Add common.sh (pierre)

diff --git a/cluster_tools/common.sh b/cluster_tools/common.sh
new file mode 100644 (file)
index 0000000..ccad419
--- /dev/null
+++ b/cluster_tools/common.sh
@@ -0,0 +1,115 @@
+
+set -u
+
+# print error message and exit immediately
+programname="$(basename ${0})"
+function error {
+    echo "${programname} **ERROR** $1"
+    exit 1
+}
+
+# ensure a valid proxy is present for at least one hour
+# if no proxy is found, try to create a new one
+# return 0 if a valid proxy is found or created
+# else return voms-proxy-init error code
+function ensure_proxy {
+    voms-proxy-info --exists -valid 1:0 > /dev/null && return 0 
+    voms-proxy-init --voms biomed -valid 24:00 || exit 1
+}
+
+# print prompt to ensure that the user want to continue further
+# the user has to answer with 'y' to continue
+function check_user {
+    prompt="${1:-is that correct?}"
+    read -p "${prompt} [y/n] " answer
+    test "${answer}" == "y" && return 0
+    test "${answer}" == "n" && return 1
+    check_user "${prompt}"
+}
+
+# checks if the lfn file exists
+function file_exists {
+    lfnfile="${1:?"provide lfn to file"}"
+    lfc-ls ${lfnfile} 2>&1 > /dev/null
+}
+
+
+# upload file to grid storage element
+# source can be a relative or an absolute path to the source file 
+# dest must be the lfn to the target **file** (not the directory) 
+# if dest already exists, it prompts the user for overwritting
+function upload_file {
+    sourcefile=${1:?"provide source file"}
+    destlfn=${2:?"provide destination file lfn"}
+    sourcefile="$(readlink -f "${sourcefile}")" # convert to absolute path
+    test -f "${sourcefile}" || error "can't find ${sourcefile}"
+    echo "uploading ${sourcefile} to ${destlfn}"
+    if file_exists "${destlfn}"; then
+       check_user "${destlfn} already exists. overwrite it?" || return 2
+       lcg-del -a "lfn:${destlfn}" || error "lcg-del error"
+    fi
+    echo "lets roll"
+
+    local pending_ses=${SES}
+    local registered=false
+    while [ "x${pending_ses}" != "x" ]
+    do 
+        #select a se from list
+        local S=`echo ${pending_ses} | awk '{print $1}'`
+        #update list of SEs
+        local new_list=""
+        for i in `echo ${pending_ses}`
+        do
+            if [ "$i" != "${S}" ]
+           then
+               new_list="${new_list} ${i}"
+            fi
+        done
+        pending_ses=${new_list}
+        local TEMP=`mktemp lcg-XXXXX`
+        if [ "${registered}" = "false" ]
+        then
+            echo -n "Registering release to ${S}..."
+            lcg-cr -v -d ${S} -l "lfn:${destlfn}" "file:${sourcefile}" &>${TEMP}
+            if [ $? != 0 ]
+           then
+               echo -e "\t [\033[31m  FAILED  \033[0m]"
+               cat ${TEMP}
+               \rm ${TEMP}
+           else
+               echo -e "\t [\033[32m  OK  \033[0m]"
+               registered=true
+               \rm ${TEMP}
+            fi
+        else
+            echo -n "Replicating release to ${S}..."
