From 43db4759634ed62fbfab4098359bee0fa4daf194 Mon Sep 17 00:00:00 2001
From: tcezard <tcezard@ebi.ac.uk>
Date: Fri, 26 Jan 2024 12:11:44 +0000
Subject: [PATCH] Extract logic from the executable to put it in the library

---
 eva_sub_cli/main.py | 64 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100755 eva_sub_cli/main.py

diff --git a/eva_sub_cli/main.py b/eva_sub_cli/main.py
new file mode 100755
index 0000000..d0f3755
--- /dev/null
+++ b/eva_sub_cli/main.py
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+import csv
+import os
+first attempt
+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.docker_validator import DockerValidator, docker_path, container_image
+from eva_sub_cli.reporter import READY_FOR_SUBMISSION_TO_EVA
+from eva_sub_cli.submit import StudySubmitter
+
+VALIDATE = 'validate'
+SUBMIT = 'submit'
+
+
+logging_config.add_stdout_handler()
+
+
+def get_vcf_files(mapping_file):
+    vcf_files = []
+    with open(mapping_file) as open_file:
+        reader = csv.DictReader(open_file, delimiter=',')
+        for row in reader:
+            vcf_files.append(row['vcf'])
+    return vcf_files
+
+
+def orchestrate_process(submission_dir, vcf_files_mapping, metadata_json, metadata_xlsx, task):
+    # load config
+    config_file_path = os.path.join(submission_dir, SUB_CLI_CONFIG_FILE)
+    sub_config = WritableConfig(config_file_path, version=__version__)
+
+    metadata_file = metadata_json or metadata_xlsx
+    vcf_files = get_vcf_files(vcf_files_mapping)
+
+
+
+    # Only run validate if it's been requested
+    if VALIDATE in tasks:
+        with DockerValidator(vcf_files_mapping, submission_dir, metadata_json, metadata_xlsx,
+                             submission_config=sub_config) as validator:
+            validator.validate()
+            validator.create_reports()
+            validator.update_config_with_validation_result()
+
+    with StudySubmitter(submission_dir, vcf_files, metadata_file, submission_config=sub_config) as submitter:
+        submitter.upload_submission()
+    # if validation is not passed, process task submit (validate and submit)
+    if READY_FOR_SUBMISSION_TO_EVA in sub_config and sub_config[READY_FOR_SUBMISSION_TO_EVA]:
+        tasks = SUBMIT
+        else:
+            # if validation is passed, upload files without validating again
+
+    if task == VALIDATE or task == SUBMIT:
+        with DockerValidator(vcf_files_mapping, submission_dir, metadata_json, metadata_xlsx,
+                             submission_config=sub_config) as validator:
+            validator.validate()
+            validator.create_reports()
+            validator.update_config_with_validation_result()
+
+    if task == SUBMIT:
+        with StudySubmitter(submission_dir, vcf_files, metadata_file, submission_config=sub_config) as submitter:
+            submitter.submit()