Difference between revisions of "Advanced Administration"

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(Created page with "Category:NCBO Virtual Appliance On this page you will find some guidelines on how Advanced administration of the BioPortal Virtual Appliance. To proceed you will need a s...")
 
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[[Category:NCBO Virtual Appliance]]
 
[[Category:NCBO Virtual Appliance]]
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[[Category:Migrated to GitHub]]
  
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].
To simplify the examples we will consider we are using a Virtual Appliance deployed at '''http://my-bioportal-vm/'''
 
  
= Solr search index =
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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].
 
 
== Access to solr ==
 
 
 
It is hosted by the tomcat on the port 8082
 
http://my-bioportal-vm:8082/solr
 
 
 
There are 2 cores:
 
 
 
* core1 is used for search
 
* core2 is used when doing a full reindexing (it allows the search to work fine when reindexing the whole bioportal)
 
 
 
 
 
To swap the 2 cores:
 
 
 
* Go to core admin tab
 
* Select core1
 
* Hit the "Swap" button
 
 
 
== Reindex all ontologies in core2 ==
 
 
 
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)
 
 
 
bin/ncbo_ontology_index -a -l logs/reindexing_all.log -c http://my-bioportal-vm:8082/solr/core2
 
 
 
 
 
== Reindex only the specified ontologies in core2 ==
 
 
 
bin/ncbo_ontology_index -o STY,SNOMED -l logs/reindexing_STY_SNOMED.log -c http://my-bioportal-vm:8082/solr/core2
 
 
 
 
 
= Annotator cache and dictionary update =
 
 
 
See the [http://www.bioontology.org/wiki/index.php/Annotator_Documentation#Update_cache_and_dictionary Annotator Documentation]
 
 
 
= Common troubles =
 
 
 
== ontologies_report.json is missing ==
 
 
 
When running some job you can face the following error:
 
ontologies_report.json : No such file or directory
 
 
 
To avoid it you have to create a ''ontologies_report.json'' file at the following location:
 
/srv/reports/ontologies_report.json
 
 
 
It has to be owned by ncbobp:ncbobp and to have permission 666
 

Latest revision as of 17:21, 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.