andreatsh
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openlab


			
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<div id="content">
<h1 class="title">OpenLab: open tools for physicists</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">1. Introduction</a>
<ul>
<li><a href="#sec-1-1">1.1. Presentation of me:</a></li>
<li><a href="#sec-1-2">1.2. Goals of this conference:</a></li>
<li><a href="#sec-1-3">1.3. Quick review of things I'd like to assume you know:</a>
<ul>
<li><a href="#sec-1-3-1">1.3.1. Open a terminal</a></li>
<li><a href="#sec-1-3-2">1.3.2. Open a file with an editor of your choice</a></li>
<li><a href="#sec-1-3-3">1.3.3. Elementary commands:</a></li>
<li><a href="#sec-1-3-4">1.3.4. Standard input, output and error</a></li>
<li><a href="#sec-1-3-5">1.3.5. Difference between absolute and relative path</a></li>
<li><a href="#sec-1-3-6">1.3.6. How to get help?</a></li>
</ul>
</li>
<li><a href="#sec-1-4">1.4. How can I improve my skills?</a></li>
</ul>
</li>
<li><a href="#sec-2">2. Start learning Bash</a>
<ul>
<li><a href="#sec-2-1">2.1. What is Bash?</a></li>
<li><a href="#sec-2-2">2.2. Why using Bash?</a>
<ul>
<li><a href="#sec-2-2-1">2.2.1. How to verify which shell you are using?</a></li>
</ul>
</li>
<li><a href="#sec-2-3">2.3. Bash scripting</a>
<ul>
<li><a href="#sec-2-3-1">2.3.1. What is a script?</a></li>
<li><a href="#sec-2-3-2">2.3.2. How can I run my script?</a></li>
<li><a href="#sec-2-3-3">2.3.3. First step: Hello World!</a></li>
<li><a href="#sec-2-3-4">2.3.4. Why is important quoting variables?</a></li>
<li><a href="#sec-2-3-5">2.3.5. Command substitutuion: backticks vs $()</a></li>
<li><a href="#sec-2-3-6">2.3.6. Why is dangerous shell scripting?</a></li>
<li><a href="#sec-2-3-7">2.3.7. Use bashisms: use Bash, don't half-use it.</a></li>
<li><a href="#sec-2-3-8">2.3.8. How to debug a script:</a></li>
</ul>
</li>
<li><a href="#sec-2-4">2.4. 7 personal advice to write a good script:</a></li>
</ul>
</li>
<li><a href="#sec-3">3. One step further: how to schedule our operations</a>
<ul>
<li><a href="#sec-3-1">3.1. Cron:</a>
<ul>
<li><a href="#sec-3-1-1">3.1.1. What is cron?</a></li>
<li><a href="#sec-3-1-2">3.1.2. How can I schedule use cron?</a></li>
</ul>
</li>
<li><a href="#sec-3-2">3.2. Systemd timers:</a>
<ul>
<li><a href="#sec-3-2-1">3.2.1. What is a systemd timer?</a></li>
<li><a href="#sec-3-2-2">3.2.2. How can I create a timer?</a></li>
</ul>
</li>
<li><a href="#sec-3-3">3.3. Exercises:</a></li>
</ul>
</li>
<li><a href="#sec-4">4. How to 'rename' large number of files?</a></li>
<li><a href="#sec-5">5. How to 'find' and do operations over multiple files?</a></li>
<li><a href="#sec-6">6. Text processing by examples: awk</a>
<ul>
<li>
<ul>
<li><a href="#sec-6-0-1">6.0.1. The worst thing you can do with Awk! (imho)</a></li>
<li><a href="#sec-6-0-2">6.0.2. Print lines based on pattern</a></li>
<li><a href="#sec-6-0-3">6.0.3. Print lines in range</a></li>
<li><a href="#sec-6-0-4">6.0.4. Remove (non consecutive) duplicated lines</a></li>
<li><a href="#sec-6-0-5">6.0.5. Find and replace</a></li>
<li><a href="#sec-6-0-6">6.0.6. Print intersection of two files</a></li>
<li><a href="#sec-6-0-7">6.0.7. Parse a CSV file</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#sec-7">7. Project example: dice rolling simulations</a></li>
<li><a href="#sec-8">8. Not covered by this talk but truly useful and important:</a>
<ul>
<li><a href="#sec-8-1">8.1. ssh</a>
<ul>
<li><a href="#sec-8-1-1">8.1.1. Generate public/private key pair for authentication</a></li>
<li><a href="#sec-8-1-2">8.1.2. Basic configuration example</a></li>
</ul>
</li>
<li><a href="#sec-8-2">8.2. git</a></li>
<li><a href="#sec-8-3">8.3. tmux</a></li>
</ul>
</li>
</ul>
</div>
</div>

<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1"><span class="section-number-2">1</span> Introduction</h2>
<div class="outline-text-2" id="text-1">
</div><div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1"><span class="section-number-3">1.1</span> Presentation of me:</h3>
<div class="outline-text-3" id="text-1-1">
<ul class="org-ul">
<li>Who I am?
</li>
<li>My contacts:
<ol class="org-ol">
<li>andrea.miglietta92@gmail.com
</li>
<li>andreatsh@lcm.mi.infn.it
</li>
</ol>
</li>
<li>GitHub: <a href="https://github.com/andreatsh/openlab">https://github.com/andreatsh/openlab</a>
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2"><span class="section-number-3">1.2</span> Goals of this conference:</h3>
<div class="outline-text-3" id="text-1-2">
<p>
Why using command line?
Why bother?
Why do I have to waste my time to learn command line?
</p>

