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DO NOT MERGE YET: Upgrade to solr6: DO NOT MERGE YET

Open cmungall opened this issue 8 years ago • 27 comments

Fixes #194

Still to do, but can be punted:

  • variable names may still say 'server' even though solrj changed class name from Server to Client
  • We use HttpSolrClient which is deprecated; change to builder

cc @kltm

cmungall avatar May 01 '17 16:05 cmungall

Tagging @nathandunn @kltm

cmungall avatar Feb 09 '18 23:02 cmungall

Just resolved a conflict. Some white-space moved around as well.

nathandunn avatar Feb 12 '18 19:02 nathandunn

  • [x] test master vs SOLR3
  • [x] test branch versus SOLR3
  • [ ] test branch versus SOLR7
    • [ ] create instructions for SOLR7 (put in PR?)
  • [ ] fix versus SOLR3 (a weird byte error)?
  • [ ] fix to make a publicly loadable gaf (client does not like https or github)
  • [ ] install biolink

nathandunn avatar Feb 13 '18 18:02 nathandunn 

#!/bin/bash 
java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx12G -jar ./OWLTools-Runner/bin/owltools http://purl.obolibrary.org/obo/go/extensions/go-lego.owl http://purl.obolibrary.org/obo/eco.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl/cl-basic.owl http://purl.obolibrary.org/obo/go/extensions/gorel.owl http://purl.obolibrary.org/obo/pato.owl http://purl.obolibrary.org/obo/po.owl http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/uberon/basic.owl http://purl.obolibrary.org/obo/wbbt.owl http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl --log-info --merge-support-ontologies --merge-imports-closure --remove-subset-entities upperlevel --remove-disjoints --silence-elk --reasoner elk --solr-taxon-subset-name amigo_grouping_subset --solr-eco-subset-name go_groupings --solr-url http://localhost:8080/solr/ --solr-log /tmp/golr_timestamp.log --solr-config /home/bbop/local/src/git/amigo/metadata/ont-config.yaml --solr-load-ontology --solr-load-ontology-general --read-panther /home/bbop/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/ --solr-load-gafs http://www.geneontology.org/gene-associations/submission/paint/pre-submission/gene_association.paint_other.gaf http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz http://www.geneontology.org/gene-associations/goa_chicken.gaf.gz http://www.geneontology.org/gene-associations/gene_association.pombase.gz http://www.geneontology.org/gene-associations/gene_association.zfin.gz --solr-load-panther --solr-load-panther-general --solr-optimize

nathandunn avatar Feb 13 '18 18:02 nathandunn

@kltm Is there a way to make this command execute quicker?

I feel as though its correct. Also, about how long should it be running for?

#!/bin/bash 
java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx12G -jar ./OWLTools-Runner/bin/owltools http://purl.obolibrary.org/obo/go/extensions/go-lego.owl http://purl.obolibrary.org/obo/eco.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl/cl-basic.owl http://purl.obolibrary.org/obo/go/extensions/gorel.owl http://purl.obolibrary.org/obo/pato.owl http://purl.obolibrary.org/obo/po.owl http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/uberon/basic.owl http://purl.obolibrary.org/obo/wbbt.owl http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl --log-info --merge-support-ontologies --merge-imports-closure --remove-subset-entities upperlevel --remove-disjoints --silence-elk --reasoner elk --solr-taxon-subset-name amigo_grouping_subset --solr-eco-subset-name go_groupings --solr-url http://localhost:8080/solr/ --solr-log /tmp/golr_timestamp.log --solr-config /home/bbop/local/src/git/amigo/metadata/ont-config.yaml --solr-load-ontology --solr-load-ontology-general --read-panther /home/bbop/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/ --solr-load-gafs http://www.geneontology.org/gene-associations/submission/paint/pre-submission/gene_association.paint_other.gaf http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz http://www.geneontology.org/gene-associations/goa_chicken.gaf.gz http://www.geneontology.org/gene-associations/gene_association.pombase.gz http://www.geneontology.org/gene-associations/gene_association.zfin.gz --solr-load-panther --solr-load-panther-general --solr-optimize

nathandunn avatar Feb 13 '18 18:02 nathandunn

@kltm / @cmungall Any reason not to do SOLR7 as it seems to be a stable release, as well.

