Update KGX code to process new merge.yaml design

[hrshdhgd]

This is w.r.t a conversation with @sierra-moxon .

The project (or rather PR) that triggered this issue: Knowledge-Graph-Hub/kg-microbe-merge#1

The issue that concerns KGX is that instead of having a physical merge.yaml file, we dynamically create the file through the following steps:

1. Create a LinkML schema that replaces the merge.yaml file.
2. Create classes using gen-python from linkml
3. Create an object [MergeKG ] using the above classes based on the transforms that need to be merged.
   • This gives the flexibility of choosing which individual transforms need to be merged. Falls perfectly into the KG modularization discussion we've been having.
4. Use yaml_dumper to dump the MergeKG into a yaml file which is then passes to the load_and_merge() in KGX.
   • This step could be avoided if KGX could accept the MergeKG object directly in the function above rather than exporting it as a file.

The old merge_yaml had the structure (displaying only parts that need to be updated):

merged_graph:
  name: kg-microbe-merge graph
  source:
    hp:
      name: "HP"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/HPTransform_nodes.tsv
          - data/transformed/ontologies/HPTransform_edges.tsv

  destination:
    merged-kg-tsv:
      format: tsv
      compression: tar.gz
      filename: merged-kg
    merged-kg-nt:
      format: nt
      compression: gz
      filename: kg_microbe_merge.nt.gz

The new format equivalent will look like this:

merged_graph:
  name: kg-microbe graph
  source:
    - name: "HP"
      input:
        format: tsv
        filename:
          - data/transformed/ontologies/hp_nodes.tsv
          - data/transformed/ontologies/hp_edges.tsv

  destination:
    - format: tsv
      compression: tar.gz
      filename: merged-kg

Just source and destination are the ones whose design is updated.

So the 2 features that can come out of this issue are:

• Update cli_utils.py to handle the updated merge.yaml
• Enable load_and_merge() to accept MergeKG object which is a linkml product.