rbbt-util 5.27.4 → 5.27.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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+  metadata.gz: d8792f1d19116c0384fd0063a5e81c8e9d9e30026e5dbaf41d5b26cf56210aa8
+  data.tar.gz: d3c1cf57d737a5255c6f31eb3ebe907c21d8449a0fae89d0208bb2935b513903
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+  data.tar.gz: 3f17849b28cfe2fd8618b72a74a9887172f90d93876ec59bbaae5d6fec4591537410958fcd5910805a6c995ebdef81e566d6056803090d8625efaccd0a3e2588

data/lib/rbbt/resource.rb

@@ -170,10 +170,12 @@ module Resource
     if type and not File.exist?(final_path) or force
       Log.medium "Producing: #{ final_path }"
       lock_filename = Persist.persistence_path(final_path, {:dir => Resource.lock_dir})
+
       Misc.lock lock_filename do
         FileUtils.rm_rf final_path if force and File.exist? final_path
-        if not File.exist?(final_path) or force
-          (remote_server and get_from_server(path, final_path)) or
+
+        if ! File.exist?(final_path) || force 
+
           begin
             case type
             when :string
@@ -291,7 +293,7 @@ url='#{url}'
           rescue
             FileUtils.rm_rf final_path if File.exist? final_path
             raise $!
-          end
+          end unless (remote_server && get_from_server(path, final_path))
         end
       end
     end
@@ -304,11 +306,12 @@ url='#{url}'
     resource ||= Rbbt
     (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys).uniq.each do |name|
       pattern = resource.search_paths[name]
-      next if patterns.nil?
+      next if pattern.nil?
+      pattern = pattern.sub('{PWD}', Dir.pwd)
       if String ===  pattern and pattern.include?('{')
         regexp = "^" + pattern.gsub(/{([^}]+)}/,'(?<\1>[^/]+)') + "(?:/(?<REST>.*))?/?$"
         if m = path.match(regexp) 
-          if m["PKGDIR"] == resource.pkgdir
+          if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == resource.pkgdir
             return self[m["TOPLEVEL"]][m["SUBPATH"]][m["REST"]]
           end
         end

data/lib/rbbt/workflow/accessor.rb

@@ -35,6 +35,7 @@ module Workflow
                            input_use = rec_input_use(name)
                            input_defaults = rec_input_defaults(name)
                            input_options = rec_input_options(name)
+                           extension = task.extension
                            export = case
                                     when (synchronous_exports.include?(name.to_sym) or synchronous_exports.include?(name.to_s))
                                       :synchronous
@@ -60,7 +61,8 @@ module Workflow
                              :input_use => input_use,
                              :result_type => result_type,
                              :result_description => result_description,
-                             :dependencies => dependencies
+                             :dependencies => dependencies,
+                             :extension => extension
                            }
                          end
   end

data/lib/rbbt/workflow/util/archive.rb

@@ -125,6 +125,7 @@ class Step
   def self.migrate(path, search_path, options = {})
     resource=Rbbt
 
+    orig_path = path
     other_rsync_args = options[:rsync]
 
     recursive = options[:recursive]
@@ -154,6 +155,7 @@ puts files * "\n"
             else
               if File.exists?(path)
                 path = resource.identify(path)
+                raise "Resource #{resource} could not identify #{orig_path}" if path.nil?
               else
                 path = Path.setup(path)
               end
@@ -178,7 +180,7 @@ puts resource[path].find(search_path)
     subpath_files = {}
     paths.sort.each do |path|
       parts = path.split("/")
-      subpath = parts[0..-4] * "/"
+      subpath = parts[0..-4] * "/" + "/"
 
       if subpath_files.keys.any? && subpath.start_with?(subpath_files.keys.last)
         subpath = subpath_files.keys.last
@@ -190,6 +192,7 @@ puts resource[path].find(search_path)
       subpath_files[subpath] << source
     end
 
+    synced_files = []
     subpath_files.each do |subpath, files|
       if options[:target]
         CMD.cmd("ssh #{options[:target]} mkdir -p '#{File.dirname(target)}'")
@@ -204,11 +207,15 @@ puts resource[path].find(search_path)
       end
       target = [options[:target], target] * ":" if options[:target]
 
+      next if File.exists?(source) && File.exists?(target) && File.expand_path(source) == File.expand_path(target)
+
       files_and_dirs = Set.new( files )
       files.each do |file|
+        synced_files << File.join(subpath, file)
+
         parts = file.split("/")[0..-2].reject{|p| p.empty?}
         while parts.any?
-          files_and_dirs << parts * "/"
+          files_and_dirs <<  parts * "/"
           parts.pop
         end
       end
@@ -218,8 +225,7 @@ puts resource[path].find(search_path)
 
         cmd = "rsync #{MAIN_RSYNC_ARGS} --progress #{test_str} --files-from='#{tmp_include_file}' #{source}/ #{target}/ #{other_rsync_args}"
 
-        cmd << " && rm -Rf #{source}" if options[:delete]
-
+        #cmd << " && rm -Rf #{source}" if options[:delete]
         if options[:print]
           ppp Open.read(tmp_include_file)
           puts cmd 
@@ -228,6 +234,26 @@ puts resource[path].find(search_path)
         end
       end
     end
+
+    if options[:delete] && synced_files.any?
+      puts Log.color :magenta, "About to erase these files:"
+      synced_files.each do |p|
+        puts Log.color :red, p
+      end 
+
+      if options[:non_interactive]
+        response = 'yes'
+      else
+        puts Log.color :magenta, "Type 'yes' if you are sure:"
+        response = STDIN.gets.chomp
+      end
+
+      if response == 'yes'
+        synced_files.each do |p|
+          Open.rm p
+        end
+      end
+    end
   end
 
   def self.purge(path, recursive = false)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.4
+  version: 5.27.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-05 00:00:00.000000000 Z
+date: 2020-05-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake