Reported from a user:

I just recently started to work with cytoscape and realized that BridgeDB eases my work a lot!
However, what puzzled me was the fact that quite a lot of IDs in my network could not be matched properly.
The BioGRID networks I am using use the gene/protein symbol as identifiers, however, all my files are based on EnsemblIDs.
So I now compared the matched IDs from BridgeDB (symbol->Ensembl) with a matched list from ensembl/biomart.
Apparently, there were quite a lot of IDs that could not be matched by BridgeDB (~250 out of 8000). Even worse, unfortunately, a lot of IDs were matched wrongly.
I figured out that in almost all cases were the IDs were matched incorrectly, the matched EnsemblID actually refers to another gene with almost similar symbols.
I.e. "Abp1" was matched to the Enseml of "Napb1",
"Cno" to the one of "Cnot11",
"Rod" to Neurod1" and so on.
All of them are no synonyms to each other, so I suppose it might be an error in the actual matchin procedure or the bridgedb database itself.
Is this already known?

After performing a mapping, a dialog asks if the user would like to perform another mapping. If you select yes, the interface should update the list of Key Attributes to include the one from the previous mapping. Otherwise, the user needs to close and reopen the interface to access this new column.

Now a have tring to fix a bug about select a mapping database file from loacl file system .

This method is a ActionEvent handle method to process the select button click event

This is the code :

/**
     * handle the click action of select button <br>
     * 2013-9-23:下午1:27:17<br>
     * <br>
     * 
     * @param evt event handle
     */
    private void pgdbButtonActionPerformed(ActionEvent evt) {// GEN-FIRST:event_pgdbButtonActionPerformed
        // In CyToscape 3.x FileUtil is a Interface with non of implementation class 
        // Reading the CyToscape 3.x javaDocs, I have found some docs about this interface
        // the link is : http://chianti.ucsd.edu/cytoscape-3.0.1/API/org/cytoscape/util/swing/FileUtil.html

        // Now I have 2 questions:
        // 0.Do we have to use FileUtil interface to load a file, and where is the impl class or maybe some example
        // 1.Could we use another way to handle this problem

        // using the util provide by CyToscape to load a file from file system  
        File source = FileUtil.getFile(
                "Select a BridgeDb file",       // friendly information 
                FileUtil.LOAD,                              // load strategy 
                new CyFileFilter[] { 
                        new CyFileFilter(                   // file filter, just allow bridge file and pgdb file 
                        new String[] { "bridge", "pgdb" }, "BridgeDb Derby file") });
        //check if there has null arguments 
        if (source == null) {
            return;
        }

        //      this is the impl of CyFileFilter in CyToscape 3.x 
        //      CyFileFilter fileFilter = new BasicCyFileFilter(extensions, contentTypes, description, category, streamUtil);
        //      CyFileFilter fileFilter = new BasicCyFileFilter(extensions, contentTypes, description, category, streamUtil);

        pgdbTextField.setText(source.getPath());
    }// GEN-LAST:event_pgdbButtonActionPerformed

allow user to select to override an existing attribute

load file not responding

Bad parameters in the dialog leads to a case that an exception is thrown for every node in the network.

org.bridgedb.IDMapperException: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
    at org.bridgedb.webservice.bridgerest.BridgeRest$RestCapabilities.isMappingSupported(BridgeRest.java:181)
    at org.bridgedb.cytoscape.internal.IDMapperClientManager$2.run(IDMapperClientManager.java:627)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
    at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.openReader(BridgeRest.java:273)
    at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.access$200(BridgeRest.java:197)
    at org.bridgedb.webservice.bridgerest.BridgeRest$RestCapabilities.isMappingSupported(BridgeRest.java:172)

Also in the ID Mapping Resource Config, in the Base URL drop-down for
BridegDb services, there's webservice.bridgedb.org/null listed multiple
times. Maybe this is a problem with bridgedb, but it might be a good idea to
check before adding urls to the list.

Doesn't seem like you're checking for the user canceling an operation. This can be really bad, forcing the user to do a force quit...

The problem is that it
is really the ID mapping step that takes the longest time and I cannot
control the internal workflow of BridgeDb. I am thinking of sending
source IDs in small batch (say 100 IDs per time) so that I can
interrupt every 100 IDs. Or maybe I can start a new thread for
BridgeDb mapping and whenever user cancels I kill the thread. Let me
play with them.

