#!/usr/bin/env bash
# First line of the script is shebang which tells the system how to execute
# the script: http://en.wikipedia.org/wiki/Shebang_(Unix)
# As you already figured, comments start with #. Shebang is also a comment.

# Simple hello world example:
echo Hello world! # => Hello world!

# Each command starts on a new line, or after semicolon:
echo 'This is the first line'; echo 'This is the second line'
# => This is the first line
# => This is the second line

# Declaring a variable looks like this:
Variable="Some string"

# But not like this:
Variable = "Some string" # => returns error "Variable: command not found"
# Bash will decide that Variable is a command it must execute and give an error
# because it can't be found.

# Or like this:
Variable= 'Some string' # => returns error: "Some string: command not found"
# Bash will decide that 'Some string' is a command it must execute and give an
# error because it can't be found. (In this case the 'Variable=' part is seen
# as a variable assignment valid only for the scope of the 'Some string'
# command.)

# Using the variable:
echo $Variable # => Some string
echo "$Variable" # => Some string
echo '$Variable' # => $Variable
# When you use the variable itself — assign it, export it, or else — you write
# its name without $. If you want to use the variable's value, you should use $.
# Note that ' (single quote) won't expand the variables!

# Parameter expansion ${ }:
echo ${Variable} # => Some string
# This is a simple usage of parameter expansion
# Parameter Expansion gets a value from a variable.  It "expands" or prints the value
# During the expansion time the value or parameter are able to be modified
# Below are other modifications that add onto this expansion

# String substitution in variables
echo ${Variable/Some/A} # => A string
# This will substitute the first occurrence of "Some" with "A"

# Substring from a variable
Length=7
echo ${Variable:0:Length} # => Some st
# This will return only the first 7 characters of the value
echo ${Variable: -5} # => tring
# This will return the last 5 characters (note the space before -5)

# String length
echo ${#Variable} # => 11

# Default value for variable
echo ${Foo:-"DefaultValueIfFooIsMissingOrEmpty"} 
# => DefaultValueIfFooIsMissingOrEmpty
# This works for null (Foo=) and empty string (Foo=""); zero (Foo=0) returns 0.
# Note that it only returns default value and doesn't change variable value.

# Declare an array with 6 elements
array0=(one two three four five six)
# Print first element
echo $array0 # => "one"
# Print first element
echo ${array0[0]} # => "one"
# Print all elements
echo ${array0[@]} # => "one two three four five six"
# Print number of elements
echo ${#array0[@]} # => "6"
# Print number of characters in third element
echo ${#array0[2]} # => "5"
# Print 2 elements starting from forth
echo ${array0[@]:3:2} # => "four five"
# Print all elements. Each of them on new line.
for i in "${array0[@]}"; do
    echo "$i"
done

# Brace Expansion { }
# Used to generate arbitrary strings
echo {1..10} # => 1 2 3 4 5 6 7 8 9 10
echo {a..z} # => a b c d e f g h i j k l m n o p q r s t u v w x y z
# This will output the range from the start value to the end value

# Builtin variables:
# There are some useful builtin variables, like
echo "Last program's return value: $?"
echo "Script's PID: $$"
echo "Number of arguments passed to script: $#"
echo "All arguments passed to script: $@"
echo "Script's arguments separated into different variables: $1 $2..."

# Now that we know how to echo and use variables,
# let's learn some of the other basics of bash!

# Our current directory is available through the command `pwd`.
# `pwd` stands for "print working directory".
# We can also use the builtin variable `$PWD`.
# Observe that the following are equivalent:
echo "I'm in $(pwd)" # execs `pwd` and interpolates output
echo "I'm in $PWD" # interpolates the variable

# If you get too much output in your terminal, or from a script, the command
# `clear` clears your screen
clear
# Ctrl-L also works for clearing output

# Reading a value from input:
echo "What's your name?"
read Name # Note that we didn't need to declare a new variable
echo Hello, $Name!

# We have the usual if structure:
# use 'man test' for more info about conditionals
if [ $Name != $USER ]
then
    echo "Your name isn't your username"
else
    echo "Your name is your username"
fi
# True if the value of $Name is not equal to the current user's login username

# NOTE: if $Name is empty, bash sees the above condition as:
if [ != $USER ]
# which is invalid syntax
# so the "safe" way to use potentially empty variables in bash is:
if [ "$Name" != $USER ] ...
# which, when $Name is empty, is seen by bash as:
if [ "" != $USER ] ...
# which works as expected

# There is also conditional execution
echo "Always executed" || echo "Only executed if first command fails"
# => Always executed
echo "Always executed" && echo "Only executed if first command does NOT fail"
# => Always executed
# => Only executed if first command does NOT fail


