From: <mg...@us...> - 2007-05-02 18:37:09
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Revision: 539 http://svn.sourceforge.net/obo/?rev=539&view=rev Author: mgibson Date: 2007-05-02 11:37:03 -0700 (Wed, 02 May 2007) Log Message: ----------- docs for release Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-release-notes.html phenote/trunk/doc/phenote-website/phenote.html phenote/trunk/src/java/phenote/datamodel/Ontology.java Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-02 18:26:05 UTC (rev 538) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-02 18:37:03 UTC (rev 539) @@ -3,13 +3,17 @@ <head> + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + <title>Phenote Release Notes</title> </head> @@ -17,241 +21,329 @@ <body> + <h1>Phenote Release Notes</h1> -1.2 -will probably come out in May<br> +1.3 +will probably come out in June<br> +<br> +<h2><span style="text-decoration: underline;">1.2</span></h2> +<a href="1.2/phenote.jnlp">Phenote 1.2</a><br> +<br> + + Features: -Can post-compose with >2 terms <br> +Can post-compose with >2 terms <br> + Term history display can be toggled on/off <br> + Synonym types display in term info<br> + Obsolete replacements displayed in term info<br> + Search filters moved into menu <br> + Loading splash screen <br> +Can configure by namespace for ontologies<br> -Bug Fixes: +Bug Fixes: Free text field text not "sticking" + <h2><span style="text-decoration: underline;">1.1</span></h2> + <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> + <br> + March 28, 2007<br> + <br> + Phenote will merge its default configuration with users configuration, preserving users changes as well as adding anything new from phenote upgrade.<br> + User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart).<br> + Tab delimited data adapter - thank you nicole!<br> + Beginnings of term history - thank you nicole!<br> + Tabbed main field panel if more than 12 fields.<br> + QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.<br> + Layout improved<br> + Can now search ALL ontologies of a field<br> + Retrieve obo from web if more up to date or no local found<br> + Refactored code for field guis<br> + Ontology chooser reflects current term (bug fix) <h2><span style="text-decoration: underline;">1.0</span></h2> + <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase webby phenote</a><br> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> + <br> + January 12, 2007<br> + <br> + The main improvement here is the ability to add any field you like, not just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence, Description, Abnormal, and Absent have been added through this new mechanism. This entailed a refactoring of the datamodel.<br> + <br> + Webby phenote is now using JSP and Spring.<br> + <br> + There has been some recent work with UVictoria for ontology graph visualization. This is coming along well and hopefully will be seen in the next release. <h2><span style="text-decoration: underline;">0.9</span></h2> + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + mid November 2006<br> + <br> + Undo<br> + Christian Pich(Zfin) has added a Quartz scheduler to phenote, which zfin takes advantage of, to schedule when to check for new obo files.<br> + Also Christian Pich upgraded the PhenoteServlet to the Spring framework - much nicer!<br> + Synonyms are now returned from auto complete with [syn] and when selected the term goes in the field (webby & standalone), obsoletes hits with [obs]<br> + Bulk update & copy in standalone.<br> + Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file saver says save not load and recognizes adapter by file extensions, psx->phenosyntax, .xml -> phenoxml <br> + Single quotes escaped for javascript fns.<br> + <h2><span style="text-decoration: underline;">0.8</span></h2> + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + 10/2/06<br> + Added post composition to standalone phenote. Logging for both webby/servlet & standalone.<br> + Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml writer (does pub & genetic context)<br> + Command line reading & writing of phenoxml & phenosyntax.<br> + Application exits on window exit (unless servlet)<br> + Can filter out stage terms from zfin anatomy<br> + <h2><span style="text-decoration: underline;">0.7</span></h2> + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + Web: entity chooser, can configure to check for new obo files and load them. (These are installed at zfin, if anyone would like to see them publicly let me know). Entity field and term info installed into zfin phenotype site. term info & completion are scrollable.<br> + Standalone: can read & write pheno-syntax with ids & term names in comments, entity chooser, pub field, use button in term info, sort table by clicking on headers, personal config file gets copied out of jar, paste mac bug fixed, file load/save remembered,layout fixed<br> + <br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote (0.6)</a><br> + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> + <br> + The main feature of release 0.6 is a webby phenote. This is in its extremely early stages (very little functionality and buggy). At this point it only does Entity and Quality fields and term info and thats it, and even thats buggy, but more coming soon! <br> + <br> + Not much new in the stand alone phenote (as Ive been working on the webby phenote). Mainly it can write pheno-xml, and it uses the latest pato (as of July 28, 2006).<br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2> + <br> + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> + <br> + 5/12/06<br> + No new additions to the gui here. In preparation for my visit to Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote first data adapter so I also laid down the foundations for data @@ -265,30 +357,39 @@ character strings.<br> + <h2><span style="text-decoration: underline;">0.4</span></h2> + <a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br> + <a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br> + <br> + 4/26/06<br> + Added Genetic Context field.<br> + Parent & child terms in term info are now clickable/navigable.<br> + Links in descriptions are clickable (should bring up default browser)<br> + Added configuration to configure ontologies & fields. This is currently at a devloper level (xml file) not a user level(gui - todo). There is a command line argument for which configuration file to use. @@ -298,16 +399,20 @@ todo is to have a gui configuration for users.<br> + Minor bugs: cant delete to 0 rows anymore, synonym search duplicates taken out<br> + <br> + Dev stuff:<br> + Refactored for configuration & adding field. Made the internal code much more generic for adding new fields from configuration, got rid of a lot of hard wiring. Part of this was instituring @@ -316,187 +421,244 @@ plop a web gui on top of the current phenote model & controller.<br> + Renamed Phenotype to Character. Added Character interface CharacterI.<br> + Added tests to test suite.<br> + <br> + <h2><span style="text-decoration: underline;">0.3.1 (CToL)<br> + </span></h2> + <a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br> + <br> + 4/7/06<br> + 0.3.1 is identical to 0.3 except that it has ontologies for CToL (fish evolution group). In particular it uses a fish taxonomy<br> + ontology for the id (in this taxonomy) choosing. On the todo is the ability to configure ontologies, but not there yet, so for now need to hardwire with seaparate jar file. This clearly makes the todo item a bit more pressing.<br> + <h2><span style="text-decoration: underline;">0.3</span></h2> + <a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br> + <br> + 4/7/06<br> + Release for NESCent fish eveolution meeting. No major new functionality here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather buggy.<br> + <br> + Completion terms now sorted alphabeitcally.<br> + Obsolete is now in addition to regular terms, not in lieu of.<br> + Filtering out attribute values (todo: change to actually filter in values)<br> + Html formatting of term info (todo: make terms selectable)<br> + Children relations are in term info<br> + Term info layout greatly improved<br> + Term info in scroller<br> + Border with label around term info<br> + Put definition at end of term info<br> + <br> + Fixed bugs:<br> + Backspace in ontology combo box<br> + Selection of item in comp list causing exception, not going in term box<br> + No terms with just 1 char<br> + Popup was staying up after selection<br> + <br> + Dev stuff:<br> + Test suite added! (todo: add more tests)<br> + Migrated to jdk 1.5 (which caused some of the bugs above)<br> + Ant file made build.xml.<br> + CompletionList refactored into Ontology (prompted by sorting)<br> + <br> + <br> + <h2><span style="text-decoration: underline;">0.2</span></h2> + <a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br> + <br> + 3/27/06<br> + Added the ability to do term completion on Synonyms, Definitions, and Obsoletes. Also can mouse over a term in a completion list and get information about it in the term info text area. <br> + <br> + The term info area needs a lot of work.<br> + TODO:<br> + layout, scrollbar, border w title, ordering & lumping parents & children, formatting. <br> + Also perhaps have children & parents be clickable in some fashion either html-like clickable text or as buttons.<br> + Theres also bugs in term completion boxes. If you start backspacing it gets wacky for instance.<br> + <br> + <a href="0.2/phenote-webstart.jnlp"><br> + </a> <h2><span style="text-decoration: underline;">0.1</span></h2> + <a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br> + <br> + 3/1/06<br> + 0.1 was the initial phenote release (known briefly as the plumper at the time). It just had a genotype, anatomy and pato fields, where anatomy and pato did term completion (just on term names) with there @@ -505,20 +667,26 @@ limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.<br> + <br> + <a href="0.2/phenote-webstart.jnlp"></a><br> + <br> + <br> + <a href="phenote.html">Phenote main page</a><br> + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote.html 2007-05-02 18:26:05 UTC (rev 538) +++ phenote/trunk/doc/phenote-website/phenote.html 2007-05-02 18:37:03 UTC (rev 539) @@ -8,6 +8,7 @@ + @@ -15,6 +16,7 @@ + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> @@ -23,6 +25,7 @@ + @@ -30,6 +33,7 @@ + <title>Phenote</title> </head> @@ -42,6 +46,7 @@ + <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br> @@ -50,6 +55,7 @@ + </h1> @@ -58,6 +64,7 @@ + <br> @@ -66,6 +73,7 @@ + Phenote is a tool to annotate phenotypes using the Entity Quality paradigm. It takes advantage of ontologies. It uses term completion to allow curators quick access to @@ -77,6 +85,7 @@ + <br> @@ -84,10 +93,14 @@ -<a href="1.1/phenote.jnlp">Phenote 1.1</a><br> +<a href="1.2/phenote.jnlp">Phenote 1.2</a><br> <br> + +<br> + + After phenote downloads the java jar files (takes a while) it will ask you what configuration you would like to use, fly, zfin, human,worm....<br> @@ -97,12 +110,14 @@ + <br> + Recent addditions include the ability to update config while preserving your changes, change config, tab delimited format, tabbed field panel, retrieve ontologies from web, retrieve from field to database, search -ALL ontols, add any field you like, post compose terms, bulk +ALL ontols, add any field you like, post compose terms with multiple diff, bulk update, undo, spring framework, and synonyms now are shown in the completion list.<br> @@ -112,6 +127,7 @@ + <br> @@ -120,6 +136,7 @@ + Zebrafish requires components of phenote(to plug into their non-public website), not a full web app. Here is a proof of concept of some of @@ -132,6 +149,7 @@ + <br> @@ -140,6 +158,7 @@ + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> @@ -149,6 +168,7 @@ + <br> @@ -157,6 +177,7 @@ + Webby phenote is a collaboration with Sohel Merchant at dictyBase. Here is what they have done:<br> @@ -166,6 +187,7 @@ + <br> @@ -174,6 +196,7 @@ + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase webby phenote</a><br> @@ -183,6 +206,7 @@ + <br> @@ -191,6 +215,7 @@ + <br> @@ -199,6 +224,7 @@ + We are doing these releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug tracker</a>) and let us know what you @@ -210,8 +236,10 @@ + <br> + [In development - the bleeding edge if you will:<a href="1.1/phenote.jnlp"> Phenote 1.2</a> coming soon]<br> @@ -220,6 +248,7 @@ + <h4>Phenote links:<br> @@ -228,6 +257,7 @@ + </h4> @@ -236,6 +266,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote email list</a><br> @@ -245,6 +276,7 @@ + <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote bug tracker</a><br> @@ -254,6 +286,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug tracker email list</a><br> @@ -263,6 +296,7 @@ + <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source code (obo sourceforge svn)</a><br> @@ -272,6 +306,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote svn commit email list</a><br> @@ -281,6 +316,7 @@ + <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty webby phenote wiki developer docs</a><br> @@ -290,11 +326,14 @@ + <a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote ncbo internal wiki (ncbo folk only)</a><br> + <a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br> + <a href="developer-docs/developer-docs.html">More developer docs</a><br> @@ -303,6 +342,7 @@ + <br> @@ -311,6 +351,7 @@ + <a href="phenote-release-notes.html">Phenote Release Notes and old webstart releases</a><br> @@ -320,6 +361,7 @@ + <br> @@ -328,6 +370,7 @@ + If the Phenote webstart link fails to do anything, then there are probably problems with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br> @@ -338,6 +381,7 @@ + page.<br> @@ -346,6 +390,7 @@ + <br> @@ -354,6 +399,7 @@ + Click here for <a href="phenote-java-requirements.html">phenote java requirements</a><br> @@ -363,6 +409,7 @@ + <br> @@ -371,6 +418,7 @@ + <br> @@ -379,6 +427,7 @@ + <br> @@ -387,6 +436,7 @@ + Old releases: <br> @@ -395,6 +445,8 @@ + +<a href="1.1/phenote.jnlp">Phenote 1.1</a><br> <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> @@ -403,6 +455,7 @@ + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> @@ -410,11 +463,13 @@ + <a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br> + <br> @@ -423,6 +478,7 @@ + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> @@ -431,6 +487,7 @@ + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> @@ -438,6 +495,7 @@ + <br> @@ -445,6 +503,7 @@ + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> @@ -453,6 +512,7 @@ + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> @@ -461,6 +521,7 @@ + <br> @@ -469,6 +530,7 @@ + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> @@ -477,6 +539,7 @@ + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> @@ -485,6 +548,7 @@ + <br> @@ -493,6 +557,7 @@ + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> @@ -501,6 +566,7 @@ + <br> @@ -509,6 +575,7 @@ + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> @@ -517,6 +584,7 @@ + <br> @@ -525,6 +593,7 @@ + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> @@ -533,6 +602,7 @@ + <br> @@ -541,6 +611,7 @@ + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> @@ -549,6 +620,7 @@ + <br> @@ -557,6 +629,7 @@ + <a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br> @@ -565,6 +638,7 @@ + <br> @@ -573,6 +647,7 @@ + <a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br> @@ -581,6 +656,7 @@ + <br> @@ -589,6 +665,7 @@ + <a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a> (a special release for the CToL group that uses fish taxonomy)<br> @@ -599,6 +676,7 @@ + <br> @@ -607,6 +685,7 @@ + <a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br> @@ -615,6 +694,7 @@ + <br> @@ -623,6 +703,7 @@ + <a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br> @@ -631,6 +712,7 @@ + <br> @@ -639,6 +721,7 @@ + <a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br> @@ -647,6 +730,7 @@ + <br> @@ -655,6 +739,7 @@ + <br> @@ -663,5 +748,6 @@ + </body> </html> Modified: phenote/trunk/src/java/phenote/datamodel/Ontology.java =================================================================== --- phenote/trunk/src/java/phenote/datamodel/Ontology.java 2007-05-02 18:26:05 UTC (rev 538) +++ phenote/trunk/src/java/phenote/datamodel/Ontology.java 2007-05-02 18:37:03 UTC (rev 539) @@ -306,6 +306,7 @@ long time = System.currentTimeMillis(); //Collection<OBOClass> // true -> cache result + // BUG - this includes obsoletes! sortedTerms = engine.query(nsQuery, true); System.out.println("got " + sortedTerms.size() + " namespace hits in " + (System.currentTimeMillis() - time) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |