[Eagle-i-admins] Institution Search shows no results after upgrading to 4.0.0

Wed Jun 29 11:19:23 EDT 2016

Hi Sukie,

It looks like possibly the repository had not come up yet and so nothing could be harvested. Could you try the following:

- set institution log4j to debug

- restart tomcat

If you are still seeing an issue with institution, could you send along:

- institution log

- catalina.out (partial is fine)

- localhost.2016-06-29.log

You can send these directly to me if you are concerned about sensitive data in your logs.

Thanks,

Sophia

________________________________
From: eagle-i-admins-bounces at open.med.harvard.edu <eagle-i-admins-bounces at open.med.harvard.edu> on behalf of Sukdith Punjasthitkul <Sukdith.Punjasthitkul at dartmouth.edu>
Sent: Wednesday, June 29, 2016 8:36 AM
To: eagle-i-admins at open.med.harvard.edu
Subject: [Eagle-i-admins] Institution Search shows no results after upgrading to 4.0.0

We just upgraded our eagle-i node to 4.0.0. Respository and SWEET works and shows results, but the Institution search page displays "No results found."

I've attached part of the institution log below. Any idea what would be causing this?

--sukie--

=========

$ tail -n 200 institution.log

2016-06-29 04:00:01,713 INFO org.eaglei.utilities.servlet.EILog4jConfigurationManager:123 - Found and loaded file: /data/eagle-i/eaglei/conf/institution.log4j.properties
2016-06-29 04:00:04,687 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://eagle-i.org/ont/app/1.0/ero-app.owl
2016-06-29 04:00:06,937 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://eagle-i.org/ont/app/1.0/ero-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:06,944 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:08,510 INFO org.eaglei.model.jena.JenaEIOntModel:799 - http://purl.obolibrary.org/obo/ERO_0000006 :  ONT UNHANDLED intersectionOperand: http://purl.obolibrary.org/obo/BFO_0000040
2016-06-29 04:00:08,511 INFO org.eaglei.model.jena.JenaEIOntModel:787 - http://purl.obolibrary.org/obo/ERO_0000006 :  ONT UNHANDLED, Resource intersection operand has null URI
2016-06-29 04:00:08,550 INFO org.eaglei.model.jena.JenaEIOntModel:817 - http://purl.obolibrary.org/obo/ERO_0002094 :  ONT UNHANDLED equivalent class construct, not an intersection.
2016-06-29 04:00:08,561 INFO org.eaglei.model.jena.JenaEIOntModel:817 - http://purl.obolibrary.org/obo/ERO_0002112 :  ONT UNHANDLED equivalent class construct, not an intersection.
2016-06-29 04:00:08,632 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 1687 msecs
2016-06-29 04:00:08,632 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://eagle-i.org/ont/app/1.0/ero-app.owl-3945msec
2016-06-29 04:00:08,641 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://eagle-i.org/ont/app/1.0/disease-import-app.owl
2016-06-29 04:00:11,923 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://eagle-i.org/ont/app/1.0/disease-import-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:11,923 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:12,104 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 180 msecs
2016-06-29 04:00:12,105 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://eagle-i.org/ont/app/1.0/disease-import-app.owl-3464msec
2016-06-29 04:00:12,105 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl
2016-06-29 04:00:12,250 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:12,250 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 28 msecs
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl-172msec
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl
2016-06-29 04:00:12,342 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:12,342 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 9 msecs
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl-73msec
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://eagle-i.org/ont/app/1.0/uberon-import-app.owl
2016-06-29 04:00:14,592 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://eagle-i.org/ont/app/1.0/uberon-import-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:14,593 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:15,011 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 418 msecs
2016-06-29 04:00:15,012 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://eagle-i.org/ont/app/1.0/uberon-import-app.owl-2660msec
2016-06-29 04:00:15,012 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl
2016-06-29 04:00:15,956 INFO org.eaglei.model.jena.JenaEIOntModel:189 - http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl ontology version: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:15,957 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...
2016-06-29 04:00:16,112 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 155 msecs
2016-06-29 04:00:16,112 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl-1100msec
2016-06-29 04:00:16,125 INFO org.eaglei.services.nodeinfo.LocalNodeInfoConfig:61 - bean local node service
2016-06-29 04:00:16,374 INFO org.eaglei.institution.server.InstitutionSearchConfig:52 - No system user defined.
2016-06-29 04:00:16,377 INFO org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig:89 - Does search require login? [false]
2016-06-29 04:00:16,381 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:68 - bean nodeRegistry
2016-06-29 04:00:16,438 WARN org.eaglei.services.nodeinfo.NodeRegistryService:324 - Unable to open and/or read config file [node-registry.xml].
2016-06-29 04:00:16,471 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:97 - bean uiConfig
2016-06-29 04:00:16,471 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:102 - bean uiConfig-local
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_SYSTEM_USER] property not found.
