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[Genoviz-cmts] SF.net SVN: genoviz:[6212] trunk/genometryImpl/src/com/affymetrix/ genometryImpl/das
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From: <jn...@us...> - 2010-06-22 12:15:41
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Revision: 6212
http://genoviz.svn.sourceforge.net/genoviz/?rev=6212&view=rev
Author: jnicol
Date: 2010-06-22 12:14:30 +0000 (Tue, 22 Jun 2010)
Log Message:
-----------
Improve synchronization and logging.
Modified Paths:
--------------
trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasServerInfo.java
trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasSource.java
Modified: trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasServerInfo.java
===================================================================
--- trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasServerInfo.java 2010-06-22 11:42:42 UTC (rev 6211)
+++ trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasServerInfo.java 2010-06-22 12:14:30 UTC (rev 6212)
@@ -92,12 +92,19 @@
* see DAS specification for returned XML format in response to "dsn" command:
* http://biodas.org/documents/spec.html
*/
- private void initialize() {
+ private boolean initialize() {
InputStream stream = null;
try {
- System.out.println("Das Request: " + getLoadURL());
+ Logger.getLogger(this.getClass().getName()).log(
+ Level.INFO, "Das Request: {0}", getLoadURL());
+
Map<String, List<String>> headers = new HashMap<String, List<String>>();
stream = LocalUrlCacher.getInputStream(getLoadURL(), true, null, headers);
+ if (stream == null) {
+ Logger.getLogger(this.getClass().getName()).log(
+ Level.SEVERE, "Could not find URL {0}", getLoadURL());
+ return false;
+ }
List<String> list;
String das_version = "";
@@ -125,8 +132,9 @@
Document doc = XMLUtils.getDocument(stream);
NodeList dsns = doc.getElementsByTagName("DSN");
- System.out.println("dsn count: " + dsns.getLength());
- for (int i = 0; i < dsns.getLength(); i++) {
+ int dsnLength = dsns.getLength();
+ System.out.println("dsn count: " + dsnLength);
+ for (int i = 0; i < dsnLength; i++) {
Element dsn = (Element) dsns.item(i);
try {
parseDSNElement(dsn);
@@ -139,11 +147,12 @@
} catch (Exception ex) {
System.out.println("Error initializing DAS server info for\n" + serverURL);
ex.printStackTrace();
- return;
+ return false;
} finally {
GeneralUtils.safeClose(stream);
}
initialized = true;
+ return true;
}
private void parseDSNElement(Element dsn) throws DOMException {
@@ -171,15 +180,18 @@
try {
URL masterURL = new URL(master_url);
if (DasSource.getID(masterURL).isEmpty()) {
- Logger.getLogger(this.getClass().getName()).log(Level.WARNING, "Skipping " + sourceid + " as MAPMASTER could not be parsed");
+ Logger.getLogger(this.getClass().getName()).log(
+ Level.WARNING, "Skipping {0} as MAPMASTER could not be parsed", sourceid);
return;
}
DasSource das_source = sources.get(DasSource.getID(masterURL));
- if (das_source == null) {
- das_source = new DasSource(serverURL, masterURL, primaryURL);
- sources.put(DasSource.getID(masterURL), das_source);
+ synchronized (this) {
+ if (das_source == null) {
+ das_source = new DasSource(serverURL, masterURL, primaryURL);
+ sources.put(DasSource.getID(masterURL), das_source);
+ }
+ das_source.add(sourceid);
}
- das_source.add(sourceid);
} catch (MalformedURLException ex) {
Logger.getLogger(this.getClass().getName()).log(Level.WARNING, "", ex);
}
Modified: trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasSource.java
===================================================================
--- trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasSource.java 2010-06-22 11:42:42 UTC (rev 6211)
+++ trunk/genometryImpl/src/com/affymetrix/genometryImpl/das/DasSource.java 2010-06-22 12:14:30 UTC (rev 6212)
@@ -97,7 +97,7 @@
return entry_points;
}
- public synchronized Set<DasType> getTypes() {
+ public Set<DasType> getTypes() {
if (!types_initialized) {
initTypes();
}
@@ -105,16 +105,18 @@
}
/** Get entry points from das server. */
- private synchronized boolean initEntryPoints() {
+ private boolean initEntryPoints() {
InputStream stream = null;
try {
URL entryURL;
- if(primary == null)
