flyway errors

[giserzhangwl]

Successfully validated 188 migrations (execution time 00:00.942s)
Executing SQL callback: beforeMigrate
Creating Schema History table: lims.flyway_schema_history
Current version of schema lims: << Empty Schema >>
WARNING: outOfOrder mode is active. Migration of schema lims may not be reproducible.
Migrating schema lims to version 0001 - base schema
Migrating schema lims to version 0002 - miso type data
Migrating schema lims to version 0003 - change logs
Migrating schema lims to version 0004 - boxes
Migrating schema lims to version 0005 - library low quality
Migrating schema lims to version 0009 - drop old pool
Migrating schema lims to version 0010 - sample hierarchy
Migrating schema lims to version 0011 - kit descriptor description
Migrating schema lims to version 0012 - identity unique external name
Migrating schema lims to version 0013 - illumina wt libtype
Migrating schema lims to version 0014 - reference genome
Migrating schema lims to version 0015 - sequencer details
Migrating schema lims to version 0016 - pool notes
Migrating schema lims to version 0017 - notification user
Migrating schema lims to version 0018 - kit change logs
Migrating schema lims to version 0019 - more platforms
Migrating schema lims to version 0020 - boolean types
Migrating schema lims to version 0021 - targeted resequencing
Migrating schema lims to version 0022 - library design
Migrating schema lims to version 0023 - tag barcode refactor
Migrating schema lims to version 0024 - library design paired
Migrating schema lims to version 0025 - add sex to identity
Migrating schema lims to version 0026 - groupId groupDescription
Migrating schema lims to version 0027 - drop project note
Migrating schema lims to version 0028 - model refactor
Migrating schema lims to version 0029 - innodb
Migrating schema lims to version 0030 - project shortName
Migrating schema lims to version 0031 - libraryDilution lastUpdated
Migrating schema lims to version 0032 - add barcodes
Migrating schema lims to version 0033 - pe pkey
Migrating schema lims to version 0034 - index all the things
Migrating schema lims to version 0035 - add description to pool
Migrating schema lims to version 0036 - change cuts to slides
Migrating schema lims to version 0037 - sampleStock concentration
Migrating schema lims to version 0040 - auto main
Migrating schema lims to version 0050 - auto main
Migrating schema lims to version 0060 - auto site
Migrating schema lims to version 0070 - auto main
Migrating schema lims to version 0080 - auto main
Migrating schema lims to version 0090 - auto main
Migrating schema lims to version 0100 - auto main
Migrating schema lims to version 0110 - auto main
Migrating schema lims to version 0120 - auto main
Migrating schema lims to version 0130 - auto main
Migrating schema lims to version 0140 - auto main
Migrating schema lims to version 0150 - auto main
Migrating schema lims to version 0160 - auto main
Migrating schema lims to version 0170 - auto main
Migrating schema lims to version 0180 - auto main
Migrating schema lims to version 0190 - auto main
Migrating schema lims to version 0200 - auto main
Migrating schema lims to version 0210 - auto main
Migrating schema lims to version 0220 - auto main
Migrating schema lims to version 0230 - auto main
Migrating schema lims to version 0240 - auto main
Migrating schema lims to version 0250 - auto main
Migrating schema lims to version 0251 - StatusXmlToRunTable
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN numCycles int(11) DEFAULT NULL;'
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN imgCycle int(11) DEFAULT NULL;'
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN scoreCycle int(11) DEFAULT NULL;'
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN callCycle int(11) DEFAULT NULL;'
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable getStatusXml
INFO: Get status xml: 'com.mysql.cj.jdbc.ClientPreparedStatement: SELECT s.runName, s.xml FROM Status AS s WHERE s.xml IS NOT NULL'
Feb 06, 2024 12:37:20 AM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable deleteXmlColumnFromStatus
INFO: Dropping xml column: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Status DROP COLUMN xml;'
Migrating schema lims to version 0260 - auto main
Migrating schema lims to version 0270 - auto main
Migrating schema lims to version 0280 - auto main
Migrating schema lims to version 0290 - auto main
Migrating schema lims to version 0300 - auto main
Migrating schema lims to version 0310 - auto main
Migrating schema lims to version 0320 - auto main
Migrating schema lims to version 0330 - auto main
Migrating schema lims to version 0340 - auto main
Migrating schema lims to version 0350 - auto main
Migrating schema lims to version 0360 - auto main
Migrating schema lims to version 0370 - auto main
Migrating schema lims to version 0380 - auto main
Migrating schema lims to version 0390 - auto main
WARNING: DB: No data - zero rows fetched, selected, or processed (SQL State: 02000 - Error Code: 1329)
Migrating schema lims to version 0400 - auto main
Migrating schema lims to version 0410 - auto main
Migrating schema lims to version 0420 - auto main
Migrating schema lims to version 0430 - auto main
Migrating schema lims to version 0440 - auto main
Migrating schema lims to version 0450 - auto main
Migrating schema lims to version 0460 - auto main
Migrating schema lims to version 0470 - auto main
Migrating schema lims to version 0480 - auto main
Migrating schema lims to version 0490 - auto main
Migrating schema lims to version 0500 - auto main
Migrating schema lims to version 0510 - auto main