+            lcg-rep -v -d ${S} "lfn:${destlfn}" &>${TEMP}
+            if [ $? != 0 ]
+           then
+               echo -e "\t [\033[31m  FAILED  \033[0m]"
+               cat ${TEMP}
+               \rm ${TEMP}
+           else
+               echo -e "\t [\033[32m  OK  \033[0m]"
+               \rm ${TEMP}
+            fi
+        fi
+    done
+}
+
+
+# common path used
+lfnbase="/grid/biomed/creatis/fgate/"
+lfnrelease="/grid/biomed/creatis/vip/data/groups/GateLab/releases/"
+lfnworkflow="${lfnbase}workflow/"
+lfngasw="${lfnbase}gasw/"
+lfnscript="${lfnbase}bin/"
+
+#list of SEs used for storage. Don't modify this list unless you know
+# what you're doing. Replicating the release in a bad place (e.g. on a
+# remote continent) can dramatically slow down the transfers
+SES="ccsrm02.in2p3.fr sbgse1.in2p3.fr marsedpm.in2p3.fr"
+
+# define the prefix for uploaded file
+# default to local machine username
+prefix="${USER:?"USER must be set"}_"

diff --git a/grid/common.sh b/grid/common.sh
deleted file mode 100644 (file)
index 106aad6..0000000
--- a/grid/common.sh
+++ /dev/null
@@ -1,115 +0,0 @@
-
-set -u
-
-# print error message and exit immediately
-programname="$(basename ${0})"
-function error {
-echo "${programname} **ERROR** $1"
-exit 1
-}
-
-# ensure a valid proxy is present for at least one hour
-# if no proxy is found, try to create a new one
-# return 0 if a valid proxy is found or created
-# else return voms-proxy-init error code
-function ensure_proxy {
-voms-proxy-info --exists -valid 1:0 > /dev/null && return 0 
-voms-proxy-init --voms biomed -valid 24:00 || exit 1
-}
-
-# print prompt to ensure that the user want to continue further
-# the user has to answer with 'y' to continue
-function check_user {
-prompt="${1:-is that correct?}"
-read -p "${prompt} [y/n] " answer
-test "${answer}" == "y" && return 0
-test "${answer}" == "n" && return 1
-check_user "${prompt}"
-}
-
-# checks if the lfn file exists
-function file_exists {
-lfnfile="${1:?"provide lfn to file"}"
-lfc-ls ${lfnfile} 2>&1 > /dev/null
-}
-
-
-# upload file to grid storage element
-# source can be a relative or an absolute path to the source file 
-# dest must be the lfn to the target **file** (not the directory) 
-# if dest already exists, it prompts the user for overwritting
-function upload_file {
-sourcefile=${1:?"provide source file"}
-destlfn=${2:?"provide destination file lfn"}
-sourcefile="$(readlink -f "${sourcefile}")" # convert to absolute path
-test -f "${sourcefile}" || error "can't find ${sourcefile}"
-echo "uploading ${sourcefile} to ${destlfn}"
-if file_exists "${destlfn}"; then
-       check_user "${destlfn} already exists. overwrite it?" || return 2
-       lcg-del -a "lfn:${destlfn}" || error "lcg-del error"
-fi
-echo "lets roll"
-
-local pending_ses=${SES}
-local registered=false
-while [ "x${pending_ses}" != "x" ]
-do 
-  #select a se from list
-  local S=`echo ${pending_ses} | awk '{print $1}'`
-  #update list of SEs
-  local new_list=""
-  for i in `echo ${pending_ses}`
-    do
-    if [ "$i" != "${S}" ]
-       then
-       new_list="${new_list} ${i}"
-    fi
-  done
-  pending_ses=${new_list}
-  local TEMP=`mktemp lcg-XXXXX`
-  if [ "${registered}" = "false" ]
-      then
-      echo -n "Registering release to ${S}..."
-      lcg-cr -v -d ${S} -l "lfn:${destlfn}" "file:${sourcefile}" &>${TEMP}
-      if [ $? != 0 ]
-         then
-         echo -e "\t [\033[31m  FAILED  \033[0m]"
-         cat ${TEMP}
-         \rm ${TEMP}
-         else
-         echo -e "\t [\033[32m  OK  \033[0m]"
-         registered=true
-         \rm ${TEMP}
-      fi
-  else
-      echo -n "Replicating release to ${S}..."
-      lcg-rep -v -d ${S} "lfn:${destlfn}" &>${TEMP}
-      if [ $? != 0 ]
-         then
-         echo -e "\t [\033[31m  FAILED  \033[0m]"
-         cat ${TEMP}
-         \rm ${TEMP}
-         else
-         echo -e "\t [\033[32m  OK  \033[0m]"
-         \rm ${TEMP}
-      fi
-  fi
-done
-}
-
-
-# common path used
-lfnbase="/grid/biomed/creatis/fgate/"
-lfnrelease="/grid/biomed/creatis/vip/data/groups/GateLab/releases/"
-lfnworkflow="${lfnbase}workflow/"
-lfngasw="${lfnbase}gasw/"
-lfnscript="${lfnbase}bin/"
-
-#list of SEs used for storage. Don't modify this list unless you know
-# what you're doing. Replicating the release in a bad place (e.g. on a
-# remote continent) can dramatically slow down the transfers
-SES="ccsrm02.in2p3.fr sbgse1.in2p3.fr marsedpm.in2p3.fr"
- 
-# define the prefix for uploaded file
-# default to local machine username
-prefix="${USER:?"USER must be set"}_"