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[Treebase-guts] SF.net SVN: treebase:[989] trunk
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From: <hs...@us...> - 2011-11-28 15:43:26
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Revision: 989
http://treebase.svn.sourceforge.net/treebase/?rev=989&view=rev
Author: hshyket
Date: 2011-11-28 15:43:15 +0000 (Mon, 28 Nov 2011)
Log Message:
-----------
Adding a read timeout when uBio takes too long to respond
Modified Paths:
--------------
trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java
trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java
trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/domain/taxon/TaxonLabelService.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -372,4 +372,6 @@
*/
Set<TaxonVariant> findTaxonVariantByName(String s);
+ boolean getuBioTimeOutError();
+
}
Modified: trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java
===================================================================
--- trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-core/src/main/java/org/cipres/treebase/service/taxon/TaxonLabelServiceImpl.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -6,6 +6,7 @@
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
+import java.io.InterruptedIOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.net.URLConnection;
@@ -52,18 +53,22 @@
private static final String NMBKID = "namebankID";
private static final String NAMESTR = "nameString";
private static final int TIMEOUT = 10000;
+ private static final int READTIMEOUT = 30000;
private static final String VALUETAG = "value";
private static final String DETAILSSERVICEURLPART = "http://www.ubio.org/browser/details.php?namebankID=";
private TaxonLabelHome mTaxonLabelHome;
private PhyloTreeHome mPhyloTreeHome;
private TaxonHome mTaxonHome;
+
+ private boolean muBioTimeOutError;
/**
* constructor.
*/
public TaxonLabelServiceImpl() {
super();
+ setuBioTimeOutError(false);
}
/**
@@ -459,7 +464,7 @@
booleanplaceholder bph = new booleanplaceholder();
longplaceholder lph = new longplaceholder();
TaxonVariant firstVariant = null;
-
+
// XXX 1. Turn label into tri- or binomial, no var./ex./etc.
testString = normalizeLabelString(pTaxonLabel.getTaxonLabel());
@@ -468,6 +473,9 @@
String result = getStringFromURL(taxonFinderFullURL, null, null);
// XXX 3. Process TaxonFinder result
+ if (getuBioTimeOutError()) {
+ return null;
+ }
if (result == null || result.indexOf(NMBKID) < 0 || result.indexOf(testString) < 0 || result.indexOf(NAMESTR) < 0) {
LOGGER.warn("Problem: uBio result is garbled or doesn't contain our testString");
return null;
@@ -755,6 +763,7 @@
URL url = new URL(urlString);
URLConnection urlconn = url.openConnection();
urlconn.setConnectTimeout(TIMEOUT);
+ urlconn.setReadTimeout(READTIMEOUT);
BufferedReader in = new BufferedReader(new InputStreamReader(urlconn.getInputStream()));
StringBuilder results = new StringBuilder();
String str;
@@ -780,7 +789,11 @@
return results.toString();
} catch (MalformedURLException mfe) {
mfe.printStackTrace();
- } catch (IOException ioe) {
+ } catch (InterruptedIOException iioe) {
+ iioe.printStackTrace();
+ setuBioTimeOutError(true);
+ }
+ catch (IOException ioe) {
ioe.printStackTrace();
}
return null;
@@ -808,6 +821,14 @@
}
return result.substring(start + 1, end);
}
+
+ public boolean getuBioTimeOutError() {
+ return muBioTimeOutError;
+ }
+
+ public void setuBioTimeOutError(Boolean pTimeOutError) {
+ muBioTimeOutError = pTimeOutError;
+ }
/**
* @return the taxonHome
@@ -1019,5 +1040,5 @@
@Override
public Class defaultResultClass() {
return TaxonLabel.class;
- }
+ }
}
Modified: trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java
===================================================================
--- trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2011-11-23 21:43:54 UTC (rev 988)
+++ trunk/treebase-web/src/main/java/org/cipres/treebase/web/controllers/ListTaxaController.java 2011-11-28 15:43:15 UTC (rev 989)
@@ -148,11 +148,20 @@
// no variants were found by uBio
if ( variant == null ) {
- ubioResultMessages.add(taxonlabel.getTaxonLabel() + " is **UNRECOGNIZED**.");
- ubioResultErrors.add(taxonlabel.getTaxonLabel()
- + " is **UNRECOGNIZED** try <a href=" + UBIOSEARCHTAXONLABEL
- + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
- + " target=_blank>UBIO</a> site.");
+ if (getTaxonLabelService().getuBioTimeOutError()) {
+ ubioResultMessages.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() + ".");
+ ubioResultErrors.add("uBio service was unavailable when checking " + taxonlabel.getTaxonLabel() +
+ " try <a href=" + UBIOSEARCHTAXONLABEL
+ + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
+ + " target=_blank>UBIO</a> site.");
+ }
+ else {
+ ubioResultMessages.add(taxonlabel.getTaxonLabel() + " is **UNRECOGNIZED**.");
+ ubioResultErrors.add(taxonlabel.getTaxonLabel()
+ + " is **UNRECOGNIZED** try <a href=" + UBIOSEARCHTAXONLABEL
+ + taxonlabel.getTaxonLabel().replace(EMPTYSPACE, "%20")
+ + " target=_blank>UBIO</a> site.");
+ }
}
// variants stored by uBio,TODO now check for homonyms
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