Merge pull request #3 from Laura190/replaceMv

Replace mv

.gitignore

@@ -1,5 +1,5 @@
 .pass.txt
-OldData.list
+*.list
 TestImport.sh
 subfunctiontest.sh
 tmp.cfg

Examples/MicroscopeImport.sh

@@ -1,24 +1,14 @@
 #!/bin/bash
 
-##Import for individual Windows computer
-# Parameters:
-# Name of microscope
-micro=laura
-# Location where data is stored
-path=/mnt/d/Data
-# Location of Imported folder
-imp_path=$path/Imported
-# Location where log files will be stored
-archive=$path/ImportLogs
-# Location of password file
-pass_file=/home/user/.pass.txt
-# Path to OMERO environment
-env=/home/user/omero-env
-# Path to configuration file
-conf_file=/home/user/import.cfg
-
-#Moves old data
-bash OMEROimport move_old --location="$path/"
+## Import for individua Windows computer
+#Read config file
+config=$( bash OMEROimport check_config )
+if [ "${config//ERROR/}" != "${config}" ]; then
+      echo "${config}"
+      exit 1
+else
+  source $config
+fi
 
 #Import data for each folder on path
 log_files=()
@@ -27,16 +17,18 @@ for folder in "$path"/*; do
   if [ $(basename "$folder") != "Imported" ] && [ $(basename "$folder") != "OldData" ] && [ $(basename "$folder") != "imported" ]; then
     user=$(bash OMEROimport read_file --file="$folder"/.username.txt)
     if [[ $user != ERROR* ]]; then
-      result=$(bash OMEROimport import_folder --password_file="$pass_file" \
-                 --environment="$env" --user="$user" --folder="$folder" \
-                 --config="$conf_file") 
+      # Move old data
+      bash OMEROimport move_old --location="$folder"
+      # Import data
+      result=$(bash OMEROimport import_folder --user="$user" --folder="$folder")
     else
       result=$user
     fi
     if [ "${result//=== No files/}" != "${result}" ] || \
        [ "${result//ERROR/}" != "${result}" ]; then
       echo "${result}"
     else
+      bash OMEROimport move_imports --logfile="${result}" --target="$imp_path"
       log_files[$i]="$result"
       i=$((i+1))
     fi
@@ -45,7 +37,6 @@ done
 
 # Move imported files to imp_path
 for log in ${log_files[@]}; do
-  bash OMEROimport move_imports --logfile="$log" --target="$imp_path"
   mv "$log" "$archive"/"$micro"_$(date +%Y%m%d)_"$log"
   rm "Before_$log"
 done

Examples/import.cfg

@@ -2,19 +2,19 @@
 # Name of microscope
 micro=microscope
 # Location where data is stored
-path=/home/laura/WMS_Files/CAMDU/SoftwareDevelopment/Autoimport/test/testDrive
+path=/home/data
 # Location of Imported folder
 imp_path=$path/Imported
 # Location where log files will be stored
 archive=$path/ImportLogs
 # Location of encrypted password file
-pass_file=/home/laura/WMS_Files/CAMDU/SoftwareDevelopment/OMEROimport/.pass.txt
+pass_file=/home/user/.pass.txt
 # Path to OMERO environment
 enviro=/home/user/omero-env
 
 ## Server
 # OMERO server details
-server=camdu.warwick.ac.uk
+server=my.omero.server
 port=4064
 # Imported user
-username=importer1
+importer=importer

commands/check_config

@@ -20,7 +20,6 @@ function check_config::run () {
  fi
 
  ## Define variables
-
  local file=$(get_file "$file_path")
  check_error $file
  declare -a list=("micro" "path" "imp_path" "archive" "pass_file" "enviro" "server" "port" "importer")
@@ -56,11 +55,11 @@ get_file() {
   fi
 }
 
-# Read password from password file
 source_file() {
   local configfile="${1}"
   local configfile_secured='tmp.cfg'
-  local micro path imp_path archive pass_file enviro server port importer
+  declare -a list=("micro" "path" "imp_path" "archive" "pass_file" "enviro" "server" "port" "importer")
+  for i in ${list[@]}; do local $i; done
 
   # check if the file contains something we don't want
   if egrep -q -v '^#|^[^ ]*=[^;]*' "$configfile"; then
@@ -69,7 +68,6 @@ source_file() {
     egrep '^#|^[^ ]*=[^;&]*'  "$configfile" > "$configfile_secured"
     configfile="$configfile_secured"
   fi
-
   # now source it, either the original or the filtered variant
   source "$configfile"
 

commands/import_folder

@@ -15,7 +15,7 @@ EOT
 
 function import_folder::usage() {
   cat <<EOT
-  -c --config          mandatory   config file containing server info and importer details
+  -c --config          optional   config file containing server info and importer details, if not given will look for import.cfg
   -f --folder          mandatory   Folder of data to be imported
   -u --user            mandatory   OMERO (LDAP) user ID, who data will be 
                                    imported for
@@ -32,8 +32,7 @@ function import_folder::run() {
  # Check if config file is given
  local conf=$(readopt -c --config)
  if [ -z "${conf}" ]; then
-   echo "ERROR: import_folder - no config file given with --config"
-   exit 1
+   conf="import.cfg"
  fi
 