Migrating schema lims to version 0520 - auto main
Migrating schema lims to version 0530 - auto main
Migrating schema lims to version 0540 - auto main
Migrating schema lims to version 0550 - auto main
Migrating schema lims to version 0560 - auto main
Migrating schema lims to version 0570 - auto main
Migrating schema lims to version 0580 - auto main
Migrating schema lims to version 0590 - auto main
Migrating schema lims to version 0600 - auto main
Migrating schema lims to version 0610 - auto main
Migrating schema lims to version 0611 - Attachments
Feb 06, 2024 12:37:27 AM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: Scanning existing attachments to save in database...
Feb 06, 2024 12:37:27 AM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: scanning directory /storage/miso/files/
Migrating schema lims to version 0620 - auto main
Migrating schema lims to version 0630 - auto main
Migrating schema lims to version 0640 - auto main
Migrating schema lims to version 0650 - auto main
Migrating schema lims to version 0660 - auto main
Migrating schema lims to version 0670 - auto main
Migrating schema lims to version 0680 - auto main
Migrating schema lims to version 0690 - auto main
Migrating schema lims to version 0700 - auto main
Migrating schema lims to version 0710 - auto main
Migrating schema lims to version 0720 - auto main
Migrating schema lims to version 0730 - auto main
Migrating schema lims to version 0740 - auto main
Migrating schema lims to version 0750 - auto main
Migrating schema lims to version 0760 - auto main
Migrating schema lims to version 0770 - auto main
Migrating schema lims to version 0780 - auto main
Migrating schema lims to version 0790 - auto main
Migrating schema lims to version 0800 - auto main
Migrating schema lims to version 0810 - auto main
Migrating schema lims to version 0820 - auto main
Migrating schema lims to version 0830 - auto main
Migrating schema lims to version 0840 - auto main
Migrating schema lims to version 0850 - auto main
Migrating schema lims to version 0860 - auto main
Migrating schema lims to version 0870 - auto main
Migrating schema lims to version 0880 - auto main
Migrating schema lims to version 0890 - auto main
Migrating schema lims to version 0900 - auto main
Migrating schema lims to version 0910 - auto main
Migrating schema lims to version 0920 - auto main
Migrating schema lims to version 0930 - auto main
Migrating schema lims to version 0940 - auto main
Migrating schema lims to version 0950 - auto main
Migrating schema lims to version 0960 - auto main
Migrating schema lims to version 0970 - auto main
Migrating schema lims to version 0980 - auto main
Migrating schema lims to version 0990 - auto main
Migrating schema lims to version 1000 - auto main
Migrating schema lims to version 1010 - auto main
Migrating schema lims to version 1020 - auto main
Migrating schema lims to version 1030 - auto main
Migrating schema lims to version 1040 - auto main
Migrating schema lims to version 1050 - auto main
Migrating schema lims to version 1060 - auto main
Migrating schema lims to version 1070 - auto main
Migrating schema lims to version 1080 - auto main
Migrating schema lims to version 1090 - auto main
Migrating schema lims to version 1100 - auto main
Migrating schema lims to version 1110 - auto main
Migrating schema lims to version 1120 - auto main
Migrating schema lims to version 1130 - auto main
Migrating schema lims to version 1140 - auto main
Migrating schema lims to version 1150 - auto main
Migrating schema lims to version 1160 - auto main
Migrating schema lims to version 1170 - auto main
Migrating schema lims to version 1180 - auto main
Migrating schema lims to version 1190 - auto main
Migrating schema lims to version 1200 - auto main
Migrating schema lims to version 1210 - auto main
Migrating schema lims to version 1220 - auto main
Migrating schema lims to version 1230 - auto main
Migrating schema lims to version 1240 - auto main
Migrating schema lims to version 1250 - auto main
Migrating schema lims to version 1260 - auto main
Migrating schema lims to version 1270 - auto main
Migrating schema lims to version 1280 - auto main
Migrating schema lims to version 1290 - auto main
Migrating schema lims to version 1300 - auto main
Migrating schema lims to version 1310 - auto main
Migrating schema lims to version 1320 - auto main
Migrating schema lims to version 1330 - auto main
Migrating schema lims to version 1340 - auto main
Migrating schema lims to version 1350 - auto main
Migrating schema lims to version 1360 - auto main
Migrating schema lims to version 1370 - auto main
Migrating schema lims to version 1380 - auto main
Migrating schema lims to version 1390 - auto main
Migrating schema lims to version 1400 - auto main
Migrating schema lims to version 1410 - auto main
Migrating schema lims to version 1420 - auto main
Migrating schema lims to version 1430 - auto main
Migrating schema lims to version 1440 - auto main
Migrating schema lims to version 1450 - auto main
Migrating schema lims to version 1460 - auto main
Migrating schema lims to version 1470 - auto main
Migrating schema lims to version 1480 - auto main
Migrating schema lims to version 1490 - auto main
Migrating schema lims to version 1500 - auto main
Migrating schema lims to version 1510 - auto main
Migrating schema lims to version 1520 - auto main
Migrating schema lims to version 1530 - auto main
Migrating schema lims to version 1540 - auto main
Migrating schema lims to version 1550 - auto main
Successfully applied 188 migrations to schema lims (execution time 00:52.873s)
Executing SQL callback: afterMigrate

