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From: <cmu...@us...> - 2007-10-16 00:58:44
|
Revision: 1060
http://obo.svn.sourceforge.net/obo/?rev=1060&view=rev
Author: cmungall
Date: 2007-10-15 17:58:48 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
Added Paths:
-----------
phenote/trunk/conf/metagenomic_sample.cfg
Added: phenote/trunk/conf/metagenomic_sample.cfg
===================================================================
--- phenote/trunk/conf/metagenomic_sample.cfg (rev 0)
+++ phenote/trunk/conf/metagenomic_sample.cfg 2007-10-16 00:58:48 UTC (rev 1060)
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns:phenote-configuration version="0.1-alpha" xmlns:ns="phenote/config/xml"
+ name="Environmental Sample"
+ author="Chris Mungall"
+ description="For annotating instances of samples obtained from geographic locations and environment types">
+ <ns:log config-file="conf/log4j-standalone.xml"/>
+
+ <!-- wipeout always means that the master will always wipeout the local copy
+ in this mode modifying the local is useless -->
+ <!-- ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"
+ overriding-master-url="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/phenote/trunk/conf/envo_sample.cfg" / -->
+
+ <!-- ********************* FILE ADAPTERS ************************** -->
+ <!-- be sure to include at least one enabled file adapter -->
+ <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+
+
+ <!-- ******************** FIELD DEFINITIONS *********************** -->
+ <ns:field name="Organism" enable="true" desc="Type of organism sampled"/>
+ <ns:field name="STRAIN" enable="true" datatag="GT" desc="Strain of organism sampled"/>
+ <ns:field name="SYMBIONT" enable="true" desc="Symbiont of organism sampled"/>
+ <ns:field name="HABITAT_DESC" enable="true" desc=""/>
+ <ns:field name="Habitat" enable="true">
+ <ns:ontology name="Relationship" is-postcomp-rel="true"
+ file="http://obofoundry.org/ro/ro.obo"/>
+ <ns:ontology name="ENVO" file="http://www.purl.org/obo/obo-all/envo/envo.obo"/>
+ <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
+ <ns:ontology name="CHEBI"
+ file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+ </ns:field>
+ <ns:field name="ISOLATION_DESC" enable="true" desc=""/>
+ <ns:field name="Isolation" enable="true">
+ <ns:ontology name="Relationship" is-postcomp-rel="true"
+ file="http://obofoundry.org/ro/ro.obo"/>
+ <ns:ontology name="ENVO" file="http://www.purl.org/obo/obo-all/envo/envo.obo"/>
+ <ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
+ <ns:ontology name="DO" file="http://purl.org/obo/obo-all/disease_ontology/disease_ontology.obo"/>
+ <ns:ontology name="CL"
+ file="http://www.berkeleybop.org/ontologies/obo-all/cell/cell.obo" />
+ <ns:ontology name="TAXSLIM" file="envo_taxslim.obo"/>
+ <ns:ontology name="CHEBI"
+ file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/chemical/chebi.obo"/>
+ </ns:field>
+ <ns:field name="Isolation Time" enable="true" desc="time at which sample was collected"/>
+ <ns:field name="COUNTRY" enable="true" desc=""/>
+ <ns:field name="Location" enable="true">
+ <ns:ontology name="Relationship" is-postcomp-rel="true"
+ file="http://obofoundry.org/ro/ro.obo"/>
+ <ns:ontology file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/environmental/gaz.obo"/>
+ </ns:field>
+ <ns:field name="GOLDSTAMP" enable="true" desc=""/>
+ <ns:field name="TAXON" enable="true">
+ <ns:ontology name="Relationship" is-postcomp-rel="true"
+ file="http://obofoundry.org/ro/ro.obo"/>
+ <ns:ontology file="envo_taxslim.obo"/>
+ </ns:field>
+
+ <!-- *********************** SETTINGS **************************** -->
+ <ns:uvic-graph enable="false"/>
+ <ns:term-history enable="false"/>
+ <ns:auto-update-ontologies enable="true"/> <!--true=update; false=don't update-->
+ <!--set to 0 if you want to bypass the check; time in seconds-->
+ <ns:update-timer timer="10"/>
+
+
+</ns:phenote-configuration>
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|
|
From: <mg...@us...> - 2007-10-15 20:49:31
|
Revision: 1059
http://obo.svn.sourceforge.net/obo/?rev=1059&view=rev
Author: mgibson
Date: 2007-10-15 13:49:35 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
ok - this took me too long to dig up but nonetheless i think i got it -
i think ive now got log4j configured to dump logs in
~/.phenote/log/
we''ll see if that actually works with webstart - boy i hope so
the trick is to use the java property
${"user.home"}
previously it was just wrting to "phenote_log4j.log"
on linux from webstart this end up in home dir
on mac webstart this actually ends up at the root of the file system
who knows where for windows
which also brings up the question where is user.home on windows - ok im
windows clueless
Modified Paths:
--------------
phenote/trunk/conf/log4j.xml
Modified: phenote/trunk/conf/log4j.xml
===================================================================
--- phenote/trunk/conf/log4j.xml 2007-10-15 19:29:38 UTC (rev 1058)
+++ phenote/trunk/conf/log4j.xml 2007-10-15 20:49:35 UTC (rev 1059)
@@ -4,7 +4,7 @@
<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
<appender name="MAIN" class="org.apache.log4j.RollingFileAppender">
- <param name="File" value="phenote_log4j.log" />
+ <param name="File" value="${user.home}/.phenote/log/phenote_log4j.log" />
<param name="Append" value="true" />
<param name="MaxFileSize" value="1MB" />
<param name="MaxBackupIndex" value="10" />
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|
|
From: <mg...@us...> - 2007-10-15 19:29:46
|
Revision: 1058
http://obo.svn.sourceforge.net/obo/?rev=1058&view=rev
Author: mgibson
Date: 2007-10-15 12:29:38 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
adding log file stuff to 1.4
Modified Paths:
--------------
phenote/tags/release-1.4/src/java/phenote/main/Phenote.java
Modified: phenote/tags/release-1.4/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/tags/release-1.4/src/java/phenote/main/Phenote.java 2007-10-15 18:58:10 UTC (rev 1057)
+++ phenote/tags/release-1.4/src/java/phenote/main/Phenote.java 2007-10-15 19:29:38 UTC (rev 1058)
@@ -7,6 +7,7 @@
import java.awt.GridLayout;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
@@ -87,6 +88,13 @@
rl.setLevel(Level.DEBUG);
LOG = LogManager.getLogger(Phenote.class);
}
+
+ org.apache.log4j.FileAppender a = (org.apache.log4j.FileAppender)rl.getAppender("MAIN");
+ if (a != null) System.out.println("log file: "+a.getFile());
+ else System.out.println("No MAIN File Appender for log4j");
+
+ File f = new File("phenote_log4j.log");
+ System.out.println("path of log file "+f.getPath()+" absolute "+f.getAbsolutePath()+" canWrite "+f.canWrite());
// writes error events to log
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|
|
From: <mg...@us...> - 2007-10-15 18:58:06
|
Revision: 1057
http://obo.svn.sourceforge.net/obo/?rev=1057&view=rev
Author: mgibson
Date: 2007-10-15 11:58:10 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
check write permissions of log file
Modified Paths:
--------------
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-15 18:54:35 UTC (rev 1056)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-15 18:58:10 UTC (rev 1057)
@@ -101,7 +101,7 @@
else System.out.println("No MAIN File Appender for log4j");
File f = new File("phenote_log4j.log");
- System.out.println("path of log file "+f.getPath()+" absolute "+f.getAbsolutePath());
+ System.out.println("path of log file "+f.getPath()+" absolute "+f.getAbsolutePath()+" canWrite "+f.canWrite());
// writes error events to log
ErrorManager.inst().addErrorListener(new LogErrorListener());
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|
|
From: <mg...@us...> - 2007-10-15 18:54:33
|
Revision: 1056
http://obo.svn.sourceforge.net/obo/?rev=1056&view=rev
Author: mgibson
Date: 2007-10-15 11:54:35 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
trying to figure out where log file ends up in webstart -
that is where is the working directory of webstart
Modified Paths:
--------------
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-15 15:42:06 UTC (rev 1055)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-15 18:54:35 UTC (rev 1056)
@@ -7,6 +7,7 @@
import java.awt.GridLayout;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
+import java.io.File;
import java.io.FileNotFoundException;
import java.lang.reflect.Constructor;
import java.lang.reflect.InvocationTargetException;
@@ -95,8 +96,13 @@
rl.setLevel(Level.DEBUG);
LOG = LogManager.getLogger(Phenote.class);
}
-
+ org.apache.log4j.FileAppender a = (org.apache.log4j.FileAppender)rl.getAppender("MAIN");
+ if (a != null) System.out.println("log file: "+a.getFile());
+ else System.out.println("No MAIN File Appender for log4j");
+ File f = new File("phenote_log4j.log");
+ System.out.println("path of log file "+f.getPath()+" absolute "+f.getAbsolutePath());
+
// writes error events to log
ErrorManager.inst().addErrorListener(new LogErrorListener());
String v = "This is Phenote version "+PhenoteVersion.versionString();
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|
|
From: <mg...@us...> - 2007-10-15 15:42:02
|
Revision: 1055
http://obo.svn.sourceforge.net/obo/?rev=1055&view=rev
Author: mgibson
Date: 2007-10-15 08:42:06 -0700 (Mon, 15 Oct 2007)
Log Message:
-----------
putting birn lex anatomy back in
Modified Paths:
--------------
phenote/trunk/conf/birn-test.cfg
phenote/trunk/conf/birn.cfg
Modified: phenote/trunk/conf/birn-test.cfg
===================================================================
--- phenote/trunk/conf/birn-test.cfg 2007-10-15 15:37:05 UTC (rev 1054)
+++ phenote/trunk/conf/birn-test.cfg 2007-10-15 15:42:06 UTC (rev 1055)
@@ -29,6 +29,7 @@
<ns:field name="Entity" datatag="E" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
+ <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
@@ -47,6 +48,7 @@
<ns:field name="Add'l Entity" datatag="E2" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
+ <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg 2007-10-15 15:37:05 UTC (rev 1054)
+++ phenote/trunk/conf/birn.cfg 2007-10-15 15:42:06 UTC (rev 1055)
@@ -25,6 +25,7 @@
<ns:field name="Entity" datatag="E" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
+ <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
@@ -43,6 +44,7 @@
<ns:field name="Add'l Entity" datatag="E2" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
+ <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
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|
|
From: <mg...@us...> - 2007-10-12 19:09:17
|
Revision: 1053
http://obo.svn.sourceforge.net/obo/?rev=1053&view=rev
Author: mgibson
Date: 2007-10-12 12:09:20 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
if a config had no ontols then was throing div by 0 exception
i have such testing configs
Modified Paths:
--------------
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-10-12 15:02:27 UTC (rev 1052)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-10-12 19:09:20 UTC (rev 1053)
@@ -151,7 +151,9 @@
}
// should we have singleOboSession instance var?? or confusing with multi?
numFiles = files.size();
- progressFactor = 1+(10/numFiles); //this is kind of a hack right now until we get threading
+ // i have funny test configs with no ontol files - / 0 exception
+ int div = numFiles == 0 ? 1 : numFiles;
+ progressFactor = 1+(10/div); //this is kind of a hack right now until we get threading
System.out.println("numfiles="+numFiles);
OBOSession os = getOboSession(files);
return os;
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|
From: <ba...@us...> - 2007-10-12 15:02:23
|
Revision: 1052
http://obo.svn.sourceforge.net/obo/?rev=1052&view=rev
Author: balhoff
Date: 2007-10-12 08:02:27 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
Started a test config with fewer ontologies for most of the tests. Sometimes a test may seem slow if you have not yet downloaded an ontology, but it will be faster afterwards.
Modified Paths:
--------------
phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java
phenote/trunk/test/java/phenote/gui/TestPhenote.java
Added Paths:
-----------
phenote/trunk/conf/test.cfg
Added: phenote/trunk/conf/test.cfg
===================================================================
--- phenote/trunk/conf/test.cfg (rev 0)
+++ phenote/trunk/conf/test.cfg 2007-10-12 15:02:27 UTC (rev 1052)
@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns:phenote-configuration version="1.1" xmlns:ns="phenote/config/xml" name="Test Configuration" author="Jim Balhoff" description="This configuration is for unit testing.">
+
+ <ns:master-to-local-config mode="WIPEOUT" when="ALWAYS"/>
+ <ns:uvic-graph enable="false"/>
+ <ns:term-history enable="true"/>
+ <ns:auto-update-ontologies enable="true"/>
+ <ns:update-timer timer="0"/>
+ <ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
+ <ns:dataadapter name="phenote.dataadapter.delimited.DelimitedFileAdapter" enable="true"/>
+ <ns:dataadapter name="phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter" enable="true"/>
+ <ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
+ <ns:dataadapter name="phenote.dataadapter.nexus.NEXUSAdapter" enable="true"/>
+
+ <ns:group name="specimen-list" title="Specimen List" container="window" interface="character-template" group_adapter="phenote.charactertemplate.SpecimenListController">
+ <ns:templatechooser title="Phylogeny Chooser" adapter="phenote.charactertemplate.TreeChooser" field="Taxon"/>
+ </ns:group>
+ <ns:group name="default" title="Default Group" container="window" interface="default"/>
+
+ <ns:field name="Publication" syntax-abbrev="PUB" enable="true" groups="default specimen-list"/>
+ <ns:field name="Taxon" syntax-abbrev="GT" enable="true" groups="default specimen-list">
+ <ns:ontology name="Taxon" file="finkandfink_Taxa.obo" namespace="teleost-taxonomy"/>
+ </ns:field>
+ <ns:field name="Catalog Number" syntax-abbrev="Specimen" enable="true" groups="default specimen-list"/>
+ <ns:field name="Specimen Count" syntax-abbrev="SpecimenCount" enable="true" groups="default specimen-list"/>
+ <ns:field name="Preparation" syntax-abbrev="SpecimenPreparation" enable="true" groups="default specimen-list"/>
+ <ns:field name="Entity" syntax-abbrev="E" enable="true" groups="default">
+ <ns:ontology name="Relationship" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo" is-postcomp-rel="true"/>
+ <ns:ontology name="Teleost" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/teleost_anatomy.obo" namespace="teleost_anatomy"/>
+ <ns:ontology name="ZFin" namespace="zebrafish_anatomy" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/zebrafish_anatomy.obo"/>
+ </ns:field>
+ <ns:field name="Quality" syntax-abbrev="Q" enable="true" groups="default">
+ <ns:ontology name="Quality" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo"/>
+ </ns:field>
+ <ns:field name="Measurement" syntax-abbrev="M" enable="true" groups="default"/>
+ <ns:field name="Unit" syntax-abbrev="U" enable="true" groups="default">
+ <ns:ontology name="Unit" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"/>
+ </ns:field>
+ <ns:field name="Textual Description" syntax-abbrev="Desc" enable="true" groups="default"/>
+ <ns:field name="Image URI" syntax-abbrev="URI" enable="true" groups="default"/>
+ <ns:field name="Notes" syntax-abbrev="Notes" enable="true" groups="default"/>
+
+</ns:phenote-configuration>
\ No newline at end of file
Modified: phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
===================================================================
--- phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java 2007-10-12 14:39:43 UTC (rev 1051)
+++ phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java 2007-10-12 15:02:27 UTC (rev 1052)
@@ -23,7 +23,7 @@
@BeforeClass public static void initialize() throws ConfigException {
Phenote.resetAllSingletons();
- Config.inst().setConfigFile("phenomap.cfg");
+ Config.inst().setConfigFile("test.cfg");
Phenote phenote = Phenote.getPhenote();
phenote.initOntologies();
phenote.initGui();
Modified: phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java
===================================================================
--- phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java 2007-10-12 14:39:43 UTC (rev 1051)
+++ phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java 2007-10-12 15:02:27 UTC (rev 1052)
@@ -20,7 +20,7 @@
@BeforeClass public static void initialize() throws ConfigException {
Phenote.resetAllSingletons();
- Config.inst().setConfigFile("ncbo.cfg");
+ Config.inst().setConfigFile("test.cfg");
Phenote phenote = Phenote.getPhenote();
phenote.initOntologies();
phenote.initGui();
Modified: phenote/trunk/test/java/phenote/gui/TestPhenote.java
===================================================================
--- phenote/trunk/test/java/phenote/gui/TestPhenote.java 2007-10-12 14:39:43 UTC (rev 1051)
+++ phenote/trunk/test/java/phenote/gui/TestPhenote.java 2007-10-12 15:02:27 UTC (rev 1052)
@@ -59,7 +59,7 @@
* @BeforeClass says to run this once before all the tests */
@BeforeClass public static void init() throws InterruptedException, InvocationTargetException, ConfigException {
Phenote.resetAllSingletons();
- Config.inst().setConfigFile("ncbo.cfg");
+ Config.inst().setConfigFile("test.cfg");
phenote = Phenote.getPhenote();
phenote.initOntologies();
phenote.initGui();
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-10-12 14:39:39
|
Revision: 1051
http://obo.svn.sourceforge.net/obo/?rev=1051&view=rev
Author: mgibson
Date: 2007-10-12 07:39:43 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
corrected svn links in download.shtlm as jim noticed -
nicole these need to be updated on the web with the script
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2007-10-12 14:34:45 UTC (rev 1050)
+++ phenote/trunk/doc/phenote-website/download.shtml 2007-10-12 14:39:43 UTC (rev 1051)
@@ -26,9 +26,9 @@
<h2>Run Phenote at the command line</h2>
<p> To run phenote on the command line, linux or MacOSX users will need to checkout Phenote from the subversion repository. This can be done with the following command:</p>
<ul>
-<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4-beta3/ phenote</b>
+<!-- <li>Beta release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4-beta3/ phenote</b>
</li>-->
- <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.4/ phenote</b>
+ <li>Stable release: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.4/ phenote</b>
</li>
<li>Latest: <b>svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/trunk phenote </b>
</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-10-12 14:34:41
|
Revision: 1050
http://obo.svn.sourceforge.net/obo/?rev=1050&view=rev
Author: mgibson
Date: 2007-10-12 07:34:45 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
DataInputServlet last minute fix to 1.4 - slipping it in
Modified Paths:
--------------
phenote/tags/release-1.4/src/java/phenote/servlet/DataInputServlet.java
Modified: phenote/tags/release-1.4/src/java/phenote/servlet/DataInputServlet.java
===================================================================
--- phenote/tags/release-1.4/src/java/phenote/servlet/DataInputServlet.java 2007-10-12 14:33:34 UTC (rev 1049)
+++ phenote/tags/release-1.4/src/java/phenote/servlet/DataInputServlet.java 2007-10-12 14:34:45 UTC (rev 1050)
@@ -1,20 +1,20 @@
package phenote.servlet;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.Date;
import java.util.Enumeration;
-import java.util.Vector;
+
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import javax.servlet.http.HttpServletRequest;
+import javax.swing.SwingUtilities;
import org.apache.log4j.Logger;
+import phenote.datamodel.CharFieldException;
import phenote.datamodel.CharacterI;
import phenote.datamodel.CharacterIFactory;
-import phenote.datamodel.CharFieldException;
import phenote.datamodel.TermNotFoundException;
import phenote.edit.EditManager;
@@ -25,30 +25,44 @@
// PhenoteServlet.class is the distinct name for this logger
private static final Logger LOG = Logger.getLogger(DataInputServlet.class);
- public void doGet(HttpServletRequest request, HttpServletResponse response)
+ public void doGet(/*final*/ HttpServletRequest request, /*final*/ HttpServletResponse response)
throws IOException, ServletException {
- System.out.println("got get" +request);
- LOG.debug("servlet doGet " + new Date());
-
- CharacterI ch = CharacterIFactory.makeChar();
- Enumeration e = request.getParameterNames();
- while (e.hasMoreElements()) {
- Object o = e.nextElement();
- LOG.debug("param "+o);
- // test if instance of String?
- String field = (String)o;
- String value = request.getParameter(field);
- try {
- ch.setValue(field,value);
+ //System.out.println("got get " +request);
+ LOG.debug("servlet doGet " + new Date()+request);
+ // need to interact with the application on the Swing thread
+ //SwingUtilities.invokeLater(new EditRunnable(request));
+ // not sure why but invokeLater made later requests be empty???
+ try { SwingUtilities.invokeAndWait(new EditRunnable(request)); }
+ catch (/*Interrupted*/Exception x) { LOG.error(x); }
+ }
+
+ private class EditRunnable implements Runnable {
+ private HttpServletRequest request;
+ private EditRunnable(HttpServletRequest req) {
+ this.request = req;
+ }
+ public void run() {
+ CharacterI ch = CharacterIFactory.makeChar();
+ Enumeration<?> e = request.getParameterNames();
+ while (e.hasMoreElements()) {
+ Object o = e.nextElement();
+ LOG.debug("param "+o);
+ // test if instance of String?
+ String field = (String)o;
+ String value = request.getParameter(field);
+ try {
+ ch.setValue(field,value);
+ }
+ catch (CharFieldException cfe) {
+ LOG.error("field not found "+cfe);
+ }
+ catch (TermNotFoundException tnfe) {
+ LOG.error("term not found in field "+field+" "+tnfe);
+ }
+ }
+ EditManager.inst().addCharacter(ch);
}
- catch (CharFieldException cfe) {
- LOG.error("field not found "+cfe);
- }
- catch (TermNotFoundException tnfe) {
- LOG.error("term not found in field "+field+" "+tnfe);
- }
- }
- EditManager.inst().addCharacter(ch);
+
}
/**
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-10-12 14:33:30
|
Revision: 1049
http://obo.svn.sourceforge.net/obo/?rev=1049&view=rev
Author: mgibson
Date: 2007-10-12 07:33:34 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
brin ontols -> 1.4
Modified Paths:
--------------
phenote/tags/release-1.4/obo-files/BIRNLex-Anatomy.obo
phenote/tags/release-1.4/obo-files/BIRNLex.obo
Modified: phenote/tags/release-1.4/obo-files/BIRNLex-Anatomy.obo
===================================================================
--- phenote/tags/release-1.4/obo-files/BIRNLex-Anatomy.obo 2007-10-12 14:32:44 UTC (rev 1048)
+++ phenote/tags/release-1.4/obo-files/BIRNLex-Anatomy.obo 2007-10-12 14:33:34 UTC (rev 1049)
@@ -1,13 +1,11 @@
format-version: 1.2
-idspace: bfo http://www.ifomis.org/bfo/1.0# ""
-idspace: bfo_pato_bridge http://purl.org/obo/owl/quality_bfo_bridge# ""
-idspace: bfo_ro_bridge http://purl.org/obo/obo-all/ro_bfo_bridge/ro_bfo_bridge.owl# ""
idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# ""
-idspace: birn_annot http://purl.org/nbirn/birnlex/1.2.3/BIRNLex_annotation_properties.owl# ""
-idspace: birn_annot_old http://purl.org/nbirn/birnlex/1.2.2/BIRNLex_annotation_properties.owl# ""
-idspace: birn_obo_ubo http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-OBO-UBO.owl# ""
-idspace: birn_org_tax http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-OrganismalTaxonomy.owl# ""
+idspace: birn_annot http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl# ""
+idspace: birn_obo_ubo http://purl.org/nbirn/birnlex/ontology/BIRNLex-OBO-UBO.owl# ""
+idspace: birn_org_tax http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl# ""
+idspace: birnlex_anatomy http://purl.org/nbirn/birnlex/ontology/BIRNLex-Anatomy.owl# ""
idspace: core http://www.w3.org/2004/02/skos/core# ""
+idspace: daml http://www.daml.org/2001/03/daml+oil# ""
idspace: dc http://purl.org/dc/elements/1.1/ ""
idspace: eor http://dublincore.org/2000/03/13/eor# ""
idspace: galen http://www.co-ode.org/ontologies/galen# ""
@@ -15,16 +13,10 @@
idspace: oban http://www.berkeleybop.org/ontologies/oban/alpha# ""
idspace: obd http://www.bioontology.org/obd/obd-ontology# ""
idspace: oboInOwl http://www.bioontology.org/oboInOwl# ""
-idspace: obo_annot http://purl.org/nbirn/birnlex/1.2.3/OBO_annotation_properties.owl# ""
-idspace: obo_annot_old http://purl.org/nbirn/birnlex/1.2.2/OBO_annotation_properties.owl# ""
-idspace: obo_base http://purl.org/obo/owl/obo# ""
-idspace: obo_rel http://purl.org/obo/owl/OBO_REL# ""
-idspace: obo_ro http://www.obofoundry.org/ro/ro.owl# ""
+idspace: obo_annot http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl# ""
idspace: owl http://www.w3.org/2002/07/owl# ""
-idspace: pato http://purl.org/obo/owl/PATO# ""
idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# ""
idspace: protege http://protege.stanford.edu/plugins/owl/protege# ""
-idspace: protege-dc http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl# ""
idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# ""
idspace: rdfs http://www.w3.org/2000/01/rdf-schema# ""
idspace: reactome http://www.reactome.org/biopax# ""
@@ -33,4601 +25,9718 @@
idspace: xsd http://www.w3.org/2001/XMLSchema# ""
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_001
-name: Anatomical_entity
-comment:
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_703 ! _birnlexAnatomy_retired_class
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description101
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_004
-name: Anatomical_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description103
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1728 ! Left parietal lobe
+union_of: birnlex_anatomy:birnlex_1729 ! Right parietal lobe
+union_of: birnlex_anatomy:birnlex_1782 ! Left occipital lobe
+union_of: birnlex_anatomy:birnlex_1783 ! Right occipital lobe
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_005
-name: Organ_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_004 ! Anatomical_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description105
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_006
-name: Neuraxis_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_005 ! Organ_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description110
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_007
-name: Regional_part_of_organ_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_005 ! Organ_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description112
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1782 ! Left occipital lobe
+union_of: birnlex_anatomy:birnlex_1783 ! Right occipital lobe
+union_of: birnlex_anatomy:birnlex_1784 ! Left temporal lobe
+union_of: birnlex_anatomy:birnlex_1785 ! Right temporal lobe
+union_of: birnlex_anatomy:birnlex_1789 ! Left sub-lobar region
+union_of: birnlex_anatomy:birnlex_1790 ! Right sub-lobar region
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_008
-name: Regional_part_of_neuraxis_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_007 ! Regional_part_of_organ_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description121
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_009
-name: Central_canal
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_008 ! Regional_part_of_neuraxis_cavity
-relationship: obo_ro:adjacent_to http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_013 ! Fourth_ventricle
-relationship: obo_ro:contained_in http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_334 ! Spinal_cord_as_regional_part_of_central_nervous_system
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description123
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1780 ! Left limbic lobe
+union_of: birnlex_anatomy:birnlex_1781 ! Right limbic lobe
+union_of: birnlex_anatomy:birnlex_1786 ! Right frontal lobe
+union_of: birnlex_anatomy:birnlex_1787 ! Left frontal lobe
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_010
-name: Cerebral_ventricular_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_008 ! Regional_part_of_neuraxis_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description135
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_011
-name: Regional_part_of_cerebral_ventricular_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_008 ! Regional_part_of_neuraxis_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description137
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1780 ! Left limbic lobe
+union_of: birnlex_anatomy:birnlex_1781 ! Right limbic lobe
+union_of: birnlex_anatomy:birnlex_1784 ! Left temporal lobe
+union_of: birnlex_anatomy:birnlex_1785 ! Right temporal lobe
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_012
-name: Cerebral_aqueduct
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_011 ! Regional_part_of_cerebral_ventricular_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description139
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_013
-name: Fourth_ventricle
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_011 ! Regional_part_of_cerebral_ventricular_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description153
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_014
-name: Lateral_ventricle
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_011 ! Regional_part_of_cerebral_ventricular_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description155
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1780 ! Left limbic lobe
+union_of: birnlex_anatomy:birnlex_1781 ! Right limbic lobe
+union_of: birnlex_anatomy:birnlex_1782 ! Left occipital lobe
+union_of: birnlex_anatomy:birnlex_1783 ! Right occipital lobe
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_015
-name: Regional_part_of_lateral_ventricle
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_011 ! Regional_part_of_cerebral_ventricular_cavity
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description167
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_016
-name: Anterior_horn_of_lateral_ventricle
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_015 ! Regional_part_of_lateral_ventricle
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description169
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1780 ! Left limbic lobe
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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-name: Spinal_cord_as_organ
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
+id: birnlex_anatomy:birnlex_1004
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[Term]
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+id: birnlex_anatomy:birnlex_1005
+name: Anterior hypothalamic region
+xref: NeuroNames:359
+is_a: birnlex_anatomy:birnlex_995 ! Regional part of hypothalamus
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[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_091
-name: Stria_terminalis
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+id: birnlex_anatomy:birnlex_1006
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+xref: NeuroNames:113
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[Term]
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-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_221 ! Regional_part_of_limbic_lobe
+id: birnlex_anatomy:birnlex_1007
+name: Parabigeminal nucleus
+xref: NeuroNames:473
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+property_value: birn_annot:neuronamesID "473" string
[Term]
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-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_192 ! Regional_part_of_diencephalon
+id: birnlex_anatomy:birnlex_1008
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+xref: NeuroNames:506
+is_a: birnlex_anatomy:birnlex_1465 ! Predominantly gray regional part of midbrain tegmentum
+property_value: birn_annot:neuronamesID "506" string
[Term]
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-name: Septum
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+id: birnlex_anatomy:birnlex_1009
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+xref: NeuroNames:611
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+property_value: birn_annot:neuronamesID "611" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_095
-name: Anterior_commissure_anterior_part
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_263 ! Predominantly_white_regional_part_of_anterior_commissure
+id: birnlex_anatomy:birnlex_1010
+name: Mesencephalic nucleus of trigeminal nerve
+xref: NeuroNames:550
+is_a: birnlex_anatomy:birnlex_1465 ! Predominantly gray regional part of midbrain tegmentum
+property_value: birn_annot:neuronamesID "550" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_096
-name: Posterior_part_of_anterior_commissure
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+id: birnlex_anatomy:birnlex_1011
+name: Anatomical cavity
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_097
-name: Cytoarchitectural_part_of_the_cerebellum
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_083 ! Regional_part_of_cerebellum
+id: birnlex_anatomy:birnlex_1012
+name: Rostral sulcus
+xref: NeuroNames:58
+is_a: birnlex_anatomy:birnlex_1324 ! Superficial feature part of frontal lobe
+property_value: birn_annot:neuronamesID "58" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_098
-name: Gross_anatomical_parts_of_the_cerebellum
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_083 ! Regional_part_of_cerebellum
+id: birnlex_anatomy:birnlex_1013
+name: Predominantly gray regional part of adenohypophysis
+is_a: birnlex_anatomy:birnlex_1004 ! Regional part of adenohypophysis
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_099
-name: Cytoarchitectural_part_of_the_cerebellar_cortex
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_097 ! Cytoarchitectural_part_of_the_cerebellum
+id: birnlex_anatomy:birnlex_1014
+name: Regional part of superior colliculus
+is_a: birnlex_anatomy:birnlex_795 ! Regional part of midbrain tectum
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_100
-name: Cerebellar_cortex
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_098 ! Gross_anatomical_parts_of_the_cerebellum
+id: birnlex_anatomy:birnlex_1015
+name: Intermediate hypothalamic region
+xref: NeuroNames:375
+is_a: birnlex_anatomy:birnlex_995 ! Regional part of hypothalamus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description407
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1189 ! Tuber cinereum
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1353 ! Hypophysis
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1558 ! Dorsomedial nucleus of hypothalamus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1564 ! Intermediate periventricular nucleus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1569 ! Retrochiasmatic area
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1572 ! Ventromedial nucleus of hypothalamus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1638 ! Arcuate nucleus of hypothalamus
+property_value: birn_annot:neuronamesID "375" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_101
-name: Cerebellar_white_matter
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_347 ! Composite_part_spanning_multiple_base_regional_parts_of_brain
+id: birnlex_anatomy:birnlex_1016
+name: Corticotectal tract
+xref: NeuroNames:476
+is_a: birnlex_anatomy:birnlex_808 ! Predominantly white regional part of tectum
+property_value: birn_annot:neuronamesID "476" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_102
-name: Deep_cerebellar_nuclei
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_098 ! Gross_anatomical_parts_of_the_cerebellum
+id: birnlex_anatomy:birnlex_1017
+name: Posterior middle temporal sulcus
+xref: NeuroNames:115
+is_a: birnlex_anatomy:birnlex_1538 ! Superficial feature part of temporal lobe
+property_value: birn_annot:neuronamesID "115" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_103
-name: Regional_part_of_cerebellar_cortex
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_098 ! Gross_anatomical_parts_of_the_cerebellum
+id: birnlex_anatomy:birnlex_1018
+name: Linear nucleus
+xref: NeuroNames:510
+is_a: birnlex_anatomy:birnlex_1465 ! Predominantly gray regional part of midbrain tegmentum
+property_value: birn_annot:neuronamesID "510" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_104
-name: Cerebellar_hemisphere
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_103 ! Regional_part_of_cerebellar_cortex
+id: birnlex_anatomy:birnlex_1019
+name: Organ cavity
+is_a: birnlex_anatomy:birnlex_1011 ! Anatomical cavity
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_105
-name: Lobe_parts_of_the_cerebellar_cortex
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_103 ! Regional_part_of_cerebellar_cortex
+id: birnlex_anatomy:birnlex_1020
+name: Medullary reticular formation
+xref: NeuroNames:722
+is_a: birnlex_anatomy:birnlex_1355 ! Regional part of medulla oblongata
+disjoint_from: birnlex_anatomy:birnlex_1151 ! Cochlear nuclear complex
+disjoint_from: birnlex_anatomy:birnlex_1164 ! Inferior olivary complex
+disjoint_from: birnlex_anatomy:birnlex_1337 ! Vestibular nuclear complex
+disjoint_from: birnlex_anatomy:birnlex_1343 ! Predominantly white regional part of medullary white matter
+disjoint_from: birnlex_anatomy:birnlex_1414 ! Medullary white matter
+disjoint_from: birnlex_anatomy:birnlex_1420 ! Medullary raphe nuclear complex
+disjoint_from: birnlex_anatomy:birnlex_1429 ! Solitary nucleus
+property_value: birn_annot:neuronamesID "722" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_106
-name: Lobular_parts_of_the_cerebellar_cortex
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_103 ! Regional_part_of_cerebellar_cortex
+id: birnlex_anatomy:birnlex_1021
+name: Spur of arcuate sulcus
+xref: NeuroNames:957388385
+is_a: birnlex_anatomy:birnlex_1324 ! Superficial feature part of frontal lobe
+property_value: birn_annot:neuronamesID "957388385" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_107
-name: Regional_part_of_a_lobe_of_the_cerebellum
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_103 ! Regional_part_of_cerebellar_cortex
+id: birnlex_anatomy:birnlex_1022
+name: Distal part of hypophysis
+xref: NeuroNames:393
+is_a: birnlex_anatomy:birnlex_1013 ! Predominantly gray regional part of adenohypophysis
+property_value: birn_annot:neuronamesID "393" string
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_108
+id: birnlex_anatomy:birnlex_1023
+name: Predominantly white regional part of superior colliculus
+is_a: birnlex_anatomy:birnlex_1014 ! Regional part of superior colliculus
+
+[Term]
+id: birnlex_anatomy:birnlex_1024
+name: Regional part of medullary white matter
+is_a: birnlex_anatomy:birnlex_1355 ! Regional part of medulla oblongata
+
+[Term]
+id: birnlex_anatomy:birnlex_1025
+name: Temporal operculum
+xref: NeuroNames:109
+is_a: birnlex_anatomy:birnlex_1538 ! Superficial feature part of temporal lobe
+property_value: birn_annot:neuronamesID "109" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1026
+name: Posterior commissure
+xref: NeuroNames:475
+is_a: birnlex_anatomy:birnlex_808 ! Predominantly white regional part of tectum
+property_value: birn_annot:neuronamesID "475" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1027
+name: Predominantly white regional part of basal part of pons
+is_a: birnlex_anatomy:birnlex_1168 ! Regional part of basal part of pons
+
+[Term]
+id: birnlex_anatomy:birnlex_1028
+name: Subcommissural organ
+xref: NeuroNames:474
+is_a: birnlex_anatomy:birnlex_795 ! Regional part of midbrain tectum
+property_value: birn_annot:neuronamesID "474" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1029
+name: Neuraxis cavity
+is_a: birnlex_anatomy:birnlex_1019 ! Organ cavity
+
+[Term]
+id: birnlex_anatomy:birnlex_1030
+name: Superior frontal sulcus
+xref: NeuroNames:42
+is_a: birnlex_anatomy:birnlex_1324 ! Superficial feature part of frontal lobe
+property_value: birn_annot:neuronamesID "42" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1031
+name: Tegmentum
+is_a: birnlex_anatomy:birnlex_1304 ! Composite part spanning multiple base regional parts of brain
+relationship: http://www.obofoundry.org/ro/ro.owl#has_part __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description94
+
+[Term]
+id: birnlex_anatomy:birnlex_1032
+name: Midbrain tectum
+def: "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." []
+xref: NeuroNames:448
+is_a: birnlex_anatomy:birnlex_763 ! Regional part of midbrain
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1007 ! Parabigeminal nucleus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1016 ! Corticotectal tract
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1026 ! Posterior commissure
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1028 ! Subcommissural organ
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1040 ! Superior colliculus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1341 ! Trochlear nerve root
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_703 ! Pretectal region
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_795 ! Regional part of midbrain tectum
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_806 ! Inferior colliculus
+property_value: birn_annot:birnlexDefinition "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." string
+property_value: birn_annot:neuronamesID "448" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1033
+name: Precommissural fornix
+is_a: birnlex_anatomy:birnlex_738 ! Predominantly white regional part of fornix
+disjoint_from: birnle...
[truncated message content] |
|
From: <mg...@us...> - 2007-10-12 14:32:40
|
Revision: 1048
http://obo.svn.sourceforge.net/obo/?rev=1048&view=rev
Author: mgibson
Date: 2007-10-12 07:32:44 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
adding SAO.obo to 1.4 tag
Modified Paths:
--------------
phenote/tags/release-1.4/obo-files/SAO.obo
Modified: phenote/tags/release-1.4/obo-files/SAO.obo
===================================================================
--- phenote/tags/release-1.4/obo-files/SAO.obo 2007-10-12 14:27:19 UTC (rev 1047)
+++ phenote/tags/release-1.4/obo-files/SAO.obo 2007-10-12 14:32:44 UTC (rev 1048)
@@ -1,10 +1,11 @@
format-version: 1.2
-idspace: bfo http://www.ifomis.org/bfo/1.0# ""
+idspace: bfo http://www.ifomis.org/bfo/1.1# ""
idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# ""
idspace: birn_annot http://www.nbirn.net/birnlex/1.0/BIRNLex_annotation_properties.owl# ""
idspace: core http://www.w3.org/2004/02/skos/core# ""
idspace: daml http://www.daml.org/2001/03/daml+oil# ""
idspace: dc http://purl.org/dc/elements/1.1/ ""
+idspace: dcterms http://purl.org/dc/terms/ ""
idspace: eor http://dublincore.org/2000/03/13/eor# ""
idspace: galen http://www.co-ode.org/ontologies/galen# ""
idspace: mged http://mged.sourceforge.net/ontologies/MGEDOntology.owl# ""
@@ -13,258 +14,297 @@
idspace: oboInOwl http://www.bioontology.org/oboInOwl# ""
idspace: obo_annot http://www.nbirn.net/birnlex/1.0/OBO_annotation_properties.owl# ""
idspace: owl http://www.w3.org/2002/07/owl# ""
-idspace: owl11 http://www.w3.org/2006/12/owl11# ""
-idspace: owl11xml http://www.w3.org/2006/12/owl11-xml# ""
idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# ""
idspace: protege http://protege.stanford.edu/plugins/owl/protege# ""
+idspace: protege-dc http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl# ""
idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# ""
idspace: rdfs http://www.w3.org/2000/01/rdf-schema# ""
idspace: reactome http://www.reactome.org/biopax# ""
+idspace: sao http://ccdb.ucsd.edu/SAO/1.2# ""
idspace: serql http://www.openrdf.org/schema/serql# ""
-idspace: snap http://www.ifomis.org/bfo/1.0/snap# ""
+idspace: snap http://www.ifomis.org/bfo/1.1/snap# ""
+idspace: span http://www.ifomis.org/bfo/1.1/span# ""
idspace: swrl http://www.w3.org/2003/11/swrl# ""
idspace: xsd http://www.w3.org/2001/XMLSchema# ""
[Typedef]
id: sao:sao1056822429
-name: psd Morphology
-namespace: sao:
+name: PSD morphology
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Describes general morphology of the post synaptic density (PSD), where it is classified as macular if the thickening is continuous, or perforated when the PSD is interrupted by electron-lucent regions (Harris KM et al., 1992).
+xref: SAO:sao1056822429
domain: sao:sao1196688972 ! Post-synaptic Density
+property_value: core:prefLabel "psd Morphology" xsd:string
property_value: sao:sao_ID "sao1056822429" xsd:string
[Typedef]
id: sao:sao1065676773
name: anatomical Location General
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: General description of the anatomical location assigned to the cell class, regardless of whether parts of the cell are located elsewhere. For neurons, this would be the location of the cell soma
comment: This property is temporarily defined as a datatype property. We anticipate that the locations of cells and cell parts will be drawn from a neuroanatomical brain region ontology in a future version.
+xref: SAO:sao1065676773
property_value: birn_annot:curationStatus "graph position temporary" xsd:string
property_value: sao:sao_ID "sao1065676773" xsd:string
[Typedef]
id: sao:sao1077517916
name: has Mass
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1077517916
property_value: sao:sao_ID "sao1077517916" xsd:string
[Typedef]
id: sao:sao1130665397
name: location CNS PNS
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Differentiates between cells and processes that are located in the central nervous system (CNS) vs peripheral nervous system (PNS). Does not refer to embyrological origin.
+xref: SAO:sao1130665397
domain: sao:sao1813327414 ! Cell
property_value: sao:sao_ID "sao1130665397" xsd:string
[Typedef]
id: sao:sao1185641609
name: species
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates the species of organism from which an observation derives
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description331
+xref: SAO:sao1185641609
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description358
property_value: sao:sao_ID "sao1185641609" xsd:string
[Typedef]
id: sao:sao1220772118
-name: molecular Weight
-namespace: sao:
+name: molecular weight
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1220772118
domain: sao:sao500241072 ! Molecule
+property_value: core:prefLabel "molecular Weight" xsd:string
property_value: sao:sao_ID "sao1220772118" xsd:string
[Typedef]
id: sao:sao1239937685
name: is Regional Part Of
-namespace: sao:
-domain: snap:FiatObjectPart ! FiatObjectPart
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1239937685
+domain: snap:FiatObjectPart ! fiat_object_part
property_value: sao:sao_ID "sao1239937685" xsd:string
[Typedef]
id: sao:sao1254683799
name: has Inherent 3D Shape
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1254683799
property_value: sao:sao_ID "sao1254683799" xsd:string
[Typedef]
id: sao:sao1267375031
name: isoform
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1267375031
domain: sao:sao500241072 ! Molecule
property_value: sao:sao_ID "sao1267375031" xsd:string
[Typedef]
id: sao:sao1356746816
name: associated Cell Component
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Used to describe a physical relationship between two or more cellular components
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description257
+xref: SAO:sao1356746816
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description283
property_value: sao:sao_ID "sao1356746816" xsd:string
[Typedef]
id: sao:sao1384659949
-name: number Of Axons
-namespace: sao:
+name: Number of Axons
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the number of axons arising from the cell soma or primary dendrite. Usually is \"1\", but may be \"0\" for some neuron types. In rare cases in mammalian neurons, may be more than 1.
+xref: SAO:sao1384659949
domain: sao:sao1417703748 ! Neuron
+property_value: core:prefLabel "number Of Axons" xsd:string
property_value: sao:sao_ID "sao1384659949" xsd:string
[Typedef]
id: sao:sao138767806
name: is Component Of
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description245
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao138767806
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description273
property_value: sao:sao_ID "sao138767806" xsd:string
[Typedef]
id: sao:sao1428515021
name: population Object
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Used to describe whether properties are derived from a single, identified object or represent a summary derived from multiple instances of the object. For example, if a source described the properties of a single filled dendrites, this would not be a population object. If a source described the general attributes of all dendrites from a single neuron, then this would be a population object because the properties represent a summary of all dendrites lumped together. The number field can be used to specify the number of objects on which the descriptions is based.
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description337
+xref: SAO:sao1428515021
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description364
property_value: sao:sao_ID "sao1428515021" xsd:string
[Typedef]
id: sao:sao1429489883
name: observation Conditions
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates under what conditions the observation was made
+xref: SAO:sao1429489883
domain: sao:sao1224657022 ! Nerve Cell
property_value: sao:sao_ID "sao1429489883" xsd:string
[Typedef]
id: sao:sao1434436507
name: has Regional Part
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
is_transitive: true
-domain: snap:IndependentContinuant ! IndependentContinuant
+xref: SAO:sao1434436507
+domain: snap:IndependentContinuant ! independent_continuant
property_value: sao:sao_ID "sao1434436507" xsd:string
[Typedef]
id: sao:sao1454173298
name: continuous With Centrifugal
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1454173298
property_value: sao:sao_ID "sao1454173298" xsd:string
[Typedef]
id: sao:sao1490541696
name: has Neurotransmitter
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Neurotransmitter associated with neuronal class
+xref: SAO:sao1490541696
domain: sao:sao1417703748 ! Neuron
property_value: sao:sao_ID "sao1490541696" xsd:string
[Typedef]
id: sao:sao152994059
name: has Molecular Constituent
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description244
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao152994059
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description271
property_value: sao:sao_ID "sao152994059" xsd:string
[Typedef]
id: sao:sao158083006
name: continuous With Centripetal
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao158083006
property_value: sao:sao_ID "sao158083006" xsd:string
[Typedef]
id: sao:sao1597912566
-name: anatomical Location Atlas
-namespace: sao:
+name: Anatomical location: atlas
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Location of a cell in a specific coordinate system
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description249
+xref: SAO:sao1597912566
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description325
+property_value: core:prefLabel "anatomical Location Atlas" xsd:string
property_value: sao:sao_ID "sao1597912566" xsd:string
[Typedef]
id: sao:sao1608074544
name: functional Type
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: functional categorization of cell, e.g., motor, sensory, secretory, myelinating
+xref: SAO:sao1608074544
domain: sao:sao195217619 ! Regional Part Of Schwann Cell
property_value: sao:sao_ID "sao1608074544" xsd:string
[Typedef]
id: sao:sao1620782974
name: standard Error
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Standard error (+/-)
+xref: SAO:sao1620782974
domain: sao:sao279801585 ! Measurement
property_value: sao:sao_ID "sao1620782974" xsd:string
[Typedef]
id: sao:sao1623809261
name: has Component
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
is_transitive: true
comment: Cellular components found in typical cells.
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description248
+xref: SAO:sao1623809261
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description275
property_value: sao:sao_ID "sao1623809261" xsd:string
[Typedef]
id: sao:sao166035570
name: shape
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Used to describe generic shape of a component or compartment
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description289
+xref: SAO:sao166035570
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description315
property_value: sao:sao_ID "sao166035570" xsd:string
[Typedef]
id: sao:sao1669593695
name: point Of Measurement
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates the point at which a described measurement was taken
+xref: SAO:sao1669593695
domain: sao:sao279801585 ! Measurement
property_value: sao:sao_ID "sao1669593695" xsd:string
[Typedef]
id: sao:sao1746944408
name: number Of Branches
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1746944408
domain: sao:sao172297168 ! Dendritic Tree
property_value: sao:sao_ID "sao1746944408" xsd:string
[Typedef]
id: sao:sao1798215493
name: is Continuant
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: A continuant is an entity that endures through time. If true, then entity is a continuant; if false, then entity is an occurrent. An occurrent is defined as a process, event or happening, e.g., a dividing cell.
+xref: SAO:sao1798215493
property_value: sao:sao_ID "sao1798215493" xsd:string
[Typedef]
id: sao:sao1804901442
-name: atlas Coordinate M-L
-namespace: sao:
+name: Atlas Coordinate M-L
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Coordinate along the medial-lateral axis
+xref: SAO:sao1804901442
domain: sao:sao2052625281 ! Atlas Location ! obsolete
+property_value: core:prefLabel "atlas Coordinate M-L" xsd:string
property_value: sao:sao_ID "sao1804901442" xsd:string
[Typedef]
id: sao:sao180517057
name: associated Cellular Element
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Cellular element derived from another cell associated with a compartment, e.g., myelin
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description254
+xref: SAO:sao180517057
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description279
property_value: sao:sao_ID "sao180517057" xsd:string
[Typedef]
id: sao:sao1844377738
name: has Boundary
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to a structure that defines the boundary of a given structure
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description251
+xref: SAO:sao1844377738
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description277
property_value: sao:sao_ID "sao1844377738" xsd:string
[Typedef]
id: sao:sao1863785805
name: is Spiny
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Denotes whether a neuron or dendrite is characterized by at least one spine.
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description288
+xref: SAO:sao1863785805
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description314
property_value: sao:sao_ID "sao1863785805" xsd:string
[Typedef]
id: sao:sao1896217670
name: continuous With
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+def: "Physical continuity between structures" []
comment: This idea was adopted from FMA but possibly needs reconsideration.
+xref: SAO:sao1896217670
property_value: birn_annot:curationStatus "graph position temporary" xsd:string
property_value: sao:definition "Physical continuity between structures" xsd:string
property_value: sao:sao_ID "sao1896217670" xsd:string
@@ -272,93 +312,107 @@
[Typedef]
id: sao:sao1896476612
name: attached To
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates an intimate contact between two anatomical entities, each with their own real boundaries
+xref: SAO:sao1896476612
+property_value: obo_annot:pendingActionNote "Need to determine whether this property is useful in conjunction with intercellular junctions, i.e., in order for two things to be attached, there must be a junction of some sort" xsd:string
property_value: sao:sao_ID "sao1896476612" xsd:string
-property_value: obo_annot:pendingActionNote "Need to determine whether this property is useful in conjunction with intercellular junctions, i.e., in order for two things to be attached, there must be a junction of some sort" xsd:string
[Typedef]
id: sao:sao1936650489
name: number Primary Dendrites Max
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the maximum number of primary dendrites generally seen in a particulary neuronal class
+xref: SAO:sao1936650489
domain: sao:sao172297168 ! Dendritic Tree
property_value: sao:sao_ID "sao1936650489" xsd:string
[Typedef]
id: sao:sao1939689633
name: is Molecular Constituent Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1939689633
domain: sao:sao500241072 ! Molecule
property_value: sao:sao_ID "sao1939689633" xsd:string
[Typedef]
id: sao:sao1945565347
-name: atlas Reference Point
-namespace: sao:
+name: Atlas reference point
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Reference point of the coordinate system used, e.g., bregma
+xref: SAO:sao1945565347
domain: sao:sao2052625281 ! Atlas Location ! obsolete
+property_value: core:prefLabel "atlas Reference Point" xsd:string
property_value: sao:sao_ID "sao1945565347" xsd:string
[Typedef]
id: sao:sao1967171150
name: circuit Type
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao1967171150
domain: sao:sao1417703748 ! Neuron
property_value: sao:sao_ID "sao1967171150" xsd:string
[Typedef]
id: sao:sao1981606713
name: parent Cell Identity
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Used to describe the method by which the parent cell to a subcellular part is identified. \"Identified cell\" means that some sort of interacellular label was used to identify the parent cell with some degree of certainty; \"asserted\" refers to the use of morphological and anatomical criteria to assign identity to a parent.
domain: sao:sao1224657022 ! Nerve Cell
-property_value: sao:sao_ID "sao1981606713" xsd:string
[Typedef]
id: sao:sao2047323768
name: associated With
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates that there is a spatial relationship other than containment or parthood between cellular regional parts or components (e.g. microtuble associates with mitochondria)
+xref: SAO:sao2047323768
property_value: sao:sao_ID "sao2047323768" xsd:string
[Typedef]
id: sao:sao2048509857
-name: atlas Coordinate A-P
-namespace: sao:
+name: Atlas Coordinate A-P
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Coordiante along the anteior-posterior axis
+xref: SAO:sao2048509857
domain: sao:sao2052625281 ! Atlas Location ! obsolete
+property_value: core:prefLabel "atlas Coordinate A-P" xsd:string
property_value: sao:sao_ID "sao2048509857" xsd:string
[Typedef]
id: sao:sao2103390115
name: has Property
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: refers to a set of property classes that reflect unique aspects of a given structure, e.g., orientation, stability
-domain: snap:IndependentContinuant ! IndependentContinuant
+xref: SAO:sao2103390115
+domain: snap:IndependentContinuant ! independent_continuant
property_value: sao:sao_ID "sao2103390115" xsd:string
[Typedef]
id: sao:sao2110623092
name: orientation Reference To
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Element with reference to which orientation is defined
+xref: SAO:sao2110623092
property_value: sao:sao_ID "sao2110623092" xsd:string
[Typedef]
id: sao:sao2134236783
-name: age Of Animal
-namespace: sao:
+name: Age of Animal
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates the age of the animal in which the observation was made
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description331
+xref: SAO:sao2134236783
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description358
+property_value: core:prefLabel "age Of Animal" xsd:string
property_value: sao:sao_ID "sao2134236783" xsd:string
[Typedef]
id: sao:sao2372462654
name: presence
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+def: "Used to denote the presence or absence of a feature. \"Found\" indicates that the feature described was observed in this instance. \"Found\" is always assumed to be the default. \"Not found\" indicates that a feature was looked for and specifically not found, e.g. microtubules were not found in dendritic spines. This value should not be used if the feature was merely not described." []
comment: This property should be updated when we switch to OBR relations to the \"lacks\" relationship
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description266
+xref: SAO:sao2372462654
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description292
property_value: birn_annot:curationStatus "graph position temporary" xsd:string
property_value: sao:definition "Used to denote the presence or absence of a feature. \"Found\" indicates that the feature described was observed in this instance. \"Found\" is always assumed to be the default. \"Not found\" indicates that a feature was looked for and specifically not found, e.g. microtubules were not found in dendritic spines. This value should not be used if the feature was merely not described." xsd:string
property_value: sao:sao_ID "sao2372462654" xsd:string
@@ -366,306 +420,478 @@
[Typedef]
id: sao:sao2422696582
name: is Aggregate Part of
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description260
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao2422696582
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description266
property_value: sao:sao_ID "sao2422696582" xsd:string
[Typedef]
id: sao:sao244654816
-name: atlas Reference
-namespace: sao:
+name: Atlas Reference
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Name and edition of atlas used to derive coordinates
+xref: SAO:sao244654816
domain: sao:sao2052625281 ! Atlas Location ! obsolete
+property_value: core:prefLabel "atlas Reference" xsd:string
property_value: sao:sao_ID "sao244654816" xsd:string
[Typedef]
id: sao:sao267012610
name: number
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description336
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao267012610
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description363
property_value: sao:sao_ID "sao267012610" xsd:string
[Typedef]
id: sao:sao333215121
name: location Component
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the cellular component with which a feature is associated, e.g., ion receptor is associated with the plasma membrane
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description256
+xref: SAO:sao333215121
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description282
property_value: sao:sao_ID "sao333215121" xsd:string
[Typedef]
id: sao:sao3610809721
name: is Morphological Type Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao3610809721
domain: sao:sao1057800815 ! Morphological Quality
property_value: sao:sao_ID "sao3610809721" xsd:string
[Typedef]
id: sao:sao375065056
name: value Type
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Describes whether the reported values are averages, estimates, ranges, or absolute values
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description299
+xref: SAO:sao375065056
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description326
property_value: sao:sao_ID "sao375065056" xsd:string
[Typedef]
id: sao:sao3762365186
name: has Vesicle Component
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao3762365186
domain: sao:sao221389602 ! Vesicle
property_value: sao:sao_ID "sao3762365186" xsd:string
[Typedef]
id: sao:sao382106499
name: density
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao382106499
domain: sao:sao500241072 ! Molecule
property_value: sao:sao_ID "sao382106499" xsd:string
[Typedef]
id: sao:sao392224970
name: sex Of Animal
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates the sex of the animal in which the observation was made.
