Move executable to bin folder

eva_sub_cli/eva_sub_cli.py → bin/eva_sub_cli.py

@@ -27,6 +27,7 @@ def get_docker_validator(vcf_files_mapping, output_dir, metadata_json, metadata_
     return DockerValidator(vcf_files_mapping, validation_output_dir, metadata_json, metadata_xlsx,
                            container, docker, sub_config)
 
+
 def get_vcf_files(mapping_file):
     vcf_files = []
     with open(mapping_file) as open_file:
@@ -35,6 +36,7 @@ def get_vcf_files(mapping_file):
             vcf_files.append(row['vcf'])
     return vcf_files
 
+
 if __name__ == "__main__":
     argparser = ArgumentParser(description='EVA Submission CLI - validate and submit data to EVA')
     argparser.add_argument('--task', required=True, choices=[VALIDATE, SUBMIT, RESUME_SUBMISSION],

docker/Dockerfile

@@ -27,4 +27,4 @@ RUN curl -L "https://github.com/nextflow-io/nextflow/releases/download/v${NXF_VE
 
 COPY . /opt/
 
-RUN python setup.py install
+RUN pip install .

eva_sub_cli/docker_validator.py

@@ -14,8 +14,8 @@
 logger = logging_config.get_logger(__name__)
 
 docker_path = 'docker'
-container_image = 'ebivariation/eva-sub-eva_sub_cli'
-container_tag = 'v0.0.1.dev0'
+container_image = 'ebivariation/eva-sub-cli'
+container_tag = 'v0.0.1.dev1'
 container_validation_dir = '/opt/vcf_validation'
 container_validation_output_dir = '/opt/vcf_validation/vcf_validation_output'
 container_etc_dir = '/opt/eva_sub_cli/etc'
@@ -92,6 +92,7 @@ def run_docker_validator(self):
 
             docker_cmd = self.get_docker_validation_cmd()
             # start validation
+            print(docker_cmd)
             # FIXME: If nextflow fails in the docker exec still exit with error code 0
             run_command_with_output("Run Validation using Nextflow", docker_cmd)
             # copy validation result to user host

setup.py

@@ -25,8 +25,5 @@
         'License :: OSI Approved :: Apache Software License',
         'Programming Language :: Python :: 3'
     ],
-    scripts=[
-        join(dirname(__file__), 'eva_sub_cli', s)
-        for s in ('xlsx2json.py', 'samples_checker.py', 'eva_sub_cli.py')
-    ]
+    scripts=glob.glob(join(dirname(__file__), 'bin', '*.py'))
 )

tests/test_docker_validator.py

@@ -58,7 +58,7 @@ def setUp(self):
             mapping_file=self.mapping_file,
             output_dir=self.output_dir,
             metadata_json=self.metadata_json,
-            container_name='eva-sub-eva_sub_cli-test'
+            container_name='eva-sub-cli-test'
         )
         shutil.copyfile(
             os.path.join(self.resources_folder, 'EVA_Submission_template.V1.1.4.xlsx'),
@@ -69,7 +69,7 @@ def setUp(self):
             mapping_file=self.mapping_file,
             output_dir=self.output_dir,
             metadata_xlsx=self.metadata_xlsx,
-            container_name='eva-sub-eva_sub_cli-test'
+            container_name='eva-sub-cli-test'
         )
 
     def tearDown(self):

tests/test_samples_checker.py

@@ -3,7 +3,7 @@
 
 import yaml
 
-from eva_sub_cli.samples_checker import check_sample_name_concordance
+from bin.samples_checker import check_sample_name_concordance
 
 
 class TestSampleChecker(TestCase):

tests/test_submit.py

@@ -7,7 +7,7 @@
 import yaml
 from ebi_eva_common_pyutils.config import WritableConfig
 
-from eva_sub_cli.eva_sub_cli import SUB_CLI_CONFIG_FILE
+from eva_sub_cli import SUB_CLI_CONFIG_FILE
 from eva_sub_cli.reporter import READY_FOR_SUBMISSION_TO_EVA
 from eva_sub_cli.submit import StudySubmitter, SUB_CLI_CONFIG_KEY_SUBMISSION_ID, SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL
 

tests/test_xlsx2json.py

@@ -5,7 +5,7 @@
 import jsonschema
 
 from eva_sub_cli import ETC_DIR
-from eva_sub_cli.xlsx2json import XlsxParser, create_xls_template_from_yaml
+from bin.xlsx2json import XlsxParser, create_xls_template_from_yaml
 
 
 class TestXlsReader(TestCase):