[ARVADOS] created: 1.3.0-139-g7b86c93c1

Git user git at public.curoverse.com
Mon Jan 7 09:16:51 EST 2019


        at  7b86c93c104581fbf7a1fc9bfeb1ae300b9ee29e (commit)


commit 7b86c93c104581fbf7a1fc9bfeb1ae300b9ee29e
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Mon Jan 7 11:12:01 2019 -0300

    14482: Handle escaped chars on manifest validation.
    
    * Escaped & unescaped chars are treated equally, except for \040.
    * Empty '.' (and \056) named file tokens are accepted.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/sdk/ruby/lib/arvados/keep.rb b/sdk/ruby/lib/arvados/keep.rb
index ce1331ac1..2d444d074 100644
--- a/sdk/ruby/lib/arvados/keep.rb
+++ b/sdk/ruby/lib/arvados/keep.rb
@@ -103,6 +103,7 @@ module Keep
   class Manifest
     STRICT_STREAM_TOKEN_REGEXP = /^(\.)(\/[^\/\s]+)*$/
     STRICT_FILE_TOKEN_REGEXP = /^[[:digit:]]+:[[:digit:]]+:([^\s\/]+(\/[^\s\/]+)*)$/
+    EMPTY_DOT_FILE_TOKEN_REGEXP = /^0:0:\.$/
 
     # Class to parse a manifest text and provide common views of that data.
     def initialize(manifest_text)
@@ -131,18 +132,25 @@ module Keep
       end
     end
 
-    def unescape(s)
+    def self.unescape(s, except=[])
+      return nil if s.nil?
+
       # Parse backslash escapes in a Keep manifest stream or file name.
       s.gsub(/\\(\\|[0-7]{3})/) do |_|
-        case $1
-        when '\\'
+        if $1 == '\\'
           '\\'
+        elsif except.include? $1
+          $1
         else
           $1.to_i(8).chr
         end
       end
     end
 
+    def unescape(s)
+      self.class.unescape(s)
+    end
+
     def split_file_token token
       start_pos, filesize, filename = token.split(':', 3)
       if filename.nil?
@@ -250,7 +258,8 @@ module Keep
         count = 0
 
         word = words.shift
-        count += 1 if word =~ STRICT_STREAM_TOKEN_REGEXP and word !~ /\/\.\.?(\/|$)/
+        unescaped_word = unescape(word, except=["040"])
+        count += 1 if unescaped_word =~ STRICT_STREAM_TOKEN_REGEXP and unescaped_word !~ /\/\.\.?(\/|$)/
         raise ArgumentError.new "Manifest invalid for stream #{line_count}: missing or invalid stream name #{word.inspect if word}" if count != 1
 
         count = 0
@@ -262,7 +271,8 @@ module Keep
         raise ArgumentError.new "Manifest invalid for stream #{line_count}: missing or invalid locator #{word.inspect if word}" if count == 0
 
         count = 0
-        while word =~ STRICT_FILE_TOKEN_REGEXP and ($~[1].split('/') & ['..','.']).empty?
+        while unescape(word) =~ EMPTY_DOT_FILE_TOKEN_REGEXP or
+          (unescape(word, except=["040"]) =~ STRICT_FILE_TOKEN_REGEXP and ($~[1].split('/') & ['..', '.']).empty?)
           word = words.shift
           count += 1
         end
diff --git a/sdk/ruby/test/test_keep_manifest.rb b/sdk/ruby/test/test_keep_manifest.rb
index 71a24a28c..bd1312701 100644
--- a/sdk/ruby/test/test_keep_manifest.rb
+++ b/sdk/ruby/test/test_keep_manifest.rb
@@ -320,6 +320,7 @@ class ManifestTest < Minitest::Test
     [true, ". 00000000000000000000000000000000+0 0:0:0\n"],
     [true, ". 00000000000000000000000000000000+0 0:0:d41d8cd98f00b204e9800998ecf8427e+0+Ad41d8cd98f00b204e9800998ecf8427e00000000 at ffffffff\n"],
     [true, ". d41d8cd98f00b204e9800998ecf8427e+0+Ad41d8cd98f00b204e9800998ecf8427e00000000 at ffffffff 0:0:empty.txt\n"],
+    [true, "./empty_dir d41d8cd98f00b204e9800998ecf8427e+0 0:0:.\n"],
     [false, '. d41d8cd98f00b204e9800998ecf8427e 0:0:abc.txt',
       "Invalid manifest: does not end with newline"],
     [false, "abc d41d8cd98f00b204e9800998ecf8427e 0:0:abc.txt\n",
@@ -334,8 +335,9 @@ class ManifestTest < Minitest::Test
       "invalid stream name \"./abc/..\""],
     [false, "./abc/./foo d41d8cd98f00b204e9800998ecf8427e 0:0:abc.txt\n",
       "invalid stream name \"./abc/./foo\""],
-    [false, ". d41d8cd98f00b204e9800998ecf8427e 0:0:.\n",
-      "invalid file token \"0:0:.\""],
+    # non-empty '.'-named file tokens aren't acceptable. Empty ones are used as empty dir placeholders.
+    [false, ". 8cf8463b34caa8ac871a52d5dd7ad1ef+1 0:1:.\n",
+      "invalid file token \"0:1:.\""],
     [false, ". d41d8cd98f00b204e9800998ecf8427e 0:0:..\n",
       "invalid file token \"0:0:..\""],
     [false, ". d41d8cd98f00b204e9800998ecf8427e 0:0:./abc.txt\n",
@@ -429,6 +431,18 @@ class ManifestTest < Minitest::Test
       "Manifest invalid for stream 1: invalid file token \"0:0:foo//bar.txt\""],
     [false, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo/\n",
       "Manifest invalid for stream 1: invalid file token \"0:0:foo/\""],
+    # escaped chars
+    [true, "./empty_dir d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\056\n"],
+    [true, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\\057bar\n"],
+    [true, ".\\057Data d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\n"],
+    [false, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\\057/bar\n",
+      "Manifest invalid for stream 1: invalid file token \"0:0:foo\\\\057/bar\""],
+    [false, ".\\057/Data d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\n",
+      "Manifest invalid for stream 1: missing or invalid stream name \".\\\\057/Data\""],
+    [true, "./Data\\040Folder d41d8cd98f00b204e9800998ecf8427e+0 0:0:foo\n"],
+    [false, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\057foo/bar\n",
+      "Manifest invalid for stream 1: invalid file token \"0:0:\\\\057foo/bar\""],
+    [true, ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:\\134057foo/bar\n"],
   ].each do |ok, manifest, expected_error=nil|
     define_method "test_validate manifest #{manifest.inspect}" do
       assert_equal ok, Keep::Manifest.valid?(manifest)

commit 58f1b2d26ba08e28307f45731be157ad61feb8ce
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Fri Jan 4 18:37:15 2019 -0300

    14482: Don't list empty dir placeholder files on collections listings.
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/apps/workbench/app/models/collection.rb b/apps/workbench/app/models/collection.rb
index 09af60fb9..f5aef841e 100644
--- a/apps/workbench/app/models/collection.rb
+++ b/apps/workbench/app/models/collection.rb
@@ -68,8 +68,8 @@ class Collection < ArvadosBase
         .sort.flat_map do |parts|
         [parts + [nil]] + dir_to_tree.call(File.join(parts))
       end
-      # Then extend that list with files in this directory.
-      subnodes + tree[File.split(dirname)]
+      # Then extend that list with files in this directory, except the empty dir placeholders (0:0:. files).
+      subnodes + tree[File.split(dirname)].reject { |_, basename, size| (basename == '.') and (size == 0) }
     end
     dir_to_tree.call('.')
   end

commit 73e01bb3eaef21828ec2ae802440077752b5b7e9
Author: Lucas Di Pentima <ldipentima at veritasgenetics.com>
Date:   Fri Jan 4 18:34:58 2019 -0300

    14482: Enhance code readability
    
    Arvados-DCO-1.1-Signed-off-by: Lucas Di Pentima <ldipentima at veritasgenetics.com>

diff --git a/sdk/ruby/lib/arvados/keep.rb b/sdk/ruby/lib/arvados/keep.rb
index b2096b5ea..ce1331ac1 100644
--- a/sdk/ruby/lib/arvados/keep.rb
+++ b/sdk/ruby/lib/arvados/keep.rb
@@ -162,15 +162,15 @@ module Keep
           elsif in_file_tokens or not Locator.valid? token
             in_file_tokens = true
 
-            file_tokens = split_file_token(token)
+            start_pos, file_size, file_name = split_file_token(token)
             stream_name_adjuster = ''
-            if file_tokens[2].include?('/')                # '/' in filename
-              parts = file_tokens[2].rpartition('/')
-              stream_name_adjuster = parts[1] + parts[0]   # /dir_parts
-              file_tokens[2] = parts[2]
+            if file_name.include?('/')                # '/' in filename
+              dirname, sep, basename = file_name.rpartition('/')
+              stream_name_adjuster = sep + dirname   # /dir_parts
+              file_name = basename
             end
 
-            yield [stream_name + stream_name_adjuster] + file_tokens
+            yield [stream_name + stream_name_adjuster, start_pos, file_size, file_name]
           end
         end
       end

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