nathandunn avatar Feb 13 '18 18:02 nathandunn

Simplified command:

java -Xms1024M -DentityExpansionLimit=4086000 -Djava.awt.headless=true -Xmx8G -jar ./OWLTools-Runner/bin/owltools  \
http://purl.obolibrary.org/obo/go/extensions/go-lego.owl  \
http://purl.obolibrary.org/obo/eco.owl  \
http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl  \
http://purl.obolibrary.org/obo/cl/cl-basic.owl  \
http://purl.obolibrary.org/obo/go/extensions/gorel.owl  \
http://purl.obolibrary.org/obo/pato.owl  \
http://purl.obolibrary.org/obo/po.owl  \
http://purl.obolibrary.org/obo/chebi.owl  \
http://purl.obolibrary.org/obo/uberon/basic.owl  \
http://purl.obolibrary.org/obo/wbbt.owl  \
http://purl.obolibrary.org/obo/go/extensions/go-modules-annotations.owl  \
http://purl.obolibrary.org/obo/go/extensions/go-taxon-subsets.owl \
--log-info --merge-support-ontologies --merge-imports-closure --remove-subset-entities upperlevel --remove-disjoints --silence-elk --reasoner elk --solr-taxon-subset-name amigo_grouping_subset --solr-eco-subset-name go_groupings \
--solr-url http://localhost:8983/solr/ --solr-log /tmp/golr_timestamp.log  --solr-load-ontology --solr-load-ontology-general  --solr-load-gafs  \
http://www.geneontology.org/gene-associations/goa_chicken.gaf.gz  \
http://www.geneontology.org/gene-associations/gene_association.pombase.gz --solr-load-panther-general --solr-optimize

nathandunn avatar Feb 13 '18 18:02 nathandunn

https://github.com/owlcollab/owltools/pull/195#issuecomment-365362432 I think this is mentioned in the various tickets, but latest Solr is fine. That said, there's a possibility of pulling ahead of the monarch stack. I think we should just jump to the latest either way.

Also, it's good to get design and work-through comments in the ticket rather than a PR.

kltm avatar Feb 13 '18 19:02 kltm

Is there a way to make this command execute quicker

I'm not sure where to document this and I don't know if it's overloading this particular task, but there is a change we need to make ubiquitously across go/monarch. We frequently initialize from a large import chain available via http URLs. This is sensitive to network timeouts etc.

Two alternate strategies are possible.

  1. We run robot mirror http://robot.obolibrary.org/mirror on the root importer to make a local cache plus catalog. You can certainly investigate this for testing purposes.
  2. There is no support for owl-zip in the OWLAPI https://github.com/owlcs/owlapi/issues/375

cmungall avatar Feb 13 '18 22:02 cmungall

https://github.com/owlcollab/owltools/pull/195#issuecomment-365430981 It's good to get design and work-through comments in the ticket rather than a PR.

I think that's probably overloading what we want to do here; I think it might be better in another ticket.

kltm avatar Feb 13 '18 22:02 kltm

Error of new branch (with these changes) vs SOLR3 using the [same script] (https://github.com/nathandunn/owltools/blob/test-fixes/test3.sh) :

