This code drives the GeOMe database.

The GeOMe database validates field data and tracks physical samples and collecting events, using globally unique and persistent identifiers, for reference in collections management systems, laboratory information management systems, seqence repositories, and publications.

Getting Started:

Tools used are gradle, java/jetty, postgresql.

Production Names/Services

The following end-points / repos are associated with this codebase and are used to get things running...

• api.geome-db.org (The backend for the GEOME database) github repo: https://github.com/biocodellc/geome-db
• bcid.geome-db.org (Manage minting identifiers) github repo: https://github.com/biocodellc/bcid
• photos.geome-db.org (Manage photo handling) github repo: https://github.com/biocodellc/biocode-fims-photos

The GEOME database is built using Gradle scripts (contained in this repository) and running on Jetty Server that stores data in a postgres database. GEOME is supported from the Gordon and Betty Moore Foundation as part of the Moorea Biocode Project (http://biocode.berkeley.edu/), the National Science Foundation as part of the Diversity of the IndoPacific (http://indopacificnetwork.wikispaces.com/), the Barcode of Wildlife Project (http://www.barcodeofwildlife.org/), the Smithsonian Museum of Natural History (http://www.mnh.si.edu/), the Berkeley Natural History Museums (http://bnhm.berkeley.edu/), and the Autonomous Reef Monitoring Network (website coming soon).

Restoring database

The dump file is stored in a non-text format, which reduces the size of the dump and allows us to temporarily disable triggers during reoload.

pg_restore --disable-triggers -d bcid bcid.pgsql
pg_restore --disable-triggers -d biscicol biscicol_all.pgsql

Restoring Other Connections

We want to restore crontab and nginx configuration files. These configurations are stored under deploy/production

Local startup (Jetty)

This app runs as a WAR in Jetty. The local flow is: use remote database credentials, build the WAR, deploy it into Jetty's webapps, then run Jetty.

Remote database notes:

• A local Postgres instance is not required if src/main/environment/local/biocode-fims-database.properties points to a remote bcidUrl.
• Current local env uses remote DB URL: jdbc:postgresql://149.165.170.158:5432/biscicol.
• If needed, confirm DB access before startup:

psql -h 149.165.170.158 -p 5432 -U biscicol -d biscicol -c "select 1;"

1. Build the WAR (uses environment = local from gradle.properties):

./gradlew -Penvironment=local war

2. Create a Jetty context file (only needed once; avoids an empty geome-db.xml parse error):

cat <<'EOF' > /usr/local/opt/jetty/libexec/webapps/geome-db.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Configure PUBLIC "-//Jetty//Configure//EN" "http://www.eclipse.org/jetty/configure_9_0.dtd">
<Configure class="org.eclipse.jetty.webapp.WebAppContext">
  <Set name="contextPath">/geome-db</Set>
  <Set name="war">/usr/local/opt/jetty/libexec/webapps/geome-db.war</Set>
</Configure>
EOF

3. Deploy the WAR:

cp build/libs/geome-db.war /usr/local/opt/jetty/libexec/webapps/geome-db.war

4. Run Jetty (use start.jar with servlets module):

java -jar /usr/local/opt/jetty/libexec/start.jar \
  --module=servlets \
  jetty.base=/usr/local/opt/jetty/libexec \
  jetty.http.port=8081

5. Check app health:

curl -sS -o /dev/null -w "%{http_code}\n" http://127.0.0.1:8081/geome-db/

Notes:

• First startup can take 1-2 minutes while Spring initializes.
• Logs are under /usr/local/opt/jetty/libexec/logs/geome-db.log.
• 403 from /geome-db/ is acceptable and usually means the app is up and auth is being enforced.
• If you see warnings about Jersey resources, they are not fatal to startup.

Generate report.json for geome-configurations

Use the reports endpoint to generate a JSON report file that can be consumed by geome-configurations. Detailed service docs: docs/reporting-service.md.

Local (Jetty on 8081):

curl -sS "http://127.0.0.1:8081/geome-db/reports/summary?includePublic=true&includePrivate=true" > report.json

Production API:

curl -sS "https://api.geome-db.org/geome-db/reports/summary?includePublic=true&includePrivate=true&access_token=YOUR_TOKEN" > report.json

Optional filters:

• teamId=<project_configurations.id>
• projectId=<projects.id>
• includePrivate=true|false (default true; requires authenticated user to include private/member projects)
• topUsersLimit=<int> (default 25, max 500)
• fieldLimit=<int>

Example with team filter:

curl -sS "https://api.geome-db.org/geome-db/reports/summary?includePublic=true&includePrivate=true&teamId=321&topUsersLimit=100&access_token=YOUR_TOKEN" > report.json

projectSummary rows include:

• latestDataModification (ISO timestamp from projects.latest_data_modification)
• public (project visibility flag)