Bug #7341
An solr exception in the mn-demo-8
100%
Description
Andrei reported:
It's a SolrException that happens as a result of MN.updateSystemMetadata() --> CN.synchronize()
The trace is below. I'll also past the scimeta doc in case it's relevant. I also didn't see any mention of the pid in CN log files.
The trace mentions an unknown "geohash_1" ... I checked in the in the scimeta, and it does contain some geographical info, but maybe "geohash_1" is a solr-specific field.
Any ideas? (May be an issue is with the test data since Jing isn't seeing this error.)
From demo-8 catalina.out:
metacat 20150910-18:04:15: [DEBUG]: Storing System Metadata to store: testSetReplicationStatus_NoChange201525311040930 [edu.ucsb.nceas.metacat.dataone.hazelcast.SystemMetadataMap]
metacat 20150910-18:04:15: [DEBUG]: Entry added/updated to System Metadata map: testSetReplicationStatus_NoChange201525311040930 [edu.ucsb.nceas.metacat.dataone.hazelcast.HazelcastService]
metacat-index 20150910-18:04:15: [ERROR]: org.apache.solr.common.SolrException: ERROR:unknown field 'geohash_1'
at org.apache.solr.update.DocumentBuilder.toDocument(DocumentBuilder.java:320)
at org.apache.solr.update.processor.RunUpdateProcessor.processAdd(RunUpdateProcessorFactory.java:60)
at org.apache.solr.handler.XMLLoader.processUpdate(XMLLoader.java:158)
at org.apache.solr.handler.XMLLoader.load(XMLLoader.java:79)
at org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:67)
at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:129)
at org.apache.solr.core.SolrCore.execute(SolrCore.java:1368)
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.request(EmbeddedSolrServer.java:140)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:105)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:64)
at edu.ucsb.nceas.metacat.index.SolrIndex.insertToIndex(SolrIndex.java:477)
at edu.ucsb.nceas.metacat.index.SolrIndex.insert(SolrIndex.java:375)
at edu.ucsb.nceas.metacat.index.SolrIndex.update(SolrIndex.java:575)
at edu.ucsb.nceas.metacat.index.SolrIndex.update(SolrIndex.java:528)
at edu.ucsb.nceas.metacat.index.SystemMetadataEventListener.entryUpdated(SystemMetadataEventListener.java:146)
at edu.ucsb.nceas.metacat.index.SystemMetadataEventListener.entryAdded(SystemMetadataEventListener.java:119)
at com.hazelcast.client.impl.EntryListenerManager.notifyListeners(EntryListenerManager.java:148)
at com.hazelcast.client.impl.EntryListenerManager.notifyListeners(EntryListenerManager.java:130)
at com.hazelcast.client.impl.ListenerManager.customRun(ListenerManager.java:88)
at com.hazelcast.client.ClientRunnable.run(ClientRunnable.java:30)
at java.lang.Thread.run(Thread.java:745)
[org.apache.solr.core.SolrCore]
metacat-index 20150910-18:04:15: [ERROR]: SolrIndex.update - could not update the solr index since org.apache.solr.client.solrj.SolrServerException: org.apache.solr.common.SolrException: ERROR:unknown field 'geohash_1' [edu.ucsb.nceas.metacat.index.SolrIndex]
org.apache.solr.client.solrj.SolrServerException: org.apache.solr.client.solrj.SolrServerException: org.apache.solr.common.SolrException: ERROR:unknown field 'geohash_1'
at org.apache.solr.client.solrj.embedded.EmbeddedSolrServer.request(EmbeddedSolrServer.java:153)
at org.apache.solr.client.solrj.request.AbstractUpdateRequest.process(AbstractUpdateRequest.java:105)
at org.apache.solr.client.solrj.SolrServer.add(SolrServer.java:64)
at edu.ucsb.nceas.metacat.index.SolrIndex.insertToIndex(SolrIndex.java:477)
at edu.ucsb.nceas.metacat.index.SolrIndex.insert(SolrIndex.java:375)
...
