Timeline



Jan 27, 2023:

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

Jan 26, 2023:

2:23 PM Changeset [7016] by Nicklas Nordborg
References #1393: Release exporter changes due to Oncoarray data The …
1:48 PM Changeset [7015] by Nicklas Nordborg
References #1452: Release importer changes due to new subtypes from …
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 Changeset [7012] by Nicklas Nordborg
References #1399: The Release importer should handle null values for …

Jan 25, 2023:

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

Jan 24, 2023:

2:34 PM Changeset [7006] by Nicklas Nordborg
References #1451: Release exporter changes due to Methylation data …
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:

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 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 now 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 now 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 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 Changeset [6996] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Display the …
8:38 AM Changeset [6995] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The …
8:32 AM Changeset [6994] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The …
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 Changeset [6992] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values The JSON …
9:51 AM Changeset [6991] by Nicklas Nordborg
References #1446: Add an annotation for extra PAD values Added a …
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 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 Changeset [6982] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
11:48 AM Changeset [6981] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
9:58 AM Changeset [6980] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …

Jan 16, 2023:

2:52 PM Changeset [6979] by Nicklas Nordborg
References #1444: Implement support for submitting jobs to a specific …
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 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 …

Jan 13, 2023:

2:07 PM Ticket #1442 (Implement an option to prefer that existing value on a NoSpecimen is ...) closed by Nicklas Nordborg
fixed: In 6975: […]
2:07 PM Changeset [6975] by Nicklas Nordborg
Fixes #1442: Implement an option to prefer that existing value on a …
1:10 PM Ticket #1443 (When comparing a date without time to a date with time they should be ...) created by Nicklas Nordborg
This may happen if, for example, time information is missing from …
1:09 PM Ticket #1442 (Implement an option to prefer that existing value on a NoSpecimen is ...) created by Nicklas Nordborg
This option should be used for the PAD, Sample date+time and RNA later …
8:39 AM Ticket #1441 (Ignore entries with only the text "(Fritext)") closed by Nicklas Nordborg
fixed: In 6974: […]
8:39 AM Changeset [6974] by Nicklas Nordborg
Fixes #1441: Ignore entries with only the text "(Fritext)" …

Jan 12, 2023:

2:30 PM Ticket #1441 (Ignore entries with only the text "(Fritext)") created by Nicklas Nordborg
This text seems to be there when an optional field has not been given …
2:16 PM Milestone Reggie v4.41.4 completed
Bug fixes and enhancements for Reggie 4.41.3. Revision Log: …
11:52 AM Changeset [6973] by Nicklas Nordborg
Merge Reggie 4.41.4 to the trunk.
11:48 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.41.4 (diff)
11:47 AM reggie-4.41.4.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.41.4
11:45 AM Changeset [6972] by Nicklas Nordborg
Tagging Reggie 4.41.4
11:44 AM Changeset [6971] by Nicklas Nordborg
Preparing to release Reggie 4.41.4
11:42 AM Ticket #1440 (Add option for running Picard MarkDuplicates with ...) closed by Nicklas Nordborg
fixed: In 6970: […]
11:42 AM Changeset [6970] by Nicklas Nordborg
Fixes #1440: Add option for running Picard MarkDuplicates? with …
11:26 AM Changeset [6969] by Nicklas Nordborg
References #1440: Add option for running Picard MarkDuplicates? with …
9:33 AM Ticket #1440 (Add option for running Picard MarkDuplicates with ...) created by Nicklas Nordborg
The BAM file produced by the Hisat/2023 pipeline contained an entry …

Jan 11, 2023:

2:02 PM Ticket #1439 (The "Use latest lot numbers" doesn't work after receiving data from ...) closed by Nicklas Nordborg
fixed: In 6968: […]
2:02 PM Changeset [6968] by Nicklas Nordborg
Fixes #1439: The "Use latest lot numbers" doesn't work after receiving …
1:46 PM Ticket #1439 (The "Use latest lot numbers" doesn't work after receiving data from ...) created by Nicklas Nordborg
The "Use latest lot numbers" functionality finds the latest RNA item …

Jan 10, 2023:

2:46 PM Ticket #1438 (Check for mismatches between the suffix in the SCANB_ID and the Sample type) closed by Nicklas Nordborg
fixed: In 6967: […]
2:46 PM Changeset [6967] by Nicklas Nordborg
Fixes #1438: Check for mismatches between the suffix in the SCANB_ID …
1:02 PM Ticket #1437 (Allow alternate options for "Sample type") closed by Nicklas Nordborg
fixed: In 6966: […]
1:02 PM Changeset [6966] by Nicklas Nordborg
Fixes #1437: Allow alternate options for "Sample type"
11:38 AM Ticket #1438 (Check for mismatches between the suffix in the SCANB_ID and the Sample type) created by Nicklas Nordborg
We found a JSON file with a SCANB_ID ending with C', but with …
11:26 AM Ticket #1437 (Allow alternate options for "Sample type") created by Nicklas Nordborg
When we see Operationspreparat in the JSON file, it should be …
10:59 AM Ticket #1436 (Re-order entries in the JSON file) closed by Nicklas Nordborg
fixed: In 6965: […]
10:59 AM Changeset [6965] by Nicklas Nordborg
Fixes #1436: Re-order entries in the JSON file
9:39 AM Ticket #1436 (Re-order entries in the JSON file) created by Nicklas Nordborg
When viewing the JSON files in the external importer wizard it would …
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