[giserzhangwl]

[giserzhangwl]

/storage/miso/log/miso_debug.log

2024-02-06 02:00:28 INFO: Checking MISO storage paths...
2024-02-06 02:00:28 INFO: Directory (/storage/miso) exists.
2024-02-06 02:00:28 INFO: Directory (/storage/miso/log) exists.
2024-02-06 02:00:28 INFO: Directory (/storage/miso/temp) exists.
2024-02-06 02:00:28 INFO: Directory (/storage/miso/files) exists.
2024-02-06 02:00:28 INFO: Directory (/storage/miso/files/submission) exists.
2024-02-06 02:00:28 INFO: All storage directories OK
2024-02-06 02:00:28 INFO: Initializing Servlet 'miso'
2024-02-06 02:00:29 INFO: Completed initialization in 39 ms
2024-02-06 02:00:43 WARN: SQL Error: 1054, SQLState: 42S22
2024-02-06 02:00:43 ERROR: Unknown column 'sampleclas2_.defaultSampleTypeId' in 'field list'

[djcooke]

Hello,

Can you describe what's happening here a little more? Does the error occur during startup or when you try to load a page? Does it show an error page? I'm guessing the timestamps are not correct because it looks like the error is at 2:00 and you ran Flyway later at 12:37?

[giserzhangwl]

i change the timestamps，

Flyway Community Edition 5.2.4 by Boxfuse
Database: jdbc:mysql://db:3306/lims (MySQL 8.0)
Successfully validated 188 migrations (execution time 00:00.896s)
Executing SQL callback: beforeMigrate
Creating Schema History table: lims.flyway_schema_history
Current version of schema lims: << Empty Schema >>
WARNING: outOfOrder mode is active. Migration of schema lims may not be reproducible.
Migrating schema lims to version 0001 - base schema
Migrating schema lims to version 0002 - miso type data
Migrating schema lims to version 0003 - change logs
Migrating schema lims to version 0004 - boxes
Migrating schema lims to version 0005 - library low quality
Migrating schema lims to version 0009 - drop old pool
Migrating schema lims to version 0010 - sample hierarchy
Migrating schema lims to version 0011 - kit descriptor description
Migrating schema lims to version 0012 - identity unique external name
Migrating schema lims to version 0013 - illumina wt libtype
Migrating schema lims to version 0014 - reference genome
Migrating schema lims to version 0015 - sequencer details
Migrating schema lims to version 0016 - pool notes
Migrating schema lims to version 0017 - notification user
Migrating schema lims to version 0018 - kit change logs
Migrating schema lims to version 0019 - more platforms
Migrating schema lims to version 0020 - boolean types
Migrating schema lims to version 0021 - targeted resequencing
Migrating schema lims to version 0022 - library design
Migrating schema lims to version 0023 - tag barcode refactor
Migrating schema lims to version 0024 - library design paired
Migrating schema lims to version 0025 - add sex to identity
Migrating schema lims to version 0026 - groupId groupDescription
Migrating schema lims to version 0027 - drop project note
Migrating schema lims to version 0028 - model refactor
Migrating schema lims to version 0029 - innodb
Migrating schema lims to version 0030 - project shortName
Migrating schema lims to version 0031 - libraryDilution lastUpdated
Migrating schema lims to version 0032 - add barcodes
Migrating schema lims to version 0033 - pe pkey
Migrating schema lims to version 0034 - index all the things
Migrating schema lims to version 0035 - add description to pool
Migrating schema lims to version 0036 - change cuts to slides
Migrating schema lims to version 0037 - sampleStock concentration
Migrating schema lims to version 0040 - auto main
Migrating schema lims to version 0050 - auto main
Migrating schema lims to version 0060 - auto site
Migrating schema lims to version 0070 - auto main
Migrating schema lims to version 0080 - auto main
Migrating schema lims to version 0090 - auto main
Migrating schema lims to version 0100 - auto main
Migrating schema lims to version 0110 - auto main
Migrating schema lims to version 0120 - auto main
Migrating schema lims to version 0130 - auto main
Migrating schema lims to version 0140 - auto main
Migrating schema lims to version 0150 - auto main
Migrating schema lims to version 0160 - auto main
Migrating schema lims to version 0170 - auto main
Migrating schema lims to version 0180 - auto main
Migrating schema lims to version 0190 - auto main
Migrating schema lims to version 0200 - auto main
Migrating schema lims to version 0210 - auto main
Migrating schema lims to version 0220 - auto main
Migrating schema lims to version 0230 - auto main
Migrating schema lims to version 0240 - auto main
Migrating schema lims to version 0250 - auto main
Migrating schema lims to version 0251 - StatusXmlToRunTable
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN numCycles int(11) DEFAULT NULL;'
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN imgCycle int(11) DEFAULT NULL;'
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN scoreCycle int(11) DEFAULT NULL;'
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable addStatusColumnsToRun
INFO: Adding column to run: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Run ADD COLUMN callCycle int(11) DEFAULT NULL;'
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable getStatusXml
INFO: Get status xml: 'com.mysql.cj.jdbc.ClientPreparedStatement: SELECT s.runName, s.xml FROM Status AS s WHERE s.xml IS NOT NULL'
Feb 20, 2024 2:10:41 PM uk.ac.bbsrc.tgac.miso.db.migration.V0251__StatusXmlToRunTable deleteXmlColumnFromStatus
INFO: Dropping xml column: 'com.mysql.cj.jdbc.ClientPreparedStatement: ALTER TABLE Status DROP COLUMN xml;'
Migrating schema lims to version 0260 - auto main
Migrating schema lims to version 0270 - auto main
Migrating schema lims to version 0280 - auto main
Migrating schema lims to version 0290 - auto main
Migrating schema lims to version 0300 - auto main
Migrating schema lims to version 0310 - auto main
Migrating schema lims to version 0320 - auto main
Migrating schema lims to version 0330 - auto main
Migrating schema lims to version 0340 - auto main
Migrating schema lims to version 0350 - auto main
Migrating schema lims to version 0360 - auto main
Migrating schema lims to version 0370 - auto main
Migrating schema lims to version 0380 - auto main
Migrating schema lims to version 0390 - auto main
WARNING: DB: No data - zero rows fetched, selected, or processed (SQL State: 02000 - Error Code: 1329)
Migrating schema lims to version 0400 - auto main
Migrating schema lims to version 0410 - auto main
Migrating schema lims to version 0420 - auto main
Migrating schema lims to version 0430 - auto main
Migrating schema lims to version 0440 - auto main
Migrating schema lims to version 0450 - auto main
Migrating schema lims to version 0460 - auto main
Migrating schema lims to version 0470 - auto main
Migrating schema lims to version 0480 - auto main
Migrating schema lims to version 0490 - auto main
