make relatedness check file downloadable (#4542)

* upload relatedness check file to slack instead of adding the link * whitespace * add timeout s * use downloadable link * Update check_for_new_samples_from_pipeline.py * Update communication_utils.py
broadinstitute · Dec 19, 2024 · bfe53b7 · bfe53b7
1 parent 7c4a3ff
commit bfe53b7
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 9 deletions.
diff --git a/reference_data/management/commands/utils/download_utils.py b/reference_data/management/commands/utils/download_utils.py
@@ -44,4 +44,3 @@ def _get_remote_file_size(url):
     except Exception:
         # file size not yet implemented for FTP and other protocols, and HEAD not supported for all http requests
         return 0
-
diff --git a/seqr/management/commands/check_for_new_samples_from_pipeline.py b/seqr/management/commands/check_for_new_samples_from_pipeline.py
@@ -179,14 +179,13 @@ def _load_new_samples(cls, metadata_path, genome_version, dataset_type, run_vers
                 if split_pdos:
                     summary += f'\n\nSkipped samples in this project have been moved to {", ".join(split_pdos)}'
 
-                relatedness_check_message = (
-                    f'\nRelatedness check results: {relatedness_check_file_path}'
-                    if (relatedness_check_file_path and check == RELATEDNESS_CHECK_NAME)
-                    else ''
-                )
+                if check == RELATEDNESS_CHECK_NAME and relatedness_check_file_path:
+                    downloadable_link = f'https://storage.cloud.google.com/{relatedness_check_file_path[5:]}'
+                    summary += f'\n\nRelatedness check results: {downloadable_link}'
+
                 safe_post_to_slack(
                     SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL,
-                    f'The following {len(failures)} families failed {check.replace("_", " ")} in {project}:\n{summary}{relatedness_check_message}'
+                    f'The following {len(failures)} families failed {check.replace("_", " ")} in {project}:\n{summary}'
                 )
 
         # Reload saved variant JSON

diff --git a/seqr/management/tests/check_for_new_samples_from_pipeline_tests.py b/seqr/management/tests/check_for_new_samples_from_pipeline_tests.py
@@ -553,7 +553,7 @@ def test_command(self, mock_email, mock_airtable_utils):
             mock.call(
                 'seqr_loading_notifications',
                 """The following 1 families failed relatedness check in 1kg project nåme with uniçøde:
-- 1: Sample NA19679 has expected relation "parent" to NA19675 but has coefficients [0.0, 0.8505002045292791, 0.14949979547072176, 0.5747498977353613]; Sample NA19678 has expected relation "sibling" to NA19675 but has coefficients [0.17424888135104177, 0.6041745754450025, 0.22157654320395614, 0.5236638309264574]\nRelatedness check results: gs://seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/test_callset_hash.tsv""",
+- 1: Sample NA19679 has expected relation "parent" to NA19675 but has coefficients [0.0, 0.8505002045292791, 0.14949979547072176, 0.5747498977353613]; Sample NA19678 has expected relation "sibling" to NA19675 but has coefficients [0.17424888135104177, 0.6041745754450025, 0.22157654320395614, 0.5236638309264574]\n\nRelatedness check results: https://storage.cloud.google.com/seqr-loading-temp/v3.1/GRCh38/SNV_INDEL/relatedness_check/test_callset_hash.tsv""",
             ),
             mock.call(
                 'seqr_loading_notifications',

diff --git a/seqr/utils/communication_utils.py b/seqr/utils/communication_utils.py
@@ -80,4 +80,3 @@ def set_email_message_stream(message, stream):
     message.esp_extra = {
         'MessageStream': stream,
     }
-
Original file line number	Diff line number	Diff line change
Expand Up		@@ -44,4 +44,3 @@ def _get_remote_file_size(url):
		except Exception:
		# file size not yet implemented for FTP and other protocols, and HEAD not supported for all http requests
		return 0
Original file line number	Diff line number	Diff line change
Expand Up		@@ -80,4 +80,3 @@ def set_email_message_stream(message, stream):
		message.esp_extra = {
		'MessageStream': stream,
		}