[UPDATE] dynatable-paginator

gargantext_web/urls.py

@@ -80,7 +80,8 @@ urlpatterns = patterns('',
     url(r'^tests/pubmedquery$', pubmedscrapper.getGlobalStats),
     url(r'^tests/project/(\d+)/pubmedquery/go$', pubmedscrapper.doTheQuery),
     url(r'^tests/project/(\d+)/ISTEXquery/go$', pubmedscrapper.testISTEX),
-    url(r'^tests/paginator/project/(\d+)/corpus/(\d+)/$', views.newpaginatorJSON)
+    url(r'^tests/paginator/corpus/(\d+)/$', views.newpaginatorJSON),
+    url(r'^tests/project/(\d+)/corpus/(\d+)/$', views.corpus_trial)
 )
 
 

gargantext_web/views.py

@@ -308,13 +308,67 @@ def corpus(request, project_id, corpus_id):
     return HttpResponse(html)
 
 
-def newpaginatorJSON(request , project_id , corpus_id):
+def corpus_trial(request, project_id, corpus_id):
+    if not request.user.is_authenticated():
+        return redirect('/login/?next=%s' % request.path)
+    
+    try:
+        offset = int(project_id)
+        offset = int(corpus_id)
+    except ValueError:
+        raise Http404()
+
+    t = get_template('corpus_trial.html')
+    
+    user = request.user
+    date = datetime.datetime.now()
+    
+    project = cache.Node[int(project_id)]
+    corpus  = cache.Node[int(corpus_id)]
+
+    
+    type_doc_id = cache.NodeType['Document'].id
+    number = session.query(func.count(Node.id)).filter(Node.parent_id==corpus_id, Node.type_id==type_doc_id).all()[0][0]
+
+    try:
+        chart = dict()
+        chart['first'] = parse(corpus.children.first().metadata['publication_date']).strftime("%Y, %m, %d")
+        # TODO write with sqlalchemy
+        #chart['first'] = parse(session.query(Node.metadata['publication_date']).filter(Node.parent_id==corpus.id, Node.type_id==type_doc_id).first()).strftime("%Y, %m, %d")
+        
+        chart['last']  = parse(corpus.children.last().metadata['publication_date']).strftime("%Y, %m, %d")
+        print(chart)
+    except Exception as error:
+        print(error)
+    
+    try:
+        processing = corpus.metadata['Processing']
+    except Exception as error:
+        print(error)
+        processing = 0
+    print('processing', processing)
+
+    html = t.render(Context({\
+            'user': user,\
+            'date': date,\
+            'project': project,\
+            'corpus' : corpus,\
+            'processing' : processing,\
+#            'documents': documents,\
+            'number' : number,\
+            'dates' : chart,\
+            }))
+    
+    return HttpResponse(html)
+
+
+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()
+    # project = session.query(Node).filter(Node.id==project_id).first()
     corpus  = session.query(Node).filter(Node.id==corpus_id).first()
     type_document_id = cache.NodeType['Document'].id
     documents  = session.query(Node).filter(Node.parent_id==corpus_id , Node.type_id == type_document_id ).all()
@@ -344,17 +398,6 @@ def newpaginatorJSON(request , project_id , corpus_id):
         "totalRecordCount":len(results)
     }
     return JsonHttpResponse(finaldict)
-    # html = t.render(Context({\
-    #         # 'user': user,\
-    #         # 'date': date,\
-    #         'project': project_id,\
-    #         'corpus' : corpus_id,\
-    #         # 'documents': results,\
-    #         # 'number' : len(filtered_docs),\
-    #         # 'dates' : chart,\
-    #         }))
-    
-    # return HttpResponse(html)
 