Migrating schema lims to version 0500 - auto main
Migrating schema lims to version 0510 - auto main
Migrating schema lims to version 0520 - auto main
Migrating schema lims to version 0530 - auto main
Migrating schema lims to version 0540 - auto main
Migrating schema lims to version 0550 - auto main
Migrating schema lims to version 0560 - auto main
Migrating schema lims to version 0570 - auto main
Migrating schema lims to version 0580 - auto main
Migrating schema lims to version 0590 - auto main
Migrating schema lims to version 0600 - auto main
Migrating schema lims to version 0610 - auto main
Migrating schema lims to version 0611 - Attachments
Feb 20, 2024 2:10:48 PM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: Scanning existing attachments to save in database...
Feb 20, 2024 2:10:48 PM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: scanning directory /storage/miso/files/
Migrating schema lims to version 0620 - auto main
Migrating schema lims to version 0630 - auto main
Migrating schema lims to version 0640 - auto main
Migrating schema lims to version 0650 - auto main
Migrating schema lims to version 0660 - auto main
Migrating schema lims to version 0670 - auto main
Migrating schema lims to version 0680 - auto main
Migrating schema lims to version 0690 - auto main
Migrating schema lims to version 0700 - auto main
Migrating schema lims to version 0710 - auto main
Migrating schema lims to version 0720 - auto main
Migrating schema lims to version 0730 - auto main
Migrating schema lims to version 0740 - auto main
Migrating schema lims to version 0750 - auto main
Migrating schema lims to version 0760 - auto main
Migrating schema lims to version 0770 - auto main
Migrating schema lims to version 0780 - auto main
Migrating schema lims to version 0790 - auto main
Migrating schema lims to version 0800 - auto main
Migrating schema lims to version 0810 - auto main
Migrating schema lims to version 0820 - auto main
Migrating schema lims to version 0830 - auto main
Migrating schema lims to version 0840 - auto main
Migrating schema lims to version 0850 - auto main
Migrating schema lims to version 0860 - auto main
Migrating schema lims to version 0870 - auto main
Migrating schema lims to version 0880 - auto main
Migrating schema lims to version 0890 - auto main
Migrating schema lims to version 0900 - auto main
Migrating schema lims to version 0910 - auto main
Migrating schema lims to version 0920 - auto main
Migrating schema lims to version 0930 - auto main
Migrating schema lims to version 0940 - auto main
Migrating schema lims to version 0950 - auto main
Migrating schema lims to version 0960 - auto main
Migrating schema lims to version 0970 - auto main
Migrating schema lims to version 0980 - auto main
Migrating schema lims to version 0990 - auto main
Migrating schema lims to version 1000 - auto main
Migrating schema lims to version 1010 - auto main
Migrating schema lims to version 1020 - auto main
Migrating schema lims to version 1030 - auto main
Migrating schema lims to version 1040 - auto main
Migrating schema lims to version 1050 - auto main
Migrating schema lims to version 1060 - auto main
Migrating schema lims to version 1070 - auto main
Migrating schema lims to version 1080 - auto main
Migrating schema lims to version 1090 - auto main
Migrating schema lims to version 1100 - auto main
Migrating schema lims to version 1110 - auto main
Migrating schema lims to version 1120 - auto main
Migrating schema lims to version 1130 - auto main
Migrating schema lims to version 1140 - auto main
Migrating schema lims to version 1150 - auto main
Migrating schema lims to version 1160 - auto main
Migrating schema lims to version 1170 - auto main
Migrating schema lims to version 1180 - auto main
Migrating schema lims to version 1190 - auto main
Migrating schema lims to version 1200 - auto main
Migrating schema lims to version 1210 - auto main
Migrating schema lims to version 1220 - auto main
Migrating schema lims to version 1230 - auto main
Migrating schema lims to version 1240 - auto main
Migrating schema lims to version 1250 - auto main
Migrating schema lims to version 1260 - auto main
Migrating schema lims to version 1270 - auto main
Migrating schema lims to version 1280 - auto main
Migrating schema lims to version 1290 - auto main
Migrating schema lims to version 1300 - auto main
Migrating schema lims to version 1310 - auto main
Migrating schema lims to version 1320 - auto main
Migrating schema lims to version 1330 - auto main
Migrating schema lims to version 1340 - auto main
Migrating schema lims to version 1350 - auto main
Migrating schema lims to version 1360 - auto main
Migrating schema lims to version 1370 - auto main
Migrating schema lims to version 1380 - auto main
Migrating schema lims to version 1390 - auto main
Migrating schema lims to version 1400 - auto main
Migrating schema lims to version 1410 - auto main
Migrating schema lims to version 1420 - auto main
Migrating schema lims to version 1430 - auto main
Migrating schema lims to version 1440 - auto main
Migrating schema lims to version 1450 - auto main
Migrating schema lims to version 1460 - auto main
Migrating schema lims to version 1470 - auto main
Migrating schema lims to version 1480 - auto main
Migrating schema lims to version 1490 - auto main
Migrating schema lims to version 1500 - auto main
Migrating schema lims to version 1510 - auto main
Migrating schema lims to version 1520 - auto main
Migrating schema lims to version 1530 - auto main
Migrating schema lims to version 1540 - auto main
Migrating schema lims to version 1550 - auto main
Successfully applied 188 migrations to schema lims (execution time 00:59.749s)
Executing SQL callback: afterMigrate

