Replace leftover UMLS custom output generation with write_compendia()

[gaurav]

The leftover UMLS file currently replicates the compendium and synonym generation code in babel_utils.write_compendia():

Babel/src/createcompendia/leftover_umls.py

Lines 165 to 195 in 41d62be

	# Write this UMLS term to UMLS.txt as a single-identifier term.
	cluster = {
	'type': biolink_type,
	'identifiers': [{
	'i': umls_id,
	'l': label,
	}]
	}
	compendiumf.write(json.dumps(cluster) + "\n")
	umls_ids_in_this_compendium.add(umls_id)
	logging.debug(f"Writing {cluster} to {compendiumf}")
	logging.info(f"Wrote out {len(umls_ids_in_this_compendium)} UMLS IDs into the leftover UMLS compendium.")
	reportf.write(f"Wrote out {len(umls_ids_in_this_compendium)} UMLS IDs into the leftover UMLS compendium.\n")
	logging.info(f"Found {count_no_umls_type} UMLS IDs without UMLS types and {count_multiple_umls_type} UMLS IDs with multiple UMLS types.")
	reportf.write(f"Found {count_no_umls_type} UMLS IDs without UMLS types and {count_multiple_umls_type} UMLS IDs with multiple UMLS types.\n")
	# Write out synonyms for all IDs in this compendium.
	synonym_ids = set()
	count_synonyms = 0
	with open(synonyms, 'r') as synonymsf, open(umls_synonyms, 'w') as umls_synonymsf:
	for line in synonymsf:
	id, relation, synonym = line.rstrip().split('\t')
	if id in umls_ids_in_this_compendium:
	synonym_ids.add(id)
	count_synonyms += 1
	umls_synonymsf.write(f"{id}\t{relation}\t{synonym}\n")
	logging.info(f"Wrote {count_synonyms} synonyms for {len(synonym_ids)} UMLS IDs into the leftover UMLS synonyms file.")
	reportf.write(f"Wrote {count_synonyms} synonyms for {len(synonym_ids)} UMLS IDs into the leftover UMLS synonyms file.\n")

This means that when the output formats change, we need to modify it in both write_compendia() and leftover UMLS.

We should replace this by having leftover UMLS generate an ID file (in e.g. intermediate/leftover_umls/ids/UMLS), and then use babel_uris.write_compendia() to generate the compendia and synonyms files.