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preecej [Tue, 18 Sep 2012 17:14:51 +0000 (17:14 +0000)]
Two tickets in progress: Trac #149, 188.
Save and Close not done yet.
Object clearing associated with file-switching is improved, but not complete.
svn path=/; revision=378
ahmedi [Mon, 27 Aug 2012 19:24:59 +0000 (19:24 +0000)]
Test commit
svn path=/; revision=377
miles [Wed, 15 Aug 2012 19:09:12 +0000 (19:09 +0000)]
Final modifications. Working download link and image generation. Notes
for future: Downloadable image doesn't have special grey and gold
squares representing 0 and 1 genes, respectively. Possibility of
modification later. If the visual effects of the scroll bars on
heatMap.php page becomes an issue, consider surrounding current div tag
with an additional div tag in order to simulate scrolling.
svn path=/; revision=376
elserj [Wed, 15 Aug 2012 17:40:48 +0000 (17:40 +0000)]
Add back code to use the heatchart.java method
svn path=/; revision=375
preecej [Mon, 13 Aug 2012 22:32:23 +0000 (22:32 +0000)]
Changed Kevin McGuinness' affiliation and added a link to the orig software download
svn path=/; revision=374
miles [Mon, 13 Aug 2012 20:07:50 +0000 (20:07 +0000)]
Deleted unneeded files
svn path=/; revision=373
miles [Mon, 13 Aug 2012 20:06:37 +0000 (20:06 +0000)]
Added Web page files
svn path=/; revision=372
miles [Thu, 9 Aug 2012 21:44:35 +0000 (21:44 +0000)]
Updates for web page compatibility.
svn path=/; revision=371
miles [Wed, 25 Jul 2012 20:48:54 +0000 (20:48 +0000)]
Added webpage stuff.
svn path=/; revision=370
elserj [Wed, 25 Jul 2012 20:35:38 +0000 (20:35 +0000)]
Added HeatChart.java and modified it from original jar file to print the species on top. Also added some color and other options to the heatchart drawing.
svn path=/; revision=369
miles [Mon, 23 Jul 2012 22:53:04 +0000 (22:53 +0000)]
Fully operational image generation, independent of JHeatChart libraries.
svn path=/; revision=368
miles [Mon, 23 Jul 2012 22:16:47 +0000 (22:16 +0000)]
Working copy with JHeatChart.java. Puts the species axis at the bottom of the graph rather than the top.
svn path=/; revision=367
elserj [Fri, 20 Jul 2012 23:37:26 +0000 (23:37 +0000)]
Fixed empty args error. Also added code to print actual SQL error messages
svn path=/; revision=366
miles [Thu, 19 Jul 2012 21:02:54 +0000 (21:02 +0000)]
Tab Delimited File option fully functional. See tmp.txt for an example output file.
svn path=/; revision=365
preecej [Wed, 18 Jul 2012 02:52:09 +0000 (02:52 +0000)]
Added TO (Trait Ontology) web service and db access, fixed Annotation
form bug on listing Publications (no more tilde wildcards.)
svn path=/; revision=364
miles [Tue, 17 Jul 2012 18:38:39 +0000 (18:38 +0000)]
Now able to handle more than one gene at a time.
svn path=/; revision=363
miles [Tue, 17 Jul 2012 18:11:08 +0000 (18:11 +0000)]
Species now unique and alphabetized, geneMaps properly constructed, no errors.
svn path=/; revision=362
miles [Tue, 17 Jul 2012 17:15:11 +0000 (17:15 +0000)]
Trying to move most of workload from java to sql. Hoping to also overcome issues with repeat species in the final list and parsing of data into heatmap format.
svn path=/; revision=361
miles [Mon, 16 Jul 2012 22:14:15 +0000 (22:14 +0000)]
Initial import.
svn path=/; revision=360
preecej [Sat, 14 Jul 2012 00:33:57 +0000 (00:33 +0000)]
Fixed curr_ontology_type bug in transform_gaf, correctly switches
between ontologies in the same file during XML generation
svn path=/; revision=359
preecej [Fri, 13 Jul 2012 17:46:16 +0000 (17:46 +0000)]
Added "Assigned By" field
svn path=/; revision=358
preecej [Fri, 13 Jul 2012 17:25:58 +0000 (17:25 +0000)]
Can now handle "Assigned By" (GAF column 15); fixed a couple of bugs;
added "Vitis vinifera" species handling
svn path=/; revision=357
miles [Mon, 9 Jul 2012 21:13:49 +0000 (21:13 +0000)]
initializing miles van de wetering's file
svn path=/; revision=356
preecej [Sat, 7 Jul 2012 01:33:59 +0000 (01:33 +0000)]
Updated to work for Vitis vinifera (grape) imports. Also handled some
"missing data" scenarios for the Gene Name and Evidence fields.
