Removed instance blacklist from gitignore

.gitignore

@@ -62,7 +62,6 @@ db.sqlite3
 db.sqlite3-journal
 
 # Flask stuff:
-instance/
 .webassets-cache
 
 # Scrapy stuff:

builder/builders/instance/mode.py

@@ -0,0 +1,53 @@
+import re 
+
+class ModeBuilder:
+    def __init__(self,builder):
+        self._builder = builder
+
+    def tree(self):
+        tree_edges = []
+        node_attrs = {}
+        seen = []
+        max_key = max([node for node in self._builder.v_nodes])
+        for n,v,e in self._builder.v_edges:
+            node_attrs[v] = self._builder.nodes[v]
+            node_attrs[n] = self._builder.nodes[n]
+            v_copy = v
+            if v in seen:
+                max_key +=1
+                v = max_key
+                node_attrs[v] = self._builder.nodes[v_copy]
+                seen.append(v)
+            else:
+                seen.append(v)
+            edge = self._create_edge_dict(e)
+            tree_edges.append((n,v,e,edge))       
+        tree_graph = self._builder.sub_graph(tree_edges,node_attrs)
+        return tree_graph
+
+    def network(self):
+        return self._builder.view
+
+    def _create_edge_dict(self,key,weight=1):
+        edge = {'weight': weight, 
+                'display_name': self._get_name(str(key))}
+        return edge
+
+    def _get_name(self,subject):
+        split_subject = self._split(subject)
+        if len(split_subject[-1]) == 1 and split_subject[-1].isdigit():
+            return split_subject[-2]
+        elif len(split_subject[-1]) == 3 and _isfloat(split_subject[-1]):
+            return split_subject[-2]
+        else:
+            return split_subject[-1]
+
+    def _split(self,uri):
+        return re.split('#|\/|:', uri)
+
+def _isfloat(x):
+    try:
+        float(x)
+        return True
+    except ValueError:
+        return False

builder/builders/instance/view.py

@@ -0,0 +1,85 @@
+#from utility.nv_identifiers import identifiers
+import re
+
+class ViewBuilder:
+    def __init__(self,builder):
+        self._builder = builder
+
+    def full(self):
+        return self._builder._graph
+
+    def pruned(self):
+        edges = []
+        node_attrs = {}
+        w_predicates = []
+        for n,v,k,e in self._builder.edges(keys=True,data=True):
+            if k not in w_predicates:
+                continue
+            node_attrs[n] = self._builder.nodes[n]
+            node_attrs[v] = self._builder.nodes[v]
+            edges.append((n,v,k,e))
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def heirarchy(self):
+        edges = []
+        node_attrs = {}
+        for entity,data in self._builder.get_entities():
+            sub_entities = self._builder.get_entities(entity)
+            if len(sub_entities) == 0:
+                continue
+            node_attrs[entity] = data
+
+            for s_entity in sub_entities:
+                key = identifiers.predicates.contains
+                s_entity,s_e_data = s_entity
+                node_attrs[s_entity] = s_e_data
+                edge = self._build_edge_attr(key)
+                edges.append((entity,s_entity,key,edge))
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def interaction_verbose(self):
+        edges = []
+        node_attrs = {}
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def interaction(self):
+        edges = []
+        node_attrs = {}
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def interaction_genetic(self):
+        edges = []
+        node_attrs = {}
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def ppi(self):
+        edges = []
+        node_attrs = {}
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def module(self):
+        edges = []
+        node_attrs = {}
+        return self._builder.sub_graph(edges,node_attrs)
+
+    def _build_edge_attr(self,key):
+        return {"display_name" : self._get_name(key)}
+
+    def _get_name(self,subject):
+        split_subject = self._split(subject)
+        if len(split_subject[-1]) == 1 and split_subject[-1].isdigit():
+            return split_subject[-2]
+        elif len(split_subject[-1]) == 3 and _isfloat(split_subject[-1]):
+            return split_subject[-2]
+        else:
+            return split_subject[-1]
+
+    def _split(self,uri):
+        return re.split('#|\/|:', uri)
+
+def _isfloat(x):
+    try:
+        float(x)
+        return True
+    except ValueError:
+        return False