metacat 20150910-18:04:20: [ERROR]: It is a DataONEBaseException and its detail code is 4961 and its code is 500 [edu.ucsb.nceas.metacat.dataone.MNodeService]
metacat 20150910-18:04:20: [ERROR]: Can't update the systemmetadata of pid testSetReplicationStatus_NoChange201525311040930 in CNs since Unexpected Exception in CN.synchronize: progress: (d) got HzSyncObjectQueue: hzSyncObjectQueue:: java.lang.NullPointerException [edu.ucsb.nceas.metacat.dataone.MNodeService]
Scimeta doc:
<?xml version="1.0" encoding="UTF-8"?>
PISCO moored temperature, TPT001
PISCO: Physical Oceanography: moored temperature data: Terrace Point, California, USA (TPT001)
<creator>
<organizationName>Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)</organizationName>
<onlineUrl>http://www.piscoweb.org</onlineUrl>
</creator>
<creator>
<individualName>
<salutation>Dr.</salutation>
<givenName>Margaret</givenName>
<surName>McManus</surName>
</individualName>
<address>
<deliveryPoint>Marine Sciences Building</deliveryPoint>
<deliveryPoint>1000 Pope Road</deliveryPoint>
<deliveryPoint>Department of Oceanography</deliveryPoint>
<deliveryPoint>University of Hawaii at Manoa</deliveryPoint>
<city>Honolulu</city>
<administrativeArea>Hawaii</administrativeArea>
<postalCode>96822</postalCode>
<country>USA</country>
</address>
<phone
phonetype="voice">(808) 956-8623</phone>
<phone
phonetype="fax">(808) 956-9225</phone>
<electronicMailAddress>mamc@hawaii.edu</electronicMailAddress>
<onlineUrl>http://www.piscoweb.org/about-pisco/people/directory/details?individual=mamc</onlineUrl>
</creator>
<associatedParty>
<individualName>
<salutation>Dr.</salutation>
<givenName>Olivia</givenName>
<surName>Cheriton</surName>
</individualName>
<address>
<deliveryPoint>Long Marine Lab</deliveryPoint>
<deliveryPoint>100 Shaffer Road</deliveryPoint>
<deliveryPoint>University of California, Santa Cruz</deliveryPoint>
<city>Santa Cruz</city>
<administrativeArea>California</administrativeArea>
<postalCode>95060</postalCode>
<country>USA</country>
</address>
<phone
phonetype="voice">(831) 459-1876</phone>
<phone
phonetype="fax">(831) 459-3383</phone>
<electronicMailAddress>cheriton at biology dot ucsc dot edu</electronicMailAddress>
<onlineUrl>http://www.piscoweb.org/about-pisco/people/directory/details?individual=cheriton</onlineUrl>
<role>Post-Doctoral Researcher</role>
</associatedParty>
<language>English</language>
<series>TPT001_018MHP2000R00_20110121</series>
<abstract>
<para>This metadata record describes moored seawater temperature data collected at Terrace Point, California, USA, by PISCO. Measurements were collected using a HOBO U22 Water Temp Pro V2 (Onset Computer Corp. U22-001) beginning 2011-01-21. The instrument depth was 000 meters, in an overall water depth of 18 meters (both relative to Mean Sea Level, MSL). The sampling interval was 4.0 minutes.</para>
</abstract>
<keywordSet>
<keyword>EARTH SCIENCE : Oceans : Ocean Temperature : Water Temperature</keyword>
<keywordThesaurus>Global Change Master Directory</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Temperature</keyword>
<keyword>Integrated Ocean Observing System</keyword>
<keyword>IOOS</keyword>
<keywordThesaurus>IOOS Vocabulary Version 1</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>Oceanographic Sensor Data</keyword>
<keyword>Moored Temperature Data</keyword>
<keywordThesaurus>PISCO Categories</keywordThesaurus>
</keywordSet>
<keywordSet>
<keyword>continental shelf</keyword>
<keyword>seawater</keyword>
<keyword>temperature</keyword>
<keyword>California</keyword>
<keyword>United States of America</keyword>
<keyword>PISCO</keyword>
</keywordSet>
<intellectualRights><para>Please cite PISCO in all publications containing these data. The citation should take the form: "This study utilized data collected by the Partnership for Interdisciplinary Studies of Coastal Oceans: a long-term ecological consortium funded by the David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation." Please send copies of any published manuscript based on these data to the PISCO Program Coordinator (http://piscoweb.org/who/coordinators). Users of these data are encouraged to contact the Principal Investigators. Where appropriate, researchers whose projects are integrally dependent on PISCO data are encouraged to consider collaboration and/or co-authorship with original PISCO investigators.</para><para>Extensive efforts are made to ensure that online data are accurate and up to date, but the authors and PISCO will not take responsibility for any errors that may exist in data provided online. Furthermore, the user assumes all responsibility for errors in analysis or judgment resulting from use of the data.</para></intellectualRights>
