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

MatInit.py

+# Without this, we couldn't use the Django environment
+
+import os
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "gargantext_web.settings")
+os.environ.setdefault("DJANGO_HSTORE_GLOBAL_REGISTER", "False")
+
+
+# We're gonna use all the models!
+
+from node.models import *
+
+
+# Node.objects.get(id=26514).children.all().make_metadata_filterable()
+# exit()
+
+
+# Reset: all data
+
+tables_to_empty = [
+    Node,
+    Node_Metadata,
+    Metadata,
+    NodeType,
+    ResourceType,
+    Resource,
+]
+for table in tables_to_empty:
+    print('Empty table "%s"...' % (table._meta.db_table, ))
+    table.objects.all().delete()
+
+
+# Integration: metadata types
+
+print('Initialize metadata...')
+metadata = {
+    'publication_date': 'datetime',
+    'authors': 'string',
+    'language_fullname': 'string',
+    'abstract': 'text',
+    'title': 'string',
+    'source': 'string',
+    'volume': 'string',
+    'text': 'text',
+    'date': 'datetime',
+    'page': 'string',
+    'doi': 'string',
+    'journal': 'string',
+}
+for name, type in metadata.items():
+    Metadata(name=name, type=type).save()
+
+
+# Integration: languages
+
+print('Initialize languages...')
+import pycountry
+Language.objects.all().delete()
+for language in pycountry.languages:
+    if 'alpha2' in language.__dict__:
+        Language(
+            iso2 = language.alpha2,
+            iso3 = language.bibliographic,
+            fullname = language.name,
+            implemented = 1 if language.alpha2 in ['en', 'fr'] else 0,
+        ).save()
+
+english = Language.objects.get(iso2='en')
+french  = Language.objects.get(iso2='fr')
+
+
+# Integration: users
+
+print('Initialize users...')
+try:
+    me = User.objects.get(username='mat')
+except:
+    me = User(username='mat')
+    me.save()
+
+
+# Integration: node types
+
+print('Initialize node types...')
+try:
+    typeProject = NodeType.objects.get(name='Project')
+except Exception as error:
+    print(error)
+    typeProject = NodeType(name='Project')
+    typeProject.save()  
+
+try:
+    typeCorpus  = NodeType.objects.get(name='Corpus')
+except Exception as error:
+    print(error)
+    typeCorpus  = NodeType(name='Corpus')
+    typeCorpus.save()
+    
+try:
+    typeDoc     = NodeType.objects.get(name='Document')
+except Exception as error:
+    print(error)
+    typeDoc     = NodeType(name='Document')
+    typeDoc.save()
+
+
+# Integration: resource types
+
+print('Initialize resource...')
+try:
+    typePubmed = ResourceType.objects.get(name='pubmed')
+    typeIsi    = ResourceType.objects.get(name='isi')
+    typeRis    = ResourceType.objects.get(name='ris')
+    typePresse = ResourceType.objects.get(name='europress')
+
+except Exception as error:
+    print(error)
+    
+    typePubmed = ResourceType(name='pubmed')
+    typePubmed.save()  
+    
+    typeIsi    = ResourceType(name='isi')
+    typeIsi.save()
+    
+    typeRis    = ResourceType(name='ris')
+    typeRis.save()
+    
+    typePresse = ResourceType(name='europress')
+    typePresse.save()
+
+
+# Integration: project
+
+print('Initialize project...')
+try:
+    project = Node.objects.get(name='Bees project')
+except:
+    project = Node(name='Bees project', type=typeProject, user=me)
+    project.save()
+
+
+# Integration: corpus
+
+print('Initialize corpus...')
+try:
+    corpus_pubmed = Node.objects.get(name='PubMed corpus')
+except:
+    corpus_pubmed = Node(parent=project, name='PubMed corpus', type=typeCorpus, user=me)
+    corpus_pubmed.save()
+
+print('Initialize resource...')
+corpus_pubmed.add_resource(
+    # file='./data_samples/pubmed.zip',
+    file='./data_samples/pubmed_2013-04-01_HoneyBeesBeeBees.xml',
+    type=typePubmed,
+    user=me
+)
+
+for resource in corpus_pubmed.get_resources():
+    print('Resource #%d - %s - %s' % (resource.id, resource.digest, resource.file))
+    
+print('Parse corpus #%d...' % (corpus_pubmed.id, ))
+corpus_pubmed.parse_resources(verbose=True)
+print('Extract corpus #%d...' % (corpus_pubmed.id, ))
+corpus_pubmed.children.all().extract_ngrams(['title',])
+print('Parsed corpus #%d.' % (corpus_pubmed.id, ))
+
+exit()
\ No newline at end of file

analysis/functions.py

@@ -11,7 +11,7 @@ def create_blacklist(user, corpus):
 def create_synonymes(user, corpus):
     pass
 
-def create_whitelist(user, corpus):
+def create_whitelist(user, corpus, size=100):
     cursor = connection.cursor()
     
     try:
@@ -60,16 +60,16 @@ def create_whitelist(user, corpus):
         ORDER BY
             occurrences DESC
         LIMIT
-            100
+            %d
         ;
-    """  % (white_list.id, corpus.id, type_document.id)
+    """  % (white_list.id, corpus.id, type_document.id, size)
 
     cursor.execute(query_whitelist)
 
     return white_list
 
 #def create_cooc(user, corpus, whitelist, blacklist, synonymes):
-def create_cooc(user=None, corpus=None, whitelist=None, size=400):
+def create_cooc(user=None, corpus=None, whitelist=None, size=150):
     cursor = connection.cursor()
 
     try:
@@ -133,7 +133,7 @@ def create_cooc(user=None, corpus=None, whitelist=None, size=400):
     cursor.execute(query_cooc)
     return cooc
 
-def get_cooc(request=None, corpus_id=None, cooc_id=None, type="node_link"):
+def get_cooc(request=None, corpus_id=None, cooc_id=None, type="node_link", n=150):
     import pandas as pd
     from copy import copy
     import numpy as np
@@ -152,9 +152,9 @@ def get_cooc(request=None, corpus_id=None, cooc_id=None, type="node_link"):
 
     if Node.objects.filter(type=type_cooc, parent=corpus).first() is None:
         print("Coocurrences do not exist yet, create it.")
-        whitelist = create_whitelist(request.user, corpus)
-        cooccurrence_node = create_cooc(user=request.user, corpus=corpus, whitelist=whitelist)
-        print(cooccurrence_matrix.id, "Cooc created")
+        whitelist = create_whitelist(request.user, corpus, size=n)
+        cooccurrence_node = create_cooc(user=request.user, corpus=corpus, whitelist=whitelist, size=n)
+        print(cooccurrence_node.id, "Cooc created")
     else:
         cooccurrence_node = Node.objects.filter(type=type_cooc, parent=corpus).first()
 
@@ -177,7 +177,7 @@ def get_cooc(request=None, corpus_id=None, cooc_id=None, type="node_link"):
     threshold = min(x.max(axis=1))
     matrix_filtered = np.where(x >= threshold, 1, 0)
     #matrix_filtered = np.where(x > threshold, x, 0)
-    
+    #matrix_filtered = matrix_filtered.resize((90,90))
     G = nx.from_numpy_matrix(matrix_filtered)
     G = nx.relabel_nodes(G, dict(enumerate([ labels[label] for label in list(df.columns)])))
     #G = nx.relabel_nodes(G, dict(enumerate(df.columns)))
@@ -189,22 +189,37 @@ def get_cooc(request=None, corpus_id=None, cooc_id=None, type="node_link"):
 
     partition = best_partition(G)
     
-    for node in G.nodes():
-        try:
-            #node,type(labels[node])
-            G.node[node]['label']   = node
-            G.node[node]['name']    = node
-            G.node[node]['size']    = weight[node]
-            G.node[node]['group']   = partition[node]
-#            G.node[node]['color'] = '19,180,300'
-            G.add_edge(node, partition[node], weight=3)
-        except Exception as error:
-            print(error)
-    
+        
     if type == "node_link":
+        for node in G.nodes():
+            try:
+                #node,type(labels[node])
+                G.node[node]['label']   = node
+                G.node[node]['name']    = node
+                G.node[node]['size']    = weight[node]
+                G.node[node]['group']   = partition[node]
+                #G.add_edge(node, partition[node], weight=3)
+#            G.node[node]['color'] = '19,180,300'
+            except Exception as error:
+                print(error)
+
         data = json_graph.node_link_data(G)
+    
     elif type == "adjacency":
-        data = json_graph.adjacency_data(G)
+        for node in G.nodes():
+            try:
+                #node,type(labels[node])
+                #G.node[node]['label']   = node
+                G.node[node]['name']    = node
+                #G.node[node]['size']    = weight[node]
+                G.node[node]['group']   = partition[node]
+                #G.add_edge(node, partition[node], weight=3)
+#            G.node[node]['color'] = '19,180,300'
+            except Exception as error:
+                print(error)
+        data = json_graph.node_link_data(G)
+     
+
 #    data = json_graph.node_link_data(G, attrs={\
 #            'source':'source',\
 #            'target':'target',\

gargantext_web/settings.py

@@ -68,6 +68,8 @@ INSTALLED_APPS = (
     'ngram',
     'django_hstore',
     'djcelery',
+    'aldjemy',
+    'rest_framework',
 )
 
 MIDDLEWARE_CLASSES = (

gargantext_web/urls.py

@@ -35,19 +35,21 @@ urlpatterns = patterns('',
     # Getting data
     url(r'^chart/corpus/(\d+)/data.csv$', views.send_csv),
     url(r'^corpus/(\d+)/node_link.json$', views.node_link),
-    url(r'^corpus/(\d+)/adjacency.json$', views.adjacency),
+    url(r'^corpus/(\d+)/adjacency.json$', views.node_link),
+
+    url(r'^api$', gargantext_web.api.Root),
+    url(r'^api/nodes/(\d+)/children/metadata$', gargantext_web.api.NodesChildrenMetatadata.as_view()),
+    url(r'^api/nodes/(\d+)/children/queries$', gargantext_web.api.NodesChildrenQueries.as_view()),
     
-    # REST views
     url(r'^api/nodes$', gargantext_web.api.NodesController.get),
-    url(r'^api/corpus/(\d+)/ngrams$', gargantext_web.api.CorpusController.ngrams),
-    url(r'^api/corpus/(\d+)/metadata$', gargantext_web.api.CorpusController.metadata),
-    url(r'^api/corpus/(\d+)/data$', gargantext_web.api.CorpusController.data),
-    
-    # Tests (to be removed soon)
+    url(r'^api/nodes/(\d+)/ngrams$', gargantext_web.api.CorpusController.ngrams),
+    url(r'^api/nodes/(\d+)/data$', gargantext_web.api.CorpusController.data),
+
     url(r'^graph-it$', views.graph_it),
     url(r'^ngrams$', views.ngrams),
 )
 
+
 from django.conf import settings
 if settings.DEBUG:
     urlpatterns += patterns('',

gargantext_web/views.py

@@ -367,7 +367,6 @@ def corpus(request, project_id, corpus_id):
     
     return HttpResponse(html)
 
-
 def delete_project(request, node_id):
     Node.objects.filter(id=node_id).all().delete()
     return HttpResponseRedirect('/projects/')

init/dependances.sh

@@ -30,3 +30,5 @@ sudo apt-get install libopenblas-dev
 sudo apt-get install liblapack-dev
 
 
+source /srv/gargantext_env/bin/activate
+pip install git+https://github.com/mathieurodic/aldjemy.git

init/requirements.txt

@@ -6,7 +6,7 @@ Pillow==2.5.3
 Pygments==1.6
 SQLAlchemy==0.9.8
 South==1.0
-aldjemy==0.3.51
+aldjemy==0.3.10
 amqp==1.4.6
 anyjson==0.3.3
 billiard==3.3.0.18
@@ -26,13 +26,14 @@ django-hstore==1.3.1
 django-mptt==0.6.1
 django-nested-inlines==0.1
 django-treebeard==2.0
+djangorestframework==3.0.0
 graphviz==0.4
 ipython==2.2.0
 kombu==3.0.23
 lxml==3.3.6
-#matplotlib==1.4.0
+matplotlib==1.4.0
 networkx==1.9
-#nltk==3.0a4
+nltk==3.0a4
 nose==1.3.4
 numpy==1.8.2
 pandas==0.14.1

node/models.py

@@ -75,6 +75,23 @@ class NodeQuerySet(CTENodeManager.CTEQuerySet):
             ngramscaches = NgramsCaches()
         for node in self:
             node.extract_ngrams(keys, ngramsextractorscache, ngramscaches)
+
+    def make_metadata_filterable(self):
+        metadata_cache = {metadata.name: metadata for metadata in Metadata.objects.all()}
+        data = []
+        for node in self:
+            print(node.id)
+            for key, value in node.metadata.items():
+                if key in metadata_cache:
+                    metadata = metadata_cache[key]
+                    if metadata.type == 'string':
+                        value = value[:255]
+                    data.append(Node_Metadata(**{
+                        'node_id' : node.id,
+                        'metadata_id' : metadata.id,
+                        ('value_'+metadata.type) : value,
+                    }))
+        Node_Metadata.objects.bulk_create(data)
     
 class NodeManager(CTENodeManager):
     """Methods available from Node.object."""
@@ -85,6 +102,10 @@ class NodeManager(CTENodeManager):
         if name.startswith("_"): 
             raise AttributeError
         return getattr(self.get_queryset(), name, *args)
+
+class Metadata(models.Model):
+    name        = models.CharField(max_length=32, db_index=True)
+    type        = models.CharField(max_length=16, db_index=True)
         
 class Node(CTENode):
     """The node."""
@@ -137,7 +158,7 @@ class Node(CTENode):
         return resource
     
     @current_app.task(filter=task_method)
-    def parse_resources(self):
+    def parse_resources(self, verbose=False):
         # parse all resources into a list of metadata
         metadata_list = []
         for node_resource in self.node_resource.filter(parsed=False):
@@ -151,22 +172,33 @@ class Node(CTENode):
                 'europress_english' : EuropressFileParser,
             })[resource.type.name]()
             metadata_list += parser.parse(str(resource.file))
-        # insert the new resources in the database!
-        type = NodeType.objects.get(name='Document')
+        # retrieve info from the database
+        type_id = NodeType.objects.get(name='Document').id
         langages_cache = LanguagesCache()
-        Node.objects.bulk_create([
+        user_id = self.user.id
+        # insert the new resources in the database!
+        for i, metadata_values in enumerate(metadata_list):
+            if verbose:
+                print(i, end='\r', flush=True)
+            name = metadata_values.get('title', '')[:200]
+            language = langages_cache[metadata_values['language_iso2']] if 'language_iso2' in metadata_values else None,
+            if isinstance(language, tuple):
+                language = language[0]
             Node(
-                user        = self.user,
-                type        = type,
-                name        = metadata['title'][0:199] if 'title' in metadata else '',
-                parent      = self,
-                language    = langages_cache[metadata['language_iso2']] if 'language_iso2' in metadata else None,
-                metadata    = metadata,
-            )
-            for metadata in metadata_list
-        ])
+                user_id  = user_id,
+                type_id  = type_id,
+                name     = name,
+                parent   = self,
+                language_id = language.id if language else None,
+                metadata = metadata_values
+            ).save()
+
+        # make metadata filterable
+        self.children.all().make_metadata_filterable()
+
         # mark the resources as parsed for this node
         self.node_resource.update(parsed=True)
+
     
