rbbt-util 5.25.32 → 5.25.33

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: '090b2d7cbaff9c7bbfa64bf7cae5fcb70e542187'
-  data.tar.gz: ff563a4afe38bdadbae449268576cf23ba41b011
+  metadata.gz: 5224ee57ce9c9356d168864d1457989ab094b579
+  data.tar.gz: ee950dc591700be501b2d1f84e23bae4492cea1d
 SHA512:
-  metadata.gz: ea1e035a6b3389913f1215ef0d804d72ddb4c95320d63f9fe66bf4f596499479a324c505fea962941771808426180cc7a655c9f2c84764c315ab85987df517a1
-  data.tar.gz: b06b23ff0dae842f397983f1a9bf6c46112814c34a6804789f4949dd18ebc3a361ca46aae7a734a6518efd8fc628da6b4f42e8d49b0eb97b6c4173ca41bec939
+  metadata.gz: 64f17229abeefc9faecec3519b347c069f2fd387205f59513fd5d2cf1b38d71eb8352dabefa9fc08c968cf76f0c6e544b061a8841d17ef9a7825930c7553b214
+  data.tar.gz: 76975c93b0151e609959817f158130d0db5e57235cc4f5a6850f3d879912b09d7a3996b6fde0da1f1435ea769ebcd921050d1a54d40c08d99118576218063e6f

data/lib/rbbt/resource/util.rb

@@ -91,13 +91,17 @@ module Resource
 
       if File.exist?(File.join(opt_dir, '.post_install')) and File.directory?(File.join(opt_dir, '.post_install'))
         Dir.glob(File.join(opt_dir, '.post_install','*')).each do |file|
-          begin
-            begin
-              File.chmod file
-              CMD.cmd(file) 
-            rescue
-              Log.warn("Could not execute #{ file }")
-            end
+
+          # Load exports
+          Open.read(file).split("\n").each do |line|
+            next unless line =~ /^\s*export\s+([^=]+)=(.*)/
+            var = $1.strip
+            value = $2.strip
+            value.sub!(/^['"]/,'')
+            value.sub!(/['"]$/,'')
+            value.gsub!(/\$[a-z_0-9]+/i){|var| ENV[var[1..-1]] }
+            Log.debug "Set variable export from .post_install: #{Misc.fingerprint [var,value]*"="}"
+            ENV[var] = value
           end
         end
       end

data/lib/rbbt/tsv/util.rb

@@ -32,8 +32,9 @@ module TSV
     TmpFile.with_file(values.uniq * "\n", false) do |value_file|
       cmd = "cat '#{ path }' | sed 's/\\t/\\tHEADERNOMATCH/' | grep -w -F -f '#{ value_file }' | sed 's/HEADERNOMATCH//' |sort -u|cut -f 2  |sort|uniq -c|sed 's/^ *//;s/ /\t/'"
       begin
-        TSV.open(CMD.cmd(cmd), :key_field => 1, :type => :single, :cast => :to_i)
+        TSV.open(CMD.cmd(cmd), :key_field => 1, :fields => [0], :type => :single, :cast => :to_i)
       rescue
+        Log.exception $!
         TSV.setup({}, :type => :single, :cast => :to_i)
       end
     end

data/lib/rbbt/tsv.rb

@@ -29,7 +29,7 @@ module TSV
   end
 
   def self.str2options(str)
-    field_options, rest =  str.split("#")
+    field_options,_sep, rest =  str.partition("#")
     key, fields_str = field_options.split("~")
 
     fields = fields_str.nil? ? [] : fields_str.split(/,\s*/)

data/lib/rbbt/util/open.rb

@@ -364,6 +364,7 @@ module Open
     rescue
       Open.ln_s(source, target, options)
     end
+    nil
   end
 
   #def self.cp(source, target, options = {})

data/lib/rbbt/util/python.rb

@@ -0,0 +1,22 @@
+require 'rbbt-util'
+
+require 'pycall/import'
+
+module RbbtPython
+  extend PyCall::Import
+  def self.run(mod = nil, &block)
+    begin
+      pyimport mod unless mod.nil?
+      case block.arity
+      when 0
+        yield 
+      when 1
+        yield self.send(mod)
+      else
+        raise "Unknown arity on block of code #{block.arity}"
+      end
+    rescue
+      Log.exception $!
+    end
+  end
+end

data/share/Rlib/util.R

@@ -526,7 +526,7 @@ rbbt.png_plot <- function(filename, p, width=500, height=500, ...){
 rbbt.pheatmap <- function(filename, data, width=800, height=800, take_log=FALSE, stdize=FALSE, positive=FALSE, ...){
     rbbt.require('pheatmap')
 
