omf_web 0.9.9 → 1.0.0

data/example/simple/simple.yaml

@@ -0,0 +1,62 @@
+
+
+
+# Simple tab showing a line chart with supporting table
+#
+
+server:
+  name: 'Simple Demo'
+  port: 4050
+
+data_sources:
+  - id: signal
+    table: wave
+    database:
+      id: sample
+      url: sqlite://sample.sq3
+
+repositories:
+  - id: simple
+    type: file
+    top_dir: .
+
+widgets:
+  - id: main
+    name: Main
+    top_level: true
+    priority: 900
+    type: layout/two_columns/33_66
+    left:
+      - name: Introduction
+        type: text
+        content:
+          url: file:simple:introduction.md
+    right:
+      - type: layout/stacked
+        info: This widget shows the output measurements of three stacked generators.
+        widgets:
+          - name: Signal
+            type: data/line_chart3
+            data_source:
+              name: signal
+            mapping:
+              x_axis:
+                property: t
+              y_axis:
+                property: y
+                max: 2.0
+              group_by: oml_sender
+            axis:
+              x:
+                legend: Time (sec)
+              y:
+                legend: V
+                ticks:
+                  format: ".1f"
+
+          - name: Table
+            type: data/table2
+            data_source:
+              name: signal
+
+

data/example/simple/simple_dynamic.yaml

@@ -0,0 +1,66 @@
+
+
+
+# Simple tab showing a line chart with supporting table
+#
+
+server:
+  name: 'Simple Demo'
+  port: 4050
+
+data_sources:
+  - id: signal
+    table: wave
+    dynamic: 2 # Check every 2 seconds
+    limit: 5 # Fetch 5 rows each time
+    database:
+      id: sample
+      url: sqlite://sample.sq3
+
+repositories:
+  - id: simple
+    type: file
+    top_dir: .
+
+widgets:
+  - id: main
+    name: Main
+    top_level: true
+    priority: 900
+    type: layout/two_columns/33_66
+    left:
+      - name: Introduction
+        type: text
+        content:
+          url: file:simple:introduction.md
+    right:
+      - type: layout/stacked
+        info: This widget shows the output measurements of three stacked generators.
+        widgets:
+          - name: Signal
+            type: data/line_chart3
+            data_source:
+              name: signal
+              dynamic: 2
+            mapping:
+              x_axis:
+                property: t
+              y_axis:
+                property: y
+                max: 2.0
+              group_by: oml_sender
+            axis:
+              x:
+                legend: Time (sec)
+              y:
+                legend: V
+                ticks:
+                  format: ".1f"
+
+          - name: Table
+            type: data/table2
+            data_source:
+              name: signal
+              dynamic: 2
+
+

data/lib/irods4r/file.rb

@@ -2,15 +2,15 @@
 require 'irods4r/directory'
 
 module IRODS4r
-  
+
   #class NotFoundException < Exception; end
-  class NoFileException < Exception; end  
-  class FileExistsException < Exception; end    
-  
+  class NoFileException < Exception; end
+  class FileExistsException < Exception; end
+
   # This class proxies a file in an iRODS environment
   #
   class File
-    
+
     # Create a file resource 'path'. If 'must_not_exist' is true,
     # throw exception if resource already exists.
     #
@@ -20,34 +20,35 @@ module IRODS4r
       end
       self.new(path, opts)
     end
-    
-    
+
+
     # Return the content of this file
     def read()
-      ICommands.read(@path)
+      ICommands.read(@path, @ticket)
     end
-    
+
     # Write content to this file.
     #
     # WARN: This will overwrite any previous content
     #
     def write(content)
-      ICommands.write(@path, content)
+      ICommands.write(@path, content, @ticket)
     end
 
     def file?
       return true
     end
-    
+
     def directory?
       return false
     end
-    
+
     attr_reader :path
-    
+
     private
     def initialize(path, opts = {})
       @path = path
+      @ticket = opts[:ticket]
     end
   end
-end
+end

data/lib/irods4r/icommands.rb

@@ -2,62 +2,62 @@
 require 'irods4r'
 
 module IRODS4r
-  
+
   # This module interfaces directly with the IRODS system
   #
   module ICommands
     class ICommandException < IRODS4rException; end
-      
-    # Return the list of files found at 'path'. 
-    def self.ls(path)
-      r = `ils #{path}`
+
+    # Return the list of files found at 'path'.
+    def self.ls(path, ticket = nil)
+      r = `ils #{"-t #{ticket}" if ticket} #{path}`
       #raise ICommandException.new($?) unless $?.exitstatus == 0
       if r.empty?
         raise NotFoundException.new("Can't find resource '#{path}'")
-      end 
+      end
       r.lines
     end
-    
+
     # Return content of resource at 'path'
     #
-    def self.read(path)
+    def self.read(path, ticket = nil)
       f = Tempfile.new('irods4r')
-      `iget -f #{path} #{f.path}`
+      `iget -f #{"-t #{ticket}" if ticket} #{path} #{f.path}`
       raise ICommandException.new($?) unless $?.exitstatus == 0
       content = f.read
       f.close
       f.unlink
       content
     end
-    
+
     # Return content of resource at 'path'
     #
-    def self.write(path, content)
+    def self.write(path, content, ticket = nil)
       f = Tempfile.new('irods4r')
       f.write(content)
       f.close
-      `iput -f #{f.path} #{path}`
+      `iput -f #{"-t #{ticket}" if ticket} #{f.path} #{path}`
       raise ICommandException.new($?) unless $?.exitstatus == 0
       f.unlink
     end
 
-    def self.exist?(path)
-      `ils #{path}`
+    def self.exist?(path, ticket = nil)
+      `ils #{"-t #{ticket}" if ticket} #{path}`
       $?.exitstatus == 0
     end
-    
+
     # Copy the resource at 'path' in iRODS to 'file_path'
     # in the local file system.
     #
-    def self.export(path, file_path, create_parent_path = true)
+    def self.export(path, file_path, create_parent_path = true, ticket = nil)
       #puts ">>>> #{path} -> #{file_path}"
       if create_parent_path
         require 'fileutils'
         FileUtils.mkpath ::File.dirname(file_path)
       end
-      `iget -f #{path} #{file_path}`
+      `iget -f #{"-t #{ticket}" if ticket} #{path} #{file_path}`
       raise ICommandException.new($?) unless $?.exitstatus == 0
     end
   end #module
 end # module
-      
+

data/lib/irods4r.rb

@@ -1,10 +1,10 @@
 
 
 module IRODS4r
-  
+
   class IRODS4rException < Exception; end
   class NotFoundException < IRODS4rException; end
-  class NoDirectoryException < IRODS4rException; end  
+  class NoDirectoryException < IRODS4rException; end
 
   # Return a IRODS4r object for 'irodsPath' if it exists.
   #
@@ -12,23 +12,23 @@ module IRODS4r
   # @param [Hash] opts Options to use for establishing context
   # @return [Directory|File]
   #
-  def self.find(irodsPath = ".", opts = {})
-    r = ICommands.ls(irodsPath)
+  def self.find(irodsPath = ".", opts = {}, ticket = nil)
+    r = ICommands.ls(irodsPath, ticket)
     name = r.to_a[0].strip
     if name.end_with? ':'
       Directory.new(name[0 ... -1])
     else
       File.new(name)
-    end 
+    end
   end
-  
+
   # Return true if 'path' exists
-  def self.exists?(path)
-    ICommands.exist?(path)
+  def self.exists?(path, ticket = nil)
+    ICommands.exist?(path, ticket)
   end
 end
 
 require 'irods4r/directory'
 require 'irods4r/file'
 require 'irods4r/icommands'
-  
+

data/lib/omf-web/config.ru

@@ -1,16 +1,19 @@
 
 require 'omf_common/lobject'
+require 'rack/accept'
 
 use ::Rack::ShowExceptions
 #use ::Rack::Lint
+use Rack::Accept
 
 OMF::Web::Runner.instance.life_cycle(:pre_rackup)
 options = OMF::Web::Runner.instance.options
+auth_opts = options[:authentication] || {required: false}
 
 require 'omf-web/rack/session_authenticator'
 use OMF::Web::Rack::SessionAuthenticator, #:expire_after => 10,
-          #:login_url => '/tab/login',
-          :no_session => ['^/resource/', '^/login', '^/logout']
+          login_page_url: auth_opts[:required] ? (auth_opts[:login_url] || '/content/login') : nil,
+          no_session: ['^/resource/', '^/auth']
 
 map "/resource/vendor/" do
   require 'omf-web/rack/multi_file'
@@ -52,25 +55,47 @@ end
   # run OMF::Web::Rack::WidgetMapper.new(options)
 # end
 
-map '/login' do
+map '/auth/login' do
   handler = Proc.new do |env|
-    # req = ::Rack::Request.new(env)
-    # #puts ">>> post?: #{req.post?} - #{req.params.inspect}"
-    # if req.post?
-      # email = req.params["email"]
-      # pw = req.params["password"]
-      # remember = req.params["remember"] == "on"
-      # Authenticator.signon(email, pw, remember)
-    # end
-    [301, {'Location' => '/tab', "Content-Type" => ""}, ['Next window!']]
+    req = ::Rack::Request.new(env)
+    accept = env['rack-accept.request']
+    begin
+      OMF::Web::Rack::SessionAuthenticator.authenticate_with(req)
+    rescue OMF::Web::Rack::AuthenticationFailedException => ax
+      if accept.media_type?('application/json')
+        body = {authenticated: false, message: ax.to_s}
+        next [200, {"Content-Type" => "application/json"}, body.to_json]
+      else
+        url = auth_opts[:login_url] || '/content/login'
+        url = "#{url}?error=#{URI.encode ax.to_s}"
+        next [307, {'Location' => url, "Content-Type" => ""}, ['Next window!']]
+      end
+    end
+
+    accept = env['rack-accept.request']
+    redirect_url = "/?#{rand(10e15)}"  # avoid some ugly URL caching
+    if accept.media_type?('application/json')
+      body = {authenticated: true, redirect: redirect_url}
+      [200, {"Content-Type" => "application/json"}, body.to_json]
+    else
+      [307, {'Location' => redirect_url, "Content-Type" => ""}, ['Next window!']]
+    end
   end
   run handler
 end
 
-map '/logout' do
+map '/auth/logout' do
   handler = Proc.new do |env|
     OMF::Web::Rack::SessionAuthenticator.logout
-    [301, {'Location' => '/tab', "Content-Type" => ""}, ['Next window!']]
+
+    accept = env['rack-accept.request']
+    redirect_url = "/?#{rand(10e15)}"  # avoid some ugly URL caching
+    if accept.media_type?('application/json')
+      body = {authenticated: false, redirect: redirect_url}
+      [200, {"Content-Type" => "application/json"}, body.to_json]
+    else
+      [307, {'Location' => redirect_url, "Content-Type" => ""}, ['Next window!']]
+    end
   end
   run handler
 end
@@ -80,9 +105,9 @@ map "/" do
     req = ::Rack::Request.new(env)
     case req.path_info
     when '/'
-      [301, {'Location' => '/tab', "Content-Type" => ""}, ['Next window!']]
+      [307, {'Location' => '/tab', "Content-Type" => ""}, ['Next window!']]
     when '/favicon.ico'
-      [301, {'Location' => '/resource/image/favicon.ico', "Content-Type" => ""}, ['Next window!']]
+      [307, {'Location' => '/resource/image/favicon.ico', "Content-Type" => ""}, ['Next window!']]
     else
       OMF::Common::Loggable.logger('rack').warn "Can't handle request '#{req.path_info}'"
       [401, {"Content-Type" => ""}, "Sorry!"]

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

@@ -12,10 +12,10 @@ module OMF::Web
   # This class provides an interface to a GIT repository
   # It retrieves, archives and versions content.
   #
-  class GitContentRepository < ContentRepository  
-    
+  class GitContentRepository < ContentRepository
+
     # @@git_repositories = {}
-#     
+#
     # # Return the repository which is referenced to by elements in 'opts'.
     # #
     # #
@@ -25,8 +25,8 @@ module OMF::Web
       # end
       # repo
     # end
-      
-    # Register an existing GIT repo to the system. It will be 
+
+    # Register an existing GIT repo to the system. It will be
     # consulted for all content url's strarting with
     # 'git:_top_dir_:'. If 'is_primary' is set to true, it will
     # become the default repo for all newly created content
@@ -43,7 +43,7 @@ module OMF::Web
         # @@primary_repository = repo
       # end
     # end
-    
+
     # def self.read_content(url, opts)
       # unless (a = url.split(':')).length == 3
         # raise "Expected 'git:some_name:some_path', but got '#{url}'"
@@ -56,13 +56,13 @@ module OMF::Web
     # end
 
     attr_reader :name, :top_dir
-    
+
     def initialize(name, opts)
       super
       @repo = Grit::Repo.new(@top_dir)
       @url_prefix = "git:#{@name}:"
     end
-    
+
     #
     # Create a URL for a file with 'path' in.
     # If 'strictly_new' is true, returns nil if 'path' already exists.
@@ -72,8 +72,8 @@ module OMF::Web
       # # TODO: Need to add code to select proper repository
       # return GitContentRepository.create_url(path, strictly_new)
     # end
-    
-    
+
+
     # Load content described by either a hash or a straightforward path
     # and return a 'ContentProxy' holding it.
     #
@@ -88,9 +88,9 @@ module OMF::Web
       url = @url_prefix + path
       key = Digest::MD5.hexdigest(url)
       descr = {}
-      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])
         Dir.chdir(@top_dir) do
@@ -100,31 +100,31 @@ module OMF::Web
       proxy = ContentProxy.create(descr, self)
       return proxy
     end
-        
+
     def write(content_descr, content, message)
       path = _get_path(content_descr)
       Dir.chdir(@top_dir) do
-        unless File.writable?(path)
+        unless File.writable?(path) || File.writable?(File.dirname(path))
           raise "Cannot write to file '#{path}'"
         end
         f = File.open(path, 'w')
         f.write(content)
         f.close
-        
+
         @repo.add(path)
         # TODO: Should set info about committing user which should be in thread context
-        @repo.commit_index(message || 'no message') 
+        @repo.commit_index(message || 'no message')
       end
     end
-    
+
     # Return a URL for a path in this repo
-    # 
+    #
     def get_url_for_path(path)
       @url_prefix + path
     end
-    
-    
-    
+
+
+
     #
     # Return an array of file names which are in the repository and
     # match 'search_pattern'
@@ -134,13 +134,13 @@ module OMF::Web
       tree = @repo.tree
       res = []
       fs = _find_files(search_pattern, tree, nil, res)
-      
+
       if (mt = opts[:mime_type])
         fs = fs.select { |f| f[:mime_type] == mt }
       end
       fs
     end
-    
+
     def _find_files(search_pattern, tree, dir_path, res)
       tree.contents.each do |e|
         d = e.name
@@ -151,11 +151,12 @@ module OMF::Web
         else
           if long_name.match(search_pattern)
             mt = mime_type_for_file(e.name)
-            path = @url_prefix + long_name
-            res << {:path => path, url => url_for_path(path), :name => e.name,
-                    :mime_type => mt,
-                    #:id => Base64.encode64(long_name).gsub("\n", ''), 
-                    :size => e.size, :blob => e.id}
+            #path = @url_prefix + long_name
+            path = long_name
+            res << {path: path, url: get_url_for_path(path), name: e.name,
+                    mime_type: mt,
+                    #:id => Base64.encode64(long_name).gsub("\n", ''),
+                    size: e.size, blob: e.id}
           end
           # name = e.name
           # if File.fnmatch(search_pattern, long_name)
@@ -165,7 +166,7 @@ module OMF::Web
       end
       res
     end
-    
+
     def _get_path(content_descr)
       if content_descr.is_a? String
         path = content_descr.to_s
@@ -191,6 +192,6 @@ module OMF::Web
       end
       return path
     end
-              
+
   end # class
-end # module
+end # module