Merge branch 'unstable' of ssh://delanoe.org:1979/gargantext into samuel

admin/utils.py

@@ -47,13 +47,12 @@ def PrintException():
 
 
 class WorkflowTracking:
-
     def __init__( self ):
         self.hola = "mundo"
 
-    def processing_(self , corpus , step):
+    def processing_(self , corpus_id , step):
         try:
-            the_query = """ UPDATE node_node SET hyperdata=\'{ \"%s\" : \"%s\"}\' WHERE id=%d """ % ( "Processing", step , corpus.id )
+            the_query = """ UPDATE node_node SET hyperdata=\'{ \"%s\" : \"%s\"}\' WHERE id=%d """ % ( "Processing", step , corpus_id )
             cursor = connection.cursor()
             try:
                 cursor.execute(the_query)
@@ -61,4 +60,4 @@ class WorkflowTracking:
             finally:
                 connection.close()
         except :
-            PrintException()
\ No newline at end of file
+            PrintException()

analysis/cooccurrences.py

@@ -5,7 +5,7 @@ from sqlalchemy.sql import func
 
 from gargantext_web.db import Node, Ngram, NodeNgram, NodeNgramNgram, \
         NodeNodeNgram, NodeHyperdataNgram, NodeHyperdata, Hyperdata
-from gargantext_web.db import session, cache, get_or_create_node, bulk_insert
+from gargantext_web.db import get_session, cache, get_or_create_node, bulk_insert
 from analysis.lists import WeightedMatrix, UnweightedList, Translations
 import inspect
 import datetime
@@ -18,7 +18,8 @@ def do_cooc(corpus=None
          , start=None, end=None
          , limit=1000
          , isMonopartite=True
-         , hapax = 3):
+         , hapax = 3
+         , mysession=None):
     '''
     Compute the cooccurence matrix and save it, returning NodeNgramNgram.node_id
     For the moment list of paramters are not supported because, lists need to
@@ -40,30 +41,35 @@ def do_cooc(corpus=None
     # Security test
     field1,field2 = str(field1), str(field2)
     
+    if mysession is None:
+        from gargantext_web.db import session
+        mysession = session
+
     # Get node
     node_cooc = get_or_create_node(nodetype='Cooccurrence', corpus=corpus
                                    , name_str="Cooccurrences corpus " \
                                     + str(corpus.id) + "list_id: " + str(miam_id)
                                     #, hyperdata={'field1': field1, 'field2':field2}
-                                   )
+                                   , mysession=mysession)
 
     
     # BEGIN
     # Saving the parameters of the analysis in the Node JSONB hyperdata field
     args, _, _, parameters = inspect.getargvalues(inspect.currentframe())
-    hyperdata = dict()
-    
-    for parameter in parameters.keys():
-        if parameter != 'corpus' and parameter != 'node_cooc':
-            hyperdata[parameter] = parameters[parameter]
-    
-    node_cooc.hyperdata = hyperdata
-    session.add(node_cooc)
-    session.commit()
+#    hyperdata = dict()
+#    
+#    for parameter in parameters.keys():
+#        if parameter != 'corpus' and parameter != 'node_cooc':
+#            hyperdata[parameter] = parameters[parameter]
+#    
+#    node_cooc.hyperdata = hyperdata
+#
+    mysession.add(node_cooc)
+    mysession.commit()
     # END
 
-    session.query(NodeNgramNgram).filter(NodeNgramNgram.node_id==node_cooc.id).delete()
-    session.commit()
+    mysession.query(NodeNgramNgram).filter(NodeNgramNgram.node_id==node_cooc.id).delete()
+    mysession.commit()
 
     doc_id = cache.NodeType['Document'].id
     
@@ -75,7 +81,7 @@ def do_cooc(corpus=None
     if isMonopartite :
         NodeNgramY = aliased(NodeNgram)
 
-        cooc_query = (session.query(NodeNgramX.ngram_id, NodeNgramY.ngram_id, cooc_score)
+        cooc_query = (mysession.query(NodeNgramX.ngram_id, NodeNgramY.ngram_id, cooc_score)
                  .join(Node, Node.id == NodeNgramX.node_id)
                  .join(NodeNgramY, NodeNgramY.node_id == Node.id)
                  .filter(Node.parent_id==corpus.id, Node.type_id==doc_id)
@@ -83,7 +89,7 @@ def do_cooc(corpus=None
     else :
         NodeNgramY = aliased(NodeNgram)
         
-        cooc_query = (session.query(NodeHyperdataNgram.ngram_id, NodeNgramY.ngram_id, cooc_score)
+        cooc_query = (mysession.query(NodeHyperdataNgram.ngram_id, NodeNgramY.ngram_id, cooc_score)
                  .join(Node, Node.id == NodeHyperdataNgram.node_id)
                  .join(NodeNgramY, NodeNgramY.node_id == Node.id)
                  .join(Hyperdata, Hyperdata.id == NodeHyperdataNgram.hyperdata_id)
@@ -167,7 +173,7 @@ def do_cooc(corpus=None
     # Select according some scores
     if cvalue_id is not None :
         #miam = get_or_create_node(nodetype='Cvalue', corpus=corpus)
-        cvalue_list = UnweightedList(session.query(NodeNodeNgram.ngram_id)
+        cvalue_list = UnweightedList(mysession.query(NodeNodeNgram.ngram_id)
                                    .filter(NodeNodeNgram.nodex_id == cvalue_id).all()
                                    )
     

analysis/diachronic_specificity.py

@@ -9,7 +9,6 @@ import numpy as np
 import collections
 
 
-session = get_session()
 
 def result2dict(query):
     results = dict()
@@ -27,6 +26,7 @@ def diachronic_specificity(corpus_id, terms, order=True):
     Values are measure to indicate diachronic specificity.
     Nowadays, the measure is rather simple: distance of frequency of period from mean of frequency of all corpus.
     '''
+    # implicit global session
     ngram_frequency_query = (session
         .query(Node.hyperdata['publication_year'], func.count('*'))
         .join(NodeNgram, Node.id == NodeNgram.node_id)
@@ -64,7 +64,6 @@ def diachronic_specificity(corpus_id, terms, order=True):
     else:
         return relative_terms_count
 
-
 # For tests
 # diachronic_specificity(102750, "bayer", order=True)
 # diachronic_specificity(26128, "bee", order=True)

analysis/distance.py

 from admin.utils import PrintException
 from gargantext_web.db import *
-from gargantext_web.db import get_or_create_node
+from gargantext_web.db import get_or_create_node, session,get_session
 
 from collections import defaultdict
 from operator import itemgetter
@@ -31,6 +31,8 @@ def do_distance(cooc_id, field1=None, field2=None, isMonopartite=True, distance=
     do_distance :: Int -> (Graph, Partition, {ids}, {weight})
     '''
     
+    # implicit global session
+
     authorized = ['conditional', 'distributional', 'cosine']
     if distance not in authorized:
         distance = 'conditional'
@@ -203,7 +205,6 @@ def do_distance(cooc_id, field1=None, field2=None, isMonopartite=True, distance=
 
 
 
-
     def getWeight(item):
         return item[1]
 #    

analysis/functions.py

@@ -9,7 +9,7 @@ from math import log
 
 import scipy
 
-from gargantext_web.db import get_or_create_node
+from gargantext_web.db import session,get_session, get_or_create_node,session
 
 from analysis.cooccurrences import do_cooc
 from analysis.distance import do_distance
@@ -39,12 +39,14 @@ def get_cooc(request=None, corpus=None
     '''
     get_ccoc : to compute the graph.
     '''
+    # implicit global session
+
     data = {}
     #if session.query(Node).filter(Node.type_id==type_cooc_id, Node.parent_id==corpus_id).first() is None:
     print("Cooccurrences do not exist yet, creating it.")
-    miam_id = get_or_create_node(nodetype='MapList', corpus=corpus).id
-    stop_id = get_or_create_node(nodetype='StopList', corpus=corpus).id
-    group_id = get_or_create_node(nodetype='Group', corpus=corpus).id
+    miam_id = get_or_create_node(nodetype='MapList', corpus=corpus, mysession=session).id
+    stop_id = get_or_create_node(nodetype='StopList', corpus=corpus, mysession=session).id
+    group_id = get_or_create_node(nodetype='Group', corpus=corpus, mysession=session).id
     
     SamuelFlag = False
     # if field1 == field2 == 'ngrams' :

analysis/lists.py

 from collections import defaultdict
 from math import sqrt
 
-from gargantext_web.db import session, NodeNgram, NodeNgramNgram, bulk_insert
+from gargantext_web.db import session,get_session, NodeNgram, NodeNgramNgram, bulk_insert
 
 
 class BaseClass:
@@ -67,6 +67,7 @@ class Translations(BaseClass):
             self.items = defaultdict(int)
             self.groups = defaultdict(set)
         elif isinstance(other, int):
+            # implicit global session
             query = (session
                 .query(NodeNgramNgram.ngramy_id, NodeNgramNgram.ngramx_id)
                 .filter(NodeNgramNgram.node_id == other)
@@ -118,6 +119,7 @@ class Translations(BaseClass):
 
     def save(self, node_id):
         # delete previous data
+        # implicit global session
         session.query(NodeNgramNgram).filter(NodeNgramNgram.node_id == node_id).delete()
         session.commit()
         # insert new data
@@ -134,6 +136,7 @@ class WeightedMatrix(BaseClass):
         if other is None:
             self.items = defaultdict(lambda: defaultdict(float))
         elif isinstance(other, int):
+            # implicit global session
             query = (session
                 .query(NodeNgramNgram.ngramx_id, NodeNgramNgram.ngramy_id, NodeNgramNgram.score)
                 .filter(NodeNgramNgram.node_id == other)
@@ -159,6 +162,7 @@ class WeightedMatrix(BaseClass):
 
     def save(self, node_id):
         # delete previous data
+        # implicit global session
         session.query(NodeNgramNgram).filter(NodeNgramNgram.node_id == node_id).delete()
         session.commit()
         # insert new data
@@ -243,6 +247,7 @@ class UnweightedList(BaseClass):
         if other is None:
             self.items = set()
         elif isinstance(other, int):
+            # implicit global session
             query = (session
                 .query(NodeNgram.ngram_id)
                 .filter(NodeNgram.node_id == other)
@@ -323,6 +328,7 @@ class UnweightedList(BaseClass):
 
     def save(self, node_id):
         # delete previous data
+        # implicit global session
         session.query(NodeNgram).filter(NodeNgram.node_id == node_id).delete()
         session.commit()
         # insert new data
@@ -339,6 +345,7 @@ class WeightedList(BaseClass):
         if other is None:
             self.items = defaultdict(float)
         elif isinstance(other, int):
+            # implicit global session
             query = (session
                 .query(NodeNgram.ngram_id, NodeNgram.weight)
                 .filter(NodeNgram.node_id == other)
@@ -435,6 +442,7 @@ class WeightedList(BaseClass):
 
     def save(self, node_id):
         # delete previous data
+        # implicit global session
         session.query(NodeNgram).filter(NodeNgram.node_id == node_id).delete()
         session.commit()
         # insert new data

