Merge remote-tracking branch 'origin/romain-testing' into testing

annotations/static/annotations/document.js

@@ -15,7 +15,7 @@
         {'docId': $rootScope.docId},
         function(data, responseHeaders) {
           $scope.authors = data.authors;
-          $scope.journal = data.journal;
+          $scope.source = data.source;
           $scope.publication_date = data.publication_date;
           //$scope.current_page_number = data.current_page_number;
           //$scope.last_page_number = data.last_page_number;
@@ -23,25 +23,34 @@
           $rootScope.docId = data.id;
           $rootScope.full_text = data.full_text;
           $rootScope.abstract_text = data.abstract_text;
-          console.log("annotations.document.DocController.getannotations")
-          // GET the annotationss
-          NgramListHttpService.get(
-            {
-              'corpusId': $rootScope.corpusId,
-              'docId': $rootScope.docId
-            },
-            function(data) {
-              $rootScope.annotations = data[$rootScope.corpusId.toString()][$rootScope.docId.toString()];
-              // eg id => 'MAPLIST'
-              $rootScope.lists = data[$rootScope.corpusId.toString()].lists;
-              // inverted 'MAPLIST' => id
-              $rootScope.listIds = _.invert($rootScope.lists)
-              $scope.dataLoading = false ;
-            },
-            function(data) {
-              console.error("unable to get the list of ngrams");
-            }
-          );
+          $rootScope.workflow_finished = data.corpus_status['complete'] ;
+
+          console.log("workflow status", $rootScope.workflow_finished)
+
+          if ($scope.workflow_finished) {
+            console.log("annotations.document.DocController.getannotations")
+            // GET the annotationss
+            NgramListHttpService.get(
+              {
+                'corpusId': $rootScope.corpusId,
+                'docId': $rootScope.docId
+              },
+              function(data) {
+                $rootScope.annotations = data[$rootScope.corpusId.toString()][$rootScope.docId.toString()];
+                // eg id => 'MAPLIST'
+                $rootScope.lists = data[$rootScope.corpusId.toString()].lists;
+                // inverted 'MAPLIST' => id
+                $rootScope.listIds = _.invert($rootScope.lists)
+                $scope.dataLoading = false ;
+              },
+              function(data) {
+                console.error("unable to get the list of ngrams");
+              }
+            );
+          }
+          else {
+            $scope.dataLoading = false ;
+          }
 
       });
 

annotations/templates/annotations/main.html

@@ -24,7 +24,7 @@
     <div id="annotationsApp" ng-cloak>
       <div class="container-fluid">
         <div class="row-fluid main-panel" ng-controller="NGramHighlightController">
-          <div class="col-md-4 col-xs-4 tabbable words-panel">
+          <div ng-if="workflow_finished" class="col-md-4 col-xs-4 tabbable words-panel">
               <div class="list-selector">
                 <h5>Select highlighted list(s)
                 <select class="selectpicker" multiple ng-change="activeListsChange()" ng-model="lists" ng-controller="ActiveListsController">
@@ -89,7 +89,7 @@
             </div>
             <div class="row-fluid">
               <ul class="list-group clearfix">
-                <li class="list-group-item small"><span class="badge">journal</span>{[{journal}]}</li>
+                <li class="list-group-item small"><span class="badge">source</span>{[{source}]}</li>
                 <li class="list-group-item small"><span class="badge">authors</span>{[{authors}]}</li>
                 <li class="list-group-item small"><span class="badge">date</span>{[{publication_date}]}</li>
               </ul>
@@ -108,12 +108,14 @@
                 <span class="badge">abstract</span>
             </div>
             <p id="abstract-text" class="text-container">
+                {[{abstract_text}]}
                 <div ng-if="abstract_text == null" class="alert alert-info small" role="alert">Empty abstract text</div>
             </p>
             <div ng-if="full_text != null">
                 <span class="badge">full article</span>
             </div>
             <p id="full-text" class="text-container">
+                {[{full_text}]}
                 <div ng-if="full_text == null" class="alert alert-info small" role="alert">Empty full text</div>
             </p>
           </div>

annotations/views.py

@@ -172,8 +172,9 @@ 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()
+        corpus = session.query(Node).filter(Node.id == node.parent_id).first()
+        corpus_workflow_status = corpus.hyperdata['statuses'][0]
         if node is None:
             raise APIException('This node does not exist', 404)
 
