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[Obo-svn-commit] SF.net SVN: obo: [1248] phenote/trunk/src/java/phenote
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From: <mg...@us...> - 2007-11-29 22:37:13
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Revision: 1248
http://obo.svn.sourceforge.net/obo/?rev=1248&view=rev
Author: mgibson
Date: 2007-11-29 14:37:17 -0800 (Thu, 29 Nov 2007)
Log Message:
-----------
fixed phenote hang bug
setting obo edits obo session queried reasoner -> prefs -> set font
-> gui revalidate... -> threadlock of loading screen
fix for now is query for prefs ahead of time
also i think ill add config for turning off loading screen
as i think we will want to try that for maryann -
but leave it in if not having a problem
Modified Paths:
--------------
phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
phenote/trunk/src/java/phenote/main/Phenote.java
Modified: phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-11-29 22:29:47 UTC (rev 1247)
+++ phenote/trunk/src/java/phenote/dataadapter/OntologyDataAdapter.java 2007-11-29 22:37:17 UTC (rev 1248)
@@ -50,7 +50,7 @@
private static OntologyDataAdapter singleton;
//private Config config; cant cache may change
- private CharFieldManager ontologyManager = CharFieldManager.inst();
+ private CharFieldManager charFieldManager = CharFieldManager.inst();
private boolean initializingOntologies = false;
private Map<String,Ontology> fileToOntologyCache = new HashMap<String,Ontology>();
private OBOMetaData adapterMetaData;
@@ -107,11 +107,16 @@
private void initOntolsOneOboSession() {
try {
+ LOG.debug("loading obo files");
OBOSession os = loadAllOboFilesIntoOneOboSession();
+ LOG.debug("initializing char fields");
initCharFields();
- ontologyManager.setOboSession(os);
+ LOG.debug("setting char field managers obo session");
+ charFieldManager.setOboSession(os);
// map namespaces to ontologies? 2 methods?
+ LOG.debug("mapping namespaces to ontologies");
mapNamespacesToOntologies(os);
+ LOG.debug("ontologies initialiazed!");
// load ontologies from namespaces
}
catch (OntologyException e) { // parse ex - not file not found ex
@@ -160,7 +165,7 @@
private void initCharFields() {
for (FieldConfig fieldConfig : cfg().getEnbldFieldCfgs()) {
CharField cf = fieldConfig.getCharField(); // creates char field (if not there)
- ontologyManager.addField(cf);
+ charFieldManager.addField(cf);
}
}
@@ -612,7 +617,7 @@
cf.setName(fieldConfig.getLabel());
}
// i think this order needs to be same as config order
- ontologyManager.addField(cf);
+ charFieldManager.addField(cf);
}
@@ -688,7 +693,7 @@
///** Checks for new obo files */
//private void synchOntologies() {
-//for (CharField cf : ontologyManager.getCharFieldList()) {
+//for (CharField cf : charFieldManager.getCharFieldList()) {
//for (Ontology o : cf.getOntologyList()) {
//if (o.getSource() == null) continue;
//String file = o.getSource();
Modified: phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java 2007-11-29 22:29:47 UTC (rev 1247)
+++ phenote/trunk/src/java/phenote/datamodel/CharFieldManager.java 2007-11-29 22:37:17 UTC (rev 1248)
@@ -65,7 +65,9 @@
public void setOboSession(OBOSession s) {
// set in obo edit
+ log().debug("Setting SessionManagers session");
SessionManager.getManager().setSession(s);
+ log().debug("SessionManagers session is set");
oboSession = s;
}
public OBOSession getOboSession() {
Modified: phenote/trunk/src/java/phenote/main/Phenote.java
===================================================================
--- phenote/trunk/src/java/phenote/main/Phenote.java 2007-11-29 22:29:47 UTC (rev 1247)
+++ phenote/trunk/src/java/phenote/main/Phenote.java 2007-11-29 22:37:17 UTC (rev 1248)
@@ -33,6 +33,8 @@
import org.apache.log4j.LogManager;
import org.apache.log4j.Logger;
+import org.oboedit.gui.Preferences;
+
import phenote.charactertemplate.CharacterTemplateController;
import phenote.config.Config;
import phenote.config.ConfigException;
@@ -92,59 +94,6 @@
standalone = true; // i think this is ok
init(args);
-
-
-// phenote = getPhenote();
-// boolean enableSplashScreen = !phenote.commandLine.writeIsSpecified();
-// //System.out.println("splash "+enableSplashScreen);
-// phenote.splashScreenInit(enableSplashScreen); //initialize the splash screen;
-
- //phenote.doCommandLine(args); // does config
-
- //new phenote.gui.ConfigGui(); // testing out
-
- /* set up the overall task of loading the software