analysis/periods.py

+
+from collections import defaultdict
+
+from gargantext_web.db import get_or_create_node, session,get_session, Node, NodeHyperdata, Hyperdata, Ngram
+
+import pandas as pd
+import numpy as np
+import scipy.spatial.distance as distance
+
+from sqlalchemy.sql import func
+from sqlalchemy import desc, asc, or_, and_, Date, cast, select
+from sqlalchemy import literal_column
+from sqlalchemy.orm import aliased
+
+from analysis.distance import do_distance
+from analysis.cooccurrences import do_cooc
+
+
+# TFIDF ngrams / period
+def periods(corpus, start=None, end=None):
+    '''
+    data
+    periods :: Corpus -> [Periods]
+    
+    # compute TFIDF matrix 
+    # a = np.asarray([1,2,3])
+    # b = np.asarray([1,2,4])
+
+    # distance.cosine(a,b)
+    # search for min and split
+    '''
+    # implicit global session
+
+    Doc    = aliased(Node)
+    Corpus = aliased(Node)
+
+    query = (session
+            .query(NodeHyperdata.value_datetime)
+            .join(Doc, Doc.id == NodeHyperdata.node_id)
+            .join(Corpus, Corpus.id == Doc.parent_id)
+            .join(Hyperdata, Hyperdata.id == NodeHyperdata.hyperdata_id)
+            .filter(Doc.type_id == cache.NodeType['Document'].id)
+            .filter(Corpus.id == corpus.id)
+            .filter(Hyperdata.name == 'publication_date')
+            )
+    
+    first = query.order_by(asc(NodeHyperdata.value_datetime)).first()[0]
+    last  = query.order_by(desc(NodeHyperdata.value_datetime)).first()[0]
+
+    duration = last - first
+    if duration.days > 365 * 3 :
+        print("OK")
+
+    miam_id = get_or_create_node(nodetype='MiamList', corpus=corpus, mysession=session).id
+
+    result_list = list()
+    for t in times:
+        for ngram in miam_list:
+            result_list.add(temporal_tfidf(ngram, time))
+
+def tfidf_temporal(corpus, start=None, end=None):
+    pass
+
+def jacquard(period1, period2):
+    '''
+    type Start :: Date
+    type End   :: Date
+
+    type Period  :: (Start, End)
+    type Periods :: [Period]
+
+    '''
+    period1 = ['start1', 'end1']
+    period2 = ['start2', 'end2']
+
+    periods = [period1, period2]
+
+    nodes = [cooc(corpus=corpus_id, start=period[0], end=period[1]) for period in periods]
+    partitions = [get_cooc(cooc_id=node_id, type='bestpartition') for node_id in nodes]
+
+    for x in nodeCom.items():
+        comNode[x[1]] = comNode.get(x[1], set()).union({x[0]})
+
+def get_partition(corpus, start=None, end=None, distance=distance):
+    # implicit global session
+    
+    miam_id = get_or_create_node(corpus=corpus, nodetype='MapList', mysession=session).id
+    print("get Partition %s - %s" % (start, end))
+    cooc_id = do_cooc(corpus=corpus
+            , start=start
+            , end=end
+            , miam_id = miam_id
+            )
+
+    G, partition, ids, weight = do_distance(cooc_id
+                                    , field1="ngrams"
+                                    , field2="ngrams"
+                                    , isMonopartite=True
+                                    , distance=distance)
+    return(partition, weight)
+
+def phylo_clusters(corpus, years):
+    '''
+    corpus :: Node Corpus
+    years  :: [Year]
+    '''
+    # implicit global session
+
+    clusters     = dict()
+    nodes_weight = dict()
+    
+    periods_start_end = [
+              ('2000-01-01', '2010-12-31')
+            , ('2011-01-01', '2012-12-31')
+            , ('2013-01-01', '2015-12-31')
+            ]
+    
+    periods = list()
+    for period in periods_start_end:
+        periods.append(' '.join(p for p in period))
+    print(periods)
+    periods_index = [ z for z in zip (periods[:-1], periods[1:])]
+    print(periods_index)
+    
+    for period in periods_start_end:
+        #start,end = period
+        index = ' '.join([str(p) for p in list(period)]) 
+        clusters[index], nodes_weight[index] = get_partition( corpus
+                , start = str(period[0])
+                , end   = str(period[1])
+                , distance='distributional')
+
+    nodes = set()
+    for period in nodes_weight.keys():
+        for node in nodes_weight[period].keys():
+            nodes.add(node)
+
+
+    id_terms = session.query(Ngram.id, Ngram.terms).filter(Ngram.id.in_(nodes)).all()
+    id_terms_dict = dict()
+    for id_term in id_terms:
+        id_terms_dict[id_term[0]] = id_term[1]
+
+    year_com_node = defaultdict(lambda: defaultdict(set))
+
+    for period in clusters.keys():
+        for node, com in clusters[period].items():
+            year_com_node[period][com].add(node)
+
+    proximity_dict = defaultdict(
+                        lambda: defaultdict(
+                            lambda: defaultdict(
+                                lambda: defaultdict( float
+                                                   )
+                                               )
+                                           )
+                                )
+
+    def t1_t2(proximity_dict, t1_t2):
+        t1,t2 = t1_t2
+        for com1 in year_com_node[t1].keys():
+            for com2 in year_com_node[t2].keys():
+                
+                set_1 = year_com_node[t1][com1]
+                set_2 = year_com_node[t2][com2]
+                
+                intersection = set_1.intersection(set_2)
+                union        = set_1.union(set_2)
+
+                proximity_dict[t1][t2][com1][com2] = len(intersection) / len(union)
+    
+    for period in periods_index:
+        t1_t2(proximity_dict, period)
+    
+    data = list()
+    data_dict = dict()
+
+    for y1 in proximity_dict.keys():
+        
+        for y2 in proximity_dict[y1].keys():
+            
+            for c1 in proximity_dict[y1][y2].keys():
+                
+                for c2 in proximity_dict[y1][y2][c1].keys():
+                    
+                    score = proximity_dict[y1][y2][c1][c2]
+                    if score > 0.05:
+                        #print(y1,y2,c1,c2,score)
+                        
+                        list_node1 = list()
+                        for node in year_com_node[y1][c1]:
+                            list_node1.append((node, nodes_weight[y1][node]))
+                        list_node1 = sorted(list_node1, key=lambda x: x[1], reverse=True)
+                        
+                        list_node2 = list()
+                        for node in year_com_node[y2][c2]:
+                            list_node2.append((node, nodes_weight[y2][node]))
+                        list_node2 = sorted(list_node2, key=lambda x: x[1], reverse=True)
+                        
+                        flow = list()
+                        from_data = [id_terms_dict[x[0]] for x in list_node1[:2]]
+                        from_data.append(str(y1))
+                        flow.append(','.join(from_data))
+
+                        to_data = [id_terms_dict[x[0]] for x in list_node2[:2]]
+                        to_data.append(str(y2))
+                        flow.append(','.join(to_data))
+
+                        flow.append(round(score*100))
+
+                        data.append(flow)
+
+    return(data)
+

annotations/views.py

@@ -13,7 +13,7 @@ from rest_framework.exceptions import APIException
 from rest_framework.authentication import SessionAuthentication, BasicAuthentication
 
 from node.models import Node
-from gargantext_web.db import session, cache, Node, NodeNgram, Ngram
+from gargantext_web.db import session,get_session, cache, Node, NodeNgram, Ngram
 from ngram.lists import listIds, listNgramIds
 from gargantext_web.db import get_or_create_node
 
@@ -68,6 +68,7 @@ class NgramEdit(APIView):
         """
         Edit an existing NGram in a given list
         """
+        # implicit global session
         list_id = int(list_id)
         list_node = session.query(Node).filter(Node.id==list_id).first()
         # TODO add 1 for MapList social score ?
@@ -97,6 +98,7 @@ class NgramEdit(APIView):
         """
         Delete a ngram from a list
         """
+        # implicit global session
         print("to del",ngram_ids)
         for ngram_id in ngram_ids.split('+'):
             print('ngram_id', ngram_id)
@@ -134,13 +136,14 @@ class NgramCreate(APIView):
     """
     renderer_classes = (JSONRenderer,)
     authentication_classes = (SessionAuthentication, BasicAuthentication)
-
+    
     def post(self, request, list_id):
         """
         create NGram in a given list
         
         example: request.data = {'text': 'phylogeny'}
         """
+        # implicit global session
         list_id = int(list_id)
         # format the ngram's text
         ngram_text = request.data.get('text', None)
@@ -175,7 +178,6 @@ class NgramCreate(APIView):
             'list_id': list_id,
         })
 
-
 class Document(APIView):
     """
     Read-only Document view, similar to /api/nodes/
@@ -184,6 +186,7 @@ class Document(APIView):
 
     def get(self, request, doc_id):
         """Document by ID"""
+        # implicit global session
         node = session.query(Node).filter(Node.id == doc_id).first()
         if node is None:
             raise APIException('This node does not exist', 404)
@@ -206,4 +209,3 @@ class Document(APIView):
         }
         return Response(data)
 
-

gargantext.ini

@@ -31,6 +31,8 @@ processes               = 10
 # the socket (use the full path to be safe)
 socket          = /tmp/gargantext.sock
 
+threads = 4
+
 # with appropriate permissions - *may* be needed
 chmod-socket    = 666
 

gargantext_web/about.py

@@ -24,10 +24,10 @@ def get_team():
              'picture' : 'david.jpg',
              'role':'principal investigator'},
 
-            { 'first_name' : 'Elias', 'last_name' : 'Showk',
-             'mail' : '',
-             'website' : 'https://github.com/elishowk',
-             'picture' : '', 'role' : 'developer'},
+#            { 'first_name' : 'Elias', 'last_name' : 'Showk',
+#             'mail' : '',
+#             'website' : 'https://github.com/elishowk',
+#             'picture' : '', 'role' : 'developer'},
 
             { 'first_name' : 'Mathieu', 'last_name' : 'Rodic',
              'mail' : '',
@@ -41,7 +41,6 @@ def get_team():
              'picture' : 'samuel.jpg',
              'role' : 'developer'},
 
-
             { 'first_name' : 'Maziyar', 'last_name' : 'Panahi',
              'mail' : '',
              'website'  : '',
@@ -51,6 +50,7 @@ def get_team():
             { 'first_name' : 'Romain', 'last_name' : 'Loth',
              'mail' : '',
              'website'  : '',
+             'picture' : 'romain.jpg',
              'role' : 'developer'},
 
             { 'first_name' : 'Alexandre', 'last_name' : 'Delanoë',

gargantext_web/api2.py

@@ -13,6 +13,7 @@ import collections
 
 from gargantext_web.views import move_to_trash
 from gargantext_web.db import *
+from gargantext_web.views import session
 from gargantext_web.validation import validate, ValidationException
 from node import models
 
@@ -101,6 +102,7 @@ class NodeNgramsQueries(APIView):
     def post(self, request, project_id):
 
         # example only
+
         input = request.data or {
             'x': {
                 'with_empty': True,
@@ -256,3 +258,4 @@ class NodeNgramsQueries(APIView):
             }, 201)
         elif input['format'] == 'csv':
             return CsvHttpResponse(sorted(result.items()), ('date', 'value'), 201)
+

gargantext_web/celery.py

@@ -3,7 +3,7 @@
 from celery import shared_task
 from node import models
 from django.db import transaction
-from admin.utils import DebugTime
+from admin.utils import DebugTime, PrintException
 
 import cProfile
 #@app.task(bind=True)
@@ -11,18 +11,12 @@ import cProfile
 def debug_task(request):
     print('Request: {0!r}'.format(request))
 
-from gargantext_web.db import session, cache, Node
+from gargantext_web.db import get_session, cache, Node
 from ngram.workflow import ngram_workflow
 
 
-@shared_task
-def apply_sum(x, y):
-    print(x+y)
-    print(session.query(Node.name).first())
-
-
 from parsing.corpustools import  parse_resources, extract_ngrams #add_resource,
-from ngram.lists import ngrams2miam
+#from ngram.lists import ngrams2miam
 
 from admin.utils import WorkflowTracking
 
@@ -33,24 +27,35 @@ def apply_workflow(corpus_id):
     dbg.show('ALL WORKFLOW')
     
     update_state = WorkflowTracking()
-
-    corpus = session.query(Node).filter(Node.id==corpus_id).first()
-
-    update_state.processing_(corpus, "Parsing")
-    #cProfile.runctx('parse_resources(corpus)', global,locals)
-    parse_resources(corpus)
-
-    update_state.processing_(corpus, "Terms extraction")
-    extract_ngrams(corpus, ['title', 'abstract'], nlp=True)
-
-    # update_state.processing_(corpus, "")
-    ngram_workflow(corpus)
-
-    #ngrams2miam(user_id=corpus.user_id, corpus_id=corpus_id)
-
-    print("End of the Workflow for corpus %d" % (corpus_id))
-    update_state.processing_(corpus, "0")
-
+    
+    try :
+        mysession = get_session()
+        corpus = mysession.query(Node).filter(Node.id==corpus_id).first()
+
+        update_state.processing_(int(corpus_id), "Parsing")
+        #cProfile.runctx('parse_resources(corpus)', global,locals)
+        parse_resources(corpus, mysession=mysession)
+
+        update_state.processing_(int(corpus_id), "Terms extraction")
+        extract_ngrams(corpus, ['title', 'abstract'], nlp=True, mysession=mysession)
+
+        # update_state.processing_(corpus, "")
+        ngram_workflow(corpus, mysession=mysession)
+
+        #ngrams2miam(user_id=corpus.user_id, corpus_id=corpus_id)
+
+        print("End of the Workflow for corpus %d" % (corpus_id))
+        update_state.processing_(int(corpus_id), "0")
+        
+        #mysession.close()
+        #get_session.remove()
+        mysession.remove()
+    except Exception as error:
+        print(error)
+        PrintException()
+        #mysession.close()
+        #get_session.remove()
+        mysession.remove()
 
 @shared_task
 def empty_trash(corpus_id):

gargantext_web/corpus_views.py

@@ -141,7 +141,6 @@ def get_ngrams(request , project_id , corpus_id ):
     return HttpResponse(html)
 
 
-
 def test_test(request , corpus_id , doc_id):
     """Get All for a doc id"""
     corpus_id = int(corpus_id)

gargantext_web/db.py

@@ -2,18 +2,20 @@ from django.conf import settings
 
 from node import models
 
-__all__ = ['literalquery', 'session', 'cache', 'Session', 'bulk_insert', 'engine', 'get_cursor', 'User']
+__all__ = ['literalquery', 'cache', 'Session', 'bulk_insert', 'engine', 'get_cursor', 'User']
 
 
 # initialize sqlalchemy
 
-from sqlalchemy.orm import Session, mapper
+from sqlalchemy.orm import Session, mapper, scoped_session, sessionmaker
 from sqlalchemy.ext.automap import automap_base
 
 from sqlalchemy import create_engine, MetaData, Table, Column, ForeignKey
 from sqlalchemy.types import Integer, String, DateTime
 from sqlalchemy.dialects.postgresql import JSON
 
