[phenotips-users] PhenoTips 1.2 installatio, ontology not indexed

Shen, Lishuang lishen at chla.usc.edu
Thu Nov 5 17:02:48 EST 2015


Actually, I had them already.

ls -la /var/lib/phenotips/solr/*
-rwxr-xr-x. 1 tomcat tomcat     26901 Nov  3 18:28 /var/lib/phenotips/solr/phenotips-authorization-1.2.jar
-rw-r--r--. 1 tomcat tomcat      2250 Nov  3 18:28 /var/lib/phenotips/solr/phenotips-authorization-1.2.pom
-rwxr-xr-x. 1 tomcat tomcat 222261865 Nov  3 18:23 /var/lib/phenotips/solr/solr-configuration-1.2.jar
-rw-r--r--. 1 tomcat tomcat      1483 Nov  4 13:26 /var/lib/phenotips/solr/solr-configuration-1.2.pom
-rwxr-xr-x. 1 tomcat tomcat 222261865 Nov  4 13:24 /var/lib/phenotips/solr/solr-configuration.jar
-rw-r--r--. 1 tomcat tomcat      1483 Nov  4 13:27 /var/lib/phenotips/solr/solr-configuration.pom
-rw-r--r--. 1 tomcat tomcat       830 Aug 25 15:17 /var/lib/phenotips/solr/solr.xml

/var/lib/phenotips/solr/lib:
total 8
drwxrwxrwx. 2 tomcat tomcat 4096 Aug 26 08:09 .
drwxrwxr-x. 3 tomcat tomcat 4096 Nov  4 17:08 ..










________________________________
From: users-bounces at phenotips.org [users-bounces at phenotips.org] on behalf of Sergiu Dumitriu [sergiu.dumitriu at gmail.com]
Sent: Thursday, November 05, 2015 1:44 PM
To: PhenoTips users
Cc: PhenoTips development
Subject: Re: [phenotips-users] PhenoTips 1.2 installatio, ontology not indexed


There's this step as well: https://phenotips.org/AdminGuide/Installation+on+Tomcat+and+MySQL#HInstallingtheontologydata

On Nov 5, 2015 3:21 PM, "Shen, Lishuang" <lishen at chla.usc.edu<mailto:lishen at chla.usc.edu>> wrote:
Hello:

I wonder anyone installed the war version of new release (the standalone version worked fine for me).

Following https://phenotips.org/AdminGuide/Installation+on+Tomcat+and+MySQL

I deployed the war to tomcat webapps/ , edited the configuration files webapps/phenotips/WEB-INF/xwiki.cfg, webapps/phenotips/WEB-INF/hibernate.cfg.xml   to use MySQL, and restarted tomcat.

The setup worked and the MySQL database was created.


But no matter I use the default HSQLDB, or the MySQL, the HPO and other ontology are not working:



Clinical symptoms and physical findings

 This patient is clinically normal
Or select observed phenotypes:

        Quick phenotype search:
Browse Categories
It looks like the Human Phenotype Ontology is not indexed, please contact an administrator.
An error has occurred while attempting to display the list of phenotypes.





Administration: Ontology index
Index a vocabulary

Human Phenotype Ontology No version could be retrieved. The URL of a file containing the vocabulary you wish to index in OBO format<http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page>.

Chemical Entities of Biological Interest Ontology No version could be retrieved. The URL of a file containing the vocabulary you wish to index in OBO format<http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page>.

HUGO Gene Nomenclature No version could be retrieved. The URL of a file containing the vocabulary you wish to index in OBO format<http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page>.


# tomcat
 sudo service tomcat stop
Using CATALINA_BASE:   /usr/local/tomcat7
Using CATALINA_HOME:   /usr/local/tomcat7
Using CATALINA_TMPDIR: /usr/local/tomcat7/temp
Using JRE_HOME:        /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.85.x86_64
Using CLASSPATH:       /usr/local/tomcat7/bin/bootstrap.jar:/usr/local/tomcat7/bin/tomcat-juli.jar



# error log:

 tail -f /usr/local/tomcat7/logs/catalina.out


2015-11-05 11:59:11,848 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  p.v.i.s.HumanPhenotypeOntology - Failed to query ontology version: No such core: hpo

2015-11-05 11:59:11,850 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  o.p.v.i.s.ChEBIOntology        - Failed to query ontology version: No such core: chebi

2015-11-05 11:59:11,851 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  o.p.v.i.GeneNomenclature       - Failed to query ontology version: No such core: hgnc




## full log:

INFO: Deploying web application archive /usr/local/tomcat7/webapps/phenotips-war-1.2.war
Nov 05, 2015 12:11:29 PM org.apache.catalina.startup.TldConfig execute
INFO: At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
2015-11-05 12:11:33,605 [localhost-startStop-1] WARN  o.a.s.c.SolrResourceLoader     - No files added to classloader from lib: lib (resolved as: /var/lib/phenotips/solr/lib).
Nov 05, 2015 12:11:35 PM ontologizer.FileCache setCacheDirectory
INFO: Cache directory set to "/usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/ontologizer/.cache"
Nov 05, 2015 12:11:35 PM ontologizer.FileCache setCacheDirectory
WARNING:
java.io.FileNotFoundException: /usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/ontologizer/.cache/.index (No such file or directory)

(
ls -la  /usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/ontologizer/
total 12
drwxr-xr-x. 3 root root 4096 Nov  5 12:11 .
drwxr-xr-x. 5 root root 4096 Nov  5 12:12 ..
drwxr-xr-x. 2 root root 4096 Nov  5 12:11 .cache
)


    at java.io.FileInputStream.open(Native Method)
    at java.io.FileInputStream.<init>(FileInputStream.java:146)
    at java.io.FileReader.<init>(FileReader.java:72)
    at ontologizer.FileCache.setCacheDirectory(FileCache.java:302)
    at org.phenotips.diagnosis.internal.BoqaUtils.loadDataFiles(BoqaUtils.java:64)
    at org.phenotips.diagnosis.internal.DefaultDiagnosisService.initialize(DefaultDiagnosisService.java:109)
    at org.xwiki.component.embed.InitializableLifecycleHandler.handle(InitializableLifecycleHandler.java:39)
    at org.xwiki.component.embed.EmbeddableComponentManager.createInstance(EmbeddableComponentManager.java:322)
    at org.xwiki.component.embed.EmbeddableComponentManager.getComponentInstance(EmbeddableComponentManager.java:424)
    at org.xwiki.component.embed.EmbeddableComponentManager.getComponentInstance(EmbeddableComponentManager.java:392)
    at org.xwiki.component.embed.EmbeddableComponentManager.getInstance(EmbeddableComponentManager.java:190)
    at org.xwiki.component.embed.EmbeddableComponentManager.getDependencyInstance(EmbeddableComponentManager.java:363)
    at org.xwiki.component.embed.EmbeddableComponentManager.createInstance(EmbeddableComponentManager.java:312)
    at org.xwiki.component.embed.EmbeddableComponentManager.getComponentInstance(EmbeddableComponentManager.java:424)
    at org.xwiki.component.embed.EmbeddableComponentManager.getInstanceMap(EmbeddableComponentManager.java:214)
    at org.xwiki.component.embed.EmbeddableComponentManager.getInstanceList(EmbeddableComponentManager.java:198)
    at org.xwiki.observation.internal.DefaultObservationManager.initializeListeners(DefaultObservationManager.java:164)
    at org.xwiki.observation.internal.DefaultObservationManager.getListenersByEvent(DefaultObservationManager.java:131)
    at org.xwiki.observation.internal.DefaultObservationManager.notify(DefaultObservationManager.java:267)
    at org.xwiki.observation.internal.DefaultObservationManager.notify(DefaultObservationManager.java:321)
    at org.xwiki.container.servlet.XWikiServletContextListener.contextInitialized(XWikiServletContextListener.java:118)
    at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:5003)
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5517)
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150)
    at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:901)
    at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:877)
    at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:652)
    at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:1095)
    at org.apache.catalina.startup.HostConfig$DeployWar.run(HostConfig.java:1930)
    at java.util.concurrent.Executors$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:745)

Nov 05, 2015 12:11:35 PM ontologizer.worksets.WorkSetLoadThread run
INFO: The name of the obo file to be loaded is "/usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/phenotips_boqa_ontology.tmp"
Nov 05, 2015 12:11:35 PM ontologizer.worksets.WorkSetLoadThread run
INFO: The name of the association file to be loaded is "/usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/phenotips_boqa_annotation.tmp"
Nov 05, 2015 12:11:35 PM ontologizer.go.OBOParser doParse
INFO: Got 10567 terms and 13733 relations in 237 ms
Nov 05, 2015 12:11:35 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Nov 05, 2015 12:11:35 PM ontologizer.worksets.WorkSetLoadThread loadFiles
INFO: Parse local association file "/usr/local/tomcat7/work/Catalina/localhost/phenotips-war-1.2/xwiki-temp/phenotips_boqa_annotation.tmp"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98476: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98477: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98478: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98479: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98480: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98481: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 98482: Expected that dbObject "158000" maps to symbol "OMIM:158000" but it maps to "ORPHANET:158000"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 105265: Expected that dbObject "32" maps to symbol "DECIPHER:32" but it maps to "ORPHANET:32"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 105266: Expected that dbObject "32" maps to symbol "DECIPHER:32" but it maps to "ORPHANET:32"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 105267: Expected that dbObject "32" maps to symbol "DECIPHER:32" but it maps to "ORPHANET:32"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 105268: Expected that dbObject "32" maps to symbol "DECIPHER:32" but it maps to "ORPHANET:32"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106677: Expected that dbObject "39" maps to symbol "DECIPHER:39" but it maps to "ORPHANET:39"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106771: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106772: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106773: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106774: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106775: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106776: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
Nov 05, 2015 12:11:35 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 106777: Expected that dbObject "44" maps to symbol "DECIPHER:44" but it maps to "ORPHANET:44"
....

Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 109754: Expected that dbObject "81" maps to symbol "DECIPHER:81" but it maps to "ORPHANET:81"
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 109755: Expected that dbObject "81" maps to symbol "DECIPHER:81" but it maps to "ORPHANET:81"
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 109756: Expected that dbObject "81" maps to symbol "DECIPHER:81" but it maps to "ORPHANET:81"
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser$1GAFByteLineScanner newLine
WARNING: Line 109757: Expected that dbObject "81" maps to symbol "DECIPHER:81" but it maps to "ORPHANET:81"
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser importAssociationFile
INFO: 112327 associations parsed, 112327 of which were kept while 0 malformed lines had to be ignored.
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser importAssociationFile
INFO: A further 0 associations were skipped due to various reasons whereas 0 of those where explicitly qualified with NOT, 0 referred to obsolete terms and 0 didn't match the requested evidence codes
Nov 05, 2015 12:11:36 PM ontologizer.association.AssociationParser importAssociationFile
INFO: A total of 6688 terms are directly associated to 7519 items.
Nov 05, 2015 12:11:36 PM ontologizer.go.Ontology assignLevel1TermsAndFixRoot
INFO: Ontology contains a single level-one term (All (HP:0000001)
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployWAR
INFO: Deployment of web application archive /usr/local/tomcat7/webapps/phenotips-war-1.2.war has finished in 25,700 ms
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/webapps/docs
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat7/webapps/docs has finished in 42 ms
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/webapps/examples
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat7/webapps/examples has finished in 193 ms
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/webapps/ROOT
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat7/webapps/ROOT has finished in 38 ms
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/webapps/host-manager
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat7/webapps/host-manager has finished in 68 ms
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deploying web application directory /usr/local/tomcat7/webapps/manager
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.HostConfig deployDirectory
INFO: Deployment of web application directory /usr/local/tomcat7/webapps/manager has finished in 38 ms
Nov 05, 2015 12:11:44 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Nov 05, 2015 12:11:44 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["ajp-bio-8009"]
Nov 05, 2015 12:11:44 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 26190 ms
2015-11-05 12:11:53,287 [XWiki initialization] INFO  .HibernateDataMigrationManager - Storage schema updates and data migrations are enabled
2015-11-05 12:11:53,545 [XWiki initialization] INFO  .HibernateDataMigrationManager - No data migration to apply for wiki [xwiki] currently in version [54693]
2015-11-05 12:11:53,547 [XWiki initialization] INFO  .HibernateDataMigrationManager - Checking Hibernate mapping and updating schema if needed for wiki [xwiki]
2015-11-05 12:12:51,716 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=dataformats] WARN  o.x.v.i.DefaultVelocityEngine  - Deprecated usage of getter [com.xpn.xwiki.api.Util.getDate] in 36:xwiki:data.WebHome at 5,172


2015-11-05 12:12:57,562 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  p.v.i.s.HumanPhenotypeOntology - Failed to query ontology version: No such core: hpo
2015-11-05 12:12:57,564 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  o.p.v.i.s.ChEBIOntology        - Failed to query ontology version: No such core: chebi
2015-11-05 12:12:57,572 [http://phenotips.chla.usc.edu:8080/phenotips-war-1.2/bin/admin/XWiki/XWikiPreferences?editor=globaladmin&section=Ontology] WARN  o.p.v.i.GeneNomenclature       - Failed to query ontology version: No such core: hgnc













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