From df9c5014adec0d2504a09206619e308a567d0ea9 Mon Sep 17 00:00:00 2001 From: Chris Schnaufer Date: Wed, 23 Sep 2020 16:21:30 -0700 Subject: [PATCH 1/2] Changing to species --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index a337cac..7c37209 100644 --- a/README.md +++ b/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. From 33e7bdbcdeba67e43d8e5ab63257ab84746ee1e2 Mon Sep 17 00:00:00 2001 From: Chris Schnaufer Date: Thu, 24 Sep 2020 13:33:53 -0700 Subject: [PATCH 2/2] Terminology changes, minor fix, fix no metadata specified --- agpypeline/entrypoint.py | 13 ++++++++----- setup.py | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/agpypeline/entrypoint.py b/agpypeline/entrypoint.py index 8555e39..e188ffe 100755 --- a/agpypeline/entrypoint.py +++ b/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') diff --git a/setup.py b/setup.py index 4320668..ad64558 100644 --- a/setup.py +++ b/setup.py @@ -8,7 +8,7 @@ setuptools.setup( name="agpypeline", - version="0.0.41", + version="0.0.43", author="Jacob van der Leeuw", author_email="jvanderleeuw@email.arizona.edu", description="Installable package for entrypoint and drone-specific environment code within a transformer",