rbbt-util 5.27.2 → 5.27.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 9adb68a2c9ddfa77a3be419dd106e4083e11933dd6653b4d6e0bfa921edab187
+  metadata.gz: ee7d7e81ee4a7981fd286ef0c5d8435aa482d0598068e7d1d19d526dd17a1e9d
+  data.tar.gz: 070db371b5d3ab7e11e52795b648e65dd5f296863cd516ce830b82e3a20e8471
 SHA512:
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+  metadata.gz: 6a7d93d19efeac98230ba8d9ba131a2e670b4ff3421606bdef8b0ec5c004e1e0aee2110dc18c64ca59066b4c3c3feb463ed86cc3295010fdb94fcd6f467e6ea0
+  data.tar.gz: 0a53f17d0bced1858aaaede6b55e30caed1347d87a120ed580a6e7bc8031ac4aba8ede384473ec92327b64d5922093e2fe1e0fa0990baca18b88873364ace8b6

data/lib/rbbt/persist/tsv.rb

@@ -148,13 +148,13 @@ module Persist
 
         data.write_and_read do
           yield data
-        end
 
-        FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
-        tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
-        tsv.persistence_path = path
+          FileUtils.mv data.persistence_path, path if File.exist? data.persistence_path and not File.exist? path
+          tsv = CONNECTIONS[path] = CONNECTIONS.delete tmp_path
+          tsv.persistence_path = path
 
-        tsv.fix_io if tsv.respond_to? :fix_io
+          tsv.fix_io if tsv.respond_to? :fix_io
+        end
 
         data
       rescue Exception

data/lib/rbbt/persist/tsv/adapter.rb

@@ -22,12 +22,6 @@ module Persist
       @closed
     end
 
-    def close
-      @closed = true
-      super
-      self
-    end
-
     def write?
       @writable
     end
@@ -47,8 +41,10 @@ module Persist
     def close(*args)
       begin
         super(*args)
+        @closed = true
       rescue NoMethodError
       end
+      self
     end
 
     def read(*args)
@@ -87,6 +83,16 @@ module Persist
       end
     end
 
+    def lock_and_close
+      lock do
+        begin
+          yield
+        ensure
+          close
+        end
+      end
+    end
+
     def write_and_read
       if write?
         begin
@@ -97,7 +103,7 @@ module Persist
       end
 
       lock do
-        write true if closed? or not write?
+        write(true) if closed? || !write?
         begin
           yield
         ensure
@@ -111,12 +117,12 @@ module Persist
         begin
           return yield
         ensure
-          close
+          close unless @locked
         end
       end
 
       lock do
-        write true if closed? || ! write?
+        write(true) if closed? || ! write?
         res = begin
                 yield
               rescue Exception
@@ -130,11 +136,12 @@ module Persist
     end
 
     def read_and_close
-      if read?
+      #return yield if @locked
+      if read? || write?
         begin
           return yield
         ensure
-          close
+          close unless @locked
         end
       end
 
@@ -161,8 +168,27 @@ module Persist
     end
 
     def include?(*args)
-      read if closed?
-      super(*args) #- TSV::ENTRY_KEYS.to_a
+      self.read_and_close do
+        super(*args) #- TSV::ENTRY_KEYS.to_a
+      end
+    end
+
+    def [](*args)
+      self.read_and_close do
+        super(*args) #- TSV::ENTRY_KEYS.to_a
+      end
+    end
+
+    def []=(*args)
+      self.write_and_close do
+        super(*args) #- TSV::ENTRY_KEYS.to_a
+      end
+    end
+
+    def keys(*args)
+      self.read_and_close do
+        super(*args) #- TSV::ENTRY_KEYS.to_a
+      end
     end
   end
 end

data/lib/rbbt/persist/tsv/tokyocabinet.rb

@@ -93,7 +93,9 @@ module Persist
 
     unless serializer == :clean
       TSV.setup database
-      database.serializer = serializer || database.serializer
+      database.write_and_read do
+        database.serializer = serializer if serializer 
+      end
     end
 
     database

data/lib/rbbt/tsv/accessor.rb

@@ -243,7 +243,7 @@ module TSV
   end
 
   def []=(key, value, clean = false)
-    return super(key, value) if clean or value.nil? or TSV::CleanSerializer == self.serializer_module 
+    return super(key, value) if clean || value.nil? || TSV::CleanSerializer == self.serializer_module 
     super(key, @serializer_module.dump(value))
   end
 

data/lib/rbbt/tsv/change_id.rb

@@ -10,7 +10,8 @@ module TSV
 
     identifiers = Organism.identifiers(tsv.namespace) if identifiers.nil? and tsv.namespace
 
