Timeline



Nov 29, 2018:

11:31 AM Changeset [5155] by olle
Refs #1029. BASE-line registration from file updated for 10x10 blood …

Nov 28, 2018:

2:48 PM Changeset [5154] by olle
Refs #1029. FFPE section order form generation updated to use a yellow …
1:17 PM Changeset [5153] by Nicklas Nordborg
References #1087: Changes needed for supporting multiple …
10:08 AM Changeset [5152] by olle
Refs #1029. BASE-line registration from file updated to use 10x10 …
9:58 AM Changeset [5151] by Nicklas Nordborg
References #1087: Changes needed for supporting multiple …
9:54 AM Changeset [5150] by Nicklas Nordborg
References #1086: Changes needed for supporting multiple …
8:57 AM Changeset [5149] by olle
Refs #1029. BASE-line registration from file updated to support CSV …

Nov 26, 2018:

10:29 AM Changeset [5148] by Nicklas Nordborg
References #1086: Changes needed for supporting multiple …
10:28 AM Changeset [5147] by Nicklas Nordborg
References #1087: Changes needed for supporting multiple …
8:54 AM Changeset [5146] by Nicklas Nordborg
References #1087: Changes needed for supporting multiple …
8:46 AM Changeset [5145] by Nicklas Nordborg
References #1087: Changes needed for supporting multiple …
8:45 AM Changeset [5144] by Nicklas Nordborg
References #1086: Changes needed for supporting multiple …
8:43 AM Changeset [5143] by Nicklas Nordborg
References #1086: Changes needed for supporting multiple …

Nov 23, 2018:

12:51 PM Ticket #1087 (Changes needed for supporting multiple authentication managers) created by Nicklas Nordborg
The OTP extension should be updated so that it works with multiple …
12:50 PM Ticket #1086 (Changes needed for supporting multiple authentication managers) created by Nicklas Nordborg
The Yubikey extension should be updated so that it works with multiple …

Nov 22, 2018:

2:51 PM Ticket #1085 (Remove the temporary hack for handling FlowThrough names with .f suffix) created by Nicklas Nordborg
The production server has been updated so that all FlowThrough items …
1:33 PM Changeset [5142] by Nicklas Nordborg
References #1081: The release exporter should export more data Added …
11:06 AM Changeset [5141] by Nicklas Nordborg
References #1080: Add "Manual" option to the DoNotUse? annotation type …
10:45 AM Changeset [5140] by Nicklas Nordborg
References #1081: The release exporter should export more data Added …
9:17 AM Changeset [5139] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
9:03 AM Changeset [5138] by Nicklas Nordborg
References #1081: The release exporter should export more data Added …
8:00 AM Changeset [5137] by olle
Refs #1029. FFPE section registration wizard updated in help text by …
7:47 AM Changeset [5136] by Nicklas Nordborg
References #1081: The release exporter should export more data Added …
7:34 AM Changeset [5135] by olle
Refs #1029. Case summary updated in FFPE block section by adding row …

Nov 21, 2018:

4:12 PM Changeset [5134] by Nicklas Nordborg
References #1074: Add more subtypes Added NoSpecimen subtype.
3:51 PM Changeset [5133] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
3:51 PM Changeset [5132] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
2:05 PM Changeset [5131] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
1:35 PM Changeset [5130] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
12:07 PM Changeset [5129] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …
12:04 PM Changeset [5128] by olle
Refs #1029. Updates due to version number change to "1.6.0a10". 1. …
11:37 AM Changeset [5127] by olle
Refs #1029. FFPE section order form wizard updated with new button …
10:14 AM Changeset [5126] by olle
Refs #1029. FFPE section (specimen) registration wizard updated to …
9:56 AM Ticket #1084 (DataFileFolder annotation should always set a default value) closed by Nicklas Nordborg
fixed: (In [5125]) Fixes #1084: DataFileFolder? annotation should always set a …
9:56 AM Changeset [5125] by Nicklas Nordborg
Fixes #1084: DataFileFolder? annotation should always set a default value
9:55 AM Ticket #1084 (DataFileFolder annotation should always set a default value) created by Nicklas Nordborg
Existing items that doesn't have a value for DataFilesFolder should …
9:48 AM Changeset [5124] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
9:11 AM Changeset [5123] by Nicklas Nordborg
References #1074: Add more subtypes The "NO" subtype should be "No".
9:10 AM Changeset [5122] by Nicklas Nordborg
References #1071: Installation wizard doesn't show error message …
9:08 AM Changeset [5121] by olle
Refs #1029. FFPE section (specimen) registration wizard updated with …
8:15 AM Ticket #1083 (Add mBAF plot column to derived bioassay list) closed by Nicklas Nordborg
fixed: (In [5120]) Fixes #1083: Add mBAF plot column to derived bioassay list …
8:15 AM Changeset [5120] by Nicklas Nordborg
Fixes #1083: Add mBAF plot column to derived bioassay list The …
8:11 AM Ticket #1083 (Add mBAF plot column to derived bioassay list) created by Nicklas Nordborg
The column should be used to display thumbnails of the mBAF plots in …
8:04 AM Changeset [5119] by olle
Refs #1029. FFPE section (specimen) registration wizard updated by …
7:56 AM Ticket #1082 (HaplotypeCaller should not write command line parameters in result file) closed by Nicklas Nordborg
fixed: (In [5118]) Fixes #1082: HaplotypeCaller? should not write command line …
7:56 AM Changeset [5118] by Nicklas Nordborg
Fixes #1082: HaplotypeCaller? should not write command line parameters …
7:41 AM Ticket #1082 (HaplotypeCaller should not write command line parameters in result file) created by Nicklas Nordborg
Just in case the command line contains some sensitive information. …