<p>
When you realize that you spend most of your time doing repetitive tasks, you
could suspect you are not doing things quite well. What you want is a way to
perform repetitive tasks with less typing and actions as possible.
Stop waste your time with boring routine stuff!
</p>

<p>
Moreover, you can have a good comprehension and a fine control of what you
are actually doing. There are lots of tasks you can perfom easily with
command line that in other way are particular complicated.
If you do not believe it, try to implement a program (for example in C++)
that:
</p>
<ul class="org-ul">
<li>search all your files into a directory
</li>
<li>evaluate the disk space occupied by each file
</li>
<li>order by size the results
</li>
<li>print them on a file
</li>
</ul>

<p>
Once you have done, compare the time spent and the length of your code with
this simple line:
</p>
<div class="org-src-container">

<pre class="src src-bash">du -sh * | sort -nr &gt; file.results
</pre>
</div>
<p>
If you are not convinced yet, please teach me your way to code in C++!
Seriously!
</p>
</div>
</div>
<div id="outline-container-sec-1-3" class="outline-3">
<h3 id="sec-1-3"><span class="section-number-3">1.3</span> Quick review of things I'd like to assume you know:</h3>
<div class="outline-text-3" id="text-1-3">
</div><div id="outline-container-sec-1-3-1" class="outline-4">
<h4 id="sec-1-3-1"><span class="section-number-4">1.3.1</span> Open a terminal</h4>
</div>
<div id="outline-container-sec-1-3-2" class="outline-4">
<h4 id="sec-1-3-2"><span class="section-number-4">1.3.2</span> Open a file with an editor of your choice</h4>
<div class="outline-text-4" id="text-1-3-2">
<p>
Choose your tools wisely and spend time to customize them.
There are many text editor, some example:
</p>
</div>
<ol class="org-ol"><li><a id="sec-1-3-2-1" name="sec-1-3-2-1"></a>Emacs, Vim<br  /><div class="outline-text-5" id="text-1-3-2-1">
<p>
Advanced and powerful editors. (Recommended)
</p>
</div>
</li>
<li><a id="sec-1-3-2-2" name="sec-1-3-2-2"></a>Nano<br  /></li>
<li><a id="sec-1-3-2-3" name="sec-1-3-2-3"></a>Gedit<br  /></li></ol>
</div>
<div id="outline-container-sec-1-3-3" class="outline-4">
<h4 id="sec-1-3-3"><span class="section-number-4">1.3.3</span> Elementary commands:</h4>
<div class="outline-text-4" id="text-1-3-3">
<ul class="org-ul">
<li>cd
</li>
<li>ls
</li>
<li>cp
</li>
<li>mv
</li>
<li>rm
</li>
<li>mkdir
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-3-4" class="outline-4">
<h4 id="sec-1-3-4"><span class="section-number-4">1.3.4</span> Standard input, output and error</h4>
<div class="outline-text-4" id="text-1-3-4">
</div><ol class="org-ol"><li><a id="sec-1-3-4-1" name="sec-1-3-4-1"></a>&gt;<br  /><div class="outline-text-5" id="text-1-3-4-1">
<p>
Redirect stdout to a file.
Creates the file if not present, otherwise overwrites it.
</p>
</div>
</li>
<li><a id="sec-1-3-4-2" name="sec-1-3-4-2"></a>&gt;&gt;<br  /><div class="outline-text-5" id="text-1-3-4-2">
<p>
Redirect stdout to a file.
Creates the file if not present, otherwise appends to it.
</p>
</div>
</li>
<li><a id="sec-1-3-4-3" name="sec-1-3-4-3"></a>1&gt;<br  /><div class="outline-text-5" id="text-1-3-4-3">
<p>
Redirect stdout
</p>
</div>
</li>
<li><a id="sec-1-3-4-4" name="sec-1-3-4-4"></a>1&gt;&gt;<br  /><div class="outline-text-5" id="text-1-3-4-4">
<p>
Redirect and append stdout
</p>
</div>
</li>
<li><a id="sec-1-3-4-5" name="sec-1-3-4-5"></a>2&gt;<br  /><div class="outline-text-5" id="text-1-3-4-5">
<p>
Redirect stderr
</p>
</div>
</li>
<li><a id="sec-1-3-4-6" name="sec-1-3-4-6"></a>2&gt;&gt;<br  /><div class="outline-text-5" id="text-1-3-4-6">
<p>
Redirect and append stderr
</p>
</div>
</li>
<li><a id="sec-1-3-4-7" name="sec-1-3-4-7"></a>&amp;&gt;<br  /><div class="outline-text-5" id="text-1-3-4-7">
<p>
Redirect both stdout and stderr
</p>
</div>
</li>
<li><a id="sec-1-3-4-8" name="sec-1-3-4-8"></a>2&gt;&amp;1<br  /><div class="outline-text-5" id="text-1-3-4-8">
<p>
Redirect both stdout and stderr
</p>
</div>
</li>
<li><a id="sec-1-3-4-9" name="sec-1-3-4-9"></a>What is /dev/null?<br  /></li></ol>
</div>
<div id="outline-container-sec-1-3-5" class="outline-4">
<h4 id="sec-1-3-5"><span class="section-number-4">1.3.5</span> Difference between absolute and relative path</h4>
</div>
<div id="outline-container-sec-1-3-6" class="outline-4">
<h4 id="sec-1-3-6"><span class="section-number-4">1.3.6</span> How to get help?</h4>
<div class="outline-text-4" id="text-1-3-6">
</div><ol class="org-ol"><li><a id="sec-1-3-6-1" name="sec-1-3-6-1"></a>man [command]<br  /><div class="outline-text-5" id="text-1-3-6-1">
<p>
Show the complete manual page of the command
</p>
</div>
</li>
<li><a id="sec-1-3-6-2" name="sec-1-3-6-2"></a>&#x2013;help, -h<br  /><div class="outline-text-5" id="text-1-3-6-2">
<p>
These flags are provided by almost every commands and show the basic usage
</p>
</div>
</li>
<li><a id="sec-1-3-6-3" name="sec-1-3-6-3"></a>GIYF<br  /><div class="outline-text-5" id="text-1-3-6-3">
<p>
Google Is Your Friend
</p>
</div>
</li></ol>
</div>
</div>
<div id="outline-container-sec-1-4" class="outline-3">
<h3 id="sec-1-4"><span class="section-number-3">1.4</span> How can I improve my skills?</h3>
<div class="outline-text-3" id="text-1-4">
<p>
A lot of study and practice, practice and practice again!
There are no other ways to gain confidence with command line.
More confidence you have, less time you spend on silly routine tasks!
</p>
</div>
</div>
</div>
<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2"><span class="section-number-2">2</span> Start learning Bash</h2>
<div class="outline-text-2" id="text-2">
</div><div id="outline-container-sec-2-1" class="outline-3">
<h3 id="sec-2-1"><span class="section-number-3">2.1</span> What is Bash?</h3>
<div class="outline-text-3" id="text-2-1">
<p>
Bash is a Unix shell and command language.
</p>
</div>
</div>
<div id="outline-container-sec-2-2" class="outline-3">
<h3 id="sec-2-2"><span class="section-number-3">2.2</span> Why using Bash?</h3>
<div class="outline-text-3" id="text-2-2">
<p>
Bash is the standard GNU shell. It's the default shell on most Linux
distributions, so your script will virtually works everywhere.
Bash is intuitive for beginner users and at the same time is a powerful tool
for advavenced and professional users.
</p>
</div>
<div id="outline-container-sec-2-2-1" class="outline-4">
<h4 id="sec-2-2-1"><span class="section-number-4">2.2.1</span> How to verify which shell you are using?</h4>
<div class="outline-text-4" id="text-2-2-1">
<p>
There are many shells available (bash, sh, zsh, ksh, fish, etc..).
Typing commands for a shell when you are running another one can cause
confusion, errors or unwanted behaviors.
To identify your default shell open a terminal and type:
</p>
<div class="org-src-container">

