[UPDATE] merge conflict resolved ?

analysis/cooccurrences.py

@@ -17,7 +17,8 @@ def do_cooc(corpus=None
          , n_min=2, n_max=None
          , start=None, end=None
          , limit=1000
-         , isMonopartite=True):
+         , isMonopartite=True
+         , apax = 2):
     '''
     Compute the cooccurence matrix and save it, returning NodeNgramNgram.node_id
     For the moment list of paramters are not supported because, lists need to
@@ -149,8 +150,7 @@ def do_cooc(corpus=None
         # Cooc is symetric, take only the main cooccurrences and cut at the limit
         cooc_query = cooc_query.filter(NodeNgramX.ngram_id < NodeNgramY.ngram_id)
     
-    cooc_query = cooc_query.having(cooc_score > 1)
-                           #.having(cooc_score > 1)
+    cooc_query = cooc_query.having(cooc_score > apax)
              
     if isMonopartite:
         cooc_query = cooc_query.group_by(NodeNgramX.ngram_id, NodeNgramY.ngram_id)

analysis/functions.py

@@ -30,7 +30,7 @@ def diag_null(x):
     return x - x * scipy.eye(x.shape[0])
 
 
-def do_distance(cooc_id, field1=None, field2=None, isMonopartite=True):
+def do_distance(cooc_id, field1=None, field2=None, isMonopartite=True, apax=2):
     '''
     do_distance :: Int -> (Graph, Partition, {ids}, {weight})
     '''
@@ -119,6 +119,7 @@ def get_cooc(request=None, corpus=None
         , field1='ngrams', field2='ngrams'
         , cooc_id=None, type='node_link', size=1000
         , start=None, end=None
+        , apax=2
         ):
     '''
     get_ccoc : to compute the graph.
@@ -141,9 +142,7 @@ def get_cooc(request=None, corpus=None
     #cooc_id = get_or_create_node(nodetype='Cooccurrence', corpus=corpus).id
     cooc_id = do_cooc(corpus=corpus, field1="ngrams", field2="ngrams"
             , miam_id=miam_id, group_id=group_id, stop_id=stop_id, limit=size
-            , isMonopartite=isMonopartite
-            , start=start
-            , end = end)
+            , isMonopartite=isMonopartite , start=start , end=end , apax=apax)
     
     G, partition, ids, weight = do_distance(cooc_id, field1="ngrams", field2="ngrams", isMonopartite=isMonopartite)
 

annotations/urls.py

@@ -5,6 +5,6 @@ from annotations import views
 urlpatterns = patterns('',
     url(r'^document/(?P<doc_id>[0-9]+)$', views.Document.as_view()), # document view
     url(r'^corpus/(?P<corpus_id>[0-9]+)/document/(?P<doc_id>[0-9]+)$', views.NgramList.as_view()), # the list associated with an ngram
-    url(r'^lists/(?P<list_id>[0-9]+)/ngrams/(?P<ngram_ids>[0-9]+\+*[0-9]*)$', views.NgramEdit.as_view()),
+    url(r'^lists/(?P<list_id>[0-9]+)/ngrams/(?P<ngram_ids>[0-9,\+]+)+$', views.NgramEdit.as_view()),
     url(r'^lists/(?P<list_id>[0-9]+)/ngrams/create$', views.NgramCreate.as_view()), #
 )

annotations/views.py

@@ -93,7 +93,9 @@ class NgramEdit(APIView):
         """
         Delete a ngram from a list
         """
+        print(ngram_ids)
         for ngram_id in ngram_ids.split('+'):
+            print('ngram_id', ngram_id)
             ngram_id = int(ngram_id)
             (session.query(NodeNgram)
                     .filter(NodeNgram.node_id==list_id)

gargantext_web/celery.py

@@ -42,7 +42,7 @@ def apply_workflow(corpus_id):
     parse_resources(corpus)
 
     update_processing(corpus, 2)
-    extract_ngrams(corpus, ['title', 'abstract'])
+    extract_ngrams(corpus, ['title', 'abstract'], nlp=True)
 
     update_processing(corpus, 3)
     ngram_workflow(corpus)

gargantext_web/views.py

@@ -699,9 +699,17 @@ def sankey_csv(request, corpus_id):
     corpus = session.query(Node).filter(Node.id==corpus_id).first()
     data = [
             ["source", "target", "value"]
-            , ["Elvis_1", "Elvis_2", 1]
-            , ["Elvis_2", "Elvis_3", 2]
-            , ["Barry", "Elvis_3", 2]
+            , ["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]
             ]
     return(CsvHttpResponse(data))
 

