Timeline
Feb 10, 2023:
- 2:16 PM Ticket #1456 (SimpleDateFormat implementation is not thread-safe) closed by
- fixed: In 7036: […]
- 2:16 PM Changeset [7036] by
- Fixes #1456: SimpleDateFormat implementation is not thread-safe …
- 12:54 PM Ticket #1453 (Make the release exporter multi-threaded) updated by
- In 7035: […]
- 12:54 PM Changeset [7035] by
- References #1453: Make the release exporter multi-threaded Changed …
- 9:31 AM Ticket #1453 (Make the release exporter multi-threaded) updated by
- In 7034: […]
- 9:31 AM Changeset [7034] by
- References #1453: Make the release exporter multi-threaded Fixed …
- 8:55 AM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) closed by
- fixed
- 8:46 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) closed by
- fixed
- 8:46 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) updated by
- 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
- In 7033: […] EDIT This change is for ticket …
- 8:43 AM Changeset [7033] by
- 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
- fixed: In 7032: […]
- 8:39 AM Changeset [7032] by
- 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
- fixed: In 7031: […]
- 2:49 PM Changeset [7031] by
- Fixes #1457: Increase the timeout for "Picard CheckIlluminaDirectory" …
- 2:16 PM Ticket #1457 (Increase the timeout for "Picard CheckIlluminaDirectory") updated by
- In 7030: […]
- 2:16 PM Changeset [7030] by
- References #1457: Increase the timeout for "Picard …
- 2:07 PM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) updated by
- In 7029: […]
- 2:07 PM Changeset [7029] by
- References #1455: SimpleDateFormat implementation is not thread-safe …
- 2:05 PM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) closed by
-
fixed: We use the
SimpleDateFormatclass only via theDateFormatter… - 1:19 PM Ticket #1458 (The timeout when executing a command seems to not work) closed by
- fixed: In 7028: […]
- 1:19 PM Changeset [7028] by
- 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
- 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
- Temporarily disabled in #1461.
- 11:29 AM Ticket #1461 (Temporarily disable importing of sampling and RNA later date in the ...) created by
- 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
- BloodDNA items are typically registered manually, but we should assume …
- 9:44 AM Ticket #1459 (Update to SSHj 0.35) closed by
- fixed: In 7027: […]
- 9:44 AM Changeset [7027] by
- Fixes #1459: Update to SSHj 0.35
- 9:30 AM Ticket #1459 (Update to SSHj 0.35) created by
- 9:26 AM Ticket #1458 (The timeout when executing a command seems to not work) created by
-
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
- 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
- In 7026: […]
- 2:07 PM Changeset [7026] by
- References #1454: SimpleDateFormat implementation is not thread-safe …
- 2:03 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by
- In 7025: […]
- 2:03 PM Changeset [7025] by
- References #1454: SimpleDateFormat implementation is not thread-safe …
- 8:58 AM Ticket #1456 (SimpleDateFormat implementation is not thread-safe) created by
-
See #1454.
We use the
SimpleDateFormatclass in some places. - 8:57 AM Ticket #1455 (SimpleDateFormat implementation is not thread-safe) created by
-
See #1454.
We use the
SimpleDateFormatclass in some places.