<pre class="src src-bash">echo "$SHELL"
</pre>
</div>
<p>
/bin/bash
</p>
</div>
</div>
</div>
<div id="outline-container-sec-2-3" class="outline-3">
<h3 id="sec-2-3"><span class="section-number-3">2.3</span> Bash scripting</h3>
<div class="outline-text-3" id="text-2-3">
</div><div id="outline-container-sec-2-3-1" class="outline-4">
<h4 id="sec-2-3-1"><span class="section-number-4">2.3.1</span> What is a script?</h4>
<div class="outline-text-4" id="text-2-3-1">
<p>
Shell scripts are interpreted, not compiled. So in few words, a shell script
is just a sequence of instructions that the shell reads from the script line
by line and executes them.
</p>
</div>
<ol class="org-ol"><li><a id="sec-2-3-1-1" name="sec-2-3-1-1"></a>Shebang: #!<br  /></li></ol>
</div>
<div id="outline-container-sec-2-3-2" class="outline-4">
<h4 id="sec-2-3-2"><span class="section-number-4">2.3.2</span> How can I run my script?</h4>
<div class="outline-text-4" id="text-2-3-2">
</div><ol class="org-ol"><li><a id="sec-2-3-2-1" name="sec-2-3-2-1"></a>Make a file executable<br  /><div class="outline-text-5" id="text-2-3-2-1">
<p>
The permissions of a file granted to a user are:
</p>
<ul class="org-ul">
<li>read (<b>r</b>)
</li>
<li>write (<b>w</b>)
</li>
<li>execute (<b>x</b>)
</li>
</ul>
<p>
You have to assign the execute attribute to your script:
</p>
<div class="org-src-container">

<pre class="src src-bash">chmod +x script.sh
</pre>
</div>
</div>
</li></ol>
</div>
<div id="outline-container-sec-2-3-3" class="outline-4">
<h4 id="sec-2-3-3"><span class="section-number-4">2.3.3</span> First step: Hello World!</h4>
<div class="outline-text-4" id="text-2-3-3">
</div><ol class="org-ol"><li><a id="sec-2-3-3-1" name="sec-2-3-3-1"></a>A simple "Hello World!"<br  /><div class="outline-text-5" id="text-2-3-3-1">
<div class="org-src-container">

<pre class="src src-bash">#!/bin/bash
echo "Hello World!"
</pre>
</div>
</div>
</li>
<li><a id="sec-2-3-3-2" name="sec-2-3-3-2"></a>Another simple "Hello World!"<br  /><div class="outline-text-5" id="text-2-3-3-2">
<div class="org-src-container">

<pre class="src src-bash">#!/bin/bash
# This is a variable
HELLO="Hello World!"
echo "$HELLO"
</pre>
</div>
</div>
</li></ol>
</div>
<div id="outline-container-sec-2-3-4" class="outline-4">
<h4 id="sec-2-3-4"><span class="section-number-4">2.3.4</span> Why is important quoting variables?</h4>
<div class="outline-text-4" id="text-2-3-4">
<p>
It's a good practice to quote your variables.
</p>
</div>
<ol class="org-ol"><li><a id="sec-2-3-4-1" name="sec-2-3-4-1"></a>Differences between using single quotes or double quotes<br  /><ol class="org-ol"><li><a id="sec-2-3-4-1-1" name="sec-2-3-4-1-1"></a>Example 1<br  /><div class="outline-text-6" id="text-2-3-4-1-1">
<ul class="org-ul">
<li>Single quotes example:
<div class="org-src-container">

<pre class="src src-sh">echo 'This is my $HOME'
</pre>
</div>
<p>
This is my $HOME
</p>
</li>
<li>Double quotes example:
<div class="org-src-container">

<pre class="src src-sh">echo "This is my $HOME"
</pre>
</div>
<p>
This is my /home/andreatsh
</p>
</li>
</ul>
</div>
</li>
<li><a id="sec-2-3-4-1-2" name="sec-2-3-4-1-2"></a>Example 2<br  /><div class="outline-text-6" id="text-2-3-4-1-2">
<ul class="org-ul">
<li>Single quotes:
<div class="org-src-container">

<pre class="src src-sh">[ '$HOME' =='/home/andreatsh' ] &amp;&amp; echo "Yuppi" || echo "Error"
</pre>
</div>
<p>
Error
</p>
</li>
<li>Example with double quotes:
<div class="org-src-container">

<pre class="src src-sh">[ "$HOME" == "/home/andreatsh" ] &amp;&amp; echo "Yuppi" || echo "Error`"
</pre>
</div>
<p>
Yuppi
</p>
</li>
</ul>
</div>
</li></ol>
</li>
<li><a id="sec-2-3-4-2" name="sec-2-3-4-2"></a>A bit more advanced example:<br  /><div class="outline-text-5" id="text-2-3-4-2">
<div class="org-src-container">

<pre class="src src-bash">#!/bin/bash

# Personal example of why quoting is important.
# What output do you expect? You might be surprised.
HELLO=Hello!; ls -l
echo "$HELLO"

# This is a script designed to learn, you can run it and nothing bad will
# happen. But if you do not write your script with care and good practices
# (even on-the-fly scripts) can do real damages!
</pre>
</div>
</div>
</li></ol>
</div>
<div id="outline-container-sec-2-3-5" class="outline-4">
<h4 id="sec-2-3-5"><span class="section-number-4">2.3.5</span> Command substitutuion: backticks vs $()</h4>
<div class="outline-text-4" id="text-2-3-5">
</div><ol class="org-ol"><li><a id="sec-2-3-5-1" name="sec-2-3-5-1"></a>From Bash manual page:<br  /><div class="outline-text-5" id="text-2-3-5-1">
<blockquote>
<p>
Command substitution allows the output of a command to replace the command
name. There are two forms:
</p>
</blockquote>
<p class="verse">
&#xa0;&#xa0;&#xa0;&#xa0;$(command)<br  />
or<br  />
&#xa0;&#xa0;&#xa0;&#xa0;`command`<br  />
</p>
<blockquote>
<p>
Bash performs the expansion by executing command in a subshell environment
and replacing the command substitution with the standard output of the
command, with any trailing newlines deleted. Embedded newlines are not
deleted, but they may be removed during word splitting.
The command substitution $(cat file) can be  replaced by the equivalent but
faster $(&lt; file). <br  />
</p>

<p>
When the old-style backquote form of substitution is used, backslash retains
its literal meaning except when followed by $, `, or \. The first backquote
not preceded by a backslash terminates the command substitution. When using
the $(command) form, all  characters between the parentheses make up the
command; none are treated specially. <br  />
</p>

<p>
Command substitutions may be nested. To nest when using the backquoted form,
escape the inner backquotes with backslashes. <br  />
</p>

<p>
If the substitution appears within double quotes, word splitting and
pathname expansion are not performed on the results.
</p>
</blockquote>
</div>
</li>
<li><a id="sec-2-3-5-2" name="sec-2-3-5-2"></a>Examples:<br  /><div class="outline-text-5" id="text-2-3-5-2">
<ol class="org-ol">
<li>Simple use of command substitutuions:
<div class="org-src-container">

<pre class="src src-sh">ex1=`echo ciao`;  echo "$ex1"
ex1=$(echo ciao); echo "$ex1"
</pre>
</div>
</li>
<li>Nested command substitutions:
<div class="org-src-container">

