Timeline



Apr 27, 2018:

12:09 PM Changeset [4786] by olle
Refs #1029. Consent registration for active project SCAN-B-rec updated …
11:43 AM Changeset [4785] by olle
Refs #1029. Import of code for consent support, taken from Reggie …

Apr 26, 2018:

9:52 AM Changeset [4784] by olle
Refs #1029. Referral form generator updated for non-sticker forms to …

Apr 25, 2018:

4:29 PM Changeset [4783] by olle
Refs #1029. Referral form generator updated for new form versions. …
9:44 AM Changeset [4782] by Nicklas Nordborg
References #1048: Release importer fails if the export contain integer …

Apr 24, 2018:

2:56 PM Ticket #1049 (Improvments to the FrozenTissueDate wizards) created by Nicklas Nordborg
See #969 for current implementation. * Duplicates should no longer …
2:42 PM Ticket #1048 (Release importer fails if the export contain integer enumerated ...) created by Nicklas Nordborg
For example: […] Stack trace: […]
9:10 AM Ticket #1047 (HaplotypeCaller should be wrapped with stdwrap.sh) created by Nicklas Nordborg
Most of the log information that is produced by HaplotypeCaller is …

Apr 23, 2018:

8:32 AM Changeset [4781] by Nicklas Nordborg
References #1046: Flagged alignments wizard Added link on the start …
8:15 AM Ticket #1046 (Flagged alignments wizard) created by Nicklas Nordborg
This is the second step in the genotype QC. Alignments that were …

Apr 20, 2018:

1:11 PM Changeset [4780] by olle
Refs #1029. Case summary updated to show consent info after hospital …
1:08 PM Ticket #1045 (Display FrozenTissueDate annotation in case summary) created by Nicklas Nordborg
11:41 AM net.sf.basedb.relax/install created by Nicklas Nordborg
Create installation instructions
11:36 AM Changeset [4779] by olle
Refs #1029. Bugs fixed in Javascript for sample registration for …
11:19 AM Changeset [4778] by Nicklas Nordborg
Changes for future Relax 1.3
11:17 AM Milestone Relax v1.2 completed
See Relax extension page for more information.
11:17 AM PluginDownload edited by Nicklas Nordborg
Released Relax 1.2 (diff)
11:16 AM net.sf.basedb.relax edited by Nicklas Nordborg
Released Relax 1.2 (diff)
11:14 AM relax-1.2.tar.gz attached to net.sf.basedb.relax by Nicklas Nordborg
Relax 1.2
11:10 AM Changeset [4777] by Nicklas Nordborg
Tagging Relax 1.2
11:09 AM Changeset [4776] by Nicklas Nordborg
Preparing to release Relax 1.2
11:09 AM Ticket #1028 (Add support for StringTie data) closed by Nicklas Nordborg
fixed: Seems to work after full test of releasing data from reggie via relax …
10:29 AM Changeset [4775] by olle
Refs #1029. Referral form generator updated for forms with sticker …
9:20 AM Changeset [4774] by olle
Refs #1029. Referral form generator updated to create a fixed number …
9:00 AM Changeset [4773] by olle
Refs #1029. Support for consent coupled to case item added, based on …

Apr 19, 2018:

1:26 PM Ticket #1044 (Selecting INCA annotations for the Level 3 exporter) closed by Nicklas Nordborg
fixed: (In [4772]) Fixes #1044: Selecting INCA annotations for the Level 3 …
1:26 PM Changeset [4772] by Nicklas Nordborg
Fixes #1044: Selecting INCA annotations for the Level 3 exporter
11:34 AM Changeset [4771] by Nicklas Nordborg
References #1028: Add support for StringTie? data The Level 3 export …
9:47 AM Ticket #1044 (Selecting INCA annotations for the Level 3 exporter) created by Nicklas Nordborg
The Level 3 export currently exports ALL INCA annotations if not a …

Apr 18, 2018:

3:11 PM Ticket #1043 (The Level 3 exporter fails if the release server has a specified port) closed by Nicklas Nordborg
fixed: (In [4770]) Fixes #1043: The Level 3 exporter fails if the release …
3:11 PM Changeset [4770] by Nicklas Nordborg
Fixes #1043: The Level 3 exporter fails if the release server has a …
2:35 PM Ticket #1043 (The Level 3 exporter fails if the release server has a specified port) created by Nicklas Nordborg
Same problem as #1042 in Reggie.
2:20 PM Changeset [4769] by Nicklas Nordborg
References #1028: Add support for StringTie? data The Cohort exporter …
8:35 AM Changeset [4768] by olle
Refs #1029. Referral form generation updated by removing menu for …

