rbbt-util 5.21.120 → 5.21.121

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3026f21eef1a3c2c1f1fc024bd95deecd9c52fce
-  data.tar.gz: 7b7cddc34c588b2895d524ee8713c47e84f68874
+  metadata.gz: 435a3cc2ef4b1d9f0838bbd85f75e8be462cbbc3
+  data.tar.gz: 7b5549e9ceee2715acc0214e92797722b04da22a
 SHA512:
-  metadata.gz: dee509e3a25d16c38e689251221de184cac742897c0d1ed34d4c6de3fe99dd34e8d632bd7c2488f17b571d1b312fb4c0ae08f88f50ecbccb6934ab8af58ed83d
-  data.tar.gz: 78e6e1a9065412d2a1b716801a8659f02302145150bd8819b04c3b5d9c05434727993769fba2869fdbe5859e13f8673030ac2ab4472802475d27b063eb792a42
+  metadata.gz: cd02ef90d9343947194eda5f35e3dcb6edc528b431e3ecff890f12dd6f7be5e7567215fc9a01009493f1a1f106eb4e2969f95f1c8ec5b75e5153b91cfca14e69
+  data.tar.gz: 86040779d87fe38a288c7e1a274ad2cd2319cad9409dac48ed0276911b8942ee06f43ad68265138ae682aac354d1e605c0c90e3cddc1fc2ffb72a0f937c45451

data/lib/rbbt/knowledge_base/query.rb

@@ -61,7 +61,7 @@ class KnowledgeBase
   def parents(name, entity)
     entity = identify_target(name, entity)
     matches = _parents(name, entity)
-    matches.each{|m| m.replace(m.partition("~").reverse*"") } unless undirected(name)
+    #matches.each{|m| m.replace(m.partition("~").reverse*"") } unless undirected(name)
     setup(name, matches, true)
   end
 

data/lib/rbbt/workflow/step/dependencies.rb

@@ -82,7 +82,8 @@ class Step
 
     if (status == 'error' && (job.recoverable_error? || job.dirty?)) ||
       job.aborted? ||
-      (job.done? && job.dirty?)  ||
+      (job.done? && ! job.updated?)  || (job.error? && ! job.updated?)
+      (job.done? && job.dirty?)  || (job.error? && job.dirty?)
       (! (job.status == :waiting || job.status == :noinfo || job.done? || job.error? || job.aborted?) && ! job.running?)
 
       job.clean 

data/lib/rbbt/workflow/step/run.rb

@@ -93,7 +93,7 @@ class Step
   end
 
   def input_checks
-    inputs.select{|i| Step === i && i.done? }
+    inputs.select{|i| Step === i }
   end
 
   def checks
@@ -106,10 +106,10 @@ class Step
     outdated_time  = []
     outdated_dep  = []
     checks.each do |dep| 
-      if File.mtime(dep.path) > File.mtime(self.path) 
+      if dep.done? && self.done? && (File.mtime(dep.path) > File.mtime(self.path))
         outdated_time << dep
       end
-      if ! dep.updated?  
+      if ! dep.done? || ! dep.updated?
         outdated_dep << dep
       end
     end
@@ -121,7 +121,7 @@ class Step
   end
 
   def updated?
-    return true unless done?
+    return true unless (done? || error?)
 
     @updated ||= out_of_date.empty?
   end
@@ -583,7 +583,7 @@ class Step
   end
 
   def grace
-    until done? or result or error? or aborted? or streaming? 
+    until done? or result or error? or aborted? or streaming? or waiting?
       sleep 1 
     end
     self
@@ -622,7 +622,7 @@ class Step
         dependencies.each{|dep| dep.join }
       end
 
-      until (path.exists? && status == :done) or error? or aborted?
+      until (path.exists? && status == :done) or error? or aborted? or waiting?
         sleep 1 
         join_stream if streaming?
       end

data/share/Rlib/util.R

@@ -722,3 +722,31 @@ rbbt.require <- function(pkg, ...){
     library(clean.packages, character.only=T)
 }
 
+rbbt.psd <- function(m){
+    e = eigen(m) 
+    library(MASS)
+
+    values = e$values  
+    values[values < 0] = 0 
+
+    p = e$vectors %*% diag(values) %*% t(e$vectors)
+
+    rownames(p) <- rownames(m)
+    colnames(p) <- colnames(m)
+
+    return(p)
+}
+
+rbbt.fix_distance <- function(data){
+    rbbt.require('Hmisc')
+
+    m = impute(as.matrix(data))
+
+    p <- rbbt.psd(m)
+    p <- m
+
+    d <- as.dist(p)   
+
+    return(d)
+}
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.120
+  version: 5.21.121
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-28 00:00:00.000000000 Z
+date: 2018-01-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -503,88 +503,88 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.8
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/association/test_database.rb
-- test/rbbt/association/test_item.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/association/test_open.rb
-- test/rbbt/association/test_util.rb
-- test/rbbt/test_association.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_traverse.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/test_entity.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/misc/test_omics.rb
 - test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_bgzf.rb
 - test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_simpleopt.rb
 - test/rbbt/util/simpleopt/test_parse.rb
 - test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/test_open.rb
+- test/rbbt/util/simpleopt/test_get.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_log.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_semaphore.rb
 - test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_attach.rb
 - test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/tsv/test_accessor.rb
 - test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_field_index.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_excel.rb
-- test/rbbt/test_monitor.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/annotations/test_util.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/test_entity.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_persist.rb
-- test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/tsv/test_cdb.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/test_association.rb
+- test/rbbt/association/test_database.rb
+- test/rbbt/association/test_item.rb
+- test/rbbt/association/test_open.rb
+- test/rbbt/association/test_util.rb
+- test/rbbt/association/test_index.rb
+- test/rbbt/test_knowledge_base.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_lmdb.rb
+- test/rbbt/persist/tsv/test_sharder.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
+- test/rbbt/persist/tsv/test_tokyocabinet.rb
 - test/rbbt/persist/test_tsv.rb
 - test/rbbt/test_tsv.rb
+- test/rbbt/test_annotations.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/resource/test_path.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/annotations/test_util.rb
+- test/rbbt/test_monitor.rb
+- test/rbbt/test_persist.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/test_helper.rb