Shell – Rename files in directory according to name of directory

In my experience fdupes can be inconsistent in the order that it outputs files (I have had my own problems using the --delete option). This should be fairly robust as it doesn't require the files to be in a specific order (as as long as there are always two dupes in different folders):

# note no trailing slash
source_dir=/home/articles
target_dir=/external/articles

fdupes "$target_dir" "$source_dir" |
  while IFS= read file; do
    case "$file" in
      "$source_dir/"*)
         source=${file##*/}
         ;;
      "$target_dir/"*)
         target=$file
         ;;
      '')
         if [ "$source" ] && [ "$target" ]; then
           echo mv -i "$target" "$target_dir/$source"
         fi
         unset source target
         ;;
    esac
  done

This will just print out the mv commands, remove the echo when you are sure you have what you want. Also the -i option for mv will prompt you if it is going to overwrite anything.

Here's the TLDR version of my solution: you can use the dirname and basename commands along with process substitution in order to construct the target path for your copy command.

A longer explanation follows.

Here is a (super verbose) script that does roughly what you want using a Bash loop:

#!/bin/bash

# copy_and_rename.bash
#
#   Copy multiple files 2 folders up and rename these files
#   to contain their parent directory as a prefix.
#

# Set internal field separator to handle spaces in file names
IFS=$'\n'

# Iterate over the list of file paths
for _file_path in $@; do

    # Get the file name
    _file_name="$(basename ${_file_path})"

    echo "${_file_name}"

    # Get the path to the target directory (two levels above the file)
    _target_directory_path=$(dirname $(dirname ${_file_path}))

    echo "${_target_directory_path}"

    # Get the parent directory of the target directory
    _parent_directory_path=$(dirname ${_target_directory_path})

    echo "${_parent_directory_path}"

    # Get the name of the parent directory
    _parent_directory_name=$(basename ${_parent_directory_path})

    echo "${_parent_directory_name}"

    # Construct the new file path
    _new_file_path="${_target_directory_path}/${_parent_directory_name}_${_file_name}"

    echo "${_new_file_path}"

    # Copy and rename the file
    echo "cp -i \"${_file_path}\" \"${_new_file_path}\""
    cp -i "${_file_path}" "${_new_file_path}"
    echo
done

You can obviously compress this a lot, but I kept it this way for explanatory value.

Here is what the preceding script looks like without any comments or superfluous variables or echo statements:

for _file_path in $@; do
    cp -i "${_file_path}" \
    "$(dirname $(dirname ${_file_path}))/$(basename $(dirname $(dirname $(dirname ${_file_path}))))_$(basename ${_file_path})"
done

It's very fragile and doesn't do much in the way of error-handling. I also left in some echo statements for debugging so you see what it's doing and can sanity-check it when you run it for the first time.

To test it I created your files by using the following script, which I include here in case you find it useful for further testing:

#!/bin/bash

# create_test_files.bash

# Set internal field separator to handle spaces in file names
IFS=$'\n'

# Choose an prefix for the file paths
_prefix="/tmp"

# Create array of sample files
_sample_files=(
    "/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam"
    "/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam"
    "/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam"
)

# Create directories and files
for _file in "${_sample_files[@]}"; do

    # Add the prefix to the path
    _path="${_prefix}${_file}"

    # Create parent directory
    mkdir -p "$(dirname ${_path})"

    # Create file
    touch "${_path}"
done

I check that the files were created properly by using the find command:

$ find /tmp/samples -type f

/tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam
/tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam
/tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam

Then I invoke the script like this:

bash copy_and_rename.bash \
/tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam \
/tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam \
/tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam

And then I check that the script worked by using find again:

$ find /tmp/samples -type f

/tmp/samples/mydata1/RUN1/ID_date/PCR2/ID_date_F3.bam
/tmp/samples/mydata1/RUN1/ID_date/PCR2/TIME1/F3.bam
/tmp/samples/mydata2/RUN1/ID2_date4/PCR2/ID2_date4_F3.bam
/tmp/samples/mydata2/RUN1/ID2_date4/PCR2/TIME7/F3.bam
/tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/IDxxx_datexxx_F3.bam
/tmp/samples/mydataxxx/RUN1/IDxxx_datexxx/PCR2/TIMExxx/F3.bam

Finally, I delete all of the test files, also using find:

find /tmp/samples -type f -exec rm {} \;