Merge pull request #41 from aanil/fix_git

Fix for when files are committed, log message changes
NationalGenomicsInfrastructure · May 29, 2024 · 61f9b7a · 61f9b7a
2 parents 002caa9 + e2af7c0
commit 61f9b7a
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Showing 3 changed files with 13 additions and 11 deletions.
diff --git a/daily_read/__main__.py b/daily_read/__main__.py
@@ -100,20 +100,18 @@ def generate_all(ctx, upload=False, develop=False):
             for upload_category, report_state in {"projects": "published", "delete_report_for": "review"}.items():
                 for status in modified_orders[owner][upload_category].keys():
                     for project in modified_orders[owner][upload_category][status]:
-                        uploaded = False
+                        request_success = False
                         report_upload = report if upload_category == "projects" else ""
                         try:
-                            uploaded = op.upload_report_to_order_portal(report_upload, project, report_state)
-                            # Stage changes only if report was uploaded
-                            if uploaded:
+                            request_success = op.upload_report_to_order_portal(report_upload, project, report_state)
+                            # Stage changes
+                            if request_success:
                                 op.projects_data.stage_data_for_project(project)
                         # catch any and every exception during upload
                         except Exception as e:
                             log.error(
                                 f"Exception Raised: Issue in uploading/hiding reports for {project.project_id}: {e}\nContinuing to next project"
                             )
-            # Commit all uploaded projects
-            op.projects_data.commit_staged_data(f"Commit reports updates for {datetime.datetime.now()}")
 
         else:
             log.info("Saving report to disk instead of uploading")
@@ -123,6 +121,10 @@ def generate_all(ctx, upload=False, develop=False):
                 config_values.STATUS_PRIORITY,
                 out_dir=config_values.REPORTS_LOCATION,
             )
+    if upload:
+        # Commit all uploaded projects
+        op.projects_data.commit_staged_data(f"Commit reports updates for {datetime.datetime.now()}")
+
     daily_read.utils.error_reporting(log)
 
 

diff --git a/daily_read/order_portal.py b/daily_read/order_portal.py
@@ -161,12 +161,12 @@ def upload_report_to_order_portal(self, report, project, status):
         # TODO: check Encoded to utf-8 to display special characters properly
         response = requests.post(url, headers=self.headers, json=indata)
 
+        operation = "updated" if report else "hidden"
         if response.status_code == 200:
-            operation = "Updated" if report else "Hid"
-            log.info(f"{operation} report for order with project id: {project.project_id}")
+            log.info(f"Report {operation} for order with project id: {project.project_id}")
             return True
         else:
             log.error(
-                f"Report not uploaded for order with project id: {project.project_id}\nReason: {response.status_code} {response.reason}"
+                f"Report not {operation} for order with project id: {project.project_id}\nReason: {response.status_code} {response.reason}"
             )
             return False
diff --git a/tests/test_order_portal.py b/tests/test_order_portal.py
@@ -29,7 +29,7 @@ def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_da
             "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published"
         )
         assert not uploaded
-        assert f"Report not uploaded for order with project id: {order_id}\nReason: 404" in caplog.text
+        assert f"Report not updated for order with project id: {order_id}\nReason: 404" in caplog.text
 
 
 def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_data_record, get_env_file_path):
@@ -108,7 +108,7 @@ def test_get_and_process_orders_open_with_report_and_upload(
             mock_post.assert_called_once_with(
                 url, headers={"X-OrderPortal-API-key": config_values.ORDER_PORTAL_API_KEY}, json=indata
             )
-            assert f"Updated report for order with project id: {order_id}" in caplog.text
+            assert f"Report updated for order with project id: {order_id}" in caplog.text
 
 
 def test_get_and_process_orders_open_to_aborted_with_report_and_upload(