Timeline



Feb 21, 2023:

9:05 AM Ticket #1464 (New pipeline for DNA whole genome sequencing) updated by Nicklas Nordborg
In 7054: […]
9:05 AM Changeset [7054] by Nicklas Nordborg
References #1464: New pipeline for DNA whole genome sequencing Added …
8:38 AM Ticket #1465 (JSON and raw FASTQ files that are submitted from external lab should ...) updated by Nicklas Nordborg
In 7053: […]
8:38 AM Changeset [7053] by Nicklas Nordborg
References #1465: JSON and raw FASTQ files that are submitted from …
8:33 AM Ticket #1464 (New pipeline for DNA whole genome sequencing) updated by Nicklas Nordborg
In 7052: […]
8:33 AM Changeset [7052] by Nicklas Nordborg
References #1464: New pipeline for DNA whole genome sequencing …

Feb 17, 2023:

4:04 PM Ticket #1465 (JSON and raw FASTQ files that are submitted from external lab should ...) updated by Nicklas Nordborg
In 7051: […]
4:04 PM Changeset [7051] by Nicklas Nordborg
References #1465: JSON and raw FASTQ files that are submitted from …
8:40 AM Ticket #1465 (JSON and raw FASTQ files that are submitted from external lab should ...) updated by Nicklas Nordborg
In 7050: […]
8:40 AM Changeset [7050] by Nicklas Nordborg
References #1465: JSON and raw FASTQ files that are submitted from …

Feb 15, 2023:

11:23 AM Ticket #1465 (JSON and raw FASTQ files that are submitted from external lab should ...) updated by Nicklas Nordborg
In 7049: […]
11:23 AM Changeset [7049] by Nicklas Nordborg
References #1465: JSON and raw FASTQ files that are submitted from …
8:45 AM Ticket #1464 (New pipeline for DNA whole genome sequencing) updated by Nicklas Nordborg
In 7048: […]
8:45 AM Changeset [7048] by Nicklas Nordborg
References #1464: New pipeline for DNA whole genome sequencing …

Feb 14, 2023:

1:49 PM Ticket #1465 (JSON and raw FASTQ files that are submitted from external lab should ...) created by Nicklas Nordborg
Currently, the JSON file is linked with the Specimen item as remote …
1:28 PM Ticket #1464 (New pipeline for DNA whole genome sequencing) updated by Nicklas Nordborg
In 7047: […]
1:28 PM Changeset [7047] by Nicklas Nordborg
References #1464: New pipeline for DNA whole genome sequencing …
11:08 AM Ticket #1464 (New pipeline for DNA whole genome sequencing) updated by Nicklas Nordborg
In 7046: […]
11:08 AM Changeset [7046] by Nicklas Nordborg
References #1464: New pipeline for DNA whole genome sequencing Added …
9:24 AM Ticket #1464 (New pipeline for DNA whole genome sequencing) created by Nicklas Nordborg
Typically samples are paired with one blood DNA sample and one (or …

Feb 13, 2023:

1:00 PM Changeset [7045] by Nicklas Nordborg
Changes for future release Reggie 4.45
12:59 PM Milestone Reggie v4.44 completed
See Reggie extension page for more information.
12:58 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.44 (diff)
12:57 PM reggie-4.44.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.44
12:55 PM Changeset [7044] by Nicklas Nordborg
Tagging Reggie 4.44
12:54 PM Changeset [7043] by Nicklas Nordborg
Preparing to release Reggie 4.44
12:02 PM Tickets #1453,​1460 batch updated by Nicklas Nordborg
fixed
12:02 PM Ticket #1401 (Update to Open Grid/Job scheduler 1.9) updated by Nicklas Nordborg
Summary changed
12:01 PM Changeset [7042] by Nicklas Nordborg
Updated to Job Scheduler 1.9
12:00 PM Changeset [7041] by Nicklas Nordborg
Updated to Job Scheduler 1.9
11:56 AM Changeset [7040] by Nicklas Nordborg
Changes for future version Job scheduler 1.10
11:54 AM Milestone Job scheduler extension v1.9 completed
See the Job scheduler extension page for …
11:54 AM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.9 (diff)
11:52 AM opengrid-1.9.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job scheduler 1.9
11:49 AM Changeset [7039] by Nicklas Nordborg
Tagging Job Scheduler extension v1.9
11:49 AM Changeset [7038] by Nicklas Nordborg
Preparing to release Job Scheduler extension v1.9
8:33 AM Ticket #1460 (Add support for BloodDNA in the Outtake wizards) updated by Nicklas Nordborg
In 7037: […]
8:33 AM Changeset [7037] by Nicklas Nordborg
References #1460: Add support for BloodDNA in the Outtake wizards …

Feb 10, 2023:

