Nathan Dunn

@keiranmraine I did something similar to this and got it to work over selenium.

Yeah, it died for me here: ``` 18-02-13 11:26:59,317 INFO (AbstractSolrLoader:61) Server at: http://localhost:8983/solr/ 2018-02-13 11:26:59,372 INFO (SolrCommandRunner:324) Trying ontology flex load. Exception in thread "main" java.lang.NullPointerException at owltools.flex.FlexCollection.wring(FlexCollection.java:196) at...

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

- [x] test master vs SOLR3 - [x] test branch versus SOLR3 - [ ] test branch versus SOLR7 - [ ] **create instructions for SOLR7** (put in PR?) -...

``` #!/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...

@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...

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

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...

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...

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://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"...