Reorganising repo, adding some docs, updating loader config etc.

.dockerignore

@@ -11,3 +11,5 @@ solr-config/data
 *.xml
 *.md
 !oxo-web/target/oxo-web.war
+__pycache__
+*.pyc

.gitignore

@@ -3,13 +3,11 @@ target/
 *.DS_store
 .idea
 *~
-data
 properties
-sorl-config/data
-db
 application.properties
-dataloading/venv/
-dataloading/oxo/config_localdev.ini
 *.pyc
 .mvn
 oxo-web/src/main/resources/templates/search-orig.html
+oxo-web/src/main/asciidoc/generated-snippets
+oxo-web/src/main/resources/static
+.settings

.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>oxo</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

README.md

@@ -0,0 +1,64 @@
+OxO is a service for finding mappings (or cross-references) between terms from
+ontologies, vocabularies and coding standards. OxO imports mappings from a
+variety of sources including the [Ontology Lookup Service](https://www.ebi.ac.uk/ols/index) and a subset of
+mappings provided by the [UMLS](https://www.nlm.nih.gov/research/umls/index.html).
+
+# OxO with Docker
+
+OxO is comprised of three components:
+
+* The loader scripts (oxo-loader/), which pull data about terms and mappings from the OLS, OBO xrefs, and UMLS and upload them to neo4j
+* The indexer (oxo-indexer/), which indexes terms and mappings found in neo4j in solr
+* The Web application (oxo-web/), which provides the user interface
+
+The OxO Web application, solr, and neo4j can be started using docker-compose:
+
+    docker-compose up
+
+The docker-compose configuration, by default, stores all persistent data (the hsqldb, neo4j, and solr data files) in the data/ directory by mounting volumes.  However, these datasets are empty until the loader and indexer have been executed.
+
+## Running the loader
+
+The loader requires neo4j to be running.  If using docker-compose, neo4j can be
+started on its own:
+
+    docker-compose up neo4j
+
+The loader scripts can then be used as documented in the oxo-loader/ directory
+to load data into neo4j.
+
+## Running the indexer
+
+The indexer requires neo4j and solr to be running.  If using docker-compose:
+
+    docker-compose up neo4j solr
+
+The indexer can be executed using Docker:
+
+    docker build -f oxo-indexer/Dockerfile -t oxo-indexer
+    docker run oxo-indexer
+
+
+# OxO without Docker
+
+Sometimes it is impractical to use Docker (e.g. for local development).  To get
+OxO up and running without Docker, first install:
+
+* neo4j community edition 3.1.1
+* solr 5.3.0
+* Java 1.8
+* Maven
+
+The instructions for the loader are not Docker-specific, and can be found in the
+oxo-loader/ directory.  For the indexer and Web application, first compile the
+project using Maven:
+
+    mvn clean package
+
+Then run the indexer:
+
+    java -Xmx10g -jar oxo-indexer.jar
+
+The Web application is a standard WAR and can be deployed using e.g. Tomcat.
+
+

docker-compose.common.yml

@@ -0,0 +1,25 @@
+version: '2'
+services:
+    solr:
+        image: solr:5.5.3-alpine
+        environment:
+          - SOLR_HOME=/mnt/solr
+        ports:
+          - 8983:8983
+        volumes:
+          - ./data/solr:/mnt/solr
+        command: ["solr", "-f"]
+    neo4j:
+        image: neo4j:3.1.1
+        environment:
+          - NEO4J_HEAP_MEMORY=10g # configure the heap memory
+          - NEO4J_dbms_memory_heap_maxSize=8g
+          - NEO4J_AUTH=neo4j/dba
+        cap_add:
+          - SYS_RESOURCE
+        ports:
+          - 7474:7474
+          - 7687:7687
+        volumes:
+          - ./data/neo4jimport:/var/lib/neo4j/import
+          - ./data/neo4j:/data

docker-compose.yml

@@ -1,44 +1,27 @@
 version: '2'
 services:
     solr:
-        image: solr:5.5.3-alpine
-        environment:
-        - SOLR_HOME=/home/mysolrhome
-        ports:
-        - 8983:8983
-        volumes:
-        - ./solr-config:/home/mysolrhome
-        - ./solr-config/data:/home/mysolrhome/mapping/data
-        command: ["solr", "-f"]
+        extends:
+          file: docker-compose.common.yml
+          service: solr
     neo4j:
-        image: neo4j:3.1.1
-        environment:
-        - NEO4J_HEAP_MEMORY=10g # configure the heap memory
-        - NEO4J_dbms_memory_heap_maxSize=8g
-        - NEO4J_AUTH=neo4j/dba
-        cap_add:
-         - SYS_RESOURCE
-        ports:
-        - 7474:7474
-        - 7687:7687
-        volumes:
-          - ./neo4jimport:/var/lib/neo4j/import
+        extends:
+          file: docker-compose.common.yml
+          service: neo4j
     oxo:
-        build: .
+        build: oxo-web
         depends_on:
           - neo4j
           - solr
         links:
           - neo4j
           - solr
         environment:
-          - spring.datasource.url=jdbc:hsqldb:file:/home/hsqldb
+          - spring.datasource.url=jdbc:hsqldb:file:/mnt/hsqldb
           - oxo.neo.driver=org.neo4j.ogm.drivers.http.driver.HttpDriver
           - oxo.neo.uri=http://neo4j:dba@neo4j:7474
           - spring.data.solr.host=http://solr:8983/solr
-        command:
-            - java
-            - -jar
-            - /home/oxo.war
+        volumes:
+          - ./data/hsqldb:/mnt/hsqldb
         ports:
         - 8080:8080

oxo-indexer/.classpath

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="target/generated-sources/annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>