root@94070f58a909:/usr/local/tomcat# cat /storage/miso/log/miso_debug.log

2024-02-20 14:10:33 INFO: Checking MISO storage paths...
2024-02-20 14:10:33 INFO: Directory (/storage/miso) exists.
2024-02-20 14:10:33 INFO: Directory (/storage/miso/log) exists.
2024-02-20 14:10:33 INFO: Directory (/storage/miso/temp) exists.
2024-02-20 14:10:33 INFO: Directory (/storage/miso/files) exists.
2024-02-20 14:10:33 INFO: Directory (/storage/miso/files/submission) exists.
2024-02-20 14:10:33 INFO: All storage directories OK
2024-02-20 14:10:34 INFO: Initializing Servlet 'miso'
2024-02-20 14:10:34 INFO: Completed initialization in 38 ms
2024-02-20 14:10:48 WARN: SQL Error: 1054, SQLState: 42S22
2024-02-20 14:10:48 ERROR: Unknown column 'sampleclas2_.defaultSampleTypeId' in 'field list'

[giserzhangwl]

[djcooke]

This seems to indicate that Flyway was still running when the error occurred:

Migrating schema lims to version 0611 - Attachments
Feb 20, 2024 2:10:48 PM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: Scanning existing attachments to save in database...
Feb 20, 2024 2:10:48 PM uk.ac.bbsrc.tgac.miso.db.migration.V0611__Attachments migrate
INFO: scanning directory /storage/miso/files/
Migrating schema lims to version 0620 - auto main
...

2024-02-20 14:10:48 ERROR: Unknown column 'sampleclas2_.defaultSampleTypeId' in 'field list'

The Flyway migration needs to be completely finished before you use MISO. Does the same error occur if you try to reload the page now?

[giserzhangwl]

@djcooke

[djcooke]

Did this error occur again after the Flyway migrate was completely finished? Is there anything else in miso_debug.log, or just the same error again?

The defaultSampleTypeId field is added in migration V1150__auto_main.sql, so the error you posted seems to indicate that that migration was not applied, but your Flyway log indicates that it was. Please also double-check in your ROOT.xml that MISO is using the same database that Flyway migrate completed successfully on.