@@ -185,9 +186,10 @@ class Document(APIView):
             pub_date = node.hyperdata.get('publication_date')
 
         data = {
+            'corpus_status': corpus_workflow_status,
             'title': node.hyperdata.get('title'),
             'authors': node.hyperdata.get('authors'),
-            'journal': node.hyperdata.get('journal'),
+            'source': node.hyperdata.get('source'),
             'publication_date': pub_date,
             'full_text': node.hyperdata.get('full_text'),
             'abstract_text': node.hyperdata.get('abstract'),

gargantext/constants.py

@@ -382,6 +382,9 @@ BATCH_NGRAMSEXTRACTION_SIZE = 3000   # how many new node-ngram relations before
 QUERY_SIZE_N_MAX     = 1000
 QUERY_SIZE_N_DEFAULT = 1000
 
+# Refresh corpora workflow status for project view's progressbar
+PROJECT_VIEW_REFRESH_INTERVAL  = 3000     # 1st refresh in ms (then increasing arithmetically)
+PROJECT_VIEW_MAX_REFRESH_ATTEMPTS = 10    # how many times before we give up
 
 # ------------------------------------------------------------------------------
 # Graph <=> nodes API parameters

gargantext/util/db_cache.py

@@ -46,6 +46,9 @@ class ModelCache(dict):
 class Cache:
 
     def __getattr__(self, key):
+        '''
+        lazy init of new modelcaches: self.Node, self.User...
+        '''
         try:
             model = getattr(models, key)
         except AttributeError:
@@ -54,4 +57,15 @@ class Cache:
         setattr(self, key, modelcache)
         return modelcache
 
+
+    def clean_all(self):
+        '''
+        re-init any existing modelcaches
+        '''
+        for modelname in self.__dict__:
+            old_modelcache = getattr(cache, modelname)
+            new_modelcache = ModelCache(old_modelcache._model)
+            del old_modelcache
+            setattr(cache, modelname, new_modelcache)
+
 cache = Cache()

gargantext/util/http.py

@@ -32,6 +32,10 @@ def requires_auth(func):
             from gargantext.util.db import session
             session.rollback()
             print("=== session rollback ok!")
+            # re init the global cache (it must still have detached instances)
+            from gargantext.util.db_cache import cache
+            cache.clean_all()
+            print("=== cache reinit ok!")
             # and relogin for safety
             url = '/auth/login/?next=%s' % urlencode(request.path)
             return redirect(url)

gargantext/util/toolchain/ngrams_addition.py

@@ -23,6 +23,8 @@ from gargantext.util.db  import bulk_insert_ifnotexists # £TODO debug
 from sqlalchemy          import distinct
 from re                  import findall, IGNORECASE
 
+from gargantext.util.toolchain.main import t   # timer
+
 # TODO from gargantext.constants import LIST_OF_KEYS_TO_INDEX = title, abstract
 
 def index_new_ngrams(ngram_ids, corpus, keys=('title', 'abstract', )):
@@ -40,6 +42,8 @@ def index_new_ngrams(ngram_ids, corpus, keys=('title', 'abstract', )):
     @param corpus: the CORPUS node
 
     @param keys: the hyperdata fields to index
+
+    # FIXME too slow: index_new_ngrams should be faster via tsvector on DB
     """
 
     # retrieve *all* the ngrams from our list
@@ -56,7 +60,11 @@ def index_new_ngrams(ngram_ids, corpus, keys=('title', 'abstract', )):
     node_ngram_to_write = {}
 
     # loop throught the docs and their text fields
-    for doc in corpus.children('DOCUMENT'):
+    for (i, doc) in enumerate(corpus.children('DOCUMENT')):
+
+        if (i % 100 == 0):
+            print('CORPUS #%d: [%s] ngrams_addition: doc %i' % (corpus.id, t(), i))
+            print()
 
