bash functions

bash_functions.sh

set -a

sjless() {
    squeue -o "%.18i %.9P %.150j %.8u %.2t %.10M %.6D %R %.20o %500Z" | awk 'NR==1 || $4 == ENVIRON["USER"]' | less -N -S
}

# tac() {
#     if [ "$#" -gt 1 ]; then
#         echo "Usage: $0 [file]" >&2
#         return 1
#     fi

#     if [ -n "$1" ]; then
#         cat "$1" | sed '1!G;h;$!d'
#     else
#         cat | sed '1!G;h;$!d'
#     fi
# }

files_only() {
    ls -p | grep -v /
}

timestamp_copy() {
    if [ $# -ne 1 ]; then
        echo "Usage: timestamp_copy <filename>" >&2
        return 1
    fi

    file="$1"

    if [ ! -f "$file" ]; then
        echo "Error: '$file' is not a file." >&2
        return 1
    fi

    # Get current timestamp
    timestamp=$(date '+___%Y-%m-%d-%H-%M-%S')

    # Extract base name and extension
    base=$(basename "$file")
    dir=$(dirname "$file")

    case "$base" in
        *.*)
            name=${base%.*}
            ext=.${base##*.}
            ;;
        *)
            name=$base
            ext=""
            ;;
    esac

    newname="${name}${timestamp}${ext}"

    cp "$file" "$dir/$newname"
	
	printf "$newname\n"
}

stavefile () {
	if [ $# -ne 1 ]; then
        echo "Usage: timestamp_copy <filename>" >&2
        return 1
    fi

    file="$1"

    if [ ! -f "$file" ]; then
        echo "Error: '$file' is not a file." >&2
        return 1
    fi

	stamped_file=$(timestamp_copy "${file}")
	
	ln -Tnfsr ./${stamped_file} $file

}

viewtable() {
	if [ $# -ne 1 ]; then
        echo "Usage: timestamp_copy <filename>" >&2
        return 1
    fi

    file="$1"
	delim=","

	if [ ! ${2+set} = "set" ]; then
		delim=${2}
	fi

    if [ ! -f "$file" ]; then
        echo "Error: '$file' is not a file." >&2
        return 1
    fi
	
	column -s${delim} -t < $file | less -#20 -N -S
}


path_append ()  { path_remove $1; export PATH="$PATH:$1"; }

path_prepend () { path_remove $1; export PATH="$1:$PATH"; }

path_remove ()  { export PATH=`echo -n $PATH | /usr/bin/awk -v RS=: -v ORS=: '$0 != "'$1'"' | /usr/bin/sed 's/:$//'`; }

cpaste () {
    cat ~/clipboard
}

clp () {
    cat ~/clipboard
}

getnextflowlog() {
	nextflow log | \
	awk -F'\t' '{print $3}' | \
	tail -n+2 | \
	xargs -I {} -P1 -L1 nextflow log {} -f container,hostname,module,time,queue,task_id,workdir,attempt,submit,start,complete,hash,name,native_id,status,process
}

gitprune () {
    git fetch -p && git branch -vv | awk "/: gone]/{print \$1}" | xargs -I {} git branch -D {}
}


gitremote() {
    git remote -v
}

gitseturl() {
    # git remote set-url $1 $2
    git remote set-url $@
}

gitsetremote() {
    local remote=$1
    if ! [ "$remote" = "origin" ]; then
	    local remote="origin"
    else
	    local remote=""
    fi
    set -x
    git remote set-url $remote $@
    set +x
}

gitsetupstream() {
    git push --set-upstream $@
}

gitgetbranches() {
    git branch -r | grep -v '\->' | while read remote; do git branch --track "${remote#origin/}" "$remote"; done
    git fetch --all
}


gitfastforward() {
    if [ $# -eq 0 ]; then
	BRANCH="master"
    else
	BRANCH="$1"
    fi
    git merge --ff-only origin/${BRANCH}
}

calculate () {
  echo "${1}" | bc -l
}

round () {
  local in=$1; if [ -z "$in" ]; then read in; fi
  # echo "${in}" | awk '{printf("%d\n",$1)}' `# Round`
  echo "$in" | xargs printf "%.*f\n" 0 `# Round`
}

appenddirs () {
    local dir_stack=$1  # Get the input argument

    if [[ -z "$dir_stack" ]]; then
        local dir_stack="~/.dir_stack"
        dir_stack="${dir_stack/#\~/$HOME}"
    fi

    tmp=$(mktemp)
    cat <(dirs -p) ${dir_stack} > ${tmp}
    mv ${tmp} > ${dir_stack}
}

savedirs () {
    local dir_stack=$1  # Get the input argument

    if [[ -z "$dir_stack" ]]; then
        local dir_stack="~/.dir_stack"
        dir_stack="${dir_stack/#\~/$HOME}"
    fi
    dirs -p > ${dir_stack}
}

adddirs () {
    local dir_stack=$1  # Get the input argument

    if [[ -z "$dir_stack" ]]; then
        local dir_stack="~/.dir_stack"
        dir_stack="${dir_stack/#\~/$HOME}"
    fi

    while read -r dir; do
        dir="${dir/#\~/$HOME}"
        pushd "${dir}" > /dev/null
    done < <(tac ${dir_stack})
}

recoverdirs () {

	is_dir_stack_present=$(test "${DIR_STACK+set}" = "set" && echo true || echo false)

	if ! $is_dir_stack_present; then
		printf "No DIR_STACK variable present\n"
		return
	fi

	cleardirs

    while read -r dir; do
        dir="${dir/#\~/$HOME}"
        pushd "${dir}" > /dev/null
    done < <(tac <(printf "$DIR_STACK\n"))
}

loaddirs() {
    local dir_stack=$1  # Get the input argument

    if [[ -z "$dir_stack" ]]; then
        local dir_stack="~/.dir_stack"
        dir_stack="${dir_stack/#\~/$HOME}"
    fi
    
    cleardirs && adddirs ${dir_stack}
}

cleardirs() {
    while [ "$(dirs -p | wc -l)" -gt 1 ]; do
        popd -n > /dev/null || break
    done
}

dirsf() {
    dirs -v
}

dirsr() {
    dirs -v | tac | awk '{print NR-1, $2}'
}

pulld(){
    local index=$1  # Get the input argument

    # Get the total number of directories in the stack
    local total_dirs
    total_dirs=$(dirs -p | wc -l)

    if [[ -z "$index" ]]; then
        # No argument: Move item 0 to the bottom, shift items 1 and below
        if (( total_dirs <= 1 )); then
            echo "Not enough directories in the stack to perform this operation."
            return 1
        fi

        pushd +1

    else
        if [[ -z "$index" || ! "$index" =~ ^[0-9]+$ ]]; then
            echo "Usage: pulld <index>"
            return 1
        fi

        # Get the total number of directories in the stack
        local total_dirs
        total_dirs=$(dirs -p | wc -l)

        if (( index >= total_dirs )); then
            echo "Index $index is out of range. Stack has $total_dirs directories."
            return 1
        fi

        # Extract the directory to move
        local dir_to_move
        dir_to_move=$(dirs -v | awk -v idx="$index" '$1 == idx {print $2}')
        dir_to_move="${dir_to_move/#\~/$HOME}"

        if [[ -z "$dir_to_move" ]]; then
            echo "Failed to locate directory at index $index."
            return 1
        fi

        # Push the directory to the top
        pushd "$dir_to_move" > /dev/null

        # Remove the original entry from the stack
        popd +"$((index + 1))" > /dev/null
    fi
}

# currentJobs () {
#     squeue --sort=+j -u $whoami --format="%.18i %.9P %.30j %.8u %.8T %.10M %.9l %.6D %R"
# }

# powerSlurm () {
#     srun --cpus-per-task=4 --mem=32GB --time=8:00:00 --pty /bin/bash -l
# }

# SCRATCH () {
#     cd /gpfs/scratch/$USER
# }

# sambamba () {
#     /gpfs/share/apps/sambamba/0.6.8/sambamba-0.6.8 $@
# }

# mkdir () {
#     /usr/bin/mkdir -m u=rwx,g=rxs,o=rx -p $@
# }

# IGV () {
#     sh ~/IGV
# }

set +a