Merge pull request #16 from AgPipeline/develop

Merging develop into master - no review

README.md

@@ -13,7 +13,7 @@ The metadata keys listed below are all defined in the [BRAPI V1.3](https://brapi
 *  studyName - the name of the study the data belongs to
 *  season - the season associated with the data
 *  observationTimeStamp - a timestamp override in ISO 8610 long format
-*  germplasmName - the name of the crop being tested in the plot
+*  species - the name of the crop being tested in the plot
 *  collectingSite - site identification
 
 If the observationTimeStamp metadata key is not specified, the EXIF information in source image files are checked and the earliest found timestamp will be used. 

agpypeline/entrypoint.py

@@ -388,21 +388,24 @@ def do_work(parser: argparse.ArgumentParser, configuration_info: Configuration,
         result = __internal__.handle_error(-100, "Unable to create transformer class instance for processing")
         return __internal__.handle_result(result, None, None)
 
-    add_parameters(parser, transformer_instance, algorithm_instance)
+    add_parameters(parser, algorithm_instance, transformer_instance)
     args = parser.parse_args()
 
     # start logging system
     logging.getLogger().setLevel(args.debug if args.debug == logging.DEBUG else args.info)
 
-    # Check that we have mandatory metadata
+    # Check that we have metadata
     if not args.metadata and __internal__.check_metadata_needed(configuration_info):
         result = __internal__.handle_error(-1, "No metadata paths were specified.")
     elif args.metadata:
         md_results = __internal__.load_metadata_files(args.metadata)
-        if 'metadata' in md_results:
-            result = __internal__.perform_processing(transformer_instance, algorithm_instance, args, md_results['metadata'])
-        else:
+        if 'metadata' not in md_results:
             result = __internal__.handle_error(-3, md_results['error'])
+    else:
+        md_results = {'metadata': []}
+
+    if not result:
+        result = __internal__.perform_processing(transformer_instance, algorithm_instance, args, md_results['metadata'])
 
     if args.working_space:
         result_path = os.path.join(args.working_space, 'result.json')

setup.py

@@ -8,7 +8,7 @@
 
 setuptools.setup(
     name="agpypeline",
-    version="0.0.42",
+    version="0.0.43",
     author="Jacob van der Leeuw",
     author_email="[email protected]",
     description="Installable package for entrypoint and drone-specific environment code within a transformer",