Linux CLI 07: File and Directory Attributes

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# File and directory attributes

On who has access to what and a nice hack for dealing with duplicate content

.footnote[Marek Šuppa<br>Ondrej Jariabka<br>Adrián Matejov]

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# Why UNIX for Data Science?

- You will almost inevitably need to set up your own server environment

- Understanding how permissions work will be crucial to you being able to effectively use it

- Setting up links here and there will give you a bit of a superpower unheard of on other systems

---
# UNIX directory structure

- On the system level, the directory structure is implemented as a tree

[![:scale 100%](https://mermaid.ink/img/eyJjb2RlIjoiZ3JhcGggVEJcbiAgICByb290KFwiL1wiKVxuICAgIHJvb3QgLS0-IGJvb3QoXCJib290XCIpXG4gICAgcm9vdCAtLT4gZGV2KFwiZGV2XCIpXG4gICAgcm9vdCAtLT4gbWVkaWEoXCJtZWRpYVwiKVxuICAgIG1lZGlhIC0tPiBjZHJvbVtjZHJvbV1cbiAgICBtZWRpYSAtLT4gdXNiW1wiVVNCXCJdXG4gICAgcm9vdCAtLT4gcHJvYyhcInByb2NcIilcbiAgICByb290IC0tPiBldGMoXCJldGNcIilcbiAgICByb290IC0tPiB1c3IoXCJ1c3JcIilcbiAgICB1c3IgLS0-IHVzcmJpbihcImJpblwiKVxuICAgIHJvb3QgLS0-IGJpbihcImJpblwiKVxuICAgIHJvb3QgLS0-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)](https://mermaid-js.github.io/mermaid-live-editor/#/edit/eyJjb2RlIjoiZ3JhcGggVEJcbiAgICByb290KFwiL1wiKVxuICAgIHJvb3QgLS0-IGJvb3QoXCJib290XCIpXG4gICAgcm9vdCAtLT4gZGV2KFwiZGV2XCIpXG4gICAgcm9vdCAtLT4gbWVkaWEoXCJtZWRpYVwiKVxuICAgIG1lZGlhIC0tPiBjZHJvbVtjZHJvbV1cbiAgICBtZWRpYSAtLT4gdXNi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- There is one more level of structure underneath.

---
# `inode`s

.center[
  ![:scale 50%](./images/inodes.png)
]

- The basic data structure is called an `inode`, uniquely identified by an ID

- Each `inode` contains information about a specific file

- A directory is actually a _special file_: it contains a list of filenames and pointers to thier `inode`s

.center[ .font-small[Image from http://faculty.salina.k-state.edu/tim/unix_sg/advanced/links.html] ]

---
# File in UNIX systems

- name (and an optional extension, e.g. `.txt`)
- attributes (metadata)
  - owner (UID) and group (GID)
  - access rights for _owner_, _group_ and _others_
  - time of last attribute change (`ctime`), modification (`mtime`) and access
    to content (`atime`)
- content

.center[

![scale: 40%](images/13-ufs.png)

.font-small[Image from https://www.cs.rutgers.edu/~pxk/416/notes/13-fs-studies.html]
]

---

# File metadata

- Not shown by default in `ls` listing

- Part of the "long listing format" (i.e. via `ls -l`)

```bash
$ ls `-l` /labs/lab06_dist.sh
-rwxr-xr-x 1 mrshu mrshu 3402021 Oct 26 15:36 lab06_dist.sh
```

- To do the same on a directory, add `-d` flag (`ls` lists directory contents
  by default)

```bash
$ ls `-l` /labs
total 20264
-rwxr-xr-x 1 root root 3389123 Sep 21 13:21 lab01_dist.sh
-rwxr-xr-x 1 root root 3428779 Sep 28 14:09 lab02_dist.sh
-rwxr-xr-x 1 root root 3644753 Oct  5 14:23 lab03_dist.sh

$ ls `-l -d` /labs
drwxr-xr-x 2 root root 4096 Oct 26 17:01 /labs/
```

---
# File metadata: File Types

.center[![:scale 60%](./images/perms1.png)]

**File types**:
- `-`
  - "normal" file
- `d`
  - directory
- `c` / `b`
  - character / block device
- `p`
  - named pipe
- `l`
  - symbolic link
- `s`
  - socket

.center[.font-small[Image from https://test-www.ics.uci.edu/computing/linux/file-security.php]]

---
# File metadata: Permissions

.center[![:scale 60%](./images/perms1.png)]

.left-eq-column[
- Permissions are set and evaluated on three levels:
  1. owner
  2. group
  3. others
- Each level can have permission to
  - read (`r`)
  - write (`w`)
  - execute (`x`)
- Can also be represented as octal (base 8)
  numbers

]
.right-eq-column[

Conversion from `rwxr-xr--` to octal:

.center[![:scale 80%](images/permissions.png)]

.font-xsmall[Image from https://danielmiessler.com/study/unixlinux_permissions/]
]

???

