Merge pull request #44 from monarch-initiative/43-error-handling-for-…

…when-no-phenotype-entries-are-found-in-the-annotation-for-a-disease

Add error handling for empty matches for a disease

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phenotype2phenopacket"
-version = "0.6.5"
+version = "0.6.6"
 description = ""
 authors = ["Yasemin Bridges <[email protected]>"]
 readme = "README.md"

src/phenotype2phenopacket/cli_convert.py

@@ -56,7 +56,7 @@
 )
 @click.option(
     "--local-ontology-cache",
-    "-l",
+    "-c",
     metavar="PATH",
     required=False,
     help="Path to the local ontology cache, e.g., path to the hp.obo.",

src/phenotype2phenopacket/cli_create.py

@@ -56,7 +56,7 @@
 )
 @click.option(
     "--local-ontology-cache",
-    "-l",
+    "-c",
     metavar="PATH",
     required=False,
     help="Path to the local ontology cache, e.g., path to the hp.obo.",

src/phenotype2phenopacket/convert/convert.py

@@ -7,6 +7,7 @@
 from phenotype2phenopacket.utils.utils import (
     filter_diseases,
     load_ontology,
+    read_omim_id_list,
     return_phenotype_annotation_data,
 )
 
@@ -36,7 +37,10 @@ def convert_to_phenopackets(
     grouped_omim_diseases = filter_diseases(
         num_disease, omim_id, omim_id_list, phenotype_annotation_data
     )
-    for omim_disease in grouped_omim_diseases:
+    for omim_id, omim_disease in zip(read_omim_id_list(omim_id_list), grouped_omim_diseases):
+        if len(omim_disease) == 0:
+            print(f"Skipping... Could not find any phenotype entries for {omim_id}!")
+            continue
         phenopacket_file = PhenotypeAnnotationToPhenopacketConverter(
             human_phenotype_ontology
         ).create_phenopacket(omim_disease, phenotype_annotation_data.version, None)