X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/19d0b4c509ec720f9ffc1ea13f758c5825308834..02377152d7e368b6b73b2a94ceb68c99f9d55959:/apps/workbench/app/controllers/collections_controller.rb

diff --git a/apps/workbench/app/controllers/collections_controller.rb b/apps/workbench/app/controllers/collections_controller.rb
index 2508d3d49a..3089a1ed3f 100644
--- a/apps/workbench/app/controllers/collections_controller.rb
+++ b/apps/workbench/app/controllers/collections_controller.rb
@@ -2,6 +2,40 @@ class CollectionsController < ApplicationController
   skip_before_filter :find_object_by_uuid, :only => [:provenance]
   skip_before_filter :check_user_agreements, :only => [:show_file]
 
+  def show_pane_list
+    %w(Files Attributes Metadata Provenance_graph Used_by JSON API)
+  end
+
+  def set_persistent
+    case params[:value]
+    when 'persistent', 'cache'
+      persist_links = Link.filter([['owner_uuid', '=', current_user.uuid],
+                                   ['link_class', '=', 'resources'],
+                                   ['name', '=', 'wants'],
+                                   ['tail_uuid', '=', current_user.uuid],
+                                   ['head_uuid', '=', @object.uuid]])
+      logger.debug persist_links.inspect
+    else
+      return unprocessable "Invalid value #{value.inspect}"
+    end
+    if params[:value] == 'persistent'
+      if not persist_links.any?
+        Link.create(link_class: 'resources',
+                    name: 'wants',
+                    tail_uuid: current_user.uuid,
+                    head_uuid: @object.uuid)
+      end
+    else
+      persist_links.each do |link|
+        link.destroy || raise
+      end
+    end
+
+    respond_to do |f|
+      f.json { render json: @object }
+    end
+  end
+
   def index
     if params[:search].andand.length.andand > 0
       tags = Link.where(any: ['contains', params[:search]])
@@ -9,14 +43,26 @@ class CollectionsController < ApplicationController
                       Collection.where(any: ['contains', params[:search]])).
         uniq { |c| c.uuid }
     else
-      @collections = Collection.limit(100)
+      if params[:limit]
+        limit = params[:limit].to_i
+      else
+        limit = 100
+      end
+
+      if params[:offset]
+        offset = params[:offset].to_i
+      else
+        offset = 0
+      end
+
+      @collections = Collection.limit(limit).offset(offset)
     end
     @links = Link.limit(1000).
       where(head_uuid: @collections.collect(&:uuid))
     @collection_info = {}
     @collections.each do |c|
       @collection_info[c.uuid] = {
-        tags: [],
+        tag_links: [],
         wanted: false,
         wanted_by_me: false,
         provenance: [],
@@ -28,7 +74,7 @@ class CollectionsController < ApplicationController
       info = @collection_info[link.head_uuid]
       case link.link_class
       when 'tag'
-        info[:tags] << link.name
+        info[:tag_links] << link
       when 'resources'
         info[:wanted] = true
         info[:wanted_by_me] ||= link.tail_uuid == current_user.uuid
@@ -52,142 +98,6 @@ class CollectionsController < ApplicationController
     self.response_body = FileStreamer.new opts
   end
 
-  def describe_node(uuid)
-    rsc = ArvadosBase::resource_class_for_uuid uuid
-    if rsc
-      "\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{url_for rsc}/#{uuid}\"];"
-    else
-      ""
-    end
-  end
-
-  def describe_script(job)
-    #"""\"#{job.script_version}\" [label=\"#{job.script}: #{job.script_version}\"];
-    #   \"#{job.uuid}\" -> \"#{job.script_version}\" [label=\"script\"];"""
-    "\"#{job.uuid}\" [label=\"#{job.script}\\n#{job.script_version}\"];"
-  end
-
-  def job_uuid(job)
-    "#{job.script}\\n#{job.script_version}"
-  end
-
-  def collection_uuid(uuid)
-    m = /([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?/.match(uuid)
-    if m
-      m[1]
-    else
-      nil
-    end
-  end
-
-  def script_param_edges(visited, job, prefix, sp)
-    gr = ""
-    if sp and not sp.empty?
-      case sp
-      when Hash
-        sp.each do |k, v|
-          if prefix.size > 0
-            k = prefix + "::" + k.to_s
-          end
-          gr += script_param_edges(visited, job, k.to_s, v)
-        end
-      when Array
-        sp.each do |v|
-          gr += script_param_edges(visited, job, prefix, v)
-        end
-      else
-        m = collection_uuid(sp)
-        if m
-          gr += "\"#{job_uuid(job)}\" -> \"#{m}\" [label=\" #{prefix}\"];"
-          gr += generate_provenance_edges(visited, m)
-        end
-      end
-    end
-    gr
-  end
-
-  def generate_provenance_edges(visited, uuid)
-    gr = ""
-    m = collection_uuid(uuid)
-
-    if not uuid or uuid.empty? or visited[uuid] or visited[m]
-      return ""
-    end
-
-    #puts "visiting #{uuid}"
-
-    if m  
-      # uuid is a collection
-      uuid = m
-      visited[uuid] = true
-
-      gr += describe_node(uuid)
-
-      Job.where(output: uuid).each do |job|
-        #gr += describe_node(job_uuid(job)) 
-        gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" output\"];"
-        gr += generate_provenance_edges(visited, job.uuid)
-      end
-
-      Job.where(log: uuid).each do |job|
-        #gr += describe_node(job_uuid(job))
-        gr += "\"#{uuid}\" -> \"#{job_uuid(job)}\" [label=\" log\"];"
-        gr += generate_provenance_edges(visited, job.uuid)
-      end
-      
-    else
-      visited[uuid] = true
-
-      # uuid is something else
-      rsc = ArvadosBase::resource_class_for_uuid uuid
-
-      if rsc == Job
-        Job.where(uuid: uuid).each do |job|
-          gr += script_param_edges(visited, job, "", job.script_parameters)
-          #gr += describe_script(job)
-        end
-      else
-        gr += describe_node(uuid)
-      end
-    end
-
-    Link.where(head_uuid: uuid, link_class: "provenance").each do |link|
-      gr += describe_node(link.tail_uuid)
-      gr += "\"#{link.head_uuid}\" -> \"#{link.tail_uuid}\" [label=\" #{link.name}\", href=\"/links/#{link.uuid}\"];"
-      gr += generate_provenance_edges(visited, link.tail_uuid)
-    end
-
-    #puts "finished #{uuid}"
-
-    gr
-  end
-
-  def create_provenance_graph(uuid)
-    require 'open3'
-    
-    gr = """strict digraph {
-//rankdir=LR;
-node [fontsize=8,shape=box];
-edge [dir=back,fontsize=8];"""
-
-    visited = {}
-    gr += generate_provenance_edges(visited, uuid)
-
-    gr += "}"
-    svg = ""
-
-    Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
-      stdin.print(gr)
-      stdin.close
-      svg = stdout.read()
-      wait_thr.value
-      stdout.close()
-    end
-
-    svg = svg.sub(/<\?xml.*?\?>/m, "")
-    svg = svg.sub(/<!DOCTYPE.*?>/m, "")
-  end
-
   def show
     return super if !@object
     @provenance = []
@@ -219,12 +129,15 @@ edge [dir=back,fontsize=8];"""
     Link.where(head_uuid: @sourcedata.keys | @output2job.keys).each do |link|
       if link.link_class == 'resources' and link.name == 'wants'
         @protected[link.head_uuid] = true
+        if link.tail_uuid == current_user.uuid
+          @is_persistent = true
+        end
       end
     end
     Link.where(tail_uuid: @sourcedata.keys).each do |link|
       if link.link_class == 'data_origin'
         @sourcedata[link.tail_uuid][:data_origins] ||= []
-        @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_kind, link.head_uuid]
+        @sourcedata[link.tail_uuid][:data_origins] << [link.name, link.head_uuid]
       end
     end
     Collection.where(uuid: @sourcedata.keys).each do |collection|
@@ -233,7 +146,18 @@ edge [dir=back,fontsize=8];"""
       end
     end
 
-    @prov_svg = create_provenance_graph(@object.uuid)
+    Collection.where(uuid: @object.uuid).each do |u|
+      puts request
+      @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+                                                            {:request => request,
+                                                              :direction => :bottom_up,
+                                                              :combine_jobs => :script_only}) rescue nil
+      @used_by_svg = ProvenanceHelper::create_provenance_graph(u.used_by, "used_by_svg",
+                                                               {:request => request,
+                                                                 :direction => :top_down,
+                                                                 :combine_jobs => :script_only,
+                                                                 :pdata_only => true}) rescue nil
+    end
   end
 
   protected