EVA-3400 Implement submission ID persistence and retrieval for user sessions

cli/eva_sub_cli.py

@@ -0,0 +1,20 @@
+from argparse import ArgumentParser
+
+from ebi_eva_common_pyutils.logger import logging_config
+
+from cli.submit import StudySubmitter
+
+if __name__ == "__main__":
+    argparse = ArgumentParser(description='EVA Submission CLI')
+    argparse.add_argument('--submission-dir', required=True, type=str,
+                          help='Full path to the submission directory where all submission info is/will be stored')
+    argparse.add_argument('--resume', action='store_true', default=False, help='resume an existing submission')
+    args = argparse.parse_args()
+
+    logging_config.add_stdout_handler()
+
+    submitter = StudySubmitter()
+    if args.resume:
+        submitter.upload_submission(args.submission_dir)
+    else:
+        submitter.submit(args.submission_dir)

cli/submit.py

@@ -1,11 +1,16 @@
 #!/usr/bin/env python
-import json
-import requests
+import os
 
+import requests
+import yaml
 from ebi_eva_common_pyutils.logger import logging_config
+
 from cli.auth import get_auth
 
 logger = logging_config.get_logger(__name__)
+SUB_CLI_CONFIG_FILE = ".eva-sub-cli-config.yml"
+SUB_CLI_CONFIG_KEY_SUBMISSION_ID = "submission_id"
+SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL = "submission_upload_url"
 SUBMISSION_INITIATE_URL = "http://www.ebi.ac.uk/eva/v1/submission/initiate"
 
 
@@ -14,21 +19,45 @@ def __init__(self, submission_initiate_url=SUBMISSION_INITIATE_URL):
         self.auth = get_auth()
         self.submission_initiate_url = submission_initiate_url
 
+    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)
+        config_data = {
+            SUB_CLI_CONFIG_KEY_SUBMISSION_ID: submission_id,
+            SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL: submission_upload_url
+        }
+        with open(submission_config_file, 'w') as open_file:
+            yaml.safe_dump(config_data, open_file)
+
+    def get_submission_id_and_upload_url(self, submission_dir):
+        submission_config_file = os.path.join(submission_dir, SUB_CLI_CONFIG_FILE)
+        if submission_config_file:
+            with (open(submission_config_file, 'r') as f):
+                submission_config_data = yaml.safe_load(f)
+                return submission_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_ID], submission_config_data[
+                    SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL]
+        else:
+            raise FileNotFoundError(f'Could not upload. No config file found for the submission in {submission_dir}')
+
     # TODO
-    def upload_submission(self, submission_id, submission_upload_url):
+    def upload_submission(self, submission_dir, submission_id=None, submission_upload_url=None):
+        if not submission_id or not submission_upload_url:
+            submission_id, submission_upload_url = self.get_submission_id_and_upload_url(submission_dir)
         pass
 
-    def submit(self):
+    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,
                                  headers={'Accept': 'application/hal+json',
                                           'Authorization': 'Bearer ' + self.auth.token})
         response.raise_for_status()
         response_json = response.json()
         logger.info("Submission ID {} received!!".format(response_json["submissionId"]))
-        self.upload_submission(response_json["submissionId"], response_json["uploadUrl"])
-
-
-if __name__ == "__main__":
-    logging_config.add_stdout_handler()
-    submitter = StudySubmitter()
-    submitter.submit()
+        self.create_submission_config_file(submission_dir, response_json["submissionId"], response_json["uploadUrl"])
+        self.upload_submission(submission_dir, response_json["submissionId"], response_json["uploadUrl"])

tests/test_submit.py

@@ -1,10 +1,15 @@
 import json
+import os
+import shutil
 import unittest
 from unittest.mock import MagicMock, patch, Mock, PropertyMock
 
+import yaml
+
 from cli import LSRI_CLIENT_ID
 from cli.auth import WebinAuth, LSRIAuth
-from cli.submit import StudySubmitter
+from cli.submit import StudySubmitter, SUB_CLI_CONFIG_FILE, SUB_CLI_CONFIG_KEY_SUBMISSION_ID, \
+    SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL
 
 
 class TestSubmit(unittest.TestCase):
@@ -13,6 +18,11 @@ def setUp(self) -> None:
         self.token = 'a token'
         with patch('cli.submit.get_auth', return_value=Mock(token=self.token)):
             self.submitter = StudySubmitter()
+        self.test_sub_dir = os.path.join(os.path.dirname(__file__), 'resources', 'test_sub_dir')
+        shutil.rmtree(self.test_sub_dir, ignore_errors=True)
+
+    def tearDown(self) -> None:
+        shutil.rmtree(self.test_sub_dir, ignore_errors=True)
 
     def test_submit(self):
         # Mock the response for post-authentication response from eva-submission-ws
@@ -24,8 +34,57 @@ def test_submit(self):
 
         # Set the side_effect attribute to return different responses
         with patch('cli.submit.requests.post', return_value=mock_submit_response) as mock_post:
-            self.submitter.submit()
+            with patch('cli.submit.StudySubmitter.create_submission_config_file'):
+                self.submitter.submit('test_submission_directory')
         mock_post.assert_called_once_with('http://www.ebi.ac.uk/eva/v1/submission/initiate',
                                           headers={'Accept': 'application/hal+json', 'Authorization': 'Bearer a token'})
 
         # TODO: Check that upload_submission was called with submission id
+
+    def test_verify_submission_dir(self):
+        self.submitter.verify_submission_dir(self.test_sub_dir)
+        assert os.path.exists(self.test_sub_dir)
+
+    def test_verify_submission_dircreate_submission_config_file(self):
+        self.submitter.verify_submission_dir(self.test_sub_dir)
+        self.submitter.create_submission_config_file(self.test_sub_dir, 1234, "/sub/upload/url")
+
+        sub_config_file = os.path.join(self.test_sub_dir, SUB_CLI_CONFIG_FILE)
+        assert os.path.exists(sub_config_file)
+
+        with (open(sub_config_file, 'r') as f):
+            sub_config_data = yaml.safe_load(f)
+            assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_ID] == 1234
+            assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL] == "/sub/upload/url"
+
+    def test_get_submission_id_and_upload_url(self):
+        self.submitter.verify_submission_dir(self.test_sub_dir)
+        self.submitter.create_submission_config_file(self.test_sub_dir, 1234, "/sub/upload/url")
+
+        submission_id, upload_url = self.submitter.get_submission_id_and_upload_url(self.test_sub_dir)
+
+        assert submission_id == 1234
+        assert upload_url == "/sub/upload/url"
+
+
+
+    def test_submit(self):
+        mock_submit_response = MagicMock()
+        mock_submit_response.status_code = 200
+        mock_submit_response.json.return_value = {
+            "submissionId": "mock_submission_id",
+            "uploadUrl": "directory to use for upload",
+        }
+        with patch('cli.submit.requests.post', return_value=mock_submit_response) as mock_post:
+            self.submitter.submit(self.test_sub_dir)
+
+        assert os.path.exists(self.test_sub_dir)
+        sub_config_file = os.path.join(self.test_sub_dir, SUB_CLI_CONFIG_FILE)
+        assert os.path.exists(sub_config_file)
+        with (open(sub_config_file, 'r') as f):
+            sub_config_data = yaml.safe_load(f)
+            assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_ID] == "mock_submission_id"
+            assert sub_config_data[SUB_CLI_CONFIG_KEY_SUBMISSION_UPLOAD_URL] == "directory to use for upload"
+
+
+