Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

raprasad · 2014-09-02T14:27:43Z

Author Name: Philip Durbin (@pdurbin)
Original Redmine Issue: 3305, https://redmine.hmdc.harvard.edu/issues/3305
Original Date: 2013-09-16

If you attempt to create a study via SWORD with an Atom entry file that doesn't exist you will see "org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException" from the client side...

murphy:dvn pdurbin$ file atom-entry-study.xml
atom-entry-study.xml: cannot open `atom-entry-study.xml' (No such file or directory)
murphy:dvn pdurbin$ curl --insecure -s --data-binary "@atom-entry-study.xml" -H "Content-Type: application/atom+xml" -u sword:sword https://localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/sword | xmllint -format -
<?xml version="1.0"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
    <title>GlassFish Server Open Source Edition 3.1.2.2 - Error report</title>
    <style type="text/css">
<!--H1 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:22px;} H2 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:16px;} H3 {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;font-size:14px;} BODY {font-family:Tahoma,Arial,sans-serif;color:black;background-color:white;} B {font-family:Tahoma,Arial,sans-serif;color:white;background-color:#525D76;} P {font-family:Tahoma,Arial,sans-serif;background:white;color:black;font-size:12px;}A {color : black;}HR {color : #525D76;}-->
    </style>
  </head>
  <body>
    <h1>HTTP Status 500 - </h1>
    <hr />
    <p><b>type</b> Exception report</p>
    <p>
      <b>message</b>
    </p>
    <p><b>description</b>The server encountered an internal error () that prevented it from fulfilling this request.</p>
    <p>
      <b>exception</b>
      ```org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException

</p>
<p>
  <b>note</b>
  <u>The full stack traces of the exception and its root causes are available in the GlassFish Server Open Source Edition 3.1.2.2 logs.</u>
</p>
<hr />
<h3>GlassFish Server Open Source Edition 3.1.2.2</h3>

murphy:dvn pdurbin$


... and in the Glassfish server.log, this error appears:

[#|2013-09-16T08:19:33.170-0400|WARNING|glassfis###1.2|javax.enterprise.system.container.web.com.sun.enterprise.web|_ThreadID=33;_ThreadName=Thread-4;|StandardWrapperValve[edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet]: PWC1406: Servlet.service() for servlet edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet threw exception
org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException
at org.apache.abdera.parser.stax.FOMParser.parse(FOMParser.java:128)
at org.apache.abdera.util.AbstractParser.parse(AbstractParser.java:65)
at org.swordapp.server.SwordAPIEndpoint.addDepositPropertiesFromEntry(SwordAPIEndpoint.java:334)
at org.swordapp.server.CollectionAPI.post(CollectionAPI.java:156)
at edu.harvard.iq.dvn.core.web.servlet.SWORDv2CollectionServlet.doPost(SWORDv2CollectionServlet.java:37)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:688)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:770)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1550)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:343)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
at com.ocpsoft.pretty.PrettyFilter.doFilter(PrettyFilter.java:115)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:217)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:279)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:161)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:655)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:595)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:328)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:231)
at com.sun.enterprise.v3.services.impl.ContainerMapper$AdapterCallable.call(ContainerMapper.java:317)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:195)
at com.sun.grizzly.http.ProcessorTask.invokeAdapter(ProcessorTask.java:860)
at com.sun.grizzly.http.ProcessorTask.doProcess(ProcessorTask.java:757)
at com.sun.grizzly.http.ProcessorTask.process(ProcessorTask.java:1056)
at com.sun.grizzly.http.DefaultProtocolFilter.execute(DefaultProtocolFilter.java:229)
at com.sun.grizzly.DefaultProtocolChain.executeProtocolFilter(DefaultProtocolChain.java:137)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:104)
at com.sun.grizzly.DefaultProtocolChain.execute(DefaultProtocolChain.java:90)
at com.sun.grizzly.http.HttpProtocolChain.execute(HttpProtocolChain.java:79)
at com.sun.grizzly.ProtocolChainContextTask.doCall(ProtocolChainContextTask.java:54)
at com.sun.grizzly.SelectionKeyContextTask.call(SelectionKeyContextTask.java:59)
at com.sun.grizzly.ContextTask.run(ContextTask.java:71)
at com.sun.grizzly.util.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:532)
at com.sun.grizzly.util.AbstractThreadPool$Worker.run(AbstractThreadPool.java:513)
at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.ArrayIndexOutOfBoundsException
at java.lang.System.arraycopy(Native Method)
at java.io.PushbackInputStream.unread(PushbackInputStream.java:218)
at org.apache.abdera.i18n.text.io.DynamicPushbackInputStream.unread(DynamicPushbackInputStream.java:91)
at org.apache.abdera.i18n.text.io.PeekAheadInputStream.peek(PeekAheadInputStream.java:61)
at org.apache.abdera.i18n.text.io.PeekAheadInputStream.peek(PeekAheadInputStream.java:52)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.detectEncoding(CharsetSniffingInputStream.java:110)
at org.apache.abdera.parser.stax.util.FOMSniffingInputStream.detectEncoding(FOMSniffingInputStream.java:39)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.(CharsetSniffingInputStream.java:81)
at org.apache.abdera.i18n.text.io.CharsetSniffingInputStream.(CharsetSniffingInputStream.java:74)
at org.apache.abdera.parser.stax.util.FOMSniffingInputStream.(FOMSniffingInputStream.java:35)
at org.apache.abdera.parser.stax.FOMParser.parse(FOMParser.java:107)
... 37 more
|#]


org.swordapp.server.SwordAPIEndpoint.addDepositPropertiesFromEntry(SwordAPIEndpoint.java:334) corresponds to https://github.com/IQSS/swordv2-java-server-library/blob/aeaef8342361bf3de7e9fc8f2a979cd742bc31ae/src/main/java/org/swordapp/server/SwordAPIEndpoint.java#L334 which is unmodified from https://github.com/swordapp/JavaServer2.0/blob/master/src/main/java/org/swordapp/server/SwordAPIEndpoint.java#L334

Here is the relevant block of code:

328 protected void addDepositPropertiesFromEntry(Deposit deposit, HttpServletRequest req)
329 throws IOException
330 {
331 InputStream entryPart = req.getInputStream();
332 Abdera abdera = new Abdera();
333 Parser parser = abdera.getParser();
334 Document entryDoc = parser.parse(entryPart);
335 Entry entry = entryDoc.getRoot();
336 deposit.setEntry(entry);
337 }


We should probably start by reporting this on the SWORD mailing list ( https://lists.sourceforge.net/lists/listinfo/sword-app-tech ) or submit another pull request as we did with https://github.com/swordapp/JavaServer2.0/pull/3

The text was updated successfully, but these errors were encountered:

raprasad · 2014-09-02T14:27:44Z

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-07-01T17:59:32Z

This bug still exists in the upstream, though it's in a different place now:

https://github.com/swordapp/JavaServer2.0/blob/sword2-server-1.0/src/main/java/org/swordapp/server/SwordAPIEndpoint.java#L355

Perhaps they should add a try/catch?

  StandardWrapperValve[edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet]: Servlet.service() for servlet edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet threw exception
org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException
    at org.apache.abdera.parser.stax.FOMParser.parse(FOMParser.java:128)
    at org.apache.abdera.util.AbstractParser.parse(AbstractParser.java:65)
    at org.swordapp.server.SwordAPIEndpoint.addDepositPropertiesFromEntry(SwordAPIEndpoint.java:355)
    at org.swordapp.server.CollectionAPI.post(CollectionAPI.java:156)
    at edu.harvard.iq.dataverse.api.datadeposit.SWORDv2CollectionServlet.doPost(SWORDv2CollectionServlet.java:34)

raprasad · 2014-09-02T14:27:44Z

Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-07-01T18:18:16Z

I filed an issue upstream: swordapp/JavaServer2.0#6

pdurbin · 2014-10-21T15:05:26Z

As of 2c1cfd5 this error should be fixed. Rather than a crazy Glassfish exception we get a sane "Unable to parse SWORD entry" message to report back to the user:

$ touch /tmp/empty-file.xml

$ curl --insecure --data-binary @/tmp/empty-file.xml -H 'Content-Type: application/atom+xml' -u pete:pete https://localhost:8181/dvn/api/data-deposit/v1/swordv2/collection/dataverse/peteTop

