Timeline


and

Dec 11, 2014:

4:48 PM Ticket #690 (MeLuDi - Registration wizard for melanoma-lung cancer projects) closed by olle
fixed: Ticket closed as MeLuDi version 1.0 has been created.
4:34 PM net.sf.basedb.meludi edited by olle
MeLuDi BASE extension version 1.0 (diff)
4:24 PM meludi-1.0.tar.gz attached to net.sf.basedb.meludi by olle
MeLuDi? BASE extension package version 1.0
4:00 PM Changeset [3030] by olle
Refs #690. Javascript file labelgeneration.js in …
3:43 PM Changeset [3029] by nicklas
References #717: Auto-confirmation service Added "Auto-confirm" …
3:04 PM Changeset [3028] by olle
Refs #690. MeLuDi BASE extension updated to version 1.0: A. New and …
1:53 PM Ticket #717 (Auto-confirmation service) created by nicklas
For the secondary analysis we should implement an auto-confirmation …
1:39 PM Ticket #716 (Add support for Reggie to the gold skin) closed by nicklas
fixed: (In [3027]) Fixes #716: Add support for Reggie to the gold skin The …
1:39 PM Changeset [3027] by nicklas
Fixes #716: Add support for Reggie to the gold skin The major visible …
1:36 PM Ticket #716 (Add support for Reggie to the gold skin) created by nicklas
Most parts of Reggie use classes, etc. defined in BASE, there are a …
1:34 PM Changeset [3026] by nicklas
References #702: Use skin features in BASE 3.4 Turned out that color …

Dec 9, 2014:

3:08 PM Ticket #711 (The 'Confirm sequencing completed' wizard should not set ...) closed by nicklas
fixed: (In [3025]) Fixes #711: The 'Confirm sequencing completed' wizard …
3:08 PM Changeset [3025] by nicklas
Fixes #711: The 'Confirm sequencing completed' wizard should not set …
2:58 PM Ticket #710 (Flow cells can be counted multiple times for 'Register sequencing started') closed by nicklas
fixed: (In [3024]) Fixes #710: Flow cells can be counted multiple times for …
2:58 PM Changeset [3024] by nicklas
Fixes #710: Flow cells can be counted multiple times for 'Register …
2:43 PM Ticket #713 (Comment for bioplate in RNA dilution registration is not updated) closed by nicklas
fixed: (In [3023]) Fixes #713: Comment for bioplate in RNA dilution …
2:43 PM Changeset [3023] by nicklas
Fixes #713: Comment for bioplate in RNA dilution registration is not …
11:42 AM Changeset [3022] by nicklas
References #706: Update LabEnv? to use BASE database capabilties …
10:17 AM Changeset [3021] by nicklas
References #706: Update LabEnv? to use BASE database capabilties …
8:40 AM Ticket #715 (Do not query the sensor for it's name every time) closed by nicklas
fixed: (In [3020]) Fixes #715: Do not query the sensor for it's name every time
8:40 AM Changeset [3020] by nicklas
Fixes #715: Do not query the sensor for it's name every time
8:40 AM Ticket #715 (Do not query the sensor for it's name every time) created by nicklas
Every time a sensor is queried for the current temperature and …
8:29 AM Ticket #714 (Get rid of warning messages from HttpMethodBase) closed by nicklas
fixed: (In [3019]) Fixes #714: Get rid of warning messages from …
8:29 AM Changeset [3019] by nicklas
Fixes #714: Get rid of warning messages from HttpMethodBase? Reading …
7:53 AM Ticket #714 (Get rid of warning messages from HttpMethodBase) created by nicklas
Every time a request is made to one of the sensors a warning message …
7:44 AM Changeset [3018] by nicklas
References #706: Update LabEnv? to use BASE database capabilties …

Dec 8, 2014:

1:46 PM Changeset [3017] by nicklas
References #706: Update LabEnv? to use BASE database capabilties …
1:35 PM Ticket #608 (Update Labenv to new scripting pattern) closed by olle
fixed: Ticket closed as the requested modifications have been added. If …
7:58 AM Changeset [3016] by nicklas
Preparing bugfix branch for Reggie 2.18
7:56 AM Changeset [3015] by nicklas
Creating bugfix branch for Reggie 2.18
7:52 AM Ticket #713 (Comment for bioplate in RNA dilution registration is not updated) created by nicklas
When starting the wizard, the bioplate comment is set to the …