+
+
 # SQLAlchemy session management
 def get_engine():
     from sqlalchemy import create_engine
@@ -129,12 +131,27 @@ def literalquery(statement, dialect=None):
     return LiteralCompiler(dialect, statement)
 
 
+#
 def get_sessionmaker():
     from sqlalchemy.orm import sessionmaker
     return sessionmaker(bind=engine)
 
-Session = get_sessionmaker()
-session = Session()
+def get_session():
+    session_factory = get_sessionmaker()
+    return scoped_session(session_factory)
+
+
+# get_session à importer, plus pratique pour les remove
+#session_factory = get_sessionmaker()
+#get_session = scoped_session(session_factory)
+
+# the global session ------------
+# pour les modules qui importent
+# directement session
+session = get_session()
+#session = get_session()()
+# -------------------------------
+
 
 
 # SQLAlchemy model objects caching
@@ -158,18 +175,22 @@ class ModelCache(dict):
             for column in self._columns
             if column.type.python_type == str or key.__class__ == column.type.python_type
         ]
+        #session = get_session()
         element = session.query(self._model).filter(or_(*conditions)).first()
         if element is None:
             raise KeyError
         self[key] = element
         return element
+        #session.remove()
 
     def preload(self):
         self.clear()
+        #session = get_session()
         for element in session.query(self._model).all():
             for column_name in self._columns_names:
                 key = getattr(element, column_name)
                 self[key] = element
+        #session.remove()
 
 class Cache():
 
@@ -231,12 +252,17 @@ class bulk_insert:
 
     readline = read
 
-def get_or_create_node(nodetype=None,corpus=None,corpus_id=None,name_str=None,hyperdata=None):
+def get_or_create_node(nodetype=None,corpus=None,corpus_id=None,name_str=None,hyperdata=None, mysession=None):
     '''
     Should be a method of the object. __get_or_create__ ?
     name_str :: String
     hyperdata :: Dict
     '''
+    
+    if mysession is None:
+        from gargantext_web.db import session
+        mysession = session
+
     if nodetype is None:
         print("Need to give a type node")
     else:
@@ -245,13 +271,13 @@ def get_or_create_node(nodetype=None,corpus=None,corpus_id=None,name_str=None,hy
         except KeyError:
             ntype = cache.NodeType[nodetype] = NodeType()
             ntype.name = nodetype
-            session.add(ntype)
-            session.commit()
+            mysession.add(ntype)
+            mysession.commit()
 
     if corpus_id is not None and corpus is None:
-        corpus = session.query(Node).filter(Node.id==corpus_id).first()
+        corpus = mysession.query(Node).filter(Node.id==corpus_id).first()
 
-    node = (session.query(Node).filter(Node.type_id    == ntype.id
+    node = (mysession.query(Node).filter(Node.type_id    == ntype.id
                                    , Node.parent_id == corpus.id
                                    , Node.user_id   == corpus.user_id
                                     )
@@ -272,7 +298,9 @@ def get_or_create_node(nodetype=None,corpus=None,corpus_id=None,name_str=None,hy
             node.name=name_str
         else:
             node.name=ntype.name
-        session.add(node)
-        session.commit()
+        mysession.add(node)
+        mysession.commit()
     #print(parent_id, n.parent_id, n.id, n.name)
     return(node)
+
+

gargantext_web/urls.py

@@ -7,7 +7,6 @@ from django.contrib.staticfiles.storage import staticfiles_storage
 from django.views.generic.base import RedirectView
 
 from gargantext_web import views, views_optimized
-import gargantext_web.corpus_views as corpus_views
 
 from annotations import urls as annotations_urls
 from annotations.views import main as annotations_main_view

gargantext_web/views.py

@@ -39,14 +39,14 @@ from django.contrib.auth import authenticate, login, logout
 
 from scrappers.scrap_pubmed.admin import Logger
 
-from gargantext_web.db import *
 
 from sqlalchemy import or_, func
 
 from gargantext_web import about
 from gargantext_web.celery import empty_trash
 
-from gargantext_web.db import cache, NodeNgram, NodeNgramNgram
+from gargantext_web.db import *
+from gargantext_web.db import session, cache, NodeNgram, NodeNgramNgram
 
 def login_user(request):
     logout(request)
@@ -69,7 +69,6 @@ def logout_user(request):
     return HttpResponseRedirect('/')
     # Redirect to a success page.
 
-
 def logo(request):
     template = get_template('logo.svg')
     group = "mines"
@@ -114,7 +113,6 @@ def css(request):
             }))
     return HttpResponse(css_data, mimetype="text/css")
 
-
 def query_to_dicts(query_string, *query_args):
     """Run a simple query and produce a generator
     that returns the results as a bunch of dictionaries
@@ -230,12 +228,12 @@ def projects(request):
 
     date = datetime.datetime.now()
     # print(Logger.write("STATIC_ROOT"))
-
+    
+    # implicit global session
     projects = session.query(Node).filter(Node.user_id == user_id, Node.type_id == project_type_id).order_by(Node.date).all()
     number = len(projects)
     
 
-
     # common_users = session.query(User_User.user_parent).filter( User_User.user_id==user_id ).all()
     # [ Getting shared projects ] #
     common_users = []
@@ -278,7 +276,7 @@ def projects(request):
             return HttpResponseRedirect('/projects/')
     else:
         form = ProjectForm()
-
+    
     return render(request, 'projects.html', {
         'debug': settings.DEBUG,
         'date': date,
@@ -288,7 +286,7 @@ def projects(request):
         'common_projects':common_projects,
         'common_users':common_users,
         })
-
+    
 
 def update_nodes(request, project_id, corpus_id, view=None):
     '''
@@ -297,6 +295,7 @@ def update_nodes(request, project_id, corpus_id, view=None):
         - permanent deletion of Trash
 
     '''
+    
     if not request.user.is_authenticated():
         return redirect('/login/?next=%s' % request.path)
 
@@ -359,6 +358,7 @@ def update_nodes(request, project_id, corpus_id, view=None):
 #
 
 def corpus(request, project_id, corpus_id):
+    
     if not request.user.is_authenticated():
         return redirect('/login/?next=%s' % request.path)
 
@@ -376,6 +376,8 @@ def corpus(request, project_id, corpus_id):
     corpus  = cache.Node[int(corpus_id)]
 
     type_doc_id = cache.NodeType['Document'].id
+    
+    # implicit global session
     number = session.query(func.count(Node.id)).filter(Node.parent_id==corpus_id, Node.type_id==type_doc_id).all()[0][0]
 
 
@@ -405,8 +407,7 @@ def corpus(request, project_id, corpus_id):
 
 def newpaginatorJSON(request , corpus_id):
 
-    results = ["hola" , "mundo"]
-
+    
     # t = get_template('tests/newpag/thetable.html')
 
     # project = session.query(Node).filter(Node.id==project_id).first()
@@ -461,7 +462,6 @@ def newpaginatorJSON(request , corpus_id):
     }
     return JsonHttpResponse(finaldict)
 
-
 def move_to_trash(node_id):
     try:
         node = session.query(Node).filter(Node.id == node_id).first()
@@ -481,9 +481,12 @@ def move_to_trash(node_id):
         #return(previous_type_id)
     except Exception as error:
         print("can not move to trash Node" + str(node_id) + ":" + str(error))
+    
 
 def move_to_trash_multiple(request):
+    
     user = request.user
+    
     if not user.is_authenticated():
         return redirect('/login/?next=%s' % request.path)
 
@@ -506,8 +509,10 @@ def move_to_trash_multiple(request):
 
 def delete_node(request, node_id):
 
+    
     # do we have a valid user?
     user = request.user
+    
     node = session.query(Node).filter(Node.id == node_id).first()
 
     if not user.is_authenticated():
@@ -523,7 +528,7 @@ def delete_node(request, node_id):
         return HttpResponseRedirect('/project/' + str(node_parent_id))
     else:
         return HttpResponseRedirect('/projects/')
-
+    
 
 def delete_corpus(request, project_id, node_id):
     # ORM Django
@@ -545,6 +550,7 @@ def delete_corpus(request, project_id, node_id):
 
 def chart(request, project_id, corpus_id):
     ''' Charts to compare, filter, count'''
+    
     t = get_template('chart.html')
     user = request.user
     date = datetime.datetime.now()
@@ -562,6 +568,7 @@ def chart(request, project_id, corpus_id):
     return HttpResponse(html)
 
 def sankey(request, corpus_id):
+    
     t = get_template('sankey.html')
     user = request.user
     date = datetime.datetime.now()
@@ -578,7 +585,6 @@ def sankey(request, corpus_id):
     return HttpResponse(html)
 
 
-
 def matrix(request, project_id, corpus_id):
     t = get_template('matrix.html')
     user = request.user
@@ -598,6 +604,7 @@ def matrix(request, project_id, corpus_id):
     return HttpResponse(html)
 
 def graph(request, project_id, corpus_id, generic=100, specific=100):
+    
     t = get_template('explorer.html')
     user = request.user
     date = datetime.datetime.now()
@@ -660,6 +667,7 @@ def corpus_csv(request, project_id, corpus_id):
     '''
     Create the HttpResponse object with the appropriate CSV header.
     '''
+    
     response = HttpResponse(content_type='text/csv')
     response['Content-Disposition'] = 'attachment; filename="corpus.csv"'
 
@@ -735,30 +743,48 @@ def node_link(request, corpus_id):
     '''
     Create the HttpResponse object with the node_link dataset.
     '''
-
     data = []
     corpus = session.query(Node).filter(Node.id==corpus_id).first()
     data = get_cooc(request=request, corpus=corpus, type="node_link")
     return JsonHttpResponse(data)
 
+from analysis.periods import phylo_clusters
 
 def sankey_csv(request, corpus_id):
+    
     data = []
     corpus = session.query(Node).filter(Node.id==corpus_id).first()
+#
+#    header = ["source", "target", "value"] 
+#    data.append(header)
+#    
+#    flows = phylo_clusters(corpus, range(2005,2013)) 
+#    for flow in flows: 
+#        data.append(flow) 
+#    print(data)
+#
+
     data = [
-            ["source", "target", "value"]
-            , ["Comment_1", "Theme_1", 1]
-            
-            , ["Comment_2", "Theme_2", 2]
-            , ["Comment_3", "Theme_2", 2]
-            , ["Comment_7", "Theme_1", 2]
-            , ["Comment_8", "Theme_3", 2]
-            
-            , ["Theme_1", "Reco_par_1", 2]
-            , ["Theme_2", "Reco_par_2", 2]
-            , ["Theme_2", "Reco_par_5", 2]
-            , ["Theme_3", "Reco_par_5", 1]
+              ['source', 'target', 'value']
+            , ['inégalités,rapports sociaux,P1', 'critique,travail social,P2', 8]
+            , ['inégalités,rapports sociaux,P1', 'inégalités,éducation,P2', 21]
+            , ['éducation,institutions,P1', 'critique,travail social,P2', 7]
+            , ['éducation,institutions,P1', 'inégalités,éducation,P2', 10]
+            #, ['éducation,institutions,P1', 'personnes âgées,pouvoirs publics,P2', 8]
+            , ['éducation,institutions,P1', 'politiques publiques,personnes âgées dépendantes,P2', 8]
+            #, ['éducation,institutions,P1', 'intervention sociale,travailleur social,P2', 8]
+            #, ['intervention sociale,travailleur social,2011-01-01 2013-12-31', 'intervention sociale,travailleur social,P3', 0]
+            , ['critique,enseignement supérieur,P1', 'critique,travail social,P2', 6]
+            #, ['critique,enseignement supérieur,P1', 'personnes âgées,pouvoirs publics,P2', 7]
+            , ['justice,exclusion,violence,P1', 'inégalités,éducation,P2', 12]
+            , ['critique,travail social,P2', 'justice,travail social,P3', 14]
+            , ['inégalités,éducation,P2', 'justice,travail social,P3', 20]
+            , ['inégalités,éducation,P2', 'justice sociale,éducation,P3', 8]
+            , ['inégalités,éducation,P2', 'action publique,institutions,P3', 9]
+            , ['inégalités,éducation,P2', 'inégalités,inégalités sociales,P3', 18]
+            , ['politiques publiques,personnes âgées dépendantes,P2', 'justice sociale,éducation,P3', 20]
             ]
+
     return(CsvHttpResponse(data))
 
 def adjacency(request, corpus_id):
@@ -818,7 +844,6 @@ def ngrams(request):
     }))
     return HttpResponse(html)
 
-
 def nodeinfo(request , node_id):
     '''Structure of the popUp for topPapers div '''
     t = get_template('node-info.html')

gargantext_web/views_optimized.py

@@ -16,6 +16,8 @@ from threading import Thread
 from node.admin import CustomForm
 from gargantext_web.db import *
 from gargantext_web.db import get_or_create_node
+from gargantext_web.views import session
+
 from gargantext_web.settings import DEBUG, MEDIA_ROOT
 from rest_v1_0.api import JsonHttpResponse
 from django.db import connection
@@ -31,7 +33,6 @@ from gargantext_web.celery import apply_workflow
 from admin.utils import ensure_dir
 
 def project(request, project_id):
-
     # do we have a valid project id?
     try:
         project_id = int(project_id)
@@ -39,6 +40,7 @@ def project(request, project_id):
         raise Http404()
 