     @current_app.task(filter=task_method)
     def extract_ngrams(self, keys, ngramsextractorscache=None, ngramscaches=None):
@@ -203,6 +235,15 @@ class Node(CTENode):
             for ngram_text, weight in associations.items()
         ])
 
+class Node_Metadata(models.Model):
+    node        = models.ForeignKey(Node)
+    metadata    = models.ForeignKey(Metadata)
+    value_int   = models.IntegerField(null=True, db_index=True)
+    value_float = models.FloatField(null=True, db_index=True)
+    value_string = models.CharField(max_length=255, null=True, db_index=True)
+    value_datetime  = models.DateTimeField(null=True, db_index=True)
+    value_text  = models.TextField(null=True)
+
 class Node_Resource(models.Model):
     node     = models.ForeignKey(Node, related_name='node_resource')
     resource = models.ForeignKey(Resource)

parsing/Caches.py

@@ -75,9 +75,10 @@ class LanguagesCache(defaultdict):
                 self[str(language.iso2.lower())] = language
                 self[str(language.iso3.lower())] = language
                 self[str(language.fullname.lower())] = language
-        betterKey = key.strip().lower()
-        self[key] = self[betterKey] if betterKey in self.keys() else None
-        return self[betterKey]
+        if key not in self.keys():
+            betterKey = key.strip().lower()
+            self[key] = self[betterKey] if betterKey in self.keys() else None
+        return self[key]
 
 
 

static/img/logo.svg

+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+
+<svg
+   xmlns:dc="http://purl.org/dc/elements/1.1/"
+   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+   xmlns:svg="http://www.w3.org/2000/svg"
+   xmlns="http://www.w3.org/2000/svg"
+   xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
+   xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
+   width="48px"
+   height="48px"
+   id="svg4362"
+   version="1.1"
+   inkscape:version="0.48.5 r10040"
+   sodipodi:docname="logo.svg">
+  <defs
+     id="defs4364" />
+  <sodipodi:namedview
+     id="base"
+     pagecolor="#ffffff"
+     bordercolor="#666666"
+     borderopacity="1.0"
+     inkscape:pageopacity="0.0"
+     inkscape:pageshadow="2"
+     inkscape:zoom="5.6897594"
+     inkscape:cx="-11.235831"
+     inkscape:cy="3.8560006"
+     inkscape:current-layer="layer1"
+     showgrid="true"
+     inkscape:grid-bbox="true"
+     inkscape:document-units="px"
+     inkscape:window-width="1360"
+     inkscape:window-height="762"
+     inkscape:window-x="0"
+     inkscape:window-y="0"
+     inkscape:window-maximized="0" />
+  <metadata
+     id="metadata4367">
+    <rdf:RDF>
+      <cc:Work
+         rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type
+           rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
+        <dc:title></dc:title>
+      </cc:Work>
+    </rdf:RDF>
+  </metadata>
+  <g
+     id="layer1"
+     inkscape:label="Layer 1"
+     inkscape:groupmode="layer">
+    <rect
+       style="fill:#fffcfc;fill-opacity:1;stroke:none"
+       id="rect3755"
+       width="29.70249"
+       height="31.108515"
+       x="0"
+       y="-0.1566938"
+       inkscape:export-filename="/srv/gargantext/static/img/logo.png"
+       inkscape:export-xdpi="53"
+       inkscape:export-ydpi="53" />
+    <g
+       inkscape:export-ydpi="53.799999"
+       inkscape:export-xdpi="53.799999"
+       inkscape:export-filename="/srv/gargantext/static/img/logo.png"
+       style="fill:#ff8080;fill-opacity:0.82014388"
+       id="g3835"
+       transform="matrix(0.2422549,0,0,0.23374214,-49.789462,-7.9055988)">
+      <path
+         inkscape:export-ydpi="100"
+         inkscape:export-xdpi="100"
+         inkscape:export-filename="/home/alexandre/projets/gargantext.py/gargantext_core/shared/LogoSimple.png"
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+         style="font-size:166.11251831px;font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;text-align:center;line-height:125%;letter-spacing:0px;word-spacing:0px;writing-mode:lr-tb;text-anchor:middle;fill:#ff8080;fill-opacity:0.82014388;stroke:none;font-family:Bitstream Charter;-inkscape-font-specification:Bitstream Charter"
+         inkscape:connector-curvature="0" />
+      <path
+         inkscape:export-ydpi="100"
+         inkscape:export-xdpi="100"
+         transform="translate(611.62306,-400.10238)"
+         sodipodi:open="true"
+         sodipodi:end="6.1660663"
+         sodipodi:start="0"
+         d="m -312.87112,480.17926 c 0,4.97881 -4.03612,9.01493 -9.01493,9.01493 -4.97881,0 -9.01493,-4.03612 -9.01493,-9.01493 0,-4.97881 4.03612,-9.01493 9.01493,-9.01493 4.57131,0 8.41901,3.42153 8.95317,7.96152"
+         sodipodi:ry="9.0149298"
+         sodipodi:rx="9.0149298"
+         sodipodi:cy="480.17926"
+         sodipodi:cx="-321.88605"
+         id="path3839"
+         style="fill:#ff8080;fill-opacity:0.82014388;stroke:none"
+         sodipodi:type="arc" />
+    </g>
+  </g>
+</svg>