Dec 5, 2014:

1:10 PM Changeset [3014] by nicklas
References #706: Update LabEnv? to use BASE database capabilties …
12:31 PM Ticket #606 (Switch to JDOM 2) closed by nicklas
fixed
12:31 PM Changeset [3013] by nicklas
References #606: Switch to JDOM 2 New JDOM 2.0.5 replaces 1.1.3. Also …
11:50 AM Changeset [3012] by nicklas
References #606: Switch to JDOM 2 Switched to depend on BASE 3.4
11:48 AM Changeset [3011] by nicklas
References #608: Update Labenv to new scripting pattern The "LabEnv?" …
11:06 AM Ticket #712 (The 'Skin options' menu is only visible for root user) closed by nicklas
fixed: (In [3010]) Fixes #712: The 'Skin options' menu is only visible for …
11:06 AM Changeset [3010] by nicklas
Fixes #712: The 'Skin options' menu is only visible for root user
11:06 AM Ticket #712 (The 'Skin options' menu is only visible for root user) created by nicklas
The menu item is configured to be visible for users with WRITE …

Dec 4, 2014:

2:04 PM Ticket #711 (The 'Confirm sequencing completed' wizard should not set ...) created by nicklas
This flag may already be present from the previous (Register …
1:59 PM Ticket #710 (Flow cells can be counted multiple times for 'Register sequencing started') created by nicklas
The counter next to the 'Register sequencing started' wizard can count …
12:41 PM Ticket #605 (Switch to JDOM 2) closed by nicklas
fixed: (In [3009]) Fixes #605: Switch to JDOM 2
12:41 PM Changeset [3009] by nicklas
Fixes #605: Switch to JDOM 2
11:02 AM Ticket #709 (Depend on BASE 3.4) closed by nicklas
fixed: (In [3008]) Fixes #709: Depend on BASE 3.4 Updated to BASE version …
11:02 AM Changeset [3008] by nicklas
Fixes #709: Depend on BASE 3.4 Updated to BASE version 3.4.0. Removed …
10:55 AM Ticket #709 (Depend on BASE 3.4) created by nicklas
Time to move on to the upcoming BASE version. Also means that we can …
10:32 AM PluginDownload edited by nicklas
Released skin collection 1.0 (diff)
10:23 AM Milestone Skin-collection 1.0 completed
See Skin collection extension page
10:02 AM Changeset [3007] by nicklas
Preparing for future release Skin collection 1.1
10:00 AM net.sf.basedb.skincollection edited by nicklas
Released skin collection 1.0 (diff)
9:56 AM skin-collection-1.0.tar.gz attached to net.sf.basedb.skincollection by nicklas
Skin collection 1.0
9:55 AM Changeset [3006] by nicklas
Tagging skin collection 1.0.
9:54 AM Changeset [3005] by nicklas
Preparing to release skin collection 1.0
9:08 AM Changeset [3004] by nicklas
Preparing for future release Reggie 2.19
9:06 AM net.sf.basedb.reggie/HistoryOfReggie edited by nicklas
Added Reggie 2.18 screenshot (diff)
9:06 AM reggie-2.18.png attached to net.sf.basedb.reggie/HistoryOfReggie by nicklas
Reggie 2.18
8:58 AM Milestone Reggie v2.18 completed
Improvements towards streamlining lab work for "real-time" sample …
8:57 AM PluginDownload edited by nicklas
Released Reggie 2.18 (diff)
8:57 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.18 (diff)
8:54 AM reggie-2.18.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.18
8:54 AM Ticket #674 (Generate document with report of sequencing results) closed by nicklas
fixed
8:53 AM Changeset [3003] by nicklas
Tagging Reggie 2.18
8:52 AM Changeset [3002] by nicklas
References #674: Generate document with report of sequencing results …
8:17 AM Changeset [3001] by nicklas
Preparing to release Reggie 2.18
8:13 AM Milestone Reggie v2.17.3 completed
Bug fixes for Reggie 2.17.2. See [wiki:net.sf.basedb.reggie Reggie …
8:12 AM Changeset [3000] by nicklas
Merge unreleased changes on 2.17-stable (#700) to trunk.