         # a new empty counting subdict
         node_ngram_to_write[doc.id] = {}

gargantext/views/api/ngramlists.py

@@ -373,6 +373,10 @@ class ListChange(APIView):
     def put(self, request):
         """
         Adds one or more ngrams to a list.
+
+        NB: we assume ngram_ids don't contain subforms !!
+            (this assumption is not checked here because it would be
+             slow: if you want to add a subform, send the mainform's id)
         """
         # union of items ----------------------------
         new_list = self.base_list + self.change_list

gargantext/views/api/nodes.py

@@ -17,7 +17,11 @@ _node_available_fields = ['id', 'parent_id', 'name', 'typename', 'hyperdata', 'n
 _node_default_fields = ['id', 'parent_id', 'name', 'typename']
 _node_available_types = NODETYPES
 
-#_hyperdata_available_fields = ['title', 'resourcetype']
+_hyperdata_available_fields = ['title', 'source', 'abstract', 'statuses',
+                               'language_name', 'language_iso3','language_iso2','language_id',
+                               'publication_date',
+                               'publication_year','publication_month', 'publication_day',
+                               'publication_hour','publication_minute','publication_second']
 #_node_available_formats = ['json', 'csv', 'bibex']
 
 
@@ -32,24 +36,38 @@ def _query_nodes(request, node_id=None):
     # parameters validation
     # fixme: this validation does not allow custom keys in url (eg '?name=' for rename action)
     parameters = get_parameters(request)
+
     parameters = validate(parameters, {'type': dict, 'items': {
         'formated': {'type': str, 'required' : False, 'default': 'json'},
-#        'hyperdata': {'type': list, 'default' : _hyperdata_available_fields, 'items': {
-#            'type': str, 'range' : _node_available_fields,
-#        }},
+
         'pagination_limit': {'type': int, 'default': 10},
         'pagination_offset': {'type': int, 'default': 0},
         'fields': {'type': list, 'default': _node_default_fields, 'items': {
             'type': str, 'range': _node_available_fields,
         }},
+        # choice of hyperdata fields
+        'hyperdata_filter': {'type': list, 'required':False,
+            'items': {
+                'type': str, 'range': _hyperdata_available_fields,
+            }},
         # optional filtering parameters
         'types': {'type': list, 'required': False, 'items': {
             'type': str, 'range': _node_available_types,
         }},
         'parent_id': {'type': int, 'required': False},
     }})
+
+    # debug
+    # print('PARAMS', parameters)
+
+    # additional validation for hyperdata_filter
+    if (('hyperdata_filter' in parameters)
+        and (not ('hyperdata' in parameters['fields']))):
+        raise ValidationException("Using the hyperdata_filter filter requires fields[]=hyperdata")
+
     # start the query
     query = user.nodes()
+
     # filter by id
     if node_id is not None:
         query = query.filter(Node.id == node_id)
@@ -63,6 +81,7 @@ def _query_nodes(request, node_id=None):
     count = query.count()
     # order
     query = query.order_by(Node.hyperdata['publication_date'], Node.id)
+
     # paginate the query
     if parameters['pagination_limit'] == -1:
         query = query[parameters['pagination_offset']:]
@@ -72,8 +91,54 @@ def _query_nodes(request, node_id=None):
             parameters['pagination_limit']
         ]
     # return the result!
+    # (the receiver function does the filtering of fields and hyperdata_filter)
     return parameters, query, count
 
+
+def _filter_node_fields(node, parameters):
+    """
+    Filters the properties of a Node object before sending them to response
+
+    @parameters: a dict comming from get_parameters
+                 that must only contain a 'fields' key
+
+    Usually the dict looks like this :
+               {'fields': ['parent_id', 'id', 'name', 'typename', 'hyperdata'],
+                'hyperdata_filter': ['title'], 'parent_id': '55054',
+                'types': ['DOCUMENT'], 'pagination_limit': '15'}
+
+    History:
+        1) this used to be single line:
+           res = {field: getattr(node, field) for field in parameters['fields']}
+
+        2) it was in both NodeResource.get() and NodeListResource.get()
+
+        3) it's now expanded to add support for parameters['hyperdata_filter']
+            - if absent, entire hyperdata is considered as one field
+                (as before)
+            - if present, the hyperdata subfields are picked
+                (new)
+    """
+    # FIXME all this filtering
+    #       could be done in rawsql
+    #       (in _query_nodes)
+
+    result = {}
+    for field in parameters['fields']:
+        # normal field or entire hyperdata
+        if field != 'hyperdata' or (not 'hyperdata_filter' in parameters):
+            result[field] = getattr(node,field)
+
+        # hyperdata if needs to be filtered
+        else:
+            this_filtered_hyp = {}
+            for hfield in parameters['hyperdata_filter']:
+                if hfield in node.hyperdata:
+                    this_filtered_hyp[hfield] = node.hyperdata[hfield]
+            result['hyperdata'] = this_filtered_hyp
+
+    return result
+
 class Status(APIView):
     '''API endpoint that represent the current status of the node'''
     renderer_classes = (JSONRenderer, BrowsableAPIRenderer)
@@ -84,17 +149,27 @@ class Status(APIView):
             return HttpResponse('Unauthorized', status=401)
 