     # do we have a valid project?
+
     project = (session
         .query(Node)
         .filter(Node.id == project_id)
@@ -205,8 +207,9 @@ def tfidf(request, corpus_id, ngram_ids):
     # filter input
     ngram_ids = ngram_ids.split('a')
     ngram_ids = [int(i) for i in ngram_ids]
-
+    
     corpus = session.query(Node).filter(Node.id==corpus_id).first()
+    
     tfidf_id = get_or_create_node(corpus=corpus, nodetype='Tfidf').id
     print(tfidf_id)
     # request data
@@ -251,49 +254,108 @@ def tfidf(request, corpus_id, ngram_ids):
     return JsonHttpResponse(nodes_list)
 
 def getCorpusIntersection(request , corpuses_ids):
-
     FinalDict = False
-    if request.method == 'POST' and "nodeids" in request.POST and len(request.POST["nodeids"])>0:
+    if request.method == 'POST' and "nodeids" in request.POST and len(request.POST["nodeids"])>0 :
+
         import ast
+        import networkx as nx
         node_ids = [int(i) for i in (ast.literal_eval( request.POST["nodeids"] )) ]
         # Here are the visible nodes of the initial semantic map.
 
         corpuses_ids = corpuses_ids.split('a')
-        corpuses_ids = [int(i) for i in corpuses_ids] # corpus[1] will be the corpus to compare
-        cooc_type_id = cache.NodeType['Cooccurrence'].id
         
-        cooc_ids  = session.query(Node.id).filter(Node.user_id == request.user.id , Node.parent_id==corpuses_ids[1] , Node.type_id == cooc_type_id ).first()
-        if len(cooc_ids)==0:
-            return JsonHttpResponse(FinalDict)
-         # If corpus[1] has a coocurrence.id then lets continue
+        corpuses_ids = [int(i) for i in corpuses_ids] 
+        print(corpuses_ids)
+        # corpus[1] will be the corpus to compare
+        
+        
 
-        Coocs = {}
-        import networkx as nx
-        G = nx.Graph() # I use an undirected graph, because direction doesnt matter here, coocs should be a triangular matrix, so...
-        ngrams_data1 = session.query(NodeNgramNgram).filter( NodeNgramNgram.node_id==cooc_ids[0], NodeNgramNgram.ngramx_id.in_( node_ids )).all()
-        for ngram in ngrams_data1: # are there visible nodes in the X-axis of corpus to compare ?
-            G.add_edge(  ngram.ngramx_id ,  ngram.ngramy_id , weight=ngram.score)
-
-        ngrams_data2 = session.query(NodeNgramNgram).filter( NodeNgramNgram.node_id==cooc_ids[0], NodeNgramNgram.ngramy_id.in_( node_ids )).all()
-        for ngram in ngrams_data2: # are there visible nodes in the Y-axis of corpus to compare ?
-            if not G.has_edge(ngram.ngramx_id,ngram.ngramy_id):
+        def get_score(corpus_id):
+
+            cooc_type_id = cache.NodeType['Cooccurrence'].id
+            cooc_ids  = (session.query(Node.id)
+                                .filter(Node.user_id == request.user.id
+                                      , Node.parent_id==corpus_id
+                                      , Node.type_id == cooc_type_id )
+                                .first()
+                                )
+            
+            if len(cooc_ids)==0:
+                return JsonHttpResponse(FinalDict)
+                # If corpus[1] has a coocurrence.id then lets continue
+
+            Coocs  = {}
+            
+            G = nx.Graph()
+            # undirected graph only
+            # because direction doesnt matter here
+            # coocs is triangular matrix
+
+            ngrams_data = ( session.query(NodeNgramNgram)
+                                   .filter( NodeNgramNgram.node_id==cooc_ids[0]
+                                          , or_(
+                                                NodeNgramNgram.ngramx_id.in_( node_ids )
+                                              , NodeNgramNgram.ngramy_id.in_( node_ids )
+                                              )
+                                              )
+                                   .group_by(NodeNgramNgram)
+                                   .all()
+                                   )
+            
+            for ngram in ngrams_data :
+                # are there visible nodes in the X-axis of corpus to compare ?
                 G.add_edge(  ngram.ngramx_id ,  ngram.ngramy_id , weight=ngram.score)
-
-        for e in G.edges_iter():
-            n1 = e[0]
-            n2 = e[1]
-            # print( G[n1][n2]["weight"] , "\t", n1,",",n2 )
-            if n1 not in Coocs:
-                Coocs[n1]=0
-            if n2 not in Coocs:
-                Coocs[n2]=0
-            Coocs[n1]+=G[n1][n2]["weight"] 
-            Coocs[n2]+=G[n1][n2]["weight"] 
+                print(corpus_id, ngram)
+
+            for e in G.edges_iter() :
+                n1 = e[0]
+                n2 = e[1]
+                # print( G[n1][n2]["weight"] , "\t", n1,",",n2 )
+                if n1 not in Coocs :
+                    Coocs[n1] = 0
+                if n2 not in Coocs :
+                    Coocs[n2] = 0
+                Coocs[n1] += G[n1][n2]["weight"]
+                Coocs[n2] += G[n1][n2]["weight"]
+
+            return(Coocs,G)
+
+        Coocs_0,G_0 = get_score( corpuses_ids[0] )
+        Coocs_1,G_1 = get_score( corpuses_ids[1] )
+        
         FinalDict = {}
-        for node in node_ids:
-            if node in Coocs:
-                FinalDict[node] = Coocs[node]/G.degree(node)
-        # Getting AVG-COOC of each ngram that exists in the cooc-matrix of the compared-corpus. 
+        measure = 'cooc'
+        
+        if measure == 'jacquard':
+            for node in node_ids :
+                if node in G_1.nodes() and node in G_0.nodes():
+                    neighbors_0 = set(G_0.neighbors(node))
+                    neighbors_1 = set(G_1.neighbors(node))
+                    jacquard = len(neighbors_0.intersection(neighbors_1)) / len(neighbors_0.union(neighbors_1))
+                    FinalDict[node] = jacquard * 3
+                elif node in G_0.nodes() and node not in G_1.nodes() :
+                    FinalDict[node] = 2
+                elif node not in G_0.nodes() and node in G_1.nodes() :
+                    FinalDict[node] = 1
+                else:
+                    FinalDict[node] = 0
+        
+        elif measure == 'cooc':
+            for node in node_ids :
+                if node in G_1.nodes() and node in G_0.nodes():
+                    score_0 = Coocs_0[node] / G_0.degree(node)
+                    score_1 = Coocs_1[node] / G_1.degree(node)
+                    FinalDict[node] = 5 * score_0 / score_1
+                elif node in G_0.nodes() and node not in G_1.nodes() :
+                    FinalDict[node] = 0.5
+                elif node not in G_0.nodes() and node in G_1.nodes() :
+                    FinalDict[node] = 0.2
+                else:
+                    FinalDict[node] = 0
+        
+        print(FinalDict)
+                #print(node,score)
+                # Getting AVG-COOC of each ngram that exists in the cooc-matrix of the compared-corpus. 
 
     return JsonHttpResponse(FinalDict)
 

ngram/cvalue.py

@@ -6,7 +6,8 @@ from admin.utils import PrintException,DebugTime
 
 from gargantext_web.db import NodeNgram,NodeNodeNgram
 from gargantext_web.db import *
-from gargantext_web.db import get_or_create_node
+from gargantext_web.db import get_or_create_node, session,get_session
+
 
 from parsing.corpustools import *
 
@@ -40,6 +41,8 @@ def getNgrams(corpus=None, limit=1000):
     '''
     getNgrams :: Corpus -> [(Int, String, String, Float)]
     '''
+    # implicit global session
+    
     terms = dict()
     tfidf_node = get_or_create_node(nodetype='Tfidf (global)'
                                     , corpus=corpus)
@@ -63,7 +66,7 @@ def getNgrams(corpus=None, limit=1000):
             PrintException()
     return(terms)
 
-def compute_cvalue(corpus=None, limit=1000):
+def compute_cvalue(corpus=None, limit=1000, mysession=None):
     '''
     computeCvalue :: Corpus
     frequency :: String -> Int -> Int
@@ -122,12 +125,11 @@ def compute_cvalue(corpus=None, limit=1000):
 
     result = cvalueAll()
     #print([n for n in result])
-    session.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==cvalue_node.id).delete()
-    session.commit()
+    mysession.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==cvalue_node.id).delete()
+    mysession.commit()
 
     #bulk_insert(NodeNodeNgram, ['nodex_id', 'nodey_id', 'ngram_id', 'score'], [n for n in islice(result,0,100)])
     bulk_insert(NodeNodeNgram, ['nodex_id', 'nodey_id', 'ngram_id', 'score'], [n for n in result])
-
 # test
 #corpus=session.query(Node).filter(Node.id==244250).first()
 #computeCvalue(corpus)

ngram/group.py

@@ -5,7 +5,7 @@ from admin.utils import PrintException,DebugTime
 
 from gargantext_web.db import NodeNgram,NodeNodeNgram
 from gargantext_web.db import *
-from gargantext_web.db import get_or_create_node
+from gargantext_web.db import get_or_create_node, get_session
 
 from analysis.lists import Translations, UnweightedList
 from parsing.corpustools import *
@@ -23,7 +23,6 @@ from math import log
 from functools import reduce
 
 
-
 def getStemmer(corpus):
     '''
     getStemmer :: Corpus -> Stemmer
@@ -48,10 +47,11 @@ def getStemmer(corpus):
 
     return(stemIt)
 
-def compute_groups(corpus, limit_inf=None, limit_sup=None, how='Stem'):
+def compute_groups(corpus, limit_inf=None, limit_sup=None, how='Stem', mysession=None):
     '''
     group ngrams according to a function (stemming or lemming)
     '''
+    
     dbg = DebugTime('Corpus #%d - group' % corpus.id)
     dbg.show('Group')
 
@@ -62,17 +62,19 @@ def compute_groups(corpus, limit_inf=None, limit_sup=None, how='Stem'):
         stemIt = getStemmer(corpus)
 
     group_to_insert = set()
-    node_group = get_or_create_node(nodetype='Group', corpus=corpus)
+    node_group = get_or_create_node(nodetype='Group', corpus=corpus, mysession=mysession)
 
     miam_to_insert = set()
-    miam_node = get_or_create_node(nodetype='MiamList', corpus=corpus)
+    miam_node = get_or_create_node(nodetype='MiamList', corpus=corpus, mysession=mysession)
 
-    stop_node = get_or_create_node(nodetype='StopList', corpus=corpus)
+    stop_node = get_or_create_node(nodetype='StopList', corpus=corpus, mysession=mysession)
     #stop_list = UnweightedList(stop_node.id)
 
     Stop = aliased(NodeNgram)
     frequency = sa.func.count(NodeNgram.weight)
-    ngrams = (session.query(Ngram.id, Ngram.terms, frequency )
+    
+
+    ngrams = (mysession.query(Ngram.id, Ngram.terms, frequency )
             .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
             .join(Node, Node.id == NodeNgram.node_id)
             #.outerjoin(Stop, Stop.ngram_id == Ngram.id)
@@ -84,7 +86,7 @@ def compute_groups(corpus, limit_inf=None, limit_sup=None, how='Stem'):
             .limit(limit_sup)
             )
     
-    stops = (session.query(Ngram.id, Ngram.terms, frequency)
+    stops = (mysession.query(Ngram.id, Ngram.terms, frequency)
                     .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
                     .join(Node, Node.id == NodeNgram.node_id)
                     .join(Stop, Stop.ngram_id == Ngram.id)
@@ -125,13 +127,14 @@ def compute_groups(corpus, limit_inf=None, limit_sup=None, how='Stem'):
             miam_to_insert.add((miam_node.id, group[key]['mainForm'], 1))
 
 #    # Deleting previous groups
-    session.query(NodeNgramNgram).filter(NodeNgramNgram.node_id == node_group.id).delete()
+    mysession.query(NodeNgramNgram).filter(NodeNgramNgram.node_id == node_group.id).delete()
 #    # Deleting previous ngrams miam list
-    session.query(NodeNgram).filter(NodeNgram.node_id == miam_node.id).delete()
-    session.commit()
+    mysession.query(NodeNgram).filter(NodeNgram.node_id == miam_node.id).delete()
+    mysession.commit()
 
     bulk_insert(NodeNgramNgram
                 , ('node_id', 'ngramx_id', 'ngramy_id', 'score')
                 , [data for data in group_to_insert])
 
     bulk_insert(NodeNgram, ('node_id', 'ngram_id', 'weight'), [data for data in list(miam_to_insert)])
+

ngram/importExport.py

@@ -12,7 +12,7 @@ TODO : REFACTOR 2) improvements in ngram creation (?bulk like node_ngram links)
 """
 
 from gargantext_web.db import Ngram, NodeNgram, NodeNodeNgram, NodeNgramNgram
-from gargantext_web.db import cache, session, get_or_create_node, bulk_insert
+from gargantext_web.db import cache, session,get_session, get_or_create_node, bulk_insert
 
