8.1. Basic concepts and simple commands

The absolute path of a file

The absolute or full path of a file specifies its unique location in the file system, its name and extension. The absolute path of every file is different and constant. It will always be the same regardless of the current directory in which you are working (unless you move the file). This path follows a hierarchy of directories where the file is located, separating each directory with the delimiting character, which is the slash (/) for Macintosh and Linux and the backslash (\) for Windows. For example, a text file named file.txt located in the Desktop of a Mac computer, will commonly have an absolute path similar to this:
/Users/user_name/Desktop/file.txt
To find the absolute path of a file you can drag and drop it into the Terminal.

For example, if this is the absolute path of a file:
/Users/user_name/Desktop/SomeFolder/Subfolder/file.txt
It means that in the user Desktop there is a folder called SomeFolder, inside SomeFolder there is another folder called Subfolder, and inside Subfolder is located the corresponding file, with name file and extension txt. Inside a directory there can be two files with the same name but in this case, they must have a different extension. There cannot be two files with both the same name and same extension inside the same folder.

The relative path of a file

The relative path of a file starts from the current working directory and represents the location of a specific file relative to this directory. It is always changing as it depends on what directory you are located in the terminal, but is a lot shorter than the absolute path.

If the absolute path of a file is the following, meaning the file is located in the Desktop:
/Users/user_name/Desktop/file.txt
And the user current working directory is the desktop, then the relative path of the file is:
file.txt or ./file.txt
Since the file is located in the current directory, the user can use just the name and extension for the relative path. Adding ./ doesn't do anything because ./ represents the current directory.

The following relative paths represent files that are located in the current working directory:
File1.txt
File2.nii.gz
./File3.nii
./File4.docx

The absolute path of these files will be something similar to this (for Mac users), if the current directory is the Desktop:
/Users/username/Desktop/File1.txt
/Users/username/Desktop/File2.nii.gz
/Users/username/Desktop/File3.nii
/Users/username/Desktop/File4.docx

The same way as a dot (.) represents the current directory in a relative path, two dots (..) represent the parent directory. So, if the absolute path of my current working directory is the following:
/Users/user_name/Desktop/SomeFolder
I can refer to files located in the parent directory (Desktop) using the double dots. So, all these files are located in the Desktop (the same as SomeFolder):
../FileA.txt
../FileB.txt
../FileC.txt

Some tips about file paths

Both the absolute and relative paths are used to reference files when doing operations with it, but I generally prefer to use the absolute path when writing scripts because that way my script will run with no issues independently of my working directory. Never the less, when doing fast operations in the Terminal (like renaming or copying a file), then it's faster to use the relative path.

It is also recommended to not use spaces or any other special characters when naming a file, because it makes it harder to write the path of that file. For example, if I have a file named Some File.txt in my Desktop (on a Mac), this is not the absolute path:
/Users/user_name/Desktop/Some File.txt
Instead, the absolute path will be:
/Users/user_name/Desktop/Some\ File.txt

The backslash is telling us to not treat the space as a special character but instead as part of the file path. This works the same way in Linux and MacOS.

The same will happen with a file which name contains the dollar sign (which is a special character). For example, if in the Desktop there is a folder named untitled$folder, this is not the absolute path:
/Users/user_name/Desktop/untitled$folder
Instead, the absolute path will be:
/Users/user_name/Desktop/untitled\$folder

Again, the backslash is indicating us to treat the special character ($) as part of the file name and not as the beginning of a variable name (which is the normal use of $ in bash). If we don't use the backslash before the dollar sign, bash will try to find a variable called folder ($folder normally refers to the value of folder as a variable, not a string). If that variable doesn't exist, then bash will read /Users/user_name/Desktop/untitled$folder as /Users/user_name/Desktop/untitled, replacing $folder for an empty space.

In the following sections you will learn how the absolute and relative paths are used to manipulate files in MacOS and Linux.

pwd command

Prints the absolute path of the current working directory.

ls command

add something about permissions here!!

Lists the files and folders inside the specified directory. If no directory is specified after ls, then it prints the contents of the current folder. If no flag is used, it lists the files in bare format (without any details such as modified date and time or permissions). Depending which flag is used (or a combination of flags), then specific information about the file will be displayed. The following table is taken from manual of the ls command as displayed in the command line.

The following examples show the usage of the flags presented in the previous table and details on the results that can be obtained when using the command ls together with those flags.

ls with no flags

Show the list of files in the current working directory:

$ ls
Applicationshome
Libraryinstaller.failurerequests
Networknet
Subjectsopt
Usersprivate
Volumessbin
binmp
coresusr
devvar
etc

Show the list of files in a different directory using the absolute path of that directory

$ ls /Volumes/MyExternalDrive
ArticlesMRIdata SharedFolder

Show the list of files in a subfolder (Applications) using the relative path

$ ls Applications/
Calculator.app
Calendar.app
Chess.app
Dashboard.app
Dictionary.app
EndNote X7
EndNote X8
FaceTime.app
Firefox.app
IBM
Image Capture.app
Launchpad.app
MATLAB_R2014b.app

ls -l

When using the flag -l, bash will not only show the list of files but also a description for each file. The output will be organized in columns, each one with a specific meaning. Most of these meanings will be discussed later as they are part of more advanced topics related to file manipulation.

$ ls -l /Volumes/MyExternalDrive
Total 0

File type and permissions from the ls -l command:

The first character of the first column, where the file type and permissions are specified, describes the type of file. It is one of the following characters:

The next three characters show the owner permissions (the things that the user listed as the owner can do):
2^nd character: will have value r if the owner can read the file, - otherwise.
3^rd character: will have value w if the file can be written by the owner, - otherwise.
4^th character: will have value - if the file is not executable by the owner. It will have value x, s or S if it is executable by the owner or if that user can search the directory.

The following three characters show the group permissions:
5^th character: will have value r if the users that are part of the group listed in the group name column can read the file, - otherwise.
6^th character: will have value w if the users that are part of the group listed in the group name column can write the file, - otherwise.
7^th character: will have value - if the file is not executable by the users that are part of the group listed in the group name column can write the file. It will have value x, s or S if it is executable by these users of if they can search the directory.

The rest of the characters represent other permissions or whether the file has extended attributes or security information. The permissions can be modified for any file, this will be explained in the chapter “File permissions”. Additionally, the total number of 512-byte blocks used by the files in the directory is displayed on a line by itself, immediately before the lines that contain the information of each file in the directory.

In the previous example, the first line of the result is, this means that the folder occupies less than one 512-block.

The second line is the following:

This means that Articles is a directory, modified the last on September 4 of the current year at 11:40am (if it was pm, the value would be 23:40 instead of 11:40). This folder is owned by the user myUser. This user can read, write and navigate through the folder. The other users can read and navigate the folder but cannot write on it.

ls -l

The information displayed in the 5^th column (file size) of the previous example is difficult to interpret by a human. In order to see this information in a human-readable format, it is only necessary to add an h to the -l flag.

When using the -lh flag, the size of the file will be followed by a letter which represents the units:

Using more than one flag

Most of the flags can be combined, except for the following group of flags which override each other (either partially or fully). If used together, only the last one specified will be the format used to display the information. Or if possible they will be applied in the order specified.

• -1, -C, -x, and -l
• -c and -u
• -B, -b, -w, and -q
• -H, -L and -P

Combine -lh, -o, and -r to print the information in long format, using human readable file sizes (-lh), omitting the group id (-o) and in reverse lexicographical order (-r):

$ ls -lhor /Volumes/MyExternalDrive
Total 0