$.fn.editable.defaults.ajaxOptions = {type: 'put', dataType: 'json'};
$.fn.editable.defaults.send = 'always';
+
+// Default for editing is popup. I experimented with inline which is a little
+// nicer in that it shows up right under the mouse instead of nearby. However,
+// the inline box is taller than the regular content, which causes the page
+// layout to shift unless we make the table rows tall, which leaves a lot of
+// wasted space when not editing. Also inline can get cut off if the page is
+// too narrow, when the popup box will just move to do the right thing.
//$.fn.editable.defaults.mode = 'inline';
+
$.fn.editable.defaults.params = function (params) {
var a = {};
var key = params.pk.key;
if (value == "***invalid***") {
return "Invalid selection";
}
-}
\ No newline at end of file
+}
};
var remove_selection_click = function(e) {
- //remove_selection($(this).attr('name'));
remove_selection($(this).val());
};
var update_count = function(e) {
var lst = get_selection_list();
$("#persistent-selection-count").text(lst.length);
-
if (lst.length > 0) {
- $('#persistent-selection-list').html('<li><a href="#" class="btn pull-right" id="clear_selections_button">Clear selections</a></li>'
- +'<li class="notification"><table style="width: 100%"></table></li>');
+ $('#selection-form-content').html(
+ '<li><a href="#" id="clear_selections_button">Clear selections</a></li>'
+ + '<li><input type="submit" name="combine_selected_files_into_collection" '
+ + ' id="combine_selected_files_into_collection" '
+ + ' value="Combine selected collections and files into a new collection" /></li>'
+ + '<li class="notification"><table style="width: 100%"></table></li>');
+
for (var i = 0; i < lst.length; i++) {
- $('#persistent-selection-list > li > table').append("<tr>"
+ $('#selection-form-content > li > table').append("<tr>"
+ "<td>"
- + "<form>"
- + "<input class='remove-selection' type='checkbox' value='" + lst[i].uuid + "' checked='true'></input>"
- + "</form>"
+ + "<input class='remove-selection' name='selection[]' type='checkbox' value='" + lst[i].uuid + "' checked='true' data-stoppropagation='true' />"
+ "</td>"
+ "<td>"
- + "<span style='padding-left: 1em'><a href=\"" + lst[i].href + "\">" + lst[i].name + "</a></span>"
+ + "<div style='padding-left: 1em'><a href=\"" + lst[i].href + "\">" + lst[i].name + "</a></div>"
+ "</td>"
+ "<td style=\"vertical-align: top\">"
+ "</tr>");
}
} else {
- $('#persistent-selection-list').html("<li class='notification empty'>No selections.</li>");
+ $('#selection-form-content').html("<li class='notification empty'>No selections.</li>");
}
var checkboxes = $('.persistent-selection:checkbox');
$(window).on('load storage', update_count);
+
+ $('#selection-form-content').on("click", function(e) {
+ e.stopPropagation();
+ });
});
add_form_selection_sources = null;
overflow-y: auto;
}
-#persistent-selection-list {
- width: 500px;
-}
-
-#persistent-selection-list li table tr {
- border-top: 1px solid rgb(221, 221, 221);
-}
--- /dev/null
+class ActionsController < ApplicationController
+
+ skip_before_filter :find_object_by_uuid, only: :post
+
+ def combine_selected_files_into_collection
+ lst = []
+ files = []
+ params["selection"].each do |s|
+ m = CollectionsHelper.match(s)
+ if m and m[1] and m[2]
+ lst.append(m[1] + m[2])
+ files.append(m)
+ end
+ end
+
+ collections = Collection.where(uuid: lst)
+
+ chash = {}
+ collections.each do |c|
+ c.reload()
+ chash[c.uuid] = c
+ end
+
+ combined = ""
+ files.each do |m|
+ mt = chash[m[1]+m[2]].manifest_text
+ if m[4]
+ IO.popen(['arv-normalize', '--extract', m[4][1..-1]], 'w+b') do |io|
+ io.write mt
+ io.close_write
+ while buf = io.read(2**20)
+ combined += buf
+ end
+ end
+ else
+ combined += chash[m[1]+m[2]].manifest_text
+ end
+ end
+
+ normalized = ''
+ IO.popen(['arv-normalize'], 'w+b') do |io|
+ io.write combined
+ io.close_write
+ while buf = io.read(2**20)
+ normalized += buf
+ end
+ end
+
+ require 'digest/md5'
+
+ d = Digest::MD5.new()
+ d << normalized
+ newuuid = "#{d.hexdigest}+#{normalized.length}"
+
+ env = Hash[ENV].
