Reference Implementation: Column 15 (score) always empty, tests working?

[Rainer]

Hi everyone,

I was updating/rebuilding our (still local) PSICQUIC reference implementation and came across a few things:

I tried our last running version 1.2.1, latest stable 1.2.3 as well as the 1.2.4 snapshot, but in all cases I get an empty column #15 for the confidence score.
First I used our data, then I tried some basic data and finally some results from the official IntAct service, but in all cases the web service ends up with perfect columns 1-14, but empty score. There are no error messages which point to incorrect formatted data, input is always PSI-MI TAB 2.5.

We already installed the latest java to be sure 1.7.0_21 (1.6 tested as well), use Maven 2.2.1 and deploy the war in Tomcat (which is quite old at ver 5.5). Maven repository was also deleted to be sure.

There are no error message when creating the index, the tests when building the war however gives always the same warnings, which seem to be unrelated to the data. Are these tests functioning correctly?

2013-06-21 15:26:07,774 [main] WARN  (InteractionConverter,569) - The id of the host organism is not a NCBI id
2013-06-21 15:26:07,774 [main] WARN  (InteractionConverter,569) - The id of the host organism is not a NCBI id
2013-06-21 15:26:07,776 [main] WARN  (InteractionConverter,569) - The id of the host organism is not a NCBI id
2013-06-21 15:26:07,776 [main] WARN  (InteractionConverter,569) - The id of the host organism is not a NCBI id
2013-06-21 15:26:07,777 [main] WARN  (InteractionConverter,569) - The id of the host organism is not a NCBI id
2013-06-21 15:26:13,859 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for HTTP://PATHWAYCOMMONS.ORG/PSI2BP#BS--1 [in vitro] (BioSource) , using Taxonomy:-1. java.lang.IllegalArgumentException: ID pattern mismatch. db=Taxonomy, id=-1, regexp: ^\d+$.
2013-06-21 15:26:13,863 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for unspecified (IntAct:EBI-1639686) (Provenance) , using null:null. java.lang.NullPointerException.
2013-06-21 15:26:13,863 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for unspecified (IntAct:EBI-446104) (Provenance) , using null:null. java.lang.NullPointerException.
2013-06-21 15:26:13,864 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for unspecified (IntAct:EBI-297231) (Provenance) , using null:null. java.lang.NullPointerException.
2013-06-21 15:26:13,864 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for unspecified (IntAct:EBI-1639830) (Provenance) , using null:null. java.lang.NullPointerException.
2013-06-21 15:26:13,865 [main] ERROR (Normalizer,301) - Cannot get a Miriam standard ID for unspecified (IntAct:EBI-1962663) (Provenance) , using null:null. java.lang.NullPointerException.
Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.001 sec

I tried to rule out Tomcat (there are no errors in its logs btw), but the in-build Jetty throws a ClassNotFoundError for the ContextLoaderListener of the spring framework:

2013-06-21 15:47:59.094:WARN:oejw.StandardDescriptorProcessor:Could not instantiate listener org.springframework.web.context.ContextLoaderListener
java.lang.ClassNotFoundException: org.springframework.web.context.ContextLoaderListener

I have to check that next week or use a standalone jetty, but wanted to finish this post first. Maybe it rings a bell? It would be great if someone could set up a reference implementation with some basic data to check if the problem is on our side.

Thanks a lot for your work on PSICQUIC, greatly appreciated!
Have a nice weekend,
Rainer

[Marine Dumousseau]

Hello Rainer,

Could you send me the MITAB file you try to index and the logs when you index your mitab file?

Cheers,

Marine

---

From: Rainer <raine...@gmail.com>
To: psic...@googlegroups.com
Sent: Friday, June 21, 2013 5:07 PM
Subject: [psicquic] Reference Implementation: Column 15 (score) always empty, tests working?

--
--
You received this message because you are subscribed to the Google
Groups PSICQUIC group.
To post to this group, send email to psic...@googlegroups.com
To unsubscribe from this group, send email to
psicquic+u...@googlegroups.com
 
http://psicquic.googlecode.com
---
You received this message because you are subscribed to the Google Groups "psicquic" group.
To unsubscribe from this group and stop receiving emails from it, send an email to psicquic+u...@googlegroups.com.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

[Rainer]

Hi Marine,

thanks for your reply! I repeated everything using the latest snapshot with Java 1.7+Jetty9 on my working PC and got the same results.

I don't get much from the indexing process, the output is posted below.
This time I used an unmodified PSI-MI TAB 2.5 output directly from IntAct, using the first 10 results from the query cbx1:
http://www.ebi.ac.uk/Tools/webservices/psicquic/intact/webservices/current/search/query/cbx1?firstResult=0&maxResults=10&format=tab25

The input data is attached as a file, it would mess up the formatting of this mail.

Thanks again,
Rainer

PS: The index log:

>mvn clean compile -P createIndex -D psicquic.index=/home/gtadmin/IntAct/psicquic_index/cbx1_10/ -D mitabFile=/home/gtadmin/IntAct/psicquic_index/cbx1_10.txt -D hasHeader=true
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Building PSI :: PSICQUIC WS Reference Implementation
[INFO]    task-segment: [clean, compile]
[INFO] ------------------------------------------------------------------------
[INFO] [clean:clean {execution: default-clean}]
[INFO] Deleting directory /home/gtadmin/IntAct/workspace2/psicquic-trunk/psicquic-webservice/target
[WARNING] While downloading org.codehaus.woodstox:wstx-asl:4.0.6
  This artifact has been relocated to org.codehaus.woodstox:woodstox-core-asl:4.0.6.


[INFO] [cxf-codegen:wsdl2java {execution: generate-sources}]
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default frontend jaxws
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default frontend jaxws21
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default databinding source
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default databinding domsource
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default databinding staxsource
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default databinding saxsource
Jun 28, 2013 7:51:44 PM org.apache.cxf.tools.wsdlto.core.PluginLoader loadPlugin
INFO: Replaced default databinding jaxb
[debug] execute contextualize
[INFO] [resources:resources {execution: default-resources}]
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 3 resources
[INFO] [compiler:compile {execution: default-compile}]
[INFO] Compiling 101 source files to /home/gtadmin/IntAct/workspace2/psicquic-trunk/psicquic-webservice/target/classes
[INFO] [exec:exec {execution: default}]
Creating index: /home/gtadmin/IntAct/psicquic_index/cbx1_10/ from file: /home/gtadmin/IntAct/psicquic_index/cbx1_10.txt
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESSFUL
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 11 seconds
[INFO] Finished at: Fri Jun 28 19:51:51 CEST 2013
[INFO] Final Memory: 73M/859M
[INFO] ------------------------------------------------------------------------

[Marine Dumousseau]

Hello Rainer,

It was indeed a bug in the version 1.2.3 of psicquic LUCENE. I fixed the bug and redeployed a new version 1.2.4 that you can use now.

I would also recommend you to have a look at the SOLR PSICQUIC implementation which can index MITAB 2.5, 2.6 and 2.7 (http://code.google.com/p/psicquic/wiki/HowToInstallPsicquicSolr)

Thanks for reporting the issue,

Cheers,

Marine

---

From: Rainer <raine...@gmail.com>
To: psic...@googlegroups.com

Cc: Marine Dumousseau <mdumo...@yahoo.com>
Sent: Friday, June 28, 2013 7:01 PM
Subject: Re: [psicquic] Reference Implementation: Column 15 (score) always empty, tests working?