INFO: {} 0 29
Feb 14, 2018 6:50:17 PM org.apache.solr.common.SolrException log
SEVERE: org.apache.solr.common.SolrException: Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)
	at org.apache.solr.handler.XMLLoader.load(XMLLoader.java:81)
	at org.apache.solr.handler.ContentStreamHandlerBase.handleRequestBody(ContentStreamHandlerBase.java:58)
	at org.apache.solr.handler.RequestHandlerBase.handleRequest(RequestHandlerBase.java:129)
	at org.apache.solr.core.SolrCore.execute(SolrCore.java:1376)
	at org.apache.solr.servlet.SolrDispatchFilter.execute(SolrDispatchFilter.java:365)
	at org.apache.solr.servlet.SolrDispatchFilter.doFilter(SolrDispatchFilter.java:260)
	at org.mortbay.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1212)
	at org.mortbay.jetty.servlet.ServletHandler.handle(ServletHandler.java:399)
	at org.mortbay.jetty.security.SecurityHandler.handle(SecurityHandler.java:216)
	at org.mortbay.jetty.servlet.SessionHandler.handle(SessionHandler.java:182)
	at org.mortbay.jetty.handler.ContextHandler.handle(ContextHandler.java:766)
	at org.mortbay.jetty.webapp.WebAppContext.handle(WebAppContext.java:450)
	at org.mortbay.jetty.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:230)
	at org.mortbay.jetty.handler.HandlerCollection.handle(HandlerCollection.java:114)
	at org.mortbay.jetty.handler.HandlerWrapper.handle(HandlerWrapper.java:152)
	at org.mortbay.jetty.Server.handle(Server.java:326)
	at org.mortbay.jetty.HttpConnection.handleRequest(HttpConnection.java:542)
	at org.mortbay.jetty.HttpConnection$RequestHandler.content(HttpConnection.java:945)
	at org.mortbay.jetty.HttpParser.parseNext(HttpParser.java:756)
	at org.mortbay.jetty.HttpParser.parseAvailable(HttpParser.java:218)
	at org.mortbay.jetty.HttpConnection.handle(HttpConnection.java:404)
	at org.mortbay.jetty.bio.SocketConnector$Connection.run(SocketConnector.java:228)
	at org.mortbay.thread.QueuedThreadPool$PoolThread.run(QueuedThreadPool.java:582)
Caused by: com.ctc.wstx.exc.WstxIOException: Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)
	at com.ctc.wstx.sr.StreamScanner.throwFromIOE(StreamScanner.java:708)
	at com.ctc.wstx.sr.BasicStreamReader.next(BasicStreamReader.java:1086)
	at org.apache.solr.handler.XMLLoader.processUpdate(XMLLoader.java:104)
	at org.apache.solr.handler.XMLLoader.load(XMLLoader.java:79)
	... 22 more
Caused by: java.io.CharConversionException: Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)
	at com.ctc.wstx.io.UTF8Reader.reportInvalidOther(UTF8Reader.java:313)
	at com.ctc.wstx.io.UTF8Reader.read(UTF8Reader.java:204)
	at com.ctc.wstx.io.ReaderSource.readInto(ReaderSource.java:84)
	at com.ctc.wstx.io.BranchingReaderSource.readInto(BranchingReaderSource.java:57)
	at com.ctc.wstx.sr.StreamScanner.loadMore(StreamScanner.java:992)
	at com.ctc.wstx.sr.StreamScanner.getNext(StreamScanner.java:763)
	at com.ctc.wstx.sr.BasicStreamReader.nextFromProlog(BasicStreamReader.java:1995)
	at com.ctc.wstx.sr.BasicStreamReader.next(BasicStreamReader.java:1069)
	... 24 more

Feb 14, 2018 6:50:17 PM org.apache.solr.core.SolrCore execute
INFO: [] webapp=/solr path=/update params={wt=javabin&version=2} status=400 QTime=29

nathandunn avatar Feb 15 '18 02:02 nathandunn

And on the client:

15","obj":"GO:0005856","pred":"part_of"}],"meta":{}}[0x0][0xf]"
2018-02-14 18:50:17,398 DEBUG (wire:72)  << "HTTP/1.1 400 Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)[\r][\n]"
2018-02-14 18:50:17,399 DEBUG (wire:72)  << "Content-Type: text/html; charset=iso-8859-1[\r][\n]"
2018-02-14 18:50:17,399 DEBUG (wire:72)  << "Cache-Control: must-revalidate,no-cache,no-store[\r][\n]"
2018-02-14 18:50:17,399 DEBUG (wire:72)  << "Content-Length: 1464[\r][\n]"
2018-02-14 18:50:17,399 DEBUG (wire:72)  << "[\r][\n]"
2018-02-14 18:50:17,399 DEBUG (DefaultClientConnection:253) Receiving response: HTTP/1.1 400 Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)
2018-02-14 18:50:17,400 DEBUG (headers:256) << HTTP/1.1 400 Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)
2018-02-14 18:50:17,400 DEBUG (headers:259) << Content-Type: text/html; charset=iso-8859-1
2018-02-14 18:50:17,400 DEBUG (headers:259) << Cache-Control: must-revalidate,no-cache,no-store
2018-02-14 18:50:17,400 DEBUG (headers:259) << Content-Length: 1464
2018-02-14 18:50:17,401 DEBUG (SystemDefaultHttpClient:510) Connection can be kept alive indefinitely
2018-02-14 18:50:17,408 DEBUG (wire:72)  << "<html>[\n]"
2018-02-14 18:50:17,408 DEBUG (wire:72)  << "<head>[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<title>Error 400 Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)</title>[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "</head>[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<body><h2>HTTP ERROR 400</h2>[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<p>Problem accessing /solr/update. Reason:[\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<pre>    Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)</pre></p><hr /><i><small>Powered by Jetty://</small></i><br/>                                                [\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,409 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,410 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "<br/>                                                [\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "[\n]"
2018-02-14 18:50:17,411 DEBUG (wire:72)  << "</body>[\n]"
2018-02-14 18:50:17,412 DEBUG (wire:72)  << "</html>[\n]"
2018-02-14 18:50:17,412 DEBUG (PoolingClientConnectionManager:262) Connection [id: 0][route: {}->http://localhost:8983][state: class org.apache.solr.client.solrj.impl.HttpSolrClient] can be kept alive indefinitely
2018-02-14 18:50:17,412 DEBUG (PoolingClientConnectionManager:269) Connection released: [id: 0][route: {}->http://localhost:8983][state: class org.apache.solr.client.solrj.impl.HttpSolrClient][total kept alive: 1; route allocated: 1 of 32; total allocated: 1 of 128]
Exception in thread "main" org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr: Expected mime type application/octet-stream but got text/html. <html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"/>
<title>Error 400 Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)</title>
</head>
<body><h2>HTTP ERROR 400</h2>
<p>Problem accessing /solr/update. Reason:
<pre>    Invalid UTF-8 middle byte 0xe0 (at char #1, byte #-1)</pre></p><hr /><i><small>Powered by Jetty://</small></i><br/>                                                
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</body>
</html>