2:16 PM Ticket #1456 (SimpleDateFormat implementation is not thread-safe) closed by Nicklas Nordborg
fixed: In 7036: […]
2:16 PM Changeset [7036] by Nicklas Nordborg
Fixes #1456: SimpleDateFormat implementation is not thread-safe …
12:54 PM Ticket #1453 (Make the release exporter multi-threaded) updated by Nicklas Nordborg
In 7035: […]
12:54 PM Changeset [7035] by Nicklas Nordborg
References #1453: Make the release exporter multi-threaded Changed …
9:31 AM Ticket #1453 (Make the release exporter multi-threaded) updated by Nicklas Nordborg
In 7034: […]
9:31 AM Changeset [7034] by Nicklas Nordborg
References #1453: Make the release exporter multi-threaded Fixed …
8:55 AM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) closed by Nicklas Nordborg
fixed
8:46 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) closed by Nicklas Nordborg
fixed
8:46 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) updated by Nicklas Nordborg
In [7033]: Fixes #1461: Temporarily disable importing of sampling and …
8:43 AM Ticket #1463 (Add activity log entries when importing JSON files) updated by Nicklas Nordborg
In 7033: […] EDIT This change is for ticket …
8:43 AM Changeset [7033] by Nicklas Nordborg
Fixes #1463: Temporarily disable importing of sampling and RNA later …
8:39 AM Ticket #1463 (Add activity log entries when importing JSON files) closed by Nicklas Nordborg
fixed: In 7032: […]
8:39 AM Changeset [7032] by Nicklas Nordborg
Fixes #1463: Add activity log entries when importing JSON files

Feb 9, 2023:

2:49 PM Ticket #1457 (Increase the timeout for "Picard CheckIlluminaDirectory") closed by Nicklas Nordborg
fixed: In 7031: […]
2:49 PM Changeset [7031] by Nicklas Nordborg
Fixes #1457: Increase the timeout for "Picard CheckIlluminaDirectory" …
2:16 PM Ticket #1457 (Increase the timeout for "Picard CheckIlluminaDirectory") updated by Nicklas Nordborg
In 7030: […]
2:16 PM Changeset [7030] by Nicklas Nordborg
References #1457: Increase the timeout for "Picard …
2:07 PM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
In 7029: […]
2:07 PM Changeset [7029] by Nicklas Nordborg
References #1455: SimpleDateFormat implementation is not thread-safe …
2:05 PM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) closed by Nicklas Nordborg
fixed: We use the SimpleDateFormat class only via the DateFormatter
1:19 PM Ticket #1458 (The timeout when executing a command seems to not work) closed by Nicklas Nordborg
fixed: In 7028: […]
1:19 PM Changeset [7028] by Nicklas Nordborg
Fixes #1458: The timeout when executing a command seems to not work …
11:32 AM Ticket #1463 (Add activity log entries when importing JSON files) created by Nicklas Nordborg
I noticed that this event was never included in the activity log, but …
11:30 AM Ticket #1462 (Re-enable importing of sampling and RNA later date in the JSON importer) created by Nicklas Nordborg
Temporarily disabled in #1461.
11:29 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) created by Nicklas Nordborg
The latest information we have is that the values in the JSON files …
11:26 AM Ticket #1460 (Add support for BloodDNA in the Outtake wizards) created by Nicklas Nordborg
BloodDNA items are typically registered manually, but we should assume …
9:44 AM Ticket #1459 (Update to SSHj 0.35) closed by Nicklas Nordborg
fixed: In 7027: […]
9:44 AM Changeset [7027] by Nicklas Nordborg
Fixes #1459: Update to SSHj 0.35
9:30 AM Ticket #1459 (Update to SSHj 0.35) created by Nicklas Nordborg
9:26 AM Ticket #1458 (The timeout when executing a command seems to not work) created by Nicklas Nordborg
The AbstractSession.execute() method has a timeout parameter which …

Feb 8, 2023:

2:36 PM Ticket #1457 (Increase the timeout for "Picard CheckIlluminaDirectory") created by Nicklas Nordborg
This is run by auto-confirmer when a sequencing has been completed and …
2:07 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
In 7026: […]
2:07 PM Changeset [7026] by Nicklas Nordborg
References #1454: SimpleDateFormat implementation is not thread-safe …
2:03 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
In 7025: […]
2:03 PM Changeset [7025] by Nicklas Nordborg
References #1454: SimpleDateFormat implementation is not thread-safe …
8:58 AM Ticket #1456 (SimpleDateFormat implementation is not thread-safe) created by Nicklas Nordborg
See #1454. We use the SimpleDateFormat class in some places.
8:57 AM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) created by Nicklas Nordborg
See #1454. We use the SimpleDateFormat class in some places.