 # import sqlalchemy as sa
 from sqlalchemy.sql import func, exists
@@ -105,6 +105,7 @@ def exportNgramLists(node,filename,delimiter="\t"):
           2  <=> mapList
         """
         # récupérer d'un coup les objets Ngram (avec terme)
+        # implicit global session
         if len(ngram_ids):
             ng_objs = session.query(Ngram).filter(Ngram.id.in_(ngram_ids)).all()
         else:
@@ -131,7 +132,6 @@ def exportNgramLists(node,filename,delimiter="\t"):
         # csv_rows = [[ligne1_a, ligne1_b..],[ligne2_a, ligne2_b..],..]
         return csv_rows
     
-    
     # on applique notre fonction ng_to_csv sur chaque liste
     # ------------------------------------------------------
     stop_csv_rows = ngrams_to_csv_rows(stop_ngram_ids, 
@@ -187,7 +187,7 @@ def importNgramLists(node,filename,delimiter="\t", del_lists=[]):
         (and ideally add its logic to analysis.lists.Translations)
     
     '''
-    
+    # implicit global session
     # the node arg has to be a corpus here
     if not hasattr(node, "type_id") or node.type_id != 4:
         raise TypeError("IMPORT: node argument must be a Corpus Node")
@@ -378,10 +378,6 @@ def importNgramLists(node,filename,delimiter="\t", del_lists=[]):
     
     print("INFO: added %i elements in the lists indices" % added_nd_ng)
     print("INFO: added %i new ngrams in the lexicon" % added_ng)
-    
-
-
-
 
 
 # à chronométrer:

ngram/lists.py

 from admin.utils import PrintException
 
-from gargantext_web.db import NodeNgram
+from gargantext_web.db import NodeNgram, session,get_session
 from gargantext_web.db import *
 from parsing.corpustools import *
 
@@ -20,6 +20,9 @@ def listIds(typeList=None, user_id=None, corpus_id=None):
     typeList  :: String, Type of the Node that should be created
     [Node]      :: List of Int, returned or created by the function
     '''
+    
+    # implicit global session
+
     if typeList is None:
         typeList = 'MiamList'
 
@@ -57,6 +60,7 @@ def listIds(typeList=None, user_id=None, corpus_id=None):
     else:
         raise Exception("Usage (Warning): Need corpus_id and user_id")
 
+
 # Some functions to manage ngrams according to the lists
 
 def listNgramIds(list_id=None, typeList=None,
@@ -74,6 +78,9 @@ def listNgramIds(list_id=None, typeList=None,
     doc_id    : to get specific ngrams related to a document with Node.id=doc_id
     user_id   : needed to create list if it does not exist
     '''
+    
+    # implicit global session
+
     if typeList is None:
         typeList = ['MiamList', 'StopList']
     elif isinstance(typeList, string):
@@ -123,6 +130,8 @@ def ngramList(do, list_id, ngram_ids=None) :
         ngram_id  = [Int]  : list of Ngrams id (Ngrams.id)
         list_id   = Int    : list id (Node.id)
     '''
+    # implicit global session
+    
     results = []
 
     if do == 'create':
@@ -174,6 +183,7 @@ def ngrams2miam(user_id=None, corpus_id=None):
     '''
     Create a Miam List only
     '''
+    # implicit global session
 
     miam_id = listIds(typeList='MiamList', user_id=user_id, corpus_id=corpus_id)[0][0]
     print(miam_id)
@@ -205,6 +215,8 @@ def ngrams2miamBis(corpus):
 
     miam_id = get_or_create_node(corpus=corpus, nodetype='MiamList')
     stop_id = get_or_create_node(corpus=corpus,nodetype='StopList')
+    
+    # implicit global session
 
     query = (session.query(
                 literal_column(str(miam_id)).label("node_id"),
@@ -247,6 +259,7 @@ def doList(
         lem     = equivalent Words which are lemmatized (but the main form)
         cvalue  = equivalent N-Words according to C-Value (but the main form)
     '''
+    # implicit global session
 
     if type_list not in ['MiamList', 'MainList']:
         raise Exception("Type List (%s) not supported, try: \'MiamList\' or \'MainList\'" % type_list)
@@ -356,4 +369,3 @@ def doList(
     return(list_dict[type_list]['id'])
 
 
-

ngram/mapList.py

@@ -5,7 +5,7 @@ from admin.env import *
 from admin.utils import PrintException,DebugTime
 
 from gargantext_web.db import NodeNgram,NodeNodeNgram,NodeNgramNgram
-from gargantext_web.db import get_or_create_node, session, bulk_insert
+from gargantext_web.db import get_or_create_node, get_session, bulk_insert
 
 from sqlalchemy.sql import func
 from sqlalchemy import desc, asc, or_, and_, Date, cast, select
@@ -15,22 +15,23 @@ from sqlalchemy.orm import aliased
 from ngram.tools import insert_ngrams
 import csv
 
-def compute_mapList(corpus,limit=500,n=1):
+def compute_mapList(corpus,limit=500,n=1, mysession=None):
     '''
     According to Specificities and stoplist,
     '''
-
+    
+ 
     monograms_part = 0.005
     monograms_limit = round(limit * monograms_part)
     multigrams_limit = limit - monograms_limit
 
     dbg = DebugTime('Corpus #%d - computing Miam' % corpus.id)
 
-    node_miam  = get_or_create_node(nodetype='MiamList', corpus=corpus)
-    node_stop  = get_or_create_node(nodetype='StopList', corpus=corpus)
-    node_group = get_or_create_node(nodetype='Group', corpus=corpus)
+    node_miam  = get_or_create_node(nodetype='MiamList', corpus=corpus, mysession=mysession)
+    node_stop  = get_or_create_node(nodetype='StopList', corpus=corpus, mysession=mysession)
+    node_group = get_or_create_node(nodetype='Group', corpus=corpus, mysession=mysession)
     
-    node_spec  = get_or_create_node(nodetype='Specificity', corpus=corpus)
+    node_spec  = get_or_create_node(nodetype='Specificity', corpus=corpus, mysession=mysession)
 
     Miam=aliased(NodeNgram)
     Stop=aliased(NodeNgram)
@@ -38,7 +39,7 @@ def compute_mapList(corpus,limit=500,n=1):
     
     Spec=aliased(NodeNodeNgram)
 
-    query = (session.query(Spec.ngram_id, Spec.score)
+    query = (mysession.query(Spec.ngram_id, Spec.score)
                 .join(Miam, Spec.ngram_id == Miam.ngram_id)
                 .join(Ngram, Ngram.id == Spec.ngram_id)
                 #.outerjoin(Group, Group.ngramy_id == Spec.ngram_id)
@@ -61,19 +62,19 @@ def compute_mapList(corpus,limit=500,n=1):
                 .limit(multigrams_limit)
                )
     
-    stop_ngrams = (session.query(NodeNgram.ngram_id)
+    stop_ngrams = (mysession.query(NodeNgram.ngram_id)
                          .filter(NodeNgram.node_id == node_stop.id)
                          .all()
                  )
 
-    grouped_ngrams = (session.query(NodeNgramNgram.ngramy_id)
+    grouped_ngrams = (mysession.query(NodeNgramNgram.ngramy_id)
                              .filter(NodeNgramNgram.node_id == node_group.id)
                              .all()
                     )
     
-    node_mapList = get_or_create_node(nodetype='MapList', corpus=corpus)
-    session.query(NodeNgram).filter(NodeNgram.node_id==node_mapList.id).delete()
-    session.commit()
+    node_mapList = get_or_create_node(nodetype='MapList', corpus=corpus, mysession=mysession)
+    mysession.query(NodeNgram).filter(NodeNgram.node_id==node_mapList.id).delete()
+    mysession.commit()
     
     data = zip(
         [node_mapList.id for i in range(1,limit)]
@@ -87,12 +88,13 @@ def compute_mapList(corpus,limit=500,n=1):
 
     dbg.show('MapList computed')
 
-def insert_miam(corpus, ngrams=None, path_file_csv=None):
+def insert_miam(corpus, ngrams=None, path_file_csv=None, mysession=None):
+    
     dbg = DebugTime('Corpus #%d - computing Miam' % corpus.id)
     
-    node_miam = get_or_create_node(nodetype='MiamList', corpus=corpus)
-    session.query(NodeNgram).filter(NodeNgram.node_id==node_miam.id).delete()
-    session.commit()
+    node_miam = get_or_create_node(nodetype='MiamList', corpus=corpus, mysession=mysession)
+    mysession.query(NodeNgram).filter(NodeNgram.node_id==node_miam.id).delete()
+    mysession.commit()
     
     stop_words = set()
     miam_words = set()
@@ -122,7 +124,4 @@ def insert_miam(corpus, ngrams=None, path_file_csv=None):
     file_csv.close()
     dbg.show('Miam computed')
 
-#corpus = session.query(Node).filter(Node.id==540420).first()
-#compute_mapList(corpus)
-#insert_miam(corpus=corpus, path_file_csv="Thesaurus_tag.csv")
 

ngram/occurrences.py

 
-from gargantext_web.db import session, cache, get_cursor
+from gargantext_web.db import get_session, cache, get_cursor
 from gargantext_web.db import Node, NodeNgram, NodeNodeNgram
 from gargantext_web.db import get_or_create_node
 from admin.utils import DebugTime
 
-def compute_occs(corpus):
+def compute_occs(corpus, mysession=None):
+    '''
+    compute_occs :: Corpus -> IO ()
+
+    '''
+    
     dbg = DebugTime('Corpus #%d - OCCURRENCES' % corpus.id)
     dbg.show('Calculate occurrences')
-    occs_node = get_or_create_node(nodetype='Occurrences', corpus=corpus)
+    occs_node = get_or_create_node(nodetype='Occurrences', corpus=corpus, mysession=mysession)
     
     #print(occs_node.id)
 
-    (session.query(NodeNodeNgram)
+    (mysession.query(NodeNodeNgram)
             .filter(NodeNodeNgram.nodex_id==occs_node.id).delete()
             )
-    session.commit()
+    mysession.commit()
 
     db, cursor = get_cursor()
     cursor.execute('''
@@ -46,5 +51,7 @@ def compute_occs(corpus):
             )
     )
     db.commit()
+
+
     #data = session.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==occs_node.id).all()
     #print([n for n in data])

ngram/specificity.py

@@ -10,17 +10,17 @@ import numpy as np
 import pandas as pd
 
 from analysis.cooccurrences import do_cooc
-from gargantext_web.db import session, cache, get_or_create_node, bulk_insert
+from gargantext_web.db import get_session, cache, get_or_create_node, bulk_insert
 from gargantext_web.db import NodeNgramNgram, NodeNodeNgram
 
 from sqlalchemy import desc, asc, or_, and_, Date, cast, select
 
-def specificity(cooc_id=None, corpus=None, limit=100):
+def specificity(cooc_id=None, corpus=None, limit=100, mysession=None):
     '''
     Compute the specificity, simple calculus.
     '''
-
-    cooccurrences = (session.query(NodeNgramNgram)
+ 
+    cooccurrences = (mysession.query(NodeNgramNgram)
                     .filter(NodeNgramNgram.node_id==cooc_id)
                     .order_by(NodeNgramNgram.score)
                     .limit(limit)
@@ -41,36 +41,37 @@ def specificity(cooc_id=None, corpus=None, limit=100):
     m = ( xs - ys) / (2 * (x.shape[0] - 1))
     m = m.sort(inplace=False)
 
-    node = get_or_create_node(nodetype='Specificity',corpus=corpus)
+    node = get_or_create_node(nodetype='Specificity',corpus=corpus, mysession=mysession)
 
     data = zip(  [node.id for i in range(1,m.shape[0])]
                , [corpus.id for i in range(1,m.shape[0])]
                , m.index.tolist()
                , m.values.tolist()
                )
-    session.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==node.id).delete()
-    session.commit()
+    mysession.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==node.id).delete()
+    mysession.commit()
 
     bulk_insert(NodeNodeNgram, ['nodex_id', 'nodey_id', 'ngram_id', 'score'], [d for d in data])
 
     return(node.id)
+    
 
-def compute_specificity(corpus,limit=100):
+def compute_specificity(corpus,limit=100, mysession=None):
     '''
     Computing specificities as NodeNodeNgram.
     All workflow is the following:
         1) Compute the cooc matrix
         2) Compute the specificity score, saving it in database, return its Node
     '''
+    
     dbg = DebugTime('Corpus #%d - specificity' % corpus.id)
+    
+    list_cvalue = get_or_create_node(nodetype='Cvalue', corpus=corpus, mysession=mysession)
+    cooc_id = do_cooc(corpus=corpus, cvalue_id=list_cvalue.id,limit=limit, mysession=mysession)
 