 
 # Im using this actually

init/requirements.txt~

+Cython==0.20.2
+Django==1.6.11
+Jinja2==2.7.3
+MarkupSafe==0.23
+Pillow==2.5.3
+Pygments==1.6
+RandomWords==0.1.12
+SQLAlchemy==0.9.8
+South==1.0
+aldjemy==0.3.10
+amqp==1.4.6
+anyjson==0.3.3
+bibtexparser==0.6.0
+billiard==3.3.0.18
+celery==3.1.15
+certifi==14.05.14
+cffi==0.8.6
+chardet==2.3.0
+cryptography==0.6
+decorator==3.4.0
+django-autoslug==1.7.2
+django-autoslug-field==0.2.3
+django-celery==3.1.16
+django-cte-trees==0.9.2
+django-extensions==1.4.0
+django-grappelli==2.5.3
+django-hstore==1.3.1
+django-maintenance==0.1
+django-mptt==0.6.1
+django-nested-inlines==0.1
+django-pgfields==1.4.4
+django-pgjson==0.2.2
+django-pgjsonb==0.0.10
+django-treebeard==2.0
+djangorestframework==3.0.0
+gensim==0.10.3
+graphviz==0.4
+ipython==2.2.0
+kombu==3.0.23
+lxml==3.4.1
+matplotlib==1.4.0
+networkx==1.9
+nltk==3.0a4
+nose==1.3.4
+numpy==1.8.2
+pandas==0.14.1
+pexpect-u==2.5.1
+psycopg2==2.5.4
+pycountry==1.8
+pycparser==2.10
+pydot2==1.0.33
+pyparsing==2.0.2
+python-dateutil==2.2
+python-igraph==0.7
+pytz==2014.7
+pyzmq==14.3.1
+readline==6.2.4.1
+redis==2.10.3
+scikit-learn==0.15.1
+scipy==0.14.0
+simplerandom==0.12.1
+six==1.7.3
+sympy==0.7.5
+tornado==4.0.1
+uWSGI==2.0.7
+ujson==1.33

parsing/FileParsers/PubmedFileParser_wYield.py

+from django.db import transaction
+from lxml import etree
+from .FileParser import FileParser
+from ..NgramsExtractors import *
+
+class PubmedFileParser(FileParser):
+    
+    def _parse(self, file):
+        # open the file as XML
+        xml_parser = etree.XMLParser(resolve_entities=False, recover=True)
+        xml = etree.parse(file, parser=xml_parser)
+        xml_articles = xml.findall('PubmedArticle')
+        # parse all the articles, one by one
+        for xml_article in xml_articles:
+            # extract data from the document
+            metadata = {}
+            metadata_path = {
+                "journal"           : 'MedlineCitation/Article/Journal/Title',
+                "title"             : 'MedlineCitation/Article/ArticleTitle',
+                "language_iso3"     : 'MedlineCitation/Article/Language',
+                "doi"               : 'PubmedData/ArticleIdList/ArticleId[@type=doi]',
+                "abstract"          : 'MedlineCitation/Article/Abstract/AbstractText',
+                "publication_year"  : 'MedlineCitation/DateCreated/Year',
+                "publication_month" : 'MedlineCitation/DateCreated/Month',
+                "publication_day"   : 'MedlineCitation/DateCreated/Day',
+                "authors"           : 'MedlineCitation/Article/AuthorList',
+            }
+            for key, path in metadata_path.items():
+                try:
+                    xml_node = xml_article.find(path)
+                    if key == 'authors':
+                        metadata[key] = ', '.join([
+                            xml_author.find('ForeName').text + ' ' + xml_author.find('LastName').text
+                            for xml_author in xml_node
+                        ])
+                    else:
+                        metadata[key] = xml_node.text
+                except:
+                    pass
+            yield metadata
\ No newline at end of file