         user = cache.User[request.user.id]
-        check_rights(request, node_id)
+        # check_rights(request, node_id)
+        # I commented check_rights because filter on user_id below does the job
+
         node = session.query(Node).filter(Node.id == node_id, Node.user_id== user.id).first()
         if node is None:
             return Response({"detail":"Node not Found for this user"}, status=HTTP_404_NOT_FOUND)
         else:
-            context = format_response(node, [n for n in node.children()])
+
+            # FIXME using the more generic strategy ---------------------------
+            # context = format_response(node, [n for n in node.children()])
+            # or perhaps ? context = format_response(None, [node])
+            # -----------------------------------------------------------------
+
+            # using a more direct strategy
+            context = {}
             try:
-                context["status"] = node.hyperdata["statuses"]
+               context["statuses"] = node.hyperdata["statuses"]
             except KeyError:
-                context["status"] = None
+               context["statuses"] = None
             return Response(context)
+
     def post(self, request, data):
         '''create a new status for node'''
         if not request.user.is_authenticated():
@@ -102,17 +177,17 @@ class Status(APIView):
             return HttpResponse('Unauthorized', status=401)
 
         raise NotImplementedError
-    
+
     def put(self, request, data):
         '''update status for node'''
-        
+
         if not request.user.is_authenticated():
             # can't use @requires_auth because of positional 'self' within class
             return HttpResponse('Unauthorized', status=401)
 
         user = cache.User[request.user.id]
-        check_rights(request, node_id)
-        node = session.query(Node).filter(Node.id == node_id).first()
+        # check_rights(request, node_id)
+        node = session.query(Node).filter(Node.id == node_id, Node.user_id== user.id).first()
 
         raise NotImplementedError
 
@@ -126,8 +201,8 @@ class Status(APIView):
             return HttpResponse('Unauthorized', status=401)
 
         user = cache.User[request.user.id]
-        check_rights(request, node_id)
-        node = session.query(Node).filter(Node.id == node_id).first()
+        # check_rights(request, node_id)
+        node = session.query(Node).filter(Node.id == node_id, Node.user_id == user.id).first()
         if node is None:
             return Response({"detail":"Node not Found"}, status=HTTP_404_NOT_FOUND)
         node.hyperdata["status"] = []
@@ -150,16 +225,22 @@ class NodeListResource(APIView):
         parameters, query, count = _query_nodes(request)
 
         if parameters['formated'] == 'json':
+            records_array = []
+            add_record = records_array.append
+
+            # FIXME filter in rawsql in _query_nodes
+            for node in query:
+                add_record(_filter_node_fields(node, parameters))
+
             return JsonHttpResponse({
                 'parameters': parameters,
                 'count': count,
-                'records': [
-                    { field: getattr(node, field) for field in parameters['fields'] }
-                    for node in query
-                ]
+                'records': records_array
             })
 
         elif parameters['formated'] == 'csv':
+            # TODO add support for fields and hyperdata_filter
+
             response = HttpResponse(content_type='text/csv')
             response['Content-Disposition'] = 'attachment; filename="Gargantext_Corpus.csv"'
 
@@ -305,9 +386,8 @@ class NodeResource(APIView):
         if not len(query):
             raise Http404()
         node = query[0]
-        return JsonHttpResponse({
-            field: getattr(node, field) for field in parameters['fields']
-        })
+
+        return JsonHttpResponse(_filter_node_fields(node, parameters))
 
