Merge pull request #70 from ncbo/66-retrieve-ontology-version-when-do…

…wnloading-and-pass-it-to-the-transformer Get more ontology metadata and pass to the transform step
ncbo · Sep 5, 2024 · 7e07fd6 · 7e07fd6
2 parents 3611c42 + ffc371a
commit 7e07fd6
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Showing 4 changed files with 188 additions and 67 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/src/kg_bioportal/cli.py b/src/kg_bioportal/cli.py
@@ -4,7 +4,7 @@
 
 import click
 
-from kg_bioportal.downloader import Downloader
+from kg_bioportal.downloader import Downloader, ONTOLOGY_LIST_NAME
 from kg_bioportal.transformer import Transformer
 
 __all__ = [
@@ -128,6 +128,20 @@ def download(
 
     onto_list = []
 
+    # If no input args provided, use the full list of ontologies
+    # But if the full list isn't available, throw an error and remind
+    # the user to download it first
+    if not ontologies and not ontology_file:
+        try:
+            with open(f"{output_dir}/{ONTOLOGY_LIST_NAME}", "r") as f:
+                for line in f:
+                    onto_list.append(line.strip())
+        except FileNotFoundError:
+            logging.error(
+                f"Ontology list file not found. Please run the 'get_ontology_list' command first."
+            )
+            return None
+
     # Parse the ontologies argument
     if ontologies:
         for ontology in ontologies.split():