[ARVADOS] created: 687a5246e161ef1d191264d3b579271bc834223c

[git at public.curoverse.com]

        at  687a5246e161ef1d191264d3b579271bc834223c (commit)


commit 687a5246e161ef1d191264d3b579271bc834223c
Author: radhika <radhika at curoverse.com>
Date:   Wed Aug 12 11:06:13 2015 -0400

    6859: added salvage_collection.rb script.

diff --git a/services/api/script/salvage_collection.rb b/services/api/script/salvage_collection.rb
new file mode 100755
index 0000000..796fa6e
--- /dev/null
+++ b/services/api/script/salvage_collection.rb
@@ -0,0 +1,106 @@
+#!/usr/bin/env ruby
+
+# Take two input parameters: a collection uuid and reason
+# Get "src" collection with the given uuid
+# Create a new collection "dest" with:
+#   src.manifest_text as "invalid manifest_text.txt"
+#   Locators from src.manifest_text as "salvaged_data"
+# Update src collection:
+#   Set src.manifest_text to: ""
+#   Append to src.name: " (reason; salvaged data at dest.uuid)"
+#   Set portable_data_hash to "d41d8cd98f00b204e9800998ecf8427e+0"
+
+require 'trollop'
+
+opts = Trollop::options do
+  banner ''
+  banner "Usage: salvage_collection.rb " +
+    "{uuid} {reason}"
+  banner ''
+  opt :uuid, <<-eos
+uuid of the collection to be salvaged.
+  eos
+  opt :reason, <<-eos
+Reason for salvaging.
+  eos
+end
+
+if ARGV.count < 1
+  Trollop::die "required uuid argument is missing"
+end
+
+uuid, reason = ARGV
+
+require File.dirname(__FILE__) + '/../config/environment'
+require 'arvados/keep'
+include ApplicationHelper
+
+def salvage_collection uuid, reason
+  act_as_system_user do
+    root_dir = '/tmp/salvage_uuids'
+    Dir.mkdir(root_dir) unless File.exists?(root_dir)
+
+    src = Collection.find_by_uuid uuid
+    if !src
+      puts "No collection found for #{uuid}"
+      return
+    end
+
+    begin
+      src_manifest_text = src.manifest_text || ''
+
+      # write the manifest_text to a file
+      dir = root_dir+"/"+uuid
+      Dir.mkdir(dir) unless File.exists?(dir)
+      File.write(dir+"/invalid_manifest_text.txt", src_manifest_text)
+
+      # also, create another file with the locators from the collection manifest_text
+      locators = []
+      src_manifest_text.each_line do |line|
+        line.split(' ').each do |word|
+          if match = Keep::Locator::LOCATOR_REGEXP.match(word)
+            word = word.split('+')[0..1].join('+')  # get rid of any hints
+            locators << word
+          end
+        end
+      end
+
+      locators_str = locators.join(' ')
+      File.write(dir+"/salvaged_data", locators_str)
+
+=begin
+      # create new collection with salvaged data
+      dest_manifest_text = ". "
+      dest_manifest_text += (src.portable_data_hash + " 0:#{src_manifest_text.length}:invalid_manifest_text.txt\n")
+      dest_manifest_text += (". " + locators_str + " 0:#{locators_str.length}:salvaged_data\n")
+      dest_name = "Salvaged from " + uuid + ", " + src.portable_data_hash
+      dest = Collection.new name: dest_name, manifest_text: dest_manifest_text
+      dest.save!
+=end
+
+      # create new collection with salvaged data using 'arv keep put'
+      created = %x(arv keep put #{dir}/*)
+      created.rstrip!
+      match = created.match HasUuid::UUID_REGEX
+      raise "uuid not found" if !match
+      puts "Created salvaged collection for #{uuid} with uuid: #{created}  #{match}"
+    rescue => error
+      puts "Error creating salvaged collection for #{uuid}: #{error}"
+      return
+    end
+
+    begin
+      # update src collection name, pdh, and manifest_text
+      src.name = (src.name || '') + ' (' + (reason || '') + '; salvaged data at ' + created + ')'
+      src.manifest_text = ''
+      src.portable_data_hash = 'd41d8cd98f00b204e9800998ecf8427e+0'
+      src.save!
+      puts "Updated collection #{uuid}"
+    rescue => error
+      puts "Error updating source collection #{uuid}: #{error}"
+    end
+  end
+end
+
+# Salvage the collection with the given uuid
+salvage_collection uuid, reason

-----------------------------------------------------------------------


hooks/post-receive
--