Nov 20, 2018:

4:09 PM Changeset [5117] by Nicklas Nordborg
References #1081: The release exporter should export more data The …
3:03 PM Changeset [5116] by olle
Refs #1029. FFPE block order form wizard updated to no longer write …
2:13 PM Changeset [5115] by olle
Refs #1029. Case summary updated to support new naming scheme for DNA …
1:42 PM Changeset [5114] by olle
Refs #1029. FFPE section (specimen) registration wizard updated: 1. …
1:06 PM Ticket #1080 (Add "Manual" option to the DoNotUse annotation type) closed by Nicklas Nordborg
fixed: (In [5113]) Fixes #1080: Add "Manual" option to the DoNotUse?
1:06 PM Changeset [5113] by Nicklas Nordborg
Fixes #1080: Add "Manual" option to the DoNotUse? annotation type
1:03 PM Ticket #1079 (The FrozenTissue date importer should ignore lines without date) closed by Nicklas Nordborg
fixed: (In [5112]) Fixes #1079: The FrozenTissue? date importer should ignore …
1:03 PM Changeset [5112] by Nicklas Nordborg
Fixes #1079: The FrozenTissue? date importer should ignore lines …
12:55 PM Ticket #1081 (The release exporter should export more data) created by Nicklas Nordborg
For existing items we should export more annotations/other data: * …
12:54 PM Changeset [5111] by olle
Refs #1029. FFPE section registration wizard prepared for new sample …
12:52 PM Ticket #1080 (Add "Manual" option to the DoNotUse annotation type) created by Nicklas Nordborg
12:51 PM Ticket #1079 (The FrozenTissue date importer should ignore lines without date) created by Nicklas Nordborg
This includes empty lines and lines with only white-space. Seems like …
10:24 AM Changeset [5110] by olle
Refs #1029. Support for showing connected "chained" items in Case …

Nov 19, 2018:

2:35 PM Changeset [5109] by Nicklas Nordborg
References #1074: Add more subtypes Added Retract, No, NotAsked, …
2:22 PM net.sf.basedb.reggie/notes421 edited by Nicklas Nordborg
Added notes about ticket #1078 (diff)
2:06 PM Changeset [5108] by Nicklas Nordborg
References #1078: "Not asked" subtype should be renamed to "NotAsked?" …
1:27 PM Ticket #1078 ("Not asked" subtype should be renamed to "NotAsked") created by Nicklas Nordborg
The change must be made manually by an administrator before updating …
1:25 PM Changeset [5107] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
10:58 AM Changeset [5106] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
8:30 AM Changeset [5105] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …

Nov 16, 2018:

2:19 PM Changeset [5104] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
12:32 PM Changeset [5103] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
9:20 AM Changeset [5102] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
8:26 AM Changeset [5101] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …

Nov 15, 2018:

2:18 PM Changeset [5100] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
1:13 PM Changeset [5099] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
11:43 AM Changeset [5098] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
9:07 AM Changeset [5097] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …

Nov 14, 2018:

2:52 PM Changeset [5096] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
2:35 PM Changeset [5095] by olle
Refs #1029. Updates needed for FFPE blocks in selection menus to show …
2:19 PM Changeset [5094] by olle
Refs #1029. MeLuDI updated with new configuration variables …
1:26 PM Changeset [5093] by olle
Refs #1029. Basic support for Histology and H&E glass items added. The …
12:05 PM Changeset [5092] by olle
Refs #1029. Support for showing connected "chained" items in Case …
10:46 AM Changeset [5091] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
9:22 AM Changeset [5090] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …
8:15 AM Changeset [5089] by Nicklas Nordborg
References #1075: Change the release exporter to work with list of …

Nov 13, 2018:

