paulstey / erddap-docker

ERDDAP Server

ERDDAP Docker

This repository contains the common setup files for the axiom/docker-erddap image. This image starts up the ERDDAP service and serves it using Apache Tomcat. ERRDAP is a Java application is a data server that provides a simple interface for downloading datasets.

Development

The configuration in this repository is designed for deployments. If you'd like to test this image locally you can use the docker-compose.dev.yml. This file differs from the production compose in two aspects:

1. The port mapping is changed from 127.0.0.1:8080:8080 to 8080.

2. In content/erddap/setup.xml the baseUrl field will point to to http://localhost:8080 instead of https://pricaimcit.services.brown.edu.

To run ERDDAP with real data locally, you'll need to grab the data from pricaimcit.services.brown.edu:/isilon_erddap/buoy_data and put it in a folder called buoy_data in the root of this project.

Running Locally

To start the container run docker-compose -f docker-compose.dev.yml up -d erddap. Then go to http://localhost:8080. To check that the service is up run docker-compose exec erddap bash and check to see that there's data in the logs/ directory. Tomcat takes a while to start up, don't be surprised if you don't see anything.

Loading data into ERDDAP

This process will guide you on how to start a local ERDDAP server and load new datasets.

Before loading data into ERDDAP it's important to get familiar with ERDDAP's data structure and data types. ERDDAP provides extensive documentation on that topic here.

ERDDAP also provides a few tools to help you create the dataset's XML file, and the data attribute structure/data descriptor structure.

To create a XML block for a dataset, run:

#development
docker-compose -f docker-compose.dev.yml run generate_dataset_xml

#production
docker-compose run generate_dataset_xml

This will run the script GenerateDatasetXml.sh provided by ERDDAP. This is an interactive tool that will ask you to enter some information about the dataset. We place data files in /erddapData/, which is mounted to isilon_erddap/erddap_data. Make sure you have downloaded the isilon_erddap folder from Google Drive. If you don't have that, ask an administrator for the link.

The logs will be saved at isilon_erddap/erddap_data/GenerateDatasetsXml.log. You can check the logs to help you debugging the dataset. If the XML block is generated successfully, it will be printed in that log file.

After that's done, copy the XML dataset block and paste it into erddap-dev/datasets.xml within the <erddapDatasets></erddapDatasets> tag.

The XML block will have the dataset ID. This ID is used to generate the dataset attribute structure (DAS) and the dataset descriptor structure (DDS). To generate the DAS/DDS, run:

#development
docker-compose -f docker-compose.dev.yml run generate_data_structure

#production
docker-compose run generate_data_structure

This will run ERDDAP's DasDds.sh script. It will ask you the enter the ID of your dataset, which was generated in the previous step. The logs for this script will be at isilon_erddap/erddap_data/DasDds.log. If that is completed successfully, you can start your local ERDDAP server:

#development
docker-compose -f docker-compose.dev.yml up erddap

#production
docker-compose up -d erddap

You can then visit localhost:8080/erddap/index.html. The server might take a few minutes to start and load all datasets.

If you can see your dataset in your local ERDDAP server, you're ready to start a Pull Request to the production server.

To do that:

• paste the dataset's XML block in the production erddap/dataset.xml file in this repo.
• add a link to the raw data files in your PR's description.

For admins:

• After merging the PR, follow the Loading data into ERDDAP process again, but with the production server.

Costumize ERDDAP text

To costumize ERDDAP's appearance and text, edit the content/erddap/setup.xml or content/erddap-dev/setup.xml file. Check the messages.xml file for costumizable blocks and add those at the end of setup.xml. There are currently two examples in setup.xml:

• <startBodyHtml5><startBodyHtml5>: Is responsible to changes made to the banner.
• <theShortDescriptionHtml></theShortDescriptionHtml>: Contains the text on the left column of the front page. To change this, you can remove [standardShortDescriptionHtml] and add content in html format.

It's recommended to use the erddap-dev/setup.xml and check if your changes are working correctly. (See development workflow above). When everything looks correct, add those changes to erddap/setup.xml