Feb 7, 2023:
- 2:23 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by
- In 7024: […]
- 2:23 PM Changeset [7024] by
- References #1454: SimpleDateFormat implementation is not thread-safe …
- 1:39 PM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) updated by
- In 7023: […]
- 1:39 PM Changeset [7023] by
- References #1454: SimpleDateFormat implementation is not thread-safe …
- 11:51 AM Ticket #1454 (SimpleDateFormat implementation is not thread-safe) created by
-
We use the
java.text.SimpleDateFormatimplementation to format and …
Feb 6, 2023:
- 2:45 PM Ticket #1453 (Make the release exporter multi-threaded) updated by
- In 7022: […]
- 2:45 PM Changeset [7022] by
- 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
- I think the performance of the release exporter can be improved by …
Jan 30, 2023:
- 2:06 PM Tickets #1452,1399 batch updated by
- fixed
- 2:06 PM Tickets #1393,1451 batch updated by
- fixed
Jan 27, 2023:
- 2:15 PM Ticket #1399 (The Release importer should handle null values for annotations) updated by
- In 7021: […]
- 2:15 PM Changeset [7021] by
- References #1399: The Release importer should handle null values for …
- 11:57 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by
- In 7020: […]
- 11:57 AM Changeset [7020] by
- References #1451: Release exporter changes due to Methylation data …
- 9:33 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by
- In 7019: […]
- 9:33 AM Changeset [7019] by
- References #1451: Release exporter changes due to Methylation data …
- 9:03 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by
- In 7018: […]
- 9:03 AM Changeset [7018] by
- References #1393: Release exporter changes due to Oncoarray data …
- 8:44 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by
- In 7017: […]
- 8:44 AM Changeset [7017] by
- 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
- In 7016: […]
- 2:23 PM Changeset [7016] by
- 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
- In 7015: […]
- 1:48 PM Changeset [7015] by
- References #1452: Release importer changes due to new subtypes from …
- 1:24 PM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by
- In 7014: […]
- 1:24 PM Changeset [7014] by
- References #1393: Release exporter changes due to Oncoarray data …
- 11:33 AM Changeset [7013] by
- 11:13 AM Ticket #1399 (The Release importer should handle null values for annotations) updated by
- In 7012: […]
- 11:13 AM Changeset [7012] by
- 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
- In 7011: […]
- 2:15 PM Changeset [7011] by
- References #1393: Release exporter changes due to Oncoarray data …
- 1:27 PM Ticket #1451 (Release exporter changes due to Methylation data) updated by
- In 7010: […]
- 1:27 PM Changeset [7010] by
- References #1451: Release exporter changes due to Methylation data …
- 9:52 AM Ticket #1451 (Release exporter changes due to Methylation data) updated by
- In 7009: […]
- 9:52 AM Changeset [7009] by
- 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
- In 7008: […]
- 9:45 AM Changeset [7008] by
- References #1452: Release importer changes due to new subtypes from …
- 8:45 AM Ticket #1393 (Release exporter changes due to Oncoarray data) updated by
- In 7007: […]
- 8:45 AM Changeset [7007] by
- 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
- In 7006: […]
- 2:34 PM Changeset [7006] by
- References #1451: Release exporter changes due to Methylation data …
- 2:32 PM Tickets #1393,1451 batch updated by
-
Status, Milestone changed
- 2:09 PM Ticket #1452 (Release importer changes due to new subtypes from Reggie) created by
- 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
- 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
-
Milestone changed
Milestone renamed - 9:00 AM Changeset [7005] by
- 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
- Released Reggie 4.43 (diff)
- 8:56 AM Changeset [7004] by
- Tagging Reggie 4.43
- 8:56 AM Changeset [7003] by
- Preparing to release Reggie 4.43
- 8:52 AM Ticket #1446 (Add an annotation for extra PAD values) closed by
- fixed
- 8:51 AM Ticket #1446 (Add an annotation for extra PAD values) updated by
- In 7002: […]
- 8:51 AM Changeset [7002] by
- 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
- fixed: In 7001: […]
- 2:59 PM Changeset [7001] by
- 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
- 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
- fixed: In 7000: […]
- 1:34 PM Changeset [7000] by
- 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
- 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
- fixed: In 6999: […]
- 1:14 PM Changeset [6999] by
- 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
- 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
- In 6998: […]