<?xml version="1.0" encoding="ISO-8859-1"?> <sword:error href="Unable to parse SWORD entry: org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException" xmlns:sword="http://purl.org/net/sword/terms/"><atom:title xmlns:atom="http://www.w3.org/2005/Atom">ERROR</atom:title><atom:updated xmlns:atom="http://www.w3.org/2005/Atom">2014-10-21T10:58:27Z</atom:updated><atom:generator uri="http://www.swordapp.org/" version="2.0" xmlns:atom="http://www.w3.org/2005/Atom"/><sword:treatment>Processing failed</sword:treatment><atom:summary xmlns:atom="http://www.w3.org/2005/Atom">Unable to parse SWORD entry: org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException</atom:summary></sword:error>

Please note that this fix required patching the upstream SWORD library. I have submitted a pull request here:

throw SwordError for unparseable Atom entry swordapp/JavaServer2.0#6 by pdurbin · Pull Request #7 · swordapp/JavaServer2.0 - swordapp/JavaServer2.0#7

If the pull request gets accepted and a new upstream version is released, we should upgrade to it. I left a note about this in our pom.xml:

dataverse/pom.xml

Line 72 in 2c1cfd5

Passing to QA.

esotiri · 2014-10-29T16:12:26Z

Create a study for non-existent atom-entry-study.xml

curl -s --insecure --data-binary "@xml/atom-entry-study-non-exixtent.xml" -H "Content-Type: application/atom+xml" https://$user:$passwd@$host/dvn/api/data-deposit/v1/swordv2/collection/dataverse/$DATAVERSE_ALIAS | xmllint -format -

Below is the sword output:

`

<sword:error xmlns:sword="http://purl.org/net/sword/terms/" href="Unable to parse SWORD entry: org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException">
<atom:title xmlns:atom="http://www.w3.org/2005/Atom">ERROR</atom:title>
<atom:updated xmlns:atom="http://www.w3.org/2005/Atom">2014-10-29T12:08:36Z</atom:updated>
<atom:generator xmlns:atom="http://www.w3.org/2005/Atom" uri="http://www.swordapp.org/" version="2.0"/>
sword:treatmentProcessing failed</sword:treatment>
<atom:summary xmlns:atom="http://www.w3.org/2005/Atom">Unable to parse SWORD entry: org.apache.abdera.parser.ParseException: java.lang.ArrayIndexOutOfBoundsException</atom:summary>
</sword:error>
`

esotiri · 2014-10-29T17:19:06Z

the message above is much better than the crazy glassfish exception, closing the issue.

raprasad added Priority: Medium labels Sep 2, 2014

raprasad added this to the Dataverse 4.0: In Review milestone Sep 2, 2014

eaquigley modified the milestones: Dataverse 4.0: In Review, In Review - Dataverse 4.0, Beta 8 - Dataverse 4.0 Sep 2, 2014

kcondon added the Status: QA label Sep 9, 2014

kcondon removed the Status: QA label Sep 23, 2014

kcondon added this to the In Review - Dataverse 4.0 milestone Sep 23, 2014

pdurbin modified the milestones: Beta 8 - Dataverse 4.0, In Review - Dataverse 4.0 Oct 14, 2014

pdurbin added a commit that referenced this issue Oct 21, 2014

forked SWORD library to handle empty Atom entry #893

2c1cfd5

pdurbin mentioned this issue Oct 21, 2014

throw SwordError for unparseable Atom entry swordapp/JavaServer2.0#6 swordapp/JavaServer2.0#7

Open

pdurbin added Status: QA and removed Status: Design labels Oct 21, 2014

kcondon assigned esotiri Oct 24, 2014

pdurbin mentioned this issue Oct 29, 2014

Expand Data Deposit API to support additional metadata #899

Closed

esotiri closed this as completed Oct 29, 2014

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Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

raprasad commented Sep 2, 2014

raprasad commented Sep 2, 2014

raprasad commented Sep 2, 2014

pdurbin commented Oct 21, 2014

esotiri commented Oct 29, 2014

esotiri commented Oct 29, 2014

Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

Fix Abdera ArrayIndexOutOfBoundsException with non-existent atom-entry-study.xml in SWORD jar (upstream ideally) #893

Comments

raprasad commented Sep 2, 2014

raprasad commented Sep 2, 2014

raprasad commented Sep 2, 2014

pdurbin commented Oct 21, 2014

esotiri commented Oct 29, 2014

esotiri commented Oct 29, 2014