-    opar = par()
+    #opar = par()
     png(filename=filename, width=width, height=height);
 
     data = as.matrix(data)
@@ -556,8 +556,8 @@ rbbt.pheatmap <- function(filename, data, width=800, height=800, take_log=FALSE,
         pheatmap(data, ...)
     }
 
+    #par(opar)
     dev.off();
-    par(opar)
 }
 
 rbbt.heatmap <- function(filename, data, width=800, height=800, take_log=FALSE, stdize=FALSE, ...){
@@ -725,18 +725,22 @@ rbbt.plot.text_scatter <- function(formula, data) {
 }
 
 rbbt.install.CRAN <- function(pkg){
+    cat("Try CRAN install:", pkg, "\n")
     res = FALSE
-    tryCatch({ install.packages(pkg); library(pkg); res = TRUE }, error = function(e){ warning(paste("Could not install CRAN ", pkg)); res = FALSE })
+    tryCatch({ install.packages(pkg); res = TRUE; }, error = function(e){ str(e); warning(paste("Could not install CRAN ", pkg)); res = FALSE })
+    cat("CRAN", res)
     return(res)
 }
 
 rbbt.install.bioc <-function(pkg){
+    cat("Try BIOC install:", pkg, "\n")
     res = FALSE
     tryCatch({ source("http://bioconductor.org/biocLite.R"); biocLite(pkg, ask=FALSE, suppressUpdates = TRUE); res = TRUE }, error = function(e){ warning(paste("Could not install Bioconductor ", pkg)); res = FALSE })
     return(res)
 }
 
 rbbt.install.github <- function(pkg, ...){
+    cat("Try GITHUB install:", pkg, "\n")
     res = FALSE
     tryCatch({ library(devtools); install_github(pkg, ...); res = TRUE }, error = function(e){ warning(paste("Could not install GITHUB ", pkg)); res = FALSE })
     return(res)

data/share/install/software/lib/install_helpers

@@ -10,10 +10,38 @@ OPT_BUILD_DIR="$SOFTWARE_DIR/.build"; [ -d $OPT_BUILD_DIR ] || mkdir -p $OPT_BUI
 
 mkdir -p "$OPT_BUILD_DIR"
 
+if command -v realpath > /dev/null; then
+	function relative_path(){
+		local basedir=$1
+		local path=$2
+		echo $(realpath --relative-to="$basedir" "$path")
+	}
+else
+	realpath(){
+			OURPWD=$PWD
+			echo "REALPATH $@" >&2
+			cd "$(dirname "$1")"
+			LINK=$(readlink "$(basename "$1")")
+			while [ "$LINK" ]; do
+				cd "$(dirname "$LINK")"
+				LINK=$(readlink "$(basename "$1")")
+			done
+			REALPATH="$PWD/$(basename "$1")"
+			cd "$OURPWD"
+			echo "$REALPATH"
+	}
+
+	function relative_path(){
+		local basedir="$(realpath $1)"
+		local path="$(realpath "$2")"
+		echo ${path/$basedir\/}
+	}
+fi
+
 function link(){
   local source="$1"
   local target="$2"
-  local rel_source=$(realpath --relative-to="$(dirname $target)" "$source")
+  local rel_source=$(relative_path "$(dirname $target)" "$source")
   
   [ -h "$target" ] && rm "$target"
   echo ln -s "$rel_source" "$target" 1>&2
@@ -31,7 +59,7 @@ function add2file(){
     file=$1
     line=$2
 
-    rel="$(realpath -s --relative-to="$OPT_DIR" "$line")"
+    local rel=$(relative_path "$OPT_DIR" "$line")
     grep "$rel" "$file" || echo "$rel" >> "$file"
 }
 
@@ -168,22 +196,15 @@ compile(){
     fi
 }
 
-build(){
+prepare_make(){
     local name=$1; shift
     local extra="$@"
 
-    echo "Building $name"
-    if [ "x$extra" != "x" ]; then
-        echo "Extra params: $extra"
-    fi
-
     local old_pwd="`expand_path $(pwd)`"
     cd "`build_dir`"
 
     [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
 
-    echo PWD: `pwd`
-    ls
 
     if [ -f config/m4 ]; then
         libtoolize --force
@@ -192,7 +213,7 @@ build(){
     fi
 
     if [ -f Makefile.am -a ! -f configure ]; then
-      autoreconf
+        autoreconf
     fi
 
     if [ -f aclocal.m4 ]; then
@@ -216,55 +237,117 @@ build(){
         ln -s config configure
     fi
 
-    if [ -f CMakeLists.txt ]; then
-      [ -d build ] || mkdir build
-      cd build
-      cmake -DCMAKE_INSTALL_PREFIX=/install_dir ..
+    cd "$old_pwd"
+}
 
-      if [ -f ../configure ]; then
-        ../configure --prefix="$(opt_dir "$name")" $extra
-        make -j4
-        make install || (cd .. ; mv build "$(opt_dir "$name")")
-      else
-        make DESTDIR="$(opt_dir "$name")"  -j4
-        make DESTDIR="$(opt_dir "$name")" install || (cd .. ; mv build "$(opt_dir "$name")")
+build_make(){
+    local name=$1; shift
+    local extra="$@"
 
-        if [ -d "$(opt_dir "$name")/install_dir" ]; then
-          mv "$(opt_dir "$name")/install_dir"/** "$(opt_dir "$name")"
-          rmdir "$(opt_dir "$name")/install_dir"
-        fi
-      fi
+    local old_pwd="`expand_path $(pwd)`"
+    cd "`build_dir`"
+    echo PWD: `pwd`
+    ls
 
-      setup "$name"
-      clean_build
-    else
-      if [ -f configure ]; then 
+
+    [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
+
+    echo "Building with configure $name"
+    if [ "x$extra" != "x" ]; then
+        echo "Extra params: $extra"
+    fi
+
+    prepare_make $name
+
+    if [ -f configure ]; then 
         ./configure --prefix="$(opt_dir "$name")" $extra
         compile "$name" $extra
         [ -d "$(opt_dir "$name")" ] || move_opt "$name"
         setup "$name"
         clean_build
-      else
+    else
         compile "$name" $extra
         move_opt "$name"
         setup "$name"
         clean_build
-      fi
     fi
-    
+
+    cd "$old_pwd"
+}
+
+buid_cmake(){
+    local name=$1; shift
+    local extra="$@"
+
+    local old_pwd="`expand_path $(pwd)`"
+    cd "`build_dir`"
+    echo PWD: `pwd`
+    ls
+
+
+    [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
+
+    echo "Building with cmake $name"
+    if [ "x$extra" != "x" ]; then
+        echo "Extra params: $extra"
+    fi
+
+    echo "Using cmake"
+    [ -d build ] || mkdir build
+
+    cd build
+    cmake -DMAKE_INSTALL_PREFIX=/ $extra ..
+    if [ ! -f Makefile -a -f ../configure ]; then
+        ../configure --prefix="$(opt_dir "$name")" $extra
+        make -j4
+        make install || (cd .. ; mv build "$(opt_dir "$name")")
+    else
+        make DESTDIR="$(opt_dir "$name")"  -j4 && make DESTDIR="$(opt_dir "$name")" install
+    fi
+    cd ..
+
+    if [ ! -d "$(opt_dir "$name")" ]; then 
+        mkdir -p "$(opt_dir "$name")"
+        for subd in bin lib lib64 include pkgdir; do
+            [ -d $subd ] && mv $subd "$(opt_dir "$name")"/$subd
+        done
+    fi
+
+    setup "$name"
+    clean_build
+
     cd "$old_pwd"
 }
 
+build(){
+    local name=$1; shift
+    local extra="$@"
+
+    echo "Building $name"
+    if [ "x$extra" != "x" ]; then
+        echo "Extra params: $extra"
+    fi
+
+    [ -d src -a ! -e CMakeLists.txt -a ! -e Makefile -a ! -e configure ] && cd src
+
+    if [ -f CMakeLists.txt ]; then
+        buid_cmake "$name" $extra
+    else
+        build_make "$name" $extra
+    fi
+    
+}
+
 #{{{ SETUP
 
-versioned?(){
+is_versioned(){
     local name="$1"
     [[ $name =~ : ]]
 }
 
 opt_dir(){
     local name="$1"
-    if versioned? "$name"; then
+    if is_versioned "$name"; then
         local real_name=`echo $1 | sed 's/:.*//'`
         local version=`echo $1 | sed 's/.*://'`
         echo "$OPT_DIR/$real_name/$version"
@@ -292,7 +375,7 @@ setup(){
     local name="$1"
     local pkg_dir="`opt_dir \"$name\"`"
 
-    if versioned? "$name"; then
+    if is_versioned "$name"; then
         rm -f "$(dirname $pkg_dir)/current"
         link "$pkg_dir" "$(dirname $pkg_dir)/current"
         pkg_dir="$(dirname $pkg_dir)/current"
@@ -326,14 +409,22 @@ setup(){
 
