Merge branch 'feature-s/refuse_full' into 'dev'

Fully refuse when deleting a sequence file

Closes #2478

See merge request !49

server/web2py/applications/vidjil/controllers/file.py

@@ -588,11 +588,11 @@ def delete():
         if not(delete_results):
             delete_sequence_file(request.vars['id'])
         else:
-            results_file = db(db.results_file.sequence_file_id == request.vars["id"]).select().first()
-            config_id = results_file.config_id
+            sample_set_ids = get_sequence_file_sample_sets(request.vars["id"])
+            config_ids = get_sequence_file_config_ids(request.vars["id"])
             db(db.results_file.sequence_file_id == request.vars["id"]).delete()
             db(db.sequence_file.id == request.vars["id"]).delete()
-            schedule_fuse(sample_set.id, config_id)
+            schedule_fuse(sample_set_ids, config_ids)
 
         res = {"redirect": "sample_set/index",
                "args" : { "id" : request.vars["redirect_sample_set_id"]},

server/web2py/applications/vidjil/models/sequence_file.py

@@ -107,3 +107,23 @@ def get_run_id(file_id):
         run_id = row.id
 
     return run_id
+
+def get_sequence_file_sample_sets(sequence_file_id):
+    '''
+    return the list of sample_sets a sequence_file belongs to
+    '''
+    query = db((db.sample_set_membership.sequence_file_id == sequence_file_id)).select(db.sample_set_membership.sample_set_id)
+    sample_set_ids = []
+    for row in query:
+        sample_set_ids.append(row.sample_set_id)
+    return sample_set_ids
+
+def get_sequence_file_config_ids(sequence_file_id):
+    '''
+    return the list of configs run ona sequence_file
+    '''
+    query = db((db.results_file.sequence_file_id == sequence_file_id)).select(db.results_file.config_id)
+    config_ids = []
+    for row in query:
+        config_ids.append(row.config_id)
+    return config_ids

server/web2py/applications/vidjil/models/task.py

@@ -128,20 +128,21 @@ def schedule_run(id_sequence, id_config, grep_reads=None):
     log.info(res)
     return res
 
-def schedule_fuse(id_sample_set, id_config):
-    sample_set = db.sample_set[id_sample_set]
-
-    sequence_file_id = db((db.sample_set_membership.sample_set_id == sample_set.id)
-                        &(db.sample_set_membership.sequence_file_id == db.sequence_file.id)
-                        ).select(db.sequence_file.id).first().id
-
-    results_file_id = db((db.results_file.sequence_file_id == sequence_file_id)
-                        & (db.results_file.config_id == id_config)
-                        ).select(db.results_file.id).first().id
-
-    args = [sequence_file_id, id_config, results_file_id, id_sample_set, False]
-    task = scheduler.queue_task('fuse', args,
-                                repeats = 1, timeout = defs.TASK_TIMEOUT)
+def schedule_fuse(sample_set_ids, config_ids):
+    args = []
+    for sample_set_id in sample_set_ids:
+        for config_id in config_ids:
+            row = db((db.sample_set_membership.sample_set_id == sample_set_id)
+                   & (db.sample_set_membership.sequence_file_id == db.results_file.sequence_file_id)
+                   & (db.results_file.config_id == config_id)
+                ).select(db.sample_set_membership.sample_set_id, db.sample_set_membership.sequence_file_id,
+                        db.results_file.id, db.results_file.config_id).first()
+            if row:
+                args.append([row.sample_set_membership.sequence_file_id, row.results_file.config_id,
+                row.results_file.id, row.sample_set_membership.sample_set_id, False])
+    if len(args) > 0:
+        task = scheduler.queue_task('refuse', [args],
+                                    repeats = 1, timeout = defs.TASK_TIMEOUT)
 
 def run_vidjil(id_file, id_config, id_data, grep_reads,
                clean_before=False, clean_after=False):
@@ -469,6 +470,10 @@ def run_copy(id_file, id_config, id_data, clean_before=False, clean_after=False)
     return "SUCCESS"
 
 
+def run_refuse(args):
+    for arg in args:
+        run_fuse(arg[0], arg[1], arg[2], arg[3], arg[4])
+    return "SUCCESS"
 
 def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clean_after=False):
     from subprocess import Popen, PIPE, STDOUT, os
@@ -778,5 +783,5 @@ def run_pre_process(pre_process_id, sequence_file_id, clean_before=True, clean_a
                                mixcr=run_mixcr,
                                none=run_copy,
                                pre_process=run_pre_process,
-                               fuse=run_fuse),
+                               refuse=run_refuse),
                         heartbeat=defs.SCHEDULER_HEARTBEAT)