gaiaCatalog contains all the materials to build the gaiaCatalog containers for use in the OHDSI/GIS toolchain as a part of the Information on Observational Health Data Sciences and Informatics (OHDSI) organization.
Status: under active development
This repository has two principal components:
- a catalog comprised of metadata descriptions for GIS datasets
- two docker build specifications to provide a SOLR index of the catalog entries and a user interface to the index.
NOTE: This is not a standalone tool. Please see the gaiaDB repository for integration into the gaiaDB project and the gaiaDocker repository for the integration into a browser-based exploration and ingestion tool.
This repository contains:
+-- datastore
# metadata descriptions used by gaiaDB and gaiaDocker
+-- data
# collection of catalog entries (see below for details)
+-- collections
# a description of the OHDSI data collection
+-- docker
# The config files for docker container builds used by gaiaDocker
+-- repository
# a flask app to provide a user interface
+-- solr
# the solr index of the catalog entries
+-- examples
# template files for the catalog entries
Note that there is more content under development.
- Linux, Mac, or Windows
- Docker 1.27.0+
- Git
Each dataset under /datastore/data follows this layout:
/datastore/data/{table_id}/
meta_json-ld_{table_id}.json ← JSON-LD metadata (dataset + variables)
meta_etl_{table_id}.json ← ETL configuration (geometry, EPSG, fields)
meta_dcat_{table_id}.json ← DCAT catalog metadata
etl/
{table_id}_osgeo.sh ← Step 1: download + ogr2ogr load
{table_id}_postgis.sh ← Step 2: geometry cleanup + local projection
{table_id}_osgeo_derivative.sh ← (publishing) create derived osgeo outputs
{table_id}_postgis_derivative.sh ← (publishing) pg_dump + tarball for download
download/ ← created at runtime by _osgeo.sh
derived/ ← created at runtime by derivative scripts
The build context for both images is the root directory of this repository.
docker build -t gaia-catalog -f ./docker/repository/Dockerfile .
docker build -t gaia-solr -f ./docker/solr/Dockerfile .Or use the docker compose on the gaiaDocker repository.
Please use the GitHub issue tracker for bugs and feature requests.
- Open an issue before starting significant work
- Create a feature branch and submit a Pull Request when ready
- PRs require review before merge to
main