# To use && and || with if statements, you need multiple pairs of square brackets:
if [ "$Name" == "Steve" ] && [ "$Age" -eq 15 ]
then
    echo "This will run if $Name is Steve AND $Age is 15."
fi

if [ "$Name" == "Daniya" ] || [ "$Name" == "Zach" ]
then
    echo "This will run if $Name is Daniya OR Zach."
fi

# There is also the =~ operator, which tests a string against a Regex pattern:
Email=me@example.com
if [[ "$Email" =~ [a-z]+@[a-z]{2,}\.(com|net|org) ]]
then
    echo "Valid email!"
fi
# Note that =~ only works within double [[ ]] square brackets,
# which are subtly different from single [ ].
# See http://www.gnu.org/software/bash/manual/bashref.html#Conditional-Constructs for more on this.

# Redefine command 'ping' as alias to send only 5 packets
alias ping='ping -c 5'
# Escape alias and use command with this name instead
\ping 192.168.1.1
# Print all aliases
alias -p

# Expressions are denoted with the following format:
echo $(( 10 + 5 )) # => 15

# Unlike other programming languages, bash is a shell so it works in the context
# of a current directory. You can list files and directories in the current
# directory with the ls command:
ls # Lists the files and subdirectories contained in the current directory

# These commands have options that control their execution:
ls -l # Lists every file and directory on a separate line
ls -t # Sorts the directory contents by last-modified date (descending)
ls -R # Recursively `ls` this directory and all of its subdirectories

# Results of the previous command can be passed to the next command as input.
# grep command filters the input with provided patterns. That's how we can list
# .txt files in the current directory:
ls -l | grep "\.txt"

# Use `cat` to print files to stdout:
cat file.txt

# We can also read the file using `cat`:
Contents=$(cat file.txt)
echo "START OF FILE\n$Contents\nEND OF FILE" # "\n" prints a new line character
# => START OF FILE
# => [contents of file.txt]
# => END OF FILE

# Use `cp` to copy files or directories from one place to another.
# `cp` creates NEW versions of the sources,
# so editing the copy won't affect the original (and vice versa).
# Note that it will overwrite the destination if it already exists.
cp srcFile.txt clone.txt
cp -r srcDirectory/ dst/ # recursively copy

# Look into `scp` or `sftp` if you plan on exchanging files between computers.
# `scp` behaves very similarly to `cp`.
# `sftp` is more interactive.

# Use `mv` to move files or directories from one place to another.
# `mv` is similar to `cp`, but it deletes the source.
# `mv` is also useful for renaming files!
mv s0urc3.txt dst.txt # sorry, l33t hackers...

# Since bash works in the context of a current directory, you might want to 
# run your command in some other directory. We have cd for changing location:
cd ~    # change to home directory
cd      # also goes to home directory
cd ..   # go up one directory
        # (^^say, from /home/username/Downloads to /home/username)
cd /home/username/Documents   # change to specified directory
cd ~/Documents/..    # still in home directory..isn't it??
cd -    # change to last directory
# => /home/username/Documents

# Use subshells to work across directories
(echo "First, I'm here: $PWD") && (cd someDir; echo "Then, I'm here: $PWD")
pwd # still in first directory

# Use `mkdir` to create new directories.
mkdir myNewDir
# The `-p` flag causes new intermediate directories to be created as necessary.
mkdir -p myNewDir/with/intermediate/directories
# if the intermediate directories didn't already exist, running the above
# command without the `-p` flag would return an error

# You can redirect command input and output (stdin, stdout, and stderr).
# Read from stdin until ^EOF$ and overwrite hello.py with the lines
# between "EOF":
cat > hello.py << EOF
#!/usr/bin/env python
from __future__ import print_function
import sys
print("#stdout", file=sys.stdout)
print("#stderr", file=sys.stderr)
for line in sys.stdin:
    print(line, file=sys.stdout)
EOF
# Variables will be expanded if the first "EOF" is not quoted

# Run the hello.py Python script with various stdin, stdout, and 
# stderr redirections:
python hello.py < "input.in" # pass input.in as input to the script
python hello.py > "output.out" # redirect output from the script to output.out
python hello.py 2> "error.err" # redirect error output to error.err
python hello.py > "output-and-error.log" 2>&1 # redirect both output and errors to output-and-error.log
python hello.py > /dev/null 2>&1 # redirect all output and errors to the black hole, /dev/null, i.e., no output
# The output error will overwrite the file if it exists,
# if you want to append instead, use ">>":
python hello.py >> "output.out" 2>> "error.err"

# Run the hello.m MatLab script with parameter from shell.
cat > hello_function.m << EOF
function hello_function(str)
disp(str)
end
EOF
str="Hello World!"
matlab -nodesktop -nosplash -r "str = '$str';hello_function(str);quit"

