FIX unnecessary writing of big cooc matrix used once just in specif + update maplist

gargantext/util/toolchain/__init__.py

@@ -136,21 +136,23 @@ def parse_extract_indexhyperdata(corpus):
 
     # ------------
     # -> cooccurrences on mainlist: compute + write (=> Node and NodeNgramNgram)
-    #                               todo: no need to write it ?
-    cooc_id = compute_coocs(corpus, on_list_id = mainlist_id, groupings_id = group_id)
-    print('CORPUS #%d: [%s] new coocs node #%i' % (corpus.id, t(), cooc_id))
+    coocs = compute_coocs(corpus,
+                            on_list_id = mainlist_id,
+                            groupings_id = group_id,
+                            just_pass_result = True)
+    print('CORPUS #%d: [%s] computed mainlist coocs for specif rank' % (corpus.id, t()))
 
     # -> specificity: compute + write (=> NodeNodeNgram)
-    spec_id = compute_specificity(corpus, cooc_id=cooc_id
-            #   ,groupings_id = group_id
-              )
+    spec_id = compute_specificity(corpus,cooc_matrix = coocs)
+    # no need here for subforms because cooc already counted them in mainform
     print('CORPUS #%d: [%s] new specificity node #%i' % (corpus.id, t(), spec_id))
 
-    # ?? maplist: compute + write (to Node and NodeNgram)
+    # maplist: compute + write (to Node and NodeNgram)
     map_id = do_maplist(corpus,
                         mainlist_id = mainlist_id,
                         specificity_id=spec_id,
-                        grouplist_id=group_id)
+                        grouplist_id=group_id
+                        )
     print('CORPUS #%d: [%s] new maplist node #%i' % (corpus.id, t(), map_id))
 
     print('CORPUS #%d: [%s] FINISHED ngram lists computation' % (corpus.id, t()))
@@ -161,7 +163,7 @@ def parse_extract_indexhyperdata(corpus):
 
 
     if DEBUG is False:
-        print('CORPUS #%d: [%s] FINISHED Sendind email notification' % (corpus.id, t()))
+        print('CORPUS #%d: [%s] FINISHED Sending email notification' % (corpus.id, t()))
         notify_owner(corpus)
 
     corpus.status('Workflow', progress=10, complete=True)

gargantext/util/toolchain/list_map.py

@@ -43,15 +43,11 @@ def do_maplist(corpus,
 
     #dbg = DebugTime('Corpus #%d - computing Miam' % corpus.id)
 
-    mainterms_subquery = (session
-                            # we want only terms within mainlist
-                            .query(NodeNgram.ngram_id)
-                            .filter(NodeNgram.node_id == mainlist_id)
-                            .subquery()
-                         )
+    MainlistTable = aliased(NodeNgram)
 
-    primary_groupterms_subquery = (session
-                            # we want only primary terms (ngram1)
+    IsSubform = (session
+                            # we want only secondary terms (ngram2)
+                            # to be able to filter them out
                             .query(NodeNgramNgram.ngram2_id)
                             .filter(NodeNgramNgram.node_id == grouplist_id)
                             .subquery()
@@ -63,8 +59,15 @@ def do_maplist(corpus,
     query = (session.query(ScoreSpec.ngram_id)
                 .join(Ngram, Ngram.id == ScoreSpec.ngram_id)
                 .filter(ScoreSpec.node_id == specificity_id)
-                .filter(ScoreSpec.ngram_id.in_(mainterms_subquery))
-                .filter(ScoreSpec.ngram_id.notin_(primary_groupterms_subquery))
+
+                # we want only terms within mainlist
+                .join(MainlistTable, Ngram.id == MainlistTable.ngram_id)
+                .filter(MainlistTable.node_id == mainlist_id)
+
+                # we remove all ngrams matching an ngram2_id from the synonyms
+                .outerjoin(IsSubform,
+                           IsSubform.c.ngram2_id == ScoreSpec.ngram_id)
+                .filter(IsSubform.c.ngram2_id == None)
             )
 
     # TODO: move these 2 pools up to mainlist selection
@@ -94,7 +97,7 @@ def do_maplist(corpus,
     new_hyperdata = { 'corpus': corpus.id,
                       'limit' : limit,
                       'monograms_part' : monograms_part,
-                     'monograms_result' : obtained_mono/obtained_total if obtained_total != 0 else obtained_mono
+                     'monograms_result' : obtained_mono/obtained_total if obtained_total != 0 else 0
                     }
     if overwrite_id:
         # overwrite pre-existing node

gargantext/util/toolchain/metric_specificity.py

@@ -9,7 +9,7 @@ from collections              import defaultdict
 from pandas                   import DataFrame
 import pandas as pd
 
-def compute_specificity(corpus, cooc_id=None, overwrite_id = None):
+def compute_specificity(corpus, cooc_id=None, cooc_matrix=None, overwrite_id = None):
     '''
     Compute the specificity, simple calculus.
 
@@ -18,18 +18,26 @@ def compute_specificity(corpus, cooc_id=None, overwrite_id = None):
         - overwrite_id: optional preexisting specificity node to overwrite
     '''
 
+    matrix = defaultdict(lambda : defaultdict(float))
+
+    if cooc_id == None and cooc_matrix == None:
+        raise TypeError("compute_specificity: needs a cooc_id or cooc_matrix param")
+
+    elif cooc_id:
         cooccurrences = (session.query(NodeNgramNgram)
                         .filter(NodeNgramNgram.node_id==cooc_id)
                         )
-    # no filtering: new choice cooc already filtered on tfidf before creation
-
-    matrix = defaultdict(lambda : defaultdict(float))
-
-    # £TODO re-rename weight => score
+        # no filtering: cooc already filtered on mainlist_id at creation
         for cooccurrence in cooccurrences:
             matrix[cooccurrence.ngram1_id][cooccurrence.ngram2_id] = cooccurrence.weight
             matrix[cooccurrence.ngram2_id][cooccurrence.ngram1_id] = cooccurrence.weight
 
+    elif cooc_matrix:
+        # copy WeightedMatrix into local matrix structure
+        for (ngram1_id, ngram2_id) in cooc_matrix.items:
+            w = cooc_matrix.items[(ngram1_id, ngram2_id)]
+            matrix[ngram1_id][ngram2_id] = w
+
     nb_ngrams = len(matrix)
 
     print("SPECIFICITY: computing on %i ngrams" % nb_ngrams)