  # Check if user is given
@@ -149,7 +148,6 @@ import() {
     done
     logname=$logname-$i
 fi
-touch -- "$logname".log
   #Increase Java Heap size for imports
   export JAVA_OPTS=-Xmx4G
   #Check if there are any files to import

commands/move_imports

@@ -47,6 +47,7 @@ function move_imports::run () {
 
  local summary=$(get_summary "$img_log")
  check_error $summary
+ echo "$summary"
 
  local images=$(get_imported_images "$img_log")
  check_error $images
@@ -57,10 +58,6 @@ function move_imports::run () {
  local result=$(move_imports "$target")
  check_error $result
 
- #Print warnings
- local errors=$(check_omero_errors "$summary" "$user")
- echo $errors
-
  # Print message if successful
  echo "=== Successfully moved imported files"
 }
@@ -118,28 +115,28 @@ get_summary() {
 get_imported_images() {
   local log_file=${1}
   # List of imported image files
-  images=$(grep -o 'IMPORT_DONE Imported file:.*' $log_file | cut -f 4- -d ' ')
-  echo $images
+  grep -o 'IMPORT_DONE Imported file:.*' $log_file | cut -f 4- -d ' ' > importedImages.list
+  echo importedImages.list
 }
 
 # Get files associated to imported image files and save to temp file
 get_imported_files(){
   local grp_file=${1}
-  local images=${3}
   # If it exists remove importsFiles so do not append to already existing file
   rm -f importedFiles.list 2> /tmp/om_imp
   rm -f allImportedFiles.list 2> /tmp/om_imp
   # Parse group log file to get all associated/additional files
   local end=$(grep "#===" $grp_file | head -1)
   local start
   local escaped_start
-  for img in $images; do
+  cat ${3} | while read img; do
     start=$(grep "# Group: $img" $grp_file | head -1)
     escaped_start=$(printf '%s\n' "$start" | sed -e 's/[\/&]/\\&/g')
 	#Read all the lines between, and including, escaped_start and end; then delete first and last lines
     sed -n "/${escaped_start}/,/${end}/ p" $grp_file | sed '1d' | sed '$d' >> allImportedFiles.list
   done
   sort allImportedFiles.list | uniq > importedFiles.list
+  cat importedFiles.list
 }
 
 # Move imports data to imported folder
@@ -155,7 +152,7 @@ move_imports() {
     if [ $? -ne 0 ]; then
       echo "ERROR: unable to create folder for $newFilename"
     fi
-    mv "$filename" "$newFilename"
+    rsync -a --remove-source-files "$filename" "$newFilename"
     ec=$?
     if [ $ec -ne 0 ]; then
       echo "ERROR: errorcode: $ec, unable to move $filename"
@@ -187,12 +184,6 @@ check_file() {
   fi
 }
 
-check_omero_errors() {
-  local errors=$(echo "${1}" | cut -d ' ' -f 10)
-  local user=${2}
-  echo "Warning: OMERO reported $errors errors occured when importing files for $user"
-}
-
 # Check for errors - all error messages start with ERROR:
 # If doing multiple levels of functions, send to error file and then parse file at end
 check_error() {

commands/move_old

@@ -86,7 +86,7 @@ move_old_data() {
         echo "ERROR: unable to create OldData folder"
         exit 1
       fi
-      mv "$filename" "$newFilename"
+      rsync -a --remove-source-files "$filename" "$newFilename"
       if [ $? -ne 0 ]; then
         echo "ERROR: unable to move $filename to $newFilename"
         exit 1
@@ -116,7 +116,7 @@ move_DV_olddata() {
     # Send command to remote microscope computer to move files
     # Need to point to specific ssh key to prevent request for password
     printf -v makeStr 'mkdir --parents %q' "$(dirname "$newFilename")"
-    printf -v moveStr1 'mv %q %q/' "$oldFilename" "$(dirname "$newFilename")"
+    printf -v moveStr1 'rsync -a --remove-source-files %q %q/' "$oldFilename" "$(dirname "$newFilename")"
     # -n needed to prevent ssh breaking while loop
     ssh -n camdu@$IP -i $ssh_key $makeStr
     if [ $? -ne 0 ]; then