+ if(primary == null) {
entryURL = new URL(master, master.getPath() + "/" + ENTRY_POINTS);
- else
+ }
+ else {
entryURL = new URL(primary,id + "/" + ENTRY_POINTS + XML);
+ }
- System.out.println("Das Entry Request: " + entryURL);
+ Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Das Entry Request: {0}", entryURL);
stream = LocalUrlCacher.getInputStream(entryURL);
if (stream == null) {
Logger.getLogger(this.getClass().getName()).log(
@@ -123,23 +125,7 @@
}
Document doc = XMLUtils.getDocument(stream);
NodeList segments = doc.getElementsByTagName("SEGMENT");
- int length = segments.getLength();
- System.out.println("segments: " + length);
- for (int i = 0; i < length; i++) {
- Element seg = (Element) segments.item(i);
- String segid = seg.getAttribute("id");
- String stopstr = seg.getAttribute("stop");
- String sizestr = seg.getAttribute("size"); // can optionally use "size" instead of "start" and "stop"
-
- int stop = 1;
- if (stopstr != null && !stopstr.isEmpty()) {
- stop = Integer.parseInt(stopstr);
- } else if (sizestr != null) {
- stop = Integer.parseInt(sizestr);
- }
- getGenome().addSeq(segid, stop);
- entry_points.add(segid);
- }
+ addSegments(segments);
} catch (MalformedURLException ex) {
ErrorHandler.errorPanel("Error initializing DAS entry points for\n" + getID() + " on " + server, ex);
} catch (ParserConfigurationException ex) {
@@ -150,12 +136,35 @@
ErrorHandler.errorPanel("Error initializing DAS entry points for\n" + getID() + " on " + server, ex);
} finally {
GeneralUtils.safeClose(stream);
- entries_initialized = true; // set even if there's an error
+ synchronized(this) {
+ entries_initialized = true; // set even if there's an error?
+ }
}
return true;
}
- private synchronized void initTypes() {
+ private void addSegments(NodeList segments) throws NumberFormatException {
+ int length = segments.getLength();
+ Logger.getLogger(this.getClass().getName()).log(Level.FINE, "segments: {0}", length);
+ for (int i = 0; i < length; i++) {
+ Element seg = (Element) segments.item(i);
+ String segid = seg.getAttribute("id");
+ String stopstr = seg.getAttribute("stop");
+ String sizestr = seg.getAttribute("size"); // can optionally use "size" instead of "start" and "stop"
+ int stop = 1;
+ if (stopstr != null && !stopstr.isEmpty()) {
+ stop = Integer.parseInt(stopstr);
+ } else if (sizestr != null) {
+ stop = Integer.parseInt(sizestr);
+ }
+ synchronized (this) {
+ getGenome().addSeq(segid, stop);
+ entry_points.add(segid);
+ }
+ }
+ }
+
+ private void initTypes() {
Set<String> badSources = new HashSet<String>();
for (String source : sources) {
@@ -164,10 +173,12 @@
}
}
/* Remove any failed sources */
- for (String source : badSources) {
- sources.remove(source);
+ synchronized (this) {
+ for (String source : badSources) {
+ sources.remove(source);
+ }
+ types_initialized = true;
}
- types_initialized = true;
}
private boolean initType(String source) {
@@ -177,7 +188,7 @@
URL typesURL = new URL(server, source + "/" + TYPES);
URL testMasterURL = new URL(master, master.getPath() + "/" + TYPES);
- System.out.println("Das Types Request: " + loadURL);
+ Logger.getLogger(this.getClass().getName()).log(Level.INFO, "Das Types Request: {0}", loadURL);
stream = LocalUrlCacher.getInputStream(loadURL);
if (stream == null) {
Logger.getLogger(this.getClass().getName()).log(
@@ -187,14 +198,17 @@
Document doc = XMLUtils.getDocument(stream);
NodeList typelist = doc.getElementsByTagName("TYPE");
int typeLength = typelist.getLength();
- System.out.println("types: " + typeLength);
+ Logger.getLogger(this.getClass().getName()).log(Level.FINE, "types: {0}", typeLength);
for (int i = 0; i < typeLength; i++) {
Element typenode = (Element) typelist.item(i);
String typeid = typenode.getAttribute("id");
/* URL.equals() does DNS lookups! */
String name = URLEquals(typesURL, testMasterURL) ? null : source + "/" + typeid;
- types.add(new DasType(server, typeid, source, name));
+ DasType type = new DasType(server, typeid, source, name);
+ synchronized(this) {
+ types.add(type);
+ }
}
} catch (MalformedURLException ex) {
ErrorHandler.errorPanel("Error initializing DAS types for\n" + getID() + " on " + server, ex);
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