static/css/jquery.dynatable.css

+/*
+ * jQuery Dynatable plugin 0.3.1
+ *
+ * Copyright (c) 2014 Steve Schwartz (JangoSteve)
+ *
+ * Dual licensed under the AGPL and Proprietary licenses:
+ *   http://www.dynatable.com/license/
+ *
+ * Date: Tue Jan 02 2014
+ */
+th {
+  background: #006a72;
+}
+th a {
+  color: #fff;
+}
+th a:hover {
+  color: #fff;
+  text-decoration: underline;
+}
+
+.dynatable-search {
+  float: right;
+  margin-bottom: 10px;
+}
+
+.dynatable-pagination-links {
+  float: right;
+}
+
+.dynatable-record-count {
+  display: block;
+  padding: 5px 0;
+}
+
+.dynatable-pagination-links span,
+.dynatable-pagination-links li {
+  display: inline-block;
+}
+
+.dynatable-page-link,
+.dynatable-page-break {
+  display: block;
+  padding: 5px 7px;
+}
+
+.dynatable-page-link {
+  cursor: pointer;
+}
+
+.dynatable-active-page,
+.dynatable-disabled-page {
+  cursor: text;
+}
+.dynatable-active-page:hover,
+.dynatable-disabled-page:hover {
+  text-decoration: none;
+}
+
+.dynatable-active-page {
+  background: #006a72;
+  border-radius: 5px;
+  color: #fff;
+}
+.dynatable-active-page:hover {
+  color: #fff;
+}
+.dynatable-disabled-page,
+.dynatable-disabled-page:hover {
+  background: none;
+  color: #999;
+}

templates/subcorpus.html

@@ -54,6 +54,7 @@ function getCookie(name) {
     return cookieValue;
 }
 
+//Delete all the duplicates using the Django-Garg API.
 function deleteDuplicates(url) {
     console.log("hello world")
     console.log(url)

templates/tests/newpag/thetable.html

+<!DOCTYPE html>
+<html ng-app="myApp">
+{% load staticfiles %}
+<head>
+  <link data-require="bootstrap-css@3.1.1" data-semver="3.1.1" rel="stylesheet" href="http://netdna.bootstrapcdn.com/bootstrap/3.1.1/css/bootstrap.min.css" />
+  <link rel="stylesheet" href="{% static "js/libs/css2/dirPagination.css" %}" />
+
+</head>
+
+<body>
+  <div class="container">
+    <div class="row">
+      <div class="col-lg-8">
+        <div ng-controller="MyController" class="my-controller">
+          <h1>Tasty Paginated Menu</h1>
+
+          <small>this is in "MyController"</small>
+
+
+          <div class="row">
+            <div class="col-xs-4">
+              <h3>Meals Page: {{ currentPage }}</h3>
+            </div>
+            <div class="col-xs-4">
+              <label for="search">Search:</label>
+              <input ng-model="q" id="search" class="form-control" placeholder="Filter text">
+            </div>
+            <div class="col-xs-4">
+              <label for="search">items per page:</label>
+              <input type="number" min="1" max="100" class="form-control" ng-model="pageSize">
+            </div>
+          </div>
+          <br>
+          <div class="panel panel-default">
+            <div class="panel-body">
+
+              <ul>
+                <li dir-paginate="meal in meals | filter:q | itemsPerPage: pageSize" current-page="currentPage">{{ meal }}</li>
+                
+              </ul>
+            </div>
+          </div>
+        </div>
+
+        <div ng-controller="OtherController" class="other-controller">
+          <small>this is in "OtherController"</small>
+          <div class="text-center">
+
+            <dir-pagination-controls boundary-links="true" on-page-change="pageChangeHandler(newPageNumber)">
+              <ul class="pagination" ng-if="1 < pages.length">
+                  <li ng-if="boundaryLinks" ng-class="{ disabled : pagination.current == 1 }">
+                      <a href="" ng-click="setCurrent(1)">&laquo;</a>
+                  </li>
+                  <li ng-if="directionLinks" ng-class="{ disabled : pagination.current == 1 }" class="ng-scope">
+                      <a href="" ng-click="setCurrent(pagination.current - 1)" class="ng-binding">‹</a>
+                  </li>
+                  <li ng-repeat="pageNumber in pages track by $index" ng-class="{ active : pagination.current == pageNumber, disabled : pageNumber == '...' }">
+                      <a href="" ng-click="setCurrent(pageNumber)">{{ pageNumber }}</a>
+                  </li>
+
+                  <li ng-if="directionLinks" ng-class="{ disabled : pagination.current == pagination.last }" class="ng-scope">
+                      <a href="" ng-click="setCurrent(pagination.current + 1)" class="ng-binding">›</a>
+                  </li>
+                  <li ng-if="boundaryLinks"  ng-class="{ disabled : pagination.current == pagination.last }">
+                      <a href="" ng-click="setCurrent(pagination.last)">&raquo;</a>
+                  </li>
+              </ul>
+            </dir-pagination-controls>
+
+          </div>
+        </div>
+      </div>
+    </div>
+  </div>
+
+
+  <script data-require="angular.js@1.3.0" data-semver="1.3.0" src="http://code.angularjs.org/1.3.0/angular.js"></script>
+  <script data-require="jquery@*" data-semver="2.0.3" src="http://code.jquery.com/jquery-2.0.3.min.js"></script>
+  <script data-require="bootstrap@3.1.1" data-semver="3.1.1" src="http://netdna.bootstrapcdn.com/bootstrap/3.1.1/js/bootstrap.min.js"></script>
+  <script src="{% static "js/libs/dirPagination.js"%}"></script>
+  
+  <script>
+  // Code goes here
+  var myApp = angular.module('myApp', ['angularUtils.directives.dirPagination']);
+
+  function MyController($scope) {
+
+    $scope.currentPage = 1;
+    $scope.pageSize = 10;
+    $scope.meals = ["a","b","c","d"];
+
+    // var dishes = [
+    //   'noodles',
+    //   'sausage',
+    //   'beans on toast',
+    //   'cheeseburger',
+    //   'battered mars bar',
+    //   'crisp butty',
+    //   'yorkshire pudding',
+    //   'wiener schnitzel',
+    //   'sauerkraut mit ei',
+    //   'salad',
+    //   'onion soup',
+    //   'bak choi',
+    //   'avacado maki'
+    // ];
+    // var sides = [
+    //   'with chips',
+    //   'a la king',
+    //   'drizzled with cheese sauce',
+    //   'with a side salad',
+    //   'on toast',
+    //   'with ketchup',
+    //   'on a bed of cabbage',
+    //   'wrapped in streaky bacon',
+    //   'on a stick with cheese',
+    //   'in pitta bread'
+    // ];
+    // for (var i = 1; i <= 100; i++) {
+    //   var dish = dishes[Math.floor(Math.random() * dishes.length)];
+    //   var side = sides[Math.floor(Math.random() * sides.length)];
+    //   $scope.meals.push('meal ' + i + ': ' + dish + ' ' + side);
+    // }
+    
+    $scope.pageChangeHandler = function(num) {
+        console.log('meals page changed to ' + num);
+    };
+  }
+
+  function OtherController($scope) {
+    $scope.pageChangeHandler = function(num) {
+      console.log('going to page ' + num);
+    };
+  }
+
+  myApp.controller('MyController', MyController);
+  myApp.controller('OtherController', OtherController);
+  </script>
+
+
+</body>
+
+</html>