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description331
+xref: SAO:sao392224970
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description358
property_value: sao:sao_ID "sao392224970" xsd:string
[Typedef]
id: sao:sao3931558608
name: has Morphological Type
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description259
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao3931558608
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description285
property_value: sao:sao_ID "sao3931558608" xsd:string
[Typedef]
id: sao:sao395752640
name: maximum
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: maximum value in a range
+xref: SAO:sao395752640
domain: sao:sao279801585 ! Measurement
property_value: sao:sao_ID "sao395752640" xsd:string
[Typedef]
id: sao:sao40919963
name: unit
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: unit of measurement
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description281
+xref: SAO:sao40919963
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description307
property_value: sao:sao_ID "sao40919963" xsd:string
[Typedef]
id: sao:sao4245285112
name: located in
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description247
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao4245285112
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description274
property_value: sao:sao_ID "sao4245285112" xsd:string
[Typedef]
id: sao:sao431495567
name: polarity Reference To
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Reference to which polarity is defined
+xref: SAO:sao431495567
domain: sao:sao349337269 ! Polarity
property_value: sao:sao_ID "sao431495567" xsd:string
[Typedef]
id: sao:sao45720944
name: is Intercellular Junction Compartment Of
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description243
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao45720944
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description269
property_value: sao:sao_ID "sao45720944" xsd:string
[Typedef]
id: sao:sao4718979881
name: has Surrounding Cellular Element
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao4718979881
property_value: sao:sao_ID "sao4718979881" xsd:string
[Typedef]
id: sao:sao528500906
name: total Dendritic Length
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Cumulative length of all dendrites in the dendritic tree
+xref: SAO:sao528500906
property_value: sao:sao_ID "sao528500906" xsd:string
[Typedef]
id: sao:sao548011359
name: anatomical Location Specific
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the specific location of an instance of a cell
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description250
+xref: SAO:sao548011359
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description276
property_value: sao:sao_ID "sao548011359" xsd:string
[Typedef]
id: sao:sao554204175
name: contains Site
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description240
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao554204175
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description267
property_value: sao:sao_ID "sao554204175" xsd:string
[Typedef]
id: sao:sao5598458770
name: has Part
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao5598458770
property_value: sao:sao_ID "sao5598458770" xsd:string
[Typedef]
id: sao:sao643761283
name: minimum
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Minimum value in a range
+xref: SAO:sao643761283
domain: sao:sao279801585 ! Measurement
property_value: sao:sao_ID "sao643761283" xsd:string
[Typedef]
id: sao:sao655061336
name: value
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: measurement value
+xref: SAO:sao655061336
domain: sao:sao279801585 ! Measurement
property_value: sao:sao_ID "sao655061336" xsd:string
[Typedef]
id: sao:sao7022761014
name: site Adjacent To
-namespace: sao:
-domain: snap:Site ! Site
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao7022761014
+domain: snap:Site ! site
property_value: sao:sao_ID "sao7022761014" xsd:string
[Typedef]
id: sao:sao7122682114
name: anatomical Location
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao7122682114
property_value: sao:sao_ID "sao7122682114" xsd:string
[Typedef]
id: sao:sao7291254923
name: inverse of has Component 6
-namespace: sao:
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description255
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao7291254923
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description281
property_value: sao:sao_ID "sao7291254923" xsd:string
[Typedef]
id: sao:sao733319732
name: intercellular Junction Compartment
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: participates in one or more types of intercellular junctions
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description242
+xref: SAO:sao733319732
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description270
property_value: sao:sao_ID "sao733319732" xsd:string
[Typedef]
id: sao:sao7905250655
name: is Population Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+comment: This is intended to describe what kind of object the members of a population are.
+xref: SAO:sao7905250655
domain: sao:sao2254405550 ! Population
property_value: sao:sao_ID "sao7905250655" xsd:string
[Typedef]
id: sao:sao796296921
name: ccdb ID
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+def: "Unique identifier of an instance found in the CCDB." []
+xref: SAO:sao796296921
property_value: sao:definition "Unique identifier of an instance found in the CCDB." xsd:string
property_value: sao:sao_ID "sao796296921" xsd:string
[Typedef]
id: sao:sao833783433
-name: atlas Coordinate D-V
-namespace: sao:
+name: Atlas Coordinate D-V
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Coordinate along the dorsal ventral axis
+xref: SAO:sao833783433
domain: sao:sao2052625281 ! Atlas Location ! obsolete
+property_value: core:prefLabel "atlas Coordinate D-V" xsd:string
property_value: sao:sao_ID "sao833783433" xsd:string
[Typedef]
id: sao:sao841626191
name: process Number
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Describes the general morphology of a class of neurons with respect to the number of processes extending from the cell soma
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description322
+xref: SAO:sao841626191
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description345
property_value: sao:sao_ID "sao841626191" xsd:string
[Typedef]
id: sao:sao872346836
name: morphometrics
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Measurement associated with compartment
-domain: snap:IndependentContinuant ! IndependentContinuant
+xref: SAO:sao872346836
+domain: snap:IndependentContinuant ! independent_continuant
property_value: sao:sao_ID "sao872346836" xsd:string
[Typedef]
id: sao:sao8839644583
name: has Aggregate Part
-namespace: sao:
-domain: snap:ObjectAggregate ! ObjectAggregate
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao8839644583
+domain: sao:sao3826089237 ! Aggregate Object
property_value: sao:sao_ID "sao8839644583" xsd:string
[Typedef]
id: sao:sao8979892663
name: has Adjacent Cellular Element
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao8979892663
property_value: sao:sao_ID "sao8979892663" xsd:string
[Typedef]
id: sao:sao923422536
name: boundary Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Indicates that the structure forms the boundary for another structure, e.g., membrane of endoplasmic reticulum is boundary of lumen of endoplasmic reticulum
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description252
+xref: SAO:sao923422536
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description278
property_value: sao:sao_ID "sao923422536" xsd:string
[Typedef]
id: sao:sao924725934
name: is Neurotransmitter Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao924725934
domain: sao:sao500241072 ! Molecule
property_value: sao:sao_ID "sao924725934" xsd:string
[Typedef]
id: sao:sao925977276
name: maximum Branch Order
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the maximum branch order of the dendritic tree
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description335
+xref: SAO:sao925977276
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description362
property_value: sao:sao_ID "sao925977276" xsd:string
[Typedef]
id: sao:sao9371595441
name: is Location Of
-namespace: sao:
-domain: snap:Site ! Site
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao9371595441
+domain: snap:Site ! site
property_value: sao:sao_ID "sao9371595441" xsd:string
[Typedef]
id: sao:sao950829914
-name: number Primary Dendrites Min
-namespace: sao:
+name: Number of Primary Dendrites
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Refers to the minimum number of primary dendrites arising from the cell soma
+xref: SAO:sao950829914
domain: sao:sao1417703748 ! Neuron
+property_value: core:prefLabel "number Primary Dendrites Min" xsd:string
property_value: sao:sao_ID "sao950829914" xsd:string
[Typedef]
id: sao:sao9906015852
name: is Part Of
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
+xref: SAO:sao9906015852
property_value: sao:sao_ID "sao9906015852" xsd:string
[Typedef]
id: sao:sao996727841
name: branch Order
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: A property of branching structures such as axons and dendrites
+xref: SAO:sao996727841
property_value: sao:sao_ID "sao996727841" xsd:string
[Typedef]
id: sao:sao99760531
name: synapse Type
-namespace: sao:
+namespace: http://ccdb.ucsd.edu/SAO/1.2#
comment: Classification of synaptic type according to Gray, except using the symmetrical (Gray's Type 2) and asymmetrical (Gray's Type 1) designations
-domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description277
+xref: SAO:sao99760531
+domain: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description303
property_value: sao:sao_ID "sao99760531" xsd:string
+[Typedef]
+id: dc:contributor
+name: Contributor
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: An entity responsible for making contributions to the\n content of the resource.
+property_value: dc:description "Examples of a Contributor include a person, an \n organisation, or a service. Typically, the name of a \n Contributor should be used to indicate the entity." string
+
+[Typedef]
+id: dc:coverage
+name: Coverage
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: The extent or scope of the content of the resource.
+property_value: dc:description "Coverage will typically include spatial location (a place name\n or geographic coordinates), temporal period (a period label,\n date, or date range) or jurisdiction (such as a named\n administrative entity).\n Recommended best practice is to select a value from a\n controlled vocabulary (for example, the Thesaurus of Geographic\n Names [TGN]) and that, where appropriate, named places or time\n periods be used in preference to numeric identifiers such as\n sets of coordinates or date ranges." string
+
+[Typedef]
+id: dc:creator
+name: Creator
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: An entity primarily responsible for making the content \n of the resource.
+property_value: dc:description "Examples of a Creator include a person, an organisation,\n or a service. Typically, the name of a Creator should \n be used to indicate the entity." string
+
+[Typedef]
+id: dc:date
+name: Date
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: A date associated with an event in the life cycle of the\n resource.
+property_value: dc:description "Typically, Date will be associated with the creation or\n availability of the resource. Recommended best practice\n for encoding the date value is defined in a profile of\n ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format." string
+
+[Typedef]
+id: dc:description
+name: Description
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: An account of the content of the resource.
+property_value: dc:description "Description may include but is not limited to: an abstract,\n table of contents, reference to a graphical representation\n of content or a free-text account of the content." string
+
+[Typedef]
+id: dc:format
+name: Format
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: The physical or digital manifestation of the resource.
+property_value: dc:description "Typically, Format may include the media-type or dimensions of\n the resource. Format may be used to determine the software,\n hardware or other equipment needed to display or operate the\n resource. Examples of dimensions include size and duration.\n Recommended best practice is to select a value from a\n controlled vocabulary (for example, the list of Internet Media\n Types [MIME] defining computer media formats)." string
+
+[Typedef]
+id: dc:identifier
+name: Resource Identifier
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: An unambiguous reference to the resource within a given context.
+property_value: dc:description "Recommended best practice is to identify the resource by means\n of a string or number conforming to a formal identification\n system.\n Example formal identification systems include the Uniform\n Resource Identifier (URI) (including the Uniform Resource\n Locator (URL)), the Digital Object Identifier (DOI) and the\n International Standard Book Number (ISBN)." string
+
+[Typedef]
+id: dc:language
+name: Language
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: A language of the intellectual content of the resource.
+property_value: dc:description "Recommended best practice is to use RFC 3066 [RFC3066],\n which, in conjunction with ISO 639 [ISO639], defines two-\n and three-letter primary language tags with optional\n subtags. Examples include \"en\" or \"eng\" for English,\n \"akk\" for Akkadian, and \"en-GB\" for English used in the\n United Kingdom." string
+
+[Typedef]
+id: dc:publisher
+name: Publisher
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: An entity responsible for making the resource available
+property_value: dc:description "Examples of a Publisher include a person, an organisation,\n or a service.\n Typically, the name of a Publisher should be used to\n indicate the entity." string
+
+[Typedef]
+id: dc:relation
+name: Relation
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: A reference to a related resource.
+property_value: dc:description " Recommended best practice is to reference the resource by means\n of a string or number conforming to a formal identification\n system.\n " string
+
+[Typedef]
+id: dc:rights
+name: Rights Management
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: Information about rights held in and over the resource.
+property_value: dc:description " Typically, a Rights element will contain a rights \n management statement for the resource, or reference \n a service providing such information. Rights information \n often encompasses Intellectual Property Rights (IPR), \n Copyright, and various Property Rights. \n If the Rights element is absent, no assumptions can be made \n about the status of these and other rights with respect to \n the resource.\n " string
+
+[Typedef]
+id: dc:source
+name: Source
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: A reference to a resource from which the present resource\n is derived.
+property_value: dc:description "The present resource may be derived from the Source resource\n in whole or in part. Recommended best practice is to reference\n the resource by means of a string or number conforming to a\n formal identification system." string
+
+[Typedef]
+id: dc:subject
+name: Subject and Keywords
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: The topic of the content of the resource.
+property_value: dc:description "Typically, a Subject will be expressed as keywords,\n key phrases or classification codes that describe a topic\n of the resource. Recommended best practice is to select \n a value from a controlled vocabulary or formal \n classification scheme." string
+
+[Typedef]
+id: dc:title
+name: Title
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: A name given to the resource.
+property_value: dc:description " Typically, a Title will be a name by which the resource is\n formally known.\n " string
+
+[Typedef]
+id: dc:type
+name: Resource Type
+namespace: http://purl.org/dc/elements/1.1/
+is_metadata_tag: true
+comment: The nature or genre of the content of the resource.
+property_value: dc:description "Type includes terms describing general categories, functions,\n genres, or aggregation levels for content. Recommended best\n practice is to select a value from a controlled vocabulary\n (for example, the DCMI Type Vocabulary [DCMITYPE]). To \n describe the physical or digital manifestation of the \n resource, use the Format element." string
+
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description118
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description119
is_anonymous: true
+intersection_of: sao:sao1211023249 ! Dendrite
+intersection_of: sao:sao3931558608 sao:sao638749545 ! Spiny
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description132
+is_anonymous: true
union_of: sao:sao1211023249 ! Dendrite
union_of: sao:sao1770195789 ! Axon
union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
@@ -673,7 +899,7 @@
union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description120
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description139
is_anonymous: true
union_of: sao:sao-1465673360 ! Pyramidal
union_of: sao:sao1595237779 ! Oval
@@ -681,27 +907,39 @@
union_of: sao:sao957949983 ! Spherical
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description142
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description160
is_anonymous: true
union_of: sao:sao1447478620 ! Pial Endfoot
union_of: sao:sao2064469343 ! Vascular Endfoot
union_of: sao:sao401910342 ! Somatic Portion
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description148
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description167
is_anonymous: true
-union_of: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description149
-union_of: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description150
+intersection_of: sao:sao1211023249 ! Dendrite
+intersection_of: sao:sao3931558608 sao:sao638749545 ! Spiny
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description16
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description169
is_anonymous: true
+union_of: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description170
+union_of: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description171
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description17
+is_anonymous: true
union_of: sao:sao-206157942 ! Internode
union_of: sao:sao-234066064 ! Paranode
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description191
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description180
is_anonymous: true
+intersection_of: sao:sao2254405550 ! Population
+intersection_of: sao:sao7905250655 sao:sao1071221672 ! Synaptic Vesicle
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description213
+is_anonymous: true
union_of: sao:sao1044911821 ! Neuronal Cell Body
union_of: sao:sao1340260079 ! Tuft
union_of: sao:sao1642908940 ! Spine Neck
@@ -711,140 +949,142 @@
union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description240
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description266
is_anonymous: true
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
+union_of: snap:ObjectBoundary ! object_boundary
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description267
+is_anonymous: true
union_of: sao:sao1860313010 ! Mitochondrion
-union_of: snap:Site ! Site
+union_of: snap:Site ! site
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description241
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description268
is_anonymous: true
union_of: sao:sao-1367457321 ! Mitochondrial Site
union_of: sao:sao-343550527 ! Mitochondrial Space
-union_of: snap:Site ! Site
+union_of: snap:Site ! site
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description242
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description269
is_anonymous: true
-union_of: sao:sao1299635018 ! Cell Cell Contact Zone
-union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
union_of: sao:sao1922892319 ! Intercellular Junction Site
-union_of: sao:sao864921383 ! Regional Part Of Neuron
+union_of: sao:sao2081625415 ! Regional Part Of Cell Cell Contact Zone ! obsolete
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description243
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description270
is_anonymous: true
+union_of: sao:sao1299635018 ! Cell Cell Contact Zone
+union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
union_of: sao:sao1922892319 ! Intercellular Junction Site
-union_of: sao:sao2081625415 ! Regional Part Of Cell Cell Contact Zone ! obsolete
+union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description244
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description271
is_anonymous: true
union_of: sao:sao1329750433 ! Membrane Surface
-union_of: http://www.ifomis.org/bfo/1.0/span#ProcessualEntity
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
+union_of: span:ProcessualEntity ! processual_entity
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description245
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description272
is_anonymous: true
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description246
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description273
is_anonymous: true
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description247
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description274
is_anonymous: true
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description248
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description275
is_anonymous: true
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description249
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description276
is_anonymous: true
union_of: sao:sao1224657022 ! Nerve Cell
-union_of: sao:sao864921383 ! Regional Part Of Neuron
-
-[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description250
-is_anonymous: true
-union_of: sao:sao1224657022 ! Nerve Cell
union_of: sao:sao1253297813 ! Glial Subcompartment
union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
union_of: sao:sao508165343 ! Supra Cellular Structure
union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description251
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description277
is_anonymous: true
-union_of: snap:Object ! Object
-union_of: snap:Site ! Site
+union_of: snap:Object ! object
+union_of: snap:Site ! site
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description252
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description278
is_anonymous: true
-union_of: snap:Object ! Object
-union_of: snap:ObjectBoundary ! ObjectBoundary
+union_of: snap:Object ! object
+union_of: snap:ObjectBoundary ! object_boundary
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description253
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description279
is_anonymous: true
union_of: sao:sao1813327414 ! Cell
union_of: sao:sao340271629 ! Regional Part Of Cell
+union_of: sao:sao85163621 ! Supracellular Object Part ! obsolete
+union_of: sao:sao9117790637 ! Extracellular Structure
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description254
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description280
is_anonymous: true
union_of: sao:sao1813327414 ! Cell
union_of: sao:sao340271629 ! Regional Part Of Cell
-union_of: sao:sao85163621 ! Supracellular Object Part ! obsolete
-union_of: sao:sao9117790637 ! Extracellular Structure
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description255
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description281
is_anonymous: true
union_of: sao:sao1455064842 ! Vesicle Subcomponent
-union_of: snap:Object ! Object
+union_of: snap:Object ! object
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description256
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description282
is_anonymous: true
union_of: sao:sao120573470 ! Cellular Inclusion
union_of: sao:sao500241072 ! Molecule
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description257
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description283
is_anonymous: true
union_of: sao:sao628508602 ! Cellular Subcomponent
union_of: sao:sao9117790637 ! Extracellular Structure
-union_of: snap:Site ! Site
+union_of: snap:Site ! site
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description258
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description284
is_anonymous: true
union_of: sao:sao1329750433 ! Membrane Surface
-union_of: http://www.ifomis.org/bfo/1.0/span#ProcessualEntity
-union_of: snap:FiatObjectPart ! FiatObjectPart
-union_of: snap:Object ! Object
-union_of: snap:ObjectAggregate ! ObjectAggregate
+union_of: snap:FiatObjectPart ! fiat_object_part
+union_of: snap:Object ! object
+union_of: snap:ObjectAggregate ! object_aggregate
+union_of: span:ProcessualEntity ! processual_entity
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description259
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description285
is_anonymous: true
union_of: sao:sao1337158144 ! Cellular Component
union_of: sao:sao1813327414 ! Cell
@@ -853,14 +1093,8 @@
union_of: sao:sao340271629 ! Regional Part Of Cell
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description260
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description292
is_anonymous: true
-union_of: owl:Thing
-union_of: snap:IndependentContinuant ! IndependentContinuant
-
-[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description266
-is_anonymous: true
union_of: sao:sao1224657022 ! Nerve Cell
union_of: sao:sao1253297813 ! Glial Subcompartment
union_of: sao:sao1515819812 ! General Cell Subcompartment ! obsolete
@@ -873,66 +1107,72 @@
union_of: sao:sao895885284 ! Regional Part Of Glial Cell
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description277
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description303
is_anonymous: true
union_of: sao:sao1922892319 ! Intercellular Junction Site
union_of: sao:sao2081625415 ! Regional Part Of Cell Cell Contact Zone ! obsolete
union_of: sao:sao914572699 ! Synapse
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description281
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description307
is_anonymous: true
union_of: sao:sao118541872 ! Gap Junction
union_of: sao:sao279801585 ! Measurement
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description288
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description314
is_anonymous: true
union_of: sao:sao1211023249 ! Dendrite
union_of: sao:sao1417703748 ! Neuron
union_of: sao:sao2034472720 ! Dendritic Shaft
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description289
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description315
is_anonymous: true
union_of: sao:sao1539965131 ! Organelle
union_of: sao:sao221389602 ! Vesicle
union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description299
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description325
is_anonymous: true
+union_of: sao:sao1224657022 ! Nerve Cell
+union_of: sao:sao864921383 ! Regional Part Of Neuron
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description326
+is_anonymous: true
union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
union_of: sao:sao279801585 ! Measurement
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description31
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description33
is_anonymous: true
union_of: sao:sao1749953771 ! Tail Portion
union_of: sao:sao901230115 ! Neck Portion
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description322
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description345
is_anonymous: true
union_of: sao:sao1224657022 ! Nerve Cell
union_of: sao:sao1355908696 ! Pericyte
union_of: sao:sao1813327414 ! Cell
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description331
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description358
is_anonymous: true
union_of: sao:sao1224657022 ! Nerve Cell
union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
union_of: sao:sao864921383 ! Regional Part Of Neuron
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description335
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description362
is_anonymous: true
union_of: sao:sao1211023249 ! Dendrite
union_of: sao:sao172297168 ! Dendritic Tree
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description336
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description363
is_anonymous: true
union_of: sao:sao1515819812 ! General Cell Subcompartment ! obsolete
union_of: sao:sao183270081 ! Subregional Part Of Neuron Process
@@ -942,7 +1182,7 @@
union_of: sao:sao914572699 ! Synapse
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description337
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description364
is_anonymous: true
union_of: sao:sao1224657022 ! Nerve Cell
union_of: sao:sao1253297813 ! Glial Subcompartment
@@ -957,32 +1197,78 @@
union_of: sao:sao895885284 ! Regional Part Of Glial Cell
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description53
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description40
is_anonymous: true
+intersection_of: sao:sao1211023249 ! Dendrite
+intersection_of: sao:sao3931558608 sao:sao638749545 ! Spiny
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description49
+is_anonymous: true
+intersection_of: sao:sao1211023249 ! Dendrite
+intersection_of: sao:sao3931558608 sao:sao128827344 ! Aspiny
+
+[Term]
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description59
+is_anonymous: true
union_of: sao:sao2034472720 ! Dendritic Shaft
union_of: sao:sao952643730 ! Spine Head
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description55
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description64
is_anonymous: true
union_of: sao:sao571652273 ! Node Of Ranvier
union_of: sao:sao758620702 ! Juxtaparanode
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description71
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description79
is_anonymous: true
union_of: sao:sao1642908940 ! Spine Neck
union_of: sao:sao2034472720 ! Dendritic Shaft
[Term]
-id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description87
+id: __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description93
is_anonymous: true
union_of: sao:sao1791490892 ! Regional Part Of Myelinated Axon
union_of: sao:sao280355188 ! Regional Part Of Axon
[Term]
+id: bfo:Entity
+name: entity
+union_of: snap:Continuant ! continuant
+union_of: span:Occurrent ! occurrent
+
+[Term]
+id: sao:GABAergic_Neuron
+name: GABAergic_Neuron
+intersection_of: sao:sao1417703748 ! Neuron
+intersection_of: sao:sao1490541696 sao:sao229636300 ! GABA
+
+[Term]
+id: sao:Glutamatergic_Neuron
+name: Glutamatergic_Neuron
+intersection_of: sao:sao1417703748 ! Neuron
+intersection_of: sao:sao1490541696 sao:sao1744435799 ! Glutamate
+
+[Term]
+id: sao:Granule_Cell
+name: Granule_Cell
+intersection_of: sao:sao1417703748 ! Neuron
+intersection_of: sao:sao3931558608 sao:sao6934064108 ! Granule
+
+[Term]
+id: sao:Spiny_Cell
+name: Spiny_Cell
+intersection_of: sao:sao1417703748 ! Neuron
+intersection_of: sao:sao1434436507 __file:///Users/cjm/.blip/data_cache/SAO.owl#__Description119
+
+[Term]
id: sao:sao-1046371754
name: Filopodium
+def: "Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward (Gene Ontology)" []
+xref: GO:0030175
+xref: SAO:sao-1046371754
+xref: UMLS:0030175
is_a: sao:sao-250931889 ! Neuron Protrusion
disjoint_from: sao:sao-961694769 ! Excrescence
disjoint_from: sao:sao1145756102 ! Spine
@@ -994,6 +1280,8 @@
[Term]
id: sao:sao-1067215520
name: Schwann Cell Paranodal Termination
+def: "Cytoplasmic pockets, or as they appear in thin sections \"loops\" formed by the Schwann cell in the paranodal region. These pockets are actually part of a continuous helical structure providing cytoplasmic continuity from the inntermost to the outermost layers of the myelin sheath through the cytoplasmic channel formed by the loop. Most are directly apposed to the paranodal axonal membrane" []
+xref: SAO:sao-1067215520
is_a: sao:sao-593830697 ! Schwann Cell Myelin Sheath
property_value: birn_annot:curationStatus "uncurated" xsd:string
property_value: sao:definition "Cytoplasmic pockets, or as they appear in thin sections \"loops\" formed by the Schwann cell in the paranodal region. These pockets are actually part of a continuous helical structure providing cytoplasmic continuity from the inntermost to the outermost layers of the myelin sheath through the cytoplasmic channel formed by the loop. Most are directly apposed to the paranodal axonal mem...
[truncated message content] |
|
From: <mg...@us...> - 2007-10-12 14:27:15
|
Revision: 1047
http://obo.svn.sourceforge.net/obo/?rev=1047&view=rev
Author: mgibson
Date: 2007-10-12 07:27:19 -0700 (Fri, 12 Oct 2007)
Log Message:
-----------
took brin lex anatomy out as i think its covered by birn lex
Modified Paths:
--------------
phenote/trunk/conf/birn.cfg
Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg 2007-10-12 14:25:47 UTC (rev 1046)
+++ phenote/trunk/conf/birn.cfg 2007-10-12 14:27:19 UTC (rev 1047)
@@ -43,7 +43,6 @@
<ns:field name="Add'l Entity" datatag="E2" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
- <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2007-10-11 22:01:53
|
Revision: 1045
http://obo.svn.sourceforge.net/obo/?rev=1045&view=rev
Author: nlw
Date: 2007-10-11 15:01:56 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
a bunch of icons for toolbars; from java l&f library
Added Paths:
-----------
phenote/trunk/images/Bookmarks24.gif
phenote/trunk/images/Copy24.gif
phenote/trunk/images/Delete24.gif
phenote/trunk/images/Edit24.gif
phenote/trunk/images/New24.gif
phenote/trunk/images/Open24.gif
phenote/trunk/images/Redo24.gif
phenote/trunk/images/Save24.gif
phenote/trunk/images/Undo24.gif
Added: phenote/trunk/images/Bookmarks24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Bookmarks24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Copy24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Copy24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Delete24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Delete24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Edit24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Edit24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/New24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/New24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Open24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Open24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Redo24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Redo24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Save24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Save24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: phenote/trunk/images/Undo24.gif
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/images/Undo24.gif
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ba...@us...> - 2007-10-11 21:26:35
|
Revision: 1044
http://obo.svn.sourceforge.net/obo/?rev=1044&view=rev
Author: balhoff
Date: 2007-10-11 14:26:37 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
All unit tests should now pass. Added reset() method to all singletons, because Eclipse runs all test classes within the same process and we need to switch configs while testing. Ant starts a new process for each test class, so this isn't an issue there.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/config/Config.java
phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
phenote/trunk/src/java/phenote/dataadapter/LoadSaveManager.java
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java
phenote/trunk/src/java/phenote/edit/EditManager.java
phenote/trunk/src/java/phenote/error/ErrorManager.java
phenote/trunk/src/java/phenote/gui/MenuManager.java
phenote/trunk/src/java/phenote/gui/SearchParams.java
phenote/trunk/src/java/phenote/gui/SelectionHistory.java
phenote/trunk/src/java/phenote/gui/ShrimpDag.java
phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
phenote/trunk/src/java/phenote/main/CommandLine.java
phenote/trunk/src/java/phenote/main/Phenote.java
phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java
phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
phenote/trunk/test/java/phenote/charactertemplate/TreeChooserTest.java
phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java
phenote/trunk/test/java/phenote/gui/TestPhenote.java
Added Paths:
-----------
phenote/trunk/test/testfiles/
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/config/Config.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -47,7 +47,7 @@
public class Config {
public final static String FLYBASE_DEFAULT_CONFIG_FILE = "flybase.cfg";
- private static Config singleton = new Config();
+ private static Config singleton;
private String configFile = FLYBASE_DEFAULT_CONFIG_FILE; // default
private List<DataAdapterConfig> dataAdapConfList;
@@ -85,8 +85,16 @@
private final static String myphenoteFile = "my-phenote";
public static Config inst() {
+ if (singleton == null) {
+ singleton = new Config();
+ }
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
+
/** singleton */
private Config() {}
Modified: phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/dataadapter/CharacterListManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -41,6 +41,10 @@
// singleton = new CharacterListManager();
// return singleton;
}
+
+ public static void reset() {
+ groupToListMan.clear();
+ }
public static CharacterListManager getCharListMan(String group) {
if (group == null) group = CharFieldManager.DEFAULT_GROUP; // ??
Modified: phenote/trunk/src/java/phenote/dataadapter/LoadSaveManager.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/LoadSaveManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/dataadapter/LoadSaveManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -45,6 +45,10 @@
return singleton;
}
+ public static void reset() {
+ singleton = null;
+ }
+
public void newData() {
// CharacterListI charList = new CharacterList();
// CharacterListManager.inst().setCharacterList(this,charList);
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -83,6 +83,10 @@
return singleton;
}
+ public static void reset() {
+ singleton = null;
+ }
+
/** just calls getInstance - but more intuitive for initialization */
public static synchronized void initialize() {
getInstance();
@@ -166,7 +170,6 @@
/** This actually creates both CharFields and Ontologies and maps namespaces from
obo file adapter meta data */
private void mapNamespacesToOntologies(OBOSession oboSession) throws OntologyException {
- int progress = phenote.loadingScreen.getStartupProgress();
for (FieldConfig fieldConfig : cfg().getEnbldFieldCfgs()) {
CharField cf = fieldConfig.getCharField(); // creates char field (if not there)
// ontology manager.addCF???
@@ -188,11 +191,8 @@
// loads ontology from spaces
//ah! but this is loading the ontologies multiple times i think!
Ontology o = new Ontology(spaces,oc,oboSession);
- progress+=progressFactor;
- phenote.loadingScreen.setMessageText("loading: "+o.getName());
- phenote.loadingScreen.setProgress(progress);
+ this.updateLoadingScreen("loading: "+o.getName(), true);
-
// ADD TO CHAR FIELD
if (oc.isPostCompRel()) { // POST COMP REL ONTOLOGY
cf.setPostCompAllowed(true);
@@ -206,6 +206,14 @@
}
}
+ private void updateLoadingScreen(String message, boolean addProgress) {
+ if (phenote.loadingScreen == null) return;
+ phenote.loadingScreen.setMessageText(message);
+ if (addProgress) {
+ final int progress = phenote.loadingScreen.getStartupProgress();
+ phenote.loadingScreen.setProgress(progress + progressFactor);
+ }
+ }
/** if configged checks if repos has more recent - if so copies to cache
@@ -215,8 +223,8 @@
private String findOboUrlString(OntologyConfig ontCfg) throws OntologyException {
return findOboUrl(ontCfg).toString();
}
-
+
/** if configged checks if repos has more recent - if so copies to cache
if no repos gets from cache(.phenote/obo-files), if no cache gets from
app/obo-files throws ontology ex if fails to find in
@@ -224,7 +232,6 @@
private URL findOboUrl(OntologyConfig ontCfg) throws OntologyException {
// first get local url (if there is one) to use to compare against repos url
// get normal/cached/local ontology
- int progress = phenote.loadingScreen.getStartupProgress();
String filename = ontCfg.getFile();
if (filename == null)
throw new OntologyException(ontCfg.getName()+" has null file");
@@ -242,9 +249,7 @@
URL reposUrl = ontCfg.getReposUrl(); // throws MalfUrlEx
//long mem = Runtime.getRuntime().totalMemory()/1000000; //startTimer();
LOG.debug(reposUrl+" checking with repos for newer ontol\n");
- phenote.loadingScreen.setMessageText("checking for updates: "+ontCfg.getName());
- progress+=progressFactor;
- phenote.loadingScreen.setProgress(progress);
+ this.updateLoadingScreen("checking for updates: "+ontCfg.getName(), true);
// if out of synch copies repos to local(.phenote/obo-files)
// url may be jar/obo-files or svn/obo-files but this function will put file
// in cache ~/.phenote/obo-files
@@ -254,14 +259,14 @@
LOG.error("URL is malformed "+m);
}
}
-
+
if (url == null)
throw new OntologyException("obo file "+filename+" not found in repos nor local");
ontCfg.setLoadUrl(url);
return url;
-
+
}
@@ -269,12 +274,10 @@
/** this copies obo file from reposUrl to local cache (~/.phenote/obo-files
called by findOboUrl which has already established that the reposUrl exists */
private URL synchWithRepositoryUrl(URL localUrl, URL reposUrl, String ontol,
- String filename)
+ String filename)
- throws OntologyException {
+ throws OntologyException {
- int progress = phenote.loadingScreen.getStartupProgress();
-
boolean useRepos = false;
if (localUrl == null) {
useRepos = true;
@@ -303,7 +306,7 @@
//if autoupdate without popup
//LOG.debug("repos date "+reposDate+" local date "+loc);
if ((autoUpdate && (timer==0)) && (reposDate > loc)) {
- useRepos = true;
+ useRepos = true;
} else if (reposDate > loc || useRepos) {
useRepos = SynchOntologyDialog.queryUserForOntologyUpdate(ontol);
}
@@ -311,27 +314,23 @@
if (useRepos) {
// i think its always better to download as http/repos is slow
-// boolean downloadToLocal = false; // from Config!
-// if (!downloadToLocal) {
-// LOG.info("Using obo file straight from repository "+reposUrl+
-// " NOT downloading to local cache");
-// return reposUrl; // just use straight from repos
-// }
+// boolean downloadToLocal = false; // from Config!
+// if (!downloadToLocal) {
+// LOG.info("Using obo file straight from repository "+reposUrl+
+// " NOT downloading to local cache");
+// return reposUrl; // just use straight from repos
+// }
// download obo to local cache (takes time!)
String file = localUrl!=null ? FileUtil.getNameOfFile(localUrl) : filename;
//String file = FileUtil.getNameOfFile(localUrl);
- phenote.loadingScreen.setMessageText("updating ontology file: "+ontol);
- progress+=progressFactor;
- phenote.loadingScreen.setProgress(progress);
+ this.updateLoadingScreen("updating ontology file: "+ontol, true);
try {
localUrl = new File(FileUtil.getDotPhenoteOboDir(),file).toURL();
LOG.info("Downloading new ontology from repository "+reposUrl+" to "+localUrl);
- phenote.loadingScreen.setMessageText("downloading from repository: "+ontol);
- progress+=progressFactor;
- phenote.loadingScreen.setProgress(progress);
+ this.updateLoadingScreen("downloading from repository: "+ontol, true);
copyReposToLocal(reposUrl,localUrl);
}
@@ -340,8 +339,8 @@
return localUrl;
}
-
+
/** Get the date of the file from the header of the obo file - just read header dont
read in whole file. should it also query urlConnection for date first?
throws OntologyException if unable to parse date DateEx?*/
@@ -354,13 +353,13 @@
String line = br.readLine();
if (i == 1 && line == null)
throw new OntologyException("readLine returns null, "+
- "url seems to have no content "+oboUrl);
+ "url seems to have no content "+oboUrl);
if (line == null)
throw new OntologyException("No date found in url "+oboUrl);
-
+
// eg date: 22:08:2006 15:38
if (!line.startsWith("date:")) continue;
- SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm");
+ SimpleDateFormat dateFormat = new SimpleDateFormat("dd:MM:yyyy HH:mm");
Date d = dateFormat.parse(line, new ParsePosition(6));
//LOG.debug("date "+d+" for url "+oboUrl+" line "+line);
br.close();
@@ -376,7 +375,7 @@
/** local url may be from distrib/jar dir, but needs to be set to
.phenote/obo-files dir as thats where the user cache is */
private void copyReposToLocal(URL reposUrl, URL localUrl)
- throws OntologyException {
+ throws OntologyException {
// is there a better way then just reading & writing lines? nio?
try {
// nio & old io do the same time - oh well (~1 minute for GO)
@@ -397,13 +396,13 @@
long size = 99999999999999l; // cant get actual size - whole file
w.transferFrom(r,0,size);
//byte[] buf = new byte[1024];
-// int i = 0;
-// //while((i=br.read())!=-1) {
-// String line;
-// while ((line=br.readLine())!=null) {
-// //bos.write(i); //buf, 0, i);
-// ps.print(line+"\n");
-// }
+// int i = 0;
+// //while((i=br.read())!=-1) {
+// String line;
+// while ((line=br.readLine())!=null) {
+// //bos.write(i); //buf, 0, i);
+// ps.print(line+"\n");
+// }
//stopTimer();
r.close();
is.close(); // ??
@@ -434,14 +433,15 @@
/** file list is a list of file/url Strings */
private OBOSession getOboSession(Collection<String> fileList)
- throws OntologyException {
+ throws OntologyException {
OBOFileAdapter fa = new OBOFileAdapter();
OBOFileAdapter.OBOAdapterConfiguration cfg = new OBOFileAdapter.OBOAdapterConfiguration();
// takes strings not urls!
cfg.setReadPaths(fileList);
cfg.setBasicSave(false); //i think i need this for dangling references
cfg.setAllowDangling(true); //setting this to true for now! should be configrable
- phenote.loadingScreen.setMessageText("loading ontologies into memory");
+ this.updateLoadingScreen("loading ontologies into memory", false);
+
try { // throws data adapter exception
OBOSession os = (OBOSession)fa.doOperation(IOOperation.READ,cfg,null);
adapterMetaData = fa.getMetaData(); // check for null?
@@ -449,7 +449,7 @@
}
catch (DataAdapterException e) {
String m = "got obo data adapter exception: "+e+" message "+e.getMessage()
- +" cause "+e.getCause(); // cause is crucial!
+ +" cause "+e.getCause(); // cause is crucial!
ErrorManager.inst().error(new ErrorEvent(this,m));
LOG.error(m); // error manager should do this for free
throw new OntologyException(e);
@@ -460,10 +460,10 @@
/** The ontology has been determined to be out of date (by quartz) and thus directed
to reload itself from its file - in other words there is a new obo file to load
in place of old one */
-// public void reloadOntology(Ontology ont) throws OntologyException {
-// URL url = findFile(ont.getSource()); // ex
-// loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
-// }
+//public void reloadOntology(Ontology ont) throws OntologyException {
+//URL url = findFile(ont.getSource()); // ex
+//loadOboSessionFromUrl(ont,url,ont.getSource()); // throws ex
+//}
public void reloadOntologies() throws OntologyException {
fileToOntologyCache = new HashMap<String,Ontology>();
// i dont think we need to clear out ontologies from OntMans char field as they
@@ -496,7 +496,7 @@
ontology.setFilter(ontCfg.getFilter());
if (ontCfg.hasSlim())
ontology.setSlim(ontCfg.getSlim());
-
+
loadOboSession(ontology,ontCfg); // throws FileNotFoundEx->OntolEx
return ontology;
}
@@ -518,7 +518,7 @@
}
private void setOboSessionFromCache(Ontology o,String filename)
- throws OntologyException {
+ throws OntologyException {
Ontology previousOntol = fileToOntologyCache.get(filename);
o.setOboSession(previousOntol.getOboSession()); // throws OntEx if error
System.out.println("obo file already loaded using, obo file from cache "+o.getOboSession());
@@ -528,41 +528,38 @@
/** If repository is configured loads obo from repos if local out of date
old - phase out - multi obo sessions*/
private void loadOboSessionCheckRepos(Ontology o,OntologyConfig oc)
- throws OntologyException {
- int progress = phenote.loadingScreen.getStartupProgress();
-// // first get normal/cached/local ontology
-// String filename = oc.getFile();
-// // throws OntologyEx if file not found -- need to catch - should still try url
-// URL url = null;
-// try { url = findFile(filename); }
-// catch (OntologyException oe) {
-// System.out.println(filename+" not found locally, trying url if configured ");
-// }
+ throws OntologyException {
+// // first get normal/cached/local ontology
+// String filename = oc.getFile();
+// // throws OntologyEx if file not found -- need to catch - should still try url
+// URL url = null;
+// try { url = findFile(filename); }
+// catch (OntologyException oe) {
+// System.out.println(filename+" not found locally, trying url if configured ");
+// }
-// // if ontCfg.hasSynchUrl() ?
-// // URL synchUrl = ontCfg.getSynchUrl
-// if (oc.hasReposUrl()) {
-// try {
-// URL reposUrl = oc.getReposUrl();
-// // if out of synch copies repos to local(.phenote/obo-files)
-// // url may be jar/obo-files or svn/obo-files but this function may put file
-// // in cache ~/.phenote/obo-files
-// url = synchWithRepositoryUrl(url,reposUrl,o.getName(),filename);
-
-// // to do - if from repos need to load repos into local obo cache!
+// // if ontCfg.hasSynchUrl() ?
+// // URL synchUrl = ontCfg.getSynchUrl
+// if (oc.hasReposUrl()) {
+// try {
+// URL reposUrl = oc.getReposUrl();
+// // if out of synch copies repos to local(.phenote/obo-files)
+// // url may be jar/obo-files or svn/obo-files but this function may put file
+// // in cache ~/.phenote/obo-files
+// url = synchWithRepositoryUrl(url,reposUrl,o.getName(),filename);
-// } catch (/*MalformedURL & IO*/Exception e) { LOG.error(e); }
-// }
+// // to do - if from repos need to load repos into local obo cache!
+// } catch (/*MalformedURL & IO*/Exception e) { LOG.error(e); }
+// }
+
URL url = findOboUrl(oc);
long mem = Runtime.getRuntime().totalMemory()/1000000;
LOG.debug(url+" checking with repos... loading obo session mem "+mem+"\n");
- progress+=progressFactor;
- phenote.loadingScreen.setMessageText("checking for updates: "+o.getName());
- phenote.loadingScreen.setProgress(progress);
+ this.updateLoadingScreen("checking for updates: "+o.getName(), true);
startTimer();
-
+
loadOboSessionFromUrl(o,url,oc.getFile());
stopTimer(url+" checked against repos... obo session loaded");
mem = Runtime.getRuntime().totalMemory()/1000000;
@@ -574,7 +571,7 @@
private void loadOboSessionFromUrl(Ontology o, URL url, String filename)
throws OntologyException {
//URL url = findFile(filename); // throws OntologyEx if file not found
- phenote.loadingScreen.setMessageText("doing something with "+o.getName());
+ this.updateLoadingScreen("doing something with "+o.getName(), false);
o.setOboSession(getOboSession(url)); // throws OntEx if error
if (filename!=null)
fileToOntologyCache.put(filename,o); // ??
@@ -619,28 +616,29 @@
// i think this order needs to be same as config order
ontologyManager.addField(cf);
}
-
-// public OntologyPropertyListener() implements PropertyChangeListener {
-// public void propertyChange(PropertyChangeEvent e) {
-// String propertyName = e.getPropertyName();
-// if ("loading".equals(propertyName) {
-// loadingScreen.
-// } else if ("config".equals(propertyName) {
-// } else {
-//
-// }
-// }
-// ...
+
+
+// public OntologyPropertyListener() implements PropertyChangeListener {
+// public void propertyChange(PropertyChangeEvent e) {
+// String propertyName = e.getPropertyName();
+// if ("loading".equals(propertyName) {
+// loadingScreen.
+// } else if ("config".equals(propertyName) {
+// } else {
+
// }
+// }
+// ...
+// }
}
-// private void loadRelationshipOntology() { hmmmmmm
-// // for now - todo configure! post comp relationship-ontology
-// // FieldConfig rfc = cfg().getRelationshipFieldConfig();
-// //CharFieldEnum relEnum = rfc.getCharFieldEnum();
-// CharFieldEnum relEnum = CharFieldEnum.RELATIONSHIP;
-// CharField cf = new CharField(relEnum);
-// }
+//private void loadRelationshipOntology() { hmmmmmm
+//// for now - todo configure! post comp relationship-ontology
+//// FieldConfig rfc = cfg().getRelationshipFieldConfig();
+////CharFieldEnum relEnum = rfc.getCharFieldEnum();
+//CharFieldEnum relEnum = CharFieldEnum.RELATIONSHIP;
+//CharField cf = new CharField(relEnum);
+//}
}
@@ -648,74 +646,74 @@
-// GARBAGE
-// // POST COMP
-// if (fieldConfig.isPostComp()) {
-// cf.setPostCompAllowed(true);
-// try {
-// //Ontology o = initRelationshipOntology(fieldConfig.getPostCompRelOntCfg());
-// Ontology o = initOntology(fieldConfig.getPostCompRelOntCfg());
-// cf.setPostCompRelOntol(o);
-// } catch (OntologyException e) {
-// LOG.error(e.getMessage()+" ignoring ontology, fix config? ");
-// }
-// }
- // i think this order needs to be same as config order
- //initRelationshipOntology();
- // refactor -> Quartz scheduler, reloadOntology()
-// private class OntologyFileCheckThread extends Thread {
+//GARBAGE
+//// POST COMP
+//if (fieldConfig.isPostComp()) {
+//cf.setPostCompAllowed(true);
+//try {
+////Ontology o = initRelationshipOntology(fieldConfig.getPostCompRelOntCfg());
+//Ontology o = initOntology(fieldConfig.getPostCompRelOntCfg());
+//cf.setPostCompRelOntol(o);
+//} catch (OntologyException e) {
+//LOG.error(e.getMessage()+" ignoring ontology, fix config? ");
+//}
+//}
+// i think this order needs to be same as config order
+//initRelationshipOntology();
+// refactor -> Quartz scheduler, reloadOntology()
+//private class OntologyFileCheckThread extends Thread {
-// public void run() {
+//public void run() {
-// int checkMilliSecs = cfg().getOntologyCheckMinutes() * 60000;
-// //int checkMilliSecs = 6000;//0.6 * 60000; // debug - 10 secs
+//int checkMilliSecs = cfg().getOntologyCheckMinutes() * 60000;
+////int checkMilliSecs = 6000;//0.6 * 60000; // debug - 10 secs
-// while(true) {
-// // sleep in milliseconds
-// try { sleep(checkMilliSecs); }
-// catch (InterruptedException e) { LOG.error("thread interrupted??"); }
+//while(true) {
+//// sleep in milliseconds
+//try { sleep(checkMilliSecs); }
+//catch (InterruptedException e) { LOG.error("thread interrupted??"); }
-// // if still loading ontologies from previous run then dont bother
-// if (initializingOntologies) {
-// //System.out.println("Ontologies are being loaded - ontology checker going "+
-// // "back to sleep");
-// LOG.info("Ontologies are being initialized - ontology checker going "+
-// "back to sleep");
-// continue;
-// }
-// LOG.info("checking for new obo files...");
-// //System.out.println("checking for new obo files...");
-// // check for files...
-// synchOntologies();
-// }
-// }
-
-// /** Checks for new obo files */
-// private void synchOntologies() {
-// for (CharField cf : ontologyManager.getCharFieldList()) {
-// for (Ontology o : cf.getOntologyList()) {
-// if (o.getSource() == null) continue;
-// String file = o.getSource();
-// long oldTimestamp = o.getTimestamp();
-// long newTimestamp = new File(file).lastModified();
-// if (newTimestamp > oldTimestamp) {
-// Date d = new Date(newTimestamp);
-// //System.out.println("loading new obo file "+file+" new date "+d);
-// LOG.info("LOG loading new obo file "+file+" new date "+d);
-// try {
-// loadOboSession(o,file);
-// } catch (FileNotFoundException e) { // shouldnt happen
-// //System.out.println(e.getMessage()+" ignoring ontology, fix config! ");
-// LOG.error(e.getMessage()+" ignoring ontology, fix config! ");
-// // LOG.debug(stacktrace)??? no string for stack trace... hmm...
-// }
-// }
-// }
-// }
-// }
+//// if still loading ontologies from previous run then dont bother
+//if (initializingOntologies) {
+////System.out.println("Ontologies are being loaded - ontology checker going "+
+//// "back to sleep");
+//LOG.info("Ontologies are being initialized - ontology checker going "+
+//"back to sleep");
+//continue;
+//}
+//LOG.info("checking for new obo files...");
+////System.out.println("checking for new obo files...");
+//// check for files...
+//synchOntologies();
+//}
+//}
-
-// if (date > 0) { // jar files have 0 date???
-// ontology.setTimestamp(date);
-// ontology.setSource(file.toString());
-// }
+///** Checks for new obo files */
+//private void synchOntologies() {
+//for (CharField cf : ontologyManager.getCharFieldList()) {
+//for (Ontology o : cf.getOntologyList()) {
+//if (o.getSource() == null) continue;
+//String file = o.getSource();
+//long oldTimestamp = o.getTimestamp();
+//long newTimestamp = new File(file).lastModified();
+//if (newTimestamp > oldTimestamp) {
+//Date d = new Date(newTimestamp);
+////System.out.println("loading new obo file "+file+" new date "+d);
+//LOG.info("LOG loading new obo file "+file+" new date "+d);
+//try {
+//loadOboSession(o,file);
+//} catch (FileNotFoundException e) { // shouldnt happen
+////System.out.println(e.getMessage()+" ignoring ontology, fix config! ");
+//LOG.error(e.getMessage()+" ignoring ontology, fix config! ");
+//// LOG.debug(stacktrace)??? no string for stack trace... hmm...
+//}
+//}
+//}
+//}
+//}
+
+
+//if (date > 0) { // jar files have 0 date???
+//ontology.setTimestamp(date);
+//ontology.setSource(file.toString());
+//}
Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -51,6 +51,10 @@
singleton = new CharFieldManager();
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
/** OntologyDataAdapter adds fields */
public void addField(CharField cf) {
Modified: phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/datamodel/CharacterIFactory.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -8,9 +8,17 @@
public class CharacterIFactory {
- private static CharacterIFactory singleton = new CharacterIFactory();
+ private static CharacterIFactory singleton;
- public static CharacterIFactory inst() { return singleton; }
+ public static CharacterIFactory inst() {
+ if (singleton == null) {
+ singleton = new CharacterIFactory();
+ }
+ return singleton; }
+
+ public static void reset() {
+ singleton = null;
+ }
/** static sugar */
public static CharacterI makeChar() {
Modified: phenote/trunk/src/java/phenote/edit/EditManager.java
===================================================================
--- phenote/trunk/src/java/phenote/edit/EditManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/edit/EditManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -53,6 +53,10 @@
// singleton = new EditManager();
// return singleton;
}
+
+ public static void reset() {
+ groupToEditMan.clear();
+ }
// ??
public static EditManager getEditManager(String group) {
Modified: phenote/trunk/src/java/phenote/error/ErrorManager.java
===================================================================
--- phenote/trunk/src/java/phenote/error/ErrorManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/error/ErrorManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -18,6 +18,10 @@
if (singleton == null) singleton = new ErrorManager();
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
public void error(ErrorEvent e) {
for (ErrorListener l : errorListeners) {
Modified: phenote/trunk/src/java/phenote/gui/MenuManager.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/MenuManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/gui/MenuManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -20,14 +20,23 @@
private SettingsMenu settingsMenu;
- private static MenuManager singleton = new MenuManager();
+ private static MenuManager singleton;
private MenuManager() {}
- public static MenuManager inst() { return singleton; }
+ public static MenuManager inst() {
+ if (singleton == null) {
+ singleton = new MenuManager();
+ }
+ return singleton;
+ }
+
+ public static void reset() {
+ singleton = null;
+ }
public static void createMenuManager(JFrame frame) {
- singleton.initMenus(frame);
+ inst().initMenus(frame);
}
public void addViewMenuItem(JMenuItem menuItem) {
Modified: phenote/trunk/src/java/phenote/gui/SearchParams.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SearchParams.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/gui/SearchParams.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -22,6 +22,10 @@
singleton = new SearchParams();
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
/**
* Set a search filter type.
Modified: phenote/trunk/src/java/phenote/gui/SelectionHistory.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/SelectionHistory.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/gui/SelectionHistory.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -81,6 +81,10 @@
singleton = new SelectionHistory();
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
// public SelectionHistory() { //TermPanel termPanel) {
Modified: phenote/trunk/src/java/phenote/gui/ShrimpDag.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/ShrimpDag.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/gui/ShrimpDag.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -12,7 +12,7 @@
import javax.swing.*;
-class ShrimpDag {
+public class ShrimpDag {
//private JFrame window;
private OBOViewer oboViewer;
@@ -22,6 +22,10 @@
if (singleton == null) singleton = new ShrimpDag();
return singleton;
}
+
+ public static void reset() {
+ singleton = null;
+ }
private ShrimpDag() {
//window = new JFrame("Shrimp ontology viewer");
Modified: phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/gui/selection/SelectionManager.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -25,6 +25,10 @@
// if (singleton == null) singleton = new SelectionManager();
// return singleton;
}
+
+ public static void reset() {
+ groupToSelMan.clear();
+ }
public static SelectionManager getSelMan(String group) {
if (group == null) group = CharFieldManager.DEFAULT_GROUP; // ??
Modified: phenote/trunk/src/java/phenote/main/CommandLine.java
===================================================================
--- phenote/trunk/src/java/phenote/main/CommandLine.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/main/CommandLine.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -44,6 +44,10 @@
commandLineSingleton = new CommandLine();
return commandLineSingleton;
}
+
+ public static void reset() {
+ commandLineSingleton = null;
+ }
/**
* Set command-line arguments passed along from main().
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -35,8 +35,12 @@
import phenote.config.ConfigException;
import phenote.config.xml.GroupDocument.Group;
import phenote.dataadapter.CharacterListManager;
+import phenote.dataadapter.LoadSaveManager;
import phenote.dataadapter.OntologyDataAdapter;
+import phenote.datamodel.CharFieldManager;
+import phenote.datamodel.CharacterIFactory;
import phenote.datamodel.CharacterListI;
+import phenote.edit.EditManager;
import phenote.error.ErrorEvent;
import phenote.error.ErrorListener;
import phenote.error.ErrorManager;
@@ -44,10 +48,14 @@
import phenote.gui.GridBagUtil;
import phenote.gui.LoadingScreen;
import phenote.gui.MenuManager;
+import phenote.gui.SearchParams;
import phenote.gui.SelectionHistory;
+import phenote.gui.ShrimpDag;
import phenote.gui.SplashScreen;
import phenote.gui.TermInfo;
import phenote.gui.field.FieldPanel;
+import phenote.gui.selection.SelectionManager;
+import phenote.servlet.PhenoteWebConfiguration;
import phenote.util.FileUtil;
public class Phenote {
@@ -442,12 +450,37 @@
}
-
-
public static Phenote getPhenote() { // singleton
if (phenote == null) phenote = new Phenote();
return phenote;
}
+
+ public static void reset() {
+ phenote = null;
+ }
+
+
+ /**
+ * This is used to reset state between unit tests.
