Timeline


and

Apr 14, 2016:

10:10 AM net.sf.basedb.reggie edited by nicklas
Link to update notes for Reggie 4.3 (diff)
10:06 AM Changeset [3854] by olle
Refs #525. INCA import updated in order to try to stabilize the …
9:22 AM net.sf.basedb.reggie/HistoryOfReggie edited by nicklas
Added Reggie 4.3 screenshot (diff)
9:22 AM reggie-4.3.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
Reggie 4.3
9:09 AM Changeset [3853] by nicklas
Preparing for future release Reggie 4.4
9:08 AM Milestone Reggie v4.3 completed
See Reggie extension page for more information.
9:07 AM PluginDownload edited by nicklas
Released Reggie 4.3 (diff)
9:07 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 4.3 (diff)
9:05 AM reggie-4.3.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 4.3
9:04 AM Changeset [3852] by nicklas
Tagging Reggie 4.3
9:03 AM Changeset [3851] by nicklas
Preparing to release Reggie 4.3
9:02 AM Changeset [3850] by nicklas
Preparing for future release External files support 1.3
9:01 AM Milestone External files support 1.2 completed
An extension package containing support for additional protocols to …
9:00 AM PluginDownload edited by nicklas
Released Xfiles 1.2 (diff)
9:00 AM net.sf.basedb.xfiles edited by nicklas
Released Xfiles 1.2 (diff)
8:58 AM xfiles-1.2.tar.gz attached to net.sf.basedb.xfiles by nicklas
XFiles 1.2
8:57 AM Changeset [3849] by nicklas
Tagging External files support 1.2
8:56 AM Changeset [3848] by nicklas
Preparing to release External files support 1.2
8:46 AM Tickets #865,​875,​876 batch updated by nicklas
fixed
8:25 AM Ticket #877 (Add counter for consent forms) closed by nicklas
fixed: (In [3847]) Fixes #877: Add counter for consent forms
8:25 AM Changeset [3847] by nicklas
Fixes #877: Add counter for consent forms
8:24 AM Ticket #877 (Add counter for consent forms) created by nicklas
It should count all cases and blood items that is missing a consent …
8:15 AM Changeset [3846] by nicklas
References #525: Import data from INCA Marked the "Inca import" as an …
8:04 AM Changeset [3845] by nicklas
References #864: Implement a service that check and update file …
7:58 AM Changeset [3844] by nicklas
References #865: Stray files wizard Added a counter for the stray …

Apr 13, 2016:

2:28 PM Changeset [3843] by nicklas
References #865: Stray files wizard Implemented support for deleting …
1:23 PM Changeset [3842] by olle
Refs #525. INCA import updated to disable step-1 input fields under …
12:11 PM Changeset [3841] by olle
Refs #525. INCA import updated by removing debug output of lines …
12:05 PM Changeset [3840] by olle
Refs #525. INCA import updated to allow the program to handle internal …
9:03 AM Changeset [3839] by nicklas
References #865: Stray files wizard Added 'owner' to the list. Added …
8:33 AM Changeset [3838] by nicklas
References #865: Stray files wizard Added support for filtering the …

Apr 12, 2016:

10:01 AM Changeset [3837] by nicklas
References #865: Stray files wizard Started to implement the stray …
9:35 AM Tickets #771,​861 batch updated by nicklas
fixed
9:28 AM Changeset [3836] by olle
Refs #525. INCA import re-written to collect INCA data for each case …

Apr 11, 2016:

11:26 AM Changeset [3835] by nicklas
References #876: NeoPrep? library registration without Caliper files …
8:26 AM Changeset [3834] by nicklas
References #876: NeoPrep? library registration without Caliper files …

Apr 8, 2016:

9:56 AM Tickets #863,​864,​867 batch updated by nicklas
fixed
9:31 AM net.sf.basedb.reggie/notes43 created by nicklas
Upgrade comments about #875
9:22 AM Changeset [3833] by nicklas
References #875: Soft and hard target amount for NeoPrep? Added …

Apr 7, 2016:

3:41 PM Changeset [3832] by nicklas
References #875: Soft and hard target amount for NeoPrep? The "Library …

Apr 6, 2016:

12:59 PM Changeset [3831] by nicklas
References #875: Soft and hard target amount for NeoPrep? The "RNA …
8:56 AM Changeset [3830] by olle
Refs #525. Attempt to speed up file check/case mapping stage for extra …
7:59 AM Changeset [3829] by nicklas
References #875: Soft and hard target amount for NeoPrep? Added …

