rbbt-util 5.32.6 → 5.32.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 83d0ae91ee88ed3283985b5d7101759bbb45db37fbb54271bc7f16fae8ab4f52
+  metadata.gz: b989d145b1a34baab93f351ea9944e73dde157e9973a9443717b84a43e7b41d5
+  data.tar.gz: d6e8f5a7e8cb2d2f0e9a99f36a7594e4fc3655dd1d4f9b571f73f0f947b19fd3
 SHA512:
-  metadata.gz: 0b83533d504d6d66b06083a7f19a689e9b3f82fefbc26278d9bd9af0efbdfb010f87cc609bf90396bb17257a643715e335ac8127f9ff1f11ccdd52f639b77ca8
-  data.tar.gz: a4b93ca7d481120edde1d65f529984e652c261f365c67bea6d1c463d360733006d29486d3851d0b071ba2005cb90cf71382eb5665c7d4e1828a25f322b570ce7
+  metadata.gz: da60531d5e35efd54b0c4de7e9ad6b034ef05e8d58d6a6b0a1b15422b324dd6eb5a4cb01b21ba60c091616d512106c278ef794088f87f844bd96e86d8f61d7da
+  data.tar.gz: 2327575017d9dbb301b8c0ba36ee691bc8be00175712e2121da019251c3735d0348cae6d18e8112b00c952e233eb806a19f2275563310360ed745a9b868a6021

data/lib/rbbt/resource.rb

@@ -313,7 +313,10 @@ url='#{url}'
   def identify(path)
     path = File.expand_path(path)
     resource ||= Rbbt
-    (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys).uniq.each do |name|
+    locations = (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys)
+    locations -= [:current, "current"]
+    locations << :current
+    locations.uniq.each do |name|
       pattern = resource.search_paths[name]
       next if pattern.nil?
       pattern = pattern.sub('{PWD}', Dir.pwd)

data/lib/rbbt/util/cmd.rb

@@ -248,16 +248,26 @@ module CMD
     pid = io.pids.first
 
     line = "" if bar
+    starting = true
     while c = io.getc
-      STDERR << c if Log.severity <= level
-      line << c if bar
-      if c == "\n"
-        bar.process(line) if bar
+      if starting
         if pid
           Log.logn "STDOUT [#{pid}]: ", level
         else
           Log.logn "STDOUT: ", level
         end
+        starting = false
+      end
+      STDERR << c if Log.severity <= level
+      line << c if bar
+      if c == "\n"
+        bar.process(line) if bar
+        starting = true
+        #if pid
+        #  Log.logn "STDOUT [#{pid}]: ", level
+        #else
+        #  Log.logn "STDOUT: ", level
+        #end
         line = "" if bar
       end
     end 

data/lib/rbbt/util/migrate.rb

@@ -0,0 +1,118 @@
+module Rbbt 
+  def self.migrate_source_paths(path, resource = Rbbt, source = nil)
+    if source
+      lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
+require 'rbbt-util'
+path = "#{path}"
+if Open.exists?(path)
+  path = #{resource.to_s}.identify(path)
+else
+  path = Path.setup(path)
+end
+puts path
+puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
+      EOF
+
+      [path, paths.collect{|p| [source, p] * ":"}, lpath]
+    else
+      if File.exists?(path)
+        path = resource.identify(path)
+      else
+        path = Path.setup(path)
+      end
+
+      [path, (path.directory? ? path.glob_all : path.find_all), path]
+    end
+  end
+
+  def self.migrate_target_path(path, search_path = 'user', resource = Rbbt, target = nil)
+    if target
+      Misc.ssh_run(target, <<-EOF).split("\n").first
+require 'rbbt-util'
+path = "#{path}"
+resource = #{resource.to_s}
+search_path = "#{search_path}"
+puts resource[path].find(search_path)
+      EOF
+    else
+      resource[path].find(search_path)
+    end
+  end
+
+  def self.migrate_files(real_paths, target, options = {})
+    excludes = %w(.save .crap .source tmp filecache open-remote)
+    excludes += (options[:exclude] || "").split(/,\s*/)
+    excludes_str = excludes.collect{|s| "--exclude '#{s}'" } * " "
+
+    other = options[:other] || []
+
+    test_str = options[:test] ? '-nv' : ''
+
+    real_paths.each do |source_path|
+      if File.directory?(source_path) || source_path =~ /\/$/
+        source_path += "/" unless source_path[-1] == "/"
+        target += "/" unless target[-1] == "/"
+      end
+
+      next if source_path == target
+
+      if options[:target]
+        CMD.cmd("ssh #{options[:target]} mkdir -p '#{File.dirname(target)}'")
+      else
+        Open.mkdir File.dirname(target)
+      end
+
+      if options[:target]
+        target_path = [options[:target], "'" + target + "'"] * ":" 
+      else
+        target_path = "'" + target + "'"
+      end
+
+      TmpFile.with_file do |tmp_files|
+        if options[:files]
+          Open.write(tmp_files, options[:files] * "\n")
+          files_from_str = "--files-from='#{tmp_files}'"
+        else
+          files_from_str = ""
+        end
+
+        cmd = "rsync -avztAXHP --copy-unsafe-links #{test_str} #{files_from_str} #{excludes_str} '#{source_path}' #{target_path} #{other * " "}"
+
+
+        cmd << " && rm -Rf #{source_path}" if options[:delete] && ! options[:files]
+
+        if options[:print]
+          puts cmd 
+          exit 0
+        else
+          CMD.cmd_log(cmd, :log => Log::INFO)
+
+          if options[:delete] && options[:files]
+            remove_files = options[:files].collect{|f| File.join(source_path, f) }
+            dirs = remove_files.select{|f| File.directory? f }
+            remove_files.each do |file|
+              next if dirs.include? file
+              Open.rm file
+            end
+            dirs.each do |dir|
+              FileUtils.rmdir dir if Dir.glob(dir).empty?
+            end
+          end 
+        end
+      end
+    end
+  end
+
+
+  def self.migrate(path, search_path, options = {})
+    search_path = 'user' if search_path.nil?
+
+    resource = Rbbt
+
+    path, real_paths, lpath = migrate_source_paths(path, resource, options[:source])
+
+    target = migrate_target_path(lpath, search_path, resource, options[:target])
+
+    migrate_files(real_paths, target, options)
+  end
+end

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

@@ -1,3 +1,4 @@
+require 'rbbt/util/migrate'
 class Step
 
   MAIN_RSYNC_ARGS="-avztAXHP --copy-links"
@@ -126,63 +127,48 @@ class Step
     end
   end
 
-  def self.migrate(path, search_path, options = {})
-    resource=Rbbt
-
-    orig_path = path
-    other_rsync_args = options[:rsync]
-
-    recursive = options[:recursive]
+  def self.migrate_source_paths(path, resource = Rbbt, source = nil, recursive = true)
     recursive = false if recursive.nil?
-
-    paths = if options[:source]
-              Misc.ssh_run(options[:source], <<-EOF).split("\n")
+    if source
+      lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
 require 'rbbt-util'
 require 'rbbt/workflow'
 
-path = "#{path}"
 recursive = #{ recursive.to_s }
+path = "#{path}"
 
-if File.exists?(path)
+if Open.exists?(path)
   path = #{resource.to_s}.identify(path)
 else
   path = Path.setup(path)
 end
 
-files = path.glob_all
-
+files = path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p }
 files = Step.job_files_for_archive(files, recursive)
 
+puts path
 puts files * "\n"
-              EOF
-
-            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
-              files = path.glob_all
-              files = Step.job_files_for_archive(files, recursive)
-              files
-            end
-
-
-    target = if options[:target] 
-               target = Misc.ssh_run(options[:target], <<-EOF).split("\n").first
-require 'rbbt-util'
-path = "var/jobs"
-resource = #{resource.to_s}
-search_path = "#{search_path}"
-puts resource[path].find(search_path)
-               EOF
-             else
-               resource['var/jobs'].find(search_path)
-             end
+      EOF
+
+      [path, paths.collect{|p| [source, p] * ":"}, lpath]
+    else
+      path = Path.setup(path.dup)
+      files = path.glob_all
+      files = Step.job_files_for_archive(files, recursive)
+
+      [path, files, path]
+    end
+  end
+
+  def self.migrate(path, search_path, options = {})
+    search_path = 'user' if search_path.nil?
+
+    resource = Rbbt
+
+    path, real_paths, lpath = self.migrate_source_paths(path, resource, options[:source], options[:recursive])
 
     subpath_files = {}
-    paths.sort.each do |path|
+    real_paths.sort.each do |path|
       parts = path.split("/")
       subpath = parts[0..-4] * "/" + "/"
 
@@ -190,73 +176,16 @@ puts resource[path].find(search_path)
         subpath = subpath_files.keys.last
       end
 
-      source = path[subpath.length..-1]
+      source = path.chars[subpath.length..-1] * ""
 
       subpath_files[subpath] ||= []
       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)}'")
-      else
-        Open.mkdir File.dirname(target)
-      end
+    target = Rbbt.migrate_target_path('var/jobs', search_path, resource, options[:target])
 
-      if options[:source]
-        source = [options[:source], subpath] * ":"
-      else
-        source = subpath
-      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 * "/"
-          parts.pop
-        end
-      end
-
-      TmpFile.with_file(files_and_dirs.sort_by{|l| l.length}.to_a * "\n") do |tmp_include_file|
-        test_str = options[:test] ? '-nv' : ''
-
-        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]
-        if options[:print]
-          ppp Open.read(tmp_include_file)
-          puts cmd 
-        else
-          CMD.cmd_log(cmd, :log => Log::INFO)
-        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
+    subpath_files.each do |subpath, files|
+      Rbbt.migrate_files([subpath], target, options.merge(:files => files))
     end
   end
 

data/share/rbbt_commands/migrate

@@ -2,7 +2,7 @@
 
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
-require 'rbbt/workflow/remote_workflow'
+require 'rbbt/util/migrate'
 
 $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
 
@@ -30,83 +30,10 @@ if options[:help]
   exit 0
 end
 
-#excludes = %w(.save .crap .source tmp filecache open-remote workflows apps software jobs PCAWG)
-excludes = %w(.save .crap .source tmp filecache open-remote)
-excludes += (options[:exclude] || "").split(/,\s*/)
-excludes_str = excludes.collect{|s| "--exclude '#{s}'" } * " "
-
-test_str = options[:test] ? '-nv' : ''
-
 path, search_path, _sep, *other = ARGV
 
 search_path = 'user' if search_path.nil?
-resource = Rbbt
-
-path, real_paths, lpath = if options[:source]
-          lpath, *paths = Misc.ssh_run(options[:source], <<-EOF).split("\n")
-require 'rbbt-util'
-path = "#{path}"
-if Open.exists?(path)
-  path = #{resource.to_s}.identify(path)
-else
-  path = Path.setup(path)
-end
-puts path
-puts path.glob_all.collect{|p| File.directory?(p) ? p + "/" : p } * "\n"
-          EOF
-          [path, paths.collect{|p| [options[:source], p] * ":"}, lpath]
-        else
-          if File.exists?(path)
-
-            path = resource.identify(path)
-          else
-            path = Path.setup(path)
-          end
-          [path, path.glob_all, path]
-        end
-
-target = if options[:target] 
-           target = Misc.ssh_run(options[:target], <<-EOF).split("\n").first
-require 'rbbt-util'
-path = "#{path}"
-resource = #{resource.to_s}
-search_path = "#{search_path}"
-puts resource[path].find(search_path)
-           EOF
-         else
-           resource[lpath].find(search_path)
-         end
-
-real_paths.each do |source|
-
-
-  if File.directory?(source) || source =~ /\/$/
-    source += "/" unless source[-1] == "/"
-    target += "/" unless target[-1] == "/"
-  end
 
-  next if source == target
+options[:other] = other
 
-  if options[:target]
-    CMD.cmd("ssh #{options[:target]} mkdir -p '#{File.dirname(target)}'")
-  else
-    Open.mkdir File.dirname(target)
-  end
-
-  if options[:target]
-   target_path = [options[:target], "'" + target + "'"] * ":" 
-  else
-   target_path = "'" + target + "'"
-  end
-
-  cmd = "rsync -avztAXHP --copy-unsafe-links #{test_str} #{excludes_str} '#{source}' #{target_path} #{other * " "}"
-
-  cmd << " && rm -Rf #{source}" if options[:delete]
-
-  if options[:print]
-    puts cmd 
-    exit 0
-  else
-    CMD.cmd_log(cmd, :log => Log::INFO)
-  end
-end
+Rbbt.migrate(path, search_path, options)

data/test/rbbt/util/test_migrate.rb

@@ -0,0 +1,36 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt-util'
+require 'rbbt/util/migrate'
+
+class TestMigrate < Test::Unit::TestCase
+  def _test_source_locate
+    assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
+    assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
+  end
+
+  def test_migrate
+    Open.rm_rf Rbbt.tmp.test.migration_test.find(:user)
+    test_file = Rbbt.tmp.test.migration_test.migration_test_file.find(:user)
+    Open.write(test_file, "TEST")
+    TmpFile.with_file do |tmpdir|
+      Misc.in_dir tmpdir do
+        Log.with_severity 0 do
+          Rbbt.migrate('tmp/test/migration_test/migration_test_file', :current)
+        end
+      end
+      assert_equal "TEST", Open.read(File.join(tmpdir, 'tmp/test/migration_test/migration_test_file'))
+    end
+  end
+
+  def __test_migrate_turbo
+    Log.with_severity 0 do
+    TmpFile.with_file do |tmpdir|
+      Misc.in_dir tmpdir do
+        Rbbt.migrate('etc/config', :current, :source => 'mn1')
+      end
+      assert_equal "TEST", Open.read(File.join(tmpdir, 'etc/config'))
+    end
+    end
+  end
+end
+

data/test/rbbt/workflow/util/test_archive.rb

@@ -0,0 +1,31 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../../..', 'test_helper.rb')
+require 'rbbt-util'
+require 'rbbt/workflow'
+require 'rbbt/workflow/util/archive'
+
+module ArchiveTestWF
+  extend Workflow
+  task :test_archive => :string do
+    Open.write(file(:file1), "Test file")
+    "TEST"
+  end
+end
+
+class TestClass < Test::Unit::TestCase
+  def test_migrate
+    job = ArchiveTestWF.job(:test_archive)
+    job.run
+
+    Log.with_severity 0 do
+      TmpFile.with_file do |tmpdir|
+        Misc.in_dir tmpdir do
+          Step.migrate(job.path, :current, :delete => false, :print => false)
+        end
+        assert_equal "TEST", Open.read(File.join(tmpdir, 'var/jobs/ArchiveTestWF/test_archive/Default'))
+      end
+    end
+
+
+  end
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.6
+  version: 5.32.7
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -282,6 +282,7 @@ files:
 - lib/rbbt/util/log/progress.rb
 - lib/rbbt/util/log/progress/report.rb
 - lib/rbbt/util/log/progress/util.rb
+- lib/rbbt/util/migrate.rb
 - lib/rbbt/util/misc.rb
 - lib/rbbt/util/misc/annotated_module.rb
 - lib/rbbt/util/misc/bgzf.rb
@@ -522,6 +523,7 @@ files:
 - test/rbbt/util/test_excel2tsv.rb
 - test/rbbt/util/test_filecache.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_migrate.rb
 - test/rbbt/util/test_misc.rb
 - test/rbbt/util/test_open.rb
 - test/rbbt/util/test_procpath.rb
@@ -536,6 +538,7 @@ files:
 - test/rbbt/workflow/test_schedule.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-util
@@ -583,12 +586,14 @@ test_files:
 - test/rbbt/workflow/test_doc.rb
 - test/rbbt/workflow/step/test_dependencies.rb
 - test/rbbt/workflow/test_schedule.rb
+- test/rbbt/workflow/util/test_archive.rb
 - test/rbbt/workflow/util/test_orchestrator.rb
 - test/rbbt/workflow/test_task.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/test_tsv.rb
 - test/rbbt/test_annotations.rb
 - test/rbbt/test_knowledge_base.rb
+- test/rbbt/util/test_migrate.rb
 - test/rbbt/util/test_simpleDSL.rb
 - test/rbbt/util/concurrency/processes/test_socket.rb
 - test/rbbt/util/concurrency/test_processes.rb