Going to use tags from graph json only

Author: adbharadwaj

applications/graphs/controllers.py

@@ -59,12 +59,15 @@ def is_user_authorized_to_view_graph(request, username, graph_id):
 
 def is_user_authorized_to_update_graph(request, username, graph_id):
 	is_authorized = False
+	user = users.controllers.get_user(request, username)
 
 	graph = db.get_graph_by_id(request.db_session, graph_id)
 
 	if graph is not None:  # Graph exists
 		if graph.owner_email == username:
 			is_authorized = True
+		elif user is not None and user.is_admin == 1:
+			is_authorized = True
 
 	return is_authorized
 

applications/graphs/dal.py

@@ -162,7 +162,6 @@ def find_graphs(db_session, owner_email=None, group_ids=None, graph_ids=None, is
 	names = [] if names is None else names
 	tags = [] if tags is None else tags
 
-
 	elements_filter = []
 	names_filter = []
 

applications/graphs/models.py

@@ -53,7 +53,7 @@ def serialize(cls):
 			'graph_json': json.loads(cls.graph_json),
 			'style_json': json.loads(cls.style_json),
 			'is_public': cls.is_public,
-			'tags': [tag.serialize() for tag in cls.tags],
+			'tags': [tag.name for tag in cls.tags],
 			'default_layout_id': cls.default_layout_id,
 			'created_at': cls.created_at.isoformat(),
 			'updated_at': cls.updated_at.isoformat()

migration/versions/755438125e7d_add_more_network_attributes.py

@@ -0,0 +1,53 @@
+"""add more network attributes
+
+Revision ID: 755438125e7d
+Revises: 97a32c589371
+Create Date: 2017-04-12 23:55:47.368030
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+import json
+from graphspace_python.graphs.classes.gsgraph import GSGraph
+from graphspace_python.graphs.formatter.json_formatter import CyJSFormat
+from graphspace_python.api.client import GraphSpace
+
+# revision identifiers, used by Alembic.
+revision = '755438125e7d'
+down_revision = '97a32c589371'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+	graphspace = GraphSpace('adb@vt.edu', 'XXXX')
+	graphspace.set_api_host('localhost:8000')
+	response = graphspace.get_public_graphs(limit=70)
+	for graph in response['graphs']:
+		graph_json = graph['graph_json']
+		G = CyJSFormat.create_gsgraph(json.dumps(graph['graph_json']))
+		tags = list(set(G.get_tags()) | set(graph['tags']))
+		G.set_tags(tags)
+
+		if '2015-bioinformatics-xtalk' in tags:
+			G.set_data({
+				'pubmed': '26400040',
+				'pubmed_title': 'Xtalk: a path-based approach for identifying crosstalk between signaling pathways.',
+				'pubmed_authors': ['Allison N. Tegge', 'Nicholas Sharp', 'T. M. Murali']
+			})
+		elif '2013-jcb-linker' in tags:
+			G.set_data({
+				'pubmed': '23641868',
+				'pubmed_title': 'Top-down network analysis to drive bottom-up modeling of physiological processes.',
+				'organism': 'Saccharomyces cerevisiae',
+				'taxon_id': '559292',
+				'pubmed_authors': ['Christopher L. Poirel', 'Richard R. Rodrigues','Katherine C. Chen','John J. Tyson','T.M. Murali']
+			})
+		print(graph['id'])
+		response = graphspace.update_graph(graph['name'], owner_email=graph['owner_email'], graph=G, is_public=graph['is_public'])
+	raise
+
+
+def downgrade():
+	pass

