importing cohort settings
29 Feb 2024 16:04:23,608 INFO : Loading visit map cohort assignments
29 Feb 2024 16:04:23,664 INFO : Done importing visit map cohort assignments
29 Feb 2024 16:04:23,683 INFO : Loading dataset cohort assignments
29 Feb 2024 16:04:23,691 INFO : Done importing dataset cohort assignments
29 Feb 2024 16:04:23,711 INFO : Loading Participant Comment Settings
29 Feb 2024 16:04:23,719 INFO : Done importing Participant Comment Settings
29 Feb 2024 16:04:23,746 INFO : Loading participant groups
29 Feb 2024 16:04:23,906 INFO : Done importing participant groups
29 Feb 2024 16:04:23,924 INFO : Loading custom participant view
29 Feb 2024 16:04:23,941 INFO : Done importing custom participant view
29 Feb 2024 16:04:23,961 INFO : Done importing study
29 Feb 2024 16:04:23,970 INFO : Loading QC states
29 Feb 2024 16:04:24,104 INFO : Done importing QC states
29 Feb 2024 16:04:24,123 INFO : Starting Sample Type Importer
29 Feb 2024 16:04:24,131 INFO : No types XAR file to process.
29 Feb 2024 16:04:24,137 INFO : Finished Sample Type Importer
29 Feb 2024 16:04:24,146 INFO : xar directory not found in folder /home/Demos/HIV Study Tutorial
29 Feb 2024 16:04:24,160 INFO : Loading reports and charts
29 Feb 2024 16:04:24,911 INFO : 5 reports imported
29 Feb 2024 16:04:24,917 INFO : Done importing reports and charts
29 Feb 2024 16:04:24,924 INFO : Loading File Browser config
29 Feb 2024 16:04:24,936 INFO : Done importing File Browser config
29 Feb 2024 16:04:24,948 INFO : Starting Sample Status Data import
29 Feb 2024 16:04:24,954 INFO : No sample types XAR file to process.
29 Feb 2024 16:04:24,960 INFO : Finished importing Sample Status Data
29 Feb 2024 16:04:25,032 INFO : Post-processing queries
29 Feb 2024 16:04:25,055 INFO : Validating all queries in all schemas...
29 Feb 2024 16:04:28,538 INFO : Finished validating queries.
29 Feb 2024 16:04:28,544 INFO : Finished validating queries: All 177 passed validation.
29 Feb 2024 16:04:28,549 INFO : Done post-processing queries
29 Feb 2024 16:04:29,096 INFO : Successfully completed task 'org.labkey.pipeline.importer.FolderImportTask'