- Permissions are evaluated in the same order as they are represented in the listing
  1. Am I the _owner_?
  2. If not, am I part of the _group_?
  3. If not, then I am part of _others_.

---
# File metadata: Permissions II

.center[![:scale 60%](./images/perms1.png)]

.left-eq-column[
Permissions can be changed with the `chmod` command:

`chmod {u,g,o,a}{+,-,=}{r,w,x} file`
  - `u`ser (owner), `g`roup, `o`ther and `a`ll
  - `+` adds, `-` removes and `=` sets
  - `r`ead, `w`rite and e`x`ecute permissions

```bash
$ chmod g+rx file.txt
$ chmod a-r file.txt
$ chmod o=rw file.txt
```

]

.right-eq-column[

It also works with numerical (octal) representation:

- `chmod 750 file`
  - set the file permissions of `file` to `rwxr-x---`

```bash
# (111 111 111) in binary
$ chmod 777 file.txt

# (111 100 101) in binary
$ chmod 745 file.txt
```
]

???

Maybe also `setUID`, `setGID` and `umask` (in the future)?

---
# File metadata: Directory Permissions

.center[![:scale 60%](./images/perms1.png)]

Permissions work a bit differently on directories:

- read (`r`)
  - allow listing of contents

- write (`w`)
  - create, modify and remove files in the directory

- execute (`x`)
  - ability to **go through** the directory
  - in other words, to include it in the path

---
# File metadata: Owner and Group

.center[![:scale 60%](./images/perms1.png)]

.left-eq-column[
- New files/folders are created with the owner's UID and their active/primary group's GID

- Only `root` can change the owner (via the `chown` command)

```bash
# Change the owner of file.txt to jane
$ chown jane file.txt

# Works on directories as well
$ chown jane ~/Downloads
```
]

.right-eq-column[
- Group can be changed by the current group's user's

- The user needs to be part of the new group

```bash
# Change the group of file.txt to root
$ chgrp root file.txt
```

- If we want to change both the owner as well as the group, we can use `chmod`

```bash
$ chown jane:users /home/jane
```

]

---
# File metadata: Timestamps

.center[![:scale 60%](./images/perms1.png)]

- `ls -l` by default shows the `mtime` -- last modified time

- The other timestamps can be viewed by the `stat` utility

```bash
$ stat /tmp
  File: /tmp
  Size: 3800            Blocks: 0          IO Block: 4096   `directory`
Device: 23h/35d Inode: 21596       Links: 129
Access: (1777/`drwxrwxrw`t)  Uid: (    0/    root)   Gid: (    0/    root)
Context: system_u:object_r:tmp_t:s0
Access: 2020-10-30 13:48:18.249475358 +0100
Modify: 2020-11-02 11:05:48.417238277 +0100
Change: 2020-11-02 11:05:48.417238277 +0100
 Birth: -
```

---
# File metadata: Timestamps II

.center[![:scale 60%](./images/perms1.png)]

.left-eq-column[
The timestamps can be changed with the `touch` utility
- `touch`
  - sets `atime` and `mtime` to the current time (by default)
  - creates an empty file if it does not exist
  - `-a`: set `atime` only
  - `-m`: set `mtime` only
  - `-t STAMP`: use `STAMP` instead of current date

`STAMP` is formatted as `[[CC]YY]MMDDhhmm[.ss]`
]

.right-eq-column[
```bash
$ touch newfile.txt

$ touch -a newfile.txt

# STAMP format: [[CC]YY]MMDDhhmm[.ss]
# Everything in [] is optional
#
# MM == 11
# DD == 02
# hh == 10
# mm == 10
$ touch -m -t 11021010 newfile.txt
```
]

---
class: inverse, middle, center

# Hardlinks and Symlinks

---
# Links as a concept

- Often times we'd like to have a file/directory with the same content
  available on various parts of the filesystem.