-    list_cvalue = get_or_create_node(nodetype='Cvalue', corpus=corpus)
-    cooc_id = do_cooc(corpus=corpus, cvalue_id=list_cvalue.id,limit=limit)
-
-    specificity(cooc_id=cooc_id,corpus=corpus,limit=limit)
+    specificity(cooc_id=cooc_id,corpus=corpus,limit=limit,mysession=mysession)
     dbg.show('specificity')
 
-
 #corpus=session.query(Node).filter(Node.id==244250).first()
 #compute_specificity(corpus)
 

ngram/stemLem.py

@@ -4,12 +4,14 @@ from parsing.corpustools import *
 
 from gargantext_web.db import NodeNgram
 from sqlalchemy import desc, asc, or_, and_, Date, cast, select
-from gargantext_web.db import get_cursor, bulk_insert
+from gargantext_web.db import get_cursor, bulk_insert, session,get_session
 
 def get_ngramogram(corpus, limit=None):
     """
     Ngram is a composition of ograms (ogram = 1gram)
     """
+    # implicit global session
+    
     try:
         query = (session
          .query(Ngram.id, Ngram.terms)
@@ -303,6 +305,7 @@ def stem_corpus(corpus_id=None):
     Returns Int as id of the Stem Node
     stem_corpus :: Int
     '''
+    # implicit global session
 
     corpus = session.query(Node).filter(Node.id == corpus_id).first()
     #print('Number of new ngrams to stem:',
@@ -329,4 +332,3 @@ def stem_corpus(corpus_id=None):
         print('Usage: stem_corpus(corpus_id=corpus.id)')
 
 
-

ngram/stop.py

@@ -2,7 +2,7 @@ import re
 from admin.utils import PrintException
 
 from gargantext_web.db import Node, Ngram, NodeNgram,NodeNodeNgram
-from gargantext_web.db import cache, session, get_or_create_node, bulk_insert
+from gargantext_web.db import cache, session,get_session, get_or_create_node, bulk_insert
 
 import sqlalchemy as sa
 from sqlalchemy.sql import func
@@ -14,6 +14,8 @@ from ngram.tools import insert_ngrams
 from analysis.lists import WeightedList, UnweightedList
 
 def importStopList(node,filename,language='fr'):
+    # implicit global session
+
     with open(filename, "r") as f:
         stop_list = f.read().splitlines()
     
@@ -72,17 +74,18 @@ def isStopWord(ngram, stop_words=None):
         if test_match(word, regex) is True :
             return(True)
 
-def compute_stop(corpus,limit=2000,debug=False):
+def compute_stop(corpus,limit=2000,debug=False, mysession=None):
     '''
     do some statitics on all stop lists of database of the same type
     '''
-    stop_node = get_or_create_node(nodetype='StopList', corpus=corpus)
+    
+    stop_node_id = get_or_create_node(nodetype='StopList', corpus=corpus, mysession=mysession).id
     
     # TODO do a function to get all stop words with social scores
-    root = session.query(Node).filter(Node.type_id == cache.NodeType['Root'].id).first()
-    root_stop_id = get_or_create_node(nodetype='StopList', corpus=root).id
+    root = mysession.query(Node).filter(Node.type_id == cache.NodeType['Root'].id).first()
+    root_stop_id = get_or_create_node(nodetype='StopList', corpus=root, mysession=mysession).id
     
-    stop_words = (session.query(Ngram.terms)
+    stop_words = (mysession.query(Ngram.terms)
                          .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
                          .filter(NodeNgram.node_id == root_stop_id)
                          .all()
@@ -91,7 +94,7 @@ def compute_stop(corpus,limit=2000,debug=False):
     #print([n for n in stop_words])
     
     frequency = sa.func.count( NodeNgram.weight )
-    ngrams = ( session.query( Ngram.id, Ngram.terms, frequency )
+    ngrams = ( mysession.query( Ngram.id, Ngram.terms, frequency )
             .join( NodeNgram, NodeNgram.ngram_id == Ngram.id )
             .join( Node, Node.id == NodeNgram.node_id )
             .filter( Node.parent_id == corpus.id, 
@@ -108,5 +111,5 @@ def compute_stop(corpus,limit=2000,debug=False):
     #print([n for n in ngrams_to_stop])
 
     stop = WeightedList({ n[0] : -1 for n in ngrams_to_stop})
-    stop.save(stop_node.id)
-
+    stop.save(stop_node_id)
+    

ngram/tfidf.py

 #from admin.env import *
 from math import log
 from gargantext_web.db import *
-from gargantext_web.db import get_or_create_node
+from gargantext_web.db import get_session, get_or_create_node
 
 from admin.utils import DebugTime
 
-def compute_tfidf(corpus):
+def compute_tfidf(corpus, mysession=None):
     # compute terms frequency sum
+    
     dbg = DebugTime('Corpus #%d - TFIDF' % corpus.id)
     dbg.show('calculate terms frequencies sums')
-    tfidf_node = get_or_create_node(nodetype='Tfidf', corpus=corpus)
+    tfidf_node = get_or_create_node(nodetype='Tfidf', corpus=corpus, mysession=mysession)
 
     db, cursor = get_cursor()
     cursor.execute('''
@@ -119,18 +120,20 @@ def compute_tfidf(corpus):
         # the end!
         db.commit()
 
-def compute_tfidf_global(corpus):
+
+def compute_tfidf_global(corpus, mysession=None):
     '''
     Maybe improve this with:
     #http://stackoverflow.com/questions/8674718/best-way-to-select-random-rows-postgresql
     '''
     dbg = DebugTime('Corpus #%d - tfidf global' % corpus.id)
     dbg.show('calculate terms frequencies sums')
-    tfidf_node = get_or_create_node(nodetype='Tfidf (global)', corpus=corpus)
+    
+    tfidf_node = get_or_create_node(nodetype='Tfidf (global)', corpus=corpus, mysession=mysession)
 
     # update would be better
-    session.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==tfidf_node.id).delete()
-    session.commit()
+    mysession.query(NodeNodeNgram).filter(NodeNodeNgram.nodex_id==tfidf_node.id).delete()
+    mysession.commit()
 
     # compute terms frequency sum
     db, cursor = get_cursor()
@@ -257,6 +260,3 @@ def compute_tfidf_global(corpus):
 
         db.commit()
         dbg.show('insert tfidf')
-
-#corpus=session.query(Node).filter(Node.id==244250).first()
-#compute_tfidf_global(corpus)

ngram/tools.py

-from gargantext_web.db import session
 from gargantext_web.db import Ngram, NodeNgram, NodeNgramNgram
 
-from gargantext_web.db import get_cursor, bulk_insert, get_or_create_node
+from gargantext_web.db import get_cursor, bulk_insert, get_or_create_node, session,get_session
 
 def insert_ngrams_to_list(list_of_ngrams, corpus, list_type='MapList', erase=True):
     '''
     Works only for Stop and Map
     '''
-    list_node = get_or_create_node(corpus=corpus, nodetype=list_type)
-    group_node = get_or_create_node(corpus=corpus, nodetype='GroupList')
+    # implicit global session
+
+    list_node = get_or_create_node(corpus=corpus, nodetype=list_type, mysession=session)
+    group_node = get_or_create_node(corpus=corpus, nodetype='GroupList', mysession=session)
     group_list = (session.query(NodeNgramNgram.ngramy_id)
                          .filter(NodeNgramNgram.id==group_node.id)
                          .all()

ngram/workflow.py

@@ -8,21 +8,21 @@ from gargantext_web.db import get_or_create_node
 from ngram.mapList import compute_mapList
 from ngram.occurrences import compute_occs
 
-from gargantext_web.db import session , Node , NodeNgram
+from gargantext_web.db import Node , NodeNgram
 from admin.utils import WorkflowTracking
 
 
-def ngram_workflow(corpus, n=5000):
+def ngram_workflow(corpus, n=5000, mysession=None):
     '''
     All the workflow to filter the ngrams.
     '''
     update_state = WorkflowTracking()
 
-    update_state.processing_(corpus, "Stop words")
-    compute_stop(corpus)
+    update_state.processing_(corpus.id, "Stop words")
+    compute_stop(corpus, mysession=mysession)
     
-    update_state.processing_(corpus, "TF-IDF global score")
-    compute_tfidf_global(corpus)
+    update_state.processing_(corpus.id, "TF-IDF global score")
+    compute_tfidf_global(corpus, mysession=mysession)
     
     part = round(n * 0.9)
 
@@ -31,28 +31,28 @@ def ngram_workflow(corpus, n=5000):
 #    part = round(part * 0.8)
     #print('spec part:', part)
 
-    update_state.processing_(corpus, "Specificity score")
-    compute_specificity(corpus,limit=part)
+    update_state.processing_(corpus.id, "Specificity score")
+    compute_specificity(corpus,limit=part, mysession=mysession)
     
     part = round(part * 0.8)
 
     limit_inf = round(part * 1)
     limit_sup = round(part * 5)
     #print(limit_inf,limit_sup)
-    update_state.processing_(corpus, "Synonyms")
+    update_state.processing_(corpus.id, "Synonyms")
     try:
-        compute_groups(corpus,limit_inf=limit_inf, limit_sup=limit_sup)
+        compute_groups(corpus,limit_inf=limit_inf, limit_sup=limit_sup, mysession=mysession)
     except Exception as error:
         print("Workflow Ngram Group error", error)
         pass
     
-    update_state.processing_(corpus, "Map list terms")
-    compute_mapList(corpus,limit=1000) # size
+    update_state.processing_(corpus.id, "Map list terms")
+    compute_mapList(corpus,limit=1000, mysession=mysession) # size
     
-    update_state.processing_(corpus, "TF-IDF local score")
-    compute_tfidf(corpus)
+    update_state.processing_(corpus.id, "TF-IDF local score")
+    compute_tfidf(corpus, mysession=mysession)
 
-    update_state.processing_(corpus, "Occurrences")
-    compute_occs(corpus)
+    update_state.processing_(corpus.id, "Occurrences")
+    compute_occs(corpus, mysession=mysession)
 
 

rest_v1_0/api.py

@@ -11,8 +11,11 @@ import datetime
 import copy
 
 from gargantext_web.views import move_to_trash
-from gargantext_web.db import session, cache, Node, NodeNgram, NodeNgramNgram, NodeNodeNgram, Ngram, Hyperdata, Node_Ngram\
+from gargantext_web.db import cache, Node, NodeNgram, NodeNgramNgram, NodeNodeNgram, Ngram, Hyperdata, Node_Ngram\
         , NodeType, Node_Hyperdata
+
+from gargantext_web.views import session
+
 from gargantext_web.validation import validate, ValidationException
 from node import models
 
@@ -100,8 +103,10 @@ def Root(request, format=None):
 class NodesChildrenNgrams(APIView):
 
     def get(self, request, node_id):
+        
         # query ngrams
         ParentNode = aliased(Node)
+        
         ngrams_query = (session
             .query(Ngram.terms, func.sum(Node_Ngram.weight).label('count'))
             .join(Node_Ngram, Node_Ngram.ngram_id == Ngram.id)
@@ -138,10 +143,12 @@ class NodesChildrenNgrams(APIView):
                 for ngram in ngrams_query[offset : offset+limit]
             ],
         })
+        
 
 class NodesChildrenNgramsIds(APIView):
 
     def get(self, request, node_id):
+        
         # query ngrams
         ParentNode = aliased(Node)
         ngrams_query = (session
@@ -180,13 +187,14 @@ class NodesChildrenNgramsIds(APIView):
                 for node, count in ngrams_query[offset : offset+limit]
             ],
         })
-
+        
 
 
 from gargantext_web.db import get_or_create_node
 
 class Ngrams(APIView):
     def get(self, request, node_id):
+        
         # query ngrams
         ParentNode = aliased(Node)
         corpus = session.query(Node).filter(Node.id==node_id).first()
@@ -303,11 +311,11 @@ class Ngrams(APIView):
 
                     ],
                                })
-    
         
 
 class NodesChildrenDuplicates(APIView):
     def _fetch_duplicates(self, request, node_id, extra_columns=None, min_count=1):
+        
         # input validation
         if extra_columns is None:
             extra_columns = []
@@ -346,6 +354,7 @@ class NodesChildrenDuplicates(APIView):
         duplicates_query = duplicates_query.having(func.count() > min_count)
         # and now, return it
         return duplicates_query
+        
 
     def get(self, request, node_id):
         # data to be returned
@@ -395,6 +404,7 @@ class NodesChildrenDuplicates(APIView):
 
 # retrieve metadata from a given list of parent node
 def get_metadata(corpus_id_list):
+    
 
     # query hyperdata keys
     ParentNode = aliased(Node)
@@ -695,6 +705,7 @@ class NodesList(APIView):
     authentication_classes = (SessionAuthentication, BasicAuthentication)
 
     def get(self, request):
+        
         print("user id : " + str(request.user))
         query = (session
             .query(Node.id, Node.name, NodeType.name.label('type'))
@@ -710,9 +721,11 @@ class NodesList(APIView):
             node._asdict()
             for node in query.all()
         ]})
+        
 
 class Nodes(APIView):
     def get(self, request, node_id):
+        
         node = session.query(Node).filter(Node.id == node_id).first()
         if node is None:
             raise APIException('This node does not exist', 404)
@@ -725,6 +738,7 @@ class Nodes(APIView):
             #'hyperdata': dict(node.hyperdata),
             'hyperdata': node.hyperdata,
         })
+        
 
