Add TPF container

README.md

@@ -1,9 +1,10 @@
 # Dockerized VIVO
 
-This project creates three dockerized containers,
+This project creates four dockerized containers,
 - `vivo` The vivo instance
 - `solr` A standalone solr instance, based on a solr docker image
-- `mariadb` A standalone mariadb instance.
+- `mariadb` A standalone mariadb instance
+- `tpf` A standalone [Triple Pattern Fragment server](https://linkeddatafragments.org/) that queries the vivo instance.
 
 These images can be used together, or independently to setup some development or working VIVO docker instances.
 
@@ -21,16 +22,25 @@ Regardless of the usage, you will need to build the images, which require the fo
    docker-compose up -d
 ```
 
+### Verification
+
+After running the above steps,
+1. Verify your VIVO by navigating to:
+   - [http://localhost:8080/vivo/](http://localhost:8080/vivo/)
+   - username: vivo_root@mydomain.edu, password: rootPassword
+1. Verify your Solr by navigating to:
+   - [http://localhost:8983/solr/](http://localhost:8983/solr/)
+1. Verify your Triple Pattern Fragment server by navigating to:
+   - [http://localhost:7070/tpf/](http://localhost:7070/tpf/)
+
 ## VIVO Runtime Example
 
 The example [docker-compose.yml](docker-compose.yml) is a typical installation for trying out a simple VIVO installation in docker. This file starts three containers and uses the standard SDB system with the mariadb backend.  This example also shows how a local directory [example-config](example-config) is used to overwrite the default `runtime.properties` as installed by the Dockerfile.  Here the root password, and the domain are modified.
 
 ```bash
 docker-compose up -d
 ```
- Will start this project.  Navigating to http://localhost:8080/vivo will then start this simple instance.
-
- If you get an error indicating that the database was not found, this could be due to a bug where the vivo instance is not waiting on the mariadb instance to initialize.  IF you have this error, try `docker-compose down; docker-compose up -d`.
+When navigating to http://localhost:8080/vivo/, if you get an error indicating that the database was not found, this could be due to a bug where the vivo instance is not waiting on the mariadb instance to initialize.  IF you have this error, try `docker-compose down; docker-compose up -d`.
 
 
 ## VIVO Development

docker-compose.yml

@@ -31,6 +31,13 @@ services:
     ports:
       - 8080:8080
 
+  tpf:
+    build:
+      context: ./tpf
+    volumes:
+      - ./tpf/config:/usr/local/tpf/config
+    ports:
+      - 7070:8080
 
 volumes:
   solr-data:

tpf/Dockerfile

@@ -0,0 +1,24 @@
+FROM tomcat:9.0.27-jdk8-openjdk
+
+MAINTAINER Andrew Woods<awoods@lyrasis.org>
+
+RUN apt-get update
+RUN apt-get install -y maven git
+
+ENV TPF_MD5 c8cdb3350a0b7cf94c6a3481ca12d8d8
+ENV TPF_VERSION v0.2.4a
+
+RUN mkdir -v /opt/tpf
+WORKDIR /opt/tpf
+RUN echo "$TPF_MD5  tpf.war" > tpf.war.md5
+RUN wget -O tpf.war https://github.com/awoods/Server.Java/releases/download/${TPF_VERSION}/ldfserver-0.2.3.war && \
+     md5sum -c tpf.war.md5
+
+RUN mkdir /usr/local/tomcat/webapps/tpf
+WORKDIR /usr/local/tomcat/webapps/tpf
+RUN jar xvf /opt/tpf/tpf.war
+
+# Update the web.xml
+COPY ./web.xml /usr/local/tomcat/webapps/tpf/WEB-INF/web.xml
+
+RUN export CATALINA_OPTS="-Xms512m -Xmx512m -XX:MaxPermSize=128m"

tpf/config/config.json

@@ -0,0 +1,46 @@
+{
+  "title": "VIVO Linked Data Fragments server",
+
+  "datasourcetypes": {   
+    "SparqlDatasource"   : "org.linkeddatafragments.datasource.sparql.SparqlDataSourceType"
+  },
+
+  "datasources": {
+    "vivo": {
+      "title": "VIVO Linked Data TPF",
+      "type": "SparqlDatasource",
+      "description": "VIVO Semantic TPF server",
+      "settings": { "endpoint": "http://vivo:8080/vivo/api/sparqlQuery",
+                    "username": "vivo_root@mydomain.edu",
+                    "password": "monkey" }
+    }
+  },
+
+  "prefixes": {
+    "rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
+    "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+    "hydra": "http://www.w3.org/ns/hydra/core#",
+    "void": "http://rdfs.org/ns/void#",
+    "bibo": "http://purl.org/ontology/bibo/",
+    "c4o": "http://purl.org/spar/c4o/",
+    "cito": "http://purl.org/spar/cito/",
+    "dcterms": "http://purl.org/dc/terms/",
+    "event": "http://purl.org/NET/c4dm/event.owl#",
+    "fabio": "http://purl.org/spar/fabio/",
+    "foaf": "http://xmlns.com/foaf/0.1/",
+    "geo": "http://aims.fao.org/aos/geopolitical.owl#",
+    "obo": "http://purl.obolibrary.org/obo/",
+    "ocrer": "http://purl.org/net/OCRe/research.owl#",
+    "ocresst": "http://purl.org/net/OCRe/statistics.owl#",
+    "ocresd": "http://purl.org/net/OCRe/study_design.owl#",
+    "ocresp": "http://purl.org/net/OCRe/study_protocol.owl#",
+    "ro": "http://purl.obolibrary.org/obo/ro.owl#",
+    "skos": "http://www.w3.org/2004/02/skos/core#",
+    "swo": "http://www.ebi.ac.uk/efo/swo/",
+    "vcard": "http://www.w3.org/2006/vcard/ns#",
+    "vitro-public": "http://vitro.mannlib.cornell.edu/ns/vitro/public#",
+    "vivo": "http://vivoweb.org/ontology/core#",
+    "scires": "http://vivoweb.org/ontology/scientific-research#",
+    "vann": "http://purl.org/vocab/vann/"
+  }
+}

tpf/web.xml

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<web-app id="WebApp_ID" version="2.5" xmlns="http://java.sun.com/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://java.sun.com/xml/ns/javaee http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd">
+    <display-name>Linked Data Fragments Server</display-name>
+    <servlet>
+        <display-name>TpfServlet</display-name>
+        <servlet-name>TpfServlet</servlet-name>
+        <servlet-class>org.linkeddatafragments.servlet.LinkedDataFragmentServlet</servlet-class>
+        <init-param>
+          <param-name>configFile</param-name>
+          <param-value>/usr/local/tpf/config/config.json</param-value>
+        </init-param>
+    </servlet>
+    <servlet-mapping>
+        <servlet-name>TpfServlet</servlet-name>
+        <url-pattern>/*</url-pattern>
+    </servlet-mapping>
+</web-app>