<distribution>
<online>
<url
function="information">http://www.piscoweb.org</url>
</online>
</distribution>
<coverage>
<geographicCoverage
id="TPT001">
<geographicDescription>Terrace Point: TPT001: This inner-shelf mooring is located offshore of the city of Santa Cruz, California, USA. The mooring lies in an overall water depth of 018 meters (referenced to Mean Sea Level, MSL). The altitudeMinimum and altitudeMaximum tags in this initial coverage section refer to the logger measurement range (with depths expressed as negative altitudes) and are also referenced to MSL. They do not represent the overall water depth.</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>-122.080450</westBoundingCoordinate>
<eastBoundingCoordinate>-122.080450</eastBoundingCoordinate>
<northBoundingCoordinate>36.943421</northBoundingCoordinate>
<southBoundingCoordinate>36.943421</southBoundingCoordinate>
<boundingAltitudes>
<altitudeMinimum>-000</altitudeMinimum>
<altitudeMaximum>-000</altitudeMaximum>
<altitudeUnits>meter</altitudeUnits>
</boundingAltitudes>
</boundingCoordinates>
</geographicCoverage>
<temporalCoverage>
<rangeOfDates>
<beginDate>
<calendarDate>2011-01-21</calendarDate>
<time>20:20:00.00Z</time>
</beginDate>
<endDate>
<calendarDate>2011-03-30</calendarDate>
<time>13:00:00.00Z</time>
</endDate>
</rangeOfDates>
</temporalCoverage>
</coverage>
<purpose>
<para>These data were collected by PISCO to understand the physical processes of the inner continental shelf and their potential effects on marine ecology.</para>
</purpose>
<contact>
<positionName>Physical Oceanographic Data Manager</positionName>
<organizationName>PISCO</organizationName>
<electronicMailAddress>phys-ocean-data-manager@lists.piscoweb.org</electronicMailAddress>
<onlineUrl>http://www.piscoweb.org</onlineUrl>
</contact>
<methods>
<methodStep>
<description>
<para>Methods for moored temperature collection and quality-control are available online, see the protocol citation.</para>
</description>
<protocol>
<title>PISCO UCSC Tidbit Temperature Protocol</title>
<creator>
<organizationName>PISCO</organizationName>
</creator>
<distribution>
<online>
<url
function="download">http://data.piscoweb.org/catalog/metacat/PISCO_UCSC_Tidbit_Temperature_Protocol.40.1/piscoweb</url>
</online>
</distribution>
</protocol>
<instrumentation>HOBO U22 Water Temp Pro V2 (Onset Computer Corp. U22-001)</instrumentation>
</methodStep>
<sampling>
<studyExtent>
<coverage>
<geographicCoverage>
<geographicDescription>In this sampling section, the altitudeMaximum tag refers to the altitude of Mean Sea Level (MSL), and the altitudeMinimum tag refers to the nominal altitude of the sea floor. In other words, the altitudeMinimum represents the overall water depth, expressed as a negative altitude.</geographicDescription>
<boundingCoordinates>
<westBoundingCoordinate>-122.080450</westBoundingCoordinate>
<eastBoundingCoordinate>-122.080450</eastBoundingCoordinate>
<northBoundingCoordinate>36.943421</northBoundingCoordinate>
<southBoundingCoordinate>36.943421</southBoundingCoordinate>
<boundingAltitudes>
<altitudeMinimum>-18</altitudeMinimum>
<altitudeMaximum>000</altitudeMaximum>
<altitudeUnits>meter</altitudeUnits>
</boundingAltitudes>
</boundingCoordinates>
</geographicCoverage>
</coverage>
</studyExtent>
<samplingDescription>
<para>Methods for PISCO moored temperature data collection and quality-control are available online, see the protocol citation. Data were collected using a HOBO U22 Water Temp Pro V2 (Onset Computer Corp. U22-001) set to a 4.0-minute sampling interval.</para>
</samplingDescription>
</sampling>
</methods>
<project>
<title>Partnership for Interdisciplinary Studies of Coastal Oceans (PISCO)</title>
<personnel>
<organizationName>PISCO</organizationName>
<role>Consortium</role>
</personnel>
<abstract>
<para>PISCO is a large-scale marine research program that focuses on understanding the near-shore ecosystems of the U.S. West Coast. An interdisciplinary collaboration of scientists from four universities, PISCO integrates long-term monitoring of ecological and oceanographic processes at dozens of coastal sites with experimental work in the lab and field. We explore how individual organisms, populations, and ecological communities vary over space and time. Findings are applied to issues of ocean conservation and management, and are shared through our public outreach and student training programs.</para>
</abstract>
<funding>
<para>PISCO is funded by the David and Lucile Packard Foundation and the Gordon and Betty Moore Foundation.</para>
</funding>
</project>
<access
authSystem="ldap://ldap.ecoinformatics.org:389/dc=ecoinformatics,dc=org"
order="denyFirst">