     # deleting node by id
     # currently, very dangerous.
@@ -732,6 +746,7 @@ class Nodes(APIView):
     # for better constistency...
     def delete(self, request, node_id):
 
+        
         user = request.user
         node = session.query(Node).filter(Node.id == node_id).first()
 
@@ -744,6 +759,7 @@ class Nodes(APIView):
 
         except Exception as error:
             msgres ="error deleting : " + node_id + str(error)
+        
 
 class CorpusController:
     @classmethod
@@ -764,7 +780,6 @@ class CorpusController:
         #     raise Http403("Unauthorized access.")
         return corpus
 
-
     @classmethod
     def ngrams(cls, request, node_id):
 
@@ -773,6 +788,7 @@ class CorpusController:
 
         # build query
         ParentNode = aliased(Node)
+        
         query = (session
             .query(Ngram.terms, func.count('*'))
             .join(Node_Ngram, Node_Ngram.ngram_id == Ngram.id)
@@ -799,3 +815,4 @@ class CorpusController:
             )
         else:
             raise ValidationError('Unrecognized "format=%s", should be "csv" or "json"' % (format, ))
+

rest_v1_0/graph.py

 from rest_v1_0.api import APIView, APIException, JsonHttpResponse, CsvHttpResponse
 from rest_framework.authentication import SessionAuthentication, BasicAuthentication
 
-from gargantext_web.db import session, Node
+from gargantext_web.db import session,get_session, Node
 from analysis.functions import get_cooc
 
 class Graph(APIView):
     authentication_classes = (SessionAuthentication, BasicAuthentication)
+    
     def get(self, request, corpus_id):
         '''
         Graph.get :: Get graph data as REST api.
@@ -13,6 +14,8 @@ class Graph(APIView):
         graph?field1=ngrams&field2=ngrams&
         graph?field1=ngrams&field2=ngrams&start=''&end=''
         '''
+        # implicit global session
+        
         field1 = request.GET.get('field1', 'ngrams')
         field2 = request.GET.get('field2', 'ngrams')
         

rest_v1_0/ngrams.py

@@ -16,8 +16,7 @@ from gargantext_web.db import cache
 
 from gargantext_web.validation import validate, ValidationException
 
-from gargantext_web.db import session, Node, NodeNgram, NodeNgramNgram\
-        , NodeNodeNgram, Ngram, Hyperdata, Node_Ngram, get_or_create_node
+from gargantext_web.db import session,get_session, Node, NodeNgram, NodeNgramNgram, NodeNodeNgram, Ngram, Hyperdata, Node_Ngram, get_or_create_node
 
 
 def DebugHttpResponse(data):
@@ -82,6 +81,8 @@ class List(APIView):
 
     def get_metadata ( self , ngram_ids , parent_id ):
 
+        # implicit global session
+        
         start_ = time.time()
 
         nodes_ngrams = session.query(Ngram.id , Ngram.terms).filter( Ngram.id.in_( list(ngram_ids.keys()))).all()
@@ -121,10 +122,10 @@ class List(APIView):
         return { "data":ngram_ids , "secs":(end_ - start_) }
 
 
-
     def get(self, request, corpus_id , list_name ):
         if not request.user.is_authenticated():
             return JsonHttpResponse( {"request" : "forbidden"} )
+        # implicit global session
         corpus = session.query(Node).filter( Node.id==corpus_id ).first()
         # if corpus==None:
         #     return JsonHttpResponse( {"request" : "forbidden"} )
@@ -162,6 +163,7 @@ class Ngrams(APIView):
     def get(self, request, node_id):
         if not request.user.is_authenticated():
             return JsonHttpResponse( {"request" : "forbidden"} )
+        # implicit global session
         corpus = session.query(Node).filter( Node.id==node_id).first()
         # if corpus==None:
         #     return JsonHttpResponse( {"request" : "forbidden"} )
@@ -340,6 +342,9 @@ class Group(APIView):
     '''
     def get_group_id(self , node_id , user_id):
         node_id = int(node_id)
+        
+        # implicit global session
+        
         corpus = session.query(Node).filter(  Node.id==node_id).first()
         if corpus==None: return None
         group = get_or_create_node(corpus=corpus, nodetype='Group')
@@ -370,6 +375,9 @@ class Group(APIView):
         import networkx as nx
         G = nx.Graph()
         DG = nx.DiGraph()
+        
+        # implicit global session
+        
         ngrams_ngrams = (session
                 .query(NodeNgramNgram)
                 .filter(NodeNgramNgram.node_id==group_id)
@@ -409,13 +417,15 @@ class Group(APIView):
         # groups["nodes"] = get_occtfidf( ngrams , request.user.id , corpus_id , "Group")
         
         return JsonHttpResponse( { "data" : groups } )
-   
+
     def post(self, request, node_id):
         return JsonHttpResponse( ["hola" , "mundo"] )
 
     def delete(self, request, corpus_id):
         
         # input validation
+        
+        # implicit global session
         input = validate(request.DATA, {'data' : {'source': int, 'target': list}})
         
         group_id = get_group_id(corpus_id , request.user.id)
@@ -434,6 +444,7 @@ class Group(APIView):
                 raise APIException('Missing parameter: "{\'data\' : [\'source\': Int, \'target\': [Int]}"', 400)
 
     def put(self , request , corpus_id ):
+        # implicit global session
 
         group_rawreq = dict(request.data)
         
@@ -448,6 +459,8 @@ class Group(APIView):
                 gdict.append(subform)
             GDict.append( gdict )
         existing_group_id = self.get_group_id(corpus_id , request.user.id)
+        
+        # implicit global session
         grouped_ngrams = (session
                 .query(NodeNgramNgram)
                 .filter(NodeNgramNgram.node_id==existing_group_id)
@@ -512,6 +525,7 @@ class Group(APIView):
                 nodengramngram = NodeNgramNgram(node_id=existing_group_id, ngramx_id=n1 , ngramy_id=n2, score=1.0)
                 session.add(nodengramngram)
         session.commit()
+        
         # [ - - - / doing links of new clique and adding to DB - - - ] #
 
 
@@ -571,6 +585,7 @@ class Keep(APIView):
     authentication_classes = (SessionAuthentication, BasicAuthentication)
 
     def get (self, request, corpus_id):
+        # implicit global session
         # list_id = session.query(Node).filter(Node.id==list_id).first()
         corpus = session.query(Node).filter( Node.id==corpus_id ).first()
         node_mapList = get_or_create_node(nodetype='MapList', corpus=corpus )
@@ -579,11 +594,12 @@ class Keep(APIView):
         for node in nodes_in_map:
             results[node.ngram_id] = True
         return JsonHttpResponse(results)
-    
+
     def put (self, request, corpus_id):
         """
         Add ngrams to map list
         """
+        # implicit global session
         group_rawreq = dict(request.data)
         ngram_2add = [int(i) for i in list(group_rawreq.keys())]
         corpus = session.query(Node).filter( Node.id==corpus_id ).first()
@@ -598,6 +614,8 @@ class Keep(APIView):
         """
         Delete ngrams from the map list
         """
+        # implicit global session
+        
         group_rawreq = dict(request.data)
         # print("group_rawreq:")
         # print(group_rawreq)
@@ -616,4 +634,3 @@ class Keep(APIView):
 
         return JsonHttpResponse(True, 201)
 
-

scrappers/scrap_pubmed/views.py

@@ -29,6 +29,7 @@ import threading
 
 from node.admin import CustomForm
 from gargantext_web.db import *
+from gargantext_web.db import get_sessionmaker, session,get_session
 from gargantext_web.settings import DEBUG, MEDIA_ROOT
 from rest_v1_0.api import JsonHttpResponse
 
@@ -45,7 +46,8 @@ def getGlobalStats(request ):
 	alist = ["bar","foo"]
 
 	if request.method == "POST":
-		N = 1000
+		#N = 1000
+		N = 300
 		query = request.POST["query"]
 		print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" query =", query )
 		print ("LOG::TIME:_ "+datetime.datetime.now().isoformat()+" N =", N )
@@ -83,14 +85,12 @@ def getGlobalStatsISTEXT(request ):
 
 
 def doTheQuery(request , project_id):
-	alist = ["hola","mundo"]
-
+	# implicit global session
 	# do we have a valid project id?
 	try:
 		project_id = int(project_id)
 	except ValueError:
 		raise Http404()
-
 	# do we have a valid project?
 	project = (session
 		.query(Node)
@@ -134,7 +134,7 @@ def doTheQuery(request , project_id):
 		)
 		session.add(corpus)
 		session.commit()
-
+		corpus_id = corpus.id
 		# """
 		# urlreqs: List of urls to query.
 		# - Then, to each url in urlreqs you do:
@@ -170,9 +170,9 @@ def doTheQuery(request , project_id):
 
 		try:
 			if not DEBUG:
-				apply_workflow.apply_async((corpus.id,),)
+				apply_workflow.apply_async((corpus_id,),)
 			else:
-				thread = threading.Thread(target=apply_workflow, args=(corpus.id, ), daemon=True)
+				thread = threading.Thread(target=apply_workflow, args=(corpus_id, ), daemon=True)
 				thread.start()
 		except Exception as error:
 			print('WORKFLOW ERROR')
@@ -188,7 +188,7 @@ def testISTEX(request , project_id):
 	print("testISTEX:")
 	print(request.method)
 	alist = ["bar","foo"]
-
+	# implicit global session
 	# do we have a valid project id?
 	try:
 		project_id = int(project_id)
@@ -247,7 +247,7 @@ def testISTEX(request , project_id):
 		)
 		session.add(corpus)
 		session.commit()
-
+		corpus_id = corpus.id
 
 		ensure_dir(request.user)
 		tasks = MedlineFetcher()
@@ -276,9 +276,9 @@ def testISTEX(request , project_id):
 		###########################
 		try:
 			if not DEBUG:
-				apply_workflow.apply_async((corpus.id,),)
+				apply_workflow.apply_async((corpus_id,),)
 			else:
-				thread = threading.Thread(target=apply_workflow, args=(corpus.id, ), daemon=True)
+				thread = threading.Thread(target=apply_workflow, args=(corpus_id, ), daemon=True)
 				thread.start()
 		except Exception as error:
 			print('WORKFLOW ERROR')
@@ -289,4 +289,3 @@ def testISTEX(request , project_id):
 
 	data = [query_string,query,N]
 	return JsonHttpResponse(data)
-

static/css/jquery.dynatable.css

@@ -69,4 +69,4 @@ th a:hover {
 .dynatable-disabled-page:hover {
   background: none;
   color: #999;
-}
\ No newline at end of file
+}

templates/corpus/terms.html

@@ -25,13 +25,34 @@
   -o-transition: height 0.1s;
   transition: height 0.1s;
 }
-th { color: #fff; }
+th { 
+  color: #fff;
+  font-weight: normal;
+  font-size: 0.9em;
+  vertical-align: top ;
+}
+
+/* specific selector to override equally specific bootstrap.css */
+.table > thead > tr > th { vertical-align: top ; }
 
 th a {
   color: #fff;
-  font-weight: normal;
   font-style: italic;
-  font-size: 0.9em;
+}
+
+th p.note {
+  color: #ccc;
+  font-size: 0.6em;
+  margin: 1em 0 0 0 ;
+}
+
+th p.note > input {
+  float: left;
+  margin: 0 .2em 0 0 ;
+}
+
+th p.note > label {
+  float: left;
 }
 
 tr:hover {
@@ -171,7 +192,7 @@ input[type=radio]:checked + label {
     <div class="panel-heading">
       <h4 class="panel-title">
         <a data-toggle="collapse" data-parent="#accordion" href="#collapseOne">
-           <p id="corpusdisplayer" onclick='Final_UpdateTable("click")' class="btn btn-primary btn-lg" style="width:200px; margin:0 auto; display:block;">Open Folder</h2></p>
+           <p id="corpusdisplayer" onclick='Final_UpdateTable("click")' class="btn btn-primary btn-lg" style="width:200px; margin:0 auto; display:block;">Close Term List</h2></p>
         </a>
       </h4>
     </div>
@@ -194,7 +215,7 @@ input[type=radio]:checked + label {
                 </p> -->
                 <p align="right">
                     <!-- <button id="Clean_All" class="btn btn-warning">Clean</button> -->
-                    <button id="Save_All" class="btn btn-primary">Save</button>
+                    <button id="Save_All" class="btn btn-primary">Save changes permanently</button>
                 </p>
 
