<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Hi Sukie,</p>
<p><br>
</p>
<p>It looks like possibly the repository had not come up yet and so nothing could be harvested. Could you try the following:</p>
<p><br>
</p>
<p>- set institution log4j to debug</p>
<p>- restart tomcat</p>
<p><br>
</p>
<p>If you are still seeing an issue with institution, could you send along:</p>
<p><br>
</p>
<p>- institution log</p>
<p>- catalina.out (partial is fine)</p>
<p>- localhost.2016-06-29.log</p>
<p><br>
</p>
<p>You can send these directly to me if you are concerned about sensitive data in your logs.</p>
<p><br>
</p>
<p>Thanks,</p>
<p>Sophia</p>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
<div>
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> eagle-i-admins-bounces@open.med.harvard.edu <eagle-i-admins-bounces@open.med.harvard.edu> on behalf of Sukdith Punjasthitkul <Sukdith.Punjasthitkul@dartmouth.edu><br>
<b>Sent:</b> Wednesday, June 29, 2016 8:36 AM<br>
<b>To:</b> eagle-i-admins@open.med.harvard.edu<br>
<b>Subject:</b> [Eagle-i-admins] Institution Search shows no results after upgrading to 4.0.0</font>
<div> </div>
</div>
</div>
<font size="2"><span style="font-size:10pt;">
<div class="PlainText">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."
<br>
<br>
I've attached part of the institution log below. Any idea what would be causing this?
<br>
<br>
--sukie--<br>
<br>
<br>
<br>
=========<br>
<br>
$ tail -n 200 institution.log<br>
<br>
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<br>
2016-06-29 04:00:04,687 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://eagle-i.org/ont/app/1.0/ero-app.owl" id="LPlnk212929">http://eagle-i.org/ont/app/1.0/ero-app.owl</a><br>
2016-06-29 04:00:06,937 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://eagle-i.org/ont/app/1.0/ero-app.owl">
http://eagle-i.org/ont/app/1.0/ero-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:06,944 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:08,510 INFO org.eaglei.model.jena.JenaEIOntModel:799 - <a href="http://purl.obolibrary.org/obo/ERO_0000006">
http://purl.obolibrary.org/obo/ERO_0000006</a> : ONT UNHANDLED intersectionOperand:
<a href="http://purl.obolibrary.org/obo/BFO_0000040">http://purl.obolibrary.org/obo/BFO_0000040</a><br>
2016-06-29 04:00:08,511 INFO org.eaglei.model.jena.JenaEIOntModel:787 - <a href="http://purl.obolibrary.org/obo/ERO_0000006">
http://purl.obolibrary.org/obo/ERO_0000006</a> : ONT UNHANDLED, Resource intersection operand has null URI<br>
2016-06-29 04:00:08,550 INFO org.eaglei.model.jena.JenaEIOntModel:817 - <a href="http://purl.obolibrary.org/obo/ERO_0002094">
http://purl.obolibrary.org/obo/ERO_0002094</a> : ONT UNHANDLED equivalent class construct, not an intersection.<br>
2016-06-29 04:00:08,561 INFO org.eaglei.model.jena.JenaEIOntModel:817 - <a href="http://purl.obolibrary.org/obo/ERO_0002112">
http://purl.obolibrary.org/obo/ERO_0002112</a> : ONT UNHANDLED equivalent class construct, not an intersection.<br>
2016-06-29 04:00:08,632 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 1687 msecs<br>
2016-06-29 04:00:08,632 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://eagle-i.org/ont/app/1.0/ero-app.owl-3945msec">http://eagle-i.org/ont/app/1.0/ero-app.owl-3945msec</a><br>
2016-06-29 04:00:08,641 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://eagle-i.org/ont/app/1.0/disease-import-app.owl">http://eagle-i.org/ont/app/1.0/disease-import-app.owl</a><br>
2016-06-29 04:00:11,923 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://eagle-i.org/ont/app/1.0/disease-import-app.owl">
http://eagle-i.org/ont/app/1.0/disease-import-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:11,923 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:12,104 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 180 msecs<br>
2016-06-29 04:00:12,105 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://eagle-i.org/ont/app/1.0/disease-import-app.owl-3464msec">http://eagle-i.org/ont/app/1.0/disease-import-app.owl-3464msec</a><br>
2016-06-29 04:00:12,105 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl">http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl</a><br>
2016-06-29 04:00:12,250 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl">
http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:12,250 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 28 msecs<br>
