omf_web 0.9.9 → 1.0.0

data/lib/omf-web/content/irods_repository.rb

@@ -11,10 +11,10 @@ module OMF::Web
   # This class provides an interface to a directory based repository
   # It retrieves, archives and versions content.
   #
-  class IRodsContentRepository < ContentRepository  
-    
+  class IRodsContentRepository < ContentRepository
+
     @@irods_repositories = {}
-    
+
     # Return the repository which is referenced to by elements in 'opts'.
     #
     #
@@ -24,8 +24,8 @@ module OMF::Web
       end
       repo
     end
-      
-    # Register an existing directory to the system. It will be 
+
+    # Register an existing directory to the system. It will be
     # consulted for all content url's starting with
     # 'irods:_top_dir_:'. If 'is_primary' is set to true, it will
     # become the default repo for all newly created content
@@ -42,17 +42,18 @@ module OMF::Web
         @@primary_repository = repo
       end
     end
-    
+
     attr_reader :name, :top_dir
-    
+
     def initialize(name, opts)
       super
       unless @top_dir
         raise "No top_dir defined (#{opts.keys.inspect})"
       end
       @url_prefix = "irods:#{name}:"
+      @ticket = opts[:ticket]
     end
-    
+
     # Load content described by either a hash or a straightforward path
     # and return a 'ContentProxy' holding it.
     #
@@ -67,38 +68,38 @@ module OMF::Web
       descr = descr ? descr.dup : {}
       url = get_url_for_path(path)
       key = Digest::MD5.hexdigest(url)
-      descr[:url] = url      
+      descr[:url] = url
       descr[:url_key] = key
-      descr[:path] = path      
+      descr[:path] = path
       descr[:name] = url # Should be something human digestable
       if (descr[:strictly_new])
-       return nil if IRODS4r.exists?(path)
+       return nil if IRODS4r.exists?(path, @ticket)
       end
       proxy = ContentProxy.create(descr, self)
       return proxy
     end
-        
+
     def write(content_descr, content, message)
       path = _get_path(content_descr)
       #puts "WRITE PATHS>>> #{path}"
-      f = IRODS4r::File.create(path, false)
+      f = IRODS4r::File.create(path, false, ticket: @ticket)
       f.write(content)
     end
-    
+
     def read(content_descr)
       path = _get_path(content_descr)
       #puts "READ PATHS>>> #{path}"
-      f = IRODS4r::File.create(path, false)
+      f = IRODS4r::File.create(path, false, ticket: @ticket)
       f.read()
-    end    
-    
+    end
+
     #
     # Return an array of file names which are in the repository and
     # match 'search_pattern'
     #
     def find_files(search_pattern, opts = {})
       begin
-        dir = IRODS4r.find(@top_dir)
+        dir = IRODS4r.find(@top_dir, {}, @ticket)
       rescue IRODS4r::IRODS4rException
         return []
       end
@@ -106,7 +107,7 @@ module OMF::Web
       _find_files(search_pattern, dir, res, opts[:mime_type])
       res
     end
-    
+
     def _find_files(search_pattern, dir, res, mime_type)
       dir.list.each do |e|
         if e.directory?
@@ -115,7 +116,7 @@ module OMF::Web
           path = e.path
           if path.match(search_pattern)
             mt = mime_type_for_file(path)
-            next if mime_type != nil && mime_type != mt 
+            next if mime_type != nil && mime_type != mt
             res << {:url => get_url_for_path(path), :path => path, #:name => 'foo',
                     :mime_type => mt}
           end
@@ -123,10 +124,10 @@ module OMF::Web
       end
       res
     end
-    
-    
+
+
     # Return a URL for a path in this repo
-    # 
+    #
     def get_url_for_path(path)
       puts "PATH>>>>> '#{path}:#{path.class}'-'#{@top_dir}:#{@top_dir.class}'"
       if m = path.match("#{@top_dir}(.*)")
@@ -134,12 +135,12 @@ module OMF::Web
       end
       url = @url_prefix + path
     end
-    
+
     # HACK ALERT!!!
-    # 
+    #
     # This method may be called by an entity which wants to access the content
-    # directly through the file system. In the absence of a FUSE mounted iRODS 
-    # repo, we 'iget' the resource to a temporary directory and return that 
+    # directly through the file system. In the absence of a FUSE mounted iRODS
+    # repo, we 'iget' the resource to a temporary directory and return that
     # path. The calling entity needs to be aware that any changes to that file
     # will NOT show up in iRODS without an iput.
     #
@@ -147,19 +148,19 @@ module OMF::Web
     #
     def absolute_path(content_descr)
       path = _get_path(content_descr)
-      
+
       require 'etc'
       tmp_dir = "#{Dir::tmpdir}/LabWiki-#{Etc.getlogin}"
       # unless Dir.exists? tmp_dir
         # Dir.mkdir tmp_dir, 0700
       # end
-      
+
       target = File.join(tmp_dir, path)
-      IRODS4r::ICommands.export(path, target)
+      IRODS4r::ICommands.export(path, target, true, @ticket)
       target
     end
 
-    
+
     def _get_path(content_descr)
       #puts ">>>GET PATH #{content_descr.inspect}"
       if content_descr.is_a? String
@@ -186,6 +187,6 @@ module OMF::Web
       end
       return path
     end
-              
+
   end # class
-end # module
+end # module

data/lib/omf-web/content/repository.rb

@@ -12,48 +12,48 @@ module OMF::Web
   # It retrieves, archives and versions content.
   #
   class ContentRepository < OMF::Common::LObject
-    
+
     MIME_TYPE = {
-      :js => 'text/javascript',       
+      :js => 'text/javascript',
       :md => 'text/markup',
-      :rb => 'text/ruby',       
-      :r => 'text/r',       
-      :svg => 'text/svg',       
-      :txt => 'text' 
+      :rb => 'text/ruby',
+      :r => 'text/r',
+      :svg => 'text/svg',
+      :txt => 'text'
     }
-    
+
     REPO_PLUGINS = {
       git: lambda do |name, opts|
-              require 'omf-web/content/git_repository' 
+              require 'omf-web/content/git_repository'
               return GitContentRepository.new(name, opts)
           end,
       file: lambda do |name, opts|
-              require 'omf-web/content/file_repository' 
+              require 'omf-web/content/file_repository'
               return FileContentRepository.new(name, opts)
           end,
       irods: lambda do |name, opts|
-              require 'omf-web/content/irods_repository' 
+              require 'omf-web/content/irods_repository'
               return IRodsContentRepository.new(name, opts)
           end,
       static: lambda do |name, opts|
-              require 'omf-web/content/static_repository' 
+              require 'omf-web/content/static_repository'
               return StaticContentRepository.new(name, opts)
           end
     }
-    
+
     # Repo to be used for all newly created content
     @@primary_repository = nil
     @@repositories = {}
-    
+
     def self.register_repo(name, opts)
       raise "ArgumentMismatch: Expected Hash, but got #{opts}" unless opts.is_a? Hash
-      
+
       name = name.to_sym
       if @@repositories[name]
         warn "Ignoring repeated registration of repo '#{name}'"
         return
       end
-      
+
       unless type = opts[:type]
         raise "Missing type in repo opts (#{opts})"
       end
@@ -62,9 +62,10 @@ module OMF::Web
       end
       @@repositories[name] = r = repo_creator.call(name, opts)
       @@primary_repository = r if opts[:is_primary]
+      r
     end
-    
-     
+
+
     # Load content described by either a hash or a straightforward url
     # and return a 'ContentProxy' holding it.
     #
@@ -75,7 +76,7 @@ module OMF::Web
       if url_or_descr.is_a? ContentProxy
         return url_or_descr
       end
-      
+
       if url_or_descr.is_a? String
         url = url_or_descr
       else
@@ -90,20 +91,20 @@ module OMF::Web
       unless url
         throw "Can't find url in '#{url_or_descr.inspect}"
       end
-      
+
       repo = find_repo_for(url)
       repo.create_content_proxy_for(url_or_descr)
     end
-    
-    
+
+
     def self.absolute_path_for(url)
       find_repo_for(url).absolute_path(url)
     end
-    
+
     def self.read_content(url, opts)
       find_repo_for(url).read(url)
     end
-    
+
     def self.find_repo_for(url)
       parts = url.split(':')
       name = parts[1]
@@ -112,23 +113,26 @@ module OMF::Web
       end
       return repo
     end
-    
-    
-    # Find files whose file name matches 'selector'. 
-    # 
+
+
+    # Find files whose file name matches 'selector'.
+    #
     # Supported options:
     #   * :max - Maximum numbers of matches to return
     #   * :mime_type - Only return files with that specific mime type.
+    #   * :repo_iterator [Iterator] - Iterator over repos to search
     #
     def self.find_files(selector, opts = {})
-      # TODO: Search across ALL registered repos
-      fs = @@primary_repository.find_files(selector, opts)
+      fsa = (opts[:repo_iterator] || [@@primary_repository]).map do |repo|
+        repo.find_files(selector, opts)
+      end
+      fs = fsa.flatten
       if (max = opts[:max])
         fs = fs[0, max]
       end
       fs
-    end    
-    
+    end
+
     #
     # Create a URL for a file with 'path' in the user's primary repository.
     # If 'strictly_new' is true, returns nil if 'path' already exists.
@@ -137,17 +141,17 @@ module OMF::Web
       # TODO: Need to add code to select proper repository
       return GitContentRepository.create_url(path, strictly_new)
     end
-    
-    
+
+
     attr_reader :name, :top_dir
-    
+
     def initialize(name, opts)
       @name = name
       if @top_dir = opts[:top_dir]
         @top_dir = File.expand_path(@top_dir)
       end
     end
-    
+
     #
     # Return an array of file names which are in the repository and
     # match 'search_pattern'
@@ -155,8 +159,8 @@ module OMF::Web
     def find_files(search_pattern, opts = {})
       raise "Missing implementation"
     end
-    
-    
+
+
     def mime_type_for_file(content_descriptor)
       fname = content_descriptor
       if content_descriptor.is_a? Hash
@@ -165,7 +169,7 @@ module OMF::Web
       ext = fname.split('.')[-1]
       mt = MIME_TYPE[ext.to_sym] || 'text'
     end
-    
+
     def read(content_descr)
       path = _get_path(content_descr)
       Dir.chdir(@top_dir) do
@@ -175,21 +179,21 @@ module OMF::Web
         content = File.open(path).read
         return content
       end
-    end    
-    
+    end
+
     def absolute_path(content_descr)
       path = _get_path(content_descr)
       File.join(@top_dir, path)
     end
-    
+
     def path(content_descr)
       path = _get_path(content_descr)
     end
-    
+
     # Return a URL for a path in this repo
-    # 
+    #
     def get_url_for_path(path)
       raise "Missing implementation"
     end
   end # class
-end # module
+end # module

data/lib/omf-web/data_source_proxy.rb

@@ -4,20 +4,30 @@ require 'omf_common/lobject'
 require 'omf_oml/network'
 
 module OMF::Web
-        
-  # This object maintains synchronization between a JS DataSource object 
+
+  # This object maintains synchronization between a JS DataSource object
   # in a web browser and the corresponding +OmlTable+ in this server.
   #
   #
   class DataSourceProxy < OMF::Common::LObject
-    
+
     @@datasources = {}
-    
+
     # Register a data source.
     #
     # params data_source - Data source to register
     # params opts:
     #          name - Name to use instead of data source's native name
+
+    #
+    # A data_source needs to support eh following methods:
+    #
+    #  * rows Returns an array of rows
+    #  * on_content_changed(lambda{action, rows}) Call provided block with actions :added, :removed
+    #  * create_sliced_table (optional)
+    #  * release Not exactly sure when that is being used
+    #  * schema Schema of row
+    #  * offset
     #
     def self.register_datasource(data_source, opts = {})
       name = (opts[:name] || data_source.name).to_sym
@@ -32,9 +42,9 @@ module OMF::Web
       # else
         # @@datasources[name] = data_source
       # end
-      @@datasources[name] = data_source      
+      @@datasources[name] = data_source
     end
-    
+
     def self.[](name)
       name = name.to_sym
       unless dsp = OMF::Web::SessionStore[name, :dsp]
@@ -46,7 +56,7 @@ module OMF::Web
       end
       dsp
     end
-    
+
     # Return proxies for 'ds_name'. Note, there can be more then
     # one proxy be needed for a datasource, such as a network which
     # has one ds for the nodes and one for the links
@@ -69,8 +79,8 @@ module OMF::Web
         top = "#{ds_name}/"
         names = @@datasources.keys.find_all { |ds_name| ds_name.to_s.start_with? top }
         unless names.empty?
-          return names.map do |ds_name| 
-            OMF::Web::SessionStore[ds_name, :dsp] ||= self.new(ds_name, @@datasources[ds_name]) 
+          return names.map do |ds_name|
+            OMF::Web::SessionStore[ds_name, :dsp] ||= self.new(ds_name, @@datasources[ds_name])
           end
         end
         # debug ">>>> #{dsa}"
@@ -93,25 +103,25 @@ module OMF::Web
         end
         return proxies
       end
-      
+
       #debug ">>>>> DS: #{ds_descr.inspect} - #{ds}"
       proxy = OMF::Web::SessionStore[ds_name, :dsp] ||= self.new(ds_name, ds)
       return [proxy]
     end
-    
+
     attr_reader :name
-    
+
     def reset()
-      # TODO: Figure out partial sending 
+      # TODO: Figure out partial sending
     end
-    
+
     def on_update(req)
       res = {:events => @data_source.rows}
       [res.to_json, "text/json"]
     end
-    
+
     # Register callback to be informed of changes to the underlying data source.
-    # Call block when new rows are becoming available. Block needs ot return 
+    # Call block when new rows are becoming available. Block needs ot return
     # true if it wants to continue receiving updates.
     #
     # offset: Number of records already downloaded
@@ -128,7 +138,7 @@ module OMF::Web
         block.call action, rows
       end
     end
-    
+
     # Create a new data source which only contains a slice of the underlying data source
     def create_slice(col_name, col_value)
       ds = @data_source.create_sliced_table(col_name, col_value)
@@ -136,7 +146,7 @@ module OMF::Web
       def dsp.release; @data_source.release end
       dsp
     end
-    
+
     def to_javascript(opts = {})
       #puts "to_java>>>>> #{opts.inspect}"
       sid = Thread.current["sessionID"]
@@ -145,23 +155,24 @@ module OMF::Web
       opts[:schema] = @data_source.schema.describe
       opts[:update_url] = "/_update/#{@name}?sid=#{sid}"
       opts[:sid] = sid
+      #opts[:is_static] = (@data_source.respond_to? :static?) ? @data_source.static? : false
       unless opts[:slice] # don't send any data if this is a sliced one
         #opts[:rows] = @data_source.rows[0 .. 20]
         opts[:rows] = []
         opts[:offset] = @data_source.offset
       end
       #puts "to_java2>>>>> #{opts.inspect}"
-      
+
       %{
         OML.data_sources.register(#{opts.to_json});
       }
-     
+
     end
-    
+
     def initialize(name, data_source)
       @name = name
       @data_source = data_source
     end
   end
-  
+
 end

data/lib/omf-web/rack/session_authenticator.rb

@@ -28,22 +28,61 @@ module OMF::Web::Rack
     # Return true if the session is authenticated
     #
     def self.authenticated?
-      debug "AUTH: #{self[:authenticated] == true}"
-      self[:authenticated] == true
+      auth = self[:authenticated] == true && self[:valid_until] > Time.now
+      #debug "AUTH: #{auth}"
+      auth
     end
 
     # Calling this method will authenticate the current session
     #
-    def self.authenticate
+    def self.authenticate(expires = nil)
       self[:authenticated] = true
       self[:valid_until] = Time.now + @@expire_after
     end
 
+    # Information about the authenticated user
+    #
+    def self.user()
+      self[:user]
+    end
+
+    # Attempt to authenticate with the provided 'req'
+    def self.authenticate_with(req)
+      p = req.params
+      #puts ">>>>>>> AA(#{req.host_with_port}): #{p}"
+      case t = p['method']
+      when 'persona'
+        require 'net/http'
+        unless assertion = p['assertion']
+          raise AuthenticationFailedException.new("Missing assertion")
+        end
+
+        http = Net::HTTP.new('verifier.login.persona.org', 443)
+        http.use_ssl = true
+        data = "assertion=#{assertion}&audience=#{req.host_with_port}"
+        headers = {'Content-Type' => 'application/x-www-form-urlencoded'}
+        reply = http.post('/verify', data, headers)
+        unless reply.code_type == Net::HTTPOK && reply.content_type == "application/json"
+          raise AuthenticationFailedException.new("Could not verify Persona - '#{reply.body}'")
+        end
+        debug "Persona reply: '#{reply.body}'"
+        r = JSON.load(reply.body)
+        unless ((email = r['email']) && (expires = r['expires']))
+          raise AuthenticationFailedException.new("Could not verify Persona - '#{r}'")
+        end
+        self[:user] = {name: email, email: email, method: 'persona'}
+        authenticate(Time.at(expires))
+      else
+        raise AuthenticationFailedException.new("Unsupported authentication type '#{t}'")
+      end
+    end
+
     # Logging out will un-authenticate this session
     #
     def self.logout
       debug "LOGOUT"
       self[:authenticated] = false
+      self[:user] = nil
     end
 
     # DO NOT CALL DIRECTLY
@@ -79,23 +118,20 @@ module OMF::Web::Rack
     end
 
     def check_authenticated
-      authenticated = self.class[:authenticated] == true
-      #puts "AUTHENTICATED: #{authenticated}"
+      authenticated = self.class.authenticated?
       raise AuthenticationFailedException.new unless authenticated
-      #self.class[:valid_until] = Time.now + @@expire_after
-
     end
 
     def call(env)
-      #puts env.keys.inspect
       req = ::Rack::Request.new(env)
       path_info = req.path_info
-      unless sid = req.cookies['sid']
+      sid = req.cookies['sid']
+      unless sid
         sid = "s#{(rand * 10000000).to_i}_#{(rand * 10000000).to_i}"
       end
       Thread.current["sessionID"] = sid  # needed for Session Store
+      debug "Request for '#{path_info}' - sid: #{sid} - #{self.class.authenticated?}"
       unless @opts[:no_session].find {|rx| rx.match(path_info) }
-
         # If 'login_page_url' is defined, check if this session is authenticated
         login_url = @opts[:login_page_url]
         if login_url && login_url != req.path_info
@@ -107,13 +143,13 @@ module OMF::Web::Rack
             end
             headers = {'Location' => login_url, "Content-Type" => ""}
             Rack::Utils.set_cookie_header!(headers, 'sid', sid)
-            return [301, headers, ['Login first']]
+            return [307, headers, ['Login first']]
           end
         end
       end
 
       status, headers, body = @app.call(env)
-      Rack::Utils.set_cookie_header!(headers, 'sid', sid) if sid
+      Rack::Utils.set_cookie_header!(headers, 'sid', sid) # if sid
       [status, headers, body]
     end
   end # class