geome-configurations

A spawning ground for GEOME projects using API calls and the command-line. Not all GEOME projects are created here, but this repository does have a set of useful tools to help manage certain projects programitically. In particular, for editing templates directly in JSON rather than relying on the interface as well as tools for editing and managing the GEOME network template. Project editing is accomplished through fetching templates in JSON format, editing offline, and then re-loading to GEOME. This is accomplished using API calls.

Retrieve available networks

Currently there is only one network. Each network defines its own entities and relationships between entities.

curl https://api.geome-db.org/v1/network/ | gunzip - | python -m json.tool > allnetworks.json

Working with the network configuration

The master configuration is the global configuration for a network. In the following example, "1" is network 1 (which is GEOME)

# Get the network configuration
curl https://api.geome-db.org/network/1/config | gunzip - | python -m json.tool > network.json

# Edit the network configuration

# Put the network configuration
curl -g -X PUT -H 'Content-Type: application/json' --data "@network.json" https://api.geome-db.org/network/1/config?access_token={ACCESS_TOKEN} | gunzip - | python -m json.tool > network_new.json

Fetch configurations

The following lists GEOME configurations. These are team configurations (networkedApproved = true), or project configurations that are not part of a team..

# Return TEAMS (networkApproved = true)
curl https://api.geome-db.org/projects/configs?networkApproved=true | python -m json.tool > teams.json

# Get all configurations  (Teams and project configurations)
curl https://api.geome-db.org/projects/configs | python -m json.tool > allprojects.json

Update project configuration files

Once you have the {ID}, obtained from the previous section we can fetch, modify, and then PUT the data. The configuration ID that we are referring to updates the configuration in the project_configurations table, which effectively updates either team or project-specific configurations.

# Get a project configuration, unzip, pretty print JSON and write to file: 
curl https://api.geome-db.org/projects/configs/{ID}?access_token={ACCESS_TOKEN} | gunzip - | python -m json.tool > {ID}.json

# Update {ID}.json using a text editor

# PUT the entire projectConfiguration object back:
curl -X PUT -H 'Content-Type: application/json' --data "@{FILE_PATH}" https://api.geome-db.org/projects/configs/{ID}?access_token={ACCESS_TOKEN}

or, you can run the convenience script in the bin directory:

$ ./bin/putConfigurationFile.sh
usage: putConfigurationFile.sh [DEV|PROD] [access_token] [projectID] [file_path]

Creating Projects on the Back-end

Either do this on the front-end or on the back-end like:

# Select either biscicoldev or biscicol as PSQL_DB
\c PSQL_DB
# The form is:
#select create_project(ID, 'PROJECT_CODE','PROJECT_TITLE',1)
select create_project(1, 'B_TEMPLATE','Biocode Template',1);
select create_project(2, 'DIPNET','Diversity of the IndoPacific',1);