Apr 17, 2018:

4:48 PM Changeset [4767] by olle
Refs #1029. Referral form generator update: Design update of referral …
2:15 PM Milestone INCA XML to CSV converter 1.2 completed
See INCA XML to CSV converter page for more …
2:15 PM Ticket #1021 (Add INCA 2.0 columns to the blacklist) closed by Nicklas Nordborg
fixed
2:13 PM Changeset [4766] by Nicklas Nordborg
Changes for future release IncaXML2CSV 1.3
2:12 PM net.sf.basedb.inca edited by Nicklas Nordborg
Released IncaXML2CSV 1.2 (diff)
2:11 PM IncaXml2Csv-1.2.tar.gz attached to net.sf.basedb.inca by Nicklas Nordborg
IncaXml2Csv 1.2
2:10 PM Changeset [4765] by Nicklas Nordborg
Tagging IncaXML2CSV 1.2
2:10 PM Changeset [4764] by Nicklas Nordborg
Preparing to release IncaXML2CSV 1.2
2:08 PM Changeset [4763] by Nicklas Nordborg
Preparing for future release Reggie 4.17.
2:07 PM Milestone Reggie v4.16 completed
See Reggie extension page for more information.
2:06 PM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.16 (diff)
2:05 PM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.16 (diff)
2:04 PM reggie-4.16.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.16
2:02 PM Changeset [4762] by Nicklas Nordborg
Tagging Reggie 4.16
2:01 PM Changeset [4761] by Nicklas Nordborg
Preparing to release Reggie 4.16
1:57 PM Tickets #1022,​1025,​1026,​1031 batch updated by Nicklas Nordborg
fixed
1:57 PM Ticket #1042 (The release exporter fails if the release server has a specified port) closed by Nicklas Nordborg
fixed: (In [4760]) Fixes #1042: The release exporter fails if the release …
1:57 PM Changeset [4760] by Nicklas Nordborg
Fixes #1042: The release exporter fails if the release server has a …
1:48 PM Changeset [4759] by Nicklas Nordborg
References #1025: Release exporter should support StringTie? data …
1:08 PM Ticket #1042 (The release exporter fails if the release server has a specified port) created by Nicklas Nordborg
The File server item in BASE that is used by the release exporter may …
12:48 PM Ticket #1041 (The release exporter should export the QC_GenoTypeHET_PCT annotation) closed by Nicklas Nordborg
fixed: (In [4758]) Fixes #1041: The release exporter should export the …
12:48 PM Changeset [4758] by Nicklas Nordborg
Fixes #1041: The release exporter should export the QC_GenoTypeHET_PCT …
11:34 AM Ticket #1041 (The release exporter should export the QC_GenoTypeHET_PCT annotation) created by Nicklas Nordborg
As for other annotations from the AlignedSequences item the …
9:54 AM Ticket #1036 (Add support for public/private key authentication) closed by Nicklas Nordborg
fixed
9:53 AM Ticket #1038 (Add support for SSH connections with private key authentication) closed by Nicklas Nordborg
fixed

Apr 16, 2018:

3:37 PM Changeset [4757] by olle
Refs #1029. MeLuDI updated in error message to refer to the correct …
3:32 PM Changeset [4756] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …
2:32 PM Ticket #1035 (Upgrade SSHj library) closed by Nicklas Nordborg
fixed
2:31 PM Ticket #1037 (Depend on BASE 3.13) closed by Nicklas Nordborg
fixed
1:44 PM Changeset [4755] by Nicklas Nordborg
References #1038: Add support for SSH connections with private key …
12:51 PM Changeset [4754] by Nicklas Nordborg
References #1038: Add support for SSH connections with private key …
12:51 PM Changeset [4753] by Nicklas Nordborg
References #1038: Add support for SSH connections with private key …
11:47 AM Changeset [4752] by Nicklas Nordborg
References #1038: Add support for SSH connections with private key …
11:44 AM Changeset [4751] by Nicklas Nordborg
References #1038: Add support for SSH connections with private key …
11:02 AM Changeset [4750] by Nicklas Nordborg
References #1036: Add support for public/private key authentication …
9:17 AM Ticket #1040 (Set max BASE version to 3.13) closed by Nicklas Nordborg
fixed: (In [4749]) Fixes #1040: Set max BASE version to 3.13
9:17 AM Changeset [4749] by Nicklas Nordborg
Fixes #1040: Set max BASE version to 3.13
9:13 AM Ticket #1040 (Set max BASE version to 3.13) created by Nicklas Nordborg
BASE 3.13 is going to include BouncyCastle? in the core distribution …
9:10 AM Ticket #1039 (Remove BouncyCastle jar files) created by Nicklas Nordborg
BASE 3.13 is going to include BouncyCastle in the core distribution …

