4. Convert MapsΒΆ

Any Escher maps built with pre-release versions of Escher will not load right away in the stable v1.0 release. To convert pre-release maps to the new format, follow these steps:

  1. Install Escher:

    pip install escher
    
  2. Find a COBRA model for your maps. This COBRA model will be used to update the content of the map in order to support all the new Escher features. You can use a COBRA model encoded as SBML or JSON (generated with COBRApy v0.3.0b4 or later). The COBRA models currently available on the Escher website can be downloaded here:

https://github.com/escher/escher.github.io/tree/master/1-0-0/models

For a refresher on the distinction between Escher maps, COBRA models, and their file types (SBML, JSON, SBML Layout), see Escher, COBRA, and COBRApy.
  1. Run the convert_map script to convert your existing Escher map (my_old_map.json) to the new format, using a COBRA model (model_file.json or model_file.xml in these examples):

    # With a JSON file model
    python -m escher.convert_map my_old_map.json path/to/model_file.json
    
    # With an SBML model
    python -m escher.convert_map my_old_map.json path/to/model_file.xml
    

Those commands will generate a new map called my_old_map_converted.json that will load in Escher v1.0 and later.

If that doesn’t work, and you were a Beta user for Escher v1, you can DM @zakandrewking with a link to a broken Escher map (using Pastbin, Dropbox, or similar) and the COBRA model you used to generate the map. As a thank you for helping out with Escher development, I will run the convert_map script and send you back a new, valid map. -Zak