========================
Bash and shell scripting
========================

Shellcheck
==========

This utility (shell linter) is installed on PMSN. **Use it without moderation**. You can also `use it online <https://www.shellcheck.net/>`_.

.. code-block:: bash

    shellcheck myscript.sh

* online version: https://www.shellcheck.net/ or https://explainshell.com/
* online explanation for error code ``SC2154`` (example): https://github.com/koalaman/shellcheck/wiki/SC2154

Debugging
=========

* Use "strict mode with pipefail" (exit without continuing at **first** error):

.. code-block:: bash

    set -euo pipefail

* Trace each command verbosely:

.. code-block:: bash

    set -x

String replace
==============

* replace ``home`` with ``scratch`` from ``$SGE_O_WORKDIR``, save into ``$SCRATCHDIR``:

.. code-block:: bash

    SCRATCHDIR=${SGE_O_WORKDIR/"home"/"scratch"}

* name ``$OUTFILE`` and ``$LOGFILE``, following ``$INFILE`` (change file extension):

.. code-block:: bash

    INFILE=$1
    TMPNAME=$(basename "${INFILE%.*}")
    OUTFILE="$TMPNAME"-done.hdf5
    LOGFILE="$TMPNAME".log

* Explicit error message in case of unset variable

.. code-block:: bash

    # ${TMPDIR:?"TMPDIR nonexistent"}

    result=$(ls "${TMPDIR:?"TMPDIR nonexistent"}")
    if [[ "$result" == "nonexistent" ]]
    then
        echo "TMPDIR do not exist!"
        exit 1
    fi


Pattern matching
================

.. code-block:: bash

    #!/bin/bash

    #shopt -s compat31

    VARIABLE="Let's test this string!"

    # This is for regular expressions:
    # See https://www.shellcheck.net/wiki/SC2076
    if [[ "$VARIABLE" =~ "Let's.*ring" ]]
    then
        echo "#1 matched"
    else
        echo "#1 nope"
    fi

    # without quotes
    if [[ "$VARIABLE" =~ Let\'s.*ring ]]
    then
        echo "#2 matched"
    else
        echo "#2 nope"
    fi

    # And here we have Bash Patterns:
    if [[ "$VARIABLE" == L*ing! ]]
    then
        echo "#3 matched"
    else
        echo "#3 nope"
    fi

Results:

.. code-block:: bash

    #1 nope
    #2 matched
    #3 matched

To get #1 matching, remove quotes around RegExpr, or set compat31 : ``shopt -s compat31``

.. code-block:: bash

    #!/bin/sh

    thisString="1 2 3 4 5"
    searchString="1 2"
    # if you single quote your input, you could do this
    # searchString=$1

    case $thisString in
        # match exact string
        "$searchString" ) echo yep, it matches exactly ;;

        # match start of string
        "$searchString"* ) echo yep, it matches at the start ;;

        # match end of string
        *"$searchString" ) echo yep, it matches at the end ;;

        # searchString can be anywhere in thisString
        *"$searchString"* ) echo yep, it matches in the middle somewhere ;;

        *) echo nope ;;
    esac

Results:

.. code-block:: bash

    yep, it matches at the start


Associatives arrays
===================

We can name array entries (aka named index).

* tips :

.. code-block:: bash

    tab[wwsi]="whatever/wwsi"
    tab[wwoz]="whatever/to/wwoz"
    tab[fip]="http://audio.scdn.arkena.com/11016/fip-midfi128.mp3"

* unroll an array:

    * brute force:

        .. code-block:: bash

            for i in "${tab[@]}"; do echo "${i}"; done


    * tip (induce loop):

        .. code-block:: bash

            printf "%s\n" "${tab[@]}"; done

Resulting in code simplification (and readability):

* Array traversal, knowing the index (here ``$value``):

    * before :

        .. code-block:: bash

            tindex=$(for i in "${tab[@]}"; do echo "${i}"; done | grep "${value}")
            for ((i=0; i<${#tab[@]}; i++))
            do
                if [[ "$tindex" == "{tab[$i]}" ]]
                then
                    data="${tab[$i]}"
                fi
            done


    * with induce loop:

        .. code-block:: bash

            tindex=$(printf "%s\n" "${tab[@]}" | grep "${value}")
            data="${tab[$tindex]}"


.. WARNING::

    Not all these examples have been tested against recent bash and/or shelcheck. **DO IT!!**