fixed #81

databio · Jan 13, 2025 · 502aa63 · 502aa63
1 parent a52a57f
commit 502aa63
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Showing 3 changed files with 19 additions and 3 deletions.
diff --git a/bedboss/cli.py b/bedboss/cli.py
@@ -665,6 +665,22 @@ def install_requirements():
     )
 
 
+@app.command(help="Verify configuration file")
+def verify_config(
+    config: str = typer.Option(
+        ...,
+        help="Path to the bedbase config file",
+        exists=True,
+        file_okay=True,
+        readable=True,
+    ),
+):
+    from bbconf.config_parser.utils import config_analyzer
+
+    if config_analyzer(config):
+        print("Configuration file is valid!")
+
+
 @app.callback()
 def common(
     ctx: typer.Context,

diff --git a/requirements/requirements-all.txt b/requirements/requirements-all.txt
@@ -5,8 +5,8 @@ peppy>=0.40.7
 yacman>=0.8.4
 requests>=2.28.2
 piper>=v0.14.3
-bbconf>=0.10.1
-# bbconf @ git+https://github.com/databio/bbconf.git@partial_processing#egg=bbconf
+# bbconf>=0.10.1
+bbconf @ git+https://github.com/databio/bbconf.git@partial_processing#egg=bbconf
 refgenconf>=0.12.2
 pandas>=2.0.0
 ubiquerg>=0.6.2

diff --git a/test/test_dependencies/bedbase_config_test.yaml b/test/test_dependencies/bedbase_config_test.yaml
@@ -10,7 +10,7 @@ database:
   port: 5432
   password: docker
   user: postgres
-  name: bedbase
+  database: bedbase
   #name: pep-db
   dialect: postgresql
   driver: psycopg