Apr 5, 2016:

3:36 PM Ticket #876 (NeoPrep library registration without Caliper files) created by nicklas
The sizes of fragments seems to be stable. It is not necessary to run …
2:47 PM Ticket #875 (Soft and hard target amount for NeoPrep) created by nicklas
The NeoPrep has a rather wide working range (25-100 ng) of input RNA. …
1:55 PM Changeset [3828] by nicklas
References #861: YellowLabel? tracking wizard Display 'In progress' …
10:00 AM Changeset [3827] by nicklas
References #861: YellowLabel? tracking wizard Added RQS/RIN column.
9:29 AM Changeset [3826] by nicklas
References #861: YellowLabel? tracking wizard Added Consent date
8:12 AM Changeset [3825] by nicklas
References #861: YellowLabel? tracking wizard Added `Re-create report …

Apr 4, 2016:

1:53 PM Changeset [3824] by nicklas
References #861: YellowLabel? tracking wizard Added dialog for setting …
12:42 PM Changeset [3823] by nicklas
References #861: YellowLabel? tracking wizard Include the site name in …
11:16 AM Changeset [3822] by nicklas
References #861: YellowLabel? tracking wizard Added flag icon to RNA …
9:26 AM Changeset [3821] by nicklas
References #861: YellowLabel? tracking wizard Added Completed date
8:34 AM Ticket #874 (<reference-gidx> is incorrect in the default reggie-config.xml file) closed by nicklas
fixed: (In [3820]) Fixes #874: <reference-gidx> is incorrect in the default …
8:34 AM Changeset [3820] by nicklas
Fixes #874: <reference-gidx> is incorrect in the default …
8:27 AM Changeset [3819] by olle
Refs #525. First (experimental) attempt at implementing support for an …

Apr 1, 2016:

2:43 PM Changeset [3818] by olle
Refs #525. INCA import refactored, in order to put code sections in …
9:58 AM Changeset [3817] by olle
Refs #525. INCA import hopefully made more stable, by reading data for …

Mar 29, 2016:

2:29 PM Changeset [3816] by olle
Refs #525. Java servlet class IncaServlet refactored to make code …

Mar 23, 2016:

2:56 PM Changeset [3815] by nicklas
References #861: YellowLabel? tracking wizard Load sites and …
2:36 PM Changeset [3814] by nicklas
References #861: YellowLabel? tracking wizard When filtering on the …
9:08 AM Changeset [3813] by nicklas
References #861: YellowLabel? tracking wizard The "PilotReportExists?" …
9:05 AM Changeset [3812] by nicklas
References #861: YellowLabel? tracking wizard Added column for …
8:53 AM Changeset [3811] by nicklas
References #861: YellowLabel? tracking wizard Added linked icons to …
8:05 AM Changeset [3810] by nicklas
References #861: YellowLabel? tracking wizard The "Pilot report" …

Mar 22, 2016:

3:27 PM Ticket #874 (<reference-gidx> is incorrect in the default reggie-config.xml file) created by nicklas
This should be changed to: hg38/hg38.analysisSet/hg38.analysisSet.fa
2:33 PM Changeset [3809] by nicklas
Merge Reggie 4.2.1 to the trunk.
2:29 PM Milestone Reggie v4.2.1 completed
Bug fixes for Reggie 4.2. Revision Log: …
2:29 PM PluginDownload edited by nicklas
Released Reggie 4.2.1 (diff)
2:28 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 4.2.1 (diff)
2:27 PM reggie-4.2.1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 4.2.1
2:25 PM Changeset [3808] by nicklas
Tagging Reggie 4.2.1
2:25 PM Changeset [3807] by nicklas
Preparing to release Reggie 4.2.1
2:19 PM Ticket #873 (Target volume for NeoPrep should be changed from 12.5 to 15) closed by nicklas
fixed
2:11 PM Changeset [3806] by nicklas
References #873: Target volume for NeoPrep? should be changed from 12.5 …
1:58 PM Changeset [3805] by nicklas
References #873: Target volume for NeoPrep? should be changed from 12.5 …
1:28 PM Ticket #873 (Target volume for NeoPrep should be changed from 12.5 to 15) created by nicklas
See also #858. Turned out that 12.5µl was not practical since it was …
9:55 AM Ticket #866 (Implement the "Start page" extension) closed by nicklas
duplicate: Duplicated by #872.
8:51 AM Changeset [3804] by nicklas
References #868: Update SSH library Use a singleton Config instance …
8:37 AM Changeset [3803] by nicklas
References #867: Update SSH library Use a singleton Config instance …

Mar 21, 2016:

2:52 PM Changeset [3802] by nicklas
References #864: Implement a service that check and update file …
12:11 PM Changeset [3801] by olle
Refs #525. Java servlet class IncaServlet refactored to make code …

Mar 18, 2016:

2:27 PM Changeset [3800] by nicklas
References #861: YellowLabel? tracking wizard Gray background for …
1:16 PM Ticket #872 (Register Reggie as a start page) created by nicklas
BASE 3.8 provides a new extension point for setting the start page …
1:08 PM Ticket #871 (NullPointerException when selecting a software item in the gene/pilot ...) closed by nicklas
fixed: (In [3799]) Fixes #871: NullPointerException? when selecting a software …
1:08 PM Changeset [3799] by nicklas
Fixes #871: NullPointerException? when selecting a software item in the …
1:05 PM Ticket #871 (NullPointerException when selecting a software item in the gene/pilot ...) created by nicklas
When running the Gene and Pilot report wizard it is possible to select …
12:05 PM Changeset [3798] by nicklas
References #870 and #869. Updated README.
12:04 PM Ticket #869 (Switch to Java 8) closed by nicklas
fixed
12:03 PM Ticket #870 (Switch to BASE 3.7) closed by nicklas
fixed: (In [3797]) Fixes #870: Switch to BASE 3.7 Noted that the FTP …
12:03 PM Changeset [3797] by nicklas
Fixes #870: Switch to BASE 3.7 Noted that the FTP connection manager …
11:44 AM Ticket #870 (Switch to BASE 3.7) created by nicklas
The usual procedure is to always require the current BASE version.
11:42 AM Ticket #868 (Update SSH library) closed by nicklas
fixed: (In [3796]) Fixes #868: Update SSH library
11:42 AM Changeset [3796] by nicklas
Fixes #868: Update SSH library
11:40 AM Changeset [3795] by nicklas
Fixes #844: Switch to Java 8
11:30 AM Ticket #869 (Switch to Java 8) created by nicklas
Java 8 is recommended since BASE 3.6. See for example #783.
11:24 AM Ticket #868 (Update SSH library) created by nicklas
See #867.
11:24 AM Changeset [3794] by nicklas
References #867: Update SSH library Changed to SSHJ 0.15.0. New …
11:15 AM Ticket #867 (Update SSH library) created by nicklas
The SSH library we use for making SSH connections to other hosts seems …
10:49 AM Changeset [3793] by nicklas
References #863: Secondary analysis scripts should set permissions on …
9:07 AM Changeset [3792] by nicklas
References #863: Secondary analysis scripts should set permissions on …

Mar 17, 2016:

2:42 PM Changeset [3791] by nicklas
References #861: YellowLabel? tracking wizard The "Create Pilot report …
1:47 PM Changeset [3790] by nicklas
References #861: YellowLabel? tracking wizard Moved yellow label files …
1:37 PM Changeset [3789] by nicklas
References #861: YellowLabel? tracking wizard Added "Create Pilot …
1:34 PM Changeset [3788] by nicklas
References #861: YellowLabel? tracking wizard Moved code from the …
12:42 PM Changeset [3787] by nicklas
References #861: YellowLabel? tracking wizard Added "Mark as …
11:08 AM Changeset [3786] by olle
Refs #525. First version of the INCA data import. It is based on the …

Mar 16, 2016:

3:42 PM Changeset [3785] by nicklas
References #861: YellowLabel? tracking wizard Fixes filtering problems …
3:33 PM Changeset [3784] by nicklas
References #861: YellowLabel? tracking wizard Added CompletedDate
1:20 PM Changeset [3783] by nicklas
References #861: YellowLabel? tracking wizard Adding counter for …
12:54 PM Ticket #866 (Implement the "Start page" extension) created by nicklas
Reggie should add itself as a "Start page". See …
8:14 AM Ticket #865 (Stray files wizard) created by nicklas
The files in the project archive may not reflect what is registered in …
8:02 AM Ticket #864 (Implement a service that check and update file permission in ProjectArchive) created by nicklas
This is related to #863. The secondary analysis scripts will not give …
7:56 AM Ticket #863 (Secondary analysis scripts should set permissions on created files in ...) created by nicklas
This is related to #864. Files generated on the project archive file …
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