init.py

@@ -151,4 +151,19 @@ session.commit()
 ###f.close()
 ##
 ##
+
+
+from ngram.stop import importStopList
+root = session.query(Node).filter(Node.type_id==cache.NodeType['Root'].id).first()
+importStopList(root, '/srv/gargantext/init/stop_lists/fr.txt', 'fr')
+importStopList(root, '/srv/gargantext/init/stop_lists/en.txt', 'en')
+
+
+root = session.query(Node).filter(Node.type_id==cache.NodeType['Root'].id).first()
+#importStopList(root, '/srv/gargantext/init/stop_lists/fr.txt', 'fr')
+importStopList(root, '/srv/gargantext/init/stop_lists/en.txt', 'en')
+
+
+
+
 #exit()

ngram/group.py

@@ -60,15 +60,17 @@ def getNgrams(corpus=None, limit_inf=600, limit_sup=3000):
 
     #print([n for n in tfidf_ngrams])
 
-    def list2set(_list,_set):
+    def list2set(_list):
+        _set = set()
         for n in _list:
             _set.add((n[0],n[1]))
+        return(_set)
 
     cvalue_set = set()
     spec_set = set()
 
-    list2set(cvalue_ngrams,cvalue_set)
-    list2set(spec_ngrams,spec_set)
+    cvalue_set = list2set(cvalue_ngrams)
+    spec_set   = list2set(spec_ngrams)
 
     cvalue_setDiff = cvalue_set.difference(spec_set)
 

ngram/miam.py

@@ -12,6 +12,8 @@ from sqlalchemy import desc, asc, or_, and_, Date, cast, select
 from sqlalchemy import literal_column
 from sqlalchemy.orm import aliased
 
+from ngram.tools import insert_ngrams
+import csv
 
 def compute_miam(corpus,limit=500):
     '''
@@ -50,5 +52,43 @@ def compute_miam(corpus,limit=500):
 
     dbg.show('Miam computed')
 
+def insert_miam(corpus, ngrams=None, path_file_csv=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()
+    
+    stop_words = set()
+    miam_words = set()
+    
+    if path_file_csv is not None:
+        file_csv = open(path_file_csv, "r")
+    reader = csv.reader(file_csv, delimiter=',')
+
+    for line in reader:
+        word = line[0]
+        tag  = line[4]
+        if tag == '1':
+            miam_words.add((word, 1))
+        elif tag == '0':
+            stop_words.add((word, 1))
+    
+    miam_ids = insert_ngrams(miam_words)
+    print(miam_ids)
+    limit = len(list(miam_words))
+    data = zip(
+        [node_miam.id for i in range(1,limit)]
+        , [miam_ids[n] for n in miam_ids.keys()]
+        , [1 for i in range(1,limit)]
+    )
+    #print([d for d in data])
+    bulk_insert(NodeNgram, ['node_id', 'ngram_id', 'weight'], [d for d in data])
+    file_csv.close()
+    dbg.show('Miam computed')
+
+#corpus = session.query(Node).filter(Node.id==556113).first()
+#insert_miam(corpus=corpus, path_file_csv="Thesaurus_tag.csv")
+
 
 

ngram/stop.py

@@ -2,49 +2,122 @@
 #from admin.env import *
 #from ngram.stemLem import *
 
+import re
 from admin.utils import PrintException
 
 from gargantext_web.db import NodeNgram,NodeNodeNgram
-from gargantext_web.db import get_or_create_node, session
+from gargantext_web.db import cache, session, get_or_create_node
 
 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 ngram.tools import insert_ngrams
+from analysis.lists import WeightedList, UnweightedList
 
+def importStopList(node,filename,language='fr'):
+    with open(filename, "r") as f:
+        stop_list = f.read().splitlines()
+    
+    stop_words = set(stop_list)
+    stop_ids = insert_ngrams([(word, len(word.split(' '))) for word in stop_words])
 
+    stop_node = get_or_create_node(nodetype='StopList', corpus=node)
+    stop_node.language_id = cache.Language[language].id
+    session.add(stop_node)
+    session.commit()
+    
+    size = len(list(stop_words))
 