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl-172msec">http://purl.obolibrary.org/obo/ero/dev/pato-imports-app.owl-172msec</a><br>
2016-06-29 04:00:12,278 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl">http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl</a><br>
2016-06-29 04:00:12,342 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl">
http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:12,342 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 9 msecs<br>
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl-73msec">http://purl.obolibrary.org/obo/ero/dev/go-imports-app.owl-73msec</a><br>
2016-06-29 04:00:12,352 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://eagle-i.org/ont/app/1.0/uberon-import-app.owl">http://eagle-i.org/ont/app/1.0/uberon-import-app.owl</a><br>
2016-06-29 04:00:14,592 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://eagle-i.org/ont/app/1.0/uberon-import-app.owl">
http://eagle-i.org/ont/app/1.0/uberon-import-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:14,593 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:15,011 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 418 msecs<br>
2016-06-29 04:00:15,012 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://eagle-i.org/ont/app/1.0/uberon-import-app.owl-2660msec">http://eagle-i.org/ont/app/1.0/uberon-import-app.owl-2660msec</a><br>
2016-06-29 04:00:15,012 INFO org.eaglei.model.jena.EagleIOntUtils:129 - LOADING model
<a href="http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl">http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl</a><br>
2016-06-29 04:00:15,956 INFO org.eaglei.model.jena.JenaEIOntModel:189 - <a href="http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl">
http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl</a> ontology version: 2.0.3 19477 2015-06-30 20:16:20<br>
2016-06-29 04:00:15,957 INFO org.eaglei.model.jena.JenaEIOntModel:254 - initializing class pre-cache...<br>
2016-06-29 04:00:16,112 INFO org.eaglei.model.jena.JenaEIOntModel:271 - class pre-cache initialized: 155 msecs<br>
2016-06-29 04:00:16,112 INFO org.eaglei.model.jena.EagleIOntUtils:149 - LOADED model
<a href="http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl-1100msec">http://purl.obolibrary.org/obo/ero/dev/mp-imports-app.owl-1100msec</a><br>
2016-06-29 04:00:16,125 INFO org.eaglei.services.nodeinfo.LocalNodeInfoConfig:61 - bean local node service<br>
2016-06-29 04:00:16,374 INFO org.eaglei.institution.server.InstitutionSearchConfig:52 - No system user defined.<br>
2016-06-29 04:00:16,377 INFO org.eaglei.ui.gwt.search.server.AbstractSearchAppConfig:89 - Does search require login? [false]<br>
2016-06-29 04:00:16,381 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:68 - bean nodeRegistry<br>
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].<br>
2016-06-29 04:00:16,471 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:97 - bean uiConfig<br>
2016-06-29 04:00:16,471 INFO org.eaglei.services.nodeinfo.NodeInfoConfig:102 - bean uiConfig-local<br>
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_SYSTEM_USER] property not found.<br>
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_SYSTEM_PW] property not found.<br>
2016-06-29 04:00:16,473 INFO org.eaglei.services.uiconfig.UIConfigRemote:389 - <a href="http://dartmouth.eagle-i.net/i/">
http://dartmouth.eagle-i.net/i/</a> - Dartmouth College - /repository/images/site/dartmouth.png<br>
2016-06-29 04:00:16,473 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_LOGOUT_URL] property not found.<br>
2016-06-29 04:00:19,885 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [UI_SEARCH_ANNOUNCEMENT_PANEL_URL] property not found.<br>
2016-06-29 04:00:19,886 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [UI_SEARCH_ANNOUNCEMENT_PANEL_URL] property not found.<br>
2016-06-29 04:00:19,886 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_STEMCELL_INFOGRAPHIC_URL] property not found.<br>
2016-06-29 04:00:19,887 WARN org.eaglei.services.uiconfig.UIConfigRemote:623 - [SEARCH_STEMCELL_INFOGRAPHIC_URL] property not found.<br>
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:799 - <a href="http://purl.obolibrary.org/obo/ERO_0001707">
http://purl.obolibrary.org/obo/ERO_0001707</a> : ONT UNHANDLED intersectionOperand:
<a href="http://purl.obolibrary.org/obo/ERO_0000007">http://purl.obolibrary.org/obo/ERO_0000007</a><br>
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:759 - <a href="http://purl.obolibrary.org/obo/ERO_0001707">
http://purl.obolibrary.org/obo/ERO_0001707</a> : ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7c87<br>
2016-06-29 04:00:21,527 INFO org.eaglei.model.jena.JenaEIOntModel:759 - <a href="http://purl.obolibrary.org/obo/ERO_0001707">
http://purl.obolibrary.org/obo/ERO_0001707</a> : ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7c85<br>
2016-06-29 04:00:21,581 INFO org.eaglei.model.jena.JenaEIOntModel:759 - <a href="http://purl.obolibrary.org/obo/OBI_0000835">
http://purl.obolibrary.org/obo/OBI_0000835</a> : ONT UNHANDLED restriction property: -23b13e49:1559b2c121a:-7bb1<br>
2016-06-29 04:00:21,692 INFO org.eaglei.model.jena.JenaEIOntModel:817 - <a href="http://purl.obolibrary.org/obo/OBI_0000094">
http://purl.obolibrary.org/obo/OBI_0000094</a> : ONT UNHANDLED equivalent class construct, not an intersection.<br>
2016-06-29 04:00:21,828 WARN org.eaglei.model.jena.JenaEIOntModel:910 - Unexpected equivalent class construct in:
<a href="http://purl.obolibrary.org/obo/ERO_0000006">http://purl.obolibrary.org/obo/ERO_0000006</a>, Resource intersection operand has null URI<br>
2016-06-29 04:00:22,036 INFO org.eaglei.model.jena.JenaEIOntModel:817 - <a href="http://www.ebi.ac.uk/efo/swo/SWO_0000580">
http://www.ebi.ac.uk/efo/swo/SWO_0000580</a> : ONT UNHANDLED equivalent class construct, not an intersection.<br>
2016-06-29 04:00:22,738 WARN org.eaglei.ui.gwt.search.instance.server.InstanceServlet:120 - Failed to find buildversion.properties<br>
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.<br>
2016-06-29 04:00:22,978 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table INSTANCE_SERVLET_LOG_V5<br>
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.<br>
2016-06-29 04:00:22,993 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table CONTACT_LOG_V5<br>
2016-06-29 04:00:22,997 ERROR org.eaglei.ui.gwt.search.server.SearchServlet:220 - Failed to find buildversion.properties<br>
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.<br>
2016-06-29 04:00:23,010 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table SEARCH_SERVLET_LOG_V5<br>
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.<br>
2016-06-29 04:00:23,016 INFO org.eaglei.services.logger.AsynchronousLogger:158 - Asynchronous Logger started for table SEARCH_SERVLET_COUNT_LOG_V5<br>
2016-06-29 04:00:23,026 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:452 - ....waiting for solr index service SolrSearchIndexer to come up.....<br>
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<br>
2016-06-29 04:00:23,032 INFO org.eaglei.solr.AbstractSolrStreamingIndexer:452 - ....waiting for solr index service DataSuggestIndexer to come up.....<br>
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<br>
2016-06-29 04:00:45,463 WARN org.eaglei.services.connection.Apache4xHttpConnectionProvider:662 - The repository is currently unavailable.<br>
2016-06-29 04:00:45,464 WARN org.eaglei.services.harvest.SingleNodeStreamHarvester:333 - Harvesting/indexing failed for node:
<a href="https://dartmouth.eagle-i.net:8443/harvest">https://dartmouth.eagle-i.net:8443/harvest</a>. Will keep trying. Caught exception: The repository is currently unavailable.<br>
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.<br>
2016-06-29 04:02:24,658 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:08:01,380 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:17:06,359 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:20:50,564 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:24:33,217 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:25:44,052 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:25:49,697 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:25:59,506 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 04:26:09,276 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
2016-06-29 08:34:24,042 INFO org.eaglei.ui.gwt.security.server.NodeSecurityServlet:133 - institution ID: noLoginInstitution; url:
<a href="https://dartmouth.eagle-i.net:8443/repository/">https://dartmouth.eagle-i.net:8443/repository/</a><br>
<br>
_______________________________________________<br>
Eagle-i-admins mailing list<br>
Eagle-i-admins@open.med.harvard.edu<br>
<a href="https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins">https://open.med.harvard.edu/mailman/listinfo/eagle-i-admins</a><br>
</div>
</span></font></div>
</div>
</body>
</html>