3:58 PM net.sf.basedb.reggie/notes421 created by Nicklas Nordborg
Adding update notes for Reggie 4.21
3:39 PM Ticket #1077 (All biosource items should have an external id (release id)) closed by Nicklas Nordborg
fixed: (In [5088]) Fixes #1077: All biosource items should have an external …
3:39 PM Changeset [5088] by Nicklas Nordborg
Fixes #1077: All biosource items should have an external id (release …
2:20 PM Ticket #1077 (All biosource items should have an external id (release id)) created by Nicklas Nordborg
Currently, among the Biosource item types it is only Patient items …
1:25 PM Ticket #1076 (The Level 3 export plug-in should generate rsync script with -L option) closed by Nicklas Nordborg
fixed: (In [5087]) Fixes #1076: The Level 3 export plug-in should generate …
1:25 PM Changeset [5087] by Nicklas Nordborg
Fixes #1076: The Level 3 export plug-in should generate rsync script …
1:12 PM Ticket #1076 (The Level 3 export plug-in should generate rsync script with -L option) created by Nicklas Nordborg
The current script only has -l option (implicit via -a) which …
10:22 AM Ticket #1075 (Change the release exporter to work with list of patients) created by Nicklas Nordborg
The current release exporter plug-in works with a list of raw …
10:17 AM Ticket #1074 (Add more subtypes) created by Nicklas Nordborg
The next release will start from the patient side and include other …

Nov 12, 2018:

11:21 AM Changeset [5086] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen …
8:58 AM Changeset [5085] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen …
8:31 AM Changeset [5084] by olle
Refs #1029. FFPE section order form wizard updated to show material …
7:56 AM Changeset [5083] by olle
Refs #1029. FFPE section order form wizard updated when creating label …
7:49 AM Changeset [5082] by olle
Refs #1029. FFPE section order form generation updated for new PDF …

Nov 9, 2018:

11:11 AM Changeset [5081] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen …
8:52 AM Changeset [5080] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen …

Nov 8, 2018:

1:30 PM Changeset [5079] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen The …
12:59 PM Changeset [5078] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen The …

Nov 7, 2018:

1:12 PM Changeset [5077] by Nicklas Nordborg
References #1072: Introduce Lysate item between RNA and Specimen …
10:39 AM Ticket #1073 (Switch to BASE 3.13) closed by Nicklas Nordborg
fixed: (In [5076]) Fixes #1073: Switch to BASE 3.13
10:39 AM Changeset [5076] by Nicklas Nordborg
Fixes #1073: Switch to BASE 3.13
9:55 AM Ticket #1073 (Switch to BASE 3.13) created by Nicklas Nordborg
Since this is the current version.
9:43 AM Ticket #1072 (Introduce Lysate item between RNA and Specimen) created by Nicklas Nordborg
The existing structure has a direct link between RNA and Specimen. We …

Nov 6, 2018:

4:42 PM Changeset [5075] by olle
Refs #1029. Annotation type Annotationtype.LOCALIZATION updated to …
8:59 AM Changeset [5074] by olle
Refs #1029. FFPE block registration wizard updated for new input …

Nov 5, 2018:

4:29 PM Changeset [5073] by olle
Refs #1029. FFPE block registration wizard updated by fixing typo: …

Nov 1, 2018:

2:34 PM Changeset [5072] by olle
Refs #1029. Updates due to version number change to "1.6.0-dev". …
2:10 PM Changeset [5071] by olle
Refs #1029. Updates due to version number change to "1.6.0a9". 1. …
8:46 AM Changeset [5070] by olle
Refs #1029. FFPE block order form wizard updated by renaming button …
8:37 AM Changeset [5069] by olle
Refs #1029. FFPE section order form wizard updated to create label …

Oct 31, 2018:

9:03 AM Changeset [5068] by olle
Refs #1029. Data access object file SpecimenTube.java in …
8:57 AM Changeset [5067] by Nicklas Nordborg
Changes for future release Reggie 4.21
8:55 AM Milestone Reggie v4.20 completed
See Reggie extension page for more information.
8:55 AM PluginDownload edited by Nicklas Nordborg
Released Reggie 4.20 (diff)
8:53 AM net.sf.basedb.reggie edited by Nicklas Nordborg
Released Reggie 4.20 (diff)
8:51 AM reggie-4.20.tar.gz attached to net.sf.basedb.reggie by Nicklas Nordborg
Reggie 4.20
8:50 AM Ticket #1054 (Even more functionality in the Flagged alignment wizard) closed by Nicklas Nordborg
fixed
8:47 AM Changeset [5066] by Nicklas Nordborg
Tagging Reggie 4.20
8:47 AM Changeset [5065] by Nicklas Nordborg
Preparing to release Reggie 4.20
8:44 AM Changeset [5064] by Nicklas Nordborg
References #1068: Add mBAF analysis step to the Hisat/StringTie?
8:39 AM Changeset [5063] by Nicklas Nordborg
References #1054: Even more functionality in the Flagged alignment …
8:35 AM Ticket #1068 (Add mBAF analysis step to the Hisat/StringTie pipeline) closed by Nicklas Nordborg
fixed

Oct 30, 2018:

2:58 PM Changeset [5062] by olle
Refs #1029. First version of registration wizard for returned FFPE …
10:49 AM Changeset [5061] by olle
Refs #1029. FFPE section block/section wizards updated for new/changed …
Note: See TracTimeline for information about the timeline view.