	at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:578)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:279)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:268)
	at org.apache.solr.client.solrj.SolrRequest.process(SolrRequest.java:160)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:106)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:71)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:85)
	at owltools.solrj.AbstractSolrLoader.addToServer(AbstractSolrLoader.java:169)
	at owltools.solrj.AbstractSolrLoader.addAllAndCommit(AbstractSolrLoader.java:153)
	at owltools.solrj.FlexSolrDocumentLoader.load(FlexSolrDocumentLoader.java:54)
	at owltools.cli.SolrCommandRunner.flexLoadOntologySolr(SolrCommandRunner.java:330)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:4312)
	at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
	at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
	at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)

nathandunn avatar Feb 15 '18 02:02 nathandunn

Instructions for SOLR7:

  • download / explode SOLR7
  • rm files managed-schema solrconfig.xml from files/conf
  • cp schema files (schema.xml solrconfig.xml) to files/conf
  • start server: ./bin/solr -e dih

nathandunn avatar Feb 15 '18 17:02 nathandunn

Redid the SOLR3 vs this PR merge and it worked (yeah!) running this (https://github.com/nathandunn/owltools/blob/test-fixes/test3-local.sh)

though requires a local copy of the GAF file as the scripts don't like https (maybe something to fix).

Going to need to try again SOLR7 next.

nathandunn avatar Feb 15 '18 18:02 nathandunn

From: https://github.com/monarch-initiative/solr-docker-monarch-golr/blob/master/files/run.sh solr6 instructions:

  • ./bin/solr start
  • ./bin/solr create -c golr
  • ./bin/solr stop
  • rm -f server/solr/golr/conf/managed-schema
  • wget https://raw.githubusercontent.com/berkeleybop/bbop-manager-golr/master/solr/server/solr/amigo/conf/managed-schema
  • cp managed-schema server/solr/golr/conf/managed-schema

  • cp ../../amigo/golr/solr/conf/schema.xml server/solr/golr/conf/ # I don't think you want the serverconfig.xml probably don't need schema.xml either

  • ./bin/solr start
  • run https://github.com/nathandunn/owltools/blob/test-fixes/test4.sh

nathandunn avatar Feb 15 '18 21:02 nathandunn

Still getting:

018-02-15 13:49:26,369 DEBUG (PoolingClientConnectionManager:269) Connection released: [id: 0][route: {}->http://localhost:8983][state: class org.apache.solr.client.solrj.impl.HttpSolrClient][total kept alive: 1; route allocated: 1 of 32; total allocated: 1 of 128]
Exception in thread "main" org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr: Expected mime type application/octet-stream but got text/html. <html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=utf-8"/>
<title>Error 404 Not Found</title>
</head>
<body><h2>HTTP ERROR 404</h2>
<p>Problem accessing /solr/update. Reason:
<pre>    Not Found</pre></p>
</body>
</html>

	at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:578)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:279)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:268)

nathandunn avatar Feb 15 '18 21:02 nathandunn

If we are truly confident that this branch is compatible with both solr3 and solr6, then we can merge it, simplifying things a lot.