<pre class="src src-sh">ex2=`echo `ls``; echo "$ex2"    # WRONG!
ex2=`echo \`ls\``; echo "$ex2"  # RIGHT
ex2=$(echo $(ls)); echo "$ex2"  # RIGHT
</pre>
</div>
</li>
</ol>
</div>
</li></ol>
</div>
<div id="outline-container-sec-2-3-6" class="outline-4">
<h4 id="sec-2-3-6"><span class="section-number-4">2.3.6</span> Why is dangerous shell scripting?</h4>
<div class="outline-text-4" id="text-2-3-6">
<p>
Many reasons. An example is worth a thousand words:
Example:
</p>
<div class="org-src-container">

<pre class="src src-bash"># This is an example of really bad code!
MYDIR=
rm -rf "$MYDIR/"*
# MYDIR variable may not be defined or be an empty string for many reasons!
# You just ran "rm -rf /*", maybe even as superuser!
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-2-3-7" class="outline-4">
<h4 id="sec-2-3-7"><span class="section-number-4">2.3.7</span> Use bashisms: use Bash, don't half-use it.</h4>
<div class="outline-text-4" id="text-2-3-7">
<ul class="org-ul">
<li>parameters expansions
</li>
<li>local and readonly variables
</li>
<li>improved conditional expressions
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-2-3-8" class="outline-4">
<h4 id="sec-2-3-8"><span class="section-number-4">2.3.8</span> How to debug a script:</h4>
<div class="outline-text-4" id="text-2-3-8">
<p>
I'm used to write very carefully my script, even on-the-fly or one-time
scripts. However, there is always something that could be have undesired
behaviors. To debug my Bash script I find useful this way to proceed:
</p>
<div class="org-src-container">

<pre class="src src-bash"># Debug mode: ON
set -x
# ...
# Your script goes here!
# ...
# Debug mode: OFF
set +x
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-2-4" class="outline-3">
<h3 id="sec-2-4"><span class="section-number-3">2.4</span> 7 personal advice to write a good script:</h3>
<div class="outline-text-3" id="text-2-4">
<p>
I summarize here the main recommendations that will be used in this
document. I think it's a good habit to use them all the time, even just
for single time scripts. A well documented, structered and organized,
versioned collection of scripts will bring you many benefits over time.
</p>

<ol class="org-ol">
<li>Comment your code!
Use comments to explain why are you doing something more than what
you are doing, and write them in english! Do not underestimate the
importance of english in writing code! You don't write production
scripts for yourself! The whole team need to understand what you have
done and why.
</li>

<li>Choose descriptive names for variables and functions!
</li>

<li>Try to write reliable and reusable code.
In this way is easier to make changes and updates without break the
application, and you can rearrange in a jiffy functions to fit your
temporary needs instead of rewrite code from scratch.
</li>

<li>Don't use a complex construct where a simpler one will do.
Complex construct are difficult to understand and decrease readability.
</li>

<li>Break complex scripts into simpler modules. Use functions where appropriate.
</li>

<li>Log what your script is doing!
Make sure to always known what your scripts are doing.
In my experience the correct way is to use standard error for logging,
so you can redirect your simulation's output (i.e. your data) into a file
without mix them with useful (and hopefully verbose) log messages.
</li>

<li>Last but not least: Keep your code under versioning!
This is really important to me! Personally I keep under versioning even
my filesystem configurations directories, like those in /etc.
Making mistakes or having unwanted behavior is easy with shell scripts,
as we will see soon in this document. A repository is really usefull to
review your code and have structured logs of what you have done and
bugs fixed.
</li>
</ol>
</div>
</div>
</div>
<div id="outline-container-sec-3" class="outline-2">
<h2 id="sec-3"><span class="section-number-2">3</span> One step further: how to schedule our operations</h2>
<div class="outline-text-2" id="text-3">
<p>
It's often useful run a script periodically, to do some cleanup, monitor a
simulation, or backup your files. To take efficiency one step further, it
would be nice if we could not sit in front of our computers and run these
scritps manually. You can get this job done by using cron or systemd-timers.
Here is a brief introduction to these topics.
</p>
</div>
<div id="outline-container-sec-3-1" class="outline-3">
<h3 id="sec-3-1"><span class="section-number-3">3.1</span> Cron:</h3>
<div class="outline-text-3" id="text-3-1">
</div><div id="outline-container-sec-3-1-1" class="outline-4">
<h4 id="sec-3-1-1"><span class="section-number-4">3.1.1</span> What is cron?</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
<i>cron</i> is a daemon to execute scheduled commands.
</p>
</div>
</div>
<div id="outline-container-sec-3-1-2" class="outline-4">
<h4 id="sec-3-1-2"><span class="section-number-4">3.1.2</span> How can I schedule use cron?</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
Each user can have his own crontab file in <i>var/spool/cron/crontabs</i>,
which can be created/modified/removed by <i>crontab</i> command.
The crontab file should not be accessed directly, the <i>crontab</i> command
should be used to access and update it.
To edit (or create) your crontab:
</p>
<div class="org-src-container">

<pre class="src src-bash">crontab -e
</pre>
</div>
<p>
To list your current crontab:
</p>
<div class="org-src-container">