     # contains a check on user.id (within _query_nodes)
     def delete(self, request, node_id):
@@ -415,11 +495,11 @@ class CorpusFavorites(APIView):
         (will test if docs 53 and 54 are among the favorites of corpus 2)
         (returns the intersection of fav docs with [53,54])
         """
-        
+
         if not request.user.is_authenticated():
             # can't use @requires_auth because of positional 'self' within class
             return HttpResponse('Unauthorized', status=401)
-        
+
         fav_node = self._get_fav_node(corpus_id)
 
         req_params = validate(

gargantext/views/pages/projects.py

@@ -54,6 +54,9 @@ def overview(request):
             # projects owned by the user's contacts
             'common_users': (contact for contact, projects in contacts_projects),
             'common_projects': sum((projects for contact, projects in contacts_projects), []),
+            # status refreshing params (when active workflows)
+            'status_refresh_initial_interval': PROJECT_VIEW_REFRESH_INTERVAL,
+            'status_refresh_max_attempts': PROJECT_VIEW_MAX_REFRESH_ATTEMPTS,
         },
     )
 

static/lib/gargantext/Docs_dyna_chart_and_table.js

@@ -592,7 +592,7 @@ function Main_test(Data) {
           // by default we always decide to search in the title
           matchInTexts = [record.rawtitle]
 
-          // if box is checked we'll also search in the abstracts
+          // if box is checked we'll also search in the abstracts (todo: via ajax)
           if (doAbstractsSearch) {
               if (typeof record.hyperdata.abstract !== 'undefined') {
                   matchInTexts.push(record.hyperdata.abstract)
@@ -630,9 +630,23 @@ function Main_test(Data) {
     MyTable.data('dynatable').sorts.functions["signatureSort"] = makeAlphaSortFunctionOnProperty('signature')
     MyTable.data('dynatable').sorts.functions["sourceSort"] = function sourceSort (rec1,rec2, attr, direction) {
         // like rawtitle but nested property
-        if (direction == 1) return rec1.hyperdata.source.localeCompare(rec2.hyperdata.source)
-        else                return rec2.hyperdata.source.localeCompare(rec1.hyperdata.source)
-    }
+        if (rec1.hyperdata && rec1.hyperdata.source
+            && rec2.hyperdata && rec2.hyperdata.source) {
+            // the alphabetic sort
+            if (direction == 1) return rec1.hyperdata.source.localeCompare(rec2.hyperdata.source)
+            else                return rec2.hyperdata.source.localeCompare(rec1.hyperdata.source)
+        }
+        else if (rec1.hyperdata && rec1.hyperdata.source) {
+            cmp = direction
+        }
+        else if (rec2.hyperdata && rec2.hyperdata.source) {
+            cmp = -direction
+        }
+        else {
+          cmp = 0
+        }
+        if (cmp == 0)       cmp = RecDict[rec1.id] < RecDict[rec2.id] ? -1 : 1
+      }
 
     // hook on page change
     MyTable.bind('dynatable:page:set', tidyAfterPageSet)
@@ -736,9 +750,20 @@ function makeAlphaSortFunctionOnProperty(property) {
     return function (rec1,rec2, attr, direction) {
         var cmp = null
 
-        // the alphabetic sort
-        if (direction == 1) cmp = rec1[property].localeCompare(rec2[property])
-        else                cmp = rec2[property].localeCompare(rec1[property])
+        if (rec1[property] && rec2[property]) {
+            // the alphabetic sort
+            if (direction == 1) cmp = rec1[property].localeCompare(rec2[property])
+            else                cmp = rec2[property].localeCompare(rec1[property])
+        }
+        else if (rec1[property]) {
+            cmp = direction
+        }
+        else if (rec2[property]) {
+            cmp = -direction
+        }
+        else {
+          cmp = 0
+        }
 
