Merge branch 'feature-s/3899-hidden-results' into 'dev'

Hide some results

Closes #3899

See merge request !477

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

@@ -313,6 +313,7 @@ def get_data():
                    & ( db.sample_set.id == db.sample_set_membership.sample_set_id )
                    & ( db.sequence_file.id == db.sample_set_membership.sequence_file_id)
                    & ( db.results_file.sequence_file_id == db.sequence_file.id )
+                   & ( db.results_file.hidden == False )
                    & ( db.results_file.config_id == request.vars["config"]  )
                    ).select(db.sequence_file.ALL,db.results_file.ALL, db.sample_set.id, orderby=db.sequence_file.id|~db.results_file.run_date)
 

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

@@ -20,6 +20,7 @@ def index():
             & (db.sequence_file.id==db.sample_set_membership.sequence_file_id)
             & (db.sample_set_membership.sample_set_id==db.patient.sample_set_id)
             & (db.results_file.config_id==db.config.id)
+            & (db.results_file.hidden == False)
         ).select(
             orderby = ~db.results_file.run_date
         )

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

@@ -59,7 +59,8 @@ def info():
             ).select(
                 left=db.results_file.on(
                     (db.results_file.sequence_file_id==db.sequence_file.id)
-                    & (db.results_file.config_id==str(config_id) )
+                    & (db.results_file.config_id==str(config_id))
+                    & (db.results_file.hidden == False)
                 ), 
                 orderby = db.sequence_file.id|~db.results_file.run_date
             )
@@ -79,6 +80,7 @@ def info():
                 left=db.results_file.on(
                     (db.results_file.sequence_file_id==db.sequence_file.id)
                     & (db.results_file.config_id==str(config_id) )
+                    & (db.results_file.hidden == False)
                 )
             )
 

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

@@ -99,7 +99,8 @@ def index():
             ).select(
                 left=db.results_file.on(
                     (db.results_file.sequence_file_id==db.sequence_file.id)
-                    & (db.results_file.config_id==str(config_id) )
+                    & (db.results_file.config_id==str(config_id))
+                    & (db.results_file.hidden == False)
                 ), 
                 orderby = db.sequence_file.id|~db.results_file.run_date
             )
@@ -118,7 +119,8 @@ def index():
             ).select(
                 left=db.results_file.on(
                     (db.results_file.sequence_file_id==db.sequence_file.id)
-                    & (db.results_file.config_id==str(config_id) )
+                    & (db.results_file.config_id==str(config_id))
+                    & (db.results_file.hidden == False)
                 )
             )
 
@@ -311,6 +313,7 @@ def result_files():
             (db.sequence_file.id == db.sample_set_membership.sequence_file_id) &
             (db.results_file.sequence_file_id == db.sequence_file.id) &
             (db.results_file.data_file != None) &
+            (db.results_file.hidden == False) &
             config_query
         )
 
@@ -600,6 +603,7 @@ def custom():
         & (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
         & (db.results_file.sequence_file_id==db.sequence_file.id)
         & (db.results_file.data_file != '')
+        & (db.results_file.hidden == False)
         & (db.config.id==db.results_file.config_id))
 
     group_ids = get_involved_groups()

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

@@ -209,6 +209,7 @@ db.define_table('results_file',
                 Field('config_id', 'reference config', ondelete='SET NULL'),
                 Field('run_date','datetime'),
                 Field('scheduler_task_id', 'integer'),
+                Field('hidden', 'boolean', default = False, notnull = True),
                 Field('data_file', 'upload', 
                       uploadfolder=defs.DIR_RESULTS,
                       length=LENGTH_UPLOAD, autodelete=AUTODELETE))

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

@@ -12,6 +12,7 @@ def get_last_results(sequence_file, config_ids=None):
         select_on_config = db.results_file.config_id.belongs(config_ids)
     # First get the max run dates for the good result files
     select_max_run = db((db.results_file.sequence_file_id == sequence_file)\
+                        & (db.results_file.hidden == False)\
                         & (select_on_config))._select(db.results_file.run_date.max().with_alias('max'),
                                                       groupby=db.results_file.config_id)
 

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

@@ -62,6 +62,7 @@ def compute_contamination(sequence_file_id, results_file_id, config_id):
                        & ( db.sequence_file.id == db.sample_set_membership.sequence_file_id)
                        & ( db.sequence_file.id != sequence_file_id[i])
                        & ( db.results_file.sequence_file_id == db.sequence_file.id )
+                       & ( db.results_file.hidden == False )
                        & ( db.results_file.config_id == config_id[i]  )
                        ).select(db.sequence_file.ALL,db.results_file.ALL, db.sample_set.id, orderby=db.sequence_file.id|~db.results_file.run_date)
 
@@ -104,6 +105,7 @@ def compute_extra(id_file, id_config, min_threshold):
     result = {}
     d = None
     results_file = db((db.results_file.sequence_file_id == id_file) &
+                      (db.results_file.hidden == False) &
                       (db.results_file.config_id == id_config)
                     ).select(orderby=~db.results_file.run_date).first()
     filename = defs.DIR_RESULTS+results_file.data_file
@@ -148,6 +150,7 @@ def schedule_run(id_sequence, id_config, grep_reads=None):
     ts = time.time()
     data_id = db.results_file.insert(sequence_file_id = id_sequence,
                                      run_date = datetime.datetime.fromtimestamp(ts).strftime('%Y-%m-%d %H:%M:%S'),
+                                     hidden = grep_reads is not None, 
                                      config_id = id_config )
         
     args = [id_sequence, id_config, data_id, grep_reads]
@@ -183,6 +186,7 @@ def schedule_fuse(sample_set_ids, 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)
+                   & (db.results_file.hidden == False)
                 ).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:
@@ -648,6 +652,7 @@ def run_fuse(id_file, id_config, id_data, sample_set_id, clean_before=True, clea
                    & ( db.sample_set_membership.sequence_file_id == db.sequence_file.id)
                    & ( db.sample_set_membership.sample_set_id == sample_set_id)
                    & ( db.results_file.config_id == id_config )
+                   & ( db.results_file.hidden == False)
                    ).select( orderby=db.sequence_file.id|~db.results_file.run_date) 
     query = []
     sequence_file_id = 0