zearcher.sh

+#!/bin/bash
+
+function FA2gephi {
+	for f in gexfs/*.gexf
+	do
+		if [[ "$f" != *_.gexf* ]]
+		then
+			java -jar tinaviz-2.0-SNAPSHOT.jar "$f" 10 &
+			break;
+		fi
+	done
+}
+
+function testing {
+	for f in gexfs/*.gexf
+	do
+		if [[ "$f" != *_.gexf* ]]
+		then
+			variable=`cat $f | grep "<description>Carla__Taramasco"`
+			if [[ "$variable" != "" ]]
+			then
+				echo $f
+			fi
+		fi
+	done
+}
+
+# Usage:
+# ./zearcher.sh "extension" "the query"
+function test2 {
+	extension=$1
+	query=$2
+	# echo "lala $extension , $query"
+	iter=`find . -name "*.$extension" -print`
+	
+	counter=0
+	for f in $iter
+	do
+		filename=`echo $f | sed s/"\.\/"//g`
+		variable=`cat $filename | grep "$query"`
+		if [[ "$variable" != "" ]]
+		then
+			echo $filename
+			counter=$((counter + 1));
+		fi
+	done
+
+	if [ $counter -eq 0 ]
+	then
+		echo "Nothing found. Die."
+	fi		
+}
+
+test2 $1 $2