Feb 7, 2023:

2:23 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
In 7024: […]
2:23 PM Changeset [7024] by Nicklas Nordborg
References #1454: SimpleDateFormat implementation is not thread-safe …
1:39 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by Nicklas Nordborg
In 7023: […]
1:39 PM Changeset [7023] by Nicklas Nordborg
References #1454: SimpleDateFormat implementation is not thread-safe …
11:51 AM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) created by Nicklas Nordborg
We use the java.text.SimpleDateFormat implementation to format and …

Feb 6, 2023:

2:45 PM Ticket #1453 (Make the release exporter multi-threaded) updated by Nicklas Nordborg
In 7022: […]
2:45 PM Changeset [7022] by Nicklas Nordborg
References #1453: Make the release exporter multi-threaded Use 1/3 of …

Feb 1, 2023:

1:38 PM Ticket #1453 (Make the release exporter multi-threaded) created by Nicklas Nordborg
I think the performance of the release exporter can be improved by …

Jan 30, 2023:

2:06 PM Tickets #1452,​1399 batch updated by Nicklas Nordborg
fixed
2:06 PM Tickets #1393,​1451 batch updated by Nicklas Nordborg
fixed

Jan 27, 2023:

2:15 PM Ticket #1399 (The Release importer should handle null values for annotations) updated by Nicklas Nordborg
In 7021: […]
2:15 PM Changeset [7021] by Nicklas Nordborg
References #1399: The Release importer should handle null values for …
11:57 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by Nicklas Nordborg
In 7020: […]
11:57 AM Changeset [7020] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data …
9:33 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by Nicklas Nordborg
In 7019: […]
9:33 AM Changeset [7019] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data …
9:03 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7018: […]
9:03 AM Changeset [7018] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data …
8:44 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7017: […]
8:44 AM Changeset [7017] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data …

Jan 26, 2023:

2:23 PM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7016: […]
2:23 PM Changeset [7016] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data The …
1:49 PM Ticket #1452 (Release importer changes due to new subtypes from Reggie) updated by Nicklas Nordborg
In 7015: […]
1:48 PM Changeset [7015] by Nicklas Nordborg
References #1452: Release importer changes due to new subtypes from …
1:24 PM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7014: […]
1:24 PM Changeset [7014] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data …
11:33 AM Changeset [7013] by Nicklas Nordborg
11:13 AM Ticket #1399 (The Release importer should handle null values for annotations) updated by Nicklas Nordborg
In 7012: […]
11:13 AM Changeset [7012] by Nicklas Nordborg
References #1399: The Release importer should handle null values for …

Jan 25, 2023:

2:15 PM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7011: […]
2:15 PM Changeset [7011] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data …
1:27 PM Ticket #1451 (Release exporter changes due to Methylation data) updated by Nicklas Nordborg
In 7010: […]
1:27 PM Changeset [7010] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data …
9:52 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by Nicklas Nordborg
In 7009: […]
9:52 AM Changeset [7009] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data A …
9:45 AM Ticket #1452 (Release importer changes due to new subtypes from Reggie) updated by Nicklas Nordborg
In 7008: […]
9:45 AM Changeset [7008] by Nicklas Nordborg
References #1452: Release importer changes due to new subtypes from …
8:45 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by Nicklas Nordborg
In 7007: […]
8:45 AM Changeset [7007] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data …

Jan 24, 2023:

2:34 PM Ticket #1451 (Release exporter changes due to Methylation data) updated by Nicklas Nordborg
In 7006: […]
2:34 PM Changeset [7006] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data …
2:32 PM Tickets #1393,​1451 batch updated by Nicklas Nordborg
Status, Milestone changed
2:09 PM Ticket #1452 (Release importer changes due to new subtypes from Reggie) created by Nicklas Nordborg
The next data release from Reggie will probably include new subtypes …
11:55 AM Ticket #1451 (Release exporter changes due to Methylation data) created by Nicklas Nordborg
In tickets #1418 and #1419, we added data from Methylation EPIC chips …

Jan 23, 2023:

1:20 PM Ticket #1445 (Add support for submitting jobs to a specific partition/queue) updated by Nicklas Nordborg
Milestone changed
Milestone renamed
9:00 AM Changeset [7005] by Nicklas Nordborg
Changes for future release Reggie 4.44
8:59 AM Milestone Reggie v4.43 completed
See Reggie extension page for more information.
8:58 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.43 (diff)
8:57 AM reggie-4.43.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.43
8:56 AM Changeset [7004] by Nicklas Nordborg
Tagging Reggie 4.43
8:56 AM Changeset [7003] by Nicklas Nordborg
Preparing to release Reggie 4.43
8:52 AM Ticket #1446 (Add an annotation for extra PAD values) closed by Nicklas Nordborg
fixed
8:51 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 7002: […]
8:51 AM Changeset [7002] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Fixed a …
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