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[Gmod-apollo-cmts] CVS: apollo/doc GUI-test-list, NONE, 1.1 README.InstallAnywhere, 1.1, 1.2 README.chado-xml, 1.1, 1.2 README.developers, 1.3, 1.4 README.schema, 1.1, 1.2 README.sim4, 1.1, 1.2 README.webstart, 1.1, 1.2 test-list, 1.4, NONE
Update of /cvsroot/gmod/apollo/doc In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv27339 Modified Files: README.InstallAnywhere README.chado-xml README.developers README.schema README.sim4 README.webstart Added Files: GUI-test-list Removed Files: test-list Log Message: Format READMEs, rename test-list --- NEW FILE: GUI-test-list --- $Id: GUI-test-list,v 1.1 2007/04/25 15:23:48 briano Exp $ This file is a list of things to test in the GUI. The idea would be anytime a GUI bug is fixed the conditions on how to reveal the bug should be put here. Then before a release we can whip through the list. These are generally GUI things that have to be tested by hand and can't be tested programatically. 1. Bug: Horizontal Scrollbar doesn't invalidate views, features disappear on scroll. Test: Zoom all the way in, scroll all the way right, reset, scroll left, hit vertical scroll. If features suddenly appear thats bad. 2. Bug: Apollo gets cleared out on a bad filename. Test: Put a bad filename into GAME:file and gff. 3. Bug: Exceptions thrown on changing from gff to a game file. Test: Load a game file (../data/example.xml) and then load a gff file. 4. Bug: Annot not changing translation when splice sites changed in EDE. Test: Zoom in to annot in main window to see its translated seq. Drag ends of exons in trans region in EDE. Translated seq should change. 5. When making installer, need to include this -D option (to allow writes back to Ensembl databases): lax.nl.java.option.additional=-mx200M -Xmx200M -Dorg.xml.sax.driver=org.apache.xerces.parsers.SAXParser - Uncomment the das-adapter from apollo config - Choose that adapter from the chooser - If you need to set up an HTTP proxy to speak to the outside world, do this by selecting the "change" button in the "Proxy Settings" row, and filling in your proxy server address and port. If you need one and you don't set one, then this step will just hang while java faffs around trying to set up a socket. - Type www.wormbase.org/db/das into the DAS Server field (yes, Ensembl is in the drop-down, but wormbase is a faster source). The sequence sources dropdown should have one value: "elegans". Select it. If you don't have the right parameter in the lax file, the last step should break, with a dialog telling you that you can't load a SAX parser because the parameter is missing. Index: README.InstallAnywhere =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.InstallAnywhere,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** README.InstallAnywhere 24 Apr 2007 19:22:20 -0000 1.1 --- README.InstallAnywhere 25 Apr 2007 15:23:48 -0000 1.2 *************** *** 1,6 **** ! # $Id$ ! ! Instructions on using InstallAnywhere to make a release of Apollo: - Launch ~nomi/install-anywhere/InstallAnywhere - Choose the Apollo project --- 1,6 ---- ! $Id$ + Installing InstallAnywhere to make an Apollo Release + ================================== - Launch ~nomi/install-anywhere/InstallAnywhere - Choose the Apollo project Index: README.chado-xml =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.chado-xml,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** README.chado-xml 24 Apr 2007 18:16:31 -0000 1.1 --- README.chado-xml 25 Apr 2007 15:23:48 -0000 1.2 *************** *** 1,8 **** ! # $Id$ ! ! Notes on Apollo's ChadoXML adapter for FlyBase ! ! -- Viewing Chado XML adapter code: See: --- 1,6 ---- ! $Id$ + Viewing Chado XML adapter code: + ======================== See: *************** *** 10,15 **** http://cvs.sourceforge.net/viewcvs.py/gmod/apollo/src/java/apollo/dataadapter/chadoxml/ChadoXmlWrite.java?view=markup ! -- Apollo and Chado XML Macros ! Don't forget that the Chado XML reader can only handle un-macroized Chado XML. If you feed it macroized Chado XML, it tries to recognize that and --- 8,13 ---- http://cvs.sourceforge.net/viewcvs.py/gmod/apollo/src/java/apollo/dataadapter/chadoxml/ChadoXmlWrite.java?view=markup ! Apollo and Chado XML Macros ! ======================= Don't forget that the Chado XML reader can only handle un-macroized Chado XML. If you feed it macroized Chado XML, it tries to recognize that and *************** *** 17,28 **** would just choke and die. ! -- Chado Needs to Know the Region ! ChadoXML input must include an _appdata section to identify the region - Apollo needs to know the chromosome (arm), start, and end for the region. ! -- Round-tripped Data ! Things that are not roundtripped by the Chado XML adapter: --- 15,26 ---- would just choke and die. ! Chado Needs to Know the Region ! ========================== ChadoXML input must include an _appdata section to identify the region - Apollo needs to know the chromosome (arm), start, and end for the region. ! Round-tripped Data ! ========================== Things that are not roundtripped by the Chado XML adapter: *************** *** 40,49 **** - Organism ID for results is hardcoded to "Computational Result". ! -- Features without Strands ! Unstranded features are forced onto the best-guess strand for display purposes and then written back out unstranded like they came in. ! Properties that can be changed inside Apollo (either by the user or automatically by Apollo): --- 38,48 ---- - Organism ID for results is hardcoded to "Computational Result". ! Features without Strands ! ========================= Unstranded features are forced onto the best-guess strand for display purposes and then written back out unstranded like they came in. ! Properties ! ====================== Properties that can be changed inside Apollo (either by the user or automatically by Apollo): *************** *** 76,92 **** allow you to add/change the result tag with a menu option.) ! -- Subject Strand ! When writing results that have a query and a subject, subject strand is hardcoded to 1. ! -- Write an Organism ! When writing out features, always try to write an organism. If organism is missing from feature, try to get from parent (all the way up to refseq of whole region). ! -- synonym_sgml ! A synonym_sgml property is added to every synonym. If synonym_sgml is not included in the synonym record, the synonym name itself is used. --- 75,91 ---- allow you to add/change the result tag with a menu option.) ! Subject Strand ! ================== When writing results that have a query and a subject, subject strand is hardcoded to 1. ! Write an Organism ! ================== When writing out features, always try to write an organism. If organism is missing from feature, try to get from parent (all the way up to refseq of whole region). ! synonym_sgml ! ===================== A synonym_sgml property is added to every synonym. If synonym_sgml is not included in the synonym record, the synonym name itself is used. *************** *** 105,110 **** */ ! -- Flat Fields ! In order to roundtrip arbitrary flat fields (e.g., <is_obsolete>0</is_obsolete>), they are stored inside Apollo as --- 104,109 ---- */ ! Flat Fields ! ================ In order to roundtrip arbitrary flat fields (e.g., <is_obsolete>0</is_obsolete>), they are stored inside Apollo as *************** *** 117,122 **** adapter, but I don't think any of the others write out properties.) ! -- Constants ! Constants for use by ChadoXmlWrite are now defined in fly.style (and can be changed - currently they match the defaults defined in ChadoXmlWrite). --- 116,121 ---- adapter, but I don't think any of the others write out properties.) ! Constants ! ================= Constants for use by ChadoXmlWrite are now defined in fly.style (and can be changed - currently they match the defaults defined in ChadoXmlWrite). Index: README.developers =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.developers,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** README.developers 24 Apr 2007 19:03:10 -0000 1.3 --- README.developers 25 Apr 2007 15:23:48 -0000 1.4 *************** *** 1,3 **** ! # $Id$ Checking out apollo from SourceForge CVS: --- 1,3 ---- ! $Id$ Checking out apollo from SourceForge CVS: Index: README.schema =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.schema,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** README.schema 24 Apr 2007 19:10:37 -0000 1.1 --- README.schema 25 Apr 2007 15:23:48 -0000 1.2 *************** *** 1,7 **** ! # $Id$ Notes on schema descriptions for GAME XML ============================== - It turns out that RELAX-NG (which can be stored as an rng file, which is XML, or an rnc file, "compact" format) is a better way to represent the --- 1,6 ---- ! $Id$ Notes on schema descriptions for GAME XML ============================== It turns out that RELAX-NG (which can be stored as an rng file, which is XML, or an rnc file, "compact" format) is a better way to represent the Index: README.sim4 =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.sim4,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** README.sim4 24 Apr 2007 18:20:10 -0000 1.1 --- README.sim4 25 Apr 2007 15:23:48 -0000 1.2 *************** *** 1,3 **** ! # $Id$ When running sim4 you need to pass in your genomic sequence file first --- 1,3 ---- ! $Id$ When running sim4 you need to pass in your genomic sequence file first Index: README.webstart =================================================================== RCS file: /cvsroot/gmod/apollo/doc/README.webstart,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** README.webstart 24 Apr 2007 19:15:04 -0000 1.1 --- README.webstart 25 Apr 2007 15:23:48 -0000 1.2 *************** *** 1,3 **** ! # $Id$ Your web server needs to have the jnlp MIME type set in etc/mime.types --- 1,3 ---- ! $Id$ Your web server needs to have the jnlp MIME type set in etc/mime.types --- test-list DELETED --- |