Ticket #612 (closed defect: worksforme)

Opened 1 year ago

Last modified 6 months ago

annotated.groovy - fedora 500 error when trying to grab annotation count for pctr article

Reported by: russ Assigned to: ebrown
Priority: high Milestone:
Component: topaz-fedora Version: 0.8
Keywords: Cc:
Blocking: Blocked By:

Description

i annotated the one pctr article i've ingested and then ran annotated.groovy to make sure it would pick up annotations on pctr articles.

i got a fedora 500 error on the pctr article only: 

[root@topaz-dev topaz]# http://clinicaltrials-dev.plos.org/article/info%3Adoi%2F10.1371%2Fjournal.pctr.0010002
[root@topaz-dev topaz]# bin/rungroovy scripts/annotated.groovy -F fedora-dev.localdomain:9090 -M mulgara-dev.localdomain:9091
info:doi/10.1371/journal.pone.0000012   The Effectiveness of Contact Tracing in Emerging Epidemics      d.klinkenberg@vet.uu.nl 3.0
info:doi/10.1371/journal.pone.0000002   Allometric Scaling of the Active Hematopoietic Stem Cell Pool across Mammals    dingli@fas.harvard.edu     1.0
info:doi/10.1371/journal.pone.0000030   Triose Phosphate Isomerase Deficiency Is Caused by Altered DimerizationâNot Catalytic Inactivityâof the Mutant Enzymes     krobitsc@molgen.mpg.de  1.0
info:doi/10.1371/journal.pone.0000120   Cooperation between Engulfment Receptors: The Case of ABCA1 and MEGF10  chimini@ciml.univ-mrs.fr   2.0
info:doi/10.1371/journal.pone.0000004   Expression of Transgenes Targeted to the Gt(ROSA)26Sor Locus Is Orientation Dependent   ds10@sanger.ac.uk  1.0
info:doi/10.1371/journal.pone.0000008   Molecular Adaptation during Adaptive Radiation in the Hawaiian Endemic Genus Schiedea   D.Filatov@bham.ac.uk       1.0
info:doi/10.1371/journal.pone.0000263   Protein Buffering in Model Systems and in Whole Human Saliva    lamanda3@hotmail.com    13.0
info:doi/10.1371/journal.pone.0000258   Urban Physiology: City Ants Possess High Heat Tolerance mangilletta@indstate.edu        14.0
info:doi/10.1371/journal.pone.0000259   A Rapid Sound-Action Association Effect in Human Insular Cortex tonio.ball@uniklinik-freiburg.de   1.0
info:doi/10.1371/journal.pone.0000056   A Low Protein Diet Increases the Hypoxic Tolerance in Drosophila        cfrelin@unice.fr  1.0
info:doi/10.1371/journal.pone.0000144   Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processesdbeard@mcw.edu  3.0
info:doi/10.1371/journal.pone.0000339   Deductive Biocomputing  jshrager@stanford.edu   1.0
info:doi/10.1371/journal.pone.0000345   Compartmental Architecture and Dynamics of Hematopoiesis        dingli.david@mayo.edu   1.0
info:doi/10.1371/journal.pone.0000282   Theory versus Data: How to Calculate R 0 ?      sblower@mednet.ucla.edu 2.0
info:doi/10.1371/journal.pone.0000308   Sharing Detailed Research Data Is Associated with Increased Citation Rate       hpiwowar@cbmi.pitt.edu     1.0
info:doi/10.1371/journal.pone.0000000   PLoS ONE Sandbox: A Place to Learn and Play     webmaster@plos.org      17.0
info:doi/10.1371/journal.pone.0000490   Experimental Selection for Drosophila Survival in Extremely Low O 2 Environment ghaddad@ucsd.edu, kpwhite@uchicago.edu     3.0
info:doi/10.1371/journal.pone.0000448   LRP1 Functions as an Atheroprotective Integrator of TGFβ and PDGF Signals in the Vascular Wall: Implications for Marfan Syndrome  joachim.herz@utsouthwestern.edu 2.0
info:doi/10.1371/journal.pone.0000527   Human Muscle Satellite Cells as Targets of Chikungunya Virus Infection  ceccaldi@pasteur.fr9.0
Exception in thread "main" java.io.IOException: Server returned HTTP response code: 500 for URL: http://fedora-dev.localdomain:9090/fedora/get/doi:10.1371%2Fjournal.pctr.0010001/XML
        at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1153)
        at java.net.URLConnection.getContent(URLConnection.java:682)
        at java.net.URL.getContent(URL.java:1021)
        at sun.reflect.GeneratedMethodAccessor14.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at org.codehaus.groovy.runtime.Invoker.invokePojoMethod(Invoker.java:104)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:77)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:158)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethod0(ScriptBytecodeAdapter.java:182)
        at annotated$_run_closure1.doCall(annotated.groovy:109)
        at sun.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at groovy.lang.Closure.call(Closure.java:174)
        at groovy.lang.Closure.call(Closure.java:187)
        at org.codehaus.groovy.runtime.DefaultGroovyMethods.each(DefaultGroovyMethods.java:823)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.NewInstanceMetaMethod.invoke(NewInstanceMetaMethod.java:90)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at groovy.lang.DelegatingMetaClass.invokeMethod(DelegatingMetaClass.java:125)
        at org.codehaus.groovy.runtime.Invoker.invokePogoMethod(Invoker.java:115)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:81)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:158)
        at annotated.run(annotated.groovy:102)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at org.codehaus.groovy.runtime.Invoker.invokePogoMethod(Invoker.java:115)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:81)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:380)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:688)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:71)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:158)
        at annotated.main(annotated.groovy)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:688)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:71)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at groovy.lang.GroovyShell.runMainOrTestOrRunnable(GroovyShell.java:240)
        at groovy.lang.GroovyShell.run(GroovyShell.java:214)
        at groovy.lang.GroovyShell.run(GroovyShell.java:143)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at org.codehaus.groovy.runtime.Invoker.invokePogoMethod(Invoker.java:115)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:81)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:158)
        at RunGroovy.run(RunGroovy.groovy:31)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:583)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:476)
        at org.codehaus.groovy.runtime.Invoker.invokePogoMethod(Invoker.java:115)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:81)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.InvokerHelper.runScript(InvokerHelper.java:380)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:585)
        at org.codehaus.groovy.runtime.metaclass.ReflectionMetaMethod.invoke(ReflectionMetaMethod.java:52)
        at org.codehaus.groovy.runtime.MetaClassHelper.doMethodInvoke(MetaClassHelper.java:714)
        at groovy.lang.MetaClassImpl.invokeStaticMethod(MetaClassImpl.java:688)
        at org.codehaus.groovy.runtime.Invoker.invokeMethod(Invoker.java:71)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:85)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:158)
        at RunGroovy.main(RunGroovy.groovy)

Dependency Graph

Change History

08/24/07 16:20:59 changed by russ

  • owner changed from pradeep to amit.
  • priority changed from unassigned to high.
  • version set to 0.8.
  • component changed from topaz to fedora.

08/24/07 16:21:10 changed by russ

  • owner changed from amit to ebrown.

08/24/07 17:12:48 changed by ebrown

  • status changed from new to assigned.

This is pretty straight forward. Just a change to the way the annotated.groovy script computes the fedora URL for the article.

In fact, in 0.8, I'm pretty sure we can stop talking to fedora at all and get all relevant information from mulgara.... Bugger... we're not migrating the right information yet! I'll look into that too and open another ticket if necessary.

08/25/07 18:18:03 changed by amit

  • milestone set to 0.8.

08/27/07 00:12:28 changed by ebrown

  • status changed from assigned to closed.
  • resolution set to worksforme.

Russ, You're having trouble with article pctr.0010001. But I'm unable to ingest that article with the latest code. I was able to ingest pctr.0020028 so I'm not really sure what's going on.

The annotated.groovy script ran fine with with pctr.0020028. It got valid XML for the fedora url http://luna.topazproject.org:9090/fedora/get/doi:10.1371%2Fjournal.pctr.0020028/XML.

I suspect that the real problem is that pctr.0010001 was only partially ingested. There are probably records for it in mulgara, but not fedora. Probably the older code that was used to ingest pctr.0010001 errored differently than the latest code which refuses to even start to ingest pctr.0010001.

To confirm, get the list of articles from fedora via:

$FEDORA_HOME/client/bin/fedora-find localhost 9090 pid '?' http | grep pid | grep '.[0-9]*$' | awk '{print $2}' | grep -P 'journal.*.[0-9]{7}$'

Get the number of articles from mulgara via:

select $s from <local:///topazproject#ri> where $s <rdf:type> <topaz:Article>;

Opened #614 to track issue of un-migrated data. For now, continuing to pull information out of fedora should work fine.

07/16/08 11:00:34 changed by

  • milestone deleted.

Milestone 0.8 deleted