<pre class="src src-bash">crontab -l
</pre>
</div>
<p>
Use 'man cron' and 'man crontab' to find all the documentation you need.
</p>
</div>
</div>
</div>
<div id="outline-container-sec-3-2" class="outline-3">
<h3 id="sec-3-2"><span class="section-number-3">3.2</span> Systemd timers:</h3>
<div class="outline-text-3" id="text-3-2">
<p>
This is an advanced topic for this conference. If you don't know what SystemD is, don't worry,
you can skip this part without losing anything.
</p>
</div>
<div id="outline-container-sec-3-2-1" class="outline-4">
<h4 id="sec-3-2-1"><span class="section-number-4">3.2.1</span> What is a systemd timer?</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
Timers are systemd unit files with a suffix of <i>.timer</i>.
</p>
</div>
</div>
<div id="outline-container-sec-3-2-2" class="outline-4">
<h4 id="sec-3-2-2"><span class="section-number-4">3.2.2</span> How can I create a timer?</h4>
<div class="outline-text-4" id="text-3-2-2">
<p>
Let's say you have a script you want to run every hour.
In <i>$HOME/</i>.config/systemd/user/ you have to create two files: one is the
the service file, the other is the timer file.
</p>
</div>
<ol class="org-ol"><li><a id="sec-3-2-2-1" name="sec-3-2-2-1"></a>Create a service file<br  /><div class="outline-text-5" id="text-3-2-2-1">
<p>
We start creating a test.service file like this:
</p>
<pre class="example">
[Unit]
Description=Simple test script

[Service]
Type=simple
ExecStart=/home/andreatsh/bin/test.sh
</pre>
</div>
</li>
<li><a id="sec-3-2-2-2" name="sec-3-2-2-2"></a>Create a timer file<br  /><div class="outline-text-5" id="text-3-2-2-2">
<p>
Now we create test.timer file:
</p>
<pre class="example">
[Unit]
Description=Runs every minute
RefuseManualStart=no
RefuseManualStop=no

[Timer]
OnCalendar=*:0/1
Unit=test.service

[Install]
WantedBy=timers.target
</pre>
</div>
</li>
<li><a id="sec-3-2-2-3" name="sec-3-2-2-3"></a>Enable/Start service and timer<br  /><div class="outline-text-5" id="text-3-2-2-3">
<div class="org-src-container">

<pre class="src src-bash">systemctl --user enable testscript.timer
systemctl --user start testscript.timer
</pre>
</div>
</div>
</li></ol>
</div>
</div>
<div id="outline-container-sec-3-3" class="outline-3">
<h3 id="sec-3-3"><span class="section-number-3">3.3</span> Exercises:</h3>
<div class="outline-text-3" id="text-3-3">
<ol class="org-ol">
<li>Find a way to check periodically (for example every hour) your available
disk space and send the result via email. For example, if your simulation
do an heavy i/o on disk and you have a limited disk quota it's a good
habit monitor it.
Difficulty: Basic
Estimated time to complete task: ~ 1 minute
</li>
</ol>
</div>
</div>
</div>
<div id="outline-container-sec-4" class="outline-2">
<h2 id="sec-4"><span class="section-number-2">4</span> How to 'rename' large number of files?</h2>
<div class="outline-text-2" id="text-4">
<p>
I have a large number of file I want to rename them,
I can do that in a easy and fast way?
</p>
<div class="org-src-container">

<pre class="src src-bash">#!/bin/bash
# Debian/Ubuntu version
rename 's/pattern/replacement/' files
# Fedora/CentOS version
rename pattern replacement files
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-5" class="outline-2">
<h2 id="sec-5"><span class="section-number-2">5</span> How to 'find' and do operations over multiple files?</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">

<pre class="src src-bash">for i in $(ls);
do
  # Do something ..
done
</pre>
</div>
<p>
You don't have control on the output, ls does not distinguish between regular
file or directory, or files with different permission.
Sure, you can use a more complex command like
</p>
<div class="org-src-container">

<pre class="src src-bash">for i in $(ls -l | awk '/^-rwx-rw--x/{print $9}');
do
  # Do something ..
done
</pre>
</div>
<p>
but is it worth? This is not an efficient way to do loop over file.
It's always better use appropriate tools: for example I prefer a syntax like:
</p>
<div class="org-src-container">

<pre class="src src-bash">find /path/to/dir -type f -exec touch {} \;
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-6" class="outline-2">
<h2 id="sec-6"><span class="section-number-2">6</span> Text processing by examples: awk</h2>
<div class="outline-text-2" id="text-6">
<p>
Awk is a really useful tool for text processing. If you have to easily
manipulate data organized in columns, strange format, or rearrange data
based on pattern this is for you.
Here you can find some basic examples that in my opinion show how much
intuitive and powerful Awk is.
These examples are deliberately more idiomatic than those that often you can
learn from standard manuals, they want to be hints on how to write shorter
and sometimes more efficient Awk programs.
</p>
</div>
<div id="outline-container-sec-6-0-1" class="outline-4">
<h4 id="sec-6-0-1"><span class="section-number-4">6.0.1</span> The worst thing you can do with Awk! (imho)</h4>
<div class="outline-text-4" id="text-6-0-1">
<p>
Suppose we want to read a file line-by-line, and we want to print the
second column. You might be tempted to do something like:
</p>
<div class="org-src-container">

<pre class="src src-bash"># Example of bad code!
while IFS= read -r line; do
    echo "$line" | awk '{ print $2 }'
done &lt; file
</pre>
</div>
<p>
Why this is not a good idea? Awk is designed and optimized to read a file
line-by-line and do operations on these lines. In this case you are calling
an instance of Awk for each line of your file, it's a waste of resources and
time! If you have to cut ten onions you take the knife, cut all the onions
and then you wash the knife and put it away; in this case you are washing
and putting the knife away after you have cut every single onion.
The right way to do this task is:
</p>
<div class="org-src-container">

<pre class="src src-bash">awk '{ print $2 }' file
</pre>
</div>
<p>
Note: Whenever is possible avoid loops in Bash!
</p>
</div>
</div>
<div id="outline-container-sec-6-0-2" class="outline-4">
<h4 id="sec-6-0-2"><span class="section-number-4">6.0.2</span> Print lines based on pattern</h4>
<div class="outline-text-4" id="text-6-0-2">
<p>
Let's say we simply want to print all lines in a file that match a pattern.
Our first attempt might be something like that:
</p>
<div class="org-src-container">

<pre class="src src-bash">awk '{ if( $0 ~ /pattern/ ) print $0 }' file
</pre>
</div>
<p>
This code works, but we can go further. If this is not the first time you
use Awk, you know it works by definition in this way:
</p>
<div class="org-src-container">

<pre class="src src-bash">awk ' CONDITION_1 { ACTION_1 } ... CONDITION_N { ACTION_N} ' file
</pre>
</div>
<p>
So the previous one-liner become:
</p>
<div class="org-src-container">

<pre class="src src-bash">awk ' $0 ~ /pattern/ { print $0 }' file
</pre>
</div>
<p>
But it's not enough! We also know from theory that every regular expression
is implicitly applied by Awk to $0; moreover, we know the default action
applied to a true condition without specified actions is 'print' ($0 is a
redundant option since 'print' alone by default print '$0').
I omit all these working intermidiate steps and come to the point:
</p>
<div class="org-src-container">

<pre class="src src-bash"># This command emulates 'grep'
awk '/pattern/' file
</pre>
</div>
<p>
Really more readable and typing saving than our first try.
</p>

<p>
And if you want to print all lines that does not match a pattern:
</p>
<div class="org-src-container">

<pre class="src src-bash"># This command emulates 'grep -v'
awk '!/pattern/' file
</pre>
</div>
</div>
<ol class="org-ol"><li><a id="sec-6-0-2-1" name="sec-6-0-2-1"></a>Exercises:<br  /><div class="outline-text-5" id="text-6-0-2-1">
<ol class="org-ol">
<li>Print lines that match both pattern1 AND pattern2
</li>
<li>Print lines that match pattern1 BUT NOT pattern2
</li>
</ol>
</div>
</li></ol>
</div>
<div id="outline-container-sec-6-0-3" class="outline-4">
<h4 id="sec-6-0-3"><span class="section-number-4">6.0.3</span> Print lines in range</h4>
<div class="outline-text-4" id="text-6-0-3">
<div class="org-src-container">

<pre class="src src-bash"># NR: The total number of input records seen so far.
# Print from line 3 to line 7 (inclusive)
awk 'NR==3,NR==7'

# Print lines between to regular expression (inclusive)
awk '/beginregex/,/endregex/'

# Print lines between to regular expression (not inclusive)
awk '/endregex/{p=0}; p; /beginregex/{p=1}/
</pre>
</div>
</div>
<ol class="org-ol"><li><a id="sec-6-0-3-1" name="sec-6-0-3-1"></a>Exercises:<br  /><div class="outline-text-5" id="text-6-0-3-1">
<ol class="org-ol">
<li>Print lines from beginregex to endregex, excluding beginregex.
</li>
<li>Print lines from beginregex to endregex, excluding endregex.
</li>
</ol>
</div>
</li></ol>
</div>
<div id="outline-container-sec-6-0-4" class="outline-4">
<h4 id="sec-6-0-4"><span class="section-number-4">6.0.4</span> Remove (non consecutive) duplicated lines</h4>
<div class="outline-text-4" id="text-6-0-4">
<div class="org-src-container">

<pre class="src src-bash">awk '!z[$0]++' file
</pre>
</div>
</div>
<ol class="org-ol"><li><a id="sec-6-0-4-1" name="sec-6-0-4-1"></a>Exercises:<br  /><div class="outline-text-5" id="text-6-0-4-1">
<ol class="org-ol">
<li>Remove duplicated lines only if these lines are consecutive.
(Emulates uniq command)
</li>
</ol>
</div>
</li></ol>
</div>
<div id="outline-container-sec-6-0-5" class="outline-4">
<h4 id="sec-6-0-5"><span class="section-number-4">6.0.5</span> Find and replace</h4>
<div class="outline-text-4" id="text-6-0-5">
<div class="org-src-container">

<pre class="src src-bash"># Find and replace only the first occurrence
awk '{sub("pattern","replacement")} 1'
# Find and replace all occurrences
awk '{gsub("pattern","replacement")} 1'
</pre>
</div>
</div>
<ol class="org-ol"><li><a id="sec-6-0-5-1" name="sec-6-0-5-1"></a>Exercises:<br  /><div class="outline-text-5" id="text-6-0-5-1">
<ol class="org-ol">
<li>Print only the lines where a replacement occurs.
</li>
</ol>
</div>
</li></ol>
</div>
<div id="outline-container-sec-6-0-6" class="outline-4">
<h4 id="sec-6-0-6"><span class="section-number-4">6.0.6</span> Print intersection of two files</h4>
<div class="outline-text-4" id="text-6-0-6">
<p>
This is a really common and powerful construct in Awk.
</p>
<div class="org-src-container">

<pre class="src src-bash"># Print only the lines that are both in file1 and file2
awk 'FNR==NR{ z[$0]++; next } $0 in z' file1 file2
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-6-0-7" class="outline-4">
<h4 id="sec-6-0-7"><span class="section-number-4">6.0.7</span> Parse a CSV file</h4>
<div class="outline-text-4" id="text-6-0-7">
<div class="org-src-container">

<pre class="src src-bash"># With the flag -F you can set the Input Field Separator (IFS)
# If the separator is comma "," you can write something like:
awk -F, '{ print $1,$3 }' file.csv

NOTE: In this case we have set IFS=, but when we print, as you already know,
there are spaces between fields and not commas! This is not desirable if we,
after some manipulation, want to have again a csv file as output.
Sure, we can print explicitly all commas:
awk -F, '{ print $1","$3 }' file.csv

# However, this is not a good solution.
# In many situation is preferable set the Output Field Separator (OFS):
awk -F, '{ print $1,$3 }' OFS=, file.csv
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-sec-7" class="outline-2">
<h2 id="sec-7"><span class="section-number-2">7</span> Project example: dice rolling simulations</h2>
<div class="outline-text-2" id="text-7">
<p>
I choose this example because it's simple and everyone has experience of
dice rolling; moreover, I write the program in C++ because there are several
courses that cover this language and I hope you are familiar with it.
The C++ code I wrote is straightforward, so you can focus on:
</p>
<ul class="org-ul">
<li>how to pass different arguments to a program
</li>
<li>how to redirect program's output to specific files
</li>
<li>how to manipulate output files
</li>
</ul>

<p>
You can find the program's code in the <i>project:dice</i> subfolder of this seminar
repository. Compile. Run. An usage message should be returned:
Usage: ./dice &lt;dice number&gt; &lt;faces number&gt; &lt;rolls number&gt;
</p>
</div>
</div>
<div id="outline-container-sec-8" class="outline-2">
<h2 id="sec-8"><span class="section-number-2">8</span> Not covered by this talk but truly useful and important:</h2>
<div class="outline-text-2" id="text-8">
</div><div id="outline-container-sec-8-1" class="outline-3">
<h3 id="sec-8-1"><span class="section-number-3">8.1</span> ssh</h3>
<div class="outline-text-3" id="text-8-1">
<p>
Some tips to improve your experience.
</p>
</div>
<div id="outline-container-sec-8-1-1" class="outline-4">
<h4 id="sec-8-1-1"><span class="section-number-4">8.1.1</span> Generate public/private key pair for authentication</h4>
<div class="outline-text-4" id="text-8-1-1">
<p>
You can generate SSH keys with the command:
</p>
<div class="org-src-container">

<pre class="src src-bash">ssh-keygen
</pre>
</div>
<p>
Once you have a key pair you have to append your public key in the file
'~/.ssh/authorized<sub>keys'</sub> on your remote host, you can do it manually or with
the command:
</p>
<div class="org-src-container">

<pre class="src src-bash">ssh-copy-id -i ~/.ssh/id_rsa.pub user@domain
</pre>
</div>
</div>
</div>
<div id="outline-container-sec-8-1-2" class="outline-4">
<h4 id="sec-8-1-2"><span class="section-number-4">8.1.2</span> Basic configuration example</h4>
<div class="outline-text-4" id="text-8-1-2">
<p>
Create file ~/.ssh/config (or edit it if you already have one).
A basic configuration file looks like:
</p>
<pre class="example">
Host *
ControlMaster auto
ControlPath ~/.ssh/master-%r@%h:%p

Host mylab
Hostname mylab.example
User mylogin
CheckHostIP no
Compression yes
Protocol 2
</pre>
<p>
From now on, when you want to open a connection via ssh just type:
</p>
<div class="org-src-container">

<pre class="src src-bash">ssh mylab
</pre>
</div>
<p>
When you connect the first time ControlMaster create a socket and from the
second time you don't need to reinsert your password or key's passphrase (if
you have set one). Note that you can configure multiple hosts and add or
remove options as you like to fit your needs.
</p>
</div>
</div>
</div>
<div id="outline-container-sec-8-2" class="outline-3">
<h3 id="sec-8-2"><span class="section-number-3">8.2</span> git</h3>
<div class="outline-text-3" id="text-8-2">
<p>
Love it! Never again without!
I truly recommend you to inform on this irreplaceable tool!
</p>
</div>
</div>
<div id="outline-container-sec-8-3" class="outline-3">
<h3 id="sec-8-3"><span class="section-number-3">8.3</span> tmux</h3>
<div class="outline-text-3" id="text-8-3">
<p>
Tmux is a terminal multiplexer.
</p>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: 2017.05.10</p>
<p class="author">Author: Andrea Miglietta</p>
<p class="date">Created: 2017-05-10 Wed 14:42</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 24.5.1 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>