svn path=/; revision=355
preecej [Fri, 6 Jul 2012 03:24:01 +0000 (03:24 +0000)]
modified to match non-Mac updates to config files
svn path=/; revision=354
preecej [Fri, 6 Jul 2012 00:22:37 +0000 (00:22 +0000)]
Trac #157: closed
#149: still working on recalculating window size and placement for a new image, maybe also need to dispose annotations and segments from previous image.
svn path=/; revision=353
preecej [Wed, 4 Jul 2012 22:29:31 +0000 (22:29 +0000)]
[Trac tickets]
Closed: 204,200,203,202,198
Held: 193,188,186
Working on Trac tickets: 149,157
svn path=/; revision=352
preecej [Wed, 4 Jul 2012 01:56:30 +0000 (01:56 +0000)]
Memory disposal work (when opening a new file) in progress.
svn path=/; revision=351
preecej [Wed, 27 Jun 2012 20:33:34 +0000 (20:33 +0000)]
Changed app name to SIA where necessary, re-added Exit menu option (under File), removed Tools menu dropdown
svn path=/; revision=350
athreyab [Tue, 12 Jun 2012 20:09:20 +0000 (20:09 +0000)]
remove annotated_keyword_listid column
svn path=/; revision=349
athreyab [Mon, 11 Jun 2012 20:13:30 +0000 (20:13 +0000)]
interaction db stuff
svn path=/; revision=348
athreyab [Mon, 11 Jun 2012 20:02:28 +0000 (20:02 +0000)]
renaming image_annotation to image_annotation_db
svn path=/; revision=347
athreyab [Mon, 11 Jun 2012 20:01:00 +0000 (20:01 +0000)]
image annotation database stuff
svn path=/; revision=346
preecej [Thu, 7 Jun 2012 22:05:21 +0000 (22:05 +0000)]
sew together SSR data from 3 different sample transcriptome assemblies
, correlate via BLAST, output SSR count differentials amongst resulting orthologs >
dimer
svn path=/; revision=345
preecej [Wed, 6 Jun 2012 22:57:35 +0000 (22:57 +0000)]
svn path=/; revision=344
athreyab [Tue, 5 Jun 2012 23:35:32 +0000 (23:35 +0000)]
documentation
svn path=/; revision=343
lingutln [Tue, 5 Jun 2012 20:53:56 +0000 (20:53 +0000)]
Coordinates saving functionality and some UI alignments. Done by Nikhil.
svn path=/; revision=342
lingutln [Thu, 31 May 2012 20:45:20 +0000 (20:45 +0000)]
Saving annotated images functionality and UI changes. Done by Nikhil.
svn path=/; revision=341
lingutln [Thu, 31 May 2012 19:34:56 +0000 (19:34 +0000)]
Data storage functionality completed. Done by Nikhil.
svn path=/; revision=340
preecej [Thu, 31 May 2012 19:12:13 +0000 (19:12 +0000)]
Added parameters to the term search web service call for prioritizing exact match and grouping branches
svn path=/; revision=339
preecej [Sat, 26 May 2012 01:38:17 +0000 (01:38 +0000)]
term detail web service fix, and some temp URL testing of the next web service version
svn path=/; revision=338
preecej [Sat, 26 May 2012 00:09:53 +0000 (00:09 +0000)]
Moved term detail synonyms to separate table; more debugging to to, alon with bolding the selected synonym
svn path=/; revision=337
lingutln [Thu, 24 May 2012 20:56:07 +0000 (20:56 +0000)]
Data retrieval functionality completed and using ontologyterm object everywhere. Done by Nikhil.
svn path=/; revision=336
preecej [Wed, 23 May 2012 23:00:53 +0000 (23:00 +0000)]
UI and term search web service adjustments
svn path=/; revision=335
preecej [Wed, 23 May 2012 20:43:06 +0000 (20:43 +0000)]
Simple gene and expression data mapping scripts for the Rice Seed Dev
project
svn path=/; revision=334
lingutln [Tue, 22 May 2012 23:41:52 +0000 (23:41 +0000)]
Modified some UI functionalities and Species terms bug. Done by Nikhil.
svn path=/; revision=333
lingutln [Mon, 21 May 2012 22:32:44 +0000 (22:32 +0000)]
Data retrieval(Fully done). Data storage(except saving boundary coordinates). Done by Nikhil.
