rbbt-util 5.21.61 → 5.21.62

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7c51f54b68b4ba9c23c5004077c51668fdbcdbe7
-  data.tar.gz: f9a1f2c86ddada5465ee07cd39548f7a36d3e46f
+  metadata.gz: 54b3148a09833544d1369d94aadeab1ff688f37b
+  data.tar.gz: a5d4a58b69dac7ec247ba3afba3404a56d426343
 SHA512:
-  metadata.gz: e55dcd5d515aed93ee78062f8951b56c8f2f9e2c7f05314e015e712118d519f7f46e4a16ba23d7c4f2331420cfb75f05c9ee98457e659095948f4508c23e87a0
-  data.tar.gz: e7a8948047115f39a4468da548d453b11c4b83de3458dfe45de4ad3c5e0048797e9842b2fb32603a8c1ab3bc03c111680de7a6d9072595b2b12eb644b94eeaa3
+  metadata.gz: f0c6e5fc9e90070866cd405f5dba447efe585a234770e70774a41156cb3f001132e2a87eeca43211d42bcbf717650b1145506a73df1ff0c23259f322c8f55b26
+  data.tar.gz: d71ed9a23bdba6b91257377d131971afe2693615779bed96ee10afe9b561598fbaeb2346f3680c1691c4b7b97dfb0de67c739ef624c1d5f0116c5498ed83c763

data/etc/app.d/entities.rb

@@ -12,7 +12,7 @@ Rbbt.etc.entities.read.split("\n").each do |name|
       include Entity::REST
     end
   rescue
-    Log.warn "Could extend REST entity: #{ name }"
+    Log.warn "Could not extend REST entity: #{ name }"
   end
 end if Rbbt.etc.entities.exists?
 

data/lib/rbbt/resource/path.rb

@@ -2,24 +2,49 @@ require 'rbbt/resource/util'
 require 'yaml'
 
 module Path
-  attr_accessor :resource, :pkgdir, :search_paths, :original
+  attr_accessor :resource, :pkgdir, :original, :search_paths, :search_order
 
-  def self.setup(string, pkgdir = nil, resource = nil, search_paths = nil)
+  def self.setup(string, pkgdir = nil, resource = nil, search_paths = nil, search_order = nil)
     return string if string.nil?
     string = string.dup if string.frozen?
     string.extend Path
     string.pkgdir = pkgdir || 'rbbt'
     string.resource = resource
     string.search_paths = search_paths
+    string.search_order = search_order
     string
   end
 
+  def search_order
+    @search_order ||= STANDARD_SEARCH.dup.uniq
+  end
+
+  def search_paths
+    @search_paths ||= SEARCH_PATHS.dup
+  end
+
+  def add_search_path(name, dir)
+    search_paths[name.to_sym] = dir
+  end
+
+  def prepend_search_path(name, dir)
+    add_search_path(name, dir)
+    search_order.unshift(name.to_sym)
+  end
+
+  def append_search_path(name, dir)
+    add_search_path(name, dir)
+    search_order.push(name.to_sym)
+  end
+
   def sub(*args)
     self.annotate super(*args)
   end
 
   def annotate(name)
-    Path.setup name.to_s, @pkgdir, @resource, @search_paths
+    name = name.to_s
+    name = Path.setup name, @pkgdir, @resource, @search_paths, @search_order
+    name
   end
 
   def join(name)
@@ -100,10 +125,17 @@ module Path
     key_elems = [where, caller_lib, rsearch_paths, paths]
     key = Misc.digest(key_elems.inspect)
     self.sub!('~/', Etc.getpwuid.dir + '/') if self.include? "~"
+
+    return @path[key] if @path[key]
+
+    if located?
+      @path[key] = self
+      return self
+    end
+
     @path[key] ||= begin
                      paths = [paths, rsearch_paths, self.search_paths, SEARCH_PATHS].reverse.compact.inject({}){|acc,h| acc.merge! h; acc }
                      where = paths[:default] if where == :default
-                     return self if located?
                      if self.match(/(.*?)\/(.*)/)
                        toplevel, subpath = self.match(/(.*?)\/(.*)/).values_at 1, 2
                      else
@@ -111,25 +143,40 @@ module Path
                      end
 
                      path = nil
-                     res = if where.nil?
-                       STANDARD_SEARCH.each do |w| 
+                     search_order = self.search_order || []
+                     res = nil
+                     if where.nil?
+
+                       (STANDARD_SEARCH - search_order).each do |w| 
                          w = w.to_sym
+                         break if res
                          next unless paths.include? w
                          path = find(w, caller_lib, paths)
-                         return path if File.exist? path
+                         res = path if File.exist? path
                        end
-                       (SEARCH_PATHS.keys - STANDARD_SEARCH).each do |w|
+
+                       search_order.each do |w| 
                          w = w.to_sym
+                         next if res
                          next unless paths.include? w
                          path = find(w, caller_lib, paths)
-                         return path if File.exist? path
-                       end
+                         res = path if File.exist? path
+                       end if res.nil?
+
+                       (paths.keys - STANDARD_SEARCH - search_order).each do |w|
+                         w = w.to_sym
+                         next if res
+                         next unless paths.include? w
+                         path = find(w, caller_lib, paths)
+                         res = path if File.exist? path
+                       end if res.nil?
 
                        if paths.include? :default
-                         find((paths[:default] || :user), caller_lib, paths)
+                         res = find((paths[:default] || :user), caller_lib, paths)
                        else
                          raise "Path '#{ path }' not found, and no default specified in search paths: #{paths.inspect}"
-                       end
+                       end if res.nil?
+
                      else
                        where = where.to_sym
                        raise "Did not recognize the 'where' tag: #{where}. Options: #{paths.keys}" unless paths.include? where
@@ -155,16 +202,19 @@ module Path
                        path = path + '.bgz' if File.exist? path + '.bgz'
 
                        self.annotate path
+
+                       res = path
                      end
 
                      res.original = self
 
                      res
                    end
+    @path[key]
   end
 
   def find_all(caller_lib = nil, search_paths = nil)
-    search_paths ||= self.search_paths || SEARCH_PATHS
+    search_paths ||= @search_paths || SEARCH_PATHS
     search_paths = search_paths.dup
 
     search_paths.keys.
@@ -173,12 +223,12 @@ module Path
   end
 
   def glob_all(caller_lib = nil, search_paths = nil)
-    search_paths ||= self.search_paths || SEARCH_PATHS
+    search_paths ||= @search_paths || SEARCH_PATHS
     search_paths = search_paths.dup
 
     search_paths.keys.
       collect{|where| Dir.glob(find(where, Path.caller_lib_dir, search_paths))}.
-      compact.flatten.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
+      compact.flatten.collect{|file| File.expand_path(file)}.uniq.collect{|path| Path.setup(path, self.resource, self.pkgdir)}
   end
   #{{{ Methods
 
@@ -313,8 +363,14 @@ module Path
   end
 
   def set_extension(new_extension = nil)
-    new_path = self.sub(/\.[^\.\/]+$/, "." << new_extension.to_s)
-    Path.setup new_path, @pkgdir, @resource
+    new_path = self + "." + new_extension.to_s
+    self.annotate(new_path)
+  end
+
+  def replace_extension(new_extension = nil)
+    new_path = self.sub(/\.[^\.\/]{2,4}$/,'')
+    new_path = new_path + "." + new_extension.to_s
+    self.annotate(new_path)
   end
 
   def doc_file(relative_to = 'lib')

data/lib/rbbt/util/log/progress/report.rb

@@ -37,9 +37,13 @@ module Log
         max_history ||= case 
                       when @ticks > 20
                         count = @ticks - @last_count
-                        times = @max / count
-                        num = times / 20
-                        num = 2 if num < 2
+                        if @max
+                          times = @max / count
+                          num = times / 20
+                          num = 2 if num < 2
+                        else
+                          num = 10
+                        end
                         count * num
                       else
                         20

data/lib/rbbt/util/misc/format.rb

@@ -110,8 +110,7 @@ module Misc
       options[:format] = :sentence
     end
 
-    values = []
-    values = value.split('_')
+    values = value.to_s.split('_')
     values.each_index do |index|
       # lower case each item in array
       # Miguel Vazquez edit: Except for acronyms

data/share/config.ru

@@ -29,6 +29,8 @@ $app_dir = FileUtils.pwd
 $app_name = app_name = File.basename($app_dir)
 $app = app = eval "class #{app_name} < Sinatra::Base; self end"
 
+Sinatra::RbbtRESTMain.add_resource_path(Rbbt.www.views.find(:lib), true)
+
 #{{{ PRE
 load_file Rbbt.etc['app.d/pre.rb'].find 
 
@@ -69,6 +71,9 @@ load_file Rbbt.etc['app.d/preload.rb'].find_all
 load_file Rbbt.lib['sinatra.rb'].find_all
 
 #{{{ RUN
+
+Sinatra::RbbtRESTMain.add_resource_path($app_dir.www.views.find, true)
+
 $title = app_name
 require 'rack'
 use Rack::Deflater

data/share/rbbt_commands/system/status

@@ -13,9 +13,10 @@ Report the status of the system
 
 $ rbbt system status <workflow> <task>
 
--a--all Print all jobs, not only uncompleted
 -h--help Print this help
 -q--quick Quick check
+-a--all Print all jobs, not only uncompleted
+-i--inputs* List of inputs to print
 EOF
 rbbt_usage and exit 0 if options[:help]
 
@@ -27,6 +28,8 @@ task = task.split "," if task
 
 all = options.delete :all
 
+inputs = (options[:inputs] || "").split(",")
+
 def pid_msg(pid)
   color = if pid and Misc.pid_exists? pid
             :green
@@ -130,8 +133,10 @@ workflows.sort.each do |workflow,tasks|
     puts "* " << Log.color(:magenta, workflow) << "#" << Log.color(:yellow, task) << ": " <<  Log.color(:blue, jobs.length.to_s)
 
     files_txt = jobs.collect do |file, i|
+      str = file.dup
       if options[:quick] and i[:done]
         status = 'done'
+        str << " #{ status_msg status }"
       else
         info = begin
                  Open.open(i[:info_file]) do |f|
@@ -152,9 +157,22 @@ workflows.sort.each do |workflow,tasks|
             status << Log.color(:red, " (dead)") 
           end
         end
+        str << " #{ status_msg status }"
+
+        if inputs and inputs.any? and info[:inputs]
+          job_inputs = info[:inputs]
+          IndiferentHash.setup(job_inputs)
+
+          iii inputs
+          inputs.each do |input|
+            value = job_inputs[input]
+            iii [input, value]
+            next if  value.nil?
+            value_str = Misc.fingerprint(value)
+            str << " #{input}=#{value_str}"
+          end
+        end
       end
-      str = file.dup
-      str << " #{ status_msg status }"
       str << "; #{pid_msg pid}" unless status == "done"
       str
     end

data/share/rbbt_commands/workflow/install

@@ -63,7 +63,18 @@ Misc.in_dir(workflow_dir) do
       Log.info "Installing: " + workflow
       if repo.nil?
         repo_base_url = Rbbt.etc.workflow_repo.exists? ? Rbbt.etc.workflow_repo.read.strip : 'https://github.com/Rbbt-Workflows/'
-        repo = File.join(repo_base_url, Misc.snake_case(workflow) + '.git')
+        begin
+          repo = File.join(repo_base_url, workflow + '.git')
+          CMD.cmd("wget '#{repo}' -O /dev/null").read
+        rescue
+          Log.debug "Workflow repo does not exist, trying snake_case: #{ repo }"
+          begin
+            repo = File.join(repo_base_url, Misc.snake_case(workflow) + '.git')
+            CMD.cmd("wget '#{repo}' -O /dev/null").read
+          rescue
+            raise "Workflow repo does not exist: #{ repo }"
+          end
+        end
       end
       Log.warn "Cloning #{ repo }"
       Misc.insist do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.61
+  version: 5.21.62
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-12-28 00:00:00.000000000 Z
+date: 2017-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -505,83 +505,83 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_workflow.rb
+- test/test_helper.rb
 - test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/util/test_concurrency.rb
 - test/rbbt/util/test_log.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/test_tmpfile.rb
 - test/rbbt/util/test_open.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_R.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
 - test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/test_resource.rb
 - test/rbbt/test_entity.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/test_tsv.rb
 - test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_doc.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/persist/tsv/test_lmdb.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
-- test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
-- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_knowledge_base.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/parallel/test_through.rb
 - test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_util.rb
 - test/rbbt/tsv/test_excel.rb
 - test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_stream.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_matrix.rb
 - test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/test_packed_index.rb
+- test/rbbt/test_persist.rb
 - test/rbbt/test_fix_width_table.rb
-- test/test_helper.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/test_annotations.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_lmdb.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/test_tsv.rb
+- test/rbbt/test_tsv.rb