EarthChem Portal (ECP)

The EarthChem Portal (ECP) is a one-stop shop for geochemistry data of the solid earth. It provides integrated search results by federating multiple data systems—including PetDB, SedDB, GEOROC, NavDat, USGS, and GANSEKI—and features mapping and visualization tools.

About This Repository

This repository offers a portable, Docker-based infrastructure to run the ECP frontend applications, which include both the ECP Web and ECP WFS servers.

Setting Up and Running the Web Server

Follow these steps to configure and deploy the ECP web server:

Obtain ECP Database Credentials
Ensure you have the necessary database credentials for connecting to the ECP database.

Create config.inc.php
In the web_server/dbconfig directory, create a file named config.inc.php with the following contents:

<?
    $dbusername = "****";
    $dbpassword = "******";
    $dbname     = "****";
    $dbserver   = "******";
    $readonly   = "";
?>

Create config.inc.python.json
In the web_server/dbconfig directory, create a file named config.inc.python.json with the following contents:

 {
     "pg_connection": {
         "host": "******",
         "user": "****",
         "passwd": "****",
         "db": "****"
     }
 }

Update Docker Compose Configuration In the docker-compose.yml
modify the source paths (e.g., on lines 11 and 14) to point to the correct directories:
```
    source: web_server_data/plots
    source: web_server_data/hist2dplots
```
Deploy the Web Server Container Build and run the web server container using Docker Compose
```
    docker compose -f docker-compose.yml up -d --build ecp_web
```

Setting Up and Running the WFS Server

To configure the ECP WFS server, complete the following steps:

Modify the Dockerfile In the wfs_server
comment out line 12 by changing it to:

    # COPY ./wfs_server/geoserver-users.xml /usr/local/tomcat/webapps/wfs/data/security/usergroup/default/users.xml

Update Docker Compose Configuration In the docker-compose.yml
update the source path on line 26 to match your directory structure:
```
    source: wfs_server_data/logs
```
Deploy the WFS Server Container Build and run the web server container using Docker Compose
```
    docker compose -f docker-compose.yml up -d --build ecp_wfs
```
Change the admin password in GeoServer
- Log into the GeoServer UI with the default admin account(username:admin, password:geoserver).
- Change the admin password
Update ECP database credential
- Navigate to the Data tab on the left navigation panel and click on the Stores link.
- You will find a record(workspace:ECP,Store Name:ECP Postgis, Type:PostGIS) on the page 'Stores' and clik on the 'ECP Postgis' link.
- Update Connection Parameters on the page Edit Vector Data Source

Create Docker Image of the Web Server

```bash
    docker build --file web_server/Dockerfile --platform linux/amd64 --no-cache --tag ecp_web:bookworm-slim .
```

Create Docker Image of the WFS Server

```bash
    docker build --file wfs_server/Dockerfile --platform linux/amd64 --no-cache --tag ecp_wfs:9.0.104-jre17-temurin-noble .
```

Running Servers with Images

```bash
    docker compose -f docker-compose-with-image.yml up
```

Documentation (ecp_web source code:web_server/www)

fonts

Contains fonts for various map interfaces.

geopass

Contains code for interacting with geopass system.

includes

Contains headers/footers for all ECP pages.

js

Contains client-side scripts.

svggraph

Library for creating SVG graphs.

advancedoptions.php

Set advanced options for search output.

advancedoutput.php

Advanced search output.

alterationrocknameresponse.php

Response for alteration rock Ajax.

bathy.map

Map file for overlaying MGDS bathymetry.

bathy.php

Mapscript for overlaying MGDS bathymetry.

bathypolar.map

Map file for overlaying MGDS bathymetry on south pole.

citation_stats.php

Return monthly citation statistics.

citation_stats_quarter.php

Return quarterly citation statistics.

clearage.php

Clear age for search query.

clearchemistry.php

Clear chemistry for search query.

clearcruiseid.php

Clear cruise id for search query.

cleargeology.php

Clear geology for search query.

clearigsn.php

Clear igsn for search query.

clearkeyword.php

Clear keyword for search query.

clearlocation.php

Clear location for search query.

clearmineral.php

Clear mineral for search query.

clearoceanfeature.php

Clear ocean feature for search query.

clearreference.php

Clear reference for search query.

clearrocktype.php

Clear rocktype for search query.

clearsampleid.php

Clear sample ID for search query.

clearvolcano.php

Clear volcano for search query.

datasources.php

Helper for getting list of datasources

db.php

Database abstraction class loader.

deletesavedquery.php

Delete saved user query.

dynmap.map

Map file for creating dynamic map with search results.

dynpolarmap.map

Map file for creating dynamic map with search results on south pole.

earthchem_polygon_map.php

Map search interface.

earthchem_south_polar_polygon_map.php

South pole map search interface.

ecdynmap.php

Dynamic mapscript for 4326 projection.

ecdynpolarmap.php

Dynamic mapscript for polar projection.

ecstaticmap.php

Output static map for search query.

ecstaticpolarmap.php

Output static polar map for search query.