.center[![:scale 30%](images/link-diagram.jpg)]

- It makes little sense to copy the same contents multiple times over (what if
  it changes?)

- The solution is called **links**

.center[.font-small[Image from https://www.computerhope.com/unix/uln.htm]]

---
# Directory as a special file

.center[
  ![:scale 50%](./images/inodes.png)
]

- Notice how the "directory contents" file has entries for both itself (`.`) and its parent directory (`..`)

- Since it can contain arbitrary filenames which point to arbitrary `inode` IDs, this can be used for simple implementation of links

---
# Hard link

.left-eq-column[

- Different filenames (or even paths) link to the same `inode` ID

- The attributes as well as contents stay exactly the same

- Only possible within a single data device (disk)
]
.right-eq-column[

- `inode` ID of a file can be viewed with `ls -i`

- `inode` counts the number of links that point to it

- When nothing does, the `inode` gets "physically" removed as well

]
.clear-both[
```bash
$ echo "This is a file." > file1.txt
$ ls -l -i file1.txt
136158 -rw-rw-r-- `1` mrshu mrshu 16 Nov  2 11:20 file1.txt

# Create a hardlink called file2.txt from file1.txt
$ ln file1.txt file2.txt

# The hardlink count has increased
$ ls -l -i file2.txt 
136158 -rw-rw-r-- `2` mrshu mrshu 16 Nov  2 11:20 file2.txt

$ cat file1.txt
This is a file.
$ cat file2.txt
This is a file.
```
]

---

# Symbolic link (symlink)

- A "standard shortcut"
  - A new "text" file gets created; its contents point to the path where the source file is located
  - The path is evaluated from the position of this new file in the filesystem

- When the source file gets removed, the symbolic link continues to live

- It is not counted among the hardlinks (e.g. in `ls -l` output)

- Can be created across the whole filesystem (not just one data device)

.left-eq-column[

.center[
  ![:scale 60%](images/link-diagram.jpg)
  .center[.font-small[Hardlink]]
]

]
.right-eq-column[
.center[
  ![:scale 60%](images/symlink-diagram.jpg)
  .center[.font-small[Symlink]]
]
]

.center[.font-small[Images from https://www.computerhope.com/unix/uln.htm]]

---

# Symbolic link (symlink)

```bash
$ echo "This is a file." > file1.txt
$ ls -l file1.txt 
136158 -rw-rw-r-- `1` mrshu mrshu 16 Nov  2 11:44 file1.txt

# Create a symlink called file2.txt pointing to file1.txt
$ ln -s file1.txt file2.txt

# The hardlink count has not increased
$ ls -l -i file2.txt 
136159 lrwxrwxrwx `1` mrshu mrshu 9 Nov  2 11:45 `file2.txt` -> file1.txt
$ ls -l -i file1.txt 
136158 -rw-rw-r-- `1` mrshu mrshu 16 Nov  2 11:44 file1.txt

$ cat file1.txt
This is a file.
$ cat file2.txt
This is a file.

# Link to the parent directory
$ mkdir dir
$ cd dir
$ ln -s ../file1.txt file3.txt

$ ls -l -i file3.txt 
393489 lrwxrwxrwx 1 mrshu mrshu 12 Nov  2 11:48 file3.txt -> `../file1.txt`

```

---
class: inverse, middle, center

# Useful commands

For checking and changing file encoding

---
# `file`

A useful command for checking the file type (e.g. is it an image, video or a text file).

- `file filename`
  - `-b` simplified output
  - `-i` output as a mime type

```bash
$ file image.jpg
image.jpg: JPEG image data, JFIF standard 1.01, resolution (DPI), density 72x72,
segment length 16, progressive, precision 8, 317x191, components 3

$ file -bi image.jpg
image/jpeg; charset=binary

$ file index.html
index.html: HTML document, UTF-8 Unicode text, with very long lines

$ file -i index.html
index.html: text/html; charset=utf-8
```

---
# `iconv`

Convert text form one character encoding to another

- `iconv -f [encoding] -t [encoding] -o [outputfile] [inputfile]`
  - `-f [encoding]`: convert encoding from this charset
  - `-t [encoding]`: convert encoding to this charset
  - `-o [outputfile]`: save output to this file (stdout by default)

```bash
$ file -bi file_iso.txt 
text/plain; charset=iso-8859-1

$ iconv -f iso-8859-1 -t utf-8 -o file_utf8.txt file_iso.txt

$ file -bi file_utf8.txt
text/plain; charset=utf-8
```