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This API is no longer supported, but its source code / data remains available in this archived copy.

osmose-web-api

Service that generates OSMOSE configuration files from data sources like Fishbase and SeaLifeBase. Please see our wiki for more information.

Build Status DOI

prerequisites

  1. download OSMOSE 3 update 2 from http://www.osmose-model.org/downloads
  2. expand to [OSMOSE_INSTALL_DIR]

usage

generate configuration

  1. (alt 1, static, for machines) download OSMOSE configuration at https://fbob.herokuapp.com/osmose_config.zip
  2. (alt 2, single species focal groups, for machines) https://fbob.herokuapp.com/osmose_config.zip?focalGroupName=ScomberomorusCavalla&focalGroupName=LutjanusCampechanus&focalGroupName=EpinephelusMorio (dynamic configuration with three named groups: Scomberomorus cavalla, Lutjanus campechanus and Epinephelus morio.).
  3. (alt 3, defined focal and background groups, for machines) by sending http post request. For example curl -X POST --data @exampleConfig.json --header "Content-Type:application/json;charset=UTF-8" https://fbob.herokuapp.com/v2/osmose_config.zip > my_osmose_config.zip . An example of a request json can be found here exampleConfig.json.
  4. (alt 4, for machines) use javascript library available at https://github.com/osmose-model/osmose-web-api-js to generate an osmose configuration for parameters defined in json.
  5. (alt 5, for humans) use wizard at https://www.config.osmose-model.org and download generated configuration archive.
  6. expand config.zip to [SOME_DIR]

run simulation

  1. open a terminal and go to directory [OSMOSE_INSTALL_DIR]/dist
  2. run OSMOSE simulation using java -jar osmose_stable_3.jar [SOME_DIR]/osm_all-parameters.csv . in the OSMOSE install directory

The output should look something like:

osmose[info] - *********************************
osmose[info] - Osmose model - Copyright 2013 IRD
osmose[info] - *********************************
osmose[info] - Osmose version Osmose 3 Update 2 (2015/03/01)
osmose[info] - Running configuration xxx/osmose_config/osm_all-parameters.csv
osmose[info] - Loading parameters from file xxx/osmose_config/osm_all-parameters.csv
osmose[info] -   Loading parameters from file xxx/osmose_config/osm_param-output.csv