static/js/graphs_page.js

@@ -205,10 +205,12 @@ var graphsPage = {
         },
         tagsFormatter: function (value, row) {
             links = "";
-            for (i in row.tags) {
-                links += $('<a>').attr('href', '#').html($('<span>').attr('class', 'label label-info tag-btn').attr('onclick', 'graphsPage.graphsTable.searchTag(this);').text(row.tags[i].name)[0])[0].outerHTML + '&nbsp;';
+            if ('data' in row.graph_json && 'tags' in row.graph_json.data) {
+                links = _.map(row.graph_json.data.tags, function(tag){
+                    return $('<a>').attr('href', '#').html($('<span>').attr('class', 'label label-info tag-btn').attr('onclick', 'graphsPage.graphsTable.searchTag(this);').text(tag)[0])[0].outerHTML + '&nbsp;';
+                });
             }
-            return links
+            return links.join('');
         },
         ownerEmailFormatter: function (value, row) {
             if (_.startsWith(row.owner_email, 'public_user_')) {
@@ -2110,7 +2112,7 @@ var cytoscapeGraph = {
     getStylesheet: function (cy) {
         /*
          *  gets stylesheet for the graph.
-         *  
+         *
          *  cy: cytoscape graph object
          */
         var selectedElementStyleAttributes = ['overlay-opacity', 'overlay-color', 'overlay-padding'];
@@ -2133,13 +2135,13 @@ var cytoscapeGraph = {
 
         if (format === 'jpg') {
             var b64key = 'base64,';
-            var b64 = cy.jpg({'full': true}).substring( cy.jpg({'full': true}).indexOf(b64key) + b64key.length );
-            blob = utils.base64ToBlob( b64, 'image/jpeg' );
+            var b64 = cy.jpg({'full': true}).substring(cy.jpg({'full': true}).indexOf(b64key) + b64key.length);
+            blob = utils.base64ToBlob(b64, 'image/jpeg');
             fileformat = '.jpg';
         } else if (format === 'png') {
             var b64key = 'base64,';
-            var b64 = cy.png({'full': true}).substring( cy.png({'full': true}).indexOf(b64key) + b64key.length );
-            blob = utils.base64ToBlob( b64, 'image/png' );
+            var b64 = cy.png({'full': true}).substring(cy.png({'full': true}).indexOf(b64key) + b64key.length);
+            blob = utils.base64ToBlob(b64, 'image/png');
             fileformat = '.png';
         } else if (format === 'cyjs') {
             MIME_TYPE = "application/json";

templates/graph/graph_details_tab.html

@@ -1,5 +1,37 @@
 <div class="margin-top-4">
-    <table>
-        {{ description|safe }}
-    </table>
+    <style>
+        img {
+            max-width: 200px;
+        }
+    </style>
+    <div class="row">
+        <div class="col-md-6">
+            <table>
+                {{ description|safe }}
+            </table>
+        </div>
+        <div class="col-md-6">
+            <div class="table-responsive">
+                <table class="table table-bordered">
+                    <tr>
+                        <th>Attribute</th>
+                        <th>Value</th>
+                    </tr>
+                    {% if 'data' in graph.graph_json %}
+                    {% for k,v in graph.graph_json.data.items %}
+                        {% if k != 'description' %}
+                            <tr>
+                                <td>{{ k|safe}}</td>
+                                <td>{{ v|safe }}</td>
+                            </tr>
+                        {% endif %}
+                    {% endfor %}
+                    {% endif %}
+
+
+                </table>
+            </div>
+        </div>
+    </div>
+
 </div>

templates/graph/index.html

@@ -130,12 +130,12 @@ <h4 class="zero-margin d-inline-block">
                     {% endif %}
                     </small>
                 </h4>
-                {% if graph.tags %}
+                {% if 'data' in graph.graph_json and 'tags' in graph.graph_json.data%}
                     <div class="tag-cloud d-inline-block" id="Tags" >
-                        {% for tag in graph.tags %}
+                        {% for tag in graph.graph_json.data.tags %}
                             <a class="tag-anchor"
-                               href="{% url 'graphs' %}?tags={{ tag.name | slugify }}">
-                                <i class="fa fa-hashtag"></i> {{ tag.name }}
+                               href="{% url 'graphs' %}?tags={{ tag | slugify }}">
+                                <i class="fa fa-hashtag"></i> {{ tag }}
                             </a>
                         {% endfor %}
                     </div>