1212from seqr .utils .middleware import ErrorsWarningsException
1313from seqr .views .utils .airtable_utils import AirtableSession , ANVIL_REQUEST_TRACKING_TABLE
1414from seqr .views .utils .export_utils import write_multiple_files
15+ from seqr .views .utils .json_utils import _to_title_case
1516from seqr .views .utils .pedigree_info_utils import JsonConstants
1617from settings import SEQR_SLACK_DATA_ALERTS_NOTIFICATION_CHANNEL , BASE_URL , ANVIL_UI_URL , PIPELINE_RUNNER_SERVER , \
1718 SEQR_SLACK_ANVIL_DATA_LOADING_CHANNEL , SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL , LOADING_DATASETS_DIR
@@ -64,6 +65,22 @@ def update_airtable_loading_tracking_status(project, status, additional_update=N
6465 update = {'Status' : status , ** (additional_update or {})},
6566 )
6667
68+ def trigger_delete_families_search (project , family_guids , user = None ):
69+ search_samples = Sample .objects .filter (is_active = True , individual__family__guid__in = family_guids )
70+ info = []
71+ if search_samples :
72+ updated_families = search_samples .values_list ("individual__family__family_id" , flat = True ).distinct ()
73+ family_summary = ", " .join (sorted (updated_families ))
74+ num_updated = search_samples .update (is_active = False )
75+ message = f'Disabled search for { num_updated } { len (updated_families )} { family_summary }
76+ info .append (message )
77+ logger .info (message , user )
78+
79+ variables = {'project_guid' : project .guid , 'family_guids' : family_guids }
80+ _enqueue_pipeline_request ('delete_families' , variables , user )
81+ info .append ('Triggered delete family data' )
82+ return info
83+
6784def trigger_data_loading (projects : list [Project ], individual_ids : list [int ], sample_type : str , dataset_type : str ,
6885 genome_version : str , data_path : str , user : User , raise_error : bool = False , skip_expect_tdr_metrics : bool = True ,
6986 skip_check_sex_and_relatedness : bool = True , vcf_sample_id_map = None ,
@@ -84,34 +101,40 @@ def trigger_data_loading(projects: list[Project], individual_ids: list[int], sam
84101 _upload_data_loading_files (individual_ids , vcf_sample_id_map or {}, user , file_path , raise_error )
85102 _write_gene_id_file (user )
86103
87- response = requests .post (f'{ PIPELINE_RUNNER_SERVER } , json = variables , timeout = 60 )
88- success = True
104+ error = _enqueue_pipeline_request ('loading_pipeline' , variables , user , raise_error )
105+ if error :
106+ safe_post_to_slack (
107+ SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL ,
108+ f'{ error_message } { error } \n Loading pipeline should be triggered with:\n ```{ json .dumps (variables , indent = 4 )} ,
109+ )
110+
111+ success = not error
112+ if success_message and (success or success_slack_channel != SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL ):
113+ safe_post_to_slack (success_slack_channel , '\n \n ' .join ([
114+ success_message ,
115+ f'Pedigree files have been uploaded to { file_path } ,
116+ f'Loading pipeline is triggered with:\n ```{ json .dumps (variables , indent = 4 )} ,
117+ ]))
118+
119+ return success
120+
121+
122+ def _enqueue_pipeline_request (name : str , variables : dict , user : User , raise_error : bool = True ):
123+ response = requests .post (f'{ PIPELINE_RUNNER_SERVER } { name } , json = variables , timeout = 60 )
124+ error = None
89125 try :
90126 response .raise_for_status ()
91- logger .info ('Triggered loading pipeline ' , user , detail = variables )
127+ logger .info (f 'Triggered { _to_title_case ( name ) } user , detail = variables )
92128 except requests .HTTPError as e :
93- success = False
94129 error = str (e )
95130 if response .status_code == 409 :
96131 error = 'Loading pipeline is already running. Wait for it to complete and resubmit'
97132 e = ErrorsWarningsException ([error ])
98133 if raise_error :
99134 raise e
100135 else :
101- logger .warning (f'Error triggering loading pipeline: { error } , user , detail = variables )
102- safe_post_to_slack (
103- SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL ,
104- f'{ error_message } { error } \n Loading pipeline should be triggered with:\n ```{ json .dumps (variables , indent = 4 )} ,
105- )
106-
107- if success_message and (success or success_slack_channel != SEQR_SLACK_LOADING_NOTIFICATION_CHANNEL ):
108- safe_post_to_slack (success_slack_channel , '\n \n ' .join ([
109- success_message ,
110- f'Pedigree files have been uploaded to { file_path } ,
111- f'Loading pipeline is triggered with:\n ```{ json .dumps (variables , indent = 4 )} ,
112- ]))
113-
114- return success
136+ logger .warning (f'Error Triggering { _to_title_case (name )} { error } , user , detail = variables )
137+ return error
115138
116139
117140def _loading_dataset_type (sample_type : str , dataset_type : str ):
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