       </div>
@@ -247,66 +268,6 @@ input[type=radio]:checked + label {
     </div>
 
 
-    <div id="pre_savechanges" class="modal fade">
-
-      <div class="modal-dialog">
-
-        <div class="modal-content">
-          
-
-          <div class="modal-header">
-            <h3 class="modal-title">Do you want to apply these to the whole Project as well?:</h3>
-          </div>
-
-          <div class="modal-body">
-
-            <div id="stoplist_content">
-            </div>
-
-            <!-- 
-              <ul class="nav nav-tabs">
-                <li class="active"><a id="stoplist" href="#stoplist_content">Stop List</a></li>
-                <li><a id="maplist" href="#maplist_content">Map List</a></li>
-                <li><a id="grouplist" href="#grouplist_content">Group List</a></li>
-              </ul>
-
-              <div class="tab-content">
-                <div id="stoplist_content" class="tab-pane fade in active">
-                  <ul>
-                    <li>jiji01</li>
-                    <li>jiji02</li>
-                    <li>jiji03</li>
-                  </ul>
-                </div>
-
-                <div id="maplist_content" class="tab-pane fade">
-                  qowieuoqiwueowq
-                </div>
-
-                <div id="grouplist_content" class="tab-pane fade">
-                  asdhasjkdhasjdh
-                </div>
-
-              </div>
-            -->
-
-            <div class="modal-footer">
-              <button onclick="SaveGlobalChanges(false)" id="nope" type="button" class="btn btn-default" data-dismiss="modal">No</button>
-              <button onclick="SaveGlobalChanges(true)" id="yep" type="button" class="btn btn-primary">Yes</button>
-            </div>
-
-
-          </div>
-
-
-        </div>
-
-      </div>
-
-    </div>
-
-
-
 
 <div id="filter_search" style="visibility:hidden">
 <select id="example-single-optgroups" onchange="SearchFilters(this);">

templates/project.html

@@ -299,7 +299,7 @@
 					var origQuery = $("#id_name").val()
 					console.log("printing the results:")
 					console.log(origQuery)
-					testISTEX(origQuery.replace(" ","+"),1000)
+					testISTEX(origQuery.replace(" ","+"),300)
 				}
 			}
 			else {
@@ -349,7 +349,7 @@
 					console.log("enabling "+"#"+value.id)
 					$("#"+value.id).attr('onclick','getGlobalResults(this);');
 					// $("#submit_thing").prop('disabled' , false)
-					$("#submit_thing").html("Process a 1000 sample!")
+					$("#submit_thing").html("Process a 300 sample!")
 
 		            thequeries = data
 		            var N=0,k=0;
@@ -388,7 +388,7 @@
 					console.log("enabling "+"#"+value.id)
 					$("#"+value.id).attr('onclick','getGlobalResults(this);');
 					// $("#submit_thing").prop('disabled' , false)
-					$("#submit_thing").html("Process a 1000 sample!")
+					$("#submit_thing").html("Process a 300 sample!")
 
 		            thequeries = data
 		            var N=data.length,k=0;

tests/ngramstable/views.py

 from django.shortcuts import redirect
-from django.shortcuts import render
-from django.db import transaction
-
-from django.http import Http404, HttpResponse, HttpResponseRedirect, HttpResponseForbidden
+# from django.shortcuts import render
+# from django.db import transaction
+# 
+from django.http import Http404, HttpResponse #, HttpResponseRedirect, HttpResponseForbidden
 from django.template.loader import get_template
 from django.template import Context
 
@@ -13,49 +13,41 @@ from django.db import connection
 #        Node, NodeType, Node_Resource, Project, Corpus, \
 #        Ngram, Node_Ngram, NodeNgramNgram, NodeNodeNgram
 
-from node.admin import CorpusForm, ProjectForm, ResourceForm, CustomForm
-
-from django.contrib.auth.models import User
-
+# from node.admin import CorpusForm, ProjectForm, ResourceForm, CustomForm
+# 
+# from django.contrib.auth.models import User
+# 
 import datetime
-from itertools import *
-from dateutil.parser import parse
-
-from django.db import connection
-from django import forms
-
-
-from collections import defaultdict
-
-from parsing.FileParsers import *
-import os
+# from itertools import *
+# from dateutil.parser import parse
+# 
+# from django.db import connection
+# from django import forms
+# 
+# 
+# from collections import defaultdict
+# 
+# from parsing.FileParsers import *
+# import os
 import json
-import math
+# import math
 
 # SOME FUNCTIONS
 
 from gargantext_web import settings
+# 
+# from django.http import *
+# from django.shortcuts import render_to_response,redirect
+# from django.template import RequestContext
 
-from django.http import *
-from django.shortcuts import render_to_response,redirect
-from django.template import RequestContext
-from django.contrib.auth.decorators import login_required
-from django.contrib.auth import authenticate, login, logout
-
-from scrappers.scrap_pubmed.admin import Logger
-
-from gargantext_web.db import *
-
-from sqlalchemy import or_, func
+# from gargantext_web.db import *
 
-from gargantext_web import about
+from gargantext_web.db import session,get_session, cache, Node, NodeNgram
+from sqlalchemy import func
 
 from rest_v1_0.api import JsonHttpResponse
 
 
-from ngram.lists import listIds, listNgramIds, ngramList , doList
-
-
 def get_ngrams(request , project_id , corpus_id ):
     if not request.user.is_authenticated():
         return redirect('/login/?next=%s' % request.path)
@@ -73,6 +65,8 @@ def get_ngrams(request , project_id , corpus_id ):
     project = cache.Node[int(project_id)]
     corpus  = cache.Node[int(corpus_id)]
     type_doc_id = cache.NodeType['Document'].id
+
+    # implicit global session
     number = session.query(func.count(Node.id)).filter(Node.parent_id==corpus_id, Node.type_id==type_doc_id).all()[0][0]
     myamlist_type_id = cache.NodeType['MiamList'].id
     miamlist = session.query(Node).filter(Node.parent_id==corpus_id , Node.type_id == myamlist_type_id ).first()
@@ -129,6 +123,8 @@ def get_journals(request , project_id , corpus_id ):
     project = cache.Node[int(project_id)]
     corpus  = cache.Node[int(corpus_id)]
     type_doc_id = cache.NodeType['Document'].id
+    
+    # implicit global session
     number = session.query(func.count(Node.id)).filter(Node.parent_id==corpus_id, Node.type_id==type_doc_id).all()[0][0]
 
     the_query = """ SELECT hyperdata FROM node_node WHERE id=%d """ % ( int(corpus_id) )
@@ -158,7 +154,10 @@ def get_journals_json(request , project_id, corpus_id ):
 
     user_id = request.user.id
     document_type_id = cache.NodeType['Document'].id
+    
+    # implicit global session
     documents  = session.query(Node).filter( Node.parent_id==corpus_id , Node.type_id == document_type_id ).all()
+    
     for doc in documents:
         if "journal" in doc.hyperdata:
             journal = doc.hyperdata["journal"]
@@ -167,25 +166,20 @@ def get_journals_json(request , project_id, corpus_id ):
             JournalsDict[journal] += 1
     return JsonHttpResponse(JournalsDict)
 
-from gargantext_web.db import session, cache, Node, NodeNgram
-from sqlalchemy import or_, func
-from sqlalchemy.orm import aliased
-
-
 def get_corpuses( request , node_ids ):
     ngrams = [int(i) for i in node_ids.split("+") ]
+    
+    # implicit global session
     results = session.query(Node.id,Node.hyperdata).filter(Node.id.in_(ngrams) ).all()
     for r in results:
         print(r)
     return JsonHttpResponse( [ "tudo" , "bem" ] )
 
-
 def get_cores( request ):
 	import multiprocessing
 	cpus = multiprocessing.cpu_count()
 	return JsonHttpResponse( {"data":cpus} )
 
-
 def get_corpus_state( request , corpus_id ):
     if not request.user.is_authenticated():
         return JsonHttpResponse( {"request" : "forbidden"} )
@@ -200,8 +194,12 @@ def get_corpus_state( request , corpus_id ):
     # processing = corpus.hyperdata['Processing']
     return JsonHttpResponse(  processing )
 
-
 def get_groups( request ):
+    """
+    User groups for current user.id
+    
+    route: /get_groups
+    """
     if not request.user.is_authenticated():
         return JsonHttpResponse( {"request" : "forbidden"} )
 
@@ -222,11 +220,9 @@ def get_groups( request ):
 
     return JsonHttpResponse(  common_users )
 
-
 def graph_share(request, generic=100, specific=100):
-
     if request.method== 'GET' and "token" in request.GET:
-        import json
+        # import json
         le_token = json.loads(request.GET["token"])[0]
         import base64
         le_query = base64.b64decode(le_token).decode("utf-8")
@@ -237,11 +233,15 @@ def graph_share(request, generic=100, specific=100):
         # resource_id = cache.ResourceType["Pubmed (xml format)"].id
         # corpus = session.query(Node).filter( Node.type_id==resource_id , Node.user_id==user_id , Node.id==corpus_id , Node.type_id == cache.NodeType['Corpus'].id ).first()
         # if corpus==None: return JsonHttpResponse( {"request" : "forbidden"} )
+        
+        # implicit global session
         miamlist = session.query(Node).filter( Node.user_id==user_id , Node.parent_id==corpus_id , Node.type_id == cache.NodeType['MiamList'].id ).first()
+        
         if miamlist==None: return JsonHttpResponse( {"request" : "forbidden"} )
         graphurl = "node_link_share.json?token="+request.GET["token"]
         date = datetime.datetime.now()
         t = get_template('explorer_share.html')
+        
         html = t.render(Context({\
                 'debug': settings.DEBUG,
                 'date'      : date,\
@@ -252,11 +252,10 @@ def graph_share(request, generic=100, specific=100):
 
     return JsonHttpResponse(request.GET["token"])
 
-
 def node_link_share(request):
     data = { "request" : "error" }
     if request.method== 'GET' and "token" in request.GET:
-        import json
+        # import json
         le_token = json.loads(request.GET["token"])[0]
         import base64
         le_query = base64.b64decode(le_token).decode("utf-8")
@@ -268,6 +267,8 @@ def node_link_share(request):
 
         from analysis.functions import get_cooc
         data = []
+        
+        # implicit global session
         corpus = session.query(Node).filter( Node.user_id==user_id , Node.id==corpus_id).first()
         data = get_cooc(request=request, corpus=corpus, type="node_link")
 
@@ -301,7 +302,10 @@ def share_resource(request , resource_id , group_id) :
 
             # [  getting all childs ids of this project  ]
             ids2changeowner = [ project2share.id ]
+            
+            # implicit global session
             corpuses = session.query(Node.id).filter(Node.user_id == request.user.id, Node.parent_id==resource_id , Node.type_id == cache.NodeType["Corpus"].id ).all()
+            
             for corpus in corpuses:
                 ids2changeowner.append(corpus.id)
                 lists = session.query(Node.id,Node.name).filter(Node.user_id == request.user.id, Node.parent_id==corpus.id ).all()
@@ -323,4 +327,4 @@ def share_resource(request , resource_id , group_id) :
             connection.close()
             # [  / changing owner  ]
 
-    return JsonHttpResponse(  results )
\ No newline at end of file
+    return JsonHttpResponse(  results )

tests/test_ngrams.py

-
-from admin.env import *
-from gargantext_web.db import session, cache, get_or_create_node
-from gargantext_web.db import Node, NodeHyperdata, Hyperdata, Ngram, NodeNgram, NodeNgramNgram, NodeHyperdataNgram
-from sqlalchemy import func, alias, asc, desc
-import sqlalchemy as sa
-from sqlalchemy.orm import aliased
-
-from ngram.group import compute_groups, getStemmer
-
-# corpus = Corpus(272)
-corpus_id = 540420
-corpus = session.query(Node).filter(Node.id==corpus_id).first()
-#group = get_or_create_node(corpus=corpus, nodetype="Group")
-
-stop_id = get_or_create_node(nodetype='StopList',corpus=corpus).id
-miam_id = get_or_create_node(nodetype='MiamList',corpus=corpus).id
-
-somme = sa.func.count(NodeNgram.weight)
-ngrams = (session.query(Ngram.id, Ngram.terms, somme )
-        .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
-        .join(Node, Node.id == NodeNgram.node_id)
-        .filter(Node.parent_id==corpus_id, Node.type_id==cache.NodeType['Document'].id)
-        .group_by(Ngram.id)
-        .order_by(desc(somme))
-        .limit(100000)
-        )
-
-stops = (session.query(Ngram.id, Ngram.terms)
-                .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
-                .filter(NodeNgram.node_id == stop_id)
-                .all()
-                )
-
-miams = (session.query(Ngram.id, Ngram.terms, somme)
-                .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
-                .filter(NodeNgram.node_id == miam_id)
-                .group_by(Ngram.id, Ngram.terms)
-                .order_by(desc(somme))
-                .all()
-                )
-
-stemmer = getStemmer(corpus)
-
-ws = ['honeybee', 'honeybees']
-
-print(stemmer(ws[0]) == stemmer(ws[1]))
-
-#
-#for n in miams:
-#    if n[1] == 'bees':
-#        print("!" * 30)
-#        print(n)
-#        print("-" * 30)
-#    else:
-#        print(n)
-#