Dec 3, 2014:

1:34 PM Changeset [2999] by nicklas
References #674: Generate document with report of sequencing results …
1:27 PM Changeset [2998] by nicklas
References #674: Generate document with report of sequencing results …
1:10 PM Changeset [2997] by nicklas
References #674: Generate document with report of sequencing results …
1:08 PM Changeset [2996] by nicklas
Revert [2995] since it was missing a commit message.
1:05 PM Changeset [2995] by nicklas
8:16 AM Changeset [2994] by olle
Refs #608. LabEnv updated to new scripting pattern: 1. XML …
8:14 AM Changeset [2993] by nicklas
References #674: Generate document with report of sequencing results …
7:57 AM Changeset [2992] by olle
Refs #608. LabEnv updated to new scripting pattern: 1. XML …

Dec 2, 2014:

2:08 PM Changeset [2991] by nicklas
References #674: Generate document with report of sequencing results …
12:49 PM Changeset [2990] by nicklas
References #674: Generate document with report of sequencing results …
12:16 PM Changeset [2989] by olle
Refs #608. LabEnv updated to new scripting pattern: 1. XML …
10:48 AM Changeset [2988] by nicklas
References #674: Generate document with report of sequencing results …

Dec 1, 2014:

1:39 PM Changeset [2987] by olle
Refs #690. Plug-in configuration XML file plugin-configurations.xml
11:53 AM Changeset [2986] by nicklas
Fixes #708: Add example skin BASE 3.4 JAR files.

Nov 28, 2014:

1:43 PM Ticket #708 (Add example skin) closed by nicklas
fixed: (In [2985]) Fixes #708: Add example skin Added the "Pink Panther" …
1:43 PM Changeset [2985] by nicklas
Fixes #708: Add example skin Added the "Pink Panther" skin. It's not …
1:22 PM Ticket #708 (Add example skin) created by nicklas
It would be nice to have a simple example skin that demonstrates a few …

Nov 27, 2014:

1:37 PM Changeset [2984] by nicklas
Removing explicit reference to JRE6 to make Eclipse stop complaining …
1:34 PM Ticket #707 (Switch to Slf4j) closed by nicklas
fixed: (In [2983]) Fixes #707: Switch to Slf4j
1:34 PM Changeset [2983] by nicklas
Fixes #707: Switch to Slf4j
1:34 PM Ticket #707 (Switch to Slf4j) created by nicklas
We don't use any logging in the example code, but since the BASE core …
1:22 PM Ticket #706 (Update LabEnv to use BASE database capabilties instead of SQLite) created by nicklas
The LabEnv extension currently uses an SQLite database for storing …

Nov 25, 2014:

3:26 PM Changeset [2982] by nicklas
References #696: Implement some skin examples for BASE A little bit …
3:18 PM Ticket #701 (Check compability with BASE 3.4) closed by nicklas
fixed
2:59 PM Changeset [2981] by nicklas
References #701: Check compability with BASE 3.4 Some minor issues …
2:57 PM Ticket #705 (Remove internal sorting methods in retraction servlet) closed by nicklas
fixed: (In [2980]) Fixes #705: Remove internal sorting methods in retraction …
2:57 PM Changeset [2980] by nicklas
Fixes #705: Remove internal sorting methods in retraction servlet
2:53 PM Ticket #705 (Remove internal sorting methods in retraction servlet) created by nicklas
Sorting is preferably done by the database.
2:50 PM Ticket #704 (NullPointerException in retraction servlet when entering a case name ...) closed by nicklas
fixed: (In [2979]) Fixes #704: NullPointerException? in retraction servlet …
2:50 PM Changeset [2979] by nicklas
Fixes #704: NullPointerException? in retraction servlet when entering a …
2:39 PM Ticket #704 (NullPointerException in retraction servlet when entering a case name ...) created by nicklas
Stack trace from Reggie 2.17.3-dev […] Seems like …
1:04 PM Changeset [2978] by nicklas
References #696: Implement some skin examples for BASE Adding a …
1:03 PM net.sf.basedb.skincollection edited by nicklas
(diff)
9:12 AM Changeset [2977] by nicklas
References #696: Implement some skin examples for BASE Updated README.
9:07 AM net.sf.basedb.skincollection/ScreenShots edited by nicklas
(diff)
9:06 AM test-server.png attached to net.sf.basedb.skincollection/ScreenShots by nicklas
Gold skin with test server + server id
9:06 AM gold-skin-2.png attached to net.sf.basedb.skincollection/ScreenShots by nicklas
Gold skin create sample dialog
9:06 AM gold-skin-1.png attached to net.sf.basedb.skincollection/ScreenShots by nicklas
Gold skin welcome page
9:05 AM net.sf.basedb.skincollection/ScreenShots created by nicklas
9:03 AM net.sf.basedb.skincollection created by nicklas
Adding wiki page for the skin collection extension
8:33 AM Changeset [2976] by nicklas
References #679: Configuration file improvments Error message was …
8:19 AM Changeset [2975] by nicklas
References #696: Implement some skin examples for BASE Changed …
7:48 AM Ticket #703 (Make print package compatible with skins) closed by nicklas
fixed: (In [2974]) Fixes #703: Make print package compatible with skins
7:48 AM Changeset [2974] by nicklas
Fixes #703: Make print package compatible with skins
7:29 AM Ticket #703 (Make print package compatible with skins) created by nicklas
The current print package is ok, but there are some things that can be …