-def computeStop(corpus,size=100):
+    data = zip(
+        [stop_node.id for i in range(0,size)]
+        , [stop_ids[word] for word in list(stop_words)]
+        , [-1 for i in range(0,size)]
+    )
+    
+    bulk_insert(NodeNgram, ['node_id', 'ngram_id', 'weight'], [d for d in data])
+
+
+def isStopWord(ngram, stop_words=None):
+    '''
+    ngram :: (Int, String) => (ngram_id, ngram_terms)
+    stop_words :: Set of String
+    (to avoid SQL query each time isStopWord is invoked, get in as parameter)
+    '''
+    word = ngram[1]
+
+    if word in stop_words:
+        return(True)
+    
+    def test_match(word, regex):
+        format_regex = re.compile(regex)
+        if format_regex.match(word) :
+            return(True)
+
+    for regex in ["(.*)\d(.*)"
+            , "^.{1,2}$"
+            , "(.*)(\.)(.*)"
+            , "(.*)(\,)(.*)"
+            , "(.*)(study)(.*)"
+            , "(.*)(result)(.*)"
+            , "(.*)(année)(.*)"
+            , "(.*)(temps)(.*)"
+            , "(.*)(%)(.*)"
+            , "(.*)(\{)(.*)"
+            , "(.*)(terme)(.*)"
+            , "(.*)(différent)(.*)"
+            , "(.*)(travers)(.*)"
+            , "(.*)(:|\|)(.*)"
+            ] :
+        if test_match(word, regex) is True :
+            return(True)
+
+
+def compute_stop(corpus,size=2000,debug=False):
     '''
     do some statitics on all stop lists of database of the same type
     '''
-    node_stop = get_or_create_node(nodetype='StopList', corpus=corpus)
-    Stop=aliased(NodeNgram)
-
-    top_spec = (session.query(NodeNodeNgram.ngram_id, NodeNodeNgram.score)
-                .outerjoin(Stop, Stop.ngram_id == NodeNodeNgram.ngram_id)
-                .filter(NodeNodeNgram.nodex_id==node_spec.id)
-                .filter(Stop.node_id==node_stop.id)
-                .order_by(desc(NodeNodeNgram.score))
+    stop_node = get_or_create_node(nodetype='StopList', corpus=corpus)
+    miam_node = get_or_create_node(nodetype='MiamList', corpus=corpus)
+    
+    # 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
+    
+    stop_words = (session.query(Ngram.terms)
+                         .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
+                         .filter(NodeNgram.node_id == root_stop_id)
+                         .all()
+                 )
+
+    top_words = (session.query(Ngram.id, Ngram.terms)
+                .join(NodeNgram, NodeNgram.ngram_id == Ngram.id)
+                .filter(NodeNgram.node_id == miam_node.id)
+                .order_by(desc(NodeNgram.weight))
                 .limit(size)
                 )
+    
+    ngrams_to_stop = filter(lambda x: isStopWord(x,stop_words=stop_words), top_words)
+    
+    stop = WeightedList({ n[0] : -1 for n in ngrams_to_stop})
+    stop.save(stop_node.id)
 
-    node_miam = get_or_create_node(nodetype='MiamList', corpus=corpus)
-    session.query(NodeNgram).filter(NodeNgram.node_id==node_miam.id).delete()
+    miam = UnweightedList(miam_node.id)
 
-    data = zip(
-        [node_miam.id for i in range(1,size)]
-        , [1 for i in range(1,size)]
-        , [n[0] for n in top_spec]
-    )
-    #print([d for d in data])
-    bulk_insert(NodeNgram, ['node_id', 'ngram_id', 'weight'], [d for d in data])
+    new_miam = miam - stop
+    new_miam.save(miam_node.id)
 
+#    data = zip(
+#        [stop_node.id for i in range(0,size)]
+#        , [ngram[0] for ngram in ngrams_to_stop]
+#        , [-1 for i in range(0,size)]
+#    )
+#    bulk_insert(NodeNgram, ['node_id', 'ngram_id', 'weight'], [d for d in data])
 
-#corpus=session.query(Node).filter(Node.id==244250).first()
-#computeMiam(corpus)
 
+#corpus=session.query(Node).filter(Node.id==545461).first()
+#compute_stop(corpus)
 
 
 

ngram/tools.py

@@ -28,8 +28,6 @@ def insert_ngrams(ngrams,get='terms-id'):
             %s AS ngram
         WHERE
             tmp__ngram.terms = ngram.terms
-        AND
-            tmp__ngram.n = ngram.n
             ''' % (Ngram.__table__.name,))
     
     cursor.execute('''
@@ -67,7 +65,6 @@ def insert_ngrams(ngrams,get='terms-id'):
     db.commit()
     return(ngram_ids)
 
-
 def insert_nodengramngram(nodengramngram):
     db, cursor = get_cursor()
     

parsing/corpustools.py

@@ -177,6 +177,8 @@ def parse_resources(corpus, user=None, user_id=None):
 
 # ngrams extraction
 from .NgramsExtractors import EnglishNgramsExtractor, FrenchNgramsExtractor, NgramsExtractor
+from nltk.tokenize import word_tokenize, wordpunct_tokenize, sent_tokenize
+
 class NgramsExtractors(defaultdict):
     def __init__(self):
         # English
@@ -201,7 +203,7 @@ class NgramsExtractors(defaultdict):
 
 ngramsextractors = NgramsExtractors()
 