<allow>
<principal>
cn=data-managers,o=PISCOGROUPS,dc=ecoinformatics,dc=org
</principal>
<permission>all</permission>
</allow>
<allow>
<principal>public</principal>
<permission>read</permission>
</allow></access>
<dataTable>
<entityName>TPT001_018MHP2000R00_20110121.40.1.txt</entityName>
<physical>
<objectName>TPT001_018MHP2000R00_20110121.40.1</objectName>
<size
unit="bytes">1242951</size>
<characterEncoding>ASCII</characterEncoding>
<dataFormat>
<textFormat>
<numHeaderLines>1</numHeaderLines>
<recordDelimiter>#x0A</recordDelimiter>
<attributeOrientation>column</attributeOrientation>
<simpleDelimited>
<fieldDelimiter>#x20</fieldDelimiter>
</simpleDelimited>
</textFormat>
</dataFormat>
<distribution
id="TPT001_018MHP2000R00_20110121.40">
<online>
<url
function="download">ecogrid://knb/TPT001_018MHP2000R00_20110121.40.1</url>
</online>
</distribution>
</physical>
<attributeList>
<attribute>
<attributeName>date</attributeName>
<attributeDefinition>calendar date of each temperature measurement record</attributeDefinition>
<storageType
typeSystem="http://www.w3.org/2001/XMLSchema-datatypes">date</storageType>
<measurementScale>
<datetime>
<formatString>YYYY-MM-DD</formatString>
<dateTimePrecision>1 day</dateTimePrecision>
<dateTimeDomain/>
</datetime>
</measurementScale>
</attribute>
<attribute>
<attributeName>time</attributeName>
<attributeDefinition>Greenwich Mean Time of each temperature measurement record</attributeDefinition>
<storageType
typeSystem="http://www.w3.org/2001/XMLSchema-datatypes">time</storageType>
<measurementScale>
<datetime>
<formatString>hh:mm:ss.ssZ</formatString>
<dateTimePrecision>1 second</dateTimePrecision>
<dateTimeDomain/>
</datetime>
</measurementScale>
<accuracy>
<attributeAccuracyReport>1 minute/month from Onset Manuals</attributeAccuracyReport>
</accuracy>
</attribute>
<attribute>
<attributeName>yearday</attributeName>
<attributeDefinition>Time of each temperature measurement record, expressed as decimal days since 12 a.m. Jan. 1 of the year measurement was made. For example, 12 noon GMT on Jan. 2 is represented by yearday 1.5, NOT yearday 2.5.</attributeDefinition>
<storageType
typeSystem="http://www.w3.org/2001/XMLSchema-datatypes">float</storageType>
<measurementScale>
<interval>
<unit>
<standardUnit>nominalDay</standardUnit>
</unit>
<precision>0.0000116</precision>
<numericDomain>
<numberType>real</numberType>
</numericDomain>
</interval>
</measurementScale>
<accuracy>
<attributeAccuracyReport>1 minute/month from Onset Manuals</attributeAccuracyReport>
</accuracy>
</attribute>
<attribute>
<attributeName>temp_c</attributeName>
<attributeDefinition>seawater temperature</attributeDefinition>
<storageType
typeSystem="http://www.w3.org/2001/XMLSchema-datatypes">float</storageType>
<measurementScale>
<interval>
<unit>
<standardUnit>celsius</standardUnit>
</unit>
<precision>0.02</precision>
<numericDomain>
<numberType>real</numberType>
</numericDomain>
</interval>
</measurementScale>
<missingValueCode>
<code>9999.00</code>
<codeExplanation>missing data</codeExplanation>
</missingValueCode>
<accuracy>
<attributeAccuracyReport>0.2 degrees Celsius from Manual</attributeAccuracyReport>
</accuracy>
</attribute>
<attribute>
<attributeName>flag</attributeName>
<attributeDefinition>data flag used to qualify data as bad, questionable, etc.</attributeDefinition>
<storageType
typeSystem="http://www.w3.org/2001/XMLSchema-datatypes">string</storageType>
<measurementScale>
<nominal>
<nonNumericDomain>
<textDomain>
<definition>
Data for each column of the data file are flagged with a single
alpha-numeric code such that the first digit holds the
first data column flag, the second digit holds the second data column
flag, etc. Possible flags are 0-9, A-Z, a-z; however flag definitions are
currently as follows:
0 - No known bad data;
1 - Known bad data: instrument malfunction/failure, loss of memory,
loss of power, bio-fouling, electronic malfunction;
2 - Suspicious data (looks bad, but no known cause);
9 - Missing data (data column has a missing value code as defined in the metadata)
[0-9A-Za-z]</definition>
<pattern>[0-9A-Za-z][0-9A-Za-z][0-9A-Za-z][0-9A-Za-z]</pattern>
<source>PISCO/NMS Physical Oceanography Team accepted flagging conventions</source>
</textDomain>
</nonNumericDomain>
</nominal>
</measurementScale>
</attribute>
</attributeList>
</dataTable>
TPT001_018MHP2000R00_20110121.40
public
read
cn=data-managers,o=PISCOGROUPS,dc=ecoinformatics,dc=org
all
/eml:eml
History
#1 Updated by Jing Tao over 8 years ago
- Status changed from New to Closed
- % Done changed from 0 to 100
The schema.xml in the machine was out of date. After I updated the schema and rebuilt the solr index, the error message was gone.
