From c6c9a70b0cf063951a44044867fb6222bfaed6d6 Mon Sep 17 00:00:00 2001
From: James Stevenson <james.stevenson@nationwidechildrens.org>
Date: Fri, 15 Sep 2023 11:23:45 -0700
Subject: [PATCH] fix: catch ETL module import errors (#249)

---
 gene/cli.py | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/gene/cli.py b/gene/cli.py
index 4c78666d..8fe852f5 100644
--- a/gene/cli.py
+++ b/gene/cli.py
@@ -15,9 +15,6 @@
     create_db,
 )
 from gene.database.database import DatabaseException
-from gene.etl import HGNC, NCBI, Ensembl  # noqa: F401
-from gene.etl.exceptions import GeneNormalizerEtlError
-from gene.etl.merge import Merge
 from gene.schemas import SourceName
 
 logger = logging.getLogger("gene")
@@ -176,6 +173,14 @@ def _load_source(
     start_load = timer()
 
     # used to get source class name from string
+    try:
+        from gene.etl import HGNC, NCBI, Ensembl  # noqa: F401
+        from gene.etl.exceptions import GeneNormalizerEtlError
+    except ModuleNotFoundError as e:
+        click.echo(
+            f"Encountered ModuleNotFoundError attempting to import {e.name}. Are ETL dependencies installed?"
+        )
+        click.get_current_context().exit()
     SourceClass = eval(n.value)  # noqa: N806
 
     source = SourceClass(database=db)
@@ -221,6 +226,15 @@ def _load_merge(db: AbstractDatabase, processed_ids: Set[str]) -> None:
     _delete_normalized_data(db)
     if not processed_ids:
         processed_ids = db.get_all_concept_ids()
+
+    try:
+        from gene.etl.merge import Merge
+    except ModuleNotFoundError as e:
+        click.echo(
+            f"Encountered ModuleNotFoundError attempting to import {e.name}. Are ETL dependencies installed?"
+        )
+        click.get_current_context().exit()
+
     merge = Merge(database=db)
     click.echo("Constructing normalized records...")
     merge.create_merged_concepts(processed_ids)