# Overwrite output.out, append to error.err, and count lines:
info bash 'Basic Shell Features' 'Redirections' > output.out 2>> error.err
wc -l output.out error.err

# Run a command and print its file descriptor (e.g. /dev/fd/123)
# see: man fd
echo <(echo "#helloworld")

# Overwrite output.out with "#helloworld":
cat > output.out <(echo "#helloworld")
echo "#helloworld" > output.out
echo "#helloworld" | cat > output.out
echo "#helloworld" | tee output.out >/dev/null

# Cleanup temporary files verbosely (add '-i' for interactive)
# WARNING: `rm` commands cannot be undone
rm -v output.out error.err output-and-error.log
rm -r tempDir/ # recursively delete

# Commands can be substituted within other commands using $( ):
# The following command displays the number of files and directories in the
# current directory.
echo "There are $(ls | wc -l) items here."

# The same can be done using backticks `` but they can't be nested - the preferred way
# is to use $( ).
echo "There are `ls | wc -l` items here."

# Bash uses a case statement that works similarly to switch in Java and C++:
case "$Variable" in
    #List patterns for the conditions you want to meet
    0) echo "There is a zero.";;
    1) echo "There is a one.";;
    *) echo "It is not null.";;
esac

# for loops iterate for as many arguments given:
# The contents of $Variable is printed three times.
for Variable in {1..3}
do
    echo "$Variable"
done
# => 1
# => 2
# => 3


# Or write it the "traditional for loop" way:
for ((a=1; a <= 3; a++))
do
    echo $a
done
# => 1
# => 2
# => 3

# They can also be used to act on files..
# This will run the command 'cat' on file1 and file2
for Variable in file1 file2
do
    cat "$Variable"
done

# ..or the output from a command
# This will cat the output from ls.
for Output in $(ls)
do
    cat "$Output"
done

# while loop:
while [ true ]
do
    echo "loop body here..."
    break
done
# => loop body here...

# You can also define functions
# Definition:
function foo ()
{
    echo "Arguments work just like script arguments: $@"
    echo "And: $1 $2..."
    echo "This is a function"
    return 0
}
# Call the function `foo` with two arguments, arg1 and arg2:
foo arg1 arg2
# => Arguments work just like script arguments: arg1 arg2
# => And: arg1 arg2...
# => This is a function

# or simply
bar ()
{
    echo "Another way to declare functions!"
    return 0
}
# Call the function `bar` with no arguments:
bar # => Another way to declare functions!

# Calling your function
foo "My name is" $Name

# There are a lot of useful commands you should learn:
# prints last 10 lines of file.txt
tail -n 10 file.txt

# prints first 10 lines of file.txt
head -n 10 file.txt

# sort file.txt's lines
sort file.txt

# report or omit repeated lines, with -d it reports them
uniq -d file.txt

# prints only the first column before the ',' character
cut -d ',' -f 1 file.txt

# replaces every occurrence of 'okay' with 'great' in file.txt
# (regex compatible)
sed -i 's/okay/great/g' file.txt

# print to stdout all lines of file.txt which match some regex
# The example prints lines which begin with "foo" and end in "bar"
grep "^foo.*bar$" file.txt

# pass the option "-c" to instead print the number of lines matching the regex
grep -c "^foo.*bar$" file.txt

# Other useful options are:
grep -r "^foo.*bar$" someDir/ # recursively `grep`
grep -n "^foo.*bar$" file.txt # give line numbers
grep -rI "^foo.*bar$" someDir/ # recursively `grep`, but ignore binary files

# perform the same initial search, but filter out the lines containing "baz"
grep "^foo.*bar$" file.txt | grep -v "baz"

# if you literally want to search for the string,
# and not the regex, use fgrep (or grep -F)
fgrep "foobar" file.txt

# The trap command allows you to execute a command whenever your script 
# receives a signal. Here, trap will execute `rm` if it receives any of the 
# three listed signals.
trap "rm $TEMP_FILE; exit" SIGHUP SIGINT SIGTERM

# `sudo` is used to perform commands as the superuser
NAME1=$(whoami)
NAME2=$(sudo whoami)
echo "Was $NAME1, then became more powerful $NAME2"

# Read Bash shell builtins documentation with the bash 'help' builtin:
help
help help
help for
help return
help source
help .

# Read Bash manpage documentation with man
apropos bash
man 1 bash
man bash

# Read info documentation with info (? for help)
apropos info | grep '^info.*('
man info
info info
info 5 info

# Read bash info documentation:
info bash
info bash 'Bash Features'
info bash 6
info --apropos bash