rbbt-rest 1.8.145 → 1.8.148

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 312766692a55969cc09bb092ff4b7e6d4984187c968585b8e704c883fa2f69f9
-  data.tar.gz: 4e6dcbe9238daea5ad9296067526086bc31a01b2b16f1f2cd35127b4e6ad8f44
+  metadata.gz: 19ee6736af5384622ccdc31ef25294aa15f0fab48099f83467820341d117013b
+  data.tar.gz: 3660821decc1a11a951c8edf818964ca1068ea263ddbb2ccb24c8dfb64c8f67d
 SHA512:
-  metadata.gz: e7b72817fa8b7a3480891c71e7b3bf0333eddf1c8332a6893bed82e8d351d2c86b3a26f9803d830d722975a204d3a40b62a094716d919d22589fce82e2978e1e
-  data.tar.gz: 5b94f09eba05284b878a87e5908d05efc30bf6bbde1297e8dbecdd62929b4ef03208dc328243da72795a770d1cb3bda4ada8a41b61aa08e94f9616ab4e0a24b2
+  metadata.gz: 5475680967fc708f51e93a16cd3694b1fb9f664330b8cc09364af52b49af993cc5cbf8bdb786f80d00f9840744d025a59150b157883f2c632a6a9aa3bcf08aae
+  data.tar.gz: 4e4e73608d2d57f8fbbdca228430cecd1f2dd393d124ea0bcf8686137bdd9e38ffb8dc3abe21ec94cb2f6f4925ce9a3b6f2e828d8d60929245377345d417e2f8

data/lib/rbbt/rest/common/cache.rb

@@ -4,6 +4,17 @@ require 'rbbt/rest/common/table'
 
 module RbbtRESTHelpers
 
+  def escape_url(url)
+    base, _sep, query = url.partition("?")
+    base = base.split("/").collect{|p| CGI.escape(p) }* "/"
+    if query && ! query.empty?
+      query = query.split("&").collect{|e| e.split("=").collect{|pe| CGI.escape(pe) } * "=" } * "&"
+      [base, query] * "?"
+    else
+      base
+    end
+  end
+
   MEMORY_CACHE = {}
 
   def old_cache(path, check)
@@ -38,7 +49,12 @@ module RbbtRESTHelpers
     path = if params[:cache_file]
              params[:cache_file] 
            else
-             name = name.gsub("/",'>') << "_" << Misc.obj2digest(params) if params.any?
+             if post_hash = params["__post_hash_id"]
+               name = name.gsub("/",'>') << "_" << post_hash
+             elsif params
+               param_hash = Misc.obj2digest(params)
+               name = name.gsub("/",'>') << "_" << param_hash 
+             end
              settings.cache_dir[name].find
            end
 
@@ -56,6 +72,12 @@ module RbbtRESTHelpers
 
     # Clean/update job
 
+    clean_url = request.url
+    clean_url = remove_GET_param(clean_url, :_update)
+    clean_url = remove_GET_param(clean_url, :_)
+
+    clean_url =  add_GET_param(clean_url, "__post_hash_id", params["__post_hash_id"]) if params.include?("__post_hash_id") && @is_method_post
+
     if not @fragment and (old_cache(step.path, check) or update == :reload)
       begin
         pid = step.info[:pid] 
@@ -65,11 +87,10 @@ module RbbtRESTHelpers
         Log.medium{$!.message}
       end
       step.clean 
+
+      redirect remove_GET_param(clean_url, "__post_hash_id")
     end
 
-    clean_url = request.url
-    clean_url = remove_GET_param(clean_url, :_update)
-    clean_url = remove_GET_param(clean_url, :_)
 
     class << step
       def url
@@ -78,6 +99,8 @@ module RbbtRESTHelpers
 
     end
 
+    #step.instance_variable_set(:@url, clean_url)
+    #step.instance_variable_set(:@url_path, URI(clean_url).path)
     step.instance_variable_set(:@url, clean_url)
     step.instance_variable_set(:@url_path, URI(clean_url).path)
     step.clean if step.error? || step.aborted?
@@ -95,6 +118,8 @@ module RbbtRESTHelpers
       step.set_info :template_file, params[:_template_file].to_s
     end
 
