extend mRNA causes 500 error about apollo

Nothing is printed onto catalina.out
But following is the exception thrown when a 500 error is produced upon trying to extend mRNA.

24/09/2014 1:58:16 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet [org.bbop.apollo.web.AnnotationEditorService] in context with path [/myGenome] threw exception
java.lang.NullPointerException
    at org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3907)
    at org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3903)
    at org.bbop.apollo.web.AnnotationEditorService.setExonBoundaries(AnnotationEditorService.java:2600)
    at org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:558)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
    at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
    at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
    at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
    at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
    at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:307)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
    at java.lang.Thread.run(Thread.java:701)

[nathandunn]

It is most likely that you might have an orphaned feature. The exon does not have a transcript, which causes a null-pointer later. Its possible that you have a bad CVTerm file, but if everything else is working fine, it is unlikely.

        Transcript transcript = exon.getTranscript();
        Transcript oldTranscript = cloneTranscript(transcript);

In the tools folder, there is a remove_orphan_features.sh script, which should fix this.

./tools/data/remove_orphan_features.sh
Missing -w <webapollo_installation_dir> or $WEBAPOLLO_DIR environment variable

[nathandunn]

This is for the WebApollo-2014-04-03 release (the most recent one).

[nathandunn]

Let us know if this works or not or if you need help with it.

Hello Nathan,

I am trying to replicate the issue on a total new instance. But this time
trying to get rid of orphan features as you said that might be causing the
problem. As Colin pointed out the GFF files should have gene -> transcript
-> CDS/exon, which in my case it is not so. So I am adding a transcript
layer into my GFF file and at the same time making it more agreeable with
SOFA. So doing a bit of manual curation on the GFF it self. So this is why
it is taking a bit time.

Sorry for not replying sooner. I was waiting till I got the new instance up
and running... but the manual curation is taking a bit longer than I
expected.

Will let you know as soon as the new instance is up and running (today or
tomorrow.).

Cheers,
Asela

On Tue, Sep 30, 2014 at 10:09 AM, Nathan Dunn [email protected]
wrote:

Let us know if this works or not or if you need help with it.

—
Reply to this email directly or view it on GitHub
#27 (comment).

I managed to replicate the error using published data on* WebApollo Release
04-03-14*. The steps I carried out are as follows...

1. Downloaded genbank and FASTA files of accession number - NC_022592.1
2. Converted genbank to GFF3 using Bioperl - genbank2gff3.pl

This produced a GFF file with the structure of gene --> mRNA --> CDS -->
exon for each gene.

3. Carried out instructions on the "Webapollo Installation
   http://www.gmod.org/wiki/WebApollo_Installation" of which the last step
   was...

bin/flatfile-to-json.pl --gff NC_022592.gff --getSubfeatures --type gene
--trackLabel GenBank --urltemplate "http://host/gene_cards/search.php"

I still get the follwoing error when I try to extend a mRNA in the 5' -->
3' direction. But no such error when trying to extend an mRNA in 3' --> 5'
direction. As mentioned earlier after fliping the strand back and forth I
can extend the mRNA in the 5' --> 3' direction.

2/10/2014 4:52:48 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet
[org.bbop.apollo.web.AnnotationEditorService] in context with path [/test]
threw exception
java.lang.NullPointerException
at
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3907)
at
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3903)
at
org.bbop.apollo.web.AnnotationEditorService.setExonBoundaries(AnnotationEditorService.java:2600)
at
org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:558)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
at
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)

Further I am trying to link each gene to a genecard. Therefore I used
the *--urltemplate
"http://host/gene_cards/search.php http://host/gene_cards/search.php" *flag.
But nothing happens when I click on a feature. The following error is
printed in some instances.

GET
/test/AnnotationChangeNotificationService?track=Annotations-DSM10061&dojo.preventCache=1412222120557
HTTP/1.1" 504 5

I am certain that I am doing something very small and foolish with regard
to the URL issue... But pointing in the right direction would be greatly
appreciated.

Cheers,
Asela

On Tue, Sep 30, 2014 at 11:51 AM, Asela Dassanayake <
[email protected]> wrote:

Hello Nathan,

I am trying to replicate the issue on a total new instance. But this time
trying to get rid of orphan features as you said that might be causing the
problem. As Colin pointed out the GFF files should have gene -> transcript
-> CDS/exon, which in my case it is not so. So I am adding a transcript
layer into my GFF file and at the same time making it more agreeable with
SOFA. So doing a bit of manual curation on the GFF it self. So this is why
it is taking a bit time.

Sorry for not replying sooner. I was waiting till I got the new instance
up and running... but the manual curation is taking a bit longer than I
expected.

Will let you know as soon as the new instance is up and running (today or
tomorrow.).

Cheers,
Asela

On Tue, Sep 30, 2014 at 10:09 AM, Nathan Dunn [email protected]
wrote:

Let us know if this works or not or if you need help with it.

—
Reply to this email directly or view it on GitHub
#27 (comment).

[nathandunn]

Notes from Asela:

I managed to replicate the error using published data on* WebApollo Release
04-03-14*. The steps I carried out are as follows...

1. Downloaded genbank and FASTA files of accession number - NC_022592.1
2. Converted genbank to GFF3 using Bioperl - genbank2gff3.pl

This produced a GFF file with the structure of gene --> mRNA --> CDS --> exon for each gene.

3. Carried out instructions on the "Webapollo Installation http://www.gmod.org/wiki/WebApollo_Installation" of which the last step was...

bin/flatfile-to-json.pl --gff NC_022592.gff --getSubfeatures --type gene --trackLabel GenBank --urltemplate "http://host/gene_cards/search.php" 

I still get the follwoing error when I try to extend a mRNA in the 5' -->
3' direction. But no such error when trying to extend an mRNA in 3' --> 5'
direction. As mentioned earlier after fliping the strand back and forth I
can extend the mRNA in the 5' --> 3' direction.

2/10/2014 4:52:48 PM org.apache.catalina.core.StandardWrapperValve invoke 
SEVERE: Servlet.service() for servlet 
[org.bbop.apollo.web.AnnotationEditorService] in context with path [/test] 
threw exception 
java.lang.NullPointerException at  
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3907) at  
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3903) at  
org.bbop.apollo.web.AnnotationEditorService.setExonBoundaries(AnnotationEditorService.java:2600) at  
org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:558) at  
javax.servlet.http.HttpServlet.service(HttpServlet.java:641) at javax.servlet.http.HttpServlet.service(HttpServlet.java:722) at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305) at  
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81) 
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129) at  
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) at  
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) at  
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224) at  
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169) at  
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) at  
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168) at  
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98) at  
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927) at  
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) at  
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) at  
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987) at  
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579) at  
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309) at  
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146) at  
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at  
java.lang.Thread.run(Thread.java:701) 

Further I am trying to link each gene to a genecard. Therefore I used
the *--urltemplate
"http://host/gene_cards/search.php http://host/gene_cards/search.php" *flag.
But nothing happens when I click on a feature. The following error is
printed in some instances.

GET /test/AnnotationChangeNotificationService?track=Annotations-DSM10061&dojo.preventCache=1412222120557 HTTP/1.1" 504 5 

I am certain that I am doing something very small and foolish with regard
to the URL issue... But pointing in the right direction would be greatly
appreciated.

Cheers,
Asela

[nathandunn]

I’ve added these notes to the bug. I will try to reproduce this under the current code base.

Nathan

On Oct 1, 2014, at 9:05 PM, aselawsd [email protected] wrote:

I managed to replicate the error using published data on* WebApollo Release
04-03-14*. The steps I carried out are as follows...

1. Downloaded genbank and FASTA files of accession number - NC_022592.1
2. Converted genbank to GFF3 using Bioperl - genbank2gff3.pl

This produced a GFF file with the structure of gene --> mRNA --> CDS -->
exon for each gene.

3. Carried out instructions on the "Webapollo Installation
   http://www.gmod.org/wiki/WebApollo_Installation" of which the last step
   was...

bin/flatfile-to-json.pl --gff NC_022592.gff --getSubfeatures --type gene
--trackLabel GenBank --urltemplate "http://host/gene_cards/search.php"

I still get the follwoing error when I try to extend a mRNA in the 5' -->
3' direction. But no such error when trying to extend an mRNA in 3' --> 5'
direction. As mentioned earlier after fliping the strand back and forth I
can extend the mRNA in the 5' --> 3' direction.

2/10/2014 4:52:48 PM org.apache.catalina.core.StandardWrapperValve invoke
SEVERE: Servlet.service() for servlet
[org.bbop.apollo.web.AnnotationEditorService] in context with path [/test]
threw exception
java.lang.NullPointerException
at
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3907)
at
org.bbop.apollo.web.AnnotationEditorService.cloneTranscript(AnnotationEditorService.java:3903)
at
org.bbop.apollo.web.AnnotationEditorService.setExonBoundaries(AnnotationEditorService.java:2600)
at
org.bbop.apollo.web.AnnotationEditorService.doPost(AnnotationEditorService.java:558)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:641)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.mortbay.servlet.UserAgentFilter.doFilter(UserAgentFilter.java:81)
at org.mortbay.servlet.GzipFilter.doFilter(GzipFilter.java:129)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:224)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:169)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:987)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:579)
at
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:309)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)

Further I am trying to link each gene to a genecard. Therefore I used
the *--urltemplate
"http://host/gene_cards/search.php http://host/gene_cards/search.php" *flag.
But nothing happens when I click on a feature. The following error is
printed in some instances.

GET
/test/AnnotationChangeNotificationService?track=Annotations-DSM10061&dojo.preventCache=1412222120557
HTTP/1.1" 504 5

I am certain that I am doing something very small and foolish with regard
to the URL issue... But pointing in the right direction would be greatly
appreciated.

Cheers,
Asela

On Tue, Sep 30, 2014 at 11:51 AM, Asela Dassanayake <
[email protected]> wrote:

Hello Nathan,

I am trying to replicate the issue on a total new instance. But this time
trying to get rid of orphan features as you said that might be causing the
problem. As Colin pointed out the GFF files should have gene -> transcript
-> CDS/exon, which in my case it is not so. So I am adding a transcript
layer into my GFF file and at the same time making it more agreeable with
SOFA. So doing a bit of manual curation on the GFF it self. So this is why
it is taking a bit time.

Sorry for not replying sooner. I was waiting till I got the new instance
up and running... but the manual curation is taking a bit longer than I
expected.

Will let you know as soon as the new instance is up and running (today or
tomorrow.).

Cheers,
Asela

On Tue, Sep 30, 2014 at 10:09 AM, Nathan Dunn [email protected]
wrote:

Let us know if this works or not or if you need help with it.

—
Reply to this email directly or view it on GitHub
#27 (comment).

—
Reply to this email directly or view it on GitHub.

[cmdcolin]

This may be unreleated but this step for loading tracks might need changing:

bin/flatfile-to-json.pl --gff NC_022592.gff --getSubfeatures --type gene --trackLabel GenBank --urltemplate "http://host/gene_cards/search.php" 

Generally we load the mRNA level or transcript level of the features. Therefore, we would use

bin/flatfile-to-json.pl --gff NC_022592.gff --getSubfeatures --type mRNA --trackLabel GenBank --urltemplate "http://host/gene_cards/search.php" 

Again this might be unrelated, but it can actually cause database corruption to import the wrong type of features into the database.

[nathandunn]

fixed in 2.0.0?

[monicacecilia]

@nathandunn I have been testing this on 2.0 and [happily] I have not been able to reproduce it. For now I am closing this issue and if it reappears on 2.0, we'll address it again.