Merge pull request #62 from ncbo/jenkins_test

Fixes for the Jenkins build

Jenkinsfile

@@ -74,15 +74,17 @@ pipeline {
                 dir('./gitrepo') {
                     script {
                         // Get the names of all BioPortal ontologies
-                        sh ". venv/bin/activate && kgbioportal get-ontology-list --api_key ${NCBO_API_KEY} --output data/raw/"
+                        // This saves the list to data/raw/ontologylist.tsv
+                        sh ". venv/bin/activate && kgbioportal get-ontology-list --api_key ${NCBO_API_KEY}"
 
                         // Now download all
                         // or at least in the future, do them all.
                         // For now just do a few
                         sh "printf 'ENVO\nPO\nSEPIO\n' > data/raw/ontologylist.tsv"
 
                         // Download the ontologies
-                        sh ". venv/bin/activate && kbbioportal download --api_key ${NCBO_API_KEY} --ontology_file data/raw/ontologylist.tsv --output_dir data/raw/"
+                        // This saves them to data/raw/
+                        sh ". venv/bin/activate && kgbioportal download --api_key ${NCBO_API_KEY} --ontology_file data/raw/ontologylist.tsv"
 
                     }
                 }

src/kg_bioportal/cli.py

@@ -77,7 +77,7 @@ def get_ontology_list(output_dir, api_key) -> None:
     required=False,
     type=click.Path(exists=True),
 )
-@click.option("output_dir", "-o", required=True, default="data/raw")
+@click.option("--output_dir", "-o", required=True, default="data/raw")
 @click.option(
     "--snippet_only",
     "-x",

src/kg_bioportal/downloader.py

@@ -50,6 +50,9 @@ def __init__(
         if not os.path.exists(self.output_dir):
             os.makedirs(self.output_dir)
 
+        if not api_key:
+            raise ValueError("API key is required for downloading from BioPortal.")
+
         return None
 
     # TODO: save NCBO ID and version for each ontology, then pass to transformer