[egs,scripts]: replace non-portable read-link -f with utils/make_abso…

…lute.sh (#1694)

* remove links

* added steps link

* REplacement script for the gnu tool readlink with the -f option

* changed sh to bash

* replaced readlink -e with utils/make_absolute.sh

* added comments and down cased variables

egs/ami/s5/local/online/run_nnet2_ms_sp_disc.sh

@@ -135,7 +135,7 @@ fi
 
 if [ $stage -le 5 ]; then
   dir=${srcdir}_${criterion}_${effective_lrate}
-  ln -sf $(readlink -f ${srcdir}_online/conf) $dir/conf # so it acts like an online-decoding directory
+  ln -sf $(utils/make_absolute.sh ${srcdir}_online/conf) $dir/conf # so it acts like an online-decoding directory
 
   for epoch in $(seq $decode_start_epoch $num_epochs); do
     for decode_set in dev eval; do

egs/aspire/s5/local/fisher_data_prep.sh

@@ -167,7 +167,7 @@ fi
 if [ $stage -le 3 ]; then
   for f in `cat $tmpdir/sph.flist`; do
     # convert to absolute path
-    readlink -e $f
+    utils/make_absolute.sh $f
   done > $tmpdir/sph_abs.flist
 
   cat $tmpdir/sph_abs.flist | perl -ane 'm:/([^/]+)\.sph$: || die "bad line $_; ";  print "$1 $_"; ' > $tmpdir/sph.scp

egs/aspire/s5/local/multi_condition/aspire_data_prep.sh

@@ -105,7 +105,7 @@ fi
 if [ $stage -le 3 ]; then
   for f in `cat $tmpdir/wav.flist`; do
     # convert to absolute path
-    readlink -e $f
+    utils/make_absolute.sh $f
   done > $tmpdir/wav_abs.flist
 
   cat $tmpdir/wav_abs.flist | python -c "
@@ -132,7 +132,7 @@ if [ $stage -le 4 ]; then
     mkdir -p $test
     for f in `cat $tmpdir/wav_${dataset}.flist`; do
       # convert to absolute path
-      readlink -e $f
+      utils/make_absolute.sh $f
     done > $tmpdir/wav_${dataset}_abs.flist
     cat $tmpdir/wav_${dataset}_abs.flist | \
     python -c "

egs/aspire/s5/local/multi_condition/rirs/prep_aalto.sh

@@ -59,7 +59,7 @@ total_files=$(echo ${data_files[@]}|wc -w)
 echo "" > $log_dir/${DBname}_type${type_num}.rir.list
 echo "Found $total_files impulse responses in ${RIR_home}/aalto_concert_hall_pori//"
 tmpdir=`mktemp -d $log_dir/aalto_XXXXXX`
-tmpdir=`readlink -e $tmpdir`
+tmpdir=`utils/make_absolute.sh $tmpdir`
 file_count=1
 for data_file in ${data_files[@]}; do
   # aalto has incompatible format of wav audio, which are not compatible with python's wav.read() function

egs/aspire/s5/local/multi_condition/rirs/prep_c4dm.sh

@@ -88,7 +88,7 @@ total_files=$(echo ${data_files[@]}|wc -w)
 echo "" > $log_dir/${DBname}_type${type_num}.rir.list
 echo "Found $total_files impulse responses in ${RIR_home}/c4dm/"
 tmpdir=`mktemp -d $log_dir/c4dm_XXXXXX`
-tmpdir=`readlink -e $tmpdir`
+tmpdir=`utils/make_absolute.sh $tmpdir`
 file_count=1
 for data_file in ${data_files[@]}; do
   # c4dm has incompatible format of wav audio, which are not compatible with python's wav.read() function

egs/aspire/s5/local/multi_condition/rirs/prep_openair.sh

@@ -29,7 +29,7 @@ log_dir=$3
 
 if [ "$download" = true ]; then
   mkdir -p $RIR_home
-  RIR_home_abs=`readlink -e $RIR_home`
+  RIR_home_abs=`utils/make_absolute.sh $RIR_home`
   #HamiltonMuseum 
   #http://www.openairlib.net/auralizationdb/content/hamilton-mausoleum 
   echo "">$log_dir/${DBname}_download_commands.sh

egs/aspire/s5/local/multi_condition/run_nnet2_ms_disc.sh

@@ -135,7 +135,7 @@ fi
 
 if [ $stage -le 5 ]; then
   dir=${srcdir}_${criterion}_${learning_rate}_nj${num_jobs_nnet}
-  #ln -sf $(readlink -f ${srcdir}_multicondition/conf) $dir/conf # so it acts like an online-decoding directory
+  #ln -sf $(utils/make_absolute.sh ${srcdir}_multicondition/conf) $dir/conf # so it acts like an online-decoding directory
   graph_dir=exp/tri5a/graph
   for epoch in $(seq $decode_start_epoch $num_epochs); do
     for data_dir in dev_rvb test_rvb dev_aspire dev test; do

egs/babel/s5/local/make_corpus_subset.sh

@@ -40,8 +40,8 @@ fi
 mkdir -p $output_data_dir/transcription
 mkdir -p $output_data_dir/audio
 
-abs_src_dir=`readlink -f $input_data_dir` 
-abs_tgt_dir=`readlink -f $output_data_dir`
+abs_src_dir=`utils/make_absolute.sh $input_data_dir` 
+abs_tgt_dir=`utils/make_absolute.sh $output_data_dir`
 
 echo "Making subset..."
 for file_basename in `cat $input_data_list`; do

egs/babel/s5/make_release.sh

@@ -57,7 +57,7 @@ function export_file {
   else
     if [ ! -f $target_file ] ; then
       if ! $dryrun ; then
-        ln -s `readlink -f $source_file` $target_file || exit 1
+        ln -s `utils/make_absolute.sh $source_file` $target_file || exit 1
       fi
     else
       echo "The file is already there, not doing anything. Either change the version (using --version), or delete that file manually)"

egs/babel/s5/run-1-main.sh

@@ -25,7 +25,7 @@ if [ ! -d data/raw_train_data ]; then
     echo ---------------------------------------------------------------------
 
     local/make_corpus_subset.sh "$train_data_dir" "$train_data_list" ./data/raw_train_data
-    train_data_dir=`readlink -f ./data/raw_train_data`
+    train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 fi
 nj_max=`cat $train_data_list | wc -l`
@@ -34,7 +34,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -d data/raw_dev2h_data ]; then
   echo ---------------------------------------------------------------------

egs/babel/s5/run-2b-bnf.sh

@@ -56,7 +56,7 @@ num_pdfs=`gmm-info exp/tri5_ali/final.mdl | grep pdfs | awk '{print $NF}'` || ex
 
 # Now we copy conf/bnf/config_limited.py or conf/bnf/config_full.py, as appropriate,
 # to ptdnn/exp_bnf/config.py, replacing a couple of things as we copy it.
-WORK=`readlink -f $working_dir`
+WORK=`utils/make_absolute.sh $working_dir`
 config_in=conf/bnf/config_${babel_type}.py
 [ ! -f $config_in ] && echo "No such config file $config_in" && exit 1;
 ! cat $config_in | sed "s|CWD|$PWD|" | sed "s|WORK|$WORK|" | sed "s/N_OUTS/${num_pdfs}/" > ptdnn/exp_bnf/config.py && \

egs/babel/s5/run-4-test.sh

@@ -131,7 +131,7 @@ else
 
     local/make_corpus_subset.sh "$my_data_dir" "$my_data_list" ./data/raw_${type}_data
   fi
-  my_data_dir=`readlink -f ./data/raw_${type}_data`
+  my_data_dir=`utils/make_absolute.sh ./data/raw_${type}_data`
 
   nj_max=`cat $my_data_list | wc -l`
   if [[ "$nj_max" -lt "$my_nj" ]] ; then

egs/babel/s5/run-5-anydecode.sh

@@ -136,7 +136,7 @@ else
 
     local/make_corpus_subset.sh "$my_data_dir" "$my_data_list" ./data/raw_${type}_data
   fi
-  my_data_dir=`readlink -f ./data/raw_${type}_data`
+  my_data_dir=`utils/make_absolute.sh ./data/raw_${type}_data`
 
   nj_max=`cat $my_data_list | wc -l`
   if [[ "$nj_max" -lt "$my_nj" ]] ; then

egs/babel/s5b/EXAMPLE.vietnamese

@@ -115,7 +115,7 @@
 #Combine results (what we call 4way-combo)
 #This is ugly, but effective
 systems=""; for sys in `ls -1 release/*dev*.ctm | grep -v RESCORED` ; do 
-  q=`readlink -f $sys`; 
+  q=`utils/make_absolute.sh $sys`; 
   decode=${q%%/dev10h.seg*}; 
   w=`dirname ${q##*score_}`; 
   echo $w; systems+=" ${decode}:$(($w - 10))";  

egs/babel/s5b/local/make_corpus_subset.sh

@@ -48,8 +48,8 @@ for i in `seq 0 $(( $num_src / 2 - 1))` ; do
   input_data_dir=${sources[ $[2 * $i] ]}
   input_data_list=${sources[ $((2 * $i + 1)) ]}
 
-  abs_src_dir=`readlink -f $input_data_dir`
-  abs_tgt_dir=`readlink -f $output_data_dir`
+  abs_src_dir=`utils/make_absolute.sh $input_data_dir`
+  abs_tgt_dir=`utils/make_absolute.sh $output_data_dir`
 
   if [[ ! -d "$input_data_dir" ]] ; then
     echo "FATAL: input data directory does not exist";

egs/babel/s5b/local/nist_eval/create_compound_set.sh

@@ -49,22 +49,22 @@ echo "Creating compound $tgtdir/compounds/$devset"
 (
   cd $tgtdir/compounds/$devset
   echo "DEVSET file list: $devset_flist"
-  ln -s `readlink -f $devset_flist` files.list
+  ln -s `utils/make_absolute.sh $devset_flist` files.list
   echo "DEVSET ECF file : $devset_ecf"
-  ln -s `readlink -f $devset_ecf` ecf.xml
+  ln -s `utils/make_absolute.sh $devset_ecf` ecf.xml
   echo "DEVSET RTTM file: $devset_rttm"
-  ln -s `readlink -f $devset_rttm` rttm
+  ln -s `utils/make_absolute.sh $devset_rttm` rttm
   echo "DEVSET STM file : $devset_stm"
-  ln -s `readlink -f $devset_stm` stm
+  ln -s `utils/make_absolute.sh $devset_stm` stm
 )
 
 echo "Creating compound $tgtdir/compounds/$evlset"
 (
   cd $tgtdir/compounds/$evlset
   echo "EVLSET file list: $evlset_flist"
-  ln -s `readlink -f $evlset_flist` files.list
+  ln -s `utils/make_absolute.sh $evlset_flist` files.list
   echo "EVLSET ECF file : $evlset_ecf"
-  ln -s `readlink -f $evlset_ecf` ecf.xml
+  ln -s `utils/make_absolute.sh $evlset_ecf` ecf.xml
 )
 
 echo "Compound creation OK."

egs/babel/s5b/local/nist_eval/make_release.sh

@@ -52,7 +52,7 @@ function export_file {
   else
     if [ ! -f $target_file ] ; then
       if ! $dryrun ; then
-        ln -s `readlink -f $source_file` $target_file || exit 1
+        ln -s `utils/make_absolute.sh $source_file` $target_file || exit 1
         ls -al $target_file
       else
         echo "$source_file -> $target_file"
@@ -158,10 +158,10 @@ function get_ecf_name {
   #echo $kwstask
   if [ -z $kwstask ] ; then
     #echo $data/kws/kwlist.xml
-    kwlist= `readlink -f $data/kws/kwlist.xml`
+    kwlist= `utils/make_absolute.sh $data/kws/kwlist.xml`
   else
     #echo $data/$kwstask/kwlist.xml
-    kwlist=`readlink -f  $data/$kwstask/kwlist.xml`
+    kwlist=`utils/make_absolute.sh  $data/$kwstask/kwlist.xml`
   fi
   ecf=`head -n 1 $kwlist | grep -Po "(?<=ecf_filename=\")[^\"]*"`
   echo -e "\tFound ECF: $ecf" >&2
@@ -302,7 +302,7 @@ else
       echo -e "\tPREPARE EXPORT: $compound_best_one"
       sysid=`create_sysid $compound_best_one`
       #ecf=`get_ecf_name $best_one`
-      ecf=`readlink -f $data/compounds/$compound/ecf.xml`
+      ecf=`utils/make_absolute.sh $data/compounds/$compound/ecf.xml`
       scase=`figure_out_scase $ecf`
       partition=`figure_out_partition $ecf`
       corpusid=`figure_out_corpusid $ecf`
@@ -340,7 +340,7 @@ else
     echo -e "\tPREPARE EXPORT: $compound_best_one"
     sysid=`create_sysid $compound_best_one`
     #ecf=`get_ecf_name $best_one`
-    ecf=`readlink -f $data/compounds/$compound/ecf.xml`
+    ecf=`utils/make_absolute.sh $data/compounds/$compound/ecf.xml`
     scase=`figure_out_scase $ecf`
     partition=`figure_out_partition $ecf`
     corpusid=`figure_out_corpusid $ecf`

egs/babel/s5b/run-1-main-extend-lex.sh

@@ -33,7 +33,7 @@ if [ ! -f data/raw_train_data/.done ]; then
     echo ---------------------------------------------------------------------
 
     local/make_corpus_subset.sh "$train_data_dir" "$train_data_list" ./data/raw_train_data
-    train_data_dir=`readlink -f ./data/raw_train_data`
+    train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
     touch data/raw_train_data/.done 
 fi
 nj_max=`cat $train_data_list | wc -l`
@@ -42,7 +42,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -d data/raw_dev2h_data ]; then
   echo ---------------------------------------------------------------------

egs/babel/s5b/run-1-main.sh

@@ -27,7 +27,7 @@ if [ ! -f data/raw_train_data/.done ]; then
     echo ---------------------------------------------------------------------
 
     local/make_corpus_subset.sh "$train_data_dir" "$train_data_list" ./data/raw_train_data
-    train_data_dir=`readlink -f ./data/raw_train_data`
+    train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
     touch data/raw_train_data/.done
 fi
 nj_max=`cat $train_data_list | wc -l`
@@ -36,7 +36,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -d data/raw_dev2h_data ]; then
   echo ---------------------------------------------------------------------

egs/babel/s5b/run-2-segmentation.sh

@@ -35,7 +35,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -f data/train_seg/.done ]; then
 

egs/babel/s5b/run-4-anydecode.sh

@@ -167,7 +167,7 @@ if [ ! -f data/raw_${dataset_type}_data/.done ]; then
   local/make_corpus_subset.sh $resource_string ./data/raw_${dataset_type}_data
   touch data/raw_${dataset_type}_data/.done
 fi
-my_data_dir=`readlink -f ./data/raw_${dataset_type}_data`
+my_data_dir=`utils/make_absolute.sh ./data/raw_${dataset_type}_data`
 [ -f $my_data_dir/filelist.list ] && my_data_list=$my_data_dir/filelist.list
 nj_max=`cat $my_data_list | wc -l` || nj_max=`ls $my_data_dir/audio | wc -l`
 

egs/babel/s5c/local/make_corpus_subset.sh

@@ -48,8 +48,8 @@ for i in `seq 0 $(( $num_src / 2 - 1))` ; do
   input_data_dir=${sources[ $[2 * $i] ]}
   input_data_list=${sources[ $((2 * $i + 1)) ]}
 
-  abs_src_dir=`readlink -f $input_data_dir`
-  abs_tgt_dir=`readlink -f $output_data_dir`
+  abs_src_dir=`utils/make_absolute.sh $input_data_dir`
+  abs_tgt_dir=`utils/make_absolute.sh $output_data_dir`
 
   if [[ ! -d "$input_data_dir" ]] ; then
     echo "FATAL: input data directory does not exist";

egs/babel/s5c/local/nist_eval/create_compound_set.sh

@@ -49,22 +49,22 @@ echo "Creating compound $tgtdir/compounds/$devset"
 (
   cd $tgtdir/compounds/$devset
   echo "DEVSET file list: $devset_flist"
-  ln -s `readlink -f $devset_flist` files.list
+  ln -s `utils/make_absolute.sh $devset_flist` files.list
   echo "DEVSET ECF file : $devset_ecf"
-  ln -s `readlink -f $devset_ecf` ecf.xml
+  ln -s `utils/make_absolute.sh $devset_ecf` ecf.xml
   echo "DEVSET RTTM file: $devset_rttm"
-  ln -s `readlink -f $devset_rttm` rttm
+  ln -s `utils/make_absolute.sh $devset_rttm` rttm
   echo "DEVSET STM file : $devset_stm"
-  ln -s `readlink -f $devset_stm` stm
+  ln -s `utils/make_absolute.sh $devset_stm` stm
 )
 
 echo "Creating compound $tgtdir/compounds/$evlset"
 (
   cd $tgtdir/compounds/$evlset
   echo "EVLSET file list: $evlset_flist"
-  ln -s `readlink -f $evlset_flist` files.list
+  ln -s `utils/make_absolute.sh $evlset_flist` files.list
   echo "EVLSET ECF file : $evlset_ecf"
-  ln -s `readlink -f $evlset_ecf` ecf.xml
+  ln -s `utils/make_absolute.sh $evlset_ecf` ecf.xml
 )
 
 echo "Compound creation OK."

egs/babel/s5c/local/nist_eval/make_release.sh

@@ -52,7 +52,7 @@ function export_file {
   else
     if [ ! -f $target_file ] ; then
       if ! $dryrun ; then
-        ln -s `readlink -f $source_file` $target_file || exit 1
+        ln -s `utils/make_absolute.sh $source_file` $target_file || exit 1
         ls -al $target_file
       else
         echo "$source_file -> $target_file"
@@ -158,10 +158,10 @@ function get_ecf_name {
   #echo $kwstask
   if [ -z $kwstask ] ; then
     #echo $data/kws/kwlist.xml
-    kwlist= `readlink -f $data/kws/kwlist.xml`
+    kwlist= `utils/make_absolute.sh $data/kws/kwlist.xml`
   else
     #echo $data/$kwstask/kwlist.xml
-    kwlist=`readlink -f  $data/$kwstask/kwlist.xml`
+    kwlist=`utils/make_absolute.sh  $data/$kwstask/kwlist.xml`
   fi
   ecf=`head -n 1 $kwlist | grep -Po "(?<=ecf_filename=\")[^\"]*"`
   echo -e "\tFound ECF: $ecf" >&2
@@ -302,7 +302,7 @@ else
       echo -e "\tPREPARE EXPORT: $compound_best_one"
       sysid=`create_sysid $compound_best_one`
       #ecf=`get_ecf_name $best_one`
-      ecf=`readlink -f $data/compounds/$compound/ecf.xml`
+      ecf=`utils/make_absolute.sh $data/compounds/$compound/ecf.xml`
       scase=`figure_out_scase $ecf`
       partition=`figure_out_partition $ecf`
       corpusid=`figure_out_corpusid $ecf`
@@ -340,7 +340,7 @@ else
     echo -e "\tPREPARE EXPORT: $compound_best_one"
     sysid=`create_sysid $compound_best_one`
     #ecf=`get_ecf_name $best_one`
-    ecf=`readlink -f $data/compounds/$compound/ecf.xml`
+    ecf=`utils/make_absolute.sh $data/compounds/$compound/ecf.xml`
     scase=`figure_out_scase $ecf`
     partition=`figure_out_partition $ecf`
     corpusid=`figure_out_corpusid $ecf`

egs/babel/s5c/run-1-main-extend-lex.sh

@@ -33,7 +33,7 @@ if [ ! -f data/raw_train_data/.done ]; then
     echo ---------------------------------------------------------------------
 
     local/make_corpus_subset.sh "$train_data_dir" "$train_data_list" ./data/raw_train_data
-    train_data_dir=`readlink -f ./data/raw_train_data`
+    train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
     touch data/raw_train_data/.done 
 fi
 nj_max=`cat $train_data_list | wc -l`
@@ -42,7 +42,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -d data/raw_dev2h_data ]; then
   echo ---------------------------------------------------------------------

egs/babel/s5c/run-1-main.sh

@@ -27,7 +27,7 @@ if [ ! -f data/raw_train_data/.done ]; then
     echo ---------------------------------------------------------------------
 
     local/make_corpus_subset.sh "$train_data_dir" "$train_data_list" ./data/raw_train_data
-    train_data_dir=`readlink -f ./data/raw_train_data`
+    train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
     touch data/raw_train_data/.done
 fi
 nj_max=`cat $train_data_list | wc -l`
@@ -36,7 +36,7 @@ if [[ "$nj_max" -lt "$train_nj" ]] ; then
     exit 1;
     train_nj=$nj_max
 fi
-train_data_dir=`readlink -f ./data/raw_train_data`
+train_data_dir=`utils/make_absolute.sh ./data/raw_train_data`
 
 if [ ! -d data/raw_dev2h_data ]; then
   echo ---------------------------------------------------------------------