Advanced Administration - Revision history

Alexskr: update links

2023-03-23T22:47:00Z

update links

Alexskr at 22:44, 23 March 2023

2023-03-23T22:44:40Z

Graybeal: tagged as Migrated

2020-06-13T01:21:20Z

tagged as Migrated

Graybeal: forwarded to new content

2020-06-13T01:03:04Z

forwarded to new content

Vemonet at 15:47, 30 March 2016

2016-03-30T15:47:36Z

Vemonet: /* Annotator cache and dictionary update */

2016-01-28T17:18:38Z

Annotator cache and dictionary update

Vemonet: 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..."

2016-01-28T17:15:54Z

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..."

New page

[[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 ssh connexion to your Appliance.<br/>
To simplify the examples we will consider we are using a Virtual Appliance deployed at '''http://my-bioportal-vm/'''

= Solr search index =

== 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

@@ Line 2: / Line 2: @@
 [[Category:Migrated to GitHub]]
-This content has been moved! Please visit it at our new [https://ontoportal.github.io/documentation/administration/ OntoPortal Virtual Appliance Administration pages].
+This content has been moved! Please visit it at our new [https://ontoportal.github.io/documentation/administration OntoPortal Virtual Appliance Administration pages].
-You can find Advanced content in each of the sections [https://ontoportal.github.io/documentation/administration/steps/ Installing OntoPortal], [https://ontoportal.github.io/documentation/administration/ontologies/ Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/documentation/administration/management/ Managing Your System].
+You can find Advanced content in each of the sections [https://ontoportal.github.io/documentation/administration/steps Installing OntoPortal], [https://ontoportal.github.io/documentation/administration/ontologies Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/documentation/administration/management Managing Your System].

@@ Line 2: / Line 2: @@
 [[Category:Migrated to GitHub]]
-This content has been moved! Please visit it at our new [https://ontoportal.github.io/administration/ OntoPortal Virtual Appliance Administration pages].
+This content has been moved! Please visit it at our new [https://ontoportal.github.io/documentation/administration/ OntoPortal Virtual Appliance Administration pages].
-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].
+You can find Advanced content in each of the sections [https://ontoportal.github.io/documentation/administration/steps/ Installing OntoPortal], [https://ontoportal.github.io/documentation/administration/ontologies/ Managing Ontologies in OntoPortal], and [https://ontoportal.github.io/documentation/administration/management/ Managing Your System].

@@ Line 1: / Line 1: @@
 [[Category:NCBO Virtual Appliance]]
 This content has been moved! Please visit it at our new [https://ontoportal.github.io/administration/ OntoPortal Virtual Appliance Administration pages].
 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].

@@ Line 1: / Line 1: @@
 [[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 ssh connexion to your Appliance.<br/>
+This content has been moved! Please visit it at our new [https://ontoportal.github.io/administration/ OntoPortal Virtual Appliance Administration pages].
-= NCBO architecture diagram =
+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].

← Older revision		Revision as of 17:18, 28 January 2016
Line 35:		Line 35:


−	= Annotator cache and dictionary ~~update~~ =	+	= Updating the Annotator cache and dictionary =

	See the [http://www.bioontology.org/wiki/index.php/Annotator_Documentation#Update_cache_and_dictionary Annotator Documentation]		See the [http://www.bioontology.org/wiki/index.php/Annotator_Documentation#Update_cache_and_dictionary Annotator Documentation]

@@ Line 3: / Line 3: @@
 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/>
 To simplify the examples we will consider we are using a Virtual Appliance deployed at '''http://my-bioportal-vm/'''
 = Solr search index =