Merge pull request nmdp-bioinformatics#244 from pbashyal-nmdp/pyard_cli

Add `--cwd` and `--validate` options to pyard command

Author: mmaiers-nmdp

Dockerfile

@@ -4,7 +4,7 @@ LABEL MAINTAINER="Pradeep Bashyal"
 
 WORKDIR /app
 
-ARG PY_ARD_VERSION=1.0.0
+ARG PY_ARD_VERSION=1.0.1
 
 COPY requirements.txt /app
 RUN pip install --no-cache-dir --upgrade pip && \

api-spec.yaml

@@ -2,7 +2,7 @@ openapi: 3.0.3
 info:
   title: ARD Reduction
   description: Reduce to ARD Level
-  version: "1.0.0"
+  version: "1.0.1"
 servers:
   - url: 'http://localhost:8080'
 tags:

pyard/__init__.py

@@ -27,7 +27,7 @@
 from .misc import get_imgt_db_versions as db_versions
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 
 
 def init(

scripts/pyard

@@ -26,7 +26,7 @@ import sys
 
 from pyard.constants import VALID_REDUCTION_TYPES
 import pyard.misc
-from pyard.exceptions import InvalidAlleleError
+from pyard.exceptions import InvalidAlleleError, InvalidTypingError
 from pyard.misc import get_data_dir, get_imgt_version
 
 if __name__ == "__main__":
@@ -63,6 +63,13 @@ if __name__ == "__main__":
         help="Reduction Method",
     )
     parser.add_argument("--splits", dest="splits", help="Find Broad and Splits")
+    parser.add_argument(
+        "--validate",
+        dest="validate",
+        action="store_true",
+        help="Validate the provided GL String",
+    )
+    parser.add_argument("--cwd", dest="cwd", help="Perform CWD redux")
 
     args = parser.parse_args()
 
@@ -83,6 +90,15 @@ if __name__ == "__main__":
         sys.exit(0)
 
     try:
+        if args.validate:
+            ard.validate(args.cwd)
+        if args.cwd:
+            if args.validate:
+                ard.validate(args.cwd)
+            cwd_redux = ard.cwd_redux(args.cwd)
+            print(cwd_redux)
+            sys.exit(0)
+
         if args.redux_type:
             print(ard.redux(args.gl_string, args.redux_type))
         else:
@@ -93,7 +109,12 @@ if __name__ == "__main__":
                 print(ard.redux(args.gl_string, redux_type))
                 print()
     except InvalidAlleleError as e:
-        print("Error:", e)
-
-    # Remove ard and close db connection
-    del ard
+        print("Allele Error:", e.message, file=sys.stderr)
+        sys.exit(1)
+    except InvalidTypingError as e:
+        print("Typing Error:", e.message, file=sys.stderr)
+        sys.exit(2)
+    else:
+        # Remove ard and close db connection
+        print("Removing")
+        del ard

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.0.1
 commit = True
 tag = True
 

setup.py

@@ -36,7 +36,7 @@
 
 setup(
     name="py-ard",
-    version="1.0.0",
+    version="1.0.1",
     description="ARD reduction for HLA with Python",
     long_description=readme,
     long_description_content_type="text/markdown",