- there will be several events:
- 1. loading configuration - display config name
- 2. checking for ontology updates - per ontology display name
- 3. updating ontologies (name) - downloading... display name
- 4. loading into datamodel - display name - this is the bulk of the time
- */
-
-// phenote.splashScreen.setProgress("Configuring...", 10);
-// phenote.loadingScreen.setMessageText("Loading configuration: "+Config.inst().getConfigName());
-// phenote.loadingScreen.setProgress(5);
-// phenote.splashScreen.setProgress("Initializing Ontologies...", 20);
-// phenote.loadingScreen.setMessageText("Initializing Ontologies");
-// phenote.loadingScreen.setProgress(10);
-// phenote.loadingScreen.setProgress(20);
-// boolean done = false;
-
-// phenote.initOntologies();
-// phenote.splashScreen.setProgress("Ontologies Initialized", 70);
-// phenote.loadingScreen.setMessageText("Ontologies Initialized");
-// phenote.loadingScreen.setProgress(70);
-// phenote.loadFromCommandLine(); // aft ontols, reads from cmd line if specified
-// phenote.splashScreen.setProgress("Phenote Loaded", 100);
-// phenote.loadingScreen.setMessageText("Phenote Loaded");
-// phenote.loadingScreen.setProgress(100);
-
-// if (phenote.commandLine.writeIsSpecified()) {
-// phenote.writeFromCommandLine();
-// // it hangs after writing - not sure why
-// System.out.println("Done writing, exiting phenote");
-// System.exit(0);
-// }
-// else // init gui if not writing (& reading) from cmd line
-// {
-// phenote.initGui();
-// phenote.splashScreenDestruct();
-// // phenote.loadingScreenDestruct();
-// }
-
-// if (Config.inst().dataInputServletIsEnabled())
-// new phenote.servlet.DataInputServer();
-
}
/** private constructor -> singleton */
@@ -152,6 +101,7 @@
private static void init(String[] args) {
initBackend(args);
+ LOG.debug("Backend initialized, initializing GUI");
phenote.initGui();
phenote.splashScreenDestruct(); // initBackend startsup splash
}
@@ -163,6 +113,8 @@
phenote.splashScreenInit();
phenote.doCommandLineAndConfig(args); // does config
phenote.initOntologies();
+ // phenote sometimes hangs right around here!???!
+ LOG.debug("Ontologies initialized, checking command line for read & write");
phenote.loadFromCommandLine(); // if load/file specified from cmd line
phenote.setProgress("Phenote Loaded", 100);
phenote.writeFromCommandLine(); // if cmd line, writes & exits
@@ -235,9 +187,11 @@
setProgress("Initializing Ontologies...", 20);
setProgressMsg("Initializing Ontologies");
setProgress(10);
+ LOG.debug("Initializing ontologies");
//OntologyDataAdapter oda = new OntologyDataAdapter(); // singleton?
// loads up OntologyManager - non intuitive?
- OntologyDataAdapter.initialize();
+ OntologyDataAdapter.initialize(); // this sometimes hangs!!!
+ LOG.debug("Ontologies initialized");
// if (config.useShrimpDagViewer())
// ShrimpDag.inst().initOntologies();
setProgress("Ontologies Initialized", 70);
@@ -275,6 +229,9 @@
public void initGui() {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
+ LOG.debug("swing thread for gui started, making main window "+new java.util.Date());
+// try { Thread.sleep(20000); } catch(Exception e){LOG.debug("interrupt");}
+// LOG.debug("done sleeping - making main window "+new java.util.Date());
makeMainWindow(); // with tabbed groups
createGroupWindows(); // template window
}
@@ -351,6 +308,10 @@
} catch (FileNotFoundException ex) { }
// ImageIcon myImage = new ImageIcon(logoFile);
+ // wacky but oboedit preference 1st call causing setting font which triggers gui stuff
+ // which can deadlock loadingScreen, setOboSession triggers this when checks for
+ // if reasoning, so do here to subdue later call
+ Preferences.getPreferences();
splashScreen = new SplashScreen(myImage); //,enable);
if (USE_LOADING_SCREEN) {
loadingScreen = new LoadingScreen();
@@ -421,7 +382,6 @@
public Frame getFrame() { return frame; }
private void makeMainWindow() {
- // this may be changed to applet...
frame = new JFrame("Phenote "+PhenoteVersion.versionString());
if (getNumGroupTabs() < 2) {
Group g = Config.inst().getDefaultGroup();
@@ -430,7 +390,7 @@
else {
JTabbedPane tabbedGroups = new JTabbedPane();
for (Group g : getGroupTabs()) {
- JPanel p = makeGroupPanel(g); //.getName());
+ JPanel p = makeGroupPanel(g);
tabbedGroups.add(g.getTitle(),p);
}
frame.getContentPane().add(tabbedGroups);
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