Installation and Setup V3: Unterschied zwischen den Versionen

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=Standalone=
 +
All-in-one server mainly intended for exploration, testing and "to-go"-scenarios.
 +
 +
==Release Files==
 +
 +
*<code>WebCts2LE-embedded-jetty.zip</code>: CTS2-LE jetty server
 +
 +
==Required Software==
 +
 +
*Java 8
 +
 +
==Installation & Running==
 +
 +
*unzip <code>WebCts2LE-embedded-jetty.zip</code> to a directory (denoted by <code><W></code> in the following)
 +
*go to directory <code><W></code>
 +
*start command: <code>./bin/startup.sh -port <port></code>
 +
*:<span style="color:DarkGray">Windows Powershell: .\bin\startup.bat -port <port></span>
 +
*shutdown command: <code>./bin/shutdown.sh <port></code>
 +
*:<span style="color:DarkGray">Windows Powershell: ctrl-c</span>
 +
*admin navigation ui: <code>http://<host>:<port>/WebCts2LE</code>
 +
 +
==Docker==
 +
 +
'''TO BE UPDATED'''
 +
 +
Let <code><DI></code> be the docker image name. Run the image with
 +
 +
*<code>docker run -dit --restart=always --name=<name> --mount source=<volume>,target=/etc/webcts2le/inst/cts2lef-resources/resources-custom -p <port>:9090 <DI></code>
 +
*:<span style="color:DarkGray">on windows git bash: you have to exec before: docker() { (export MSYS_NO_PATHCONV=1; "docker.exe" "$@"); }</span>
 +
 +
where
 +
 +
*<code><name></code> is the container name
 +
*<code><volume></code> is the volume name (it will be created if it does not exist and it will be reused !)
 +
*<code><port></code> is the delivered port (cf. [[#Installation_.26_Running|Installation & Running]] above)
 +
 +
<!--
 +
= External Storage/Index Backends =
 +
This version is intended for use in environments where the data backend can run on separate machines.
 +
 
== Release Files ==
 
== Release Files ==
  
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== Required Software/Server ==
 
== Required Software/Server ==
  
−
=== Fuseki Installation ===
+
* Java 8
 +
 
 +
=== Fuseki Installation & Running ===
 
* unzip <code>fuseki-cts2le.zip</code> to a directory (denoted by <code><F1></code> in the following)
 
* unzip <code>fuseki-cts2le.zip</code> to a directory (denoted by <code><F1></code> in the following)
 
* unzip <code>apache-jena-fuseki-3.8.0.zip</code> from <code>https://jena.apache.org/download/</code> (the extracted directory <code>apache-jena-fuseki-3.8.0</code> is denoted by <code><F2></code> in the following)
 
* unzip <code>apache-jena-fuseki-3.8.0.zip</code> from <code>https://jena.apache.org/download/</code> (the extracted directory <code>apache-jena-fuseki-3.8.0</code> is denoted by <code><F2></code> in the following)
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*: <span style="color:DarkGray">Windows Powershell: ctrl-c</span>
 
*: <span style="color:DarkGray">Windows Powershell: ctrl-c</span>
  
−
=== Solr Installation ===  
+
=== Solr Installation & Running ===  
 
* unzip <code>solr-cts2le.zip</code> to a directory (denoted by <code><S1></code> in the following)
 
* unzip <code>solr-cts2le.zip</code> to a directory (denoted by <code><S1></code> in the following)
 
* unzip <code>solr-7.6.0.zip</code> from <code>http://lucene.apache.org/solr/downloads.html</code> (the extracted directory <code>solr-7.6.0</code> is denoted by <code><S2></code> in the following)
 
* unzip <code>solr-7.6.0.zip</code> from <code>http://lucene.apache.org/solr/downloads.html</code> (the extracted directory <code>solr-7.6.0</code> is denoted by <code><S2></code> in the following)
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* shutdown command: <code>./bin/solr stop -all</code>
 
* shutdown command: <code>./bin/solr stop -all</code>
  
−
== WebCts2LE Installation ==
+
== Installation & Running ==
−
 
 
−
=== General ===
 
 
* unzip <code>WebCts2LE-embedded-jetty.zip</code> to a directory (denoted by <code><W></code> in the following)
 
* unzip <code>WebCts2LE-embedded-jetty.zip</code> to a directory (denoted by <code><W></code> in the following)
−
 
−
=== Embedded Jetty Variant ===
 
−
 
 
* edit file <code><W>/CTS2LE_resources/resources-custom/setting.json</code>. The following fragment shows the relevant lines to adapt:
 
* edit file <code><W>/CTS2LE_resources/resources-custom/setting.json</code>. The following fragment shows the relevant lines to adapt:
 
<syntaxhighlight lang="javascript">
 
<syntaxhighlight lang="javascript">
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* shutdown command: <code>./bin/shutdown.sh <port></code>
 
* shutdown command: <code>./bin/shutdown.sh <port></code>
 
*: <span style="color:DarkGray">Windows Powershell: ctrl-c</span>
 
*: <span style="color:DarkGray">Windows Powershell: ctrl-c</span>
−
* navigation ui: <code>http://<host>:<port>/WebCts2LE</code>
+
* admin navigation ui: <code>http://<host>:<port>/WebCts2LE</code>
  
−
== WebCts2LE Basic Security ==
 
−
The Embedded Jetty Variant supports simple security based on Basic Access Authentication for services that modify the data base (advanced security will not be supported at this architecture level, instead special security components should be placed on top of WebCts2LE).
 