svn path=/; revision=332
athreyab [Sat, 19 May 2012 17:23:55 +0000 (17:23 +0000)]
remove first \1
svn path=/; revision=331
preecej [Wed, 16 May 2012 22:45:21 +0000 (22:45 +0000)]
PO web service term detail call complete; still needs UI refinement (i.e. nested list for synonyms with annotated synonym highlighted, proper horiz and vert expansion of composite) but the basics are there
svn path=/; revision=330
preecej [Tue, 15 May 2012 23:58:32 +0000 (23:58 +0000)]
in progress: ontologyTerm refactoring associated with term detail web service call
svn path=/; revision=329
preecej [Tue, 15 May 2012 21:36:26 +0000 (21:36 +0000)]
in progress: term details web service call
svn path=/; revision=328
athreyab [Tue, 1 May 2012 02:36:13 +0000 (02:36 +0000)]
pair/singleton script update
svn path=/; revision=327
athreyab [Tue, 1 May 2012 00:20:22 +0000 (00:20 +0000)]
bash script for creating singleton/pair
svn path=/; revision=326
athreyab [Mon, 16 Apr 2012 20:47:29 +0000 (20:47 +0000)]
illumina parse scripts
svn path=/; revision=325
preecej [Thu, 12 Apr 2012 19:13:58 +0000 (19:13 +0000)]
Changed PO web service term_search URL: removed branch filter
svn path=/; revision=324
preecej [Wed, 11 Apr 2012 23:42:19 +0000 (23:42 +0000)]
Moved permanently to /plantontology repo (/html/services/)
svn path=/; revision=323
preecej [Wed, 11 Apr 2012 23:09:50 +0000 (23:09 +0000)]
changed PO aspect (branch) reference to
"plant_structure_development_stage"
svn path=/; revision=322
preecej [Wed, 11 Apr 2012 22:59:50 +0000 (22:59 +0000)]
Made this service environment-independent. Now refers to db connection
string values with generic names.
svn path=/; revision=321
preecej [Wed, 11 Apr 2012 20:41:51 +0000 (20:41 +0000)]
Updated "plant growth and development stage" to "plant structure
development stage"
svn path=/; revision=320
lingutln [Tue, 10 Apr 2012 20:49:54 +0000 (20:49 +0000)]
Resolved refactoring of segment label. Done by Nikhil.
svn path=/; revision=319
lingutln [Mon, 9 Apr 2012 23:21:19 +0000 (23:21 +0000)]
svn path=/; revision=318
lingutln [Mon, 9 Apr 2012 23:05:07 +0000 (23:05 +0000)]
Base64 Decoding for UBio webservice. Done by Nikhil.
svn path=/; revision=317
lingutln [Mon, 9 Apr 2012 21:05:21 +0000 (21:05 +0000)]
Implemented Ubio Web service integration.(yet to complete reloading functionality) Done by Nikhil.
svn path=/; revision=316
preecej [Wed, 4 Apr 2012 23:53:59 +0000 (23:53 +0000)]
Adding an html_mocks folder for design mocks, first set of content for
PO Image Annotation popup
svn path=/; revision=315
elserj [Wed, 14 Mar 2012 22:20:44 +0000 (22:20 +0000)]
Fix broken relative link with absolute link. Relative would be better but because of the structure of drupal, absolute is required
svn path=/; revision=314
preecej [Tue, 13 Mar 2012 20:39:00 +0000 (20:39 +0000)]
Limited "Recent blog posts" retrieval to 5 lines.
svn path=/; revision=313
preecej [Tue, 13 Mar 2012 20:38:07 +0000 (20:38 +0000)]
New directory used to hold small changes to Drupal basecode. If large
changes start to pile up, consider moving to a complete SVN repo of our
Drupal install.
svn path=/; revision=312
preecej [Mon, 12 Mar 2012 23:21:01 +0000 (23:21 +0000)]
added bullets to right nav blog posts (class item-list)
svn path=/; revision=311
lingutln [Mon, 12 Mar 2012 18:56:49 +0000 (18:56 +0000)]
Latest Commits. Done by Nikhil.
svn path=/; revision=310
preecej [Wed, 7 Mar 2012 22:02:01 +0000 (22:02 +0000)]
stylesheet adjustment for transparent banner background
svn path=/; revision=309
preecej [Wed, 7 Mar 2012 21:30:05 +0000 (21:30 +0000)]
made banner background match general background; should move to new style in CSS
svn path=/; revision=308
preecej [Wed, 7 Mar 2012 21:15:03 +0000 (21:15 +0000)]
Modified DRUPAL HEADER to use Jaiswal Lab logo if no $site_name is provided; need to eventually make this a configurable setting via osu_confident.info
svn path=/; revision=307
lingutln [Mon, 5 Mar 2012 21:08:08 +0000 (21:08 +0000)]
Saving as a zip file functionality. Done by Nikhil.
svn path=/; revision=306
lingutln [Mon, 5 Mar 2012 18:55:24 +0000 (18:55 +0000)]
Saving as a zip functionality. Done by Nikhil.
svn path=/; revision=305
lingutln [Thu, 1 Mar 2012 00:23:54 +0000 (00:23 +0000)]
Saving imagemap as a zip file functionality. Done by Nikhil.
