Difference between revisions of "Advanced Administration"

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[[Category:NCBO Virtual Appliance]]
 
[[Category:NCBO Virtual Appliance]]
  
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On this page you will find some guidelines on how Advanced administration of the BioPortal Virtual Appliance. To proceed you will need a ssh connexion to your Appliance.<br/>
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This content has been moved! Please visit it at our new [https://ontoportal.github.io/administration/ OntoPortal Virtual Appliance Administration pages].
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To simplify the examples we will consider we are using a Virtual Appliance deployed at '''http://my-bioportal-vm/'''
 
  
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= NCBO architecture diagram =
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You can find Advanced content in each of the sections [https://ontoportal.github.io/administration/steps/ Installing OntoPortal], [https://ontoportal.github.io/administration/ontologies/ Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/administration/management/ Managing Your System].
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[[File:Ncbo_architecture.png]]
 
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= Solr search index =
 
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== Access to solr ==
 
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It is hosted by the tomcat on the port 8082
 
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http://my-bioportal-vm:8082/solr
 
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There are 2 cores:
 
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* core1 is used for search
 
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* core2 is used when doing a full reindexing (it allows the search to work fine when reindexing the whole bioportal)
 
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To swap the 2 cores:
 
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* Go to core admin tab
 
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* Select core1
 
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* Hit the "Swap" button
 
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== Reindex all ontologies in core2 ==
 
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Re-indexing in the core2 allows the BioPortal Appliance to not stop working during the reindexing (you just have to swap the cores when the reindexing is over)
 
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bin/ncbo_ontology_index -a -l logs/reindexing_all.log -c http://my-bioportal-vm:8082/solr/core2
 
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== Reindex only the specified ontologies in core2 ==
 
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bin/ncbo_ontology_index -o STY,SNOMED -l logs/reindexing_STY_SNOMED.log -c http://my-bioportal-vm:8082/solr/core2
 
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= Updating the Annotator cache and dictionary =
 
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See the [http://www.bioontology.org/wiki/index.php/Annotator_Documentation#Update_cache_and_dictionary Annotator Documentation]
 
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= Common troubles =
 
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== ontologies_report.json is missing ==
 
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When running some job you can face the following error:
 
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ontologies_report.json : No such file or directory
 
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To avoid it you have to create a ''ontologies_report.json'' file at the following location:
 
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/srv/reports/ontologies_report.json
 
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It has to be owned by ncbobp:ncbobp and to have permission 666
 

Revision as of 17:03, 12 June 2020


This content has been moved! Please visit it at our new OntoPortal Virtual Appliance Administration pages.

You can find Advanced content in each of the sections Installing OntoPortal, Managing Ontologies in OntoPortal, and Managing Your System.

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=Advanced_Administration&oldid=13016"