The haddock3 uses **/defaults.yaml files to specify the module parameteres while the i-VRESSE workflow builder uses a catalog.
The ./generate_haddock3_catalog.py script can be used to generate a catalog from the haddock3 defaults.yaml files.
To install haddock3 see https://github.com/haddocking/haddock3/blob/main/docs/INSTALL.md
Run with
# Reads modules from haddock3 in Python path
./generate_haddock3_catalog.py
# Writes catalog files in public/catalog/ dir
# TODO add command to check JSON schemas are valid.Translations from haddock3 -> i-VRESSE workflow builder:
- module -> node
- generic parameters-> global parameters
- Module info
- haddock.modules...doc -> node.label
- haddock.modules...HaddockModule.doc -> node.description
- Category info
- haddock.modules..doc -> category.description
- Module DEFAULT_CONFIG -> JSON schema + UI schema:
- short -> description
- long -> $comment
- type=float or type=integer -> type=number
- type=list -> type=array
- type=file -> type=string + format=uri-reference + ui:widget=file
- type=dir -> type=string + format=uri-reference
- type missing -> {type:object, parameters: <key/value pairs>}
- min -> minimum
- max -> maximum
- minchars -> minLength
- maxchars -> maxLength
- minitems -> minItems
- maxitems -> maxItems
- accept -> ui:options={accept: ','.join(...)}
- choices -> enum
- explevel -> each explevel gets generated into own catalog
- group -> ui:group in ui schema
- expandable (*_1) -> arrays and objects + tomlschema
- mol_* or __1_1 -> maxItemsFrom:molecules aka array should have same size as global molecules parameter
- 'residue number' in title -> format:residue
- 'chain' or 'segment id' in title -> format:chain