C2110 UNIX and programming
Lesson 5 / Module 3
PS / 2020 Distance form of teaching: Rev2
Petr Kulhánek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science Masaryk University, Kamenice 5, CZ-62500 Brno
10 UNIX and programming
Lesson 5 / Module 3
Bash
https://www.gnu.org/software/bash/
10 UNIX and programming
Lesson 5 / Module 3
Bash - Overview
Unix shell (also command processor, literally "unix shell") is the name of text user interface, which is the predecessor of the graphical user interface. One of the Unix shells is Bash.
Bash is POSIX shell with several extensions. It is designed for operating systems based on the GNU project and can be run on most Unix operating systems. It is used as the default command interpreter in systems built on Linux kernel, as well as on Mac OS X or Darvin system. It can also be used on Microsoft Windows using the subsystem for Unix application (SUA), or POSIX emulation using software Cygwin and MSYS.
https://cs.wikipedia.org
10 UNIX and programming
Lesson 5 / Module 3
Interactive Mode
Prompt - type of user / prompt ($ regular user, # super user, other possible %, >)
[kulhanek@wolf ~]$ _
username ^ /       I place for command
computer name
current directory (~ means home directory /home/username)
The command is executed by pressing Enter key.
History: Use the up and down arrow keys to scroll through the list of commands you have already entered. The history command can be reused or modified and the modified one can be used. The history is also accessible by command history.
Autocomplete: by pressing Tab key the command line interpreter tries to complete the spelled word. Command names, paths and file names are added (if one press does not cause anything, there are more options to add and repeated press will display them).
Shell interprets (expands) wild characters and other special characters, before the actual execution of the command. In interactive mode it is possible to run control structures of
bash language. a - +     •   + au a
Interactive mode is terminated by command exit.
i UNIX and programming Lesson 5 / Module 3
Bash Script
#!/bin/bash
# this is a comment
echo AThis is a script in Bash interpreter!1 echo "Content of directory xpwcT is:"
Is
# prints content of directory
A=6      # sets value of variable A
echo "Value of variable A is $A
if
echo "first command"; echo "second command"
./mycommand first_argument second_argument V
third argument
c o
+-> u
cu
X
cu
~a c
05
o
u
immediately follows new line
• blank lines are ignored
• text preceded by a character # is ignored (used to comment script functionality)
• multiple commands can be specified per line, commands are separated by a semicolon ;
• one command can be written on multiple lines using a backslash \
10 UNIX and programming
Lesson 5 / Module 3
Where to write scripts (/program
Because scripts and program source codes are text files, you can use any text editor that allows you to save text in plain form (without formatting metadata).
Text editors:
• vi
• kwrite
• kate
• gedit
A specialized development environment can also be used to write scripts and program source codes - IDE (Integrated Development Environment). In addition to the editor, the IDE also contains a project manager, debugging tools (debugger) and more. Mostly available for more complex languages: C, C++, Fortran, JavaScript, Python, PHP, etc.
Development environment:
• Kdevelop
• qtcreator
• NetBeans
• Eclipse
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Lesson 5 / Module 3
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Flowchart and Bash Script
9 ~~
writestr "Contents of directory is: 11
E
2=
order of command execution
#!/bin/bash
echo  'This is a script in bash interpreter!'
echo "Contents of directory is:"
Is
10 UNIX and programming
Lesson 5 / Module 3
Non-interactive Mode - Scripts
1) Indirect start
We run the language interpreter and give the name of the script as an argument.
$ bash my bash script
Scripts do not have to have the x flag set (executable).
2) Direct start
We run the script directly (shell automatically starts the interpreter).
$ chmod u+x my bash script $   ./my_bash_s cript
Scripts must have the x flag (executable) and interpreter set (part of the script).
#!/bin/bash ^
echo  'This is a script in Bash interpreter1
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Change of Access Rights
Access rights determine what operations a user can perform on files or directories in the file system.
Access rights:
r   ability to read file to list contents of directory
w ability to change file to change contents of directory (create or delete file/directory)
x  ability to run the file to enter directory
Each file or directory has a designated owner and user group. Access rights are listed separately for file owner (u), user group (g) and other users (o).
$ is -1 ___access rights
u    g o
-rw-rw-r—    1 kulhanek lcc      858 2008-10-17 11:58 script.sh
$ chmod u+x script, sh       add (+) / remove (-) of a right $ Is -1
-rwxrw-r--    1 kulhanek lcc      858 2008-10-17 11:58 script.sh
I UNIX and programming Lesson 5 / Module 3
Specification of Interpreter
Interpreter specification (first line of script):
#!/absolute/to/interpreter/of/script
Bash script
Gnuplot script
#!/bin/bash
echo "This is a bash script!"
#!/usr/bin/gnuplot
set xrange[0:6]
plot sin(x)
pause -1
• If script interpreter is not specified when it is run directly, the system interpreter is used shell (bash).
• The interpreter specified in the script is ignored during indirect execution.
• It is apropriate to always include the interpreter in the script, because it is used by text editors to highlight syntax.
10 UNIX and programming
Lesson 5 / Module 3
Commands for Exercises
echo   prints the entered text (string)
grep    prints lines that contain the specified PATTERN
Examples of use:
$ echo "The result is:"
prints the string "The result is:"
$ grep TEMP rst.out
prints each line from the file rst.out which contains the string "TEMP"
The grep command is very useful, so I recommend that you go through its detailed documentation (man grep)
10 UNIX and programming
Lesson 5 / Module 3
Exercise 1
Interactive mode:
1. Run the command bash in the terminal. What happened? End the second session with the exit command.
2. Using commands ps, find out the number of the process that interprets the command line.
3. End the process with the command kill (kill -9 pid, where pid the process number). What will happen?
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Lesson 5 / Module 3
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Exercises 2
Scripting:
1. Create a directory named script.
2. To the directory, copy the file script.bash from the directory book /home/kulhanek/Documents/C2110/Lesson05/programs.
3. Run directly script script.bash.
4. Create a directory named measurement.
5. To the directory, copy the file merenil.log from the directory /home/kulhanek/Documents/C2110/Lesson05/data.
6. Using suitable commands, extract the line containing the temperature of measurement from file merenil.log (a description of the data is given in the analyzed file).
7. In a text editor, write a script that will print he temperature and pressure of the measurement from the file merenil.log
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Lesson 5 / Module 3
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Additional Information
10 UNIX and programming
Lesson 5 / Module 3
Specification of Interpreter II
In case the absolute path to the interpreter changes (e.g., when using software modules), it is advisable to use the following construction:
#!/usr/bin/env interpreter
The interpreter must be in one of the directories specified by the PATH system variable.
Bash script
#!/usr/bin/env bash
echo "This is bash script!"
Script in gnuplot
#!/usr/bin/env gnuplot
set xrange[0:6]
plot sin(x)
pause -1
10 UNIX and programming
Lesson 5 / Module 3