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pass OutOfMemory errors upstream from EBI fetch client
author
jprocter
<Jim Procter>
Fri, 29 Aug 2008 11:02:29 +0000
(11:02 +0000)
committer
jprocter
<Jim Procter>
Fri, 29 Aug 2008 11:02:29 +0000
(11:02 +0000)
src/jalview/ws/ebi/EBIFetchClient.java
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diff --git
a/src/jalview/ws/ebi/EBIFetchClient.java
b/src/jalview/ws/ebi/EBIFetchClient.java
index
683f465
..
4fc0900
100644
(file)
--- a/
src/jalview/ws/ebi/EBIFetchClient.java
+++ b/
src/jalview/ws/ebi/EBIFetchClient.java
@@
-119,9
+119,10
@@
public class EBIFetchClient
}
\r
\r
\r
}
\r
\r
\r
- public File fetchDataAsFile(String ids, String f, String s)
\r
+ public File fetchDataAsFile(String ids, String f, String s) throws OutOfMemoryError
\r
{
\r
String[] data = fetchData(ids, f, s);
\r
{
\r
String[] data = fetchData(ids, f, s);
\r
+ // TODO: after JV 2.4 - test data==null and pass error(s) back up if possible (OutOfMemoryErrors are usual problem)
\r
File outFile = null;
\r
try
\r
{
\r
File outFile = null;
\r
try
\r
{
\r
@@
-150,7
+151,7
@@
public class EBIFetchClient
*
\r
* @return Raw string array result of query set
\r
*/
\r
*
\r
* @return Raw string array result of query set
\r
*/
\r
- public String[] fetchData(String ids, String f, String s)
\r
+ public String[] fetchData(String ids, String f, String s) throws OutOfMemoryError
\r
{
\r
// Need to split
\r
// ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
\r
{
\r
// Need to split
\r
// ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
\r
@@
-183,7
+184,7
@@
public class EBIFetchClient
return fetchBatch(querystring.toString(), db, f, s);
\r
}
\r
\r
return fetchBatch(querystring.toString(), db, f, s);
\r
}
\r
\r
- public String[] fetchBatch(String ids, String db, String f, String s)
\r
+ public String[] fetchBatch(String ids, String db, String f, String s) throws OutOfMemoryError
\r
{
\r
// max 50 ids can be added at one time
\r
try
\r
{
\r
// max 50 ids can be added at one time
\r
try
\r
@@
-214,10
+215,12
@@
public class EBIFetchClient
}
\r
catch (OutOfMemoryError er)
\r
{
\r
}
\r
catch (OutOfMemoryError er)
\r
{
\r
+
\r
System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
\r
ids);
\r
System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM " + db + ":\n" +
\r
ids);
\r
+ throw er;
\r
}
\r
}
\r
- return null;
\r
+ // return null;
\r
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r