Navigate the file system

Back to Week 1

Now that we have learned about the shell and the anatomy of a command, let's dive into different helpful programs (that you can run as commands) that you typically encounter while working on UNIX systems.

As a user, you can picture a filesystem as a series of nested files and folders(a.k.a. directories).

pwd:

pwd is a program that is occasionally helpful, but is a good way to get your feet wet in trying out different UNIX commands. All it does is print out what directory (folder) you are currently in. Usually you will already know where you're at from the prompt, but it can be helpful to know the full path. pwd stands for print working directory:

$ pwd
/home/username

What directory are you in when you open your shell?

Most shells start in your home directory!

$ pwd
/home/username

ls:

ls is one of the most common UNIX programs that you may use while on UNIX systems. By default, it lists the contents of your current working directory:

$ ls
data.csv        Documents       bin      Desktop

There are many options that ls can use to modify its behavior. In addition, you can specify a directory as an argument to list contents of that directory.

File Extensions

In UNIX systems, file extensions are technically meaningless, however, convention is important. Executables don't need to end in .exe and text files don't need to end in .txt. It is helpful if they do, so that people (including yourself) know what type of file it is.

Hidden Files

Files and directories that start with a "." are hidden by default. You can use the -a or --all options to see them!

Wildcards

Wildcards are special characters that let you match multiple files or directories at once, instead of typing each name manually. Bash expands wildcards before a command runs, so the program receives a list of matching filenames. These can be used to match a specific subset of files based on their name. The primary wildcards used are:

• * matches any number of characters
• ? - matches exactly one character
• [abc] or [a-z] - matches one character from a set or range

You can substitute these in to match specific patterns like so:

$ ls *.txt
file1.txt file2.txt file3.txt

$ ls data?.[ct]sv
data1.csv data2.tsv data3.csv

What files and folders are hidden in your home directory?

Check with $ ls --all! These will vary depending on what you have installed, but most will be configuration files for programs you have installed. Common ones are:

.bashrc     - bash startup customization file
.conda      - Conda python environments
.cache      - Cached data (like photo thumbnails)
.ssh        - Configuration files for SSH

How would you list all of the png files in your Downloads folder?

Use $ ls Downloads/*.png!

cd

Another one of the most common programs to run on UNIX systems is cd, which stands for change directory, but should be thought of as change working directory. This will change which directory you are currently working in.

$ pwd
/home/username
$ cd Desktop/data
$ pwd
/home/username/Desktop/data

Autocomplete

Most terminal interfaces support using tab to autocomplete file and folders that exist in your working directory. This works for most commands, but is especially helpful with cd.

Returning Home

If you run the cd command without arguments, you will return back to your home directory.

How can we move to our Documents folder?

Use $ cd Documents!

How can we move back to your Home directory?

There's several ways!

• Specify the whole path with $ cd /home/username
• You can always return home with just cd
• You can also use cd .. to move up a directory, or cd - to move to your previous directory (more on this later!)

mkdir

The last program we'll go over in this section is the mkdir or make directory command. This does what it sounds like and will create the directory noted in the argument if it doesn't already exist.

$ mkdir example-data

You can also put multiple arguments and mkdir will create all of them. A helpful option to pass to the mkdir program is -p, which will create parent directories as needed.

$ mkdir -p another_one/test1

Which will create the another_one directory in your current directory and the test1 directory within the another_one directory.

How would you make a folder on your Desktop titled myfolder?

There are several ways! We could first cd to the Desktop, and run mkdir:

cd /home/user/Desktop
mkdir myfolder

Or we could make it from our home directory by specifying the path:

mkdir Desktop/myfolder

Paths

All files in UNIX systems are organized into directories, and those directories may have subdirectories, creating a tree of files that span the entire operating system. Directory paths in UNIX systems can be absolute or relative. Absolute paths start at the root of the file system and thus always start with a slash (/). Relative paths are relative to your current working directory and do not start with a slash.

Absolute path

$ ls /home/username/Desktop
output_of_ls

Relative path

$ ls Desktop
output_of_ls

Special paths

There four special paths that are commonly used in navigating UNIX file systems:

Previous Working Directory: -

• The - represents the previous working directory (the directory you were in before your current one)
• You can run cd - to navigate to the previous directory you were in.

$ cd Desktop/data
$ cd -
$ pwd
/home/username

Home Directory: ~

• The ~ represents your home directory. You can cd ~ to move back to your home directory, or cd ~/Desktop to move to your desktop
• You can also just type cd (without any arguments) to return to your home directory

Current Working Directory: .

• The . represents the directory you are currently in. You can use it to reference certain files in your current directory (like ls ./myfile.txt)

Parent Working Directory: ..

• The .. represents the parent directory of the directory you are currently in. For example, if you are in /home/username/Documents/mydata, the command cd .. will change your directory to /home/username/Documents
• You can also stack these! For example, to move "up" two directories, you could use the command cd ../../

$ cd Desktop/data
$ cd ..
$ pwd
/home/username/Desktop

How would we move from the data directory to the Downloads directory with one command?

cd ../../Downloads

Permissions

Since everything in UNIX systems is a file, file permissions are of supreme importance. To check the permissions of a file, run the command ls -l which runs the ls program with the l option which tells ls to print out more information about the files.

The following code block shows an example of what you might see from the longer ls output:

$ ls -a -l -h ~/.ssh
total 6.0K
drwxr-xr-x  2 username student    4 Jul 17 11:19 .
drwx------ 14 username student   28 Jul 16 22:26 ..
-rw-r--r--  1 username student 2.0K Oct 18  2021 authorized_keys
-rw-r--r--  1 username student    0 Jul 17 11:19 config

The three program options used here are: a, which displays all files/folders, even hidden ones; l which lists out more information about each listing; and h which shows the size of items in a human-readable format.

In the first ten columns of the output are the permissions of that item, details of which will be discussed in the next paragraph. The next number is the number of hardlinks to the file, which for most use cases isn't important.

After that, we have the username of the owner of the file and then the name of the group that owns access to the file. The number after that is the size of the item. Then comes the date that the item was most recently modified. Last of all is the name of the actual item.

The four items in the .ssh folder of this home directory are:

1) The current directory (.)

2) A link to the parent directory (..)

3) Two files:

• authorized_keys

• config

Let's talk permissions. The first ten characters of each row represent the permissions for each item listed:

-rw-r--r-- 1 username groupname 4096 Jan 5 notes.txt

The first column shows whether it's a directory (with a d) or not (with a dash):

drwxr-x--- 2 username groupname 4096 Jan 5 secure_dir

Then the next nine columns are broken into three groups of three:

1) First three - User (u)

-rw-r---- 1 username groupname 4096 Jan 5 notes.txt

2) Second three - Group (g)

-rw-r--r-- 1 username groupname 4096 Jan 5 notes.txt

3) Last three - Others (o)

-rw-r--r-- 1 username groupname 4096 Jan 5 notes.txt

Each group of three is made up of the read (r), write (w), and execute (x) bits. The read bit controls whether someone can look at the data contained in the file. The write bit controls whether someone can edit the data in the file. And the execute bit controls if someone can run that file as a program. We'll talk more about the "execute" bit in the Week 3 "Scripting" section.

Learning about command options

man

Another helpful program is man, which stands for manual. You may hear the term man page which is just short for manual page, or running the program man with the argument being the program you want more information about.

$ man ls

The man program pulls up a page that you can scroll up and down with your arrow keys or the j/k keys and quit out of by pressing the q key. It is up to each program to provide its own man page, so not all programs have them, but when they do it can be helpful.

Next section: Editing Files