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_SYSTEM_PW] property not found.
2016-06-29 04:00:16,473 INFO org.eaglei.services.uiconfig.UIConfigRemote:389 - http://dartmouth.eagle-i.net/i/ - Dartmouth College - /repository/images/site/dartmouth.png
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_LOGOUT_URL] property not found.
2016-06-29 04:00:19,885 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [UI_SEARCH_ANNOUNCEMENT_PANEL_URL] property not found.
2016-06-29 04:00:19,886 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [UI_SEARCH_ANNOUNCEMENT_PANEL_URL] property not found.
2016-06-29 04:00:19,886 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_STEMCELL_INFOGRAPHIC_URL] property not found.
2016-06-29 04:00:19,887 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_STEMCELL_INFOGRAPHIC_URL] property not found.
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:799 - http://purl.obolibrary.org/obo/ERO_0001707 :  ONT UNHANDLED intersectionOperand: http://purl.obolibrary.org/obo/ERO_0000007
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:759 - http://purl.obolibrary.org/obo/ERO_0001707 :  ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7c87
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:759 - http://purl.obolibrary.org/obo/ERO_0001707 :  ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7c85
2016-06-29 04:00:21,581 INFO org.eaglei.model.jena.JenaEIOntModel:759 - http://purl.obolibrary.org/obo/OBI_0000835 :  ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7bb1
2016-06-29 04:00:21,692 INFO org.eaglei.model.jena.JenaEIOntModel:817 - http://purl.obolibrary.org/obo/OBI_0000094 :  ONT UNHANDLED equivalent class construct, not an intersection.
2016-06-29 04:00:21,828 WARN org.eaglei.model.jena.JenaEIOntModel:910 - Unexpected equivalent class construct in: http://purl.obolibrary.org/obo/ERO_0000006, Resource intersection operand has null URI
2016-06-29 04:00:22,036 INFO org.eaglei.model.jena.JenaEIOntModel:817 - http://www.ebi.ac.uk/efo/swo/SWO_0000580 :  ONT UNHANDLED equivalent class construct, not an intersection.
2016-06-29 04:00:22,738 WARN org.eaglei.ui.gwt.search.instance.server.InstanceServlet:120 - Failed to find buildversion.properties
2016-06-29 04:00:22,740 INFO org.eaglei.services.logger.AsynchronousLogger:177 - AsynchronousLogger using Unknown as build identifier, and 2.0.3 19477  2015-06-30 20:16:20 as ontology identifer.
2016-06-29 04:00:22,978 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table INSTANCE_SERVLET_LOG_V5
2016-06-29 04:00:22,979 INFO org.eaglei.services.logger.AsynchronousLogger:177 - AsynchronousLogger using Unknown as build identifier, and 2.0.3 19477  2015-06-30 20:16:20 as ontology identifer.
2016-06-29 04:00:22,993 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table CONTACT_LOG_V5
2016-06-29 04:00:22,997 ERROR org.eaglei.ui.gwt.search.server.SearchServlet:220 - Failed to find buildversion.properties
2016-06-29 04:00:22,998 INFO org.eaglei.services.logger.AsynchronousLogger:177 - AsynchronousLogger using Unknown as build identifier, and 2.0.3 19477  2015-06-30 20:16:20 as ontology identifer.
2016-06-29 04:00:23,010 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table SEARCH_SERVLET_LOG_V5
2016-06-29 04:00:23,011 INFO org.eaglei.services.logger.AsynchronousLogger:177 - AsynchronousLogger using Unknown as build identifier, and 2.0.3 19477  2015-06-30 20:16:20 as ontology identifer.
2016-06-29 04:00:23,016 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table SEARCH_SERVLET_COUNT_LOG_V5
2016-06-29 04:00:23,026 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:452 - ....waiting for solr index service SolrSearchIndexer to come up.....
2016-06-29 04:00:23,032 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:468 - Ontology version indexed: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:23,032 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:452 - ....waiting for solr index service DataSuggestIndexer to come up.....
2016-06-29 04:00:23,032 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:468 - Ontology version indexed: 2.0.3 19477  2015-06-30 20:16:20
2016-06-29 04:00:45,463 WARN org.eaglei.services.connection.Apache4xHttpConnectionProvider:662 - The repository is currently unavailable.
2016-06-29 04:00:45,464 WARN org.eaglei.services.harvest.SingleNodeStreamHarvester:333 - Harvesting/indexing failed for node: https://dartmouth.eagle-i.net:8443/harvest.  Will keep trying. Caught exception: The repository is currently unavailable.
2016-06-29 04:00:45,464 INFO org.eaglei.services.harvest.MultiSourceHarvester:131 -      institution Dartmouth College harvest failed, indices may not be up to date.
2016-06-29 04:02:24,658 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:08:01,380 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:17:06,359 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:20:50,564 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:24:33,217 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:25:44,052 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:25:49,697 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:25:59,506 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 04:26:09,276 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/
2016-06-29 08:34:24,042 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url: https://dartmouth.eagle-i.net:8443/repository/

_______________________________________________
Eagle-i-admins mailing list
Eagle-i-admins at open.med.harvard.edu
https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://open.med.harvard.edu/pipermail/eagle-i-admins/attachments/20160629/d0848a61/attachment-0001.html>