Add http upload capability for the data files

cli/auth.py

@@ -27,8 +27,9 @@ def token(self):
             'scope': 'openid'
         }
         response = requests.post(self.device_authorization_url, data=payload)
-        response_json = response.json()
+        response.raise_for_status()
 
+        response_json = response.json()
         device_code = response_json['device_code']
         user_code = response_json['user_code']
         verification_uri = response_json['verification_uri']

cli/submit.py

@@ -1,9 +1,12 @@
 #!/usr/bin/env python
 import os
+from urllib.parse import urljoin
 
 import requests
 import yaml
-from ebi_eva_common_pyutils.logger import logging_config
+
+from ebi_eva_common_pyutils.logger import logging_config, AppLogger
+from retry import retry
 
 from cli.auth import get_auth
 
@@ -15,9 +18,11 @@
 
 
 class StudySubmitter:
-    def __init__(self, submission_initiate_url=SUBMISSION_INITIATE_URL):
+    def __init__(self, vcf_files, metadata_file, submission_initiate_url=SUBMISSION_INITIATE_URL):
         self.auth = get_auth()
         self.submission_initiate_url = submission_initiate_url
+        self.vcf_files = vcf_files
+        self.metadata_file = metadata_file
 
     def create_submission_config_file(self, submission_dir, submission_id, submission_upload_url):
         submission_config_file = os.path.join(submission_dir, SUB_CLI_CONFIG_FILE)
@@ -38,19 +43,26 @@ def get_submission_id_and_upload_url(self, submission_dir):
         else:
             raise FileNotFoundError(f'Could not upload. No config file found for the submission in {submission_dir}')
 
-    # TODO
-    def upload_submission(self, submission_dir, submission_id=None, submission_upload_url=None):
-        if not submission_id or not submission_upload_url:
+    def upload_submission(self, submission_upload_url, submission_dir):
+        if not submission_upload_url:
             submission_id, submission_upload_url = self.get_submission_id_and_upload_url(submission_dir)
-        pass
+
+        for f in self.vcf_files:
+            self.upload_file(submission_upload_url, f)
+        self.upload_file(submission_upload_url, self.metadata_file)
+
+    @retry(tries=5, delay=10, backoff=5, logger=logger)
+    def upload_file(self, submission_upload_url, input_file):
+        base_name = os.path.basename(input_file)
+        r = requests.put(urljoin(submission_upload_url, base_name), data=open(input_file, 'rb'))
+        r.raise_for_status()
 
     def verify_submission_dir(self, submission_dir):
         if not os.path.exists(submission_dir):
             os.makedirs(submission_dir)
         if not os.access(submission_dir, os.W_OK):
             raise Exception(f"The directory '{submission_dir}' does not have write permissions.")
 
-
     def submit(self, submission_dir):
         self.verify_submission_dir(submission_dir)
         response = requests.post(self.submission_initiate_url,

tests/test_submit.py

@@ -1,18 +1,20 @@
 import json
+import os
 import unittest
-from unittest.mock import MagicMock, patch, Mock, PropertyMock
+from unittest.mock import MagicMock, patch, Mock
 
-from cli import LSRI_CLIENT_ID
-from cli.auth import WebinAuth, LSRIAuth
 from cli.submit import StudySubmitter
 
 
 class TestSubmit(unittest.TestCase):
+    resource_dir = os.path.join(os.path.dirname(__file__), 'resources')
 
     def setUp(self) -> None:
         self.token = 'a token'
         with patch('cli.submit.get_auth', return_value=Mock(token=self.token)):
-            self.submitter = StudySubmitter()
+            vcf_files = [os.path.join(self.resource_dir, 'vcf_files', 'example2.vcf.gz')]
+            metadata_file = [os.path.join(self.resource_dir, 'EVA_Submission_template.V1.1.4.xlsx')]
+            self.submitter = StudySubmitter(vcf_files=vcf_files, metadata_file=metadata_file)
 
     def test_submit(self):
         # Mock the response for post-authentication response from eva-submission-ws
@@ -30,3 +32,10 @@ def test_submit(self):
                                           headers={'Accept': 'application/hal+json', 'Authorization': 'Bearer a token'})
 
         # TODO: Check that upload_submission was called with submission id
+
+    def test_upload_file(self):
+        resource_dir = os.path.join(os.path.dirname(__file__), 'resources')
+
+        file_to_upload = os.path.join(resource_dir, 'EVA_Submission_template.V1.1.4.xlsx')
+        self.submitter.upload_file(submission_upload_url='',
+                                   input_file=file_to_upload)