+ merge({
+ 'ARVADOS_API_HOST' =>
+ $arvados_api_client.arvados_v1_base.
+ sub(/\/arvados\/v1/, '').
+ sub(/^https?:\/\//, ''),
+ 'ARVADOS_API_TOKEN' => Thread.current[:arvados_api_token],
+ 'ARVADOS_API_HOST_INSECURE' =>
+ Rails.configuration.arvados_insecure_https ? 'true' : 'false'
+ })
+
+ IO.popen([env, 'arv-put', '--raw'], 'w+b') do |io|
+ io.write normalized
+ io.close_write
+ while buf = io.read(2**20)
+
+ end
+ end
+
+ newc = Collection.new({:uuid => newuuid, :manifest_text => normalized})
+ newc.save!
+
+ chash.each do |k,v|
+ l = Link.new({
+ tail_kind: "arvados#collection",
+ tail_uuid: k,
+ head_kind: "arvados#collection",
+ head_uuid: newuuid,
+ link_class: "provenance",
+ name: "provided"
+ })
+ l.save!
+ end
+
+ redirect_to controller: 'collections', action: :show, id: newc.uuid
+ end
+
+ def post
+ if params["combine_selected_files_into_collection"]
+ combine_selected_files_into_collection
+ else
+ redirect_to :back
+ end
+ end
+end
end
Collection.where(uuid: @object.uuid).each do |u|
- @prov_svg = ProvenanceHelper::create_provenance_graph u.provenance, "provenance_svg", {:direction => :top_down, :combine_jobs => :script_only} rescue nil
- @used_by_svg = ProvenanceHelper::create_provenance_graph u.used_by, "used_by_svg", {:direction => :top_down, :combine_jobs => :script_only, :pdata_only => true} rescue nil
+ puts request
+ @prov_svg = ProvenanceHelper::create_provenance_graph(u.provenance, "provenance_svg",
+ {:request => request,
+ :direction => :top_down,
+ :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
nodes << c
end
- @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {:all_script_parameters => true, :script_version_nodes => true}
+ @svg = ProvenanceHelper::create_provenance_graph nodes, "provenance_svg", {
+ :request => request,
+ :all_script_parameters => true,
+ :script_version_nodes => true}
end
def index
provenance, pips = graph(@pipelines)
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
@pipelines = @objects
@prov_svg = ProvenanceHelper::create_provenance_graph provenance, "provenance_svg", {
+ :request => request,
:all_script_parameters => true,
:combine_jobs => :script_and_version,
:script_version_nodes => true,
end
def self.match(uuid)
- /^([a-f0-9]{32}(\+[0-9]+)?)(\+.*)?$/.match(uuid.to_s)
+ /^([a-f0-9]{32})(\+[0-9]+)?(\+.*?)?(\/.*)?$/.match(uuid.to_s)
end
end
@visited = {}
@jobs = {}
end
-
+
def self.collection_uuid(uuid)
m = CollectionsHelper.match(uuid)
if m
- #if m[2]
- return m[1]
- #else
+ if m[2]
+ return m[1]+m[2]
+ else
+ return m[1]
+ end
# Collection.where(uuid: ['contains', m[1]]).each do |u|
# puts "fixup #{uuid} to #{u.uuid}"
# return u.uuid
end
def describe_node(uuid)
+ uuid = uuid.to_sym
bgcolor = determine_fillcolor @opts[:pips][uuid] if @opts[:pips]
rsc = ArvadosBase::resource_class_for_uuid uuid.to_s
if rsc
- href = "/#{rsc.to_s.underscore.pluralize rsc}/#{uuid}"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => rsc.to_s.tableize,
+ :action => :show,
+ :id => uuid.to_s,
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
#"\"#{uuid}\" [label=\"#{rsc}\\n#{uuid}\",href=\"#{href}\"];\n"
if rsc == Collection
#puts "empty!"
return "\"#{uuid}\" [label=\"(empty collection)\"];\n"
end
+ puts "#{uuid.class} #{@pdata[uuid]}"
if @pdata[uuid]
#puts @pdata[uuid]
if @pdata[uuid][:name]
return "\"#{uuid}\" [label=\"#{@pdata[uuid][:name]}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
- else
+ else
files = nil
if @pdata[uuid].respond_to? :files
files = @pdata[uuid].files
if i < files.length
label += "\\n⋮"
end
+ #puts "#{uuid} #{label} #{files}"
return "\"#{uuid}\" [label=\"#{label}\",href=\"#{href}\",shape=oval,#{bgcolor}];\n"
end
end
gr = "\"#{head}\" -> \"#{tail}\""
end
if extra.length > 0
- gr += "["
+ gr += " ["
extra.each do |k, v|
gr += "#{k}=\"#{v}\","
end
gr += edge(job_uuid(job), job[:script_version], {:label => "script_version"})
end
end
+ elsif rsc == Link
+ # do nothing
else
gr += describe_node(uuid)
end
@pdata.each do |k, link|
if link[:head_uuid] == uuid.to_s and link[:link_class] == "provenance"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => Link.to_s.tableize,
+ :action => :show,
+ :id => link[:uuid],
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
+
gr += describe_node(link[:tail_uuid])
- gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => "/links/#{link[:uuid]}"})
+ gr += edge(link[:head_uuid], link[:tail_uuid], {:label => link[:name], :href => href})
gr += generate_provenance_edges(link[:tail_uuid])
end
end
def describe_jobs
gr = ""
@jobs.each do |k, v|
- gr += "\"#{k}\" [href=\"/jobs?"
+ href = Rails.application.routes.url_helpers.url_for ({:controller => Job.to_s.tableize,
+ :action => :index,
+ :host => @opts[:request].host,
+ :port => @opts[:request].port})
+
+ gr += "\"#{k}\" [href=\"#{href}?"
n = 0
v.each do |u|
gr += "\",label=\""
if @opts[:combine_jobs] == :script_only
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}"
elsif @opts[:combine_jobs] == :script_and_version
- gr += uuid = "#{v[0][:script]}"
+ gr += "#{v[0][:script]}" # Just show the name but the nodes will be distinct
else
- gr += uuid = "#{v[0][:script]}\\n#{v[0][:finished_at]}"
+ gr += "#{v[0][:script]}\\n#{v[0][:finished_at]}"
end
gr += "\",#{determine_fillcolor n}];\n"
end
gr += "}"
svg = ""
- #puts gr
-
+ puts gr
+
require 'open3'
Open3.popen2("dot", "-Tsvg") do |stdin, stdout, wait_thr|
class Collection < ArvadosBase
+
def total_bytes
if files
tot = 0
$arvados_api_client.api "collections/#{self.uuid}/", "used_by"
end
- # def selection_label
- # name = ''
- # i = 0
- # if self.files.length > 3
- # m = 3
- # else
- # m = self.files.length
- # end
- # while i < m
- # name += "#{self.files[i][1]}"
- # i += 1
- # name += ", " if i < m
- # end
- # if i < self.files.length
- # name += "&ellip;"
- # end
- # name
- # end
end
</tr>
</thead><tbody>
<% if @object then @object.files.sort_by{|f|[f[0],f[1]]}.each do |file| %>
- <% file_path = "#{file[0]}/#{file[1]}" %>
- <tr>
- <td>
- <% fp2 = file_path[2..-1] if file_path[0..1] == './' %>
- <% fp2 ||= file_path %>
-<%= check_box_tag 'uuids[]', @object.uuid+file_path, false, {
- :class => 'persistent-selection',
- :friendly_type => "File",
- :friendly_name => "#{@object.uuid}/#{fp2}",
- :href => "#{url_for controller: 'collections', action: 'show', id: @object.uuid }/#{file_path}"
- } %>
- </td>
- <td>
- <%= file[0] %>
- </td>
+ <% f0 = file[0] %>
+ <% f0 = '' if f0 == '.' %>
+ <% f0 = f0[2..-1] if f0[0..1] == './' %>
+ <% f0 += '/' if not f0.empty? %>
+ <% file_path = "#{f0}#{file[1]}" %>
+ <tr>
+ <td>
+ <%= check_box_tag 'uuids[]', @object.uuid+'/'+file_path, false, {
+ :class => 'persistent-selection',
+ :friendly_type => "File",
+ :friendly_name => "#{@object.uuid}/#{file_path}",
+ :href => "#{url_for controller: 'collections', action: 'show', id: @object.uuid }/#{file_path}"
+ } %>
+ </td>
+ <td>
+ <%= file[0] %>
+ </td>
- <td>
- <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
- </td>
+ <td>
+ <%= link_to file[1], {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'inline'}, {title: 'View in browser'} %>
+ </td>
- <td style="text-align:right">
- <%= raw(human_readable_bytes_html(file[2])) %>
- </td>
+ <td style="text-align:right">
+ <%= raw(human_readable_bytes_html(file[2])) %>
+ </td>
- <td>
- <div style="display:inline-block">
- <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
- </div>
- </td>
- </tr>
+ <td>
+
<div style="display:inline-block">
+ <%= link_to raw('<i class="glyphicon glyphicon-download-alt"></i>'), {controller: 'collections', action: 'show_file', uuid: @object.uuid, file: file_path, size: file[2], disposition: 'attachment'}, {class: 'btn btn-info btn-sm', title: 'Download'} %>
+ </div>
+ </td>
+ </tr>
<% end; end %>
</tbody>
</table>
<span class="badge" id="persistent-selection-count"></span>
<span class="caret"></span>
</a>
- <ul class="dropdown-menu" role="menu" id="persistent-selection-list">
+ <ul class="dropdown-menu" role="menu" id="persistent-selection-list">
+ <%= form_tag '/actions' do %>
+ <div id="selection-form-content"></div>
+ <% end %>
</ul>
</li>
match '/collections/graph' => 'collections#graph'
resources :collections
get '/collections/:uuid/*file' => 'collections#show_file', :format => false
+
+ post 'actions' => 'actions#post'
+
root :to => 'users#welcome'
# Send unroutable requests to an arbitrary controller
parser = argparse.ArgumentParser(
description='Read manifest on standard input and put normalized manifest on standard output.')
+parser.add_argument('--extract', type=str, help="The file to extract from the input manifest")
+
args = parser.parse_args()
import arvados
cr = arvados.CollectionReader(r)
-print cr.manifest_text()
+if args.extract:
+ i = args.extract.rfind('/')
+ if i == -1:
+ stream = '.'
+ fn = args.extract
+ else:
+ stream = args.extract[:i]
+ fn = args.extract[(i+1):]
+ for s in cr.all_streams():
+ if s.name() == stream:
+ if fn in s.files():
+ sys.stdout.write(s.files()[fn].as_manifest())
+else:
+ sys.stdout.write(cr.manifest_text())
projects / arvados.git / commitdiff