Merge 1df7476 into 8ec9368

knowledge_repo/app/app.py

@@ -64,7 +64,6 @@ def __init__(self, repo, db_uri=None, debug=None, config=None, **kwargs):
             repo = config.prepare_repo(repo)
         self.repository = repo
         assert isinstance(self.repository, knowledge_repo.KnowledgeRepository), "Invalid repository object provided."
-
         # Set debug mode from kwargs or else maintain current setting
         if debug is not None:
             self.config['DEBUG'] = debug
@@ -77,6 +76,7 @@ def __init__(self, repo, db_uri=None, debug=None, config=None, **kwargs):
             self.config['SQLALCHEMY_DATABASE_URI'] = db_uri
         logger.debug(u"Using database: {}".format(self.config['SQLALCHEMY_DATABASE_URI']))
 
+
         # Register database schema with flask app
         sqlalchemy_db.init_app(self)
 
@@ -143,6 +143,7 @@ def load_user_from_request(request):
         # anonymous users too.
         self.principal.identity_loaders.append(lambda: AnonymousIdentity())
 
+
         # Synchronise user permissions with data model
         @user_loaded_from_request.connect
         def on_user_loaded_from_request(sender, user):
@@ -273,10 +274,26 @@ def format_date(date):
             except:
                 return date
 
+
+
+    def append_repo(self,name,uri):
+        temp = self.repository
+        self.repository = knowledge_repo.KnowledgeRepository.append_for_uri(name,uri,temp)
+        self.db_update_index(check_timeouts=False, force=True, reindex=True)
+        return self.repository
+
+    def append_repo_obj(self,name,obj):
+        temp = self.repository
+        self.repository = knowledge_repo.KnowledgeRepository.append_obj(name,obj,temp)
+        self.db_update_index(check_timeouts=False, force=True, reindex=True)
+        return self.repository
+
+
     @property
     def repository(self):
         return getattr(self, '_repository')
 
+
     @repository.setter
     def repository(self, repo):
         self._repository = repo

knowledge_repo/app/auth_providers/oauth2.py

@@ -156,15 +156,17 @@ def extract_from_dict(d, key):
             if isinstance(key, (list, tuple)):
                 if len(key) == 1:
                     key = key[0]
-                else:
-                    return extract_from_dict(d[key[0]], key[1:])
-            if isinstance(key, six.string_types):
+                elif d[key[0]] is None:
+                    return extract_from_dict(d, key[1:])
+            else:
+                return extract_from_dict(d, key[0])
+            if isinstance(key, str):
                 return d[key]
             raise RuntimeError("Invalid key type: {}.".format(key))
-
+       
         response = self.oauth_client.get(self.get_endpoint_url(self.user_info_endpoint), verify=self.verify_ssl_certs)
         try:
-            response_dict = json.loads(response.content)
+            response_dict = json.loads(request.content.decode('utf-8'))
             identifier = extract_from_dict(response_dict, self.user_info_mapping['identifier'])
             if identifier is None:
                 raise ValueError("identifier '{}' not found in authentication response".format(self.user_info_mapping['identifier']))

knowledge_repo/app/routes/index.py

@@ -51,6 +51,19 @@ def render_index():
     return redirect('/feed')
 
 
+@blueprint.route('/testupload')
+@PageView.logged
+def test_upload():
+    global current_repo,current_app
+    #repo = current_app.append_repo("3","kr-test")
+    #current_repo = repo
+    dbobj = current_repo.migrate_to_dbrepo("ucla_rnaseq_tcga_analysis","ucla-kr")
+
+    current_repo = current_app.append_repo_obj("3",dbobj)
+    return redirect('/feed')    
+
+
+
 @blueprint.route('/favorites')
 @PageView.logged
 @login_required
@@ -82,10 +95,12 @@ def render_favorites():
 @permissions.index_view.require()
 def render_feed():
     """ Renders the index-feed view """
+    global current_repo,current_app
     feed_params = from_request_get_feed_params(request)
     posts, post_stats = get_posts(feed_params)
     for post in posts:
         post.tldr = render_post_tldr(post)
+
 
     return render_template("index-feed.html",
                            feed_params=feed_params,

knowledge_repo/app/routes/posts.py

@@ -61,10 +61,10 @@ def render(path):
         return render_template("error.html")
 
     if post.private and not (username in post.authors or username in current_repo.config.editors):
+        print "so we came here"
         allowed_users = set(user.id for group in post.groups for user in group.users)
         if user_id not in allowed_users:
             return render_template("permission_ask.html", authors=post.authors_string)
-
     rendered = render_post(post, with_toc=True)
     raw_post = render_post_raw(post) if mode == 'raw' else None
 

knowledge_repo/app/templates/base.html

@@ -97,6 +97,8 @@
               Write a Post!
             </a>
 
+
+
             <!-- Drop down menu to surface less used links on large screens -->
             <ul class="nav navbar-nav navbar-right visible-sm-block visible-md-block visible-lg-block">
               <li class="dropdown">

knowledge_repo/repository.py

@@ -58,6 +58,42 @@ def for_uris(cls, uri):
         krs = {name: cls.for_uri(uri) for name, uri in list(uris.items())}
         return MetaKnowledgeRepository(krs)
 
+    @classmethod
+    def migrate_to_dbrepo(cls,gitpath,newpath):
+        # A new (supposedly) git repository is going to be uploaded
+        # That must be migrated to the database. 
+        # Inputs : 
+        # gitpath
+        # newpath
+
+        from .repositories.dbrepository import DbKnowledgeRepository
+        newpath = "mysql://abhi:1234@localhost/knowledgerepo:%s"%newpath
+        db_obj = DbKnowledgeRepository(newpath)
+        gitkr = cls.for_uri(gitpath)
+        for post in gitkr.posts():
+            new_post = db_obj.add(post)
+            new_post_status = new_post.status
+            db_obj.submit(new_post.path)
+            db_obj.accept(new_post.path)
+            db_obj.publish(new_post.path)
+        return db_obj
+
+    @classmethod
+    def append_obj(cls,name,new_obj,meta_repo):
+        from .repositories.meta import MetaKnowledgeRepository
+        krs = meta_repo.uri
+        krs[name] = new_obj
+        meta_repo = MetaKnowledgeRepository(krs)
+        return meta_repo
+
+    @classmethod
+    def append_for_uri(cls,name,uri,meta_repo):
+        from .repositories.meta import MetaKnowledgeRepository
+        krs = meta_repo.uri
+        krs[name] = cls.for_uri(uri)
+        meta_repo = MetaKnowledgeRepository(krs)
+        return meta_repo
+
     @classmethod
     def from_uri(cls, url, *args, **kwargs):
         return cls(url, *args, **kwargs)

scripts/knowledge_repo

@@ -42,6 +42,15 @@ if os.path.exists(os.path.join(contrib_dir, '__init__.py')):
 # we finish constructing the entire parser so that the syntax and arguments can change
 # from version to version of this script.
 
+# Repeating what the argparse already does
+def parse_repo_string(repo_str):
+    prefix_pattern = re.compile('^(?:\{(?P<name>[a-zA-Z_0-9]*)\})?(?P<uri>.*)$')
+
+    prefix = prefix_pattern.match(repo_str)
+    return prefix.groups()
+
+
+
 class ParseRepositories(argparse.Action):
 
     def __init__(self, **kwargs):
@@ -97,7 +106,6 @@ try:
 except (ValueError, git.GitError, gitdb.exc.ODBError):  # TODO: Generalise error to cater for all KnowledgeRepository instances.
     repo = None
 
-
 # Update repository so that we can ensure git repository configuration is up to date
 # We wrap this in a try/except block because failing to update a repository can
 # happen for all sorts of reasons that should not inhibit other actions
@@ -237,6 +245,10 @@ if args.dev and os.path.exists(os.path.join(os.path.dirname(__file__), '..', '.g
 
 args = parser.parse_args()
 
+
+
+
+
 if not hasattr(args, 'action'):
     parser.print_help()
     sys.exit(1)