-def extract_ngrams(corpus, keys):
+def extract_ngrams(corpus, keys, nlp=True):
     dbg = DebugTime('Corpus #%d - ngrams' % corpus.id)
     default_language_iso2 = None if corpus.language_id is None else cache.Language[corpus.language_id].iso2
     # query the hyperdata associated with the given keys
@@ -220,7 +222,7 @@ def extract_ngrams(corpus, keys):
 
     ngrams_data = set()
     ngrams_language_data = set()
-    ngrams_tag_data = set()
+    #ngrams_tag_data = set()
 
     node_ngram_list = defaultdict(lambda: defaultdict(int))
     for nodeinfo in hyperdata_query:
@@ -237,17 +239,25 @@ def extract_ngrams(corpus, keys):
         ngramsextractor = ngramsextractors[language_iso2]
         for text in nodeinfo[2:]:
             if text is not None and len(text):
-                ngrams = ngramsextractor.extract_ngrams(text.replace("[","").replace("]",""))
+                if nlp == True:
+                    ngrams = ngramsextractor.extract_ngrams(text.replace("[","").replace("]",""))
+                else:
+                    ngrams = wordpunct_tokenize(text.lower())
+
                 for ngram in ngrams:
-                    n = len(ngram)
-                    terms    = ' '.join([token for token, tag in ngram]).lower()
+                    if nlp == True:
+                        n = len(ngram)
+                        terms    = ' '.join([token for token, tag in ngram]).lower()
+                    else:
+                        terms = ngram
+                        n = 1
                     # TODO BUG here
-                    if n == 1:
+                    #if n == 1:
                         #tag_id   = cache.Tag[ngram[0][1]].id
-                        tag_id   =  1
+                    #    tag_id   =  1
                         #print('tag_id', tag_id)
-                    elif n > 1:
-                        tag_id   =  1
+                    #elif n > 1:
+                    #    tag_id   =  1
                         #tag_id   = cache.Tag[ngram[0][1]].id
                         #tag_id   = cache.Tag['NN'].id
                         #tag_id   =  14
@@ -255,7 +265,7 @@ def extract_ngrams(corpus, keys):
                     node_ngram_list[node_id][terms] += 1
                     ngrams_data.add((terms[:255],n))
                     ngrams_language_data.add((terms, language_id))
-                    ngrams_tag_data.add((terms, tag_id))
+                    #ngrams_tag_data.add((terms, tag_id))
 
     # insert ngrams to temporary table
     dbg.show('find ids for the %d ngrams' % len(ngrams_data))
@@ -263,12 +273,12 @@ def extract_ngrams(corpus, keys):
     ngram_ids = insert_ngrams(ngrams_data)
 
     dbg.show('insert associations')
-    node_ngram_data = list()
+    node_ngram_data = set()
     for node_id, ngrams in node_ngram_list.items():
         for terms, weight in ngrams.items():
             try:
                 ngram_id = ngram_ids[terms]
-                node_ngram_data.append((node_id, ngram_id, weight, ))
+                node_ngram_data.add((node_id, ngram_id, weight, ))
             except Exception as e:
                 print("err01:",e)
     bulk_insert(Node_Ngram, ['node_id', 'ngram_id', 'weight'], node_ngram_data, cursor=cursor)

rest_v1_0/graph.py

@@ -21,19 +21,21 @@ class Graph(APIView):
         
         format_   =  request.GET.get('format', 'json')
         type_    = request.GET.get('type', 'node_link')
+        apax    = request.GET.get('apax', 2)
         
 
         corpus = session.query(Node).filter(Node.id==corpus_id).first()
         
         accepted_field1 = ['ngrams', 'journal', 'source', 'authors']
         accepted_field2 = ['ngrams',]
+        options = ['start', 'end', 'apax']
         
         if field1 in accepted_field1 :
             if field2 in accepted_field2 :
                 if start is not None and end is not None :
-                    data = get_cooc(corpus=corpus,field1=field1, field2=field2, start=start, end=end)
+                    data = get_cooc(corpus=corpus,field1=field1, field2=field2, start=start, end=end, apax=apax)
                 else:
-                    data = get_cooc(corpus=corpus,field1=field1, field2=field2)
+                    data = get_cooc(corpus=corpus,field1=field1, field2=field2, apax=apax)
                 if format_ == 'json':
                     return JsonHttpResponse(data)
         else:
@@ -41,4 +43,5 @@ class Graph(APIView):
                 'Warning USAGE' : 'One field for each range:'
                 , 'field1' : accepted_field1
                 , 'field2' : accepted_field2
+                , 'options': options
                 })