−
Changing security (see HashLoginService at https://www.eclipse.org/jetty/documentation/9.4.x/configuring-security.html for details):
 
−
* edit <code><W>/conf/basic-realm.properties</code>. It contains <code>username: password,rolename</code>, e.g. <code>admin: webcts2le-admin,admin</code>. Change username or password if needed. Role name <code>admin</code> should not be changed.
 
−
 
−
* run service with basic authentication via option flag: <code>./bin/startup.sh -port <port> -basic_auth</code>
 
  
 
== (Bulk-)Loading of Terminologies ==
 
== (Bulk-)Loading of Terminologies ==
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*: <span style="color:DarkGray">if WebCts2LE is started with <code>-basic_auth</code> then the command has to be extended by <code>--user <user> --passwd <passwd></code></span>
 
*: <span style="color:DarkGray">if WebCts2LE is started with <code>-basic_auth</code> then the command has to be extended by <code>--user <user> --passwd <passwd></code></span>
  
−
Currently, the estimated load time (fuseki quad store) is about 30 minutes (~3GHz/16GB) for all public terminologies exclusive SNOMED.
+
Currently, the estimated load time (fuseki quad store) is about 40 minutes (~3GHz/16GB) for all public terminologies exclusive SNOMED.
 
Due to quad store constraints (i.e. load time roughly equals removal time) it is recommended to delete all store files on <code><F2>/run/databases/cts2le</code> (for <code><F2></code> see '''Fuseki Installation''' above) if an existing filled store is the target of bulk load.
 
Due to quad store constraints (i.e. load time roughly equals removal time) it is recommended to delete all store files on <code><F2>/run/databases/cts2le</code> (for <code><F2></code> see '''Fuseki Installation''' above) if an existing filled store is the target of bulk load.
  
−
index update (possibly with basic auth credentials):
+
Subsequently, perform an index and suggester update (possibly with basic auth credentials):
 
* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/update</code> to update the search index
 
* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/update</code> to update the search index
  
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* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/suggester/update</code> to update the suggester index
 
* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/suggester/update</code> to update the suggester index
−
* restart WebCts2LE server
+
* restart server
  
 
=== Custom FHIR Terminologies ===
 
=== Custom FHIR Terminologies ===
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* run <code>java -jar cts2le-3-command-bulk.jar --command fileToStore --format fhir --sourceLoc <F> --targetLoc http://<host>:<port>/WebCts2LE</code>
 
* run <code>java -jar cts2le-3-command-bulk.jar --command fileToStore --format fhir --sourceLoc <F> --targetLoc http://<host>:<port>/WebCts2LE</code>
 
* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/suggester/update</code> to update the suggester index (possibly with basic auth credentials)
 
* run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/suggester/update</code> to update the suggester index (possibly with basic auth credentials)
−
* restart WebCts2LE server
+
* restart server
 +
 
 +
-->
 +
 
 +
=Basic Security=
 +
The Embedded Jetty Variant supports simple security based on Basic Access Authentication for services that modify the data base (advanced security will not be supported at this architecture level, instead special security components should be placed on top of WebCts2LE).
 +
Changing security (see HashLoginService at https://www.eclipse.org/jetty/documentation/9.4.x/configuring-security.html for details):
 +
 
 +
*edit <code><W>/conf/basic-realm.properties</code>. It contains <code>username: password,rolename</code>, e.g. <code>admin: webcts2le-admin,admin</code>. Change username or password if needed. Role name <code>admin</code> should not be changed.
 +
 
 +
*run service with basic authentication via option flag: <code>./bin/startup.sh -port <port> -basic_auth</code>

Aktuelle Version vom 4. September 2020, 14:37 Uhr

Standalone

All-in-one server mainly intended for exploration, testing and "to-go"-scenarios.

Release Files

  • WebCts2LE-embedded-jetty.zip: CTS2-LE jetty server

Required Software

  • Java 8

Installation & Running

  • unzip WebCts2LE-embedded-jetty.zip to a directory (denoted by <W> in the following)
  • go to directory <W>
  • start command: ./bin/startup.sh -port <port>
    Windows Powershell: .\bin\startup.bat -port <port>
  • shutdown command: ./bin/shutdown.sh <port>
    Windows Powershell: ctrl-c
  • admin navigation ui: http://<host>:<port>/WebCts2LE

Docker

TO BE UPDATED

Let <DI> be the docker image name. Run the image with

  • docker run -dit --restart=always --name=<name> --mount source=<volume>,target=/etc/webcts2le/inst/cts2lef-resources/resources-custom -p <port>:9090 <DI>
    on windows git bash: you have to exec before: docker() { (export MSYS_NO_PATHCONV=1; "docker.exe" "$@"); }

where

  • <name> is the container name
  • <volume> is the volume name (it will be created if it does not exist and it will be reused !)
  • <port> is the delivered port (cf. Installation & Running above)


Basic Security

The Embedded Jetty Variant supports simple security based on Basic Access Authentication for services that modify the data base (advanced security will not be supported at this architecture level, instead special security components should be placed on top of WebCts2LE). Changing security (see HashLoginService at https://www.eclipse.org/jetty/documentation/9.4.x/configuring-security.html for details):

  • edit <W>/conf/basic-realm.properties. It contains username: password,rolename, e.g. admin: webcts2le-admin,admin. Change username or password if needed. Role name admin should not be changed.
  • run service with basic authentication via option flag: ./bin/startup.sh -port <port> -basic_auth
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