svn path=/; revision=304
athreyab [Tue, 28 Feb 2012 22:44:18 +0000 (22:44 +0000)]
committing missed files and minor changes to the sif script
svn path=/; revision=303
athreyab [Tue, 28 Feb 2012 19:13:12 +0000 (19:13 +0000)]
modifications to add date and column type changes
svn path=/; revision=302
lingutln [Mon, 20 Feb 2012 20:05:09 +0000 (20:05 +0000)]
Minor alignments in Linux and Windows OS. Done by Nikhil.
svn path=/; revision=301
lingutln [Sun, 19 Feb 2012 01:19:09 +0000 (01:19 +0000)]
Minor alignments in Windows machine. Done by Nikhil.
svn path=/; revision=300
lingutln [Sat, 18 Feb 2012 22:49:37 +0000 (22:49 +0000)]
Latest Changes. Done by Nikhil.
svn path=/; revision=299
lingutln [Fri, 10 Feb 2012 21:54:14 +0000 (21:54 +0000)]
Saving metadata to HTML imagemap. Done by Nikhil.
svn path=/; revision=298
lingutln [Fri, 10 Feb 2012 02:46:16 +0000 (02:46 +0000)]
svn path=/; revision=297
preecej [Tue, 7 Feb 2012 01:32:27 +0000 (01:32 +0000)]
Changed curator names in application.properties; added SelectionListener to term lookup combobox
svn path=/; revision=296
lingutln [Mon, 6 Feb 2012 22:25:11 +0000 (22:25 +0000)]
Right panel elements added. Done by Nikhil.
svn path=/; revision=295
preecej [Fri, 3 Feb 2012 23:47:46 +0000 (23:47 +0000)]
Corrected relative path of rotating images gallery when no custom path
provided
svn path=/; revision=294
preecej [Thu, 2 Feb 2012 21:23:36 +0000 (21:23 +0000)]
New themes for the Jaiswal Lab site, provided by OSU CWS in Jan 2012.
Not dependent on CWS, will branch and modify/debug locally only as
needed. Note: Standard and Confident themes each have dependencies on OSU
Drupal 1_11 theme. All must be present in Drupal instance for proper
operation.
svn path=/; revision=293
lingutln [Wed, 1 Feb 2012 23:47:37 +0000 (23:47 +0000)]
Added two fields and alignments to the right panel. Done by Nikhil.
svn path=/; revision=292
preecej [Tue, 31 Jan 2012 23:25:19 +0000 (23:25 +0000)]
Refactored web service response term data into Term object. Created Term class; now used by term lookup dropdown and "term edit" popup dialogue. Should also be added to term label, term detail web service response and file metadata export.
svn path=/; revision=291
athreyab [Tue, 31 Jan 2012 22:56:55 +0000 (22:56 +0000)]
allow sif file to be a source of gene information
svn path=/; revision=290
lingutln [Tue, 31 Jan 2012 21:56:32 +0000 (21:56 +0000)]
Right panel modifications. Done by Nikhil.
svn path=/; revision=289
preecej [Tue, 31 Jan 2012 01:33:35 +0000 (01:33 +0000)]
updated list of termDetailTable items to build from an enum (up in declarations)
svn path=/; revision=288
preecej [Tue, 31 Jan 2012 00:09:44 +0000 (00:09 +0000)]
Moved PO web service calls to application.properties file; added lookup label focus listener for PO term details call
svn path=/; revision=287
athreyab [Mon, 30 Jan 2012 22:04:22 +0000 (22:04 +0000)]
removed sample data files and other unwanted script files
svn path=/; revision=286
elserj [Mon, 30 Jan 2012 21:46:02 +0000 (21:46 +0000)]
Updated for newer version of physcomitrella fasta file
svn path=/; revision=285
lingutln [Mon, 30 Jan 2012 21:23:23 +0000 (21:23 +0000)]
Layout changes. Done by Nikhil.
svn path=/; revision=284
lingutln [Mon, 30 Jan 2012 00:03:11 +0000 (00:03 +0000)]
ImageMap functionality for multiple labels. Done by Nikhil.
svn path=/; revision=283
athreyab [Sun, 29 Jan 2012 19:11:02 +0000 (19:11 +0000)]
support for looking up existing species information
svn path=/; revision=282
preecej [Thu, 26 Jan 2012 23:50:30 +0000 (23:50 +0000)]
Stubbed out termDetailTable control on the right panel
svn path=/; revision=281
lingutln [Thu, 26 Jan 2012 19:42:18 +0000 (19:42 +0000)]
Multi segment saving to imagemaps (partially done). Done by Nikhil.
svn path=/; revision=280
athreyab [Thu, 26 Jan 2012 01:50:36 +0000 (01:50 +0000)]
addressed a few review comments from Justin
svn path=/; revision=279
projects / old-jaiswallab-svn / .git / log