Merge for latest release

.gitignore

@@ -1,3 +1,6 @@
+#Node install files
+node_modules/
+
 # Emacs backup files
 *~
 

README.md

@@ -1,5 +1,7 @@
 # Whyis
 
+[Visit our project web site for more details on how to use Whyis.](http://tetherless-world.github.io/whyis)
+
 Whyis is a nano-scale knowledge graph publishing, management, and analysis framework. 
 Whyis aims to support domain-aware management and curation of knowledge from many different sources. Its primary goal is to enable creation of useful domain- and data-driven knowledge graphs. Knowledge can be contributed and managed through direct user interaction, statistical analysis, or data ingestion from many different kinds of data sources. Every contribution to the knowledge graph is managed as a separate entity so that its provenance (publication status, attribution, and justification) is transparent and can be managed and used. 
 

authenticator.py

@@ -0,0 +1,83 @@
+from flask import current_app
+from flask_login import AnonymousUserMixin, login_user
+import datetime
+
+class InvitedAnonymousUser(AnonymousUserMixin):
+    '''A user that has been referred via an external application references but does not have a user account.'''
+    def __init__(self):
+        self.roles = ImmutableList()
+
+    def has_role(self, *args):
+        """Returns `False`"""
+        return False
+
+    def is_active(self):
+        return True
+
+    @property
+    def is_authenticated(self):
+        return True
+
+
+class Authenticator:
+    def authenticate(self, request, datastore, config):
+        pass
+
+class APIKeyAuthenticator:
+    def __init__(self, key, request_arg='API_KEY'):
+        self.key = key
+        self.request_arg = request_arg
+
+    def authenticate(self, request, datastore, config):
+        if self.request_arg in request.args and request.args[self.request_arg] == self.key:
+            print 'logging in invited user'
+            user = InvitedAnonymousUser()
+            login_user(user)
+            return user
+
+default_jwt_mapping = {
+    'identifier':'sub',
+    'email': 'mail',
+    'admin': 'isAdmin',
+    'givenName' : 'givenName',
+    'roles' : 'roles',
+    'familyName' : 'sn'
+}
+
+class JWTAuthenticator:
+    def __init__(self,  key, cookie="token", algorithm='HS256', mapping=default_jwt_mapping):
+        import jwt
+        self.jwt = jwt
+        self.cookie = cookie
+        self.key = key
+        self.algorithm = algorithm
+        self.mapping = mapping
+
+    def authenticate(self, request, datastore, config):
+        token = request.cookies.get(self.cookie)
+        if token is not None:
+            try:
+                payload = self.jwt.decode(token, self.key, algorithms=[self.algorithm])
+                user = datastore.get_user(identifier=payload[self.mapping['identifier']])
+                if user is None:
+                    role_objects = []
+                    if self.mapping['roles'] in payload:
+                        role_objects = payload[self.mapping['roles']]
+                    if self.mapping['admin'] in payload:
+                        if payload[self.mapping['admin']] == True:
+                            role_objects.append('admin')
+                    user = dict(identifier=payload[self.mapping['identifier']],
+                                email=payload[self.mapping['email']],
+                                givenName=payload[self.mapping['givenName']],
+                                familyName=payload[self.mapping['familyName']],
+                                confirmed_at = datetime.datetime.utcnow(),
+                                roles = role_objects)
+                    #user_obj = flask.current_app.datastore.create_user(**user)
+                    user_obj = current_app.datastore.create_user(**user)
+                else :
+                  user_obj = user
+                login_user(user_obj)
+                return user_obj
+            except self.jwt.ExpiredSignatureError:
+                return None
+

autonomic.py

@@ -15,6 +15,8 @@
 
 import tempfile
 
+from depot.io.interfaces import StoredFile
+
 whyis = rdflib.Namespace('http://vocab.rpi.edu/whyis/')
 whyis = rdflib.Namespace('http://vocab.rpi.edu/whyis/')
 np = rdflib.Namespace("http://www.nanopub.org/nschema#")
@@ -510,12 +512,21 @@ def process(self, i, o):
                 #triples += len(new_np)
                 #if triples > 10000:
                 self.app.nanopub_manager.publish(*to_publish)
+                nanopub_prepare_graph.store.close()
             print 'Published'
+        for resource, obj in resources.items():
+            if hasattr(i, 'close'):
+                print "Closing", resource
+                try:
+                    i.close()
+                except:
+                    pass
 
 class Deductor(UpdateChangeService):
     def __init__(self, where, construct, explanation, resource="?resource", prefixes=None): # prefixes should be 
         if resource is not None:
             self.resource = resource
+	self.prefixes = {}
         if prefixes is not None:
             self.prefixes = prefixes
         self.where = where
@@ -530,19 +541,18 @@ def getOutputClass(self):
 
     def get_query(self):
         self.app.db.store.nsBindings={}
-        return '''%s SELECT DISTINCT %s WHERE {\n%s \nFILTER NOT EXISTS {\n%s\n\t}\n}''' %( self.prefixes, self.resource, self.where, self.construct )
+        return '''SELECT DISTINCT %s WHERE {\n%s \nFILTER NOT EXISTS {\n%s\n\t}\n}''' %( self.resource, self.where, self.construct )
 
     def get_context(self, i):
         context = {}
-        context_vars = self.app.db.query('''%s SELECT DISTINCT * WHERE {\n%s\nFILTER(str(%s)="%s") .\n}''' %( self.prefixes, self.where, self.resource, i.identifier) )
+        context_vars = self.app.db.query('''SELECT DISTINCT * WHERE {\n%s\nFILTER(str(%s)="%s") .\n}''' %( self.where, self.resource, i.identifier) , initNs=self.app.NS.prefixes )
         for key in context_vars.json["results"]["bindings"][0].keys():
             context[key]=context_vars.json["results"]["bindings"][0][key]["value"]
         return context
 
     def process(self, i, o):
-        self.app.db.store.nsBindings={}
         npub = Nanopublication(store=o.graph.store)
-        triples = self.app.db.query('''%s CONSTRUCT {\n%s\n} WHERE {\n%s \nFILTER NOT EXISTS {\n%s\n\t}\nFILTER(str(%s)="%s") .\n}''' %( self.prefixes,self.construct, self.where, self.construct, self.resource, i.identifier) ) # init.bindings = prefix, dict for identifier (see graph.query in rdflib)
+        triples = self.app.db.query('''CONSTRUCT {\n%s\n} WHERE {\n%s \nFILTER NOT EXISTS {\n%s\n\t}\nFILTER(str(%s)="%s") .\n}''' %( self.construct, self.where, self.construct, self.resource, i.identifier) , initNs=self.prefixes ) 
         for s, p, o, c in triples:
             print "Deductor Adding ", s, p, o
             npub.assertion.add((s, p, o))

commands.py

@@ -45,6 +45,7 @@ def get_options(self):
         ]
 
     def run(self, input_file, file_format="trig", was_revision_of=None):
+        flask.current_app.managed = True
         if was_revision_of is not None:
             wasRevisionOf = set(flask.current_app.db.objects(predicate=np.hasAssertion,
                                                                subject=rdflib.URIRef(was_revision_of)))

config-template/{{cookiecutter.location}}/config.py

@@ -28,7 +28,7 @@
 
     site_name = "{{cookiecutter.project_name}}",
 
-    site_header_image = '/static/images/random_network.png',
+    site_header_image = 'static/images/random_network.png',
 
     site_description = '',