Reactome Curator Service

What is the Reactome Curator Service

The Curator Service is the Reactome CRUD API to access curation-related data in Neo4J graph database. It is based on Spring MVC, based on REST and fully documented in Open API (previously Swagger).

Git Clone

git clone https://github.com/reactome/curator-service.git
cd curator-service

Configuring Maven Profile 📝

Maven Profile is a set of configuration values which can be used to set or override default values of Maven build. Using a build profile, you can customize build for different environments such as Production v/s Development environments. Add the following code-snippet containing all the Reactome properties inside the tag <profiles> into your ~/.m2/settings.xml. Please refer to Maven Profile Guideline if you don't have settings.xml

<profile>
    <id>Reactome-Server</id>
    <properties>
        <mail.host>localhost</mail.host>
        <mail.port>8181</mail.port>
        <mail.username>username</mail.username>
        <mail.password>password</mail.password>
        <mail.enable.auth>true</mail.enable.auth>

        <!-- Neo4J Configuration -->
        <neo4j.host>localhost</neo4j.host>
        <neo4j.port>7474</neo4j.port>
        <neo4j.user>neo4j</neo4j.user>
        <neo4j.password>password</neo4j.password>

        <!-- Solr Configuration -->
        <solr.host>http://localhost:8983/solr</solr.host>
        <solr.core>reactome</solr.core>
        <solr.user>admin</solr.user>
        <solr.password>password</solr.password>

        <!-- MySQL Configuration -->
        <mysql.host>localhost</mysql.host>
        <mysql.port>3306</mysql.port>
        <mysql.reactome.database>reactome</mysql.reactome.database>
        <mysql.report.database>report</mysql.report.database>
        <mysql.user>curator</mysql.user>
        <mysql.password>password</mysql.password>

        <template.server>https://localhost/</template.server>

        <!-- Log report -->
        <cnf.mail.error.subject>Automated Error Report</cnf.mail.error.subject>
        <cnf.mail.error.name>Error Report Agent</cnf.mail.error.name>
        <cnf.mail.error.from>noreply@reactome.org</cnf.mail.error.from>
        <cnf.mail.error.to>mail@domain.ac.uk</cnf.mail.error.to>

        <!-- Report mail Configuration -->
        <cnf.mail.report.hostname>reactome.org</cnf.mail.report.hostname>
        <cnf.mail.report.from>noreply@reactome.org</cnf.mail.report.from>
        <cnf.mail.report.to>mail@domain.ac.uk</cnf.mail.report.to>

        <!-- Results not found internal Report -->
        <report.user>reportadmin</report.user>
        <report.password>password</report.password>

        <!-- Logging -->
        <logging.level>ERROR</logging.level>
        <logging.dir>/var/log/tomcat7</logging.dir>

        <!-- Analysis intermediate file  -->
        <analysis.structure.file>/usr/local/reactomes/Reactome/production/AnalysisService/input/analysis.bin</analysis.structure.file>
        <analysis.result.root>/usr/local/reactomes/Reactome/production/AnalysisService/temp</analysis.result.root>

        <!-- Common folders and file locations -->
        <fireworks.json.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/fireworks</fireworks.json.folder>
        <diagram.json.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/diagram</diagram.json.folder>
        <diagram.exporter.temp.folder>/usr/local/reactomes/Reactome/production/ContentService/exporter/</diagram.exporter.temp.folder>
        <tuples.uploaded.files.folder>/usr/local/reactomes/Reactome/production/ContentService/custom</tuples.uploaded.files.folder>

        <!-- Needed for the Content-Service / Raster exporter -->
        <ehld.folder>/usr/local/reactomes/Reactome/production/Website/static/download/current/ehld</ehld.folder>
        <svg.summary.file>/usr/local/reactomes/Reactome/production/Website/static/download/current/ehld/svgsummary.txt</svg.summary.file>

        <!-- Path to the experiments binary file -->
        <experiments.data.file>/usr/local/reactomes/Reactome/production/AnalysisService/digester/experiments.bin</experiments.data.file>
    </properties>
</profile>

Running ContentService activating Reactome-Server profile.

mvn spring-boot:run -P Reactome-Server

Check if Tomcat has been initialised

[INFO] Using existing Tomcat server configuration at /Users/reactome/content-service/target/tomcat
INFO: Starting ProtocolHandler ["http-bio-8686"]

Usage

• 💻 Access your local installation