+    redirect clean_url if params.include?("__post_hash_id") && @is_method_post
+
     # Return fragment
 
     if @fragment
@@ -150,10 +175,9 @@ module RbbtRESTHelpers
           list_id = "List of #{type} in table #{ @fragment }"
           list_id << " (#{ @filter })" if @filter
           Entity::List.save_list(type.to_s, list_id, list, user)
-          header "Location", Entity::REST.entity_list_url(list_id, type)
-          url = Entity::REST.entity_list_url(list_id, type)
+          url =  Entity::REST.entity_list_url(list_id, type)
           url = url + '?_layout=false' unless @layout
-          url = URI.encode(url)
+          url = escape_url(url)
           redirect to(url)
         when "map"
           raw_tsv, tsv_options = load_tsv(fragment_file)
@@ -175,7 +199,7 @@ module RbbtRESTHelpers
           Entity::Map.save_map(type.to_s, column, map_id, tsv, user)
           url = Entity::REST.entity_map_url(map_id, type, column)
           url = url + '?_layout=false' unless @layout
-          url = URI.encode(url)
+          url = escape_url(url)
           redirect to(url)
         when "excel"
           require 'rbbt/tsv/excel'
@@ -274,10 +298,6 @@ data = NULL
       end
     end
 
-    if update == :reload
-      redirect to(clean_url)
-    end
-
     # Monitor
     
     begin

data/lib/rbbt/rest/common/misc.rb

@@ -57,15 +57,20 @@ module RbbtRESTHelpers
 
   def process_common_parameters
     @ajax = request.xhr?
-    @ajax_url = headers["AJAX-URL"]
 
     @uri = request.env["REQUEST_URI"]
+    @uri = remove_GET_param(@uri, ["_update", "_", "_layout"])
+    @request_method = request.env["REQUEST_METHOD"]
+    @is_method_post = @request_method.to_s.downcase == 'post'
+
+    @uri = post_uri if @is_method_post
+
     @path = request.env["PATH_INFO"]
     @query = request.env["QUERY_STRING"]
-
-    #@fullpath = request.fullpath
     @fullpath = (@query && ! @query.empty?) ? @path + "?" + @query : @path
-    @fullpath = remove_GET_param(@fullpath, ["_update", "_"])
+    @fullpath = remove_GET_param(@fullpath, ["_update", "_", "_layout"])
+
+    @ajax_url = @uri
 
     @layout = consume_parameter(:_layout)
 

data/lib/rbbt/rest/common/render.rb

@@ -42,15 +42,15 @@ module RbbtRESTHelpers
   end
 
   def wait_on(job, layout = nil)
+    layout = @layout if layout.nil?
+
     3.times do |rep|
       raise RbbtRESTHelpers::Retry if job.done? or job.error?
       sleep 1
-    end
+    end if layout
 
     raise RbbtRESTHelpers::Retry if job.done? or job.error?
 
-    layout = @layout if layout.nil?
-
     layout_file = (layout ? locate_template('layout') : nil)
     template_file = locate_template('wait')
 
@@ -232,7 +232,7 @@ module RbbtRESTHelpers
     filename = Misc.sanitize_filename(Misc.name2basename(filename))
 
     if @step
-      url = add_GET_param(remove_GET_param(@fullpath, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
+      url = add_GET_param(remove_GET_param(@uri, ["_update", "_"]), "_fragment", "html_resources/#{ filename }")
       f = @step.file(:html_resources)[filename].find
     else
       url = "/files/#{ filename }"
@@ -270,7 +270,7 @@ module RbbtRESTHelpers
     filename = File.basename(TmpFile.tmp_file) if filename.nil?
 
     if @step
-      url = add_GET_param(remove_GET_param(@fullpath, ["_update", "_"]), "_fragment", "json_resources/#{ filename }")
+      url = add_GET_param(remove_GET_param(@uri, ["_update", "_"]), "_fragment", "json_resources/#{ filename }")
       f = @step.file(:json_resources)[filename].find
     else
       url = "/files/#{ filename }"

data/lib/rbbt/rest/common/table.rb

@@ -402,7 +402,7 @@ module RbbtRESTHelpers
     if @step
       table_file = @step.file(table_code) if @step
 
-      url = add_GET_param(@fullpath, "_fragment", File.basename(table_file))
+      url = add_GET_param(@uri, "_fragment", File.basename(table_file))
       url = remove_GET_param(url, "_update")
       url = remove_GET_param(url, "_layout")
       url = remove_GET_param(url, "_")

data/lib/rbbt/rest/common/users.rb

@@ -12,7 +12,7 @@ module Sinatra
 
       def authorize!
         return true if authorized?
-        target_url = request.env["REQUEST_URI"]
+        target_url = @uri
         Log.warn{ "Unauthorized access to #{target_url}" }
         session[:target_url] = target_url
         redirect to('/login')

data/lib/rbbt/rest/helpers.rb

@@ -1,5 +1,31 @@
 module Sinatra
   module RbbtMiscHelpers
+    def param_file(name)
+      name = name.to_s
+      if @params[name + '__param_file']
+        @params[name + '__param_file']['tempfile']
+      elsif @params[name]
+        StringIO.new @params[name]
+      else
+        nil
+      end
+    end
+
+    def post_uri
+      new_params = {}
+      @params.each do |k,v|
+        if m = k.match(/(.*)__param_file/)
+          new_params[m[1]] = v['filename']
+        else
+          new_params[k] = v
+        end
+      end
+      hash = Misc.obj2digest(new_params)
+      params["__post_hash_id"] = hash
+      @uri + "?__post_hash_id=#{hash}"
+    end
+
+
     def file_mimetype(path)
       require 'mimemagic'
       mime = nil

data/lib/rbbt/rest/main.rb

@@ -123,10 +123,10 @@ module Sinatra
             dir = settings.file_dir
             FileUtils.mkdir_p dir unless File.exists? dir
             printer.print(:path => dir, :profile => 'profile')
-            Log.info{ "Profile saved at #{ dir }: #{request.env["REQUEST_URI"]}" }
+            Log.info{ "Profile saved at #{ dir }: #{@uri}" }
           end
 
-          response.header["URI"] = request.env["REQUEST_URI"]
+          response.header["URI"] = @uri
         end
 
         add_sass_load_path Rbbt.views.compass.find
@@ -186,6 +186,12 @@ module Sinatra
           template_render(template, params, name, :cache_type => :asynchronous)
         end
 
+        post '/main/*' do |file|
+          template = File.join 'main', file
+          name = template.gsub(/\//,' - ')
+          template_render(template, params, name, :cache_type => :asynchronous)
+        end
+
         get '/help/?:section?' do
           if params[:section]
             section = params[:section]

data/lib/rbbt/rest/workflow/stream_task.rb

@@ -9,7 +9,7 @@ class StreamWorkflowTask
   EOL = "\r\n"
 
   def parse_uri(env)
-    uri = env["REQUEST_URI"]
+    uri = @uri
     _n, workflow, task = uri.split("/")
     workflow = begin
                  Kernel.const_get(workflow)
@@ -195,9 +195,9 @@ class StreamWorkflowTask
   end
 
   def do_stream(env)
-    uri = env["REQUEST_URI"]
+    uri = @uri
 
-    post = env["REQUEST_METHOD"]
+    post = @request_method
     return false unless post == "POST"
 
     hijack = !!env["rack.hijack"]

data/lib/rbbt/rest/workflow.rb

@@ -292,7 +292,7 @@ module Sinatra
         job  = consume_parameter(:job)
         filename = params[:splat].first
 
-        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include? task.to_sym
+        raise Workflow::TaskNotFoundException.new workflow, task unless workflow.tasks.include?(task.to_sym)
 
         execution_type = execution_type(workflow, task)
 

data/share/views/compass/misc.sass

@@ -94,9 +94,21 @@ table
   .caption, .title
     color: $subtle-font
 
+// USED?
 .info > .meta dt
   font-weight: bold
 
+//
+.card_sidebar .meta
+  & dt
+    font-weight: bold
+
+  & dd
+    min-height: 1em
+    &:empty
+      width: 3em
+      background-color: #eee
+
 dd > ul
   margin-top: 0px
 

data/share/views/entity_partials/action_card.haml

@@ -49,7 +49,7 @@
 
     .action_content
       - if require_parameters
-        %p Please configure the parameters to execute the action
+        .ui.message.warning Please configure the parameters to execute the action
       - else
         = capture_haml &block
 

data/share/views/entity_partials/entity_card.haml

@@ -25,6 +25,7 @@
     - if info.any? or card.meta or card.list_container
       .meta
         - if info.any?
+          - empty = false
           %h3 Meta data
           .entity_info
             = hash2dl(info)

data/share/views/entity_partials/entity_map_card.haml

@@ -21,7 +21,7 @@
               %input(type='submit')
 
           - if (%w(pvalue p.value p-value pvalues p.values p-values qvalue q.value q-value qvalues q.values q-values) & map.fields.first.downcase.split(/\s+/)).any? and map.fields.first.downcase !~ /score$/
-            - url = add_GET_param(@fullpath, '_format', 'pvalue_score')
+            - url = add_GET_param(@uri, '_format', 'pvalue_score')
             %a.ui.small.button(href=url) Pvalue score
 
             = reveal "QQ-plot", nil, :class => 'ui small button plot' do
@@ -56,16 +56,16 @@
 
           - if Gene == Entity.formats[map.key_field]
             - if map.key_field != "Ensembl Gene ID"
-              - url = add_GET_param(@fullpath, '_format', 'ensembl')
+              - url = add_GET_param(@uri, '_format', 'ensembl')
               %a.ensembl.ui.small.button(href=url) Ensembl
             - if map.key_field != "Associated Gene Name"
-              - url = add_GET_param(@fullpath, '_format', 'name')
+              - url = add_GET_param(@uri, '_format', 'name')
               %a.name.ui.small.button(href=url) Name
           - if "Rank" == map.fields.first
-            - url = add_GET_param(@fullpath, '_format', 'invert_ranks')
+            - url = add_GET_param(@uri, '_format', 'invert_ranks')
             %a.invert_ranks.ui.small.button(href=url) Invert ranks
           - else
-            - url = add_GET_param(@fullpath, '_format', 'ranks')
+            - url = add_GET_param(@uri, '_format', 'ranks')
             %a.ranks.ui.small.button(href=url) Ranks
           - if NumericValue == Entity.formats[map.fields.first] or (map.entity_templates[map.fields.first] and map.entity_templates[map.fields.first].annotation_types.include? NumericValue)
             - $page_entity_base_type = page_entity_base_type 

data/share/views/error.haml

@@ -20,19 +20,19 @@
     
 
 
-  - if defined? job.info_file and Open.exists? job.info_file and request.env["REQUEST_URI"].include? job.name
-    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "clean")
+  - if defined? job.info_file and Open.exists? job.info_file and @uri.include? job.name
+    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")
     %a.ui.button.blue.clean(href=clean_url) Clean
   - else
-    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "reload")
+    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
-  - info_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/info'
-  - if request.env["REQUEST_URI"].include? job.name
+  - info_url = @uri.sub(/\?.*/,'') + '/info'
+  - if @uri.include? job.name
     %a.ui.blue.button.reload(href=info_url) Info
 
-  - if job.files.any? and request.env["REQUEST_URI"].include? job.name
-    - files_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/files'
+  - if job.files.any? and @uri.include? job.name
+    - files_url = @uri.sub(/\?.*/,'') + '/files'
     %a.ui.blue.button.reload(href=files_url) Files
 
 

data/share/views/job_files.haml

@@ -1,7 +1,7 @@
 
 - files = job.files 
 - task = job.task_name
-- workflow = job.workflow
+- workflow = job.workflow if job.workflow
 - jobname = job.name
 - files.reject!{|f| File.basename(File.dirname(f)) == ".html"}
 

data/share/views/job_info.haml

@@ -25,7 +25,7 @@
         - autofill_id = "autofill_" << Misc.digest(job.name)
         .ui.button.autofill(id=autofill_id) Auto-fill form with inputs
         .ui.button.autofill(id=autofill_id)
-          %a(href="#{@ajax_path}?_format=input_bundle") Download input bundle
+          %a(href="#{@ajax_url}?_format=input_bundle") Download input bundle
         :deferjs
           $('##{autofill_id}').click(function(){
             var inputs = #{inputs.to_hash.to_json};

data/share/views/job_result/job_control.haml

@@ -1,5 +1,8 @@
 .ui.buttons.job_control
-  %a.ui.small.basic.red.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_update=clean") clean job
+  - if Open.exists?(job.info_file)
+    %a.ui.small.basic.red.button(href="/#{[workflow.to_s, task, jobname] * "/"}?_update=clean") clean job
+  - else
+    %a.ui.small.basic.red.button.disabled(href="/#{[workflow.to_s, task, jobname] * "/"}?_update=clean") clean job
   %a.ui.small.basic.blue.button(href="/#{[workflow.to_s, task, jobname, "info"] * "/"}") job info
   - if job.files.any?
     %a.ui.small.basic.blue.button(href="/#{[workflow.to_s, task, jobname, "files"] * "/"}") job files

data/share/views/partials/form.haml

@@ -9,6 +9,7 @@
 
 - klass = "#{klass} custom"
 
+- action = remove_GET_param(action, '__post_hash_id') if action
 - if defined?(description) and description
   .form_description
     =description
@@ -66,7 +67,7 @@
       - input_options = options[input]
       - input_options = input_options.dup unless input_options.nil?
       - description = descriptions[input]
-      - if use[input]
+      - if use[input] && description
         - description += "\n\nUsed in:\n"
         - uses.each do |workflow, tasks|
           - tasks.each do |task|

data/share/views/public/js/helpers/_ajax_replace.js

@@ -113,14 +113,14 @@ function replace_object(object, href, embedd, complete){
       href = remove_parameter(href, '_update');
       href = remove_parameter(href, '_');
 
-
-      if (req.responseText.match('error_message') != null){
-        error_message = $(req.responseText).find('.error_message').html()
+      text = req.responseText
+      if (text.match('error_message') != null){
+        error_message = $(text).find('.error_message').html()
       }else{
-        if (req.responseText.match('summary') != null){
-          error_message = $(req.responseText).find('#summary').text()
+        if (text.match('summary') != null){
+          error_message = $(text).find('#summary').text()
         }else{
-          error_message = req.responseText.split("\n")[0]
+          error_message = text.split("\n")[0]
         }
       }
 
@@ -204,7 +204,7 @@ function update_embedded(object, reload, complete){
 
 
 function capture_embedded_form(object){
-
+  object = $(object)
   object.find('form').submit(function(){ 
     var form = $(this);
     var embedded = object;

data/share/views/public/js/rbbt.modal.js

@@ -59,6 +59,13 @@ ModalComponent = function(element){
       })
     }
 
+    ctrl.capture_embedded_form = function(){
+      var content = $(this.vm.element).find('> .content')
+      content.attr('target-href', this.vm.url)
+      console.log(content)
+      capture_embedded_form(content)
+    }
+
     ctrl.close = function(){
       ctrl.vm.visible(false)
       ctrl.vm.url = undefined

data/share/views/tools/nvd3/chart.haml

@@ -6,7 +6,7 @@
 
 - extra = "" unless defined? extra
 
-- url = @fullpath
+- url = @uri
 
 %svg.nvd3(id=id)
 

data/share/views/wait.haml

@@ -66,21 +66,21 @@
             $('.step.progress').progress({label: 'ratio',text:{ratio: '{value}'}})
 
   %hr
-  - if defined? job.info_file and File.exists? job.info_file and request.env["REQUEST_URI"].include? job.name
-    - abort_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "abort")
+  - if defined? job.info_file and File.exists? job.info_file and @uri.include? job.name
+    - abort_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "abort")
     %a.ui.button.red.abort(href=abort_url) Abort
-    -#- clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "clean")
+    -#- clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "clean")
     -#%a.ui.button.blue.clean(href=clean_url) Clean
   - else
-    - clean_url = add_GET_param(remove_GET_param(request.env["REQUEST_URI"], "_layout"), "_update", "reload")
+    - clean_url = add_GET_param(remove_GET_param(@uri, "_layout"), "_update", "reload")
     %a.ui.blue.button.reload(href=clean_url) Reload
 
-  - if request.env["REQUEST_URI"].include? job.name
-    - info_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/info'
+  - if @uri.include? job.name
+    - info_url = @uri.sub(/\?.*/,'') + '/info'
     %a.ui.blue.button.reload(href=info_url) Info
 
-  - if job.files.any? and request.env["REQUEST_URI"].include? job.name
-    - files_url = request.env["REQUEST_URI"].sub(/\?.*/,'') + '/files'
+  - if job.files.any? and @uri.include? job.name
+    - files_url = @uri.sub(/\?.*/,'') + '/files'
     %a.ui.blue.button.reload(href=files_url) Files
 
 - if ! progress

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-rest
 version: !ruby/object:Gem::Version
-  version: 1.8.145
+  version: 1.8.148
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-11-24 00:00:00.000000000 Z
+date: 2022-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -1881,7 +1881,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.6
+rubygems_version: 3.1.4
 signing_key: 
 specification_version: 4
 summary: Rbbt Web and REST interfaces