refactor and clean up imports

EBIvariation · Feb 16, 2024 · a1f20e0 · a1f20e0
1 parent 9b5aef9
commit a1f20e0
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Showing 12 changed files with 409 additions and 435 deletions.
diff --git a/eva_sub_cli/main.py b/eva_sub_cli/main.py
@@ -2,12 +2,11 @@
 import csv
 import os
 from ebi_eva_common_pyutils.config import WritableConfig
-from ebi_eva_common_pyutils.logger import logging_config
 
 from eva_sub_cli import SUB_CLI_CONFIG_FILE, __version__
 from eva_sub_cli.validators.docker_validator import DockerValidator
 from eva_sub_cli.validators.native_validator import NativeValidator
-from eva_sub_cli.reporter import READY_FOR_SUBMISSION_TO_EVA
+from eva_sub_cli.validators.validator import READY_FOR_SUBMISSION_TO_EVA
 from eva_sub_cli.submit import StudySubmitter
 
 VALIDATE = 'validate'
@@ -58,14 +57,12 @@ def orchestrate_process(submission_dir, vcf_files_mapping, vcf_files, assembly_f
         if executor == DOCKER:
             with DockerValidator(vcf_files_mapping, submission_dir, metadata_json, metadata_xlsx,
                                  submission_config=sub_config) as validator:
-                validator.validate()
-                validator.report()
+                validator.validate_and_report()
         # default to native execution
         else:
             with NativeValidator(vcf_files_mapping, submission_dir, metadata_json, metadata_xlsx,
                                  submission_config=sub_config) as validator:
-                validator.validate()
-                validator.report()
+                validator.validate_and_report()
     if SUBMIT in tasks:
         with StudySubmitter(submission_dir, vcf_files, metadata_file, submission_config=sub_config,
                             username=username, password=password) as submitter:

diff --git a/eva_sub_cli/reporter.py b/eva_sub_cli/reporter.py
diff --git a/eva_sub_cli/submit.py b/eva_sub_cli/submit.py
@@ -9,7 +9,7 @@
 
 from eva_sub_cli import SUB_CLI_CONFIG_FILE, __version__, SUBMISSION_WS_VAR
 from eva_sub_cli.auth import get_auth
-from eva_sub_cli.reporter import READY_FOR_SUBMISSION_TO_EVA
+from eva_sub_cli.validators.validator import READY_FOR_SUBMISSION_TO_EVA
 
 SUB_CLI_CONFIG_KEY_SUBMISSION_ID = "submission_id"
 SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL = "submission_upload_url"

diff --git a/eva_sub_cli/validators/docker_validator.py b/eva_sub_cli/validators/docker_validator.py
@@ -54,7 +54,6 @@ def get_docker_validation_cmd(self):
         return docker_cmd
 
     def run_docker_validator(self):
-        self.verify_files_present()
         # check if docker container is ready for running validation
         self.verify_docker_env()
 

diff --git a/eva_sub_cli/validators/native_validator.py b/eva_sub_cli/validators/native_validator.py
@@ -19,11 +19,10 @@ def __init__(self, mapping_file, output_dir, metadata_json=None, metadata_xlsx=N
         self.assembly_checker_path = assembly_checker_path
         self.biovalidator_path = biovalidator_path
 
-    def validate(self):
+    def _validate(self):
         self.run_validator()
 
     def run_validator(self):
-        self.verify_files_present()
         self.verify_executables_installed()
         try:
             command = self.get_validation_cmd()