Nov 24, 2014:

3:33 PM Ticket #672 (RNA concentration normalization wizard) closed by nicklas
fixed
2:21 PM Changeset [2973] by nicklas
References #674: Generate document with report of sequencing results. …
2:16 PM Changeset [2972] by nicklas
References #696: Implement some skin examples for BASE Added color …
11:21 AM Changeset [2971] by nicklas
References #696: Implement some skin examples for BASE Need more …
11:20 AM Changeset [2970] by nicklas
References #701: Check compability with BASE 3.4 Print buttons on lab …
11:01 AM Ticket #702 (Use skin features in BASE 3.4) created by nicklas
BASE 3.4 introduces the possibility to install 'skins' to change the …
11:00 AM Ticket #701 (Check compability with BASE 3.4) created by nicklas
BASE 3.4 introduces the possibility to install 'skins' to change the …
9:27 AM Changeset [2969] by nicklas
References #696: Implement some skin examples for BASE Added …

Nov 21, 2014:

2:35 PM Changeset [2968] by nicklas
References #696: Implement some skin examples for BASE Added "Server …
12:55 PM Changeset [2967] by nicklas
References #696: Implement some skin examples for BASE Added "Gold" …

Nov 20, 2014:

12:31 PM Changeset [2966] by olle
Refs #690. Since no biopsy type annotation is currently used in …
11:25 AM Changeset [2965] by olle
Refs #690. Javascript file persinfo.js in resources/personal/
9:17 AM Changeset [2964] by olle
Refs #690. The case registration section is updated with an initial …
8:01 AM Ticket #700 (Missing '-' between plate name and library name in start alignment and ...) closed by nicklas
fixed: (In [2963]) Fixes #700: Missing '-' between plate name and library …
8:01 AM Changeset [2963] by nicklas
Fixes #700: Missing '-' between plate name and library name in start …
7:59 AM Ticket #700 (Missing '-' between plate name and library name in start alignment and ...) created by nicklas

Nov 19, 2014:

3:34 PM Changeset [2962] by olle
Refs #690. Two new sites, "Karlskrona" and "Växjö" added, both …
2:03 PM Changeset [2961] by nicklas
References #674: Generate document with report of sequencing results …
1:34 PM Changeset [2960] by nicklas
Merge Reggie 2.17.2 to trunk.
1:01 PM Changeset [2959] by nicklas
Preparing for future release Reggie 2.17.3
12:59 PM Milestone Reggie v2.17.2 completed
Bug fixes for Reggie 2.17.1. See [wiki:net.sf.basedb.reggie Reggie …
12:57 PM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.17.2 (diff)
12:56 PM reggie-2.17.2.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.17.2
12:56 PM Ticket #697 (Can't start alignment if there are libraries without a library plate) closed by nicklas
fixed
12:54 PM Changeset [2958] by nicklas
Tagging Reggie 2.17.2
12:53 PM Ticket #699 (Library registration doesn't warn about missing values in Caliper well ...) closed by nicklas
fixed: (In [2957]) Fixes #699: Caliper importer doesn't warn about missing …
12:53 PM Changeset [2957] by nicklas
Fixes #699: Caliper importer doesn't warn about missing values in …
11:58 AM Ticket #699 (Library registration doesn't warn about missing values in Caliper well ...) created by nicklas
If a Caliper well table CSV file contains a row for a sample that has …
10:57 AM Changeset [2956] by nicklas
Preparing to release Reggie 2.17.2
10:51 AM Changeset [2955] by nicklas
References #697: Can't start alignment if there are libraries without …
9:27 AM Changeset [2954] by nicklas
References #697: Can't start alignment if there are libraries without …
8:48 AM Ticket #698 (Set number of nodes in the demux wizard) closed by nicklas
fixed: (In [2953]) Fixes #698: Set number of nodes in the demux wizard
8:48 AM Changeset [2953] by nicklas
Fixes #698: Set number of nodes in the demux wizard
8:39 AM Changeset [2952] by nicklas
References #697: Can't start alignment if there are libraries without …
7:52 AM Ticket #698 (Set number of nodes in the demux wizard) created by nicklas
The number of nodes to use for a demux job is currently configured in …
7:49 AM Ticket #697 (Can't start alignment if there are libraries without a library plate) created by nicklas
The javascript is not prepared for this case since it tries to add the …

Nov 18, 2014:

1:10 PM Changeset [2951] by olle
Refs #690. Text file README updated to describe MeLuDi v.1.0-a01.
10:43 AM Changeset [2950] by olle
Refs #690. Currently unused files and directories removed (file …
10:40 AM Changeset [2949] by olle
Refs #690. Ant build file build.xml updated to not include removed …
8:46 AM Changeset [2948] by olle
Refs #690. Currently unused files and directories removed, forcing …
8:18 AM Changeset [2947] by olle
Refs #690. SVN properties svn:ignore updated/created for two …

Nov 17, 2014:

11:21 AM Changeset [2946] by olle
Refs #690. Java servlet ExportServlet removed, since it is not used …
10:00 AM Changeset [2945] by olle
Refs #690. Java classes/files updated to allow a "MeLuDi" column to …
9:52 AM Changeset [2944] by olle
Refs #690. Java servlet class/file InstallServlet.java in …
9:26 AM Changeset [2943] by nicklas
Merge Reggie 2.17.1 to trunk.
9:23 AM Changeset [2942] by nicklas
Preparing for future release Reggie 2.17.2
9:21 AM Milestone Reggie v2.17.1 completed
Bug fixes for Reggie 2.17. See [wiki:net.sf.basedb.reggie Reggie …
9:21 AM net.sf.basedb.reggie edited by nicklas
Released Reggie 2.17.1 (diff)
9:19 AM reggie-2.17.1.tar.gz attached to net.sf.basedb.reggie by nicklas
Reggie 2.17.1
9:18 AM Changeset [2941] by nicklas
Tagging Reggie 2.17.1
9:17 AM Changeset [2940] by nicklas
Preparing to release Reggie 2.17.1
8:48 AM Changeset [2939] by olle
Refs #690. CSS files case_summary.css and printable.css in …
8:41 AM Changeset [2938] by olle
Refs #690. Javascript file case-summary.js in resources/scripts/
8:29 AM Changeset [2937] by olle
Refs #690. Files README and RELEASE updated to refer to meludi
8:14 AM Changeset [2936] by olle
Refs #690. File LICENSE updated to refer to MeLuDi instead of Reggie.
7:45 AM Changeset [2935] by olle
Refs #690. File meludi.jar removed from source code control, since …
7:39 AM Changeset [2934] by olle
Refs #690. File json-simple-1.1.1.jar in lib/compile/ removed, …

Nov 14, 2014:

4:08 PM Changeset [2933] by olle
Refs #690. Initial check-in of source code for MeLuDi BASE extension. …
3:02 PM Changeset [2932] by nicklas
References #696: Implement some skin examples for BASE Initial …
1:57 PM Ticket #628 (Add right-click menu to create pools wizard) closed by nicklas
fixed: (In [2931]) Fixes #628: Add right-click menu to create pools wizard
1:57 PM Changeset [2931] by nicklas
Fixes #628: Add right-click menu to create pools wizard
1:56 PM Changeset [2930] by nicklas
References #672: RNA concentration normalization wizard .n instead of …
12:50 PM Changeset [2929] by nicklas
Adding trunk and tags to skin-collection.
12:49 PM Changeset [2928] by nicklas
Fixing typo.
12:49 PM Changeset [2927] by nicklas
Adding root folder for "Skin-collection" extension.
12:45 PM Ticket #696 (Implement some skin examples for BASE) created by nicklas
See http://base.thep.lu.se/ticket/1886 and …
8:28 AM Ticket #695 (New reporter annotations) created by nicklas
The default GTF file we use (UCSC_hg38_knownGenes_22sep2014.gtf) has …
8:25 AM Ticket #694 (Path-element tags should use subclass instad of clazz) closed by nicklas
fixed: (In [2926]) Fixes #694: Path-element tags should use subclass instad …
8:25 AM Changeset [2926] by nicklas
Fixes #694: Path-element tags should use subclass instad of clazz
8:22 AM Ticket #694 (Path-element tags should use subclass instad of clazz) created by nicklas
The case summary page uses clazz which effectively replaces the …

Nov 13, 2014:

9:54 AM Ticket #693 (Move debug utilities to a toolbar at bottom of page) closed by nicklas
fixed: (In [2925]) Fixes #693: Move debug utilities to a toolbar at bottom of …
9:54 AM Changeset [2925] by nicklas
Fixes #693: Move debug utilities to a toolbar at bottom of page Fixed …
9:35 AM Changeset [2924] by nicklas
References #693: Move debug utilities to a toolbar at bottom of page …

Nov 12, 2014:

2:55 PM Ticket #693 (Move debug utilities to a toolbar at bottom of page) created by nicklas
In some wizards there are debug utilities, for example, for generating …
2:50 PM Changeset [2923] by nicklas
References #672: RNA concentration normalization wizard Adding a …
9:31 AM Ticket #635 (Include analysis information in the case summary) closed by nicklas
fixed
9:11 AM Ticket #673 (Register RNA QC results from BioAnalyzer runs) closed by nicklas
fixed: (In [2922]) Fixes #673: Register RNA QC results from BioAnalyzer? runs …
9:11 AM Changeset [2922] by nicklas
Fixes #673: Register RNA QC results from BioAnalyzer? runs Manual …

Nov 11, 2014:

2:12 PM Changeset [2921] by nicklas
References #635: Include analysis information in the case summary Use …
1:53 PM Changeset [2920] by nicklas
References #689: Use new script for checking Illumina data files …
1:43 PM Ticket #692 (Some icons in case summary are broken in print version) closed by nicklas
fixed: (In [2919]) Fixes #692: Some icons in case summary are broken in print …
1:43 PM Changeset [2919] by nicklas
Fixes #692: Some icons in case summary are broken in print version
1:18 PM Changeset [2918] by nicklas
References #635: Include analysis information in the case summary …
1:16 PM Ticket #692 (Some icons in case summary are broken in print version) created by nicklas
For example, PDF file icons linked from some bioplates (eg. mRNA plate).
12:36 PM Ticket #691 (Items in case summary are not sorted) closed by nicklas
fixed: (In [2917]) Fixes #691: Items in case summary are not sorted Also …
12:36 PM Changeset [2917] by nicklas
Fixes #691: Items in case summary are not sorted Also added …
12:00 PM Ticket #691 (Items in case summary are not sorted) created by nicklas
For some item types, there is no specific ordering if there are …
11:40 AM Changeset [2916] by nicklas
References #635: Include analysis information in the case summary Add …
11:13 AM Changeset [2915] by nicklas
References #635: Include analysis information in the case summary Add …
11:01 AM Changeset [2914] by nicklas
References #635: Include analysis information in the case summary …
8:29 AM Changeset [2913] by nicklas
References #635: Include analysis information in the case summary …
8:05 AM Changeset [2912] by nicklas
References #635: Include analysis information in the case summary …
Note: See TracTimeline for information about the timeline view.