cellannotation / cap-pipeline-config

Building ontology pipeline configurations for the Cell Annotation Platform
3 stars 0 forks source link

Split out manually edited neo4j2owl-config.yaml #81

Closed dosumis closed 2 years ago

dosumis commented 2 years ago

All content in neo4j2owl-config.yaml that is manually edited should live in a separate file here: https://github.com/kharchenkolab/cap-pipeline-config/blob/development/config/prod

let's call it neo4j2owl-config_manual.yaml

Right now this means everything except for the programatically added content under neo_node_labelling.

Once this is split out, update should use the manually edited file as input, extend it and write to the file used by the pipeline

Concretely

Script will need option to specify input files and output files:

https://github.com/kharchenkolab/cap-pipeline-config/blob/development/src/write_organ_tags.py#L36

https://github.com/kharchenkolab/cap-pipeline-config/blob/development/src/write_organ_tags.py#L68 needs to load neo4j2owl-config_manual.yaml

and

https://github.com/kharchenkolab/cap-pipeline-config/blob/development/src/write_organ_tags.py#L73 writes neo4j2owl-config.yaml