         // second level sorting on key = id in records array
         // (this one volontarily not reversable by direction
@@ -768,7 +793,10 @@ function tidyAfterPageSet() {
 $.ajax({
   url: '/api/nodes?types[]=DOCUMENT&pagination_limit=-1&parent_id='
         + corpus_id
-        +'&fields[]=parent_id&fields[]=id&fields[]=name&fields[]=typename&fields[]=hyperdata',
+        +'&fields[]=parent_id&fields[]=id&fields[]=name&fields[]=typename&fields[]=hyperdata'
+        // +'&hyperdata_filter[]=title&hyperdata_filter[]=source&hyperdata_filter[]=language_iso2'
+        +'&hyperdata_filter[]=title&hyperdata_filter[]=source&hyperdata_filter[]=language_iso2&hyperdata_filter[]=abstract'
+        +'&hyperdata_filter[]=publication_year&hyperdata_filter[]=publication_month&hyperdata_filter[]=publication_day',
   success: function(maindata){
       // unfortunately favorites info is in a separate request (other nodes)
       $.ajax({
@@ -838,6 +866,10 @@ $.ajax({
                                  rec.hyperdata.publication_day
                                 )
 
+              // and a bool property for remote search results
+              // (will be updated by ajax)
+              rec.matched_remote_search = false      // TODO use it
+
           }
 
           AjaxRecords = maindata.records; // backup-ing in global variable!

templates/pages/corpora/terms.html

@@ -131,7 +131,7 @@ em {
                            
                           <!-- save/import button -->
                           <button id="ImportListOrSaveAll" class="btn btn-warning" style="font-size:120%"
-                                   onclick="$('#csvimport').modal('show');">
+                                   onclick="$('#csvimport').modal('show'); document.getElementById('importsubmit').disabled = false ;">
                               <b>Import a Termlist</b>
                           </button>
                       </div>
@@ -437,13 +437,22 @@ function listmergeCsvPost(theFile){
                  // reload after 3s
                  setTimeout("location.reload(true)", 3000);
                  },
-              error: function(result) {
-                  my_html  = '<h3 style="color:red">Error</h3>'
-                  my_html += "<p class='note'>please correct your CSV file and retry</p>"
-                  my_html += "<p>"+ result.responseJSON['err']+"</p>"
+              error: function(result, t) {
+                  if (t != 'timeout') {
+                    my_html  = '<h3 style="color:red">Error</h3>'
+                    my_html += "<p class='note'>please correct your CSV file and retry</p>"
+                    my_html += "<p>"+ result.responseJSON['err']+"</p>"
+                  }
+                  else {
+                    my_html  = '<h3 style="color:red">Timeout</h3>'
+                    my_html += "<p>The CSV import timed out.</p>"
+                    my_html += "<p>(This bug is currently being fixed. <br/>The import and indexation are now continuing in background on our servers. Results will show in a few minutes.)</p>"
+                    document.getElementById('importsubmit').disabled = true
+                  }
                   $('#formanswer').html(my_html);
                   console.error(result);
                  },
+              timeout: 15000  // 15s
             });
     }
 };

templates/pages/corpora/titles.html

@@ -21,12 +21,12 @@
     <div class="col-md-3 col-md-offset-2">
         <div id="monthly-move-chart">
             <center>
-                   Select a time range in the chart with blue bars to zoom in
-                <p align="center">
+              Select a time range in the chart with blue bars to zoom in
+              <p align="center">
                 <!--<a class="btn btn-xs btn-default" role="button" href="/chart/corpus/{{ corpus.id }}/data.csv">Save</a>-->
-                <a class="btn btn-xs btn-default" href="javascript:volumeChart.filterAll();dc.redrawAll();">Reset</a></p>
-
-                <div class="clearfix"></div>
+                <a class="btn btn-xs btn-default" href="javascript:volumeChart.filterAll();dc.redrawAll();">Reset</a>
+              </p>
+              <div class="clearfix"></div>
             </center>
         </div>
 
@@ -68,10 +68,14 @@
                     <span style="font-size:70%;">
                     <span class="glyphicon glyphicon-filter" aria-hidden="true"></span>
                       <!-- Used by the #doubleSearch associated function -->
-                      <input title="Search in Titles" id="searchTI" name="searchTI" type="checkbox" checked onclick="return false">TI&nbsp;
-                    <span class="glyphicon glyphicon-filter" aria-hidden="true"></span>
-                      <input title="Search in Abstracts" id="searchAB" name="searchAB" type="checkbox">AB
-                    </span>&nbsp;&nbsp;
+                      <input title="Search in Titles" id="searchTI" name="searchTI" type="checkbox" checked onclick="return false">
+                        TI&nbsp;
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