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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 == | ||
| + | |||
| + | * <code>fuseki-cts2le.zip</code>: config files for fuseki | ||
| + | * <code>solr-cts2le.zip</code>: config files and blank index directory for solr | ||
| + | * <code>WebCts2LE-embedded-jetty.zip</code>: CTS2-LE jetty server | ||
| + | * <code>cts2le-3-command-bulk.jar</code>: CLI for bulk loading | ||
| + | * <code>ntriples-collection.zip</code>: standard terminologies for bulk loading | ||
| + | |||
== 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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* run <code>./fuseki start</code> and <code>./fuseki stop</code> subsequently (in order to let directory <code><F2>/run</code> be generated) | * run <code>./fuseki start</code> and <code>./fuseki stop</code> subsequently (in order to let directory <code><F2>/run</code> be generated) | ||
* copy <code><F1>/cts2le.ttl</code> to <code><F2>/run/configuration</code> | * copy <code><F1>/cts2le.ttl</code> to <code><F2>/run/configuration</code> | ||
| + | * copy <code><F1>/log4j.properties</code> to <code><F2>/run</code> | ||
* start command: <code>./fuseki start</code> | * start command: <code>./fuseki start</code> | ||
| + | *: <span style="color:DarkGray">Windows Powershell: .\fuseki-server.bat</span> | ||
* shutdown command: <code>./fuseki stop</code> | * shutdown command: <code>./fuseki stop</code> | ||
| − | === Solr Installation === | + | *: <span style="color:DarkGray">Windows Powershell: ctrl-c</span> |
| + | |||
| + | === 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) | ||
| Zeile 16: | Zeile 70: | ||
* shutdown command: <code>./bin/solr stop -all</code> | * shutdown command: <code>./bin/solr stop -all</code> | ||
| − | == | + | == Installation & Running == |
| − | |||
| − | |||
* 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) | ||
| − | |||
| − | |||
* 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"> | ||
| Zeile 38: | Zeile 88: | ||
* go to directory <code><W></code> | * go to directory <code><W></code> | ||
* start command: <code>./bin/startup.sh -port <port></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> | * shutdown command: <code>./bin/shutdown.sh <port></code> | ||
| − | * navigation ui: <code>http://<host>:<port>/WebCts2LE</code> | + | *: <span style="color:DarkGray">Windows Powershell: ctrl-c</span> |
| + | * admin navigation ui: <code>http://<host>:<port>/WebCts2LE</code> | ||
| + | |||
| + | |||
| + | == (Bulk-)Loading of Terminologies == | ||
| + | |||
| + | === Standard Terminologies (RDF-ntriples) === | ||
| + | |||
| + | * unzip <code>ntriples-collection.zip</code> to a directory (denoted by <code><N></code> in the following) | ||
| + | * unzip <code>cts2le-3-command-bulk.jar</code> to a directory (denoted by <code><C></code> in the following) | ||
| + | * go to directory <code><C></code> | ||
| + | * run <code>java -jar cts2le-3-command-bulk.jar --command fileToStore --format ntriples --sourceLoc <N> --targetLoc http://<host>:<port>/WebCts2LE</code> | ||
| + | *: <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 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. | ||
| + | |||
| + | 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 | ||
| + | |||
| + | Currently, the estimated index time (solr) is about 15 minutes (~3GHz/16GB). | ||
| + | You can delete all index files on <code><S1>/core-cts2le/data/index</code> (for <code><S1></code> see '''Solr Installation''' above). | ||
| + | |||
| + | * run <code>GET http://<host>:<port>/WebCts2LE/service/manage/index/suggester/update</code> to update the suggester index | ||
| + | * restart server | ||
| + | |||
| + | === Custom FHIR Terminologies === | ||
| + | |||
| + | * let <code><F></code> denote a directory containing FHIR xml files | ||
| + | * go to directory <code><C></code> (see above) | ||
| + | * 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) | ||
| + | * 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. | |
| − | |||
| − | |||
| − | * edit <code><W>/conf/basic-realm.properties</code>. It contains <code>username: password | ||
| − | * run service with basic authentication via option flag: <code>./bin/startup.sh -port <port> -basic_auth</code> | + | *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
Inhaltsverzeichnis
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.zipto 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 containsusername: password,rolename, e.g.admin: webcts2le-admin,admin. Change username or password if needed. Role nameadminshould not be changed.
- run service with basic authentication via option flag:
./bin/startup.sh -port <port> -basic_auth