Perhaps set up a different PR for discussion of solr7 client code, or for dockerizing solr6/7?

cmungall avatar Feb 15 '18 21:02 cmungall

Lemme bounce over and test...

kltm avatar Feb 15 '18 22:02 kltm

...or not. The build fails for me on this branch, but not master with: mvn clean install -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true in OWLTools-Parent

kltm avatar Feb 15 '18 22:02 kltm

Confident with 3. Not confident with 6, though its probably an error on my part. I'm pretty confident that the migration between 6 and 7 shouldn't pose any problem.

nathandunn avatar Feb 15 '18 22:02 nathandunn

It works for me. . . . How is it failing for you?

On Feb 15, 2018, at 2:18 PM, kltm [email protected] wrote:

...or not. The build fails for me on this branch, but not master with: mvn clean install -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true in OWLTools-Parent

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/owlcollab/owltools/pull/195#issuecomment-366080653, or mute the thread https://github.com/notifications/unsubscribe-auth/AAt2qi9JLsWerD4JkVaJ_ktLdVCeqEMRks5tVK1NgaJpZM4NNLEh.

nathandunn avatar Feb 15 '18 22:02 nathandunn

Are you running the top-level build.sh?

About a hundred unfound symbols a la:

[ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[565,22] cannot find symbol
  symbol:   class SolrInputDocument
  location: class owltools.solrj.GafSolrDocumentLoader
[ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[570,17] cannot find symbol
  symbol:   class SolrInputDocument
  location: class owltools.solrj.GafSolrDocumentLoader
[ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[570,53] cannot find symbol
  symbol:   class SolrInputDocument
  location: class owltools.solrj.GafSolrDocumentLoader
[ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/PANTHERSolrDocumentLoader.java:[49,33] cannot find symbol
  symbol:   class SolrInputDocument
  location: class owltools.solrj.PANTHERSolrDocumentLoader
[INFO] 102 errors

kltm avatar Feb 15 '18 22:02 kltm

That’s what I did originally. I’m wondering if you need to blow out your maven because of the version changes?

That is weird. I have done about 3 clean checkouts as well with different branches and no problems.

On Feb 15, 2018, at 2:37 PM, kltm [email protected] wrote:

Are you running the top-level build.sh?

About a hundred unfound symbols a la:

[ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[565,22] cannot find symbol symbol: class SolrInputDocument location: class owltools.solrj.GafSolrDocumentLoader [ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[570,17] cannot find symbol symbol: class SolrInputDocument location: class owltools.solrj.GafSolrDocumentLoader [ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/GafSolrDocumentLoader.java:[570,53] cannot find symbol symbol: class SolrInputDocument location: class owltools.solrj.GafSolrDocumentLoader [ERROR] /home/sjcarbon/local/src/git/owltools/OWLTools-Solr/src/main/java/owltools/solrj/PANTHERSolrDocumentLoader.java:[49,33] cannot find symbol symbol: class SolrInputDocument location: class owltools.solrj.PANTHERSolrDocumentLoader [INFO] 102 errors

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nathandunn avatar Feb 15 '18 22:02 nathandunn

I think its working, but I need to update the schema.xml file for 6 / 7:

golr: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Unable to use updateLog: _version_ field must exist in schema and be searchable (indexed or docValues) and retrievable(stored or docValues) and not multiValued (_version_ does not exist)

if you have one, great, otherwise I'll work through this:

https://stackoverflow.com/questions/36942477/solr-version-field-must-exist-in-schema-and-be-searchable

nathandunn avatar Feb 15 '18 22:02 nathandunn

Works using the managed schema: https://raw.githubusercontent.com/berkeleybop/bbop-manager-golr/master/solr/server/solr/amigo/conf/managed-schema

nathandunn avatar Feb 15 '18 23:02 nathandunn

and change the --solr-url from http://localhost:8983/solr/ to http://localhost:8983/solr/golr/

nathandunn avatar Feb 15 '18 23:02 nathandunn 

2018-02-15 15:33:36,056 DEBUG (PoolingClientConnectionManager:269) Connection released: [id: 0][route: {}->http://localhost:8983][state: class org.apache.solr.client.solrj.impl.HttpSolrClient][total kept alive: 1; route allocated: 1 of 32; total allocated: 1 of 128]
Exception in thread "main" org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr/golr: SolrCore 'golr' is not available due to init failure: fieldType 'text_general' not found in the schema
	at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:610)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:279)
	at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:268)
	at org.apache.solr.client.solrj.SolrRequest.process(SolrRequest.java:160)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:106)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:71)
	at org.apache.solr.client.solrj.SolrClient.add(SolrClient.java:85)

nathandunn avatar Feb 15 '18 23:02 nathandunn