templates/corpus.html

@@ -116,9 +116,9 @@
 						<div class="jumbotron">
 								<h3><a href="/ngrams">Dictionaries</a></h3>
 						<ol>
-								<li>White Lists</li>
-								<li>Black Lists</li>
 								<li>Synonyms</li>
+								<li>Black Lists</li>
+								<li>White Lists</li>
 						</ol>
 						</div>
 				</div>
@@ -129,7 +129,7 @@
 						<ol>
 								<li><a href="/corpus/{{ corpus.id }}/matrix">Adjacency matrix</a></li>
 								<li><a href="/corpus/{{ corpus.id }}/explorer">Static maps</a></li>
-								<li>Dynamics maps</li>
+								<li>Dynamic maps</li>
 						</ol>
 						</div>
 				</div>

templates/matrix.html

@@ -33,7 +33,9 @@ text.active {
         </div>
 </div>
 
-<div id="graphid" style="visibility: hidden;">/corpus/{{ corpus.id }}/node_link.json</div>
+
+<div class="container">
+<div id="graphid" style="visibility: hidden;">/corpus/{{ corpus.id }}/adjacency.json</div>
 
 
 <script src="{% static "js/jquery/jquery.min.js" %}" type="text/javascript"></script>
@@ -46,6 +48,8 @@ text.active {
 </select>
 </p>
 
+</div>
+
 <script>
 
 var margin = {top: 80, right: 0, bottom: 10, left: 80},

templates/menu.html

@@ -6,6 +6,7 @@
 
 </head>
 
+{% load staticfiles %}
 <body>
 <!-- Fixed navbar -->
     <div id="dafixedtop" class="navbar navbar-inverse navbar-fixed-top" role="navigation">
@@ -16,7 +17,7 @@
             <span class="icon-bar"></span>
             <span class="icon-bar"></span>
           </button>
-          <a class="navbar-brand" href="/">Gargantext</a>
+					<a class="navbar-brand" style="line-height:15px; height:10px; padding: 10px 10px;" href="/"><img src="{% static "img/logo.svg" %}"></a>
         </div>
         
         <div class="navbar-collapse collapse">