- 1:02 PM Changeset [6998] by
- 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
- fixed: In 6997: […]
- 11:02 AM Changeset [6997] by
- 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
- 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
- In 6996: […]
- 10:55 AM Changeset [6996] by
- 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
- In 6995: […]
- 8:38 AM Changeset [6995] by
- References #1446: Add an annotation for extra PAD values The …
- 8:32 AM Ticket #1446 (Add an annotation for extra PAD values) updated by
- In 6994: […]
- 8:32 AM Changeset [6994] by
- References #1446: Add an annotation for extra PAD values The …
- 7:56 AM Ticket #1446 (Add an annotation for extra PAD values) updated by
- In 6993: […]
- 7:56 AM Changeset [6993] by
- 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
- In 6992: […]
- 1:30 PM Changeset [6992] by
- 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
- In 6991: […]
- 9:51 AM Changeset [6991] by
- 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
- In 6990: […]
- 8:32 AM Changeset [6990] by
- 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
- In some cases an extra PAD value is created for samples that are …
Jan 17, 2023:
- 2:28 PM PluginDownload edited by
- Released Reggie 4.42 and Job scheduler 1.8 (diff)
- 2:28 PM Changeset [6989] by
- 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
- Released Reggie 4.42 (diff)
- 2:23 PM Changeset [6988] by
- Tagging Reggie 4.42
- 2:23 PM Changeset [6987] by
- Preparing to release Reggie 4.42
- 2:22 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) closed by
- fixed
- 2:21 PM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by
- In 6986: […]
- 2:21 PM Changeset [6986] by
- References #1444: Implement support for submitting jobs to a specific …
- 2:20 PM Changeset [6985] by
- 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
- Released Job scheduler extension 1.8 (diff)
- 2:16 PM Ticket #1445 (Add support for submitting jobs to a specific partition/queue) closed by
- fixed
- 2:14 PM Changeset [6984] by
- Tagging Job scheduler extension 1.8
- 2:14 PM Changeset [6983] by
- 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
- In 6982: […]
- 1:34 PM Changeset [6982] by
- 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
- In 6981: […]
- 11:48 AM Changeset [6981] by
- 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
- In 6980: […]
- 9:58 AM Changeset [6980] by
- 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
- In 6979: […]
- 2:52 PM Changeset [6979] by
- 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
- In 6978: […]
- 1:43 PM Changeset [6978] by
- 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
-
In slurm this is specified with
-por--partitionparameter and in … - 11:25 AM Ticket #1444 (Implement support for submitting jobs to a specific Slurm partition ...) updated by
- In 6977: […]
- 11:25 AM Changeset [6977] by
- 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
-
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
- fixed: In 6976: […]
- 8:39 AM Changeset [6976] by
- 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
- fixed: In 6975: […]
- 2:07 PM Changeset [6975] by
- 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
- 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
- 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
- fixed: In 6974: […]
- 8:39 AM Changeset [6974] by
- Fixes #1441: Ignore entries with only the text "(Fritext)" …
Jan 12, 2023:
- 2:30 PM Ticket #1441 (Ignore entries with only the text "(Fritext)") updated by
-
Summary changed
- 2:30 PM Ticket #1441 (Ignore entries with only the text "(Fritext)") created by
- 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
- Merge Reggie 4.41.4 to the trunk.
- 11:48 AM net.sf.basedb.reggie edited by
- Released Reggie 4.41.4 (diff)
- 11:45 AM Changeset [6972] by
- Tagging Reggie 4.41.4
- 11:44 AM Changeset [6971] by
- Preparing to release Reggie 4.41.4
- 11:42 AM Ticket #1440 (Add option for running Picard MarkDuplicates with ...) closed by
- fixed: In 6970: […]
- 11:42 AM Changeset [6970] by
- Fixes #1440: Add option for running Picard MarkDuplicates with …
- 11:26 AM Ticket #1440 (Add option for running Picard MarkDuplicates with ...) updated by
- In 6969: […]
- 11:26 AM Changeset [6969] by
- References #1440: Add option for running Picard MarkDuplicates with …
- 9:33 AM Ticket #1440 (Add option for running Picard MarkDuplicates with ...) created by
- 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
- fixed: In 6968: […]
- 2:02 PM Changeset [6968] by
- 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
- The "Use latest lot numbers" functionality finds the latest RNA item …
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