Apr 13, 2018:

2:03 PM Changeset [4748] by Nicklas Nordborg
References #1036: Add support for public/private key authentication …
1:46 PM net.sf.basedb.opengrid/install edited by Nicklas Nordborg
References #1036. Documented the new configuration options for using … (diff)
11:26 AM Changeset [4747] by Nicklas Nordborg
References #1022: INCA import/statistics wizards changes due to INCA …
9:18 AM Changeset [4746] by Nicklas Nordborg
References #1022: INCA import/statistics wizards changes due to INCA …

Apr 10, 2018:

3:29 PM Changeset [4745] by Nicklas Nordborg
References #1025: Release exporter should support StringTie? data …
1:08 PM Changeset [4744] by Nicklas Nordborg
References #1034: Remove expression matrix from release exporter …
1:06 PM Changeset [4743] by Nicklas Nordborg
References #1025 and #1034. Removed check that all raw bioassays must …
8:57 AM Ticket #1038 (Add support for SSH connections with private key authentication) created by Nicklas Nordborg
Implemented in BASE: http://base.thep.lu.se/ticket/2112 We need to …

Apr 9, 2018:

11:35 AM Changeset [4742] by Nicklas Nordborg
References #1036: Add support for public/private key authentication …
9:25 AM Changeset [4741] by Nicklas Nordborg
References #1036: Add support for public/private key authentication …
8:25 AM Changeset [4740] by Nicklas Nordborg
References #1037: Depend on BASE 3.13 Updated to BASE 3.13 and …

Apr 6, 2018:

1:20 PM Ticket #1037 (Depend on BASE 3.13) reopened by Nicklas Nordborg

Apr 5, 2018:

12:44 PM Ticket #1037 (Depend on BASE 3.13) closed by Nicklas Nordborg
fixed: (In [4739]) Fixes #1037: Depend on BASE 3.12
12:44 PM Changeset [4739] by Nicklas Nordborg
Fixes #1037: Depend on BASE 3.12
12:41 PM Ticket #1037 (Depend on BASE 3.13) created by Nicklas Nordborg
Since we are making big changes, it is better to use the latest BASE …
12:38 PM Changeset [4738] by Nicklas Nordborg
References #1035: Upgrade SSHj library
11:37 AM Changeset [4737] by Nicklas Nordborg
References #1028: Add support for StringTie? data The Level 3 exporter …
11:33 AM Ticket #1036 (Add support for public/private key authentication) created by Nicklas Nordborg
Instead of a username/password, it would be nice to be able to use …
11:32 AM Ticket #1035 (Upgrade SSHj library) created by Nicklas Nordborg
Latest version is 0.23.0. https://github.com/hierynomus/sshj
11:20 AM Changeset [4736] by olle
Refs #1029. Updates due to version number change to "1.6.0a1". 1. …
9:32 AM Changeset [4735] by Nicklas Nordborg
References #1028: Add support for StringTie? data The Relax …
8:55 AM Changeset [4734] by olle
Refs #1029. Case/sample registration in SCAN-B-rec project updated for …
8:24 AM Changeset [4733] by olle
Refs #1029. Code fork introduced for case/sample registration in …

Apr 4, 2018:

3:56 PM Changeset [4732] by olle
Refs #1029. Specimen tube registration updated in the case section …
1:47 PM Changeset [4731] by olle
Refs #1029. MeLuDI updated in sample report servlet code with debug …
12:30 PM Changeset [4730] by olle
Refs #1029. Specimen tube registration updated in the set of mutation …
11:23 AM Changeset [4729] by olle
Refs #1029. MeLuDI updated by extending list of menu options for …
10:41 AM Changeset [4728] by Nicklas Nordborg
References #1031: Define a genotype QC flag that can be set on …
9:18 AM Changeset [4727] by olle
Refs #1029. MeLuDI updated in most wizards by specifying that a …

Apr 3, 2018:

8:45 AM Changeset [4726] by olle
Refs #1029. Referral generation updated in servlet by exchanging …
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