Timeline



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 …

Jan 20, 2023:

2:59 PM Ticket #1450 (Hisat/2023 alignments should not show up in the Genotype QC wizards) closed by Nicklas Nordborg
fixed: In 7001: […]
2:59 PM Changeset [7001] by Nicklas Nordborg
Fixes #1450: Hisat/2023 alignments should now show up in the Genotype …
1:40 PM Ticket #1450 (Hisat/2023 alignments should not show up in the Genotype QC wizards) created by Nicklas Nordborg
The Hisat/2023 alignment are normally disabled for use with the …
1:34 PM Ticket #1449 (The JSON import wizard should not reserve specimen names in advance) closed by Nicklas Nordborg
fixed: In 7000: […]
1:34 PM Changeset [7000] by Nicklas Nordborg
Fixes #1449: The JSON import wizard should not reserve specimen names …
1:30 PM Ticket #1449 (The JSON import wizard should not reserve specimen names in advance) created by Nicklas Nordborg
When the import wizard can't find an existing NoSpecimen item to link …
1:14 PM Ticket #1448 (The "ReferenceDate" annotation should not be used as a timepoint for ...) closed by Nicklas Nordborg
fixed: In 6999: […]
1:14 PM Changeset [6999] by Nicklas Nordborg
Fixes #1448: The "ReferenceDate" annotation should not be used as a …
1:05 PM Ticket #1448 (The "ReferenceDate" annotation should not be used as a timepoint for ...) created by Nicklas Nordborg
The ReferenceDate is used in cases when there is no registered …
1:02 PM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6998: […]
1:02 PM Changeset [6998] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Added a link …
11:02 AM Ticket #1447 (The "All first names" field in the pathology referral form is ...) closed by Nicklas Nordborg
fixed: In 6997: […]
11:02 AM Changeset [6997] by Nicklas Nordborg
Fixes #1447: The "All first names" field in the pathology referral …
11:00 AM Ticket #1447 (The "All first names" field in the pathology referral form is ...) created by Nicklas Nordborg
It seems like if the user uses the ENTER key to step between fields …
10:55 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6996: […]
10:55 AM Changeset [6996] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Display the …
8:38 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6995: […]
8:38 AM Changeset [6995] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The …
8:32 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6994: […]
8:32 AM Changeset [6994] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The …
7:56 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6993: […]
7:56 AM Changeset [6993] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values If the …

Jan 19, 2023:

1:30 PM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6992: […]
1:30 PM Changeset [6992] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The JSON …
9:51 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6991: […]
9:51 AM Changeset [6991] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Added a …
8:32 AM Ticket #1446 (Add an annotation for extra PAD values) updated by Nicklas Nordborg
In 6990: […]
8:32 AM Changeset [6990] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Added …

Jan 18, 2023:

2:46 PM Ticket #1446 (Add an annotation for extra PAD values) created by Nicklas Nordborg
In some cases an extra PAD value is created for samples that are …

Jan 17, 2023:

2:28 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.42 and Job scheduler 1.8 (diff)
2:28 PM Changeset [6989] by Nicklas Nordborg
Changes for future release Reggie 4.43
2:27 PM Milestone Reggie v4.42 completed
See Reggie extension page for more information.
2:26 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.42 (diff)
2:25 PM reggie-4.42.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.42
2:23 PM Changeset [6988] by Nicklas Nordborg
Tagging Reggie 4.42
2:23 PM Changeset [6987] by Nicklas Nordborg
Preparing to release Reggie 4.42
2:22 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) closed by Nicklas Nordborg
fixed
2:21 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6986: […]
2:21 PM Changeset [6986] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
2:20 PM Changeset [6985] by Nicklas Nordborg
Changes for future release Job scheduler extension 1.9
2:19 PM Milestone Job scheduler extension v1.8 completed
See the Job scheduler extension page for …
2:17 PM net.sf.basedb.opengrid edited by Nicklas Nordborg
Released Job scheduler extension 1.8 (diff)
2:16 PM opengrid-1.8.tar.gz attached to net.sf.basedb.opengrid by Nicklas Nordborg
Job scheduler 1.8
2:16 PM Ticket #1445 (Add support for submitting jobs to a specific partition/queue) closed by Nicklas Nordborg
fixed
2:14 PM Changeset [6984] by Nicklas Nordborg
Tagging Job scheduler extension 1.8
2:14 PM Changeset [6983] by Nicklas Nordborg
Preparing to release Job scheduler extension 1.8
1:34 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6982: […]
1:34 PM Changeset [6982] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
11:48 AM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6981: […]
11:48 AM Changeset [6981] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
9:58 AM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6980: […]
9:58 AM Changeset [6980] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …

Jan 16, 2023:

2:52 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6979: […]
2:52 PM Changeset [6979] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
1:43 PM Ticket #1445 (Add support for submitting jobs to a specific partition/queue) updated by Nicklas Nordborg
In 6978: […]
1:43 PM Changeset [6978] by Nicklas Nordborg
References #1445: Add support for submitting jobs to a specific …
12:49 PM Ticket #1445 (Add support for submitting jobs to a specific partition/queue) created by Nicklas Nordborg
In slurm this is specified with -p or --partition parameter and in …
11:25 AM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by Nicklas Nordborg
In 6977: […]
11:25 AM Changeset [6977] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
9:44 AM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) created by Nicklas Nordborg
This is done by adding -p <name-of-partion> to the parameter list …
8:39 AM Ticket #1443 (When comparing a date without time to a date with time they should be ...) closed by Nicklas Nordborg
fixed: In 6976: […]
8:39 AM Changeset [6976] by Nicklas Nordborg
Fixes #1443: When comparing a date without time to a date with time …
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