Consider the following entries:

shared name name GeneID HEKScore JurkatScore protein Name Gene Symbol Gene Synonyms
O15258 O15258 11079 0.0 0.753 RER1_HUMAN Protein RER1 RER1 -
28872818 28872818 0.989 0.967 NP_057857 NefFull_HIV-1 - -
NEF NEF

The first row is a Uniprot ID, the second is a GI number, and the third is just a label. So I figured for illustrative purposes (since I can't map from GI to Uniprot) I would map from Uniprot to a new gene symbol column. If I use the web service (http://webservice.bridgedb.org/Human/attributes/S/O15258?attributeName=Symbol), I get:

Description Protein RER1
Synonyms O95322
Symbol RER1_HUMAN
Type Uniprot/SWISSPROT

OK, good. If I use the BridgeDB app, it tells me that no IDs were mapped. I also see lots of errors in the console:

org.bridgedb.IDMapperException: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
at org.bridgedb.webservice.bridgerest.BridgeRest.getAttributes(BridgeRest.java:466)
at org.bridgedb.IDMapperStack.getAttributes(IDMapperStack.java:338)
at org.bridgedb.cytoscape.internal.util.IDMapperWrapper.mapID(IDMapperWrapper.java:155)

at org.bridgedb.cytoscape.internal.AttributeBasedIDMappingImpl.map(AttributeBasedIDMappingImpl.java:111)
at org.bridgedb.cytoscape.internal.task.AttributeBasedIDMappingTask.run(AttributeBasedIDMappingTask.java:109)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)

Caused by: java.io.IOException: HTTP response: 404 - The server has not found anything matching the request URI
at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.openReader(BridgeRest.java:273)
at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.access$200(BridgeRest.java:197)
at org.bridgedb.webservice.bridgerest.BridgeRest.getAttributes(BridgeRest.java:454)
... 11 more

I assume that a lot of those are because of the non-matchable attributes (label and GI#), but it looks to me like every entry is getting that error. Any ideas?

In ID Mapping Resource Config, with BioMart set as the type, the second
drop-down, for Mart/Database, is too wide (presumably because of one really
long entry), so it gets cutoff. See attached.

to solve the problem when there is no current network.

I could get GI using Synergizer, but I keep getting a backtrace:
java.lang.NullPointerException
at org.cytoscape.filter.internal.column.ColumnFilter.accepts(ColumnFilter.java:190)
at org.cytoscape.filter.internal.column.ColumnFilter.accepts(ColumnFilter.java:24)
at org.cytoscape.filter.internal.composite.CompositeFilterImpl.accepts(CompositeFilterImpl.java:106)
at org.cytoscape.filter.internal.view.FilterWorker.doWork(FilterWorker.java:62)
at org.cytoscape.filter.internal.view.LazyWorkQueue$1.run(LazyWorkQueue.java:35)
at java.lang.Thread.run(Thread.java:744)
java.lang.NullPointerException
at org.cytoscape.filter.internal.column.ColumnFilter.accepts(ColumnFilter.java:190)
at org.cytoscape.filter.internal.column.ColumnFilter.accepts(ColumnFilter.java:24)
at org.cytoscape.filter.internal.composite.CompositeFilterImpl.accepts(CompositeFilterImpl.java:106)
at org.cytoscape.filter.internal.view.FilterWorker.doWork(FilterWorker.java:62)
at org.cytoscape.filter.internal.view.LazyWorkQueue$1.run(LazyWorkQueue.java:35)
at java.lang.Thread.run(Thread.java:744)
java.lang.NullPointerException
at java.net.URLEncoder.encode(URLEncoder.java:205)
at org.bridgedb.webservice.bridgerest.BridgeRest$UrlBuilder.named(BridgeRest.java:255)
at org.bridgedb.webservice.bridgerest.BridgeRest.mapID(BridgeRest.java:346)
at org.bridgedb.impl.InternalUtils.mapMultiFromSingle(InternalUtils.java:69)
at org.bridgedb.webservice.bridgerest.BridgeRest.mapID(BridgeRest.java:331)
at org.bridgedb.IDMapperStack.mapIDnormal(IDMapperStack.java:294)
at org.bridgedb.IDMapperStack.mapID(IDMapperStack.java:274)
at org.bridgedb.cytoscape.internal.util.IDMapperWrapper.mapID(IDMapperWrapper.java:117)
at org.bridgedb.cytoscape.internal.AttributeBasedIDMappingImpl.map(AttributeBasedIDMappingImpl.java:111)
at org.bridgedb.cytoscape.internal.task.AttributeBasedIDMappingTask.run(AttributeBasedIDMappingTask.java:109)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.innerRun(JDialogTaskManager.java:321)
at org.cytoscape.work.internal.task.JDialogTaskManager$TaskRunnable.run(JDialogTaskManager.java:350)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:744)
Task-Thread-21-Factory-0x2c0ea67 ERROR [TaskMonitor.org.bridgedb.cytoscape.internal.task.AttributeBasedIDMappingTask] - No IDs were mapped. Please make sure you seleceted the corrected ID mapping resources and source ID types.

It would be really helpful if the URLs for the various bridge DB services were alphabetized.