-    if not tsv.fields.include? format
+
+    if ! tsv.fields.include?(format)
       new = {}
       tsv.each do |k,v|
         if v === String or v === Array
@@ -32,6 +33,7 @@ module TSV
         tsv = tsv.attach identifiers, :fields => [format], :persist_input => true
       end
 
+
       tsv = tsv.reorder(format, tsv.fields[0..-2])
 
       tsv = tsv.to_flat  if orig_type == :flat

data/lib/rbbt/workflow.rb

@@ -607,7 +607,7 @@ module Workflow
   end
 
   def self.load_step(path)
-    Path.setup(path) unless Path === path
+    path = Path.setup(path.dup) unless Path === path
     path = path.find
 
     begin

data/share/install/software/lib/install_helpers

@@ -71,7 +71,7 @@ get_pkg(){
     local url="$2"
 
     if [ ! -f "$OPT_SRC_DIR/$name.pkg" ]; then
-        wget "$url" -O "$OPT_SRC_DIR/$name.pkg"  || wget "$url" -O "$OPT_SRC_DIR/$name.pkg" --no-check-certificate
+      wget "$url" -O "$OPT_SRC_DIR/$name.pkg"  || wget "$url" -O "$OPT_SRC_DIR/$name.pkg" --no-check-certificate || (rm -f "$OPT_SRC_DIR/$name.pkg"; echo "Error downloading"; exit -1)
     fi
 }
 
@@ -85,7 +85,7 @@ uncompress_pkg(){
     mkdir -p "$OPT_BUILD_DIR"
     cd "$OPT_BUILD_DIR"
 
-    (tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || echo "Error decompressing") 2> /dev/null
+    (tar xvfz $pkg || tar xvfJ $pkg || tar xvfj $pkg || unzip $pkg || (echo "Error decompressing" & cd & rmdir "$OPT_BUILD_DIR" & exit -1 ) ) 2> /dev/null
 
     cd "$old_pwd"
 }
@@ -207,6 +207,8 @@ prepare_make(){
 
     [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
 
+    [ -f bootstrap ] && (./bootstrap || exit -1)
+
     if [ -f config/m4 ]; then
         libtoolize --force
         aclocal
@@ -275,6 +277,8 @@ build_make(){
         setup "$name"
         clean_build
     fi
+
+    cd "$old_pwd"
 }
 
 buid_cmake(){
@@ -489,7 +493,7 @@ install_jar(){
     local url="$2"
 
     [ -d  "$OPT_DIR/$name/" ] || mkdir -p  "$OPT_DIR/$name/"
-    wget "$url" -O "$OPT_DIR/$name/$name.jar" --no-check-certificate
+    wget "$url" -O "$OPT_DIR/jars/$name.jar" || wget "$url" -O "$OPT_DIR/jars/$name.jar" --no-check-certificate || (rm "$OPT_DIR/jars/$name.jar"; exit -1)
     link "$OPT_DIR/$name/$name.jar" "$OPT_JAR_DIR/$name.jar" 
 }
 

data/share/rbbt_commands/migrate_job

@@ -3,7 +3,7 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
-require 'rbbt/workflow/remote/ssh/get'
+require 'rbbt/workflow/remote_workflow'
 
 $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
 
@@ -34,4 +34,6 @@ end
 
 path, search_path, _sep, *other = ARGV
 
+search_path = 'user' if search_path.nil?
+
 Step.migrate(path, search_path, options)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.2
+  version: 5.27.3
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-29 00:00:00.000000000 Z
+date: 2020-05-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake