hrquest workflow v0.1

diff --git a/bin/hrquest.sh b/bin/hrquest.sh
new file mode 100755 (executable)
index 0000000..61b07c4
--- /dev/null
+++ b/bin/hrquest.sh
@@ -0,0 +1,215 @@
+#!/bin/sh -l
+
+function unziptar {
+       echo "unziptar $1"
+        zipname=`echo $1 | grep '\.zip'`
+        echo $zipname
+        tarname=`echo $1 | grep '\.tar'`
+        echo $tarname
+        tgzname=`echo $1 | grep '\.tgz'`
+        echo $tgzname
+        if [ "x$zipname" != "x" ]
+                then
+                echo "ZIP File"
+                unzip -j $1 -d data
+        else
+                if [ "x$tarname" != "x" ]
+                        then
+                        echo "TAR File"
+                       COMP=`tar -tvf $1 | awk 'END{print}' |   awk -F' ' '{print $NF}' | awk -F'/' '{print NF-1}'`
+                       tar -xvf $1 --strip-components=${COMP} -C data
+                else
+                        if [ "x$tgzname" != "x" ]
+                                then
+                                echo "TGZ File"
+                               COMP=`tar -tvf $1 | awk 'END{print}' |   awk -F' ' '{print $NF}' | awk -F'/' '{print NF-1}'`
+                               tar -zxvf $1 --strip-components=${COMP} -C data
+                        else
+                                echo "Unknown File Type"
+                                exit 6
+                        fi
+                fi
+        fi
+
+        if [ $? != 0 ]
+                then
+                echo "A problem occurred while untargzing the input: giving up!"
+                exit 2
+        fi
+}
+
+function checkdir {
+        lfc-ls $1 > /dev/null
+        if [ $? != 0 ]
+        then
+                echo "Directory $1 not found, creating it!"
+               lfc-mkdir -p $1
+                #exit 6
+        fi
+}
+
+
+function downloadDir {
+        checkdir $1
+        LOCALDIR=`basename $1`
+        mkdir -p ${LOCALDIR}
+        for i in `lfc-ls $1 | grep -v garbage`
+        do
+                lcg-cp -v lfn:$1/$i file:$PWD/${LOCALDIR}/$i
+                if [ $? != 0 ]
+                then
+                        echo "lcg-cp failed: trying once more"
+                        lcg-cp -v lfn:$1/$i file:$PWD/${LOCALDIR}/$i
+                        if [ $? != 0 ]
+                        then
+                                echo "Unable to download file lfn:$1/$i: giving up."
+                                exit 1
+                        fi
+                fi
+        done
+}
+
+function downloadFile {
+       local fname=`basename $1`
+       test -f $fname
+       CODE=$?
+       if [ ${CODE} != 0 ]
+       then
+
+                lcg-cp -v lfn:$1 file:$PWD/$fname
+                if [ $? != 0 ]
+                then
+                        echo "lcg-cp failed: trying once more"
+                        lcg-cp -v lfn:$1 file:$PWD/$fname
+                        if [ $? != 0 ]
+                        then
+                                echo "Unable to download file lfn:$1: giving up."
+                                exit 1
+                        fi
+                fi
+       else
+               echo "File $fname already exists locally"
+       fi
+}
+
+in=$@
+suffix=" ] "
+echo $in | grep '\['
+CODE=$?
+if [ ${CODE} != 0 ]
+#simple arguments, no arrays
+then
+  SIGFILE=$1
+  PARAMFILE=$2
+  INFOLDER=$3
+  RESDIR=$4
+else
+#split inputs based on [] and retrieve contents
+  SIGFILE=`echo $in | awk -F'\\\[' '{print $2}' | awk -F'\\\]' '{print $1}'`
+  mySigArray=( $SIGFILE )
+  PARAMFILE=`echo $in | awk -F'\\\]' '{print $2}' | awk -F' ' '{print $1}'`
+  INFOLDER=`echo $in | awk -F'\\\]' '{print $2}' | awk -F' ' '{print $2}'`
+  RESDIR=`echo $in | awk -F'\\\] ' '{print $2}' | awk -F' ' '{print $3}'`
+
+  echo "Resdir is $RESDIR"  
+
+fi
+
+
+DATADIR=`dirname ${INFOLDER}`
+
+echo "Downloading inputs"
+
+downloadFile $PARAMFILE
+
+((n_elements=${#mySigArray[@]}, max_index=n_elements - 1))
+for ((i = 0; i <= max_index; i++)); do
+  downloadFile ${mySigArray[i]}
+done
+
+
+#COMPDATA=$4
+#RESDIR=$5
+#preparing input data
+#export LD_LIBRARY_PATH=/usr/local/matlab/MCR/v84/runtime/glnxa64:/usr/local/matlab/MCR/v84/bin/glnxa64:/usr/local/matlab/MCR/v84/sys/os/glnxa64:$LD_LIBRARY_PATH
+#export XAPPLRESDIR=/usr/local/matlab/MCR/v84/X11/app-defaults
+
+hname=`hostname`
+if [ "${hname}" != "moteur1.grid.creatis.insa-lyon.fr" ] && [ "${hname}" != "moteur2.grid.creatis.insa-lyon.fr" ]
+then
+       echo "hrquest not yest supported on grid resources"
+
+else
+       export PATH=/usr/local/hrquest:$PATH
+       export LD_LIBRARY_PATH=/usr/local/hrquest/lib:$LD_LIBRARY_PATH
+       echo "LD_LIBRARY_PATH is $LD_LIBRARY_PATH"
+fi
+
+
+#export LFC_HOST=lfc-biomed.in2p3.fr
+#export LCG_GFAL_INFOSYS=cclcgtopbdii02.in2p3.fr:2170
+
+#echo "whoami, Printing env"
+#whoami
+#env
+
+echo "result dir is $RESDIR"
+checkdir $RESDIR
+
+#preparing comparison data
+#mkdir ${DATADIR}
+#cd ${DATADIR}
+downloadDir ${INFOLDER}
+#cd ..
+
+echo "pwd is `pwd`, creating outputs folder"
+mkdir outputs
+#launching program
+echo "launching the program"
+((n_elements=${#mySigArray[@]}, max_index=n_elements - 1))
+PF=`basename ${PARAMFILE}`
+for ((i = 0; i <= max_index; i++)); do
+  echo "launching the program for i = $i"
+  SIG=`basename ${mySigArray[i]}`
+  echo "hrquestCml -f $PF $SIG"
+  hrquestCml -f $PF ${SIG}
+  CODE=$?
+  if [ ${CODE} != 0 ]
+  then
+    echo "Execution failed with code ${CODE}"
+    exit ${CODE}
+  fi
+  #echo "mySigarray is ${SIG}"
+  basefilename=`basename ${SIG%.*}`
+  mv ${basefilename}_* outputs/
+done
+
+
+RESULT=results.tgz
+LFN=${RESDIR}/${RESULT}
+lfc-ls ${LFN}
+        if [ $? = 0 ]
+        then
+                echo "deleting previous ${LFN}"
+                lcg-del -a lfn:/${LFN}
+                        if [ $? != 0 ]
+                        then
+                                echo "not able to lcg-del lfn:/${LFN}, renaming it"
+                                d=`date -d "" +%s`
+                                lfc-rename ${LFN} ${LFN}-garbage-${d}
+                        fi
+        fi
+
+
+
+tar -czvf $RESULT outputs 
+test -f ${RESULT}
+CODE=$?
+if [ ${CODE} != 0 ]
+then
+    echo "Execution failed: exiting with code ${CODE} since ${RESULT} does not exist"
+    exit ${CODE}
+else
+    echo "Execution done, ${RESULT} created."
+fi
+

diff --git a/gasw/hrquest.xml b/gasw/hrquest.xml
new file mode 100644 (file)
index 0000000..7b4a512
--- /dev/null
+++ b/gasw/hrquest.xml
@@ -0,0 +1,23 @@
+<description>
+       <executable name="hrquest.sh">
+               <access type="LFN" cached="true">       
+               </access>
+               <executor value="LOCAL"/>
+               <value value="[BIN_DIR]/hrquest.sh"/>
+       
+               <input name="SignalFile" option="no1">
+               </input>
+                <input name="ParamFile" option="no2">
+               </input>
+                <input name="InputFolder" option="no3">
+               </input>
+               <input name="OutputFolder" option="no4">
+                </input>
+               <output name="results" option="no5">
+                 <template value="$dir4/$na4/results.tgz"/>
+                       <access type="LFN">
+                       </access>
+
+               </output>
+       </executable> 
+</description>

diff --git a/workflow/hrquest.gwendia b/workflow/hrquest.gwendia
new file mode 100644 (file)
index 0000000..eaa2d13
--- /dev/null
+++ b/workflow/hrquest.gwendia
@@ -0,0 +1,53 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<workflow name="hrquest" version="0.1">
+
+  <description>There is no description for this application. Please contact the developers to know what it is about.</description>
+
+  <interface>
+    <source name="ParamFile" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: Text file containing the description of  Metabolite Basis Spectra and  Metabolite Fitting Constraints
+      </source-comment>
+    </source>
+    <source name="InputFolder" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: Folder containing  the MRUI files (database) described in the ParamFile. Take care to use the same folder name in the ParamFile
+      </source-comment>
+    </source>
+    <source name="OutputFolder" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: The folder to which the outputs will be uploaded
+      </source-comment>
+    </source>
+    <source name="SignalFile" type="string">
+      <source-comment>&lt;b&gt;&lt;font color="blue"&gt;new input&lt;/font&gt;&lt;/b&gt;: MRUI file containing the signal to be analyzed
+      </source-comment>
+    </source>
+    <sink name="output.tgz" type="uri" />
+  </interface>
+
+  <processors>
+    <processor name="hrquest" >
+      <in name="input3" type="string" depth="0" />
+      <in name="input2" type="string" depth="0" />
+      <in name="input1" type="string" depth="0" />
+      <in name="input0" type="string" depth="1" />
+      <out name="out" type="uri" depth="0" />
+      <iterationstrategy>
+        <cross>
+          <port name="input0" />
+          <port name="input1" />
+          <port name="input2" />
+          <port name="input3" />
+        </cross>
+      </iterationstrategy>
+      <gasw descriptor="[GASW_DIR]/hrquest.xml"/>
+    </processor>
+  </processors>
+
+  <links>
+      <link from="hrquest:out" to="output.tgz" />
+      <link from="SignalFile" to="hrquest:input0" />
+      <link from="ParamFile" to="hrquest:input1" />
+      <link from="InputFolder" to="hrquest:input2" />
+      <link from="OutputFolder" to="hrquest:input3" />
+  </links>
+
+</workflow>