rbbt-util 5.23.26 → 5.23.27

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 523b38a8f29fd560ffc459beb5916fc56a05d9dc
-  data.tar.gz: e89da52590052d42bc3b76aab1a314c7562851bc
+  metadata.gz: 727fd7ea14a972a4bbd10a93b3d5ff270f049d7d
+  data.tar.gz: 8f60c11ea14eca70d231e8a4e55208a51207d989
 SHA512:
-  metadata.gz: cdbb5baa368689965925f8ba68a9c2216adc94acff0e116759374176fbf6d2e2cda5b46f9f8b018f8bc211ac051deb0aa286f0482fd6eb21b23751248252c11a
-  data.tar.gz: 5bb7aa53e0c9f21225775f2c4bb1439b0e7a65287ae572e3ce03aa87dab01b6dd119f15c5523b75bfe9aa7d97bd30b6f2326f6d76ccf0b7a332fc39c12ce05db
+  metadata.gz: 4bfcfd6f510295128945a4f3a759b755777063776f5b9478e3c94865854ecbc755714d61a9bb783b5beb18fd88f85ce03b4e87aa26f4bf794e40acee282f3972
+  data.tar.gz: 9c7d620f5acd24e129c210fe35476b8f055bb5170ce5698217b90406fc314b3b9a02d2d80142a5c744f5817f0c84ccdae6a1dd4a57b34703aa47a4a6b70ba8c9

data/lib/rbbt/persist.rb

@@ -31,6 +31,7 @@ module Persist
     file = file.find if Path === file
     patht = Open.mtime(path)
     filet = Open.mtime(file)
+    return true if patht.nil? || filet.nil?
     diff = patht - filet
     return diff if diff < 0
     return false

data/lib/rbbt/resource.rb

@@ -132,7 +132,17 @@ module Resource
       rake_dir, content = rake_for(path)
       rake_dir = Path.setup(rake_dir.dup, self.pkgdir, self)
     else
-      raise "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
+      begin
+        if path !~ /\.(gz|bgz)$/
+          begin
+            produce(path + '.gz', force)
+          rescue
+            produce(path + '.bgz', force)
+          end
+        end
+      rescue
+        raise "Resource is missing and does not seem to be claimed: #{ self } -- #{ path } "
+      end
     end
 
     if path.respond_to?(:find) 

data/lib/rbbt/util/open.rb

@@ -2,6 +2,7 @@ require 'rbbt/util/cmd'
 require 'rbbt/util/tmpfile'
 require 'rbbt/util/misc'
 require 'rbbt/util/misc/bgzf'
+require 'pathname'
 
 require 'zlib'
 
@@ -710,7 +711,12 @@ module Open
       get_time_from_repo(*dir_sub_path)
     else
       file = file.find if Path === file
-      File.mtime(file)
+      file = Pathname.new(file).realpath.to_s if File.symlink?(file)
+      begin
+        File.mtime(file)
+      rescue
+        nil
+      end
     end
   end
 

data/lib/rbbt/workflow/accessor.rb

@@ -945,7 +945,7 @@ module Workflow
                      all_d = (real_dependencies + real_dependencies.flatten.collect{|d| d.rec_dependencies} ).flatten.compact.uniq
 
                      _inputs = assign_dep_inputs(_inputs, options, all_d, workflow.task_info(dep_task))
-                     jobname = _inputs[:jobname] if _inputs.include? :jobname
+                     jobname = _inputs.delete :jobname if _inputs.include? :jobname
 
                      job = workflow._job(dep_task, jobname, _inputs)
                      ComputeDependency.setup(job, compute) if compute

data/share/rbbt_commands/stat/heatmap

@@ -53,6 +53,6 @@ else
 data = rbbt.tsv2matrix(rbbt.tsv('#{file}'))
 rbbt.pheatmap('#{png}', data, width=#{ width }, height=#{ height }, take_log=#{R.ruby2R logs}, positive=#{R.ruby2R positive})
         EOF
-        `op #{png}`
+        `eog #{png}`
     end
 end

data/share/rbbt_commands/workflow/prov

@@ -70,7 +70,12 @@ def report_msg(status, name, path, info = nil)
     task, status, workflow = Log.color(:yellow, info[:task_name]), Log.color(:blue, "file"), Log.color(:magenta, "-")
   end
 
-  str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and ($main_mtime - Open.mtime(path)) < 0)
+  path_mtime = begin
+                   Open.mtime(path)
+               rescue
+                   nil
+               end
+  str = if not Open.remote?(path) and (Open.exists?(path) and $main_mtime and path_mtime and ($main_mtime - path_mtime) < 0)
     status_msg(status.to_s) << " " << [workflow, task, path].compact * " " << " (#{Log.color(:red, "Mtime out of sync") })"
   else
     status_msg(status.to_s) << " " << [workflow, task, path].compact * " " 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.26
+  version: 5.23.27
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-10-16 00:00:00.000000000 Z
+date: 2018-10-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake