rbbt-util 5.23.28 → 5.23.29

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 2275f8b0ef9e0fd2bf6a6b964aa0bb8541f7bd35
-  data.tar.gz: 3ddc1b829d1990a27fbbfec708cc41e89a7b4926
+  metadata.gz: d79b37d85261eb8752a28f32688774224fc9d99f
+  data.tar.gz: 3d3b98478b25ef4185166e437bcf40deedffcd66
 SHA512:
-  metadata.gz: fd83f6e4487f0f36f33720ded3a875cb123c4bb1398b69ab49affb229af0b1b5e63a464ea74bf1a4946929a68bf334087163de762cc1edc6b7ae85c4cd908947
-  data.tar.gz: 19109b2be3083248f31b1fb9cad1596b201f4801566d7c3a608fe24536557e44611f5a224f9cdd1e7a76aab17c7e3834c84037243e2a16254b80b7903319c6d6
+  metadata.gz: d82e5d8c6f47d92b887d757e8f6f317fb4fd5284f756027de4a70ecaf785d4577e8f13b854d549969d122069adccc7e5b7e7e497ba9af5e6adf1d51ce9903694
+  data.tar.gz: c6e7f5d41afd0fb98004bdcc01a8b1d5a4576d5f68b42e753d0be302e63b7baa97fc8cea4e252300bf6176841f2793e533130c398365b58bc637a30c60b17ca5

data/lib/rbbt-util.rb

@@ -16,4 +16,3 @@ require 'rbbt/util/cmd'
 require 'rbbt/tsv'
 
 require 'rbbt/util/config'
-

data/lib/rbbt/util/open.rb

@@ -216,7 +216,7 @@ module Open
 
   def self.find_repo_dir(file)
     self.repository_dirs.each do |dir|
-      dir = dir + '/' unless dir[-1] == "/"
+      dir = dir + '/' unless dir.chars[-1] == "/"
 
       begin
         if file.start_with? dir

data/lib/rbbt/workflow/step.rb

@@ -32,6 +32,7 @@ class Step
 
   def overriden
     if @overriden.nil? 
+      return [] if dependencies.nil?
       dependencies.select{|dep| dep.overriden }.any?
     else
       @overriden
@@ -325,7 +326,7 @@ class Step
 
     # A step result with no info_file means that it was manually
     # placed. In that case, do not consider its dependencies
-    return [] if not (defined? WorkflowRESTClient and  WorkflowRESTClient::RemoteStep === self) and Open.exists?(self.path.to_s) and not Open.exists? self.info_file
+    return [] if not (defined? WorkflowRESTClient and  WorkflowRESTClient::RemoteStep === self) and not Open.exists?(self.info_file) and Open.exists?(self.path.to_s) 
 
     return [] if dependencies.nil? or dependencies.empty?
 

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

@@ -141,18 +141,24 @@ class Step
     outdated_time  = []
     outdated_dep  = []
     canfail_paths = self.canfail_paths
+    this_mtime = Open.mtime(self.path) if Open.exists?(self.path)
+
     checks.each do |dep| 
       next unless dep.updatable?
+      dep_done = dep.done?
 
       begin
-
-        if dep.done? && self.done? && Open.exists?(dep.path) && Open.exists?(self.path) && (Open.mtime(dep.path) > Open.mtime(self.path))
+        if this_mtime && dep_done && Open.exists?(dep.path) && (Open.mtime(dep.path) > this_mtime)
           outdated_time << dep
         end
       rescue
       end
 
-      if (! dep.done? && ! canfail_paths.include?(dep.path)) || ! dep.updated?
+      # Is this pointless? this would mean some dep got updated after a later
+      # dep but but before this one.
+      #if (! dep.done? && ! canfail_paths.include?(dep.path)) || ! dep.updated?
+
+      if (! dep_done && ! canfail_paths.include?(dep.path))
         outdated_dep << dep
       end
     end

data/share/install/software/lib/install_helpers

@@ -42,7 +42,7 @@ 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"  || wget "$url" -O "$OPT_SRC_DIR/$name.pkg" --no-check-certificate
     fi
 }
 
@@ -56,7 +56,7 @@ uncompress_pkg(){
     mkdir -p "$OPT_BUILD_DIR"
     cd "$OPT_BUILD_DIR"
 
-    (tar xvfz $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") 2> /dev/null
 
     cd "$old_pwd"
 }
@@ -81,7 +81,8 @@ get_svn(){
         cd "$name" 
         svn update
     else
-        git checkout "$url" "$name"
+        echo svn checkout "$url" "$name"
+        svn checkout "$url" "$name"
     fi
 
     clean_build
@@ -146,6 +147,8 @@ compile(){
 
     [ -f setup.rb ] && (ruby -Ilib/ setup.rb --prefix="$(opt_dir "$name")" $extra || exit -1)
 
+    [ -f install.rb ] && ruby -Ilib/ install.rb config --prefix="$(opt_dir "$name")" $extra && ruby -Ilib/ install.rb install
+
     if [ -f setup.py ]; then 
         python setup.py build &&  python setup.py install --user || exit -1
         clean_build 
@@ -157,12 +160,21 @@ build(){
     local extra="$@"
 
     echo "Building $name"
+    if [ "x$extra" != "x" ]; then
+        echo "Extra params: $extra"
+    fi
 
     local old_pwd="`expand_path $(pwd)`"
     cd "`build_dir`"
     echo PWD: `pwd`
     ls
 
+    if [ -f config/m4 ]; then
+        libtoolize --force
+        aclocal
+        autoheader
+    fi
+
     if [ -f Makefile.am -a ! -f configure ]; then
       autoreconf
     fi
@@ -176,22 +188,43 @@ build(){
     fi
 
     if [ -f aclocal.m4 ]; then
+        autoreconf -i
+        autoconf
+        automake
+    else
         autoconf
+        automake
     fi
 
+    if [ -f config ]; then
+        ln -s config configure
+    fi
+
+    if [ -f CMakeLists.txt ]; then
+        mkdir build
+        cd build
+        cmake -DCMAKE_INSTALL_PREFIX:PATH=/ ..
+        make -j4
+        make DESTDIR="$(opt_dir "$name")" install
+        setup "$name"
+        clean_build
+    fi
+    
     if [ -f configure ]; then 
+        echo ./configure --prefix="$(opt_dir "$name")" $extra
         ./configure --prefix="$(opt_dir "$name")" $extra
         compile "$name" $extra
         setup "$name"
         clean_build
-        cd "$old_pwd"
     else
         compile "$name" $extra
         move_opt "$name"
         setup "$name"
         clean_build
     fi
+
     
+    cd "$old_pwd"
 }
 
 #{{{ SETUP
@@ -261,6 +294,7 @@ setup(){
         cd "$old_pwd"
     fi
     
+    ([ -d "$pkg_dir/include" ]       && add2file "$OPT_DIR/.c-paths" "$pkg_dir/include")
     ([ -d "$pkg_dir/lib" ]           && add2file "$OPT_DIR/.ld-paths" "$pkg_dir/lib")
     ([ -d "$pkg_dir/lib/pkgconfig" ] && add2file "$OPT_DIR/.pkgconfig-paths" "$pkg_dir/lib/pkgconfig")
 }
@@ -278,6 +312,16 @@ install_src(){
     build "$name"  "$extra"
 }
 
+install_svn(){
+    local name="$1"
+    local url="$2"
+    shift;shift;
+    local extra="$@"
+    
+    get_svn "$name" "$url"
+    build "$name" $extra
+}
+
 custom_build(){
     local name="$1"
     shift;
@@ -314,7 +358,7 @@ install_jar(){
     local url="$2"
 
     [ -d  "$OPT_DIR/$name/" ] || mkdir -p  "$OPT_DIR/$name/"
-    wget "$url" -O "$OPT_DIR/$name/$name.jar"
+    wget "$url" -O "$OPT_DIR/jars/$name.jar" | wget "$url" -O "$OPT_DIR/jars/$name.jar" --no-check-certificate
     link "$OPT_DIR/$name/$name.jar" "$OPT_JAR_DIR/$name.jar" 
 }
 

data/share/rbbt_commands/stat/compare_lists

@@ -0,0 +1,50 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*" "} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Compare two lists and do confusion matrix
+
+$ #{$0} [options] <filename1> <filename2>
+
+-h--help Print this help
+-c--common Print the common entries
+-o1--only_1 Print entries only in file 1
+-o2--only_2 Print entries only in file 2
+
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
+raise ParameterException, "Please provide two files with the entities to compare" unless ARGV.length == 2
+file1, file2 = ARGV
+
+list1 = Open.read(file1).split("\n")
+list2 = Open.read(file2).split("\n")
+
+common = list1 & list2
+only_1 = list1 - list2
+only_2 = list2 - list1
+
+case
+when options[:common]
+  puts common * "\n"
+when options[:only_1]
+  puts only_1 * "\n"
+when options[:only_2]
+  puts only_2 * "\n"
+else
+  puts "Common: #{common.length}"
+  puts "Unique to 1 (#{File.basename(file1)}): #{only_1.length}"
+  puts "Unique to 2 (#{File.basename(file2)}): #{only_2.length}"
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.23.28
+  version: 5.23.29
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-06 00:00:00.000000000 Z
+date: 2018-11-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -357,6 +357,7 @@ files:
 - share/rbbt_commands/resource/produce
 - share/rbbt_commands/rsync
 - share/rbbt_commands/stat/abs
+- share/rbbt_commands/stat/compare_lists
 - share/rbbt_commands/stat/density
 - share/rbbt_commands/stat/heatmap
 - share/rbbt_commands/stat/log