#1368 generate-import-slots-regardless --mixs-schema-url option

nmdc_schema/generate_import_slots_regardless.py

@@ -3,18 +3,19 @@
 
 
 class ImportSlotsRegardless:
-    mixs_slots_used_in_schema_tsv = "../assets/mixs_slots_used_in_schema.tsv"
-    mixs_slots_used_in_schema = list()
-
-    static_value_dict = {
-        "source class": "soil MIMS",
-        # "source file or URL": "https://raw.githubusercontent.com/GenomicsStandardsConsortium/mixs/main/model/schema/mixs.yaml",
-        "source file or URL": "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml",
-        "slot": "",
-        "section": "",
-        "column order": "",
-        "destination class": "placeholder_class"
-    }
+
+    def __init__(self, mixs_schema_url, slots_tsv):
+        self.static_value_dict = {
+            "source class": "soil MIMS",
+            "source file or URL": mixs_schema_url,
+            "slot": "",
+            "section": "",
+            "column order": "",
+            "destination class": "placeholder_class"
+        }
+
+        self.mixs_slots_used_in_schema_tsv = slots_tsv
+        self.mixs_slots_used_in_schema = list()
 
     def populate_mixs_slots_used_in_schema(self, input_file):
         with open(input_file, 'r') as file:
@@ -44,8 +45,11 @@ def write_import_slots_regardless_rows(self, output_file, input_file):
 @click.command()
 @click.option("--input_file", required=True, help="input file path from get-mixs-slots-used-in-schema")
 @click.option("--output_file", required=True, help="output file path for sheets_and_friends")
-def main(output_file, input_file):
-    import_slots = ImportSlotsRegardless()
+@click.option("--slots-tsv", default="assets/mixs_slots_used_in_schema.tsv")
+@click.option("--mixs-schema-url",
+              default="https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml")
+def main(output_file, input_file, slots_tsv, mixs_schema_url):
+    import_slots = ImportSlotsRegardless(mixs_schema_url=mixs_schema_url, slots_tsv=slots_tsv)
     import_slots.write_import_slots_regardless_rows(output_file, input_file)
     click.echo("Import slots regardless file generated successfully.")
 

project.Makefile

@@ -79,7 +79,11 @@ local/mixs_regen/slots_associated_with_biosample_omics_processing.tsv
 
 local/mixs_regen/import_slots_regardless_gen.tsv: \
 local/mixs_regen/mixs_slots_associated_with_biosample_omics_processing.tsv
-	$(RUN) generate-import-slots-regardless --input_file $< --output_file $@
+	$(RUN) generate-import-slots-regardless \
+		--input_file $< \
+		--mixs-schema-url "https://raw.githubusercontent.com/microbiomedata/mixs/1da849346a80b717810a02d7c8ed74a22bcd84de/model/schema/mixs.yaml" \
+		--output_file $@ \
+		--slots-tsv assets/mixs_slots_used_in_schema.tsv
 
 local/mixs_regen/mixs_subset.yaml: local/mixs_regen/import_slots_regardless_gen.tsv
 	$(RUN) do_shuttle \