+ */
+ public static void resetAllSingletons() {
+ CharacterListManager.reset();
+ LoadSaveManager.reset();
+ OntologyDataAdapter.reset();
+ CharacterIFactory.reset();
+ CharFieldManager.reset();
+ EditManager.reset();
+ ErrorManager.reset();
+ MenuManager.reset();
+ SearchParams.reset();
+ SelectionHistory.reset();
+ ShrimpDag.reset();
+ SelectionManager.reset();
+ CommandLine.reset();
+ PhenoteWebConfiguration.reset();
+ Config.reset();
+ Phenote.reset();
+ }
/** listens for errors and shoots them to the log */
private static class LogErrorListener implements ErrorListener {
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteWebConfiguration.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -18,6 +18,10 @@
}
return instance;
}
+
+ public static void reset() {
+ instance = null;
+ }
public String getWebRoot() {
Modified: phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
===================================================================
--- phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -9,6 +9,8 @@
import org.junit.BeforeClass;
import org.junit.Test;
+import phenote.config.Config;
+import phenote.config.ConfigException;
import phenote.dataadapter.CharacterListManager;
import phenote.datamodel.CharFieldException;
import phenote.datamodel.CharacterI;
@@ -19,9 +21,12 @@
private CharacterTemplateController controller;
- @BeforeClass public static void initialize() {
- final String[] emptyArgs = {};
- Phenote.main(emptyArgs);
+ @BeforeClass public static void initialize() throws ConfigException {
+ Phenote.resetAllSingletons();
+ Config.inst().setConfigFile("phenomap.cfg");
+ Phenote phenote = Phenote.getPhenote();
+ phenote.initOntologies();
+ phenote.initGui();
}
@Before public void setup() throws InterruptedException, InvocationTargetException {
Modified: phenote/trunk/test/java/phenote/charactertemplate/TreeChooserTest.java
===================================================================
--- phenote/trunk/test/java/phenote/charactertemplate/TreeChooserTest.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/test/java/phenote/charactertemplate/TreeChooserTest.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -16,6 +16,8 @@
import org.junit.BeforeClass;
import org.junit.Test;
+import phenote.config.Config;
+import phenote.config.ConfigException;
import phenote.datamodel.CharFieldException;
import phenote.datamodel.CharFieldManager;
import phenote.datamodel.CharacterI;
@@ -28,9 +30,12 @@
private TreeChooser treeChooser;
private static final String[] termIDs = {"TTO:1003114", "TTO:1004143", "TTO:1030110"};
- @BeforeClass public static void initialize() {
- final String[] emptyArgs = {};
- Phenote.main(emptyArgs);
+ @BeforeClass public static void initialize() throws ConfigException {
+ Phenote.resetAllSingletons();
+ Config.inst().setConfigFile("phenomap.cfg");
+ Phenote phenote = Phenote.getPhenote();
+ phenote.initOntologies();
+ phenote.initGui();
}
@Before public void setup() throws InterruptedException, InvocationTargetException {
Modified: phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java
===================================================================
--- phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -9,6 +9,8 @@
import org.junit.BeforeClass;
import org.junit.Test;
+import phenote.config.Config;
+import phenote.config.ConfigException;
import phenote.dataadapter.CharacterListManager;
import phenote.main.Phenote;
@@ -16,9 +18,12 @@
private CharacterTableController controller;
- @BeforeClass public static void initialize() {
- final String[] emptyArgs = {};
- Phenote.main(emptyArgs);
+ @BeforeClass public static void initialize() throws ConfigException {
+ Phenote.resetAllSingletons();
+ Config.inst().setConfigFile("ncbo.cfg");
+ Phenote phenote = Phenote.getPhenote();
+ phenote.initOntologies();
+ phenote.initGui();
}
@Before public void setup() throws InterruptedException, InvocationTargetException {
Modified: phenote/trunk/test/java/phenote/gui/TestPhenote.java
===================================================================
--- phenote/trunk/test/java/phenote/gui/TestPhenote.java 2007-10-11 20:06:27 UTC (rev 1043)
+++ phenote/trunk/test/java/phenote/gui/TestPhenote.java 2007-10-11 21:26:37 UTC (rev 1044)
@@ -24,6 +24,8 @@
import org.junit.Ignore;
import org.junit.Test;
+import phenote.config.Config;
+import phenote.config.ConfigException;
import phenote.dataadapter.CharacterListManager;
import phenote.dataadapter.fly.FlyCharList;
import phenote.dataadapter.fly.FlyCharListTransferable;
@@ -53,14 +55,16 @@
/** @throws InvocationTargetException
* @throws InterruptedException
+ * @throws ConfigException
* @BeforeClass says to run this once before all the tests */
- @BeforeClass public static void init() throws InterruptedException, InvocationTargetException {
- System.out.println("Initializing Phenote...");
- final String[] emptyArgs = {};
- Phenote.main(emptyArgs);
+ @BeforeClass public static void init() throws InterruptedException, InvocationTargetException, ConfigException {
+ Phenote.resetAllSingletons();
+ Config.inst().setConfigFile("ncbo.cfg");
+ phenote = Phenote.getPhenote();
+ phenote.initOntologies();
+ phenote.initGui();
SwingUtilities.invokeAndWait(new Runnable() {
public void run() {
- phenote = Phenote.getPhenote();
fieldPanel = phenote.getFieldPanel();
searchParamPanel = fieldPanel.getSearchParamPanel();
entityComboBox = fieldPanel.getEntityComboBox();
@@ -72,7 +76,7 @@
}
});
}
-
+
@Ignore @Test public void displayTermInfoOnCompMouseOverTest() throws InterruptedException, InvocationTargetException {
SwingUtilities.invokeAndWait(new Runnable() {
public void run() {
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|
|
From: <mg...@us...> - 2007-10-11 20:06:23
|
Revision: 1043
http://obo.svn.sourceforge.net/obo/?rev=1043&view=rev
Author: mgibson
Date: 2007-10-11 13:06:27 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
Put birn lex into config as its the bit we could convert to obo
Modified Paths:
--------------
phenote/trunk/conf/birn.cfg
Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg 2007-10-11 20:02:59 UTC (rev 1042)
+++ phenote/trunk/conf/birn.cfg 2007-10-11 20:06:27 UTC (rev 1043)
@@ -43,6 +43,7 @@
<ns:field name="Add'l Entity" datatag="E2" enable="true">
<ns:ontology name="Relationship" is-postcomp-rel="true" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro.obo"/>
<ns:ontology name="SAO" file="SAO.obo"/>
+ <ns:ontology name="BIRNLex-Anatomy" file="BIRNLex-Anatomy.obo"/>
<ns:ontology name="BIRNLex" file="BIRNLex.obo"/>
<ns:ontology name="FMA" file="http://obo.svn.sourceforge.net/viewvc/*checkout*/obo/fma-conversion/trunk/fma_obo.obo"/>
<ns:ontology name="Mouse" file="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/mouse/adult_mouse_anatomy.obo"/>
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|
|
From: <mg...@us...> - 2007-10-11 20:02:55
|
Revision: 1042
http://obo.svn.sourceforge.net/obo/?rev=1042&view=rev
Author: mgibson
Date: 2007-10-11 13:02:59 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
threading was causing requests to go empty - not sure why
but with change from invokeLater to invokeAndWait this was cleared up
Modified Paths:
--------------
phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
Modified: phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 19:51:47 UTC (rev 1041)
+++ phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 20:02:59 UTC (rev 1042)
@@ -27,12 +27,13 @@
public void doGet(/*final*/ HttpServletRequest request, /*final*/ HttpServletResponse response)
throws IOException, ServletException {
- System.out.println("got get " +request);
- LOG.debug("servlet doGet " + new Date());
- Enumeration<?> e = request.getParameterNames();
- while (e.hasMoreElements()) LOG.debug("param -prethread "+e.nextElement());
+ //System.out.println("got get " +request);
+ LOG.debug("servlet doGet " + new Date()+request);
// need to interact with the application on the Swing thread
- SwingUtilities.invokeLater(new EditRunnable(request));
+ //SwingUtilities.invokeLater(new EditRunnable(request));
+ // not sure why but invokeLater made later requests be empty???
+ try { SwingUtilities.invokeAndWait(new EditRunnable(request)); }
+ catch (/*Interrupted*/Exception x) { LOG.error(x); }
}
private class EditRunnable implements Runnable {
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|
|
From: <mg...@us...> - 2007-10-11 19:51:47
|
Revision: 1041
http://obo.svn.sourceforge.net/obo/?rev=1041&view=rev
Author: mgibson
Date: 2007-10-11 12:51:47 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
yea the threading is causing the request to go to hell and i cant figure out
why
i thought the final might be a problem but apparently not
hmmmmm.....
Modified Paths:
--------------
phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
Modified: phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 18:44:11 UTC (rev 1040)
+++ phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 19:51:47 UTC (rev 1041)
@@ -25,12 +25,21 @@
// PhenoteServlet.class is the distinct name for this logger
private static final Logger LOG = Logger.getLogger(DataInputServlet.class);
- public void doGet(final HttpServletRequest request, final HttpServletResponse response)
+ public void doGet(/*final*/ HttpServletRequest request, /*final*/ HttpServletResponse response)
throws IOException, ServletException {
- System.out.println("got get" +request);
+ System.out.println("got get " +request);
LOG.debug("servlet doGet " + new Date());
+ Enumeration<?> e = request.getParameterNames();
+ while (e.hasMoreElements()) LOG.debug("param -prethread "+e.nextElement());
// need to interact with the application on the Swing thread
- SwingUtilities.invokeLater(new Runnable() {
+ SwingUtilities.invokeLater(new EditRunnable(request));
+ }
+
+ private class EditRunnable implements Runnable {
+ private HttpServletRequest request;
+ private EditRunnable(HttpServletRequest req) {
+ this.request = req;
+ }
public void run() {
CharacterI ch = CharacterIFactory.makeChar();
Enumeration<?> e = request.getParameterNames();
@@ -52,7 +61,7 @@
}
EditManager.inst().addCharacter(ch);
}
- });
+
}
/**
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|
|
From: <ba...@us...> - 2007-10-11 18:44:12
|
Revision: 1040
http://obo.svn.sourceforge.net/obo/?rev=1040&view=rev
Author: balhoff
Date: 2007-10-11 11:44:11 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
Fixing glazed list exceptions caused by data input servlet.
Modified Paths:
--------------
phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
Modified: phenote/trunk/src/java/phenote/servlet/DataInputServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 18:44:11 UTC (rev 1039)
+++ phenote/trunk/src/java/phenote/servlet/DataInputServlet.java 2007-10-11 18:44:11 UTC (rev 1040)
@@ -1,20 +1,20 @@
package phenote.servlet;
import java.io.IOException;
-import java.io.PrintWriter;
import java.util.Date;
import java.util.Enumeration;
-import java.util.Vector;
+
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
+import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-import javax.servlet.http.HttpServletRequest;
+import javax.swing.SwingUtilities;
import org.apache.log4j.Logger;
+import phenote.datamodel.CharFieldException;
import phenote.datamodel.CharacterI;
import phenote.datamodel.CharacterIFactory;
-import phenote.datamodel.CharFieldException;
import phenote.datamodel.TermNotFoundException;
import phenote.edit.EditManager;
@@ -25,30 +25,34 @@
// PhenoteServlet.class is the distinct name for this logger
private static final Logger LOG = Logger.getLogger(DataInputServlet.class);
- public void doGet(HttpServletRequest request, HttpServletResponse response)
+ public void doGet(final HttpServletRequest request, final HttpServletResponse response)
throws IOException, ServletException {
System.out.println("got get" +request);
LOG.debug("servlet doGet " + new Date());
-
- CharacterI ch = CharacterIFactory.makeChar();
- Enumeration e = request.getParameterNames();
- while (e.hasMoreElements()) {
- Object o = e.nextElement();
- LOG.debug("param "+o);
- // test if instance of String?
- String field = (String)o;
- String value = request.getParameter(field);
- try {
- ch.setValue(field,value);
+ // need to interact with the application on the Swing thread
+ SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ CharacterI ch = CharacterIFactory.makeChar();
+ Enumeration<?> e = request.getParameterNames();
+ while (e.hasMoreElements()) {
+ Object o = e.nextElement();
+ LOG.debug("param "+o);
+ // test if instance of String?
+ String field = (String)o;
+ String value = request.getParameter(field);
+ try {
+ ch.setValue(field,value);
+ }
+ catch (CharFieldException cfe) {
+ LOG.error("field not found "+cfe);
+ }
+ catch (TermNotFoundException tnfe) {
+ LOG.error("term not found in field "+field+" "+tnfe);
+ }
+ }
+ EditManager.inst().addCharacter(ch);
}
- catch (CharFieldException cfe) {
- LOG.error("field not found "+cfe);
- }
- catch (TermNotFoundException tnfe) {
- LOG.error("term not found in field "+field+" "+tnfe);
- }
- }
- EditManager.inst().addCharacter(ch);
+ });
}
/**
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|
|
From: <mg...@us...> - 2007-10-11 18:44:12
|
Revision: 1039
http://obo.svn.sourceforge.net/obo/?rev=1039&view=rev
Author: mgibson
Date: 2007-10-11 11:44:11 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
new birn lex anatomy - this isnt actually used in configs
but the question to birn is is this sufficient as the full birn lex
seems problematic for owl to obo converter
Modified Paths:
--------------
phenote/trunk/obo-files/BIRNLex-Anatomy.obo
Modified: phenote/trunk/obo-files/BIRNLex-Anatomy.obo
===================================================================
--- phenote/trunk/obo-files/BIRNLex-Anatomy.obo 2007-10-11 18:39:08 UTC (rev 1038)
+++ phenote/trunk/obo-files/BIRNLex-Anatomy.obo 2007-10-11 18:44:11 UTC (rev 1039)
@@ -1,13 +1,11 @@
format-version: 1.2
-idspace: bfo http://www.ifomis.org/bfo/1.0# ""
-idspace: bfo_pato_bridge http://purl.org/obo/owl/quality_bfo_bridge# ""
-idspace: bfo_ro_bridge http://purl.org/obo/obo-all/ro_bfo_bridge/ro_bfo_bridge.owl# ""
idspace: biopax1 http://www.biopax.org/release/biopax-level1.owl# ""
-idspace: birn_annot http://purl.org/nbirn/birnlex/1.2.3/BIRNLex_annotation_properties.owl# ""
-idspace: birn_annot_old http://purl.org/nbirn/birnlex/1.2.2/BIRNLex_annotation_properties.owl# ""
-idspace: birn_obo_ubo http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-OBO-UBO.owl# ""
-idspace: birn_org_tax http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-OrganismalTaxonomy.owl# ""
+idspace: birn_annot http://purl.org/nbirn/birnlex/ontology/annotation/BIRNLex_annotation_properties.owl# ""
+idspace: birn_obo_ubo http://purl.org/nbirn/birnlex/ontology/BIRNLex-OBO-UBO.owl# ""
+idspace: birn_org_tax http://purl.org/nbirn/birnlex/ontology/BIRNLex-OrganismalTaxonomy.owl# ""
+idspace: birnlex_anatomy http://purl.org/nbirn/birnlex/ontology/BIRNLex-Anatomy.owl# ""
idspace: core http://www.w3.org/2004/02/skos/core# ""
+idspace: daml http://www.daml.org/2001/03/daml+oil# ""
idspace: dc http://purl.org/dc/elements/1.1/ ""
idspace: eor http://dublincore.org/2000/03/13/eor# ""
idspace: galen http://www.co-ode.org/ontologies/galen# ""
@@ -15,16 +13,10 @@
idspace: oban http://www.berkeleybop.org/ontologies/oban/alpha# ""
idspace: obd http://www.bioontology.org/obd/obd-ontology# ""
idspace: oboInOwl http://www.bioontology.org/oboInOwl# ""
-idspace: obo_annot http://purl.org/nbirn/birnlex/1.2.3/OBO_annotation_properties.owl# ""
-idspace: obo_annot_old http://purl.org/nbirn/birnlex/1.2.2/OBO_annotation_properties.owl# ""
-idspace: obo_base http://purl.org/obo/owl/obo# ""
-idspace: obo_rel http://purl.org/obo/owl/OBO_REL# ""
-idspace: obo_ro http://www.obofoundry.org/ro/ro.owl# ""
+idspace: obo_annot http://purl.org/nbirn/birnlex/ontology/annotation/OBO_annotation_properties.owl# ""
idspace: owl http://www.w3.org/2002/07/owl# ""
-idspace: pato http://purl.org/obo/owl/PATO# ""
idspace: propreo http://lsdis.cs.uga.edu/projects/glycomics/propreo# ""
idspace: protege http://protege.stanford.edu/plugins/owl/protege# ""
-idspace: protege-dc http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl# ""
idspace: rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# ""
idspace: rdfs http://www.w3.org/2000/01/rdf-schema# ""
idspace: reactome http://www.reactome.org/biopax# ""
@@ -33,4601 +25,9718 @@
idspace: xsd http://www.w3.org/2001/XMLSchema# ""
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_001
-name: Anatomical_entity
-comment:
-is_a: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_703 ! _birnlexAnatomy_retired_class
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description101
+is_anonymous: true
+intersection_of: http://purl.org/obo/owl/PATO#PATO_0001471
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_004
-name: Anatomical_cavity
-comment: __file:///Users/cjm/tmp/BIRNLex-Anatomy.owl#__Description1
+id: __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description103
+is_anonymous: true
+union_of: birnlex_anatomy:birnlex_1728 ! Left parietal lobe
+union_of: birnlex_anatomy:birnlex_1729 ! Right parietal lobe
+union_of: birnlex_anatomy:birnlex_1782 ! Left occipital lobe
+union_of: birnlex_anatomy:birnlex_1783 ! Right occipital lobe
[Term]
-id: http://purl.org/nbirn/birnlex/1.2.2/BIRNLex-Anatomy.owl#birnAnatomy_005
-name: Organ_cavity
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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[Term]
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+id: birnlex_anatomy:birnlex_1024
+name: Regional part of medullary white matter
+is_a: birnlex_anatomy:birnlex_1355 ! Regional part of medulla oblongata
+
+[Term]
+id: birnlex_anatomy:birnlex_1025
+name: Temporal operculum
+xref: NeuroNames:109
+is_a: birnlex_anatomy:birnlex_1538 ! Superficial feature part of temporal lobe
+property_value: birn_annot:neuronamesID "109" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1026
+name: Posterior commissure
+xref: NeuroNames:475
+is_a: birnlex_anatomy:birnlex_808 ! Predominantly white regional part of tectum
+property_value: birn_annot:neuronamesID "475" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1027
+name: Predominantly white regional part of basal part of pons
+is_a: birnlex_anatomy:birnlex_1168 ! Regional part of basal part of pons
+
+[Term]
+id: birnlex_anatomy:birnlex_1028
+name: Subcommissural organ
+xref: NeuroNames:474
+is_a: birnlex_anatomy:birnlex_795 ! Regional part of midbrain tectum
+property_value: birn_annot:neuronamesID "474" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1029
+name: Neuraxis cavity
+is_a: birnlex_anatomy:birnlex_1019 ! Organ cavity
+
+[Term]
+id: birnlex_anatomy:birnlex_1030
+name: Superior frontal sulcus
+xref: NeuroNames:42
+is_a: birnlex_anatomy:birnlex_1324 ! Superficial feature part of frontal lobe
+property_value: birn_annot:neuronamesID "42" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1031
+name: Tegmentum
+is_a: birnlex_anatomy:birnlex_1304 ! Composite part spanning multiple base regional parts of brain
+relationship: http://www.obofoundry.org/ro/ro.owl#has_part __file:///Users/cjm/.blip/data_cache/BIRNLex-Anatomy.owl#__Description94
+
+[Term]
+id: birnlex_anatomy:birnlex_1032
+name: Midbrain tectum
+def: "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." []
+xref: NeuroNames:448
+is_a: birnlex_anatomy:birnlex_763 ! Regional part of midbrain
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1007 ! Parabigeminal nucleus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1016 ! Corticotectal tract
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1026 ! Posterior commissure
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1028 ! Subcommissural organ
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1040 ! Superior colliculus
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_1341 ! Trochlear nerve root
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_703 ! Pretectal region
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_795 ! Regional part of midbrain tectum
+relationship: http://www.obofoundry.org/ro/ro.owl#has_proper_part birnlex_anatomy:birnlex_806 ! Inferior colliculus
+property_value: birn_annot:birnlexDefinition "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." string
+property_value: birn_annot:neuronamesID "448" string
+
+[Term]
+id: birnlex_anatomy:birnlex_1033
+name: Precommissural fornix
+is_a: birnlex_anatomy:birnlex_738 ! Predominant...
[truncated message content] |
|
From: <mg...@us...> - 2007-10-11 18:39:04
|
Revision: 1038
http://obo.svn.sourceforge.net/obo/?rev=1038&view=rev
Author: mgibson
Date: 2007-10-11 11:39:08 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
javadoc
Modified Paths:
--------------
phenote/trunk/src/java/phenote/gui/CharacterTableController.java
phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
Modified: phenote/trunk/src/java/phenote/gui/CharacterTableController.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/CharacterTableController.java 2007-10-11 18:05:12 UTC (rev 1037)
+++ phenote/trunk/src/java/phenote/gui/CharacterTableController.java 2007-10-11 18:39:08 UTC (rev 1038)
@@ -72,6 +72,8 @@
return this.characterTablePanel;
}
+ /** in swixml config conf/character_table_panel.xml the add button New is set up to
+ call this method */
public void addNewCharacter() {
this.getEditManager().addNewCharacter();
}
@@ -267,4 +269,4 @@
}
}
-
\ No newline at end of file
+
Modified: phenote/trunk/src/java/phenote/gui/field/FieldPanel.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-10-11 18:05:12 UTC (rev 1037)
+++ phenote/trunk/src/java/phenote/gui/field/FieldPanel.java 2007-10-11 18:39:08 UTC (rev 1038)
@@ -83,10 +83,11 @@
if (addSearchPanel)
initSearchPanel();
- // should there be a GroupConfig object?
+ // should there be a GroupConfig object? cant GroupAdap do this itself?
if (Config.inst().hasGroupAdapter(group)) {
GroupAdapterI groupAdap = Config.inst().getGroupAdapter(group);
if (groupAdap.hasCharChangeListener()) {
+ // this is doing for all groups, should probably just for its own group
editManager.addCharChangeListener(groupAdap.getCharChangeListener());
}
if (groupAdap.hasCharListChangeListener()) {
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2007-10-11 18:05:08
|
Revision: 1037
http://obo.svn.sourceforge.net/obo/?rev=1037&view=rev
Author: mgibson
Date: 2007-10-11 11:05:12 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
woops forgot to enable servlet for birn.cfg to be used by smart atlas
Modified Paths:
--------------
phenote/trunk/conf/birn.cfg
Modified: phenote/trunk/conf/birn.cfg
===================================================================
--- phenote/trunk/conf/birn.cfg 2007-10-11 15:43:41 UTC (rev 1036)
+++ phenote/trunk/conf/birn.cfg 2007-10-11 18:05:12 UTC (rev 1037)
@@ -12,6 +12,7 @@
<ns:dataadapter name="phenote.dataadapter.phenoxml.PhenoXmlAdapter" enable="true"/>
<!--******************** FIELD DEFINITIONS ***********************-->
<ns:autocomplete-settings term="true" synonym="true" definition="false" obsolete="false"/>
+
<ns:field name="Pub" datatag="PUB" enable="true" desc="The provenance for this data"/>
@@ -66,12 +67,13 @@
<ns:field name="Slice Number" datatag="slicenumber" enable="true" desc="images have many slices(?)"/>
<!--*********************** SETTINGS ****************************-->
- <ns:uvic-graph enable="false"/>
+ <ns:data-input-servlet enable="true"/>
<ns:term-history enable="false"/>
+ <!--true=update; false=don't update-->
<ns:auto-update-ontologies enable="true"/>
- <!--true=update; false=don't update-->
<!--set to 0 if you want to bypass the check; time in seconds-->
<ns:update-timer timer="10"/>
+ <ns:uvic-graph enable="false"/>
<!--******************** REVISION HISTORY ***********************-->
<!--08.14.2007 - Sarah M. copied from birn2
- added comment field
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ba...@us...> - 2007-10-11 15:43:40
|
Revision: 1036
http://obo.svn.sourceforge.net/obo/?rev=1036&view=rev
Author: balhoff
Date: 2007-10-11 08:43:41 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
Moving the rest of the tests.
Added Paths:
-----------
phenote/trunk/test/java/phenote/gui/TestPhenote.java
phenote/trunk/test/java/phenote/util/
phenote/trunk/test/java/phenote/util/FileUtilTest.java
phenote/trunk/test/java/phenote/util/TermLinkComparatorTest.java
Removed Paths:
-------------
phenote/trunk/src/java/phenote/gui/TestPhenote.java
phenote/trunk/src/java/phenote/util/FileUtilTest.java
phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
Deleted: phenote/trunk/src/java/phenote/gui/TestPhenote.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TestPhenote.java 2007-10-11 15:28:04 UTC (rev 1035)
+++ phenote/trunk/src/java/phenote/gui/TestPhenote.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -1,307 +0,0 @@
-package phenote.gui;
-
-// move to main package??
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.ClipboardOwner;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.datatransfer.UnsupportedFlavorException;
-import java.awt.event.KeyEvent;
-import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-
-import javax.swing.SwingUtilities;
-import javax.swing.event.HyperlinkEvent;
-
-import org.junit.BeforeClass;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import phenote.dataadapter.CharacterListManager;
-import phenote.dataadapter.fly.FlyCharList;
-import phenote.dataadapter.fly.FlyCharListTransferable;
-import phenote.dataadapter.fly.FlyCharacter;
-import phenote.dataadapter.fly.FlybaseDataAdapter;
-import phenote.datamodel.CharacterI;
-import phenote.datamodel.CharacterListI;
-import phenote.gui.field.AbstractAutoCompList;
-import phenote.gui.field.FieldPanel;
-import phenote.gui.field.SearchParamPanel;
-import phenote.main.Phenote;
-import phenote.util.HtmlUtil;
-
-// making same package as phenotes giving us access to package methods!
-
-// dont need to subclass TestCase - does tests thgough annotations (1.5)
-public class TestPhenote {
-
- // dont have handle on instance - have to do statics - wierd
- private static Phenote phenote;
- private static FieldPanel fieldPanel;
- private static SearchParamPanel searchParamPanel;
- private static AbstractAutoCompList entityComboBox;
- private static AbstractAutoCompList qualityComboBox;
- private static TermInfo termInfo;
- private static CharacterTableController tableController;
-
- /** @throws InvocationTargetException
- * @throws InterruptedException
- * @BeforeClass says to run this once before all the tests */
- @BeforeClass public static void init() throws InterruptedException, InvocationTargetException {
- System.out.println("Initializing Phenote...");
- final String[] emptyArgs = {};
- Phenote.main(emptyArgs);
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- phenote = Phenote.getPhenote();
- fieldPanel = phenote.getFieldPanel();
- searchParamPanel = fieldPanel.getSearchParamPanel();
- entityComboBox = fieldPanel.getEntityComboBox();
- entityComboBox.setTestMode(true); // turns off popup, hanging bug only in test
- qualityComboBox = fieldPanel.getQualityComboBox();
- qualityComboBox.setTestMode(true);
- termInfo = phenote.getTermInfo();
- tableController = phenote.getCharacterTableController();
- }
- });
- }
-
- @Ignore @Test public void displayTermInfoOnCompMouseOverTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- System.out.println("Testing comp list mouse over term info...");
- // "he" should have plenty of completion terms associated, heart, head...
- boolean doCompletion = true;
- System.out.println("set entity text to hea");
- //entityComboBox.setText("hea",doCompletion);
- // already have list from l from previous test - for some reason 2nd l doesnt jibe
- // even though there are lots of quality terms with 'll' ???
- //qualityComboBox.simulateLKeyStroke(); // just does 'l'
- System.out.println("set text - getting 3rd term");
- //JList entityJList = entityComboBox.getJList();
- // pick 3rd item
- //String thirdTerm = (String)entityJList.getModel().getElementAt(2);
- //String thirdTerm = getEntityThirdAutoTerm();
- String thirdTerm = getQualityThirdAutoTerm();
- assertNotNull("3rd term from quality combo shouldnt be null",thirdTerm);
- //entityJList.setSelectedIndex(2);
- //entityComboBox.doMouseOver(2); // 2 is 3rd - 0 indexing
- qualityComboBox.doMouseOver(2);
-
- //String info = termInfo.getText();
- // gets text in term field part where name is displayed
- String info = termInfo.getTermFieldText();
- //String properInfoPrefix = "Term: "+thirdTerm;
- // this doesnt work anymore with mtml stuff in there...
- //boolean isInfoProper = info.startsWith(properInfoPrefix);
- boolean isInfoProper = info.contains(thirdTerm);
-
- String msg = "term info should contain '"+thirdTerm
- +"' not getting mouseover but its ["+info+"]";
- assertTrue(msg,isInfoProper);
- System.out.println("Completion mouse over term info test succeeded!");
- }
- });
-
- }
-
- private String getEntityThirdAutoTerm() {
- return entityComboBox.getJComboBox().getModel().getElementAt(2).toString();
- }
-
- private String getQualityThirdAutoTerm() {
- assertNotNull(qualityComboBox.getJComboBox().getModel());
- assertNotNull("3rd term from quality combo shouldnt be null",
- qualityComboBox.getJComboBox().getModel().getElementAt(2));
- return qualityComboBox.getJComboBox().getModel().getElementAt(2).toString();
- }
-
- private String getQualityTerm(int index) {
- assertNotNull(qualityComboBox.getJComboBox().getModel());
- assertNotNull(index+" term from quality combo shouldnt be null",
- qualityComboBox.getJComboBox().getModel().getElementAt(index));
- return qualityComboBox.getJComboBox().getModel().getElementAt(index).toString();
- }
-
- /** Selecting item in entity combo box should cause that item to appear in
- table in entity column
- * @throws InvocationTargetException
- * @throws InterruptedException */
- @Ignore @Test public void comboTermSelectionGoesToTableTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- // selecting item should make it go in table...
- tableController.addNewCharacter();
- tableController.getSelectionModel().setSelectionInterval(0,0);
- System.out.println("Selecting 3rd entity item");
- qualityComboBox.getJComboBox().setSelectedIndex(2); // 2 is 3rd
- String selectedQualityTerm = getQualityThirdAutoTerm();
- CharacterI selPheno = tableController.getSelectionModel().getSelected().get(0);
- String tableQuality = selPheno.getQuality().getName(); // oboclass
- assertEquals(selectedQualityTerm,tableQuality);
- System.out.println("term to table test passed, selected quality term "
- +selectedQualityTerm+" quality in table "+tableQuality+"\n");
- }
- });
-
- }
-
- // cant get null pointer to fly - gotta love testing guis
- /** theres a null pointer on selcting item for 1st time, not sure i can replicate
- this is an awful test - assumes lacking physical part is the 2nd indexed
- L term in quality
- ontology - assumes theres a quality ontology
- * @throws InvocationTargetException
- * @throws InterruptedException */
- @Ignore @Test public void compListSelectionTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- //qualityComboBox.setText("larg",true);
- qualityComboBox.simulateLKeyStroke();
- qualityComboBox.getJComboBox().setSelectedIndex(2);
- // this is admittedly presumptious of quality
- assertEquals("lacking physical part",qualityComboBox.getText());
- System.out.println("comp list sel ok "+qualityComboBox.getText());
- }
- });
- }
-
- /** After term selected in comp list popup should not come up - this doesnt actually
- test this - the popup does go away with setSelInd - only with mouse click it
- sometimes doesnt - need simulated mouse click!
- * @throws InvocationTargetException
- * @throws InterruptedException */
- @Ignore @Test public void selectionPopupTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- qualityComboBox.setText("larg",true);
- qualityComboBox.getJComboBox().setSelectedIndex(2);
- assertFalse(qualityComboBox.getJComboBox().isPopupVisible());
- }
- });
-
- }
-
- /** with searching on synonyms hit bug where terms come in more than once if have
- 2 syns
- * @throws InvocationTargetException
- * @throws InterruptedException */
- @Ignore @Test public void synonymDupTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- qualityComboBox.setText("");
- // searchParamPanel not used anymore - need to set in menu
- //searchParamPanel.setTermSearch(false);
- //searchParamPanel.setSynonymSearch(true);
- SearchParams.inst().setParam(SearchFilterType.TERM,false);
- SearchParams.inst().setParam(SearchFilterType.SYN,true);
- simulateAQualityKeyStroke();
- String first = getQualityTerm(0);
- String second = getQualityTerm(1);
- assertFalse(first.equals(second));
- }
- });
-
- }
-
- // utlimatley need to do mouse click on term - how to do that???
- @Test public void termInfoSelectTermTest() throws InterruptedException, InvocationTargetException {
- SwingUtilities.invokeAndWait(new Runnable() {
- public void run() {
- simulatePhenoteHyperlinkUpdate();
- String m = "term info hyper link test fail, term info should have body tone val "
- +" term info: "+termInfo.getTermFieldText();
- // how to make this test not so pato specific??
- assertTrue(m,termInfo.getTermFieldText().contains("body tone value"));
- }
- });
- }
-
- private void simulatePhenoteHyperlinkUpdate() {
- HyperlinkEvent.EventType type = HyperlinkEvent.EventType.ACTIVATED;
- // 0000732 -> "BodyToneValue"
- String desc = HtmlUtil.makePhenoIdLink("PATO:0000732");
- HyperlinkEvent e = new HyperlinkEvent(termInfo,type,null,desc);
- termInfo.simulateHyperlinkEvent(e);
- }
-
- private void simulateAQualityKeyStroke() {
- simulateQualityKeyStroke(KeyEvent.VK_A,'a');
- }
-
- private void simulateQualityKeyStroke(int keyCode, char c) {
- qualityComboBox.simulateKeyStroke(keyCode,c);
- }
-
- @Ignore @Test public void flyDataAdapterTest() throws UnsupportedFlavorException, IOException {
- CharacterListI cl = CharacterListManager.main().getCharacterList();
- DataFlavor charListFlavor = FlyCharListTransferable.getCharListDataFlavor();
- Object o = getClipboard().getData(charListFlavor);
- String m = "Failure: clipboard transferrable is not a FlyCharList "+o;
- assertTrue(m,o instanceof FlyCharList);
- FlyCharList fcl = (FlyCharList)o;
- CharacterListI clipboardCharList = fcl.getCharacterList();
- //assertEquals(clipboardCharList,cl); // its a clone???
- assertTrue(clipboardCharList.equals(cl));
-
- // simulate proforma - grab strings and recreate char list & shove in clipboard
- // & load it up
- FlyCharList newFlyCharList = new FlyCharList();
- for (FlyCharacter fc : fcl.getFlyCharList()) {
- FlyCharacter fcNew = new FlyCharacter(fc.getGenotype(),fc.getEVString());
- newFlyCharList.addFlyChar(fcNew);
- }
- Transferable tr = new FlyCharListTransferable(newFlyCharList);
- ClipboardOwner clipboardOwner = FlybaseDataAdapter.getClipboardOwner();
- getClipboard().setContents(tr,clipboardOwner);
-
- MenuManager.inst().getFileMenu().clickLoad();
- CharacterListI newCL = CharacterListManager.inst().getCharacterList();
- //assertEquals(cl,newCL); == NOT .equals()
- assertTrue(cl.equals(newCL));
- }
-
-// // put in CharList class?
-// private boolean charListEquals(CharacterListI c1, CharacterListI c2) {
-// if (c1.size() != c2.size()) return false;
-// for (int i=0; i<c1.size(); i++) {
-// if (!c1.get(i).equals(c2,get(i)))
-// return false;
-// }
-// return true;
-// }
-
- private Clipboard getClipboard() {
- Toolkit t = Toolkit.getDefaultToolkit();
- return t.getSystemClipboard();
- }
-
-
- // I cant find a way to simulate a backspace in jcombobox - very frustrating!!
-// /** there is/was a bug where delete/backspace was not triggering a new
-// completion list */
-// private void backspaceInComboBoxTest() {
-// boolean doCompletion = true;
-// qualityComboBox.clear();
-// qualityComboBox.setText("larg",doCompletion);
-// int preBackspaceCount = qualityComboBox.getItemCount();
-
-// // simulate backspace/delete key
-// KeyEvent ke = new KeyEvent(qualityComboBox,KeyEvent.VK_DELETE,Calendar.getInstance().getTimeInMillis(),0,KeyEvent.VK_UNDEFINED,KeyEvent.CHAR_UNDEFINED);
-// //qualityComboBox.processKeyEvent(ke);
-// qualityComboBox.getEditor().getEditorComponent().processKeyEvent(ke);
-
-// String postDelText = qualityComboBox.getText();
-// int postBackspaceCount = qualityComboBox.getItemCount();
-// System.out.println("post text "+postDelText+" pre count "+preBackspaceCount+" post count "+postBackspaceCount);
-// assertTrue(preBackspaceCount != postBackspaceCount);
-// }
-
-}
Deleted: phenote/trunk/src/java/phenote/util/FileUtilTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtilTest.java 2007-10-11 15:28:04 UTC (rev 1035)
+++ phenote/trunk/src/java/phenote/util/FileUtilTest.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -1,127 +0,0 @@
-package phenote.util;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import org.junit.Test;
-import org.junit.After;
-import org.junit.Before;
-
-
-import java.io.File;
-import java.io.IOException;
-
-/**
- * Unit test class for FileUtil.
- */
-public class FileUtilTest {
-
- private static final File testArchiveDir = new File("src" + FileUtil.FILE_SEPARATOR +
- "java" + FileUtil.FILE_SEPARATOR +
- "test", "test-archive-dir");
- private static final File testLoadDirectory = new File("src" + FileUtil.FILE_SEPARATOR +
- "java" + FileUtil.FILE_SEPARATOR +
- "test", "test-load-dir");
- private File testLoadFile;
- private File testPurgeFile;
-
- @Before
- public void setUp() {
- setTestDirectories();
- }
-
- @After
- public void tearDown() {
- cleanupTestFilesStructure();
- }
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- */
- @Test
- public void archiveFile() {
- File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
- File[] files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
- assertTrue("Original File still exists", testLoadFile.exists());
- }
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- * Sleep for a second and then archive another file and then purge the first file while the
- * second file does not get purged.
- */
- @Test
- public void purgeArchiveFile() {
- File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
- File[] files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
- assertTrue("Original File still exists", testLoadFile.exists());
-
- // create the second file and wait a second before archiving it.
- testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
- try {
- Thread.sleep(1000);
- testPurgeFile.createNewFile();
- } catch (IOException e) {
- e.printStackTrace();
- } catch (InterruptedException e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
-
- archivedFile = FileUtil.archiveFile(testPurgeFile, testArchiveDir);
- files = testArchiveDir.listFiles();
- assertEquals("Number of files", 2, files.length);
- FileUtil.purgeArchiveDirectory(testArchiveDir, 990);
-
- files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
-
- }
-
- @Test
- public void pureFilename() {
- String fileNameOnly = "filenameAlpha.txt";
- String filename = FileUtil.FILE_SEPARATOR + "dire" + FileUtil.FILE_SEPARATOR + fileNameOnly;
- String pureFilename = FileUtil.getPureFileName(filename);
- assertEquals("Pure File Name", fileNameOnly, pureFilename);
-
- fileNameOnly = "";
- pureFilename = FileUtil.getPureFileName(fileNameOnly);
- assertEquals("Pure File Name", fileNameOnly, pureFilename);
- }
-
-
- /**
- * Create the test directories before the tests are run.
- */
- private void setTestDirectories() {
- testLoadDirectory.mkdir();
-
- testLoadFile = new File(testLoadDirectory, "test-file-one.txt");
- testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
- try {
- testLoadFile.createNewFile();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- /**
- * Remove test directories after the tests are done.
- */
- private void cleanupTestFilesStructure() {
- testLoadFile.delete();
- testPurgeFile.delete();
- testLoadDirectory.delete();
- File[] files = testArchiveDir.listFiles();
- if (files != null)
- for (File file : files) {
- file.delete();
- }
- testArchiveDir.delete();
- }
-
-}
Deleted: phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:28:04 UTC (rev 1035)
+++ phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -1,81 +0,0 @@
-package phenote.util;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-import org.geneontology.oboedit.datamodel.Link;
-import org.geneontology.oboedit.datamodel.OBOProperty;
-import org.geneontology.oboedit.datamodel.impl.InstancePropertyValue;
-import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
-import org.junit.Assert;
-import org.junit.Test;
-
-
-/**
- * Unit test class for FileUtil.
- */
-public class TermLinkComparatorTest {
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- */
- @Test public void testIS_A_Before_PART_Of() {
- List<InstancePropertyValue> links = new ArrayList<InstancePropertyValue>();
- links.add(getLinkUnknownOne());
- links.add(getLinkUnknownTwo());
- links.add(getLinkDevelops_From());
- links.add(getLinkPart_Of());
- links.add(getLinkIS_A());
-
- Collections.sort(links, new TermLinkComparator());
-
- Link link = (Link) links.get(0);
- Assert.assertEquals("IS a first", "is_a", link.getType().getName());
- link = (Link) links.get(1);
- Assert.assertEquals("Part of is second", "part of", link.getType().getName());
- link = (Link) links.get(2);
- Assert.assertEquals("Part of is second", "develops from", link.getType().getName());
- link = (Link) links.get(3);
- Assert.assertEquals("IS a first", "Unknown A", link.getType().getName());
- link = (Link) links.get(4);
- Assert.assertEquals("IS a first", "Unknown B", link.getType().getName());
-
- }
-
- private InstancePropertyValue getLinkIS_A(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.IS_A.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkPart_Of(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.PART_OF.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkDevelops_From(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.DEVELOPS_FROM.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkUnknownOne(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl("Unknown B");
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkUnknownTwo(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl("Unknown A");
- link.setType(prop);
- return link;
- }
-
-}
Copied: phenote/trunk/test/java/phenote/gui/TestPhenote.java (from rev 1035, phenote/trunk/src/java/phenote/gui/TestPhenote.java)
===================================================================
--- phenote/trunk/test/java/phenote/gui/TestPhenote.java (rev 0)
+++ phenote/trunk/test/java/phenote/gui/TestPhenote.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -0,0 +1,307 @@
+package phenote.gui;
+
+// move to main package??
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.event.KeyEvent;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
+
+import org.junit.BeforeClass;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import phenote.dataadapter.CharacterListManager;
+import phenote.dataadapter.fly.FlyCharList;
+import phenote.dataadapter.fly.FlyCharListTransferable;
+import phenote.dataadapter.fly.FlyCharacter;
+import phenote.dataadapter.fly.FlybaseDataAdapter;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterListI;
+import phenote.gui.field.AbstractAutoCompList;
+import phenote.gui.field.FieldPanel;
+import phenote.gui.field.SearchParamPanel;
+import phenote.main.Phenote;
+import phenote.util.HtmlUtil;
+
+// making same package as phenotes giving us access to package methods!
+
+// dont need to subclass TestCase - does tests thgough annotations (1.5)
+public class TestPhenote {
+
+ // dont have handle on instance - have to do statics - wierd
+ private static Phenote phenote;
+ private static FieldPanel fieldPanel;
+ private static SearchParamPanel searchParamPanel;
+ private static AbstractAutoCompList entityComboBox;
+ private static AbstractAutoCompList qualityComboBox;
+ private static TermInfo termInfo;
+ private static CharacterTableController tableController;
+
+ /** @throws InvocationTargetException
+ * @throws InterruptedException
+ * @BeforeClass says to run this once before all the tests */
+ @BeforeClass public static void init() throws InterruptedException, InvocationTargetException {
+ System.out.println("Initializing Phenote...");
+ final String[] emptyArgs = {};
+ Phenote.main(emptyArgs);
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ phenote = Phenote.getPhenote();
+ fieldPanel = phenote.getFieldPanel();
+ searchParamPanel = fieldPanel.getSearchParamPanel();
+ entityComboBox = fieldPanel.getEntityComboBox();
+ entityComboBox.setTestMode(true); // turns off popup, hanging bug only in test
+ qualityComboBox = fieldPanel.getQualityComboBox();
+ qualityComboBox.setTestMode(true);
+ termInfo = phenote.getTermInfo();
+ tableController = phenote.getCharacterTableController();
+ }
+ });
+ }
+
+ @Ignore @Test public void displayTermInfoOnCompMouseOverTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ System.out.println("Testing comp list mouse over term info...");
+ // "he" should have plenty of completion terms associated, heart, head...
+ boolean doCompletion = true;
+ System.out.println("set entity text to hea");
+ //entityComboBox.setText("hea",doCompletion);
+ // already have list from l from previous test - for some reason 2nd l doesnt jibe
+ // even though there are lots of quality terms with 'll' ???
+ //qualityComboBox.simulateLKeyStroke(); // just does 'l'
+ System.out.println("set text - getting 3rd term");
+ //JList entityJList = entityComboBox.getJList();
+ // pick 3rd item
+ //String thirdTerm = (String)entityJList.getModel().getElementAt(2);
+ //String thirdTerm = getEntityThirdAutoTerm();
+ String thirdTerm = getQualityThirdAutoTerm();
+ assertNotNull("3rd term from quality combo shouldnt be null",thirdTerm);
+ //entityJList.setSelectedIndex(2);
+ //entityComboBox.doMouseOver(2); // 2 is 3rd - 0 indexing
+ qualityComboBox.doMouseOver(2);
+
+ //String info = termInfo.getText();
+ // gets text in term field part where name is displayed
+ String info = termInfo.getTermFieldText();
+ //String properInfoPrefix = "Term: "+thirdTerm;
+ // this doesnt work anymore with mtml stuff in there...
+ //boolean isInfoProper = info.startsWith(properInfoPrefix);
+ boolean isInfoProper = info.contains(thirdTerm);
+
+ String msg = "term info should contain '"+thirdTerm
+ +"' not getting mouseover but its ["+info+"]";
+ assertTrue(msg,isInfoProper);
+ System.out.println("Completion mouse over term info test succeeded!");
+ }
+ });
+
+ }
+
+ private String getEntityThirdAutoTerm() {
+ return entityComboBox.getJComboBox().getModel().getElementAt(2).toString();
+ }
+
+ private String getQualityThirdAutoTerm() {
+ assertNotNull(qualityComboBox.getJComboBox().getModel());
+ assertNotNull("3rd term from quality combo shouldnt be null",
+ qualityComboBox.getJComboBox().getModel().getElementAt(2));
+ return qualityComboBox.getJComboBox().getModel().getElementAt(2).toString();
+ }
+
+ private String getQualityTerm(int index) {
+ assertNotNull(qualityComboBox.getJComboBox().getModel());
+ assertNotNull(index+" term from quality combo shouldnt be null",
+ qualityComboBox.getJComboBox().getModel().getElementAt(index));
+ return qualityComboBox.getJComboBox().getModel().getElementAt(index).toString();
+ }
+
+ /** Selecting item in entity combo box should cause that item to appear in
+ table in entity column
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void comboTermSelectionGoesToTableTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ // selecting item should make it go in table...
+ tableController.addNewCharacter();
+ tableController.getSelectionModel().setSelectionInterval(0,0);
+ System.out.println("Selecting 3rd entity item");
+ qualityComboBox.getJComboBox().setSelectedIndex(2); // 2 is 3rd
+ String selectedQualityTerm = getQualityThirdAutoTerm();
+ CharacterI selPheno = tableController.getSelectionModel().getSelected().get(0);
+ String tableQuality = selPheno.getQuality().getName(); // oboclass
+ assertEquals(selectedQualityTerm,tableQuality);
+ System.out.println("term to table test passed, selected quality term "
+ +selectedQualityTerm+" quality in table "+tableQuality+"\n");
+ }
+ });
+
+ }
+
+ // cant get null pointer to fly - gotta love testing guis
+ /** theres a null pointer on selcting item for 1st time, not sure i can replicate
+ this is an awful test - assumes lacking physical part is the 2nd indexed
+ L term in quality
+ ontology - assumes theres a quality ontology
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void compListSelectionTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ //qualityComboBox.setText("larg",true);
+ qualityComboBox.simulateLKeyStroke();
+ qualityComboBox.getJComboBox().setSelectedIndex(2);
+ // this is admittedly presumptious of quality
+ assertEquals("lacking physical part",qualityComboBox.getText());
+ System.out.println("comp list sel ok "+qualityComboBox.getText());
+ }
+ });
+ }
+
+ /** After term selected in comp list popup should not come up - this doesnt actually
+ test this - the popup does go away with setSelInd - only with mouse click it
+ sometimes doesnt - need simulated mouse click!
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void selectionPopupTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ qualityComboBox.setText("larg",true);
+ qualityComboBox.getJComboBox().setSelectedIndex(2);
+ assertFalse(qualityComboBox.getJComboBox().isPopupVisible());
+ }
+ });
+
+ }
+
+ /** with searching on synonyms hit bug where terms come in more than once if have
+ 2 syns
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void synonymDupTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ qualityComboBox.setText("");
+ // searchParamPanel not used anymore - need to set in menu
+ //searchParamPanel.setTermSearch(false);
+ //searchParamPanel.setSynonymSearch(true);
+ SearchParams.inst().setParam(SearchFilterType.TERM,false);
+ SearchParams.inst().setParam(SearchFilterType.SYN,true);
+ simulateAQualityKeyStroke();
+ String first = getQualityTerm(0);
+ String second = getQualityTerm(1);
+ assertFalse(first.equals(second));
+ }
+ });
+
+ }
+
+ // utlimatley need to do mouse click on term - how to do that???
+ @Test public void termInfoSelectTermTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ simulatePhenoteHyperlinkUpdate();
+ String m = "term info hyper link test fail, term info should have body tone val "
+ +" term info: "+termInfo.getTermFieldText();
+ // how to make this test not so pato specific??
+ assertTrue(m,termInfo.getTermFieldText().contains("body tone value"));
+ }
+ });
+ }
+
+ private void simulatePhenoteHyperlinkUpdate() {
+ HyperlinkEvent.EventType type = HyperlinkEvent.EventType.ACTIVATED;
+ // 0000732 -> "BodyToneValue"
+ String desc = HtmlUtil.makePhenoIdLink("PATO:0000732");
+ HyperlinkEvent e = new HyperlinkEvent(termInfo,type,null,desc);
+ termInfo.simulateHyperlinkEvent(e);
+ }
+
+ private void simulateAQualityKeyStroke() {
+ simulateQualityKeyStroke(KeyEvent.VK_A,'a');
+ }
+
+ private void simulateQualityKeyStroke(int keyCode, char c) {
+ qualityComboBox.simulateKeyStroke(keyCode,c);
+ }
+
+ @Ignore @Test public void flyDataAdapterTest() throws UnsupportedFlavorException, IOException {
+ CharacterListI cl = CharacterListManager.main().getCharacterList();
+ DataFlavor charListFlavor = FlyCharListTransferable.getCharListDataFlavor();
+ Object o = getClipboard().getData(charListFlavor);
+ String m = "Failure: clipboard transferrable is not a FlyCharList "+o;
+ assertTrue(m,o instanceof FlyCharList);
+ FlyCharList fcl = (FlyCharList)o;
+ CharacterListI clipboardCharList = fcl.getCharacterList();
+ //assertEquals(clipboardCharList,cl); // its a clone???
+ assertTrue(clipboardCharList.equals(cl));
+
+ // simulate proforma - grab strings and recreate char list & shove in clipboard
+ // & load it up
+ FlyCharList newFlyCharList = new FlyCharList();
+ for (FlyCharacter fc : fcl.getFlyCharList()) {
+ FlyCharacter fcNew = new FlyCharacter(fc.getGenotype(),fc.getEVString());
+ newFlyCharList.addFlyChar(fcNew);
+ }
+ Transferable tr = new FlyCharListTransferable(newFlyCharList);
+ ClipboardOwner clipboardOwner = FlybaseDataAdapter.getClipboardOwner();
+ getClipboard().setContents(tr,clipboardOwner);
+
+ MenuManager.inst().getFileMenu().clickLoad();
+ CharacterListI newCL = CharacterListManager.inst().getCharacterList();
+ //assertEquals(cl,newCL); == NOT .equals()
+ assertTrue(cl.equals(newCL));
+ }
+
+// // put in CharList class?
+// private boolean charListEquals(CharacterListI c1, CharacterListI c2) {
+// if (c1.size() != c2.size()) return false;
+// for (int i=0; i<c1.size(); i++) {
+// if (!c1.get(i).equals(c2,get(i)))
+// return false;
+// }
+// return true;
+// }
+
+ private Clipboard getClipboard() {
+ Toolkit t = Toolkit.getDefaultToolkit();
+ return t.getSystemClipboard();
+ }
+
+
+ // I cant find a way to simulate a backspace in jcombobox - very frustrating!!
+// /** there is/was a bug where delete/backspace was not triggering a new
+// completion list */
+// private void backspaceInComboBoxTest() {
+// boolean doCompletion = true;
+// qualityComboBox.clear();
+// qualityComboBox.setText("larg",doCompletion);
+// int preBackspaceCount = qualityComboBox.getItemCount();
+
+// // simulate backspace/delete key
+// KeyEvent ke = new KeyEvent(qualityComboBox,KeyEvent.VK_DELETE,Calendar.getInstance().getTimeInMillis(),0,KeyEvent.VK_UNDEFINED,KeyEvent.CHAR_UNDEFINED);
+// //qualityComboBox.processKeyEvent(ke);
+// qualityComboBox.getEditor().getEditorComponent().processKeyEvent(ke);
+
+// String postDelText = qualityComboBox.getText();
+// int postBackspaceCount = qualityComboBox.getItemCount();
+// System.out.println("post text "+postDelText+" pre count "+preBackspaceCount+" post count "+postBackspaceCount);
+// assertTrue(preBackspaceCount != postBackspaceCount);
+// }
+
+}
Copied: phenote/trunk/test/java/phenote/util/FileUtilTest.java (from rev 1035, phenote/trunk/src/java/phenote/util/FileUtilTest.java)
===================================================================
--- phenote/trunk/test/java/phenote/util/FileUtilTest.java (rev 0)
+++ phenote/trunk/test/java/phenote/util/FileUtilTest.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -0,0 +1,125 @@
+package phenote.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+import org.junit.After;
+import org.junit.Before;
+
+
+import java.io.File;
+import java.io.IOException;
+
+/**
+ * Unit test class for FileUtil.
+ */
+public class FileUtilTest {
+
+ private static final File testArchiveDir = new File("test" + FileUtil.FILE_SEPARATOR + FileUtil.FILE_SEPARATOR +
+ "testfiles", "test-archive-dir");
+ private static final File testLoadDirectory = new File("test" + FileUtil.FILE_SEPARATOR + FileUtil.FILE_SEPARATOR +
+ "testfiles", "test-load-dir");
+ private File testLoadFile;
+ private File testPurgeFile;
+
+ @Before
+ public void setUp() {
+ setTestDirectories();
+ }
+
+ @After
+ public void tearDown() {
+ cleanupTestFilesStructure();
+ }
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ */
+ @Test
+ public void archiveFile() {
+ File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
+ File[] files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+ assertTrue("Original File still exists", testLoadFile.exists());
+ }
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ * Sleep for a second and then archive another file and then purge the first file while the
+ * second file does not get purged.
+ */
+ @Test
+ public void purgeArchiveFile() {
+ File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
+ File[] files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+ assertTrue("Original File still exists", testLoadFile.exists());
+
+ // create the second file and wait a second before archiving it.
+ testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
+ try {
+ Thread.sleep(1000);
+ testPurgeFile.createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (InterruptedException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+
+ archivedFile = FileUtil.archiveFile(testPurgeFile, testArchiveDir);
+ files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 2, files.length);
+ FileUtil.purgeArchiveDirectory(testArchiveDir, 990);
+
+ files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+
+ }
+
+ @Test
+ public void pureFilename() {
+ String fileNameOnly = "filenameAlpha.txt";
+ String filename = FileUtil.FILE_SEPARATOR + "dire" + FileUtil.FILE_SEPARATOR + fileNameOnly;
+ String pureFilename = FileUtil.getPureFileName(filename);
+ assertEquals("Pure File Name", fileNameOnly, pureFilename);
+
+ fileNameOnly = "";
+ pureFilename = FileUtil.getPureFileName(fileNameOnly);
+ assertEquals("Pure File Name", fileNameOnly, pureFilename);
+ }
+
+
+ /**
+ * Create the test directories before the tests are run.
+ */
+ private void setTestDirectories() {
+ testLoadDirectory.mkdir();
+
+ testLoadFile = new File(testLoadDirectory, "test-file-one.txt");
+ testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
+ try {
+ testLoadFile.createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Remove test directories after the tests are done.
+ */
+ private void cleanupTestFilesStructure() {
+ testLoadFile.delete();
+ testPurgeFile.delete();
+ testLoadDirectory.delete();
+ File[] files = testArchiveDir.listFiles();
+ if (files != null)
+ for (File file : files) {
+ file.delete();
+ }
+ testArchiveDir.delete();
+ }
+
+}
Copied: phenote/trunk/test/java/phenote/util/TermLinkComparatorTest.java (from rev 1035, phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java)
===================================================================
--- phenote/trunk/test/java/phenote/util/TermLinkComparatorTest.java (rev 0)
+++ phenote/trunk/test/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:43:41 UTC (rev 1036)
@@ -0,0 +1,81 @@
+package phenote.util;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.geneontology.oboedit.datamodel.Link;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.impl.InstancePropertyValue;
+import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
+import org.junit.Assert;
+import org.junit.Test;
+
+
+/**
+ * Unit test class for FileUtil.
+ */
+public class TermLinkComparatorTest {
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ */
+ @Test public void testIS_A_Before_PART_Of() {
+ List<InstancePropertyValue> links = new ArrayList<InstancePropertyValue>();
+ links.add(getLinkUnknownOne());
+ links.add(getLinkUnknownTwo());
+ links.add(getLinkDevelops_From());
+ links.add(getLinkPart_Of());
+ links.add(getLinkIS_A());
+
+ Collections.sort(links, new TermLinkComparator());
+
+ Link link = (Link) links.get(0);
+ Assert.assertEquals("IS a first", "is_a", link.getType().getName());
+ link = (Link) links.get(1);
+ Assert.assertEquals("Part of is second", "part of", link.getType().getName());
+ link = (Link) links.get(2);
+ Assert.assertEquals("Part of is second", "develops from", link.getType().getName());
+ link = (Link) links.get(3);
+ Assert.assertEquals("IS a first", "Unknown A", link.getType().getName());
+ link = (Link) links.get(4);
+ Assert.assertEquals("IS a first", "Unknown B", link.getType().getName());
+
+ }
+
+ private InstancePropertyValue getLinkIS_A(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.IS_A.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkPart_Of(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.PART_OF.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkDevelops_From(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.DEVELOPS_FROM.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkUnknownOne(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl("Unknown B");
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkUnknownTwo(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl("Unknown A");
+ link.setType(prop);
+ return link;
+ }
+
+}
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|
|
From: <ba...@us...> - 2007-10-11 15:28:01
|
Revision: 1035
http://obo.svn.sourceforge.net/obo/?rev=1035&view=rev
Author: balhoff
Date: 2007-10-11 08:28:04 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
Started moving tests back into their own folder. Updated Ant targets to find tests via JUnit 1.4 annotations.
Modified Paths:
--------------
phenote/trunk/build.xml
phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java
phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
Added Paths:
-----------
phenote/trunk/src/java/phenote/gui/TestPhenote.java
phenote/trunk/src/java/phenote/util/FileUtilTest.java
phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
phenote/trunk/test/
phenote/trunk/test/java/
phenote/trunk/test/java/phenote/
phenote/trunk/test/java/phenote/charactertemplate/
phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
phenote/trunk/test/java/phenote/charactertemplate/TreeChooserTest.java
phenote/trunk/test/java/phenote/dataadapter/
phenote/trunk/test/java/phenote/dataadapter/nexus/
phenote/trunk/test/java/phenote/dataadapter/nexus/NEXUSAdapterTest.java
phenote/trunk/test/java/phenote/gui/
phenote/trunk/test/java/phenote/gui/CharacterTableControllerTest.java
Removed Paths:
-------------
phenote/trunk/src/java/phenote/UnitTests.java
phenote/trunk/src/java/phenote/gui/TestPhenote.java
phenote/trunk/src/java/phenote/util/FileUtilTest.java
phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
phenote/trunk/src/java/test/
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/build.xml 2007-10-11 15:28:04 UTC (rev 1035)
@@ -16,7 +16,7 @@
<property environment="env"/>
<!-- property name="src-svn" value="./src/java" / -->
<property name="src" value="./src/java"/>
- <property name="test" value="./src/java/test"/>
+ <property name="test" value="./test/java"/>
<!-- where classes go -->
<property name="classfiles" value="classfiles"/>
<property name="web-classfiles" value="${env.PHENOTE_WEB_CLASSFILES}"/>
@@ -176,39 +176,34 @@
</java>
</target>
-
- <target name="test" depends="build-test">
- <java classname="org.junit.runner.JUnitCore" fork="yes" jvmargs="-Xmx200M">
- <arg value="phenote.gui.TestPhenote"/>
- <classpath>
+ <target name="test" depends="build-test" description="Unit tests">
+ <junit fork="yes" printsummary="on" maxmemory="1024m">
+ <classpath>
<pathelement path="${classfiles}"/>
<fileset dir="${lib}">
<include name="*.jar"/>
<exclude name="phenote.jar"/>
</fileset>
</classpath>
- </java>
- </target>
+ <batchtest>
+ <fileset dir="${test}"/>
+ </batchtest>
+ </junit>
+ </target>
+
+ <target name="runatest" depends="build-test">
+ <junit fork="yes" printsummary="on" maxmemory="1024m">
+ <classpath>
+ <pathelement path="${classfiles}"/>
+ <fileset dir="${lib}">
+ <include name="*.jar"/>
+ <exclude name="phenote.jar"/>
+ </fileset>
+ </classpath>
+ <test name="${junit.test.class.name}"/>
+ </junit>
+ </target>
- <target name="runtests" depends="build-test" description="Unit tests">
- <antcall target="runatest">
- <param name="junit.test.class.name" value="phenote.UnitTests"/>
- </antcall>
- </target>
-
- <target name="runatest" depends="build-test">
- <java fork="yes" classname="junit.textui.TestRunner" taskname="junit" failonerror="true">
- <arg value="${junit.test.class.name}"/>
- <classpath>
- <pathelement path="${classfiles}"/>
- <fileset dir="${lib}">
- <include name="*.jar"/>
- <exclude name="phenote.jar"/>
- </fileset>
- </classpath>
- </java>
- </target>
-
<!-- The clean target just erases the classes -->
<target name="clean">
<delete dir="${classfiles}"/>
@@ -218,7 +213,6 @@
<!-- clean and compile everything -->
<target name="build-all" depends="clean,compile,build-test"/>
-
<target name="build-test" depends="compile">
<javac srcdir="${test}" destdir="${classfiles}" debug="yes">
<classpath refid="project.classpath"/>
Deleted: phenote/trunk/src/java/phenote/UnitTests.java
===================================================================
--- phenote/trunk/src/java/phenote/UnitTests.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/UnitTests.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -1,26 +0,0 @@
-package phenote;
-
-import junit.framework.TestSuite;
-import junit.framework.JUnit4TestAdapter;
-import junit.textui.TestRunner;
-import phenote.util.FileUtilTest;
-import phenote.gui.TestPhenote;
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-
-/**
- * This is the master unit test class that runs all registered unit tests (suite).
- * Add your new unit test here if it is ready to be included in regular builds.
- */
-@RunWith(Suite.class)
-...@Su...iteClasses({
- FileUtilTest.class,
- TestPhenote.class
- })
-
-public class UnitTests {
-
- public static junit.framework.Test suite() {
- return new JUnit4TestAdapter(UnitTests.class);
- }
-}
Modified: phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/charactertemplate/CharacterTemplateController.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -187,6 +187,10 @@
return this.selectionModel;
}
+ public List<CharacterI> getAllCharacters() {
+ return this.sortedCharacters;
+ }
+
public JFrame getWindow() {
if (this.window == null) {
this.window = new JFrame(this.getGroupTitle());
Modified: phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java
===================================================================
--- phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/charactertemplate/TreeChooser.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -106,7 +106,7 @@
return taxa;
}
- private TreeViewer getTreeViewer() {
+ protected TreeViewer getTreeViewer() {
if (this.treeViewer == null) {
this.treeViewer = this.createViewer();
// starting out with a tree helps the TreeViewer to display correctly
Modified: phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/dataadapter/nexus/NEXUSAdapter.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -15,30 +15,33 @@
import java.util.Set;
import java.util.Map.Entry;
+import org.apache.log4j.Logger;
import org.geneontology.oboedit.datamodel.Link;
import org.geneontology.oboedit.datamodel.OBOClass;
import org.geneontology.oboedit.datamodel.TermCategory;
import phenote.dataadapter.AbstractFileAdapter;
+import phenote.datamodel.CharFieldException;
import phenote.datamodel.CharacterI;
import phenote.datamodel.CharacterListI;
+import phenote.main.PhenoteVersion;
/** Writes Phenote characters to a NEXUS file.
* Phenote characters are grouped into NEXUS characters via shared "attribute" heritage
* within PATO.
* The exporter supports only up to 36 values for any particular attribute, due to
* various limitations of other widely used NEXUS implementations (e.g. Mesquite & MacClade).
- * There is no support for reading of NEXUS files.
+ * There is currently no support for reading of NEXUS files.
*/
public class NEXUSAdapter extends AbstractFileAdapter {
private File file;
- private static String[] extensions = {"nex", "nxs"};
- private static String description = "NEXUS [.nex, .nxs]";
- private static String GENOTYPE_KEY = "Genotype";
- private static String ENTITY_KEY = "Entity";
- private static String VALUE_KEY = "Quality";
+ private static final String[] extensions = {"nex", "nxs"};
+ private static final String description = "NEXUS [.nex, .nxs]";
+ private static final String TAXON_KEY = "Taxon";
+ private static final String ENTITY_KEY = "Entity";
+ private static final String VALUE_KEY = "Quality";
private static String STATE_SYMBOLS = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ";
private LinkedHashMap<String, ArrayList<Integer>> genotypes; // ordered map of genotype names and value lists
private LinkedHashMap<NEXUSCharacter, List<OBOClass>> nexusCharacters; // ordered map of character names and state lists
@@ -49,25 +52,33 @@
public void commit(CharacterListI charList) {
if (this.file == null)
return;
+ this.commit(charList, this.file);
+ }
+
+ public void commit(CharacterListI charList, File f) {
+ this.file = f;
+ try {
+ this.commit(charList, new BufferedWriter(new FileWriter(this.file)));
+ } catch (IOException e) {
+ log().error("Failed to write NEXUS file", e);
+ }
+ }
+
+ public void commit(CharacterListI charList, Writer writer) {
this.setGenotypes(new LinkedHashMap<String, ArrayList<Integer>>());
this.setNexusCharacters(new LinkedHashMap<NEXUSCharacter, List<OBOClass>>());
this.populateGenotypesAndCharacters(charList);
this.createDefaultCharacterValues();
this.populateCharacterValues(charList);
- this.writeNexus(this.file);
+ this.writeNexus(writer);
}
- public void commit(CharacterListI charList, File f) {
- this.file = f;
- commit(charList);
- }
-
public List<String> getExtensions() {
return Arrays.asList(NEXUSAdapter.extensions);
}
public void load() {
- System.out.println("Cannot read: NEXUS adapter is for import only.");
+ log().error("Cannot read: NEXUS adapter is for import only.");
}
public CharacterListI load(File f) {
@@ -102,16 +113,16 @@
OBOClass entityTerm;
OBOClass valueTerm;
try {
- genotype = ch.getValueString(GENOTYPE_KEY);
+ genotype = ch.getValueString(TAXON_KEY);
entityTerm = ch.getTerm(ENTITY_KEY);
valueTerm = ch.getTerm(VALUE_KEY);
- } catch (Exception e) {
- System.out.println("Could not get terms from character: " + e);
+ } catch (CharFieldException e) {
+ log().error("Could not get terms from character: " + ch, e);
continue;
}
OBOClass attributeTerm = this.getAttributeForValue(valueTerm);
if (attributeTerm == null) {
- System.out.println("Failed to find attribute for value.");
+ log().error("Failed to find attribute for value: " + valueTerm);
continue;
}
if (!(this.genotypes.containsKey(genotype))) {
@@ -140,34 +151,34 @@
private void populateCharacterValues(CharacterListI characterList) {
for (CharacterI ch : characterList.getList()) {
if (this.isValidCharacter(ch)) {
- String genotype;
+ OBOClass taxonTerm;
OBOClass entityTerm;
OBOClass valueTerm;
try {
- genotype = ch.getValueString(GENOTYPE_KEY);
+ taxonTerm = ch.getTerm(TAXON_KEY);
entityTerm = ch.getTerm(ENTITY_KEY);
valueTerm = ch.getTerm(VALUE_KEY);
- } catch (Exception e) {
- System.out.println("Could not get terms from character: " + e);
+ } catch (CharFieldException e) {
+ log().error("Could not get terms from character: " + ch, e);
continue;
}
OBOClass attributeTerm = this.getAttributeForValue(valueTerm);
if (attributeTerm == null) {
- System.out.println("Failed to find attribute for value.");
+ log().error("Failed to find attribute for value: " + valueTerm);
continue;
}
NEXUSCharacter currentCharacter = new NEXUSCharacter(entityTerm, attributeTerm);
List<OBOClass> currentValueList = this.getNexusCharacters().get(currentCharacter);
int indexOfCharacter = Arrays.asList(this.getNexusCharacters().values().toArray()).indexOf(currentValueList);
int indexOfValue = currentValueList.indexOf(valueTerm);
- this.getGenotypes().get(genotype).set(indexOfCharacter, indexOfValue);
+ this.getGenotypes().get(taxonTerm.getName()).set(indexOfCharacter, indexOfValue);
}
}
}
private boolean isValidCharacter(CharacterI character) {
try {
- return (character.hasValue(GENOTYPE_KEY) && (character.hasValue(ENTITY_KEY)) && (character.hasValue(VALUE_KEY)));
+ return ((character.hasValue(TAXON_KEY)) && (character.hasValue(ENTITY_KEY)) && (character.hasValue(VALUE_KEY)));
} catch (Exception e) {
return false;
}
@@ -181,9 +192,7 @@
}
if (categoryNames.contains("attribute_slim")) {
return valueTerm;
- }
- // isRoot no longer there - not sure what replaces it yet...
- else if ((categoryNames.contains("value_slim"))) { //&& !(valueTerm.isRoot())) {
+ } else if ((categoryNames.contains("value_slim"))) {
return this.getAttributeForValue(this.getParentForTerm(valueTerm));
}
return null;
@@ -199,10 +208,9 @@
return null;
}
- private void writeNexus(File f) {
+ private void writeNexus(Writer writer) {
try {
- BufferedWriter writer = new BufferedWriter(new FileWriter(f));
- writer.write("#NEXUS\n[Generated by Phenote]\n\n");
+ writer.write("#NEXUS\n[Generated by Phenote " + PhenoteVersion.versionString() + "]\n\n");
writer.write("BEGIN TAXA;\n");
writer.write("\tDIMENSIONS NTAX=" + this.getGenotypes().size() + ";\n");
this.writeTaxLabels(writer);
@@ -215,7 +223,7 @@
writer.write("END;\n");
writer.close();
} catch (IOException e) {
- System.out.println("Failed to write NEXUS file " + e);
+ log().error("Failed to write NEXUS file", e);
}
}
@@ -273,8 +281,11 @@
return ("'" + text + "'");
}
+ private static Logger log() {
+ return Logger.getLogger(NEXUSAdapter.class);
+ }
- private class NEXUSCharacter {
+ private static class NEXUSCharacter {
private OBOClass entity;
private OBOClass attribute;
Deleted: phenote/trunk/src/java/phenote/gui/TestPhenote.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TestPhenote.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/gui/TestPhenote.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -1,300 +0,0 @@
-package phenote.gui;
-
-// move to main package??
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Toolkit;
-import java.awt.datatransfer.Clipboard;
-import java.awt.datatransfer.ClipboardOwner;
-import java.awt.datatransfer.DataFlavor;
-import java.awt.datatransfer.Transferable;
-import java.awt.event.KeyEvent;
-
-import javax.swing.event.HyperlinkEvent;
-
-import org.junit.BeforeClass;
-import org.junit.Test;
-
-import phenote.dataadapter.CharacterListManager;
-import phenote.dataadapter.fly.FlyCharList;
-import phenote.dataadapter.fly.FlyCharListTransferable;
-import phenote.dataadapter.fly.FlyCharacter;
-import phenote.dataadapter.fly.FlybaseDataAdapter;
-import phenote.datamodel.CharacterI;
-import phenote.datamodel.CharacterListI;
-import phenote.gui.field.AbstractAutoCompList;
-import phenote.gui.field.FieldPanel;
-import phenote.gui.field.SearchParamPanel;
-import phenote.main.Phenote;
-import phenote.util.HtmlUtil;
-
-// making same package as phenotes giving us access to package methods!
-
-// dont need to subclass TestCase - does tests thgough annotations (1.5)
-public class TestPhenote {
-
- // dont have handle on instance - have to do statics - wierd
- private static Phenote phenote;
- private static FieldPanel fieldPanel;
- private static SearchParamPanel searchParamPanel;
- private static AbstractAutoCompList entityComboBox;
- private static AbstractAutoCompList qualityComboBox;
- private static TermInfo termInfo;
- private static CharacterTableController tableController;
-
- /** @BeforeClass says to run this once before all the tests */
- @BeforeClass public static void init() {
- System.out.println("Initializing Phenote...");
- Phenote.main(null);
- // so the gui actually needs a little time to do layout on gui thread
- // or else ACB.doComp() showPopup causes a hang - wierd!
-// System.out.println("sleeping...");
-// try {Thread.currentThread().sleep(5000); } // millis
-// catch (InterruptedException e) { System.out.println(e); }
-// System.out.println("^^^done sleeping - is gui ready?");
- phenote = Phenote.getPhenote();
- fieldPanel = phenote.getFieldPanel();
- searchParamPanel = fieldPanel.getSearchParamPanel();
- entityComboBox = fieldPanel.getEntityComboBox();
- entityComboBox.setTestMode(true); // turns off popup, hanging bug only in test
- qualityComboBox = fieldPanel.getQualityComboBox();
- qualityComboBox.setTestMode(true);
- termInfo = phenote.getTermInfo();
- tableController = phenote.getCharacterTableController();
- }
-
- /** @Test is an annotation defined in Test - Test looks for Test methods */
- @Test public void test() {
- //selectionPopupTest(); not done proper
- compListSelectionTest();
- displayTermInfoOnCompMouseOverTest();
- comboTermSelectionGoesToTableTest();
- //synonymDupTest(); -- uses pase searchParamPanel
- termInfoSelectTermTest();
- //attributeInQualityCompletionTest(); --> need 3 keystrokes 'ttr'
- //backspaceInComboBoxTest(); cant sim backspace.....
- //flyDataAdapterTest(); out of date its now doing phenoxml - soon will be syntax
- }
-
- private void displayTermInfoOnCompMouseOverTest() {
- System.out.println("Testing comp list mouse over term info...");
- // "he" should have plenty of completion terms associated, heart, head...
- boolean doCompletion = true;
- System.out.println("set entity text to hea");
- //entityComboBox.setText("hea",doCompletion);
- // already have list from l from previous test - for some reason 2nd l doesnt jibe
- // even though there are lots of quality terms with 'll' ???
- //qualityComboBox.simulateLKeyStroke(); // just does 'l'
- System.out.println("set text - getting 3rd term");
- //JList entityJList = entityComboBox.getJList();
- // pick 3rd item
- //String thirdTerm = (String)entityJList.getModel().getElementAt(2);
- //String thirdTerm = getEntityThirdAutoTerm();
- String thirdTerm = getQualityThirdAutoTerm();
- assertNotNull("3rd term from quality combo shouldnt be null",thirdTerm);
- //entityJList.setSelectedIndex(2);
- //entityComboBox.doMouseOver(2); // 2 is 3rd - 0 indexing
- qualityComboBox.doMouseOver(2);
-
- //String info = termInfo.getText();
- // gets text in term field part where name is displayed
- String info = termInfo.getTermFieldText();
- //String properInfoPrefix = "Term: "+thirdTerm;
- // this doesnt work anymore with mtml stuff in there...
- //boolean isInfoProper = info.startsWith(properInfoPrefix);
- boolean isInfoProper = info.contains(thirdTerm);
-
- String msg = "term info should contain '"+thirdTerm
- +"' not getting mouseover but its ["+info+"]";
- assertTrue(msg,isInfoProper);
- System.out.println("Completion mouse over term info test succeeded!");
- }
-
- private String getEntityThirdAutoTerm() {
- return entityComboBox.getJComboBox().getModel().getElementAt(2).toString();
- }
-
- private String getQualityThirdAutoTerm() {
- assertNotNull(qualityComboBox.getJComboBox().getModel());
- assertNotNull("3rd term from quality combo shouldnt be null",
- qualityComboBox.getJComboBox().getModel().getElementAt(2));
- return qualityComboBox.getJComboBox().getModel().getElementAt(2).toString();
- }
-
- private String getQualityTerm(int index) {
- assertNotNull(qualityComboBox.getJComboBox().getModel());
- assertNotNull(index+" term from quality combo shouldnt be null",
- qualityComboBox.getJComboBox().getModel().getElementAt(index));
- return qualityComboBox.getJComboBox().getModel().getElementAt(index).toString();
- }
-
- /** Selecting item in entity combo box should cause that item to appear in
- table in entity column */
- private void comboTermSelectionGoesToTableTest() {
- // selecting item should make it go in table...
- tableController.addNewCharacter();
- tableController.getSelectionModel().setSelectionInterval(0,0);
- System.out.println("Selecting 3rd entity item");
- qualityComboBox.getJComboBox().setSelectedIndex(2); // 2 is 3rd
- String selectedQualityTerm = getQualityThirdAutoTerm();
- CharacterI selPheno = tableController.getSelectionModel().getSelected().get(0);
- String tableQuality = selPheno.getQuality().getName(); // oboclass
- assertEquals(selectedQualityTerm,tableQuality);
- System.out.println("term to table test passed, selected quality term "
- +selectedQualityTerm+" quality in table "+tableQuality+"\n");
- }
-
- /** Test that attributes are being filtered out of quality term completion list */
- private void attributeInQualityCompletionTest() {
- boolean doCompletion = true;
- System.out.println("Testing quality for attribute filtering");
- // need to do this with key strokes now - set text doesnt work
- // need at least 3 key strokes 'ttr' for attributes - i seem to have problems
- // getting more than one key stroke in - hmmmmm
- qualityComboBox.setText("attribute",doCompletion);
- int count = qualityComboBox.getJComboBox().getItemCount();
- String m = "Attributes are not being filtered out of Quality completion "+
- "There are "+count+" terms with 'attribute'";
- System.out.println("There are "+count+" attributes in comp list");
- assertTrue(m,count == 0);
- }
-
- // cant get null pointer to fly - gotta love testing guis
- /** theres a null pointer on selcting item for 1st time, not sure i can replicate
- this is an awful test - assumes lacking physical part is the 2nd indexed
- L term in quality
- ontology - assumes theres a quality ontology */
- private void compListSelectionTest() {
- //qualityComboBox.setText("larg",true);
- qualityComboBox.simulateLKeyStroke();
- qualityComboBox.getJComboBox().setSelectedIndex(2);
- // this is admittedly presumptious of quality
- assertEquals("lacking physical part",qualityComboBox.getText());
- System.out.println("comp list sel ok "+qualityComboBox.getText());
- }
-
- /** After term selected in comp list popup should not come up - this doesnt actually
- test this - the popup does go away with setSelInd - only with mouse click it
- sometimes doesnt - need simulated mouse click! */
- private void selectionPopupTest() {
- qualityComboBox.setText("larg",true);
- qualityComboBox.getJComboBox().setSelectedIndex(2);
- assertFalse(qualityComboBox.getJComboBox().isPopupVisible());
- }
-
- /** with searching on synonyms hit bug where terms come in more than once if have
- 2 syns */
- private void synonymDupTest() {
- qualityComboBox.setText("");
- // searchParamPanel not used anymore - need to set in menu
- //searchParamPanel.setTermSearch(false);
- //searchParamPanel.setSynonymSearch(true);
- SearchParams.inst().setParam(SearchFilterType.TERM,false);
- SearchParams.inst().setParam(SearchFilterType.SYN,true);
- simulateAQualityKeyStroke();
- String first = getQualityTerm(0);
- String second = getQualityTerm(1);
- assertFalse(first.equals(second));
- }
-
- // utlimatley need to do mouse click on term - how to do that???
- private void termInfoSelectTermTest() {
- simulatePhenoteHyperlinkUpdate();
- String m = "term info hyper link test fail, term info should have body tone val "
- +" term info: "+termInfo.getTermFieldText();
- // how to make this test not so pato specific??
- assertTrue(m,termInfo.getTermFieldText().contains("body tone value"));
- }
-
- private void simulatePhenoteHyperlinkUpdate() {
- HyperlinkEvent.EventType type = HyperlinkEvent.EventType.ACTIVATED;
- // 0000732 -> "BodyToneValue"
- String desc = HtmlUtil.makePhenoIdLink("PATO:0000732");
- HyperlinkEvent e = new HyperlinkEvent(termInfo,type,null,desc);
- termInfo.simulateHyperlinkEvent(e);
- }
-
- private void simulateAQualityKeyStroke() {
- simulateQualityKeyStroke(KeyEvent.VK_A,'a');
- }
-
- private void simulateQualityKeyStroke(int keyCode, char c) {
- qualityComboBox.simulateKeyStroke(keyCode,c);
- }
-
- private void flyDataAdapterTest() {
- CharacterListI cl = CharacterListManager.main().getCharacterList();
-
- DataFlavor charListFlavor = FlyCharListTransferable.getCharListDataFlavor();
- try {
- Object o = getClipboard().getData(charListFlavor);
- String m = "Failure: clipboard transferrable is not a FlyCharList "+o;
- assertTrue(m,o instanceof FlyCharList);
- FlyCharList fcl = (FlyCharList)o;
- CharacterListI clipboardCharList = fcl.getCharacterList();
- //assertEquals(clipboardCharList,cl); // its a clone???
- assertTrue(clipboardCharList.equals(cl));
-
- // simulate proforma - grab strings and recreate char list & shove in clipboard
- // & load it up
- FlyCharList newFlyCharList = new FlyCharList();
- for (FlyCharacter fc : fcl.getFlyCharList()) {
- FlyCharacter fcNew = new FlyCharacter(fc.getGenotype(),fc.getEVString());
- newFlyCharList.addFlyChar(fcNew);
- }
- Transferable tr = new FlyCharListTransferable(newFlyCharList);
- ClipboardOwner clipboardOwner = FlybaseDataAdapter.getClipboardOwner();
- getClipboard().setContents(tr,clipboardOwner);
-
- MenuManager.inst().getFileMenu().clickLoad();
- CharacterListI newCL = CharacterListManager.inst().getCharacterList();
- //assertEquals(cl,newCL); == NOT .equals()
- assertTrue(cl.equals(newCL));
- }
- catch (Exception e) {
- System.out.println("FAILURE: Exception thrown "+e);
- e.printStackTrace();
- }
- }
-
-// // put in CharList class?
-// private boolean charListEquals(CharacterListI c1, CharacterListI c2) {
-// if (c1.size() != c2.size()) return false;
-// for (int i=0; i<c1.size(); i++) {
-// if (!c1.get(i).equals(c2,get(i)))
-// return false;
-// }
-// return true;
-// }
-
- private Clipboard getClipboard() {
- Toolkit t = Toolkit.getDefaultToolkit();
- return t.getSystemClipboard();
- }
-
-
- // I cant find a way to simulate a backspace in jcombobox - very frustrating!!
-// /** there is/was a bug where delete/backspace was not triggering a new
-// completion list */
-// private void backspaceInComboBoxTest() {
-// boolean doCompletion = true;
-// qualityComboBox.clear();
-// qualityComboBox.setText("larg",doCompletion);
-// int preBackspaceCount = qualityComboBox.getItemCount();
-
-// // simulate backspace/delete key
-// KeyEvent ke = new KeyEvent(qualityComboBox,KeyEvent.VK_DELETE,Calendar.getInstance().getTimeInMillis(),0,KeyEvent.VK_UNDEFINED,KeyEvent.CHAR_UNDEFINED);
-// //qualityComboBox.processKeyEvent(ke);
-// qualityComboBox.getEditor().getEditorComponent().processKeyEvent(ke);
-
-// String postDelText = qualityComboBox.getText();
-// int postBackspaceCount = qualityComboBox.getItemCount();
-// System.out.println("post text "+postDelText+" pre count "+preBackspaceCount+" post count "+postBackspaceCount);
-// assertTrue(preBackspaceCount != postBackspaceCount);
-// }
-
-}
Added: phenote/trunk/src/java/phenote/gui/TestPhenote.java
===================================================================
--- phenote/trunk/src/java/phenote/gui/TestPhenote.java (rev 0)
+++ phenote/trunk/src/java/phenote/gui/TestPhenote.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -0,0 +1,307 @@
+package phenote.gui;
+
+// move to main package??
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.ClipboardOwner;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.awt.event.KeyEvent;
+import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.SwingUtilities;
+import javax.swing.event.HyperlinkEvent;
+
+import org.junit.BeforeClass;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import phenote.dataadapter.CharacterListManager;
+import phenote.dataadapter.fly.FlyCharList;
+import phenote.dataadapter.fly.FlyCharListTransferable;
+import phenote.dataadapter.fly.FlyCharacter;
+import phenote.dataadapter.fly.FlybaseDataAdapter;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.CharacterListI;
+import phenote.gui.field.AbstractAutoCompList;
+import phenote.gui.field.FieldPanel;
+import phenote.gui.field.SearchParamPanel;
+import phenote.main.Phenote;
+import phenote.util.HtmlUtil;
+
+// making same package as phenotes giving us access to package methods!
+
+// dont need to subclass TestCase - does tests thgough annotations (1.5)
+public class TestPhenote {
+
+ // dont have handle on instance - have to do statics - wierd
+ private static Phenote phenote;
+ private static FieldPanel fieldPanel;
+ private static SearchParamPanel searchParamPanel;
+ private static AbstractAutoCompList entityComboBox;
+ private static AbstractAutoCompList qualityComboBox;
+ private static TermInfo termInfo;
+ private static CharacterTableController tableController;
+
+ /** @throws InvocationTargetException
+ * @throws InterruptedException
+ * @BeforeClass says to run this once before all the tests */
+ @BeforeClass public static void init() throws InterruptedException, InvocationTargetException {
+ System.out.println("Initializing Phenote...");
+ final String[] emptyArgs = {};
+ Phenote.main(emptyArgs);
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ phenote = Phenote.getPhenote();
+ fieldPanel = phenote.getFieldPanel();
+ searchParamPanel = fieldPanel.getSearchParamPanel();
+ entityComboBox = fieldPanel.getEntityComboBox();
+ entityComboBox.setTestMode(true); // turns off popup, hanging bug only in test
+ qualityComboBox = fieldPanel.getQualityComboBox();
+ qualityComboBox.setTestMode(true);
+ termInfo = phenote.getTermInfo();
+ tableController = phenote.getCharacterTableController();
+ }
+ });
+ }
+
+ @Ignore @Test public void displayTermInfoOnCompMouseOverTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ System.out.println("Testing comp list mouse over term info...");
+ // "he" should have plenty of completion terms associated, heart, head...
+ boolean doCompletion = true;
+ System.out.println("set entity text to hea");
+ //entityComboBox.setText("hea",doCompletion);
+ // already have list from l from previous test - for some reason 2nd l doesnt jibe
+ // even though there are lots of quality terms with 'll' ???
+ //qualityComboBox.simulateLKeyStroke(); // just does 'l'
+ System.out.println("set text - getting 3rd term");
+ //JList entityJList = entityComboBox.getJList();
+ // pick 3rd item
+ //String thirdTerm = (String)entityJList.getModel().getElementAt(2);
+ //String thirdTerm = getEntityThirdAutoTerm();
+ String thirdTerm = getQualityThirdAutoTerm();
+ assertNotNull("3rd term from quality combo shouldnt be null",thirdTerm);
+ //entityJList.setSelectedIndex(2);
+ //entityComboBox.doMouseOver(2); // 2 is 3rd - 0 indexing
+ qualityComboBox.doMouseOver(2);
+
+ //String info = termInfo.getText();
+ // gets text in term field part where name is displayed
+ String info = termInfo.getTermFieldText();
+ //String properInfoPrefix = "Term: "+thirdTerm;
+ // this doesnt work anymore with mtml stuff in there...
+ //boolean isInfoProper = info.startsWith(properInfoPrefix);
+ boolean isInfoProper = info.contains(thirdTerm);
+
+ String msg = "term info should contain '"+thirdTerm
+ +"' not getting mouseover but its ["+info+"]";
+ assertTrue(msg,isInfoProper);
+ System.out.println("Completion mouse over term info test succeeded!");
+ }
+ });
+
+ }
+
+ private String getEntityThirdAutoTerm() {
+ return entityComboBox.getJComboBox().getModel().getElementAt(2).toString();
+ }
+
+ private String getQualityThirdAutoTerm() {
+ assertNotNull(qualityComboBox.getJComboBox().getModel());
+ assertNotNull("3rd term from quality combo shouldnt be null",
+ qualityComboBox.getJComboBox().getModel().getElementAt(2));
+ return qualityComboBox.getJComboBox().getModel().getElementAt(2).toString();
+ }
+
+ private String getQualityTerm(int index) {
+ assertNotNull(qualityComboBox.getJComboBox().getModel());
+ assertNotNull(index+" term from quality combo shouldnt be null",
+ qualityComboBox.getJComboBox().getModel().getElementAt(index));
+ return qualityComboBox.getJComboBox().getModel().getElementAt(index).toString();
+ }
+
+ /** Selecting item in entity combo box should cause that item to appear in
+ table in entity column
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void comboTermSelectionGoesToTableTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ // selecting item should make it go in table...
+ tableController.addNewCharacter();
+ tableController.getSelectionModel().setSelectionInterval(0,0);
+ System.out.println("Selecting 3rd entity item");
+ qualityComboBox.getJComboBox().setSelectedIndex(2); // 2 is 3rd
+ String selectedQualityTerm = getQualityThirdAutoTerm();
+ CharacterI selPheno = tableController.getSelectionModel().getSelected().get(0);
+ String tableQuality = selPheno.getQuality().getName(); // oboclass
+ assertEquals(selectedQualityTerm,tableQuality);
+ System.out.println("term to table test passed, selected quality term "
+ +selectedQualityTerm+" quality in table "+tableQuality+"\n");
+ }
+ });
+
+ }
+
+ // cant get null pointer to fly - gotta love testing guis
+ /** theres a null pointer on selcting item for 1st time, not sure i can replicate
+ this is an awful test - assumes lacking physical part is the 2nd indexed
+ L term in quality
+ ontology - assumes theres a quality ontology
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void compListSelectionTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ //qualityComboBox.setText("larg",true);
+ qualityComboBox.simulateLKeyStroke();
+ qualityComboBox.getJComboBox().setSelectedIndex(2);
+ // this is admittedly presumptious of quality
+ assertEquals("lacking physical part",qualityComboBox.getText());
+ System.out.println("comp list sel ok "+qualityComboBox.getText());
+ }
+ });
+ }
+
+ /** After term selected in comp list popup should not come up - this doesnt actually
+ test this - the popup does go away with setSelInd - only with mouse click it
+ sometimes doesnt - need simulated mouse click!
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void selectionPopupTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ qualityComboBox.setText("larg",true);
+ qualityComboBox.getJComboBox().setSelectedIndex(2);
+ assertFalse(qualityComboBox.getJComboBox().isPopupVisible());
+ }
+ });
+
+ }
+
+ /** with searching on synonyms hit bug where terms come in more than once if have
+ 2 syns
+ * @throws InvocationTargetException
+ * @throws InterruptedException */
+ @Ignore @Test public void synonymDupTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ qualityComboBox.setText("");
+ // searchParamPanel not used anymore - need to set in menu
+ //searchParamPanel.setTermSearch(false);
+ //searchParamPanel.setSynonymSearch(true);
+ SearchParams.inst().setParam(SearchFilterType.TERM,false);
+ SearchParams.inst().setParam(SearchFilterType.SYN,true);
+ simulateAQualityKeyStroke();
+ String first = getQualityTerm(0);
+ String second = getQualityTerm(1);
+ assertFalse(first.equals(second));
+ }
+ });
+
+ }
+
+ // utlimatley need to do mouse click on term - how to do that???
+ @Test public void termInfoSelectTermTest() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ simulatePhenoteHyperlinkUpdate();
+ String m = "term info hyper link test fail, term info should have body tone val "
+ +" term info: "+termInfo.getTermFieldText();
+ // how to make this test not so pato specific??
+ assertTrue(m,termInfo.getTermFieldText().contains("body tone value"));
+ }
+ });
+ }
+
+ private void simulatePhenoteHyperlinkUpdate() {
+ HyperlinkEvent.EventType type = HyperlinkEvent.EventType.ACTIVATED;
+ // 0000732 -> "BodyToneValue"
+ String desc = HtmlUtil.makePhenoIdLink("PATO:0000732");
+ HyperlinkEvent e = new HyperlinkEvent(termInfo,type,null,desc);
+ termInfo.simulateHyperlinkEvent(e);
+ }
+
+ private void simulateAQualityKeyStroke() {
+ simulateQualityKeyStroke(KeyEvent.VK_A,'a');
+ }
+
+ private void simulateQualityKeyStroke(int keyCode, char c) {
+ qualityComboBox.simulateKeyStroke(keyCode,c);
+ }
+
+ @Ignore @Test public void flyDataAdapterTest() throws UnsupportedFlavorException, IOException {
+ CharacterListI cl = CharacterListManager.main().getCharacterList();
+ DataFlavor charListFlavor = FlyCharListTransferable.getCharListDataFlavor();
+ Object o = getClipboard().getData(charListFlavor);
+ String m = "Failure: clipboard transferrable is not a FlyCharList "+o;
+ assertTrue(m,o instanceof FlyCharList);
+ FlyCharList fcl = (FlyCharList)o;
+ CharacterListI clipboardCharList = fcl.getCharacterList();
+ //assertEquals(clipboardCharList,cl); // its a clone???
+ assertTrue(clipboardCharList.equals(cl));
+
+ // simulate proforma - grab strings and recreate char list & shove in clipboard
+ // & load it up
+ FlyCharList newFlyCharList = new FlyCharList();
+ for (FlyCharacter fc : fcl.getFlyCharList()) {
+ FlyCharacter fcNew = new FlyCharacter(fc.getGenotype(),fc.getEVString());
+ newFlyCharList.addFlyChar(fcNew);
+ }
+ Transferable tr = new FlyCharListTransferable(newFlyCharList);
+ ClipboardOwner clipboardOwner = FlybaseDataAdapter.getClipboardOwner();
+ getClipboard().setContents(tr,clipboardOwner);
+
+ MenuManager.inst().getFileMenu().clickLoad();
+ CharacterListI newCL = CharacterListManager.inst().getCharacterList();
+ //assertEquals(cl,newCL); == NOT .equals()
+ assertTrue(cl.equals(newCL));
+ }
+
+// // put in CharList class?
+// private boolean charListEquals(CharacterListI c1, CharacterListI c2) {
+// if (c1.size() != c2.size()) return false;
+// for (int i=0; i<c1.size(); i++) {
+// if (!c1.get(i).equals(c2,get(i)))
+// return false;
+// }
+// return true;
+// }
+
+ private Clipboard getClipboard() {
+ Toolkit t = Toolkit.getDefaultToolkit();
+ return t.getSystemClipboard();
+ }
+
+
+ // I cant find a way to simulate a backspace in jcombobox - very frustrating!!
+// /** there is/was a bug where delete/backspace was not triggering a new
+// completion list */
+// private void backspaceInComboBoxTest() {
+// boolean doCompletion = true;
+// qualityComboBox.clear();
+// qualityComboBox.setText("larg",doCompletion);
+// int preBackspaceCount = qualityComboBox.getItemCount();
+
+// // simulate backspace/delete key
+// KeyEvent ke = new KeyEvent(qualityComboBox,KeyEvent.VK_DELETE,Calendar.getInstance().getTimeInMillis(),0,KeyEvent.VK_UNDEFINED,KeyEvent.CHAR_UNDEFINED);
+// //qualityComboBox.processKeyEvent(ke);
+// qualityComboBox.getEditor().getEditorComponent().processKeyEvent(ke);
+
+// String postDelText = qualityComboBox.getText();
+// int postBackspaceCount = qualityComboBox.getItemCount();
+// System.out.println("post text "+postDelText+" pre count "+preBackspaceCount+" post count "+postBackspaceCount);
+// assertTrue(preBackspaceCount != postBackspaceCount);
+// }
+
+}
Deleted: phenote/trunk/src/java/phenote/util/FileUtilTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtilTest.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/util/FileUtilTest.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -1,126 +0,0 @@
-package phenote.util;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-import org.junit.Test;
-import org.junit.After;
-import org.junit.Before;
-
-import java.io.File;
-import java.io.IOException;
-
-/**
- * Unit test class for FileUtil.
- */
-public class FileUtilTest {
-
- private static final File testArchiveDir = new File("src" + FileUtil.FILE_SEPARATOR +
- "java" + FileUtil.FILE_SEPARATOR +
- "test", "test-archive-dir");
- private static final File testLoadDirectory = new File("src" + FileUtil.FILE_SEPARATOR +
- "java" + FileUtil.FILE_SEPARATOR +
- "test", "test-load-dir");
- private File testLoadFile;
- private File testPurgeFile;
-
- @Before
- public void setUp() {
- setTestDirectories();
- }
-
- @After
- public void tearDown() {
- cleanupTestFilesStructure();
- }
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- */
- @Test
- public void archiveFile() {
- File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
- File[] files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
- assertTrue("Original File still exists", testLoadFile.exists());
- }
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- * Sleep for a second and then archive another file and then purge the first file while the
- * second file does not get purged.
- */
- @Test
- public void purgeArchiveFile() {
- File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
- File[] files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
- assertTrue("Original File still exists", testLoadFile.exists());
-
- // create the second file and wait a second before archiving it.
- testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
- try {
- Thread.sleep(1000);
- testPurgeFile.createNewFile();
- } catch (IOException e) {
- e.printStackTrace();
- } catch (InterruptedException e) {
- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
- }
-
- archivedFile = FileUtil.archiveFile(testPurgeFile, testArchiveDir);
- files = testArchiveDir.listFiles();
- assertEquals("Number of files", 2, files.length);
- FileUtil.purgeArchiveDirectory(testArchiveDir, 990);
-
- files = testArchiveDir.listFiles();
- assertEquals("Number of files", 1, files.length);
- assertEquals("File Name", archivedFile.getName(), files[0].getName());
-
- }
-
- @Test
- public void pureFilename() {
- String fileNameOnly = "filenameAlpha.txt";
- String filename = FileUtil.FILE_SEPARATOR + "dire" + FileUtil.FILE_SEPARATOR + fileNameOnly;
- String pureFilename = FileUtil.getPureFileName(filename);
- assertEquals("Pure File Name", fileNameOnly, pureFilename);
-
- fileNameOnly = "";
- pureFilename = FileUtil.getPureFileName(fileNameOnly);
- assertEquals("Pure File Name", fileNameOnly, pureFilename);
- }
-
-
- /**
- * Create the test directories before the tests are run.
- */
- private void setTestDirectories() {
- testLoadDirectory.mkdir();
-
- testLoadFile = new File(testLoadDirectory, "test-file-one.txt");
- testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
- try {
- testLoadFile.createNewFile();
- } catch (IOException e) {
- e.printStackTrace();
- }
- }
-
- /**
- * Remove test directories after the tests are done.
- */
- private void cleanupTestFilesStructure() {
- testLoadFile.delete();
- testPurgeFile.delete();
- testLoadDirectory.delete();
- File[] files = testArchiveDir.listFiles();
- if (files != null)
- for (File file : files) {
- file.delete();
- }
- testArchiveDir.delete();
- }
-
-}
Added: phenote/trunk/src/java/phenote/util/FileUtilTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/FileUtilTest.java (rev 0)
+++ phenote/trunk/src/java/phenote/util/FileUtilTest.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -0,0 +1,127 @@
+package phenote.util;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Test;
+import org.junit.After;
+import org.junit.Before;
+
+
+import java.io.File;
+import java.io.IOException;
+
+/**
+ * Unit test class for FileUtil.
+ */
+public class FileUtilTest {
+
+ private static final File testArchiveDir = new File("src" + FileUtil.FILE_SEPARATOR +
+ "java" + FileUtil.FILE_SEPARATOR +
+ "test", "test-archive-dir");
+ private static final File testLoadDirectory = new File("src" + FileUtil.FILE_SEPARATOR +
+ "java" + FileUtil.FILE_SEPARATOR +
+ "test", "test-load-dir");
+ private File testLoadFile;
+ private File testPurgeFile;
+
+ @Before
+ public void setUp() {
+ setTestDirectories();
+ }
+
+ @After
+ public void tearDown() {
+ cleanupTestFilesStructure();
+ }
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ */
+ @Test
+ public void archiveFile() {
+ File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
+ File[] files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+ assertTrue("Original File still exists", testLoadFile.exists());
+ }
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ * Sleep for a second and then archive another file and then purge the first file while the
+ * second file does not get purged.
+ */
+ @Test
+ public void purgeArchiveFile() {
+ File archivedFile = FileUtil.archiveFile(testLoadFile, testArchiveDir);
+ File[] files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+ assertTrue("Original File still exists", testLoadFile.exists());
+
+ // create the second file and wait a second before archiving it.
+ testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
+ try {
+ Thread.sleep(1000);
+ testPurgeFile.createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ } catch (InterruptedException e) {
+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
+ }
+
+ archivedFile = FileUtil.archiveFile(testPurgeFile, testArchiveDir);
+ files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 2, files.length);
+ FileUtil.purgeArchiveDirectory(testArchiveDir, 990);
+
+ files = testArchiveDir.listFiles();
+ assertEquals("Number of files", 1, files.length);
+ assertEquals("File Name", archivedFile.getName(), files[0].getName());
+
+ }
+
+ @Test
+ public void pureFilename() {
+ String fileNameOnly = "filenameAlpha.txt";
+ String filename = FileUtil.FILE_SEPARATOR + "dire" + FileUtil.FILE_SEPARATOR + fileNameOnly;
+ String pureFilename = FileUtil.getPureFileName(filename);
+ assertEquals("Pure File Name", fileNameOnly, pureFilename);
+
+ fileNameOnly = "";
+ pureFilename = FileUtil.getPureFileName(fileNameOnly);
+ assertEquals("Pure File Name", fileNameOnly, pureFilename);
+ }
+
+
+ /**
+ * Create the test directories before the tests are run.
+ */
+ private void setTestDirectories() {
+ testLoadDirectory.mkdir();
+
+ testLoadFile = new File(testLoadDirectory, "test-file-one.txt");
+ testPurgeFile = new File(testLoadDirectory, "test-file-two.txt");
+ try {
+ testLoadFile.createNewFile();
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+
+ /**
+ * Remove test directories after the tests are done.
+ */
+ private void cleanupTestFilesStructure() {
+ testLoadFile.delete();
+ testPurgeFile.delete();
+ testLoadDirectory.delete();
+ File[] files = testArchiveDir.listFiles();
+ if (files != null)
+ for (File file : files) {
+ file.delete();
+ }
+ testArchiveDir.delete();
+ }
+
+}
Deleted: phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:18:54 UTC (rev 1034)
+++ phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -1,90 +0,0 @@
-package phenote.util;
-
-import junit.framework.Test;
-import junit.framework.TestCase;
-import junit.framework.TestSuite;
-import junit.textui.TestRunner;
-import org.geneontology.oboedit.datamodel.Link;
-import org.geneontology.oboedit.datamodel.OBOProperty;
-import org.geneontology.oboedit.datamodel.impl.InstancePropertyValue;
-import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * Unit test class for FileUtil.
- */
-public class TermLinkComparatorTest extends TestCase {
-
- public static void main(String args[]) {
- TestRunner.run(TermLinkComparatorTest.suite());
- }
-
- public static Test suite() {
- return new TestSuite(TermLinkComparatorTest.class);
- }
-
- /**
- * Create a single file and archive it. Make sure it moved into the archive directory.
- */
- public void testIS_A_Before_PART_Of() {
- List<InstancePropertyValue> links = new ArrayList<InstancePropertyValue>();
- links.add(getLinkUnknownOne());
- links.add(getLinkUnknownTwo());
- links.add(getLinkDevelops_From());
- links.add(getLinkPart_Of());
- links.add(getLinkIS_A());
-
- Collections.sort(links, new TermLinkComparator());
-
- Link link = (Link) links.get(0);
- assertEquals("IS a first", "is_a", link.getType().getName());
- link = (Link) links.get(1);
- assertEquals("Part of is second", "part of", link.getType().getName());
- link = (Link) links.get(2);
- assertEquals("Part of is second", "develops from", link.getType().getName());
- link = (Link) links.get(3);
- assertEquals("IS a first", "Unknown A", link.getType().getName());
- link = (Link) links.get(4);
- assertEquals("IS a first", "Unknown B", link.getType().getName());
-
- }
-
- private InstancePropertyValue getLinkIS_A(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.IS_A.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkPart_Of(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.PART_OF.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkDevelops_From(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.DEVELOPS_FROM.getName());
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkUnknownOne(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl("Unknown B");
- link.setType(prop);
- return link;
- }
-
- private InstancePropertyValue getLinkUnknownTwo(){
- InstancePropertyValue link = new InstancePropertyValue();
- OBOProperty prop = new OBOPropertyImpl("Unknown A");
- link.setType(prop);
- return link;
- }
-
-}
Added: phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java
===================================================================
--- phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java (rev 0)
+++ phenote/trunk/src/java/phenote/util/TermLinkComparatorTest.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -0,0 +1,81 @@
+package phenote.util;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.geneontology.oboedit.datamodel.Link;
+import org.geneontology.oboedit.datamodel.OBOProperty;
+import org.geneontology.oboedit.datamodel.impl.InstancePropertyValue;
+import org.geneontology.oboedit.datamodel.impl.OBOPropertyImpl;
+import org.junit.Assert;
+import org.junit.Test;
+
+
+/**
+ * Unit test class for FileUtil.
+ */
+public class TermLinkComparatorTest {
+
+ /**
+ * Create a single file and archive it. Make sure it moved into the archive directory.
+ */
+ @Test public void testIS_A_Before_PART_Of() {
+ List<InstancePropertyValue> links = new ArrayList<InstancePropertyValue>();
+ links.add(getLinkUnknownOne());
+ links.add(getLinkUnknownTwo());
+ links.add(getLinkDevelops_From());
+ links.add(getLinkPart_Of());
+ links.add(getLinkIS_A());
+
+ Collections.sort(links, new TermLinkComparator());
+
+ Link link = (Link) links.get(0);
+ Assert.assertEquals("IS a first", "is_a", link.getType().getName());
+ link = (Link) links.get(1);
+ Assert.assertEquals("Part of is second", "part of", link.getType().getName());
+ link = (Link) links.get(2);
+ Assert.assertEquals("Part of is second", "develops from", link.getType().getName());
+ link = (Link) links.get(3);
+ Assert.assertEquals("IS a first", "Unknown A", link.getType().getName());
+ link = (Link) links.get(4);
+ Assert.assertEquals("IS a first", "Unknown B", link.getType().getName());
+
+ }
+
+ private InstancePropertyValue getLinkIS_A(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.IS_A.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkPart_Of(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.PART_OF.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkDevelops_From(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl(TermLinkComparator.RelationshipEnum.DEVELOPS_FROM.getName());
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkUnknownOne(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl("Unknown B");
+ link.setType(prop);
+ return link;
+ }
+
+ private InstancePropertyValue getLinkUnknownTwo(){
+ InstancePropertyValue link = new InstancePropertyValue();
+ OBOProperty prop = new OBOPropertyImpl("Unknown A");
+ link.setType(prop);
+ return link;
+ }
+
+}
Added: phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java
===================================================================
--- phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java (rev 0)
+++ phenote/trunk/test/java/phenote/charactertemplate/CharacterTemplateControllerTest.java 2007-10-11 15:28:04 UTC (rev 1035)
@@ -0,0 +1,93 @@
+package phenote.charactertemplate;
+
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.SwingUtilities;
+
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import phenote.dataadapter.CharacterListManager;
+import phenote.datamodel.CharFieldException;
+import phenote.datamodel.CharacterI;
+import phenote.datamodel.TermNotFoundException;
+import phenote.main.Phenote;
+
+public class CharacterTemplateControllerTest {
+
+ private CharacterTemplateController controller;
+
+ @BeforeClass public static void initialize() {
+ final String[] emptyArgs = {};
+ Phenote.main(emptyArgs);
+ }
+
+ @Before public void setup() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ controller = new CharacterTemplateController("specimen-list");
+ }
+ });
+ }
+
+ @Test public void addNewCharacter() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ controller.addNewCharacter();
+ Assert.assertEquals("Should be one character", 1, controller.getAllCharacters().size());
+ }
+ });
+ }
+
+ @Test public void markCharacter() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ CharacterI character = addAndMarkNewCharacter();
+ Assert.assertTrue("Character should be marked", controller.getMarkedCharacters().contains(character));
+ }
+ });
+ }
+
+ @Test public void invertMarkedCharacters() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ CharacterI character = addAndMarkNewCharacter();
+ controller.invertMarkedCharacters();
+ Assert.assertFalse("No characters should be marked", controller.getMarkedCharacters().contains(character));
+ }
+ });
+ }
+
+ @Test public void generateCharacters() throws InterruptedException, InvocationTargetException {
+ SwingUtilities.invokeAndWait(new Runnable() {
+ public void run() {
+ try {
+ CharacterListManager.main().clear();
+ CharacterI template = addAndMarkNewCharacter();
+ template.setValue("Textual Description", "testCharacter");
+ template.setValue("Quality", "PATO:0000001");
+ controller.generateCharac...
[truncated message content] |
|
From: <mg...@us...> - 2007-10-11 15:18:53
|
Revision: 1034
http://obo.svn.sourceforge.net/obo/?rev=1034&view=rev
Author: mgibson
Date: 2007-10-11 08:18:54 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
Tagging the 1.4 release of phenote - comp optimizations, obo edit annotations,template, mac, splash...
Added Paths:
-----------
phenote/tags/release-1.4/
Copied: phenote/tags/release-1.4 (from rev 1033, phenote/trunk)
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|
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