 #{{{ HELPERS
 
-install_src(){
+prepare_src_pkg(){
     local name="$1"
     local url="$2"
     shift;shift;
-    local extra="$@"
-    
+
     get_pkg "$name" "$url"
     uncompress_pkg "$name"
+}
+
+install_src(){
+    local name="$1"
+    local url="$2"
+    shift;shift;
+    local extra="$@"
+
+    prepare_src_pkg "$name" "$url"
     build "$name"  "$extra"
 }
 
@@ -342,7 +433,7 @@ install_svn(){
     local url="$2"
     shift;shift;
     local extra="$@"
-    
+
     get_svn "$name" "$url"
     build "$name" $extra
 }
@@ -384,6 +475,7 @@ install_jar(){
 
     [ -d  "$OPT_DIR/$name/" ] || mkdir -p  "$OPT_DIR/$name/"
     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" 
 }
 
 jar2bin(){

data/share/rbbt_commands/tsv/info

@@ -56,7 +56,7 @@ else
     end
   end
 
-  if String === file and not Open.remote? file and File.exist? file
+  if String === file and not Open.remote? file and File.exist? file and not Open.gzip? file
     rows = `wc -l '#{ file }' 2> /dev/null|cut -f 1 -d' '`.strip
     header_rows = `(head '#{ file }' |grep "#" | wc -l) 2> /dev/null|cut -f 1 -d' '`
     if header_rows.to_i <= 2 and header_rows.to_i >= 1
@@ -65,7 +65,7 @@ else
       rows << ' (possibly including header)'
     end
   else
-    rows = "Could not get rows of #{Misc.fingerprint file}"
+    rows = "Could not get number of rows for #{Misc.fingerprint file}"
   end
   
   puts "Rows: #{Log.color :blue, rows}" 

data/share/rbbt_commands/workflow/info

@@ -146,15 +146,14 @@ if all
 end
 
 if recursive
-  inputs = step.info[:inputs]
-  inputs = {}
-  deps = (step.info[:dependencies] || []).collect{|v| get_step v.last }
+  inputs = step.info[:inputs] || {}
+  deps = step.dependencies
 
   while deps.any? do
     dep = deps.shift
     inputs = {} if inputs.nil?
     inputs = inputs.merge(dep.info[:inputs] || {})
-    deps.concat (dep.info[:dependencies] || []).collect{|v| get_step v.last }
+    deps = deps.concat dep.dependencies
   end
 
   if inputs.any?

data/share/workflow_config.ru

@@ -51,11 +51,11 @@ end
 #{{{ BASE
 app_eval app, etc_dir['app.d/base.rb'].find
 
-app.add_workflow wf, :priority
-
 #{{{ WORKFLOWS
 app_eval app, etc_dir['app.d/workflows.rb'].find_all
 
+app.add_workflow wf, :priority
+
 #{{{ RESOURCES
 load_file etc_dir['app.d/resources.rb'].find
 
@@ -123,13 +123,22 @@ app.get '/reload_workflow' do
     halt 500, "Not allowed in production" 
   end
 
-  workflow = params[:workflow] if params[:workflow]
-  wf_file = Workflow.local_workflow_filename(workflow)
-  wf_dir = File.dirname(wf_file)
-  $LOADED_FEATURES.delete_if do |path|
-    Misc.path_relative_to(wf_dir, path)
+  begin
+      workflow = params[:workflow] if params[:workflow]
+      wf_file = Workflow.local_workflow_filename(workflow)
+      wf_dir = File.dirname(wf_file)
+      $LOADED_FEATURES.delete_if do |path|
+          Misc.path_relative_to(wf_dir, path)
+      end
+      load wf_file
+  rescue Exception
+      if File.exists?(Rbbt.etc['target_workflow'].read.strip)
+          load Rbbt.etc['target_workflow'].read.strip
+      else
+          raise $!
+      end
   end
-  load wf_file
+
   halt 200, "Workflow #{ workflow } reloaded"
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.25.32
+  version: 5.25.33
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-05 00:00:00.000000000 Z
+date: 2019-03-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -302,6 +302,7 @@ files:
 - lib/rbbt/util/misc/system.rb
 - lib/rbbt/util/named_array.rb
 - lib/rbbt/util/open.rb
+- lib/rbbt/util/python.rb
 - lib/rbbt/util/semaphore.rb
 - lib/rbbt/util/simpleDSL.rb
 - lib/rbbt/util/simpleopt.rb