├── .gitignore ├── CNAME ├── collaborators.md ├── guide.html ├── guide ├── 01-install.html ├── 02-link.html ├── 03-modify.html ├── 04-live.html ├── 05-website.html ├── 06-dat-git-partial.html ├── 06-sparse.html ├── 100-beaker.html ├── 101-science-data.html ├── 102-desktop-application.html ├── 103-genomic-data.html └── index.html ├── img ├── Beaker-fork.png ├── Beaker-more.png ├── Beaker-screenshot-2.png ├── Dat-git-example-files.png └── beaker-screenshot-1.png ├── index.html ├── index.js ├── markdown ├── 01-install.md ├── 02-link.md ├── 03-modify.md ├── 04-live.md ├── 05-website.md ├── 06-dat-git-partial.md ├── 100-beaker.md ├── 101-science-data.md ├── 102-desktop-application.md └── 103-genomic-data.md ├── package.json ├── readme.md ├── static ├── css │ ├── bootstrap.min.css │ ├── normalize.min.css │ ├── railscasts.css │ ├── reset.min.css │ └── style.css └── img │ ├── cat.png │ ├── dat-directory.png │ ├── dat-hex-small.png │ ├── datcat.jpeg │ ├── octocat-green.png │ └── wildcat.jpg ├── terminal.html ├── terminal.js └── wip ├── 01-using-docker.md ├── 05-dat-json-config.md └── beta-use-cases.md /.gitignore: -------------------------------------------------------------------------------- 1 | .dat 2 | dat.json 3 | people.json 4 | .DS_Store 5 | node_modules 6 | bundle.js 7 | terminal-bundle.js -------------------------------------------------------------------------------- /CNAME: -------------------------------------------------------------------------------- 1 | try-dat.com 2 | -------------------------------------------------------------------------------- /collaborators.md: -------------------------------------------------------------------------------- 1 | ## Collaborators 2 | 3 | get-dat is only possible due to the excellent work of the following collaborators: 4 | 5 | 6 | 7 | 8 | 9 |

maxogden	GitHub/maxogden
mafintosh	GitHub/mafintosh
karissa	GitHub/karissa
sethvincent	GitHub/sethvincent

10 | -------------------------------------------------------------------------------- /guide.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | {{> header }} 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | {{#if index}} 13 |

14 |

15 |

Welcome!

16 |

This is try-dat, a tutorial that teaches you how to work with datasets using dat. In this tutorial you will play around with data versioning and syncing workflows, and play with some awesome tools to publish or share data over the peer-to-peer web.

17 |

18 |

19 |

{{ name }}

24 |

25 | We used to host an interactive version of Try Dat that included a web based terminal, but unfortunately someone decided to take advantage of our servers to mine Bitcoin, stealing the limited resources of our nonprofit for their private gain :( 26 |

27 |

28 | What you now find here is a tutorial you can do with a friend (recommended) using two computers, or by yourself (still works OK but not quite as fun as with a friend) using one computer. 29 |

30 |

Ok, ready to dive in? Let's go! »

31 |

32 | {{/if}} 33 | 34 | {{#if content}} 35 |

36 |

table of contents

37 | {{{ content }}} 38 |

39 | {{#if next}} 40 | OK, next! » 41 | {{#if previous}} 42 | « back 43 | {{/if}} 44 | {{/if}} 45 |

46 | {{/if}} 47 |

48 |

49 | 50 | 51 | 52 | -------------------------------------------------------------------------------- /guide/01-install.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Installation

16 |

First you'll need to install the dat command line tool if you haven't already. There are two ways to do this, using npm or downloading a binary. If you don't have a preference we recommend using npm which you can do by downloading the Node LTS installer from the Node.js website:

17 |

Download node and npm here

20 |

If you run into problems, you can view more detailed installation instructions here.

21 |

You'll also need a Terminal application on your local computer. If you're using Windows, you should use the Git Shell app as your terminal. It is installed with GitHub Desktop. In Mac and Linux you can use the app Terminal, which is already on your computer.

22 |

If you've never used the command line before, check out Command Line Bootcamp to get comfortable navigating your computer via the command line.

23 |

Once you have downloaded npm, install dat on your local machine. Type the following in your local terminal:

24 |

npm install -g dat
25 |

This means that dat is now installed on your system:

26 |

$ dat
27 | 
28 | Usage: dat <cmd> [<dir>] [options]
29 | 
30 | Sharing Files:
31 |    dat share                   create dat, import files, share to network
32 |    dat create                  create empty dat and dat.json
33 |    dat sync                    import files to existing dat & sync with network
34 | 
35 | Downloading Files:
36 |    dat clone <link> [<dir>]    download a dat via link to <dir>
37 |    dat pull                    update dat & exit
38 |    dat sync                    live sync files with the network
39 | 
40 | Info:
41 |    dat log                     log history for a dat
42 |    dat status                  get key & info about a local dat
43 | 
44 | Dat public registries:
45 |    dat <cmd> [<registry>]      All commands take <registry> option
46 |    dat register                register new account
47 |    dat login                   login to your account
48 |    dat publish                 publish a dat
49 |    dat whoami                  print active login information
50 |    dat logout                  logout from active login
51 | 
52 | Stateless/Shortcut Commands:
53 |    dat <link> [<dir>]          clone or sync link to <dir>
54 |    dat <dir>                   create and sync dat in directory
55 | 
56 | Troubleshooting & Help:
57 |    dat doctor                  run the dat network doctor
58 |    dat help                    print this usage guide
59 |    dat <command> --help, -h    print help for a specific command
60 |    dat --version, -v           print the dat version
61 | 
62 | 
63 | Have fun using Dat! Learn more at docs.datproject.org
64 |

Once you have this installed, you're good to go! Let's move on to the good stuff.

65 | 66 |

67 | OK, next! » 68 |

69 |

70 |

71 | 72 | 73 | 74 | -------------------------------------------------------------------------------- /guide/02-link.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 | 16 |

We are going to start by using dat to share a folder. First you have to pick a folder with some files in it on your machine. If you can't find one, try making one on your Desktop called 'dat-test' and put a couple screenshots or other images in it. The folder can be any size, but something at least a couple megabytes in total size will be more fun to test out.

17 |

`dat share`

18 |

First, let's create a link to share these files. If you're new to the command line, check out Command Line Bootcamp before moving on.

19 |

Type the following in your terminal (replacing the cd path with the actual path your test folder):

20 |

$ cd ~/Desktop/dat-test
21 | $ dat share
22 |

This will create a link, that looks like dat://.... Your output should look something like this:

23 |

$ dat share
24 | Created new dat
25 | dat://5a4575c632d1a573...
26 |

Behind the scenes dat created a new hidden folder called .dat in your test folder. The appearance of the .dat folder means that everything in this directory can now be versioned with Dat.

27 |

As long as the dat share process stays open and running the data will be available via the global Dat decentralized network to anyone who has that link. The link is secret and unguessable. Only people who you share the link with will be able to access your dat.

28 |

Downloading

29 |

First, copy the dat link from the source terminal. Windows users beware - please right-click to copy, as cntrl-C will quit dat and dat needs to keep running.

30 |

If you are doing this tutorial using a single computer, open up a second terminal window, we will refer to this second one as the destination terminal. The first one is the source terminal.

31 |

If you are doing this tutorial with a second computer, then use the second computer as the destination. Find a way to send them the dat link (email, text message).

32 |

On the destination terminal: Move to a directory where you'd like to add these files. To download the files from the source, type dat clone followed by the link dat://, and a folder name like try-dat.

33 |

The full command should look like this:

34 |

dat clone dat://replace-with-your-dat-link-here try-dat
35 |

The files will be downloaded to the destination, to the current working directory, into a folder called try-dat. Take a minute now to check that the files on your destination match the files from the source.

36 |

Lastly, on the source, type control-C to stop running dat. You should now be back to the command prompt on both terminals.

37 | 38 |

39 | OK, next! » 40 | « back 41 |

42 |

43 |

44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /guide/03-modify.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 | 16 |

Now you have a copy of the files on your destination a folder called try-dat! But what happens if the contents of the files change? Let's find out.

17 |

On the source create a new file called welcome.txt and open it in your favorite text editor app (such as TextEdit or Sublime Text). Make some changes to the text in the file. Once you've edited it, save the file. The file on the source will no longer match the one on the destination. To rectify this and sync the new changes to the destination copy, run dat share again on the source.

18 |

Type the following in the source terminal:

19 |

$ dat share
20 |

This will create a link, that looks like dat://.... Your output in the source terminal will look something like this:

21 |

$ dat share
22 | Created new dat
23 | dat://5a4575c632d1a573...
24 |

Now lets switch to the destination terminal. cd into the try-dat folder, and run dat sync.

25 |

Type the following in the destination terminal:

26 |

$ dat sync
27 |

Your output should look like this:

28 |

$ dat sync
29 | dat v13.8.1
30 | Downloading dat: 2 files (2.7 MB)
31 | 
32 | 1 connection | Download 0 B/s Upload 0 B/s
33 | 
34 | dat synced, waiting for updates.
35 | [==========================================] 100.00%
36 |

Check the file on both sides - they should match.

37 | 38 |

39 | OK, next! » 40 | « back 41 |

42 |

43 |

44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /guide/04-live.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Live syncing data

16 |

Currently, you're running Dat both on the source and at your destination. Don't quit Dat! Leave it running on both terminals.

17 |

Notice that your source terminal window says:

18 |

dat synced, waiting for updates.
19 |

What happens if you make changes to the source file while your destination is watching? On the source side, edit the welcome.txt rapidly, saving after each edit in your text editor program.

20 |

Watch what happens in your destionation terminal window as you save.

21 |

Since this is a tiny text time, the updates will download extremely fast. Your source terminal window will look something like this:

22 |

1 connection | Download 445 KB/s Upload 0 B/s
23 | 
24 | Downloading updates...
25 | [====================================------] 86.05%
26 |

Meanwhile, Dat running in the destination machine is watching for file updates:

27 |

Watching for file updates                                                          
28 | ADD: welcome.txt (329 B)                                                           
29 | ADD: welcome.txt (328 B)                                                           
30 | ADD: welcome.txt (323 B)                                                           
31 | ADD: welcome.txt (0 B)
32 |

The file will live sync to your machine as you save. Isn't that cool?

33 | 34 |

35 | OK, next! » 36 | « back 37 |

38 |

39 |

40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /guide/05-website.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Hosting a website

16 |

We've covered sharing, syncing, and live syncing of data. But what about sharing via the web? We can create a Dat link that can be viewed in any browser. Dat has an http server that can be turned on by adding --http$PORT_XX, where XX is specific to the server port.

17 |

To share your data via the web, create a file called index.html using the command touch. 18 | Type the following into the virtual terminal:

19 |

touch index.html

20 |

You will see a new file, index.html, has been added to the directory on the virtual server.

21 |

Let's make it fun! Use the test editor in the browser to add to the new index.html. Edit it and add some stuff in your html. Here's a silly template to get you started.

22 |

<!DOCTYPE html>
23 | <html>
24 | <head>
25 |   <meta charset="utf-8">
26 |   <title>Hello Friends!</title>
27 | </head>
28 | <body>
29 | <h1>Welcome to my data website!</h1>
30 | <p>More things about my data. And cat!</p>
31 |   <img src="cat.png" alt="cat" height="300" width="450"> 
32 | <br>
33 |   <img id="rickroll" src="https://media.giphy.com/media/13tTN4ccM3R6us/giphy.gif"/>  
34 | </body>
35 | </html>
36 |

To share this, type the following in the source terminal:

37 |

dat share --http=8080

38 |

Check out your new website at http://localhost:8080!

39 |

When you modify file, the site will update when you refresh the browser window. Pretty cool, huh?

40 | 41 |

42 | OK, next! » 43 | « back 44 |

45 |

46 |

47 | 48 | 49 | 50 | -------------------------------------------------------------------------------- /guide/06-dat-git-partial.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Downloading a partial dataset from git

16 |

Here's an example of hosting code on Github that includes a link to a Dat dataset. This Github repo contains a dat.json file, which contains the Dat link (dat://...) for the dataset as well as other metadata about these data.

17 |

The author has included a .datdownload file which specifies which files users will download by default. Without this, all files would be downloaded upon dat cloning this repository. You can imagine a scenario where a larger dataset is availble, but only segments of it are required to reproduce an analysis. Or a dataset that won't fit in git, but fits in dat. Because this author has a dat.json file in their git repository, you don't need to work with their Dat link. In this exercise, you will clone the repository with git and then access the data with dat.

18 |

To clone the repository to your local machine using git, type the following in your local terminal:

19 |

git clone https://github.com/joehand/dat-git-example.git
20 |

Now you have a copy of dat-git-example that includes text and code files, but none of the data files. Check the index.html to see that the pictures are missing by typing the following in your local terminal:

21 |

open index.html
22 |

To get the data, run dat clone --empty to fetch the .dat metadata (but none of the files). Type the following in your source terminal:

23 |

dat clone ./dat-git-example --empty
24 |

Then sync to get the files, specified by the .datdownload, type the following in your source terminal:

25 |

dat sync ./dat-git-example
26 |

You should now have downloaded both the code (index.html) and the data files that were specificed by the .datdownload file.

27 | 28 |

29 | OK, next! » 30 | « back 31 |

32 |

33 |

34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /guide/06-sparse.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Downloading a dataset from GitHub

16 |

Here's an example of a dataset hosted on GitHub, where the author has included a dat.json file. This file contains the Dat link for the dataset as well as other metadata about these data.

17 |

git clone https://github.com/joehand/dat-git-example.git
18 | dat clone ./dat-git-example --empty
19 | dat sync ./dat-git-example
20 |

21 |

22 | OK, next! » 23 | « back 24 |

25 |

26 |

27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /guide/100-beaker.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Extra Credit: Host your site in Beaker

16 |

Beaker is a browser built on Dat. It's fun to play with, it enables sercure sharing of data through the browser, and Beaker makes it super easy to host a website. We :heart: Beaker Browser!

17 |

Install beaker on your machine

18 |

To see the data you've been working with, simply type the Dat-link (generated by the dat share command in the virtual terminal) into the Beaker browser address bar:

19 |

dat://83726...whatever-your-link-is-goes-here...a594/

20 |

If you haven't added an index.html, Beaker should show you something like this:

21 |

Beaker-image

22 |

If you've added an index.htl file, it will render the html and look more like this:

23 |

Beaker-image

24 |

You can send the dat link to a friend and they can fork and edit their version of the site. They can also download the files.

25 |

Beaker-image

26 |

Sites on Beaker can be saved to a library to view offline.

27 |

Beaker-image

28 |

Play around with Beaker! And follow them @beakerbrowser for updates.

29 | 30 |

31 | OK, next! » 32 | « back 33 |

34 |

35 |

36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /guide/101-science-data.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Extra Credit: Distributing Scientific Data

16 |

Now that you've used Dat to share example data, give it a spin using some of your own research data, or data that you've used in the past.

17 |

Here are some example pages with data on them to give you ideas, but we encourage you to give Dat a spin with some data that you already have downloaded or published before.

18 |

Recent Earthquake CSVs: https://earthquake.usgs.gov/earthquakes/feed/v1.0/csv.php
Recently published DOIs (JSON): https://api.crossref.org/works?sort=updated&order=desc&rows=10&select=DOI,title,link,deposited

22 |

Once you have data files in a folder on your machine, simply run dat create in the folder to start tracking the data with Dat.

23 |

To complete this lesson, run dat share and share the link with another workshop attendee and see if they can access your data.

24 | 25 |

26 | OK, next! » 27 | « back 28 |

29 |

30 |

31 | 32 | 33 | 34 | -------------------------------------------------------------------------------- /guide/102-desktop-application.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Extra Credit: Desktop Application

16 |

If you'd like to try a different workflow for managing Dat repositories, we have developed a Desktop application called Dat Desktop. You can install it from https://datproject.org/install for Mac or Linux (Windows coming soon).

17 |

18 |

The Desktop application is intended to make Dat more approachable for users that prefer not to use the command line for everything. Give it a try and let us know what you think!

19 | 20 |

21 | OK, next! » 22 | « back 23 |

24 |

25 |

26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /guide/103-genomic-data.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 | 13 |

14 |

table of contents

15 |

Extra Credit: Import genomic data into Dat with the JavaScript API

16 |

We are going to download the flu virus genome from NCBI with Bionode and import it into Dat!

17 |

Create a new folder named infuenza, enter that folder with your local terminal (cd) and install bionode-ncbi.

18 |

npm install bionode-ncbi
19 |

20 |

Create a script.js file with the following content:

21 |

var Dat = require('dat')
22 | var Bionode = require('bionode-ncbi')
23 | 
24 | Dat('.', function (err, dat) {
25 |   if (err) throw err
26 |   var download = Bionode.download('assembly', 'ViralMultiSegProj15622')
27 |   download.on('data', console.log)
28 |   download.on('end', function() {
29 |     dat.importFiles()
30 |     dat.joinNetwork()
31 |     console.log('My Dat link is: dat://', dat.key.toString('hex'))
32 |   })
33 | })
34 |

35 |

Run it:

36 |

node script.js
37 |

38 |

Clone this Dat archive into another folder (change it to your Dat link):

39 |

❯ dat clone d3457d9e11c9548faa704a799e6553d1dfb672264cdd0374a62564213c3c3474 influenzaCopy
40 |

41 |

Check that you got a copy of the influenza genome from Dat:

42 |

❯ gunzip -c influenzaCopy/266481/GCF_000865085.1_ViralMultiSegProj15622_genomic.fna.gz | head -n 5
43 |

44 |

Should give you:

45 |

>NC_007373.1 Influenza A virus (A/New York/392/2004(H3N2)) segment 1, complete sequence
46 | AGCAAAAGCAGGTCAATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAACCTGATGTCGCAGTCTCGCACTCGCGA
47 | GATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCAC
48 | TTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAAT
49 | GAACAAGGACAAACTCTATGGAGTAAAATGAGTGATGCTGGATCAGATCGAGTGATGGTATCACCTTTGGCTGTAACATG
50 |

51 | 52 |

53 |

54 |

55 |

56 | 57 | 58 | 59 | -------------------------------------------------------------------------------- /guide/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Submarine 5 | 6 | 7 | 8 | 9 | 10 | 11 |

12 |

13 |

14 |

Welcome!

15 |

16 |

17 |

18 |

30 |

31 | We used to host an interactive version of Try Dat that included a web based terminal, but unfortunately someone decided to take advantage of our servers to mine Bitcoin, stealing the limited resources of our nonprofit for their private gain :( 32 |

33 |

34 | What you now find here is a tutorial you can do with a friend (recommended) using two computers, or by yourself (still works OK but not quite as fun as with a friend) using one computer. 35 |

36 |

Ok, ready to dive in? Let's go! »

37 |

38 | 39 | 40 |

41 | 42 | 43 | 44 | -------------------------------------------------------------------------------- /img/Beaker-fork.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/img/Beaker-fork.png -------------------------------------------------------------------------------- /img/Beaker-more.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/img/Beaker-more.png -------------------------------------------------------------------------------- /img/Beaker-screenshot-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/img/Beaker-screenshot-2.png -------------------------------------------------------------------------------- /img/Dat-git-example-files.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/img/Dat-git-example-files.png -------------------------------------------------------------------------------- /img/beaker-screenshot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/img/beaker-screenshot-1.png -------------------------------------------------------------------------------- /index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | dat adventure 6 | 7 | 8 | 9 | 10 | 14 |

15 |

16 |

17 |

18 |

19 |

20 |

21 | toggle editor 22 |

23 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /index.js: -------------------------------------------------------------------------------- 1 | var url = require('url') 2 | var querystring = require('querystring') 3 | var adventureTime = require('adventure-time') 4 | 5 | var production = !location.port // a bit hackish but assume production if no custom port 6 | var qs = url.parse(window.location.href, true).query 7 | 8 | if (!qs.id) { 9 | qs.id = Math.random().toString(36).slice(2) 10 | window.location.href = window.location.href.split('?')[0] + '?' + querystring.stringify(qs) 11 | } 12 | 13 | var opts = { 14 | guide: 'guide/', 15 | console: 'terminal.html', 16 | server: qs.server || (production ? 'docker.try-dat.com' : 'dev.try-dat.com:8080'), 17 | id: qs.id, 18 | secure: production 19 | } 20 | 21 | 22 | if (production) qs.secure = 'true' 23 | if (!qs.server) qs.server = opts.server 24 | 25 | // for debugging production w/ local frontend 26 | // qs.server = 'docker.try-dat.com' 27 | // qs.secure = 'true' 28 | 29 | opts.console += '?'+querystring.stringify(qs) 30 | 31 | var adventure = adventureTime(opts) 32 | -------------------------------------------------------------------------------- /markdown/01-install.md: -------------------------------------------------------------------------------- 1 | # Installation 2 | 3 | First you'll need to install the `dat` command line tool if you haven't already. There are two ways to do this, using `npm` or downloading a binary. If you don't have a preference we recommend using `npm` which you can do by downloading the Node LTS installer from the Node.js website: 4 | 5 | - [Download node and npm here](https://nodejs.org/en/) 6 | 7 | If you run into problems, you can view more detailed installation instructions [here](https://github.com/datproject/dat/blob/master/README.md#installing-the--dat-command-line-tool). 8 | 9 | You'll also need a Terminal application on your local computer. If you're using Windows, you should use the **Git Shell** app as your terminal. It is installed with [GitHub Desktop](http://desktop.github.com). In Mac and Linux you can use the app **Terminal**, which is already on your computer. 10 | 11 | If you've never used the command line before, check out [Command Line Bootcamp](http://rik.smith-unna.com/command_line_bootcamp/?id=bfv5p9l1w5g) to get comfortable navigating your computer via the command line. 12 | 13 | Once you have downloaded npm, install dat on your local machine. Type the following in your **local terminal**: 14 | 15 | ``` 16 | npm install -g dat 17 | ``` 18 | 19 | This means that dat is now installed on your system: 20 | 21 | ``` 22 | $ dat 23 | 24 | Usage: dat [] [options] 25 | 26 | Sharing Files: 27 | dat share create dat, import files, share to network 28 | dat create create empty dat and dat.json 29 | dat sync import files to existing dat & sync with network 30 | 31 | Downloading Files: 32 | dat clone [] download a dat via link to 33 | dat pull update dat & exit 34 | dat sync live sync files with the network 35 | 36 | Info: 37 | dat log log history for a dat 38 | dat status get key & info about a local dat 39 | 40 | Dat public registries: 41 | dat [] All commands take option 42 | dat register register new account 43 | dat login login to your account 44 | dat publish publish a dat 45 | dat whoami print active login information 46 | dat logout logout from active login 47 | 48 | Stateless/Shortcut Commands: 49 | dat [] clone or sync link to 50 | dat create and sync dat in directory 51 | 52 | Troubleshooting & Help: 53 | dat doctor run the dat network doctor 54 | dat help print this usage guide 55 | dat --help, -h print help for a specific command 56 | dat --version, -v print the dat version 57 | 58 | 59 | Have fun using Dat! Learn more at docs.datproject.org 60 | ``` 61 | 62 | Once you have this installed, you're good to go! Let's move on to the good stuff. 63 | -------------------------------------------------------------------------------- /markdown/02-link.md: -------------------------------------------------------------------------------- 1 | # Sharing data 2 | 3 | We are going to start by using `dat` to share a folder. First you have to pick a folder with some files in it on your machine. If you can't find one, try making one on your Desktop called 'dat-test' and put a couple screenshots or other images in it. The folder can be any size, but something at least a couple megabytes in total size will be more fun to test out. 4 | 5 | ## `dat share` 6 | 7 | First, let's create a link to share these files. If you're new to the command line, check out [Command Line Bootcamp](http://rik.smith-unna.com/command_line_bootcamp/?id=ocd6pv8xa0i) before moving on. 8 | 9 | Type the following in your terminal (replacing the `cd` path with the actual path your test folder): 10 | 11 | ``` 12 | $ cd ~/Desktop/dat-test 13 | $ dat share 14 | ``` 15 | 16 | This will create a link, that looks like `dat://...`. Your output should look something like this: 17 | 18 | ``` 19 | $ dat share 20 | Created new dat 21 | dat://5a4575c632d1a573... 22 | ``` 23 | 24 | Behind the scenes dat created a new hidden folder called `.dat` in your test folder. The appearance of the `.dat` folder means that everything in this directory can now be versioned with Dat. 25 | 26 | As long as the `dat share` process stays open and running the data will be available via the global Dat decentralized network to anyone who has that link. The link is secret and unguessable. Only people who you share the link with will be able to access your dat. 27 | 28 | ## Downloading 29 | 30 | First, copy the dat link from the source terminal. Windows users beware - please right-click to copy, as `cntrl-C` will quit dat and dat needs to keep running. 31 | 32 | If you are doing this tutorial using a single computer, open up a second terminal window, we will refer to this second one as the **destination** terminal. The first one is the **source** terminal. 33 | 34 | If you are doing this tutorial with a second computer, then use the second computer as the **destination**. Find a way to send them the dat link (email, text message). 35 | 36 | On the **destination** terminal: Move to a directory where you'd like to add these files. To download the files from the source, type `dat clone` followed by the link `dat://`, and a folder name like `try-dat`. 37 | 38 | The full command should look like this: 39 | 40 | ``` 41 | dat clone dat://replace-with-your-dat-link-here try-dat 42 | ``` 43 | 44 | The files will be downloaded to the destination, to the current working directory, into a folder called `try-dat`. Take a minute now to check that the files on your destination match the files from the source. 45 | 46 | **Lastly**, on the source, type `control-C` to stop running dat. You should now be back to the command prompt on both terminals. 47 | -------------------------------------------------------------------------------- /markdown/03-modify.md: -------------------------------------------------------------------------------- 1 | # Editing & sharing data 2 | 3 | Now you have a copy of the files on your destination a folder called `try-dat`! But what happens if the contents of the files change? Let's find out. 4 | 5 | On the **source** create a new file called `welcome.txt` and open it in your favorite text editor app (such as TextEdit or Sublime Text). Make some changes to the text in the file. Once you've edited it, save the file. The file on the source will no longer match the one on the destination. To rectify this and sync the new changes to the destination copy, run `dat share` again on the source. 6 | 7 | Type the following in the **source** terminal: 8 | 9 | ``` 10 | $ dat share 11 | ``` 12 | 13 | This will create a link, that looks like `dat://...`. Your output in the **source** terminal will look something like this: 14 | 15 | ``` 16 | $ dat share 17 | Created new dat 18 | dat://5a4575c632d1a573... 19 | ``` 20 | 21 | Now lets switch to the **destination** terminal. `cd` into the `try-dat` folder, and run `dat sync`. 22 | 23 | Type the following in the **destination terminal**: 24 | 25 | ``` 26 | $ dat sync 27 | ``` 28 | 29 | Your output should look like this: 30 | 31 | ``` 32 | $ dat sync 33 | dat v13.8.1 34 | Downloading dat: 2 files (2.7 MB) 35 | 36 | 1 connection | Download 0 B/s Upload 0 B/s 37 | 38 | dat synced, waiting for updates. 39 | [==========================================] 100.00% 40 | ``` 41 | 42 | Check the file on both sides - they should match. 43 | -------------------------------------------------------------------------------- /markdown/04-live.md: -------------------------------------------------------------------------------- 1 | # Live syncing data 2 | 3 | Currently, you're running Dat both on the source and at your destination. Don't quit Dat! Leave it running on both terminals. 4 | 5 | Notice that your **source** terminal window says: 6 | 7 | ``` 8 | dat synced, waiting for updates. 9 | ``` 10 | 11 | What happens if you make changes to the source file while your destination is watching? On the **source** side, edit the `welcome.txt` rapidly, saving after each edit in your text editor program. 12 | 13 | Watch what happens in your **destionation terminal** window as you save. 14 | 15 | Since this is a tiny text time, the updates will download extremely fast. Your **source terminal** window will look something like this: 16 | 17 | ``` 18 | 1 connection | Download 445 KB/s Upload 0 B/s 19 | 20 | Downloading updates... 21 | [====================================------] 86.05% 22 | 23 | ``` 24 | 25 | Meanwhile, Dat running in the **destination machine** is watching for file updates: 26 | 27 | ``` 28 | Watching for file updates 29 | ADD: welcome.txt (329 B) 30 | ADD: welcome.txt (328 B) 31 | ADD: welcome.txt (323 B) 32 | ADD: welcome.txt (0 B) 33 | ``` 34 | 35 | The file will live sync to your machine as you save. Isn't that cool? 36 | -------------------------------------------------------------------------------- /markdown/05-website.md: -------------------------------------------------------------------------------- 1 | # Hosting a website 2 | 3 | We've covered sharing, syncing, and live syncing of data. But what about sharing via the web? We can create a Dat link that can be viewed in any browser. Dat has an http server that can be turned on by adding `--http$PORT_XX`, where XX is specific to the server port. 4 | 5 | To share your data via the web, create a file called `index.html` using the command `touch`. 6 | Type the following into the **virtual terminal**: 7 | 8 | `touch index.html` 9 | 10 | You will see a new file, `index.html`, has been added to the directory on the virtual server. 11 | 12 | Let's make it fun! Use the test editor in the browser to add to the new `index.html`. Edit it and add some stuff in your html. Here's a silly template to get you started. 13 | ``` 14 | 15 | 16 | 17 | 18 | Hello Friends! 19 | 20 | 21 |

Welcome to my data website!

22 |

More things about my data. And cat!

23 |

24 |
25 |

26 | 27 | 28 | ``` 29 | 30 | To share this, type the following in the **source terminal**: 31 | 32 | `dat share --http=8080` 33 | 34 | Check out your new website at http://localhost:8080! 35 | 36 | When you modify file, the site will update when you refresh the browser window. Pretty cool, huh? 37 | -------------------------------------------------------------------------------- /markdown/06-dat-git-partial.md: -------------------------------------------------------------------------------- 1 | # Downloading a partial dataset from git 2 | 3 | Here's an example of hosting code on Github that includes a link to a Dat dataset. This Github repo contains a `dat.json` file, which contains the Dat link (dat://...) for the dataset as well as other metadata about these data. 4 | 5 | The author has included a `.datdownload` file which specifies which files users will download by default. Without this, all files would be downloaded upon dat cloning this repository. You can imagine a scenario where a larger dataset is availble, but only segments of it are required to reproduce an analysis. Or a dataset that won't fit in git, but fits in dat. Because this author has a `dat.json` file in their git repository, you don't need to work with their Dat link. In this exercise, you will clone the repository with git and then access the data with dat. 6 | 7 | To clone the repository to your local machine using git, type the following in your **local terminal**: 8 | 9 | ``` 10 | git clone https://github.com/joehand/dat-git-example.git 11 | ``` 12 | 13 | Now you have a copy of `dat-git-example` that includes text and code files, but none of the data files. Check the `index.html` to see that the pictures are missing by typing the following in your **local terminal**: 14 | 15 | ``` 16 | open index.html 17 | ``` 18 | 19 | To get the data, run `dat clone --empty` to fetch the `.dat` metadata (but none of the files). Type the following in your **source terminal**: 20 | 21 | ``` 22 | dat clone ./dat-git-example --empty 23 | ``` 24 | 25 | Then sync to get the files, specified by the `.datdownload`, type the following in your **source terminal**: 26 | 27 | ``` 28 | dat sync ./dat-git-example 29 | ``` 30 | 31 | You should now have downloaded both the code (`index.html`) and the data files that were specificed by the `.datdownload` file. 32 | -------------------------------------------------------------------------------- /markdown/100-beaker.md: -------------------------------------------------------------------------------- 1 | # Extra Credit: Host your site in Beaker 2 | 3 | [Beaker](https://beakerbrowser.com/) is a browser built on Dat. It's fun to play with, it enables sercure sharing of data through the browser, and Beaker makes it super easy to host a website. We :heart: Beaker Browser! 4 | 5 | [Install beaker on your machine](https://beakerbrowser.com/docs/install/) 6 | 7 | To see the data you've been working with, simply type the Dat-link (generated by the `dat share` command in the virtual terminal) into the **Beaker browser address bar**: 8 | 9 | `dat://83726...whatever-your-link-is-goes-here...a594/` 10 | 11 | If you haven't added an index.html, Beaker should show you something like this: 12 | 13 | ![Beaker-image](/img/beaker-screenshot-1.png) 14 | 15 | If you've added an index.htl file, it will render the html and look more like this: 16 | 17 | ![Beaker-image](/img/Beaker-screenshot-2.png) 18 | 19 | You can send the dat link to a friend and they can fork and edit their version of the site. They can also download the files. 20 | 21 | ![Beaker-image](/img/Beaker-fork.png) 22 | 23 | Sites on Beaker can be saved to a library to view offline. 24 | 25 | ![Beaker-image](/img/Beaker-more.png) 26 | 27 | Play around with Beaker! And follow them [@beakerbrowser](https://twitter.com/beakerbrowser) for updates. 28 | -------------------------------------------------------------------------------- /markdown/101-science-data.md: -------------------------------------------------------------------------------- 1 | # Extra Credit: Distributing Scientific Data 2 | 3 | Now that you've used Dat to share example data, give it a spin using some of your own research data, or data that you've used in the past. 4 | 5 | Here are some example pages with data on them to give you ideas, but we encourage you to give Dat a spin with some data that you already have downloaded or published before. 6 | 7 | - Recent Earthquake CSVs: https://earthquake.usgs.gov/earthquakes/feed/v1.0/csv.php 8 | - Recently published DOIs (JSON): https://api.crossref.org/works?sort=updated&order=desc&rows=10&select=DOI,title,link,deposited 9 | 10 | Once you have data files in a folder on your machine, simply run `dat create` in the folder to start tracking the data with Dat. 11 | 12 | To complete this lesson, run `dat share` and share the link with another workshop attendee and see if they can access your data. 13 | -------------------------------------------------------------------------------- /markdown/102-desktop-application.md: -------------------------------------------------------------------------------- 1 | # Extra Credit: Desktop Application 2 | 3 | If you'd like to try a different workflow for managing Dat repositories, we have developed a Desktop application called Dat Desktop. You can install it from [https://datproject.org/install](https://datproject.org/install) for Mac or Linux (Windows coming soon). 4 | 5 | ![screenshot-dat-desktop.png](https://datproject.org/public/img/screenshot-dat-desktop.png) 6 | 7 | The Desktop application is intended to make Dat more approachable for users that prefer not to use the command line for everything. Give it a try and let us know what you think! 8 | -------------------------------------------------------------------------------- /markdown/103-genomic-data.md: -------------------------------------------------------------------------------- 1 | # Extra Credit: Import genomic data into Dat with the JavaScript API 2 | 3 | We are going to download the flu virus genome from [NCBI](https://www.ncbi.nlm.nih.gov) with [Bionode](https://bionode.io) and import it into Dat! 4 | 5 | Create a new folder named `infuenza`, enter that folder with your local terminal (`cd`) and install [bionode-ncbi](https://doc.bionode.io/#bionode-ncbi). 6 | 7 | ```bash 8 | npm install bionode-ncbi 9 | ``` 10 | 11 | Create a `script.js` file with the following content: 12 | 13 | ```javascript 14 | var Dat = require('dat') 15 | var Bionode = require('bionode-ncbi') 16 | 17 | Dat('.', function (err, dat) { 18 | if (err) throw err 19 | var download = Bionode.download('assembly', 'ViralMultiSegProj15622') 20 | download.on('data', console.log) 21 | download.on('end', function() { 22 | dat.importFiles() 23 | dat.joinNetwork() 24 | console.log('My Dat link is: dat://', dat.key.toString('hex')) 25 | }) 26 | }) 27 | ``` 28 | 29 | Run it: 30 | 31 | ```bash 32 | node script.js 33 | ``` 34 | 35 | Clone this Dat archive into another folder (change it to your Dat link): 36 | 37 | ```bash 38 | ❯ dat clone d3457d9e11c9548faa704a799e6553d1dfb672264cdd0374a62564213c3c3474 influenzaCopy 39 | ``` 40 | 41 | Check that you got a copy of the influenza genome from Dat: 42 | 43 | ```bash 44 | ❯ gunzip -c influenzaCopy/266481/GCF_000865085.1_ViralMultiSegProj15622_genomic.fna.gz | head -n 5 45 | ``` 46 | 47 | Should give you: 48 | 49 | ```bash 50 | >NC_007373.1 Influenza A virus (A/New York/392/2004(H3N2)) segment 1, complete sequence 51 | AGCAAAAGCAGGTCAATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAACCTGATGTCGCAGTCTCGCACTCGCGA 52 | GATACTGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCCGTCAC 53 | TTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGGATAACAGAAATGGTTCCGGAGAGAAAT 54 | GAACAAGGACAAACTCTATGGAGTAAAATGAGTGATGCTGGATCAGATCGAGTGATGGTATCACCTTTGGCTGTAACATG 55 | ``` -------------------------------------------------------------------------------- /package.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "get-dat", 3 | "version": "2.0.0", 4 | "description": "workshop content for learning dat", 5 | "main": "index.js", 6 | "scripts": { 7 | "render": "submarine markdown guide --template=guide.html", 8 | "deploy": "gh-pages-deploy", 9 | "build": "browserify index.js -o bundle.js && browserify terminal.js -o terminal-bundle.js", 10 | "start": "wzrd index.js:bundle.js terminal.js:terminal-bundle.js" 11 | }, 12 | "author": "max ogden", 13 | "license": "BSD", 14 | "watch": { 15 | "build": "workshop/*.md" 16 | }, 17 | "gh-pages-deploy": { 18 | "prep": [ 19 | "build", 20 | "render" 21 | ], 22 | "noprompt": "true" 23 | }, 24 | "dependencies": { 25 | "adventure-time": "^2.0.0", 26 | "gh-pages-deploy": "^0.1.1", 27 | "submarine": "0.2.4" 28 | }, 29 | "devDependencies": { 30 | "browserify": "^14.4.0", 31 | "wzrd": "^1.5.0" 32 | }, 33 | "dat": {} 34 | } 35 | -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- 1 | # try-dat 2 | 3 | ## A command line tutorial to learn `dat` 4 | 5 | This repo contains the content for the workshop. 6 | 7 | First install dat on your command line: `npm install dat -g` 8 | 9 | Then follow the instructions from each markdown (`.md`) file in this repo, in order. 10 | 11 | More lessons coming soon! Leave feedback in the issue tracker. 12 | 13 | ## development 14 | 15 | ``` 16 | npm install 17 | npm run render 18 | npm start 19 | ``` -------------------------------------------------------------------------------- /static/css/bootstrap.min.css: -------------------------------------------------------------------------------- 1 | /*! 2 | * Bootstrap v3.2.0 (http://getbootstrap.com) 3 | * Copyright 2011-2014 Twitter, Inc. 4 | * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE) 5 | *//*! normalize.css v3.0.1 | MIT License | git.io/normalize */html{font-family:sans-serif;-webkit-text-size-adjust:100%;-ms-text-size-adjust:100%}body{margin:0}article,aside,details,figcaption,figure,footer,header,hgroup,main,nav,section,summary{display:block}audio,canvas,progress,video{display:inline-block;vertical-align:baseline}audio:not([controls]){display:none;height:0}[hidden],template{display:none}a{background:0 0}a:active,a:hover{outline:0}abbr[title]{border-bottom:1px 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59 | } 60 | 61 | .hljs-identifier { 62 | color: #d0d0ff; 63 | } 64 | 65 | .hljs-class .hljs-title, 66 | .hljs-type, 67 | .smalltalk .hljs-class, 68 | .hljs-doctag { 69 | text-decoration: none; 70 | } 71 | 72 | .hljs-constant, 73 | .hljs-name { 74 | color: #da4939; 75 | } 76 | 77 | 78 | .hljs-symbol, 79 | .hljs-built_in, 80 | .ruby .hljs-symbol .hljs-string, 81 | .ruby .hljs-symbol .hljs-identifier, 82 | .asciidoc .hljs-link_url, 83 | .markdown .hljs-link_url, 84 | .hljs-attribute { 85 | color: #6d9cbe; 86 | } 87 | 88 | .asciidoc .hljs-link_url, 89 | .markdown .hljs-link_url { 90 | text-decoration: underline; 91 | } 92 | 93 | 94 | 95 | .hljs-params, 96 | .hljs-variable, 97 | .clojure .hljs-attribute { 98 | color: #d0d0ff; 99 | } 100 | 101 | .css .hljs-tag, 102 | .hljs-rule .hljs-property, 103 | .hljs-pseudo, 104 | .tex .hljs-special { 105 | color: #cda869; 106 | } 107 | 108 | .css .hljs-class { 109 | color: #9b703f; 110 | } 111 | 112 | .hljs-rule .hljs-keyword { 113 | color: #c5af75; 114 | } 115 | 116 | .hljs-rule .hljs-value { 117 | color: #cf6a4c; 118 | } 119 | 120 | .css .hljs-id { 121 | color: #8b98ab; 122 | } 123 | 124 | .hljs-annotation, 125 | .apache .hljs-sqbracket, 126 | .nginx .hljs-built_in { 127 | color: #9b859d; 128 | } 129 | 130 | .hljs-preprocessor, 131 | .hljs-preprocessor *, 132 | .hljs-pragma { 133 | color: #8996a8 !important; 134 | } 135 | 136 | .hljs-hexcolor, 137 | .css .hljs-value .hljs-number { 138 | color: #a5c261; 139 | } 140 | 141 | .hljs-title, 142 | .hljs-decorator, 143 | .css .hljs-function { 144 | color: #ffc66d; 145 | } 146 | 147 | .diff .hljs-header, 148 | .hljs-chunk { 149 | background-color: #2f33ab; 150 | color: #e6e1dc; 151 | display: inline-block; 152 | width: 100%; 153 | } 154 | 155 | .diff .hljs-change { 156 | background-color: #4a410d; 157 | color: #f8f8f8; 158 | display: inline-block; 159 | width: 100%; 160 | } 161 | 162 | .hljs-addition { 163 | background-color: #144212; 164 | color: #e6e1dc; 165 | display: inline-block; 166 | width: 100%; 167 | } 168 | 169 | .hljs-deletion { 170 | background-color: #600; 171 | color: #e6e1dc; 172 | display: inline-block; 173 | width: 100%; 174 | } 175 | 176 | .coffeescript .javascript, 177 | .javascript .xml, 178 | .tex .hljs-formula, 179 | .xml .javascript, 180 | .xml .vbscript, 181 | .xml .css, 182 | .xml .hljs-cdata { 183 | opacity: 0.7; 184 | } 185 | -------------------------------------------------------------------------------- /static/css/reset.min.css: -------------------------------------------------------------------------------- 1 | html,body,div,span,applet,object,iframe,h1,h2,h3,h4,h5,h6,p,blockquote,pre,a,abbr,acronym,address,big,cite,code,del,dfn,em,img,ins,kbd,q,s,samp,small,strike,strong,sub,sup,tt,var,b,u,i,center,dl,dt,dd,ol,ul,li,fieldset,form,label,legend,table,caption,tbody,tfoot,thead,tr,th,td,article,aside,canvas,details,embed,figure,figcaption,footer,header,hgroup,menu,nav,output,ruby,section,summary,time,mark,audio,video{margin:0;padding:0;border:0;font-size:100%;font:inherit;vertical-align:baseline}article,aside,details,figcaption,figure,footer,header,hgroup,menu,nav,section{display:block}body{line-height:1}ol,ul{list-style:none}blockquote,q{quotes:none}blockquote:before,blockquote:after,q:before,q:after{content:'';content:none}table{border-collapse:collapse;border-spacing:0} -------------------------------------------------------------------------------- /static/css/style.css: -------------------------------------------------------------------------------- 1 | @import "normalize.min.css"; 2 | @import "bootstrap.min.css"; 3 | @import "railscasts.css"; 4 | 5 | /* Colors */ 6 | /* Containers */ 7 | body { 8 | font-family: 'Source Sans Pro', sans-serif; 9 | margin: 0; 10 | padding: 0; 11 | background-color: #f4f5f6; 12 | font-size: 18px; 13 | } 14 | h1, 15 | h2, 16 | h3 { 17 | color: #333; 18 | } 19 | h4, h5 { 20 | color: #777; 21 | } 22 | h4 { 23 | font-size: 2rem; 24 | } 25 | .mono { 26 | font-family: monospace; 27 | } 28 | a { 29 | transition: all 0.15s ease; 30 | color: #35b44f; 31 | } 32 | a:hover { 33 | color: #35b44f; 34 | text-decoration: underline; 35 | } 36 | p { 37 | padding: 10px 0px; 38 | } 39 | pre { 40 | padding: .5em; 41 | font-size: 16px; 42 | background-color: #232323; 43 | color: #e6e1dc; 44 | } 45 | .muted, 46 | .dark-text { 47 | color: #959ba4; 48 | } 49 | .caption { 50 | color: #959ba4; 51 | font-size: 14px; 52 | } 53 | .navlinks { 54 | padding: 20px 20px 100px 30px; 55 | } 56 | .toc { 57 | padding: 40px 0px 0px 0px; 58 | } 59 | .button { 60 | display: inline-block; 61 | font-size: 22px; 62 | font-weight: 600; 63 | color: white; 64 | background-color: #35b44f; 65 | padding: 18px 14px; 66 | border-radius: 5px; 67 | } 68 | .button.button-light { 69 | background-color: white; 70 | } 71 | .button:hover { 72 | background-color: #a9ce7f; 73 | text-decoration: none !important; 74 | } 75 | /** SPLASH **/ 76 | .rsaquo { 77 | color: #35B44F; 78 | margin-right: 10px; 79 | font-family: "Times New Roman", Times, serif; 80 | font-size: 20px; 81 | } 82 | /** CONTENT **/ 83 | .small-dat-title-icon { 84 | height: 2.5rem; 85 | padding-right: 8px; 86 | } 87 | .content { 88 | padding: 0px 15px; 89 | } 90 | html, body { 91 | font-family: 'Source Sans Pro', sans-serif; 92 | margin: 0; 93 | padding: 0; 94 | background-color: #fff; 95 | } 96 | 97 | .button:hover { 98 | background-color: #a9ce7f; 99 | } 100 | .buttons { 101 | bottom: 0; 102 | right: 0; 103 | position: absolute; 104 | z-index: 99999; 105 | } 106 | .button { 107 | display: inline-block; 108 | font-size: 18px; 109 | font-weight: 600; 110 | color: white; 111 | background-color: #35b44f; 112 | padding: 7px 14px; 113 | border-radius: 5px; 114 | } 115 | .CodeMirror { font-size: 12px; height: 100% !important; } 116 | .CodeMirror-scroll { height: 100%; } 117 | .CodeMirror div.CodeMirror-selected { background: rgba(0,0,0,0.1); } 118 | .CodeMirror-focused div.CodeMirror-selected { background: rgba(0,0,255,0.1); } 119 | .CodeMirror .errorLine { background: rgba(255,0,0,0.25); } 120 | .container { } 121 | 122 | .nextp { 123 | float: right; 124 | } 125 | 126 | .datLogo { 127 | padding: 3px 5px 0 5px; 128 | height: 28px; 129 | display: block; 130 | float: left; 131 | } 132 | 133 | .datTitle { 134 | line-height: 34px; 135 | display: block; 136 | float: left; 137 | } 138 | 139 | .hidden { 140 | display: none; 141 | } 142 | 143 | .topbar { 144 | font-weight: 300; 145 | height: 34px; 146 | position: absolute; 147 | right: 0; 148 | left: 0; 149 | top: 0; 150 | background: #fdfdfd; 151 | border-bottom: 1px solid #f0f0f0; 152 | } 153 | 154 | .topbar ul { padding: 0; margin: 0; list-style: none; padding-right: 5px; } 155 | .topbar li { line-height: 34px; display: inline; } 156 | .topbar li a { padding: 0px 3px; } 157 | 158 | .panels { 159 | position: absolute; 160 | top: 35px; 161 | right: 0; 162 | left: 0; 163 | bottom: 0; 164 | } 165 | 166 | .editor { 167 | position: absolute; 168 | top: 50%; 169 | left: 57%; 170 | right: 0; 171 | bottom: 0; 172 | } 173 | 174 | .console { 175 | position: absolute; 176 | top: 0; 177 | left: 45%; 178 | right: 0; 179 | bottom: 50%; 180 | padding: 20px; 181 | border-bottom: 1px solid #ddd; 182 | } 183 | 184 | .tree { 185 | position: absolute; 186 | top: 50%; 187 | left: 45%; 188 | right: 45%; 189 | bottom: 0; 190 | padding: 0 0 0 4px; 191 | overflow-y: scroll; 192 | } 193 | 194 | .guide { 195 | position: absolute; 196 | top: 0; 197 | left: 0; 198 | right: 55%; 199 | bottom: 0; 200 | border-bottom: 1px solid #ddd; 201 | border-right: 5px solid #f4f5f6; 202 | } 203 | 204 | .console iframe { 205 | width: 100%; 206 | height: 100%; 207 | border: none; 208 | border-width: 0; 209 | } 210 | 211 | .tall { 212 | bottom: 0%; 213 | } 214 | 215 | /** footer **/ 216 | .footer { 217 | position: absolute; 218 | bottom: -40px; 219 | height: 40px; 220 | font-size: 12px; 221 | line-height: 40px; 222 | width: 100%; 223 | background-color: #2a3749; 224 | overflow: auto; 225 | text-align: center; 226 | color: #959ba4; 227 | } 228 | .footer a { 229 | color: #fff; 230 | text-decoration: none; 231 | } 232 | .footer a:hover { 233 | text-decoration: underline; 234 | } 235 | .octocat-green { 236 | display: inline-block; 237 | position: relative; 238 | top: 3px; 239 | width: 17px; 240 | height: 17px; 241 | background-image: url('../img/octocat-green.png'); 242 | } 243 | 244 | /* overrides */ 245 | 246 | .tree-view .entry.selected:before { 247 | background-color: #f7f7f7; 248 | } 249 | 250 | img { 251 | max-width: 100%; 252 | } -------------------------------------------------------------------------------- /static/img/cat.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/cat.png -------------------------------------------------------------------------------- /static/img/dat-directory.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/dat-directory.png -------------------------------------------------------------------------------- /static/img/dat-hex-small.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/dat-hex-small.png -------------------------------------------------------------------------------- /static/img/datcat.jpeg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/datcat.jpeg -------------------------------------------------------------------------------- /static/img/octocat-green.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/octocat-green.png -------------------------------------------------------------------------------- /static/img/wildcat.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/max-mapper/get-dat/ff6c47f7498a2e2d15454b696012d43fdbe96052/static/img/wildcat.jpg -------------------------------------------------------------------------------- /terminal.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | dat terminal 6 | 36 | 37 | 38 |

39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /terminal.js: -------------------------------------------------------------------------------- 1 | var terminal = require('adventure-time/terminal') 2 | terminal() -------------------------------------------------------------------------------- /wip/01-using-docker.md: -------------------------------------------------------------------------------- 1 | # Using docker 2 | 3 | Once you have some data, and you want to do fun things with it, you usually have to install extra software. 4 | 5 | This can be really difficult if the software requires installing lots of dependencies, e.g. specific versions of Python or Ruby. 6 | 7 | To make this process easier we have been using docker to build lightweight linux containers that come pre-installed with various data processing tools and all of their dependencies. 8 | 9 | We have written a data processing program that you can stream data into and it will render a bar chart. It uses a bar chart rendering program written in Python but in order to make it easier to use we also published a docker container that has Python + all the other dependencies for the bar chart pre-installed. 10 | 11 | To render the bar chart, first make sure your terminal is inside the `eukaryota` dat repository, and run the following command: 12 | 13 | ``` 14 | dat cat | docker run -i bmpvieira/barchart 15 | ``` 16 | 17 | This pipes the `dat cat` JSON data into the barchart program running in docker. You should see a barchart show up in your terminal. 18 | -------------------------------------------------------------------------------- /wip/05-dat-json-config.md: -------------------------------------------------------------------------------- 1 | # `dat.json` 2 | 3 | ## How to configure dat 4 | 5 | The `dat.json` file that gets created when you do `dat init` can be used to override dat's default behavior and extend it with new functionality. 6 | 7 | There is [full documentation available](https://github.com/maxogden/dat/blob/master/docs/dat-json-config.md) for the `dat.json` file. In this file we will cover some common use cases. 8 | 9 | ### Default port 10 | 11 | Dat's default port is `6461`. Edit your `dat.json` file (create a new empty dat if you don't already have one) and add a port: 12 | 13 | ```JSON 14 | { 15 | "name": "get-dat", 16 | "port": 9000 17 | } 18 | ``` 19 | 20 | Now run `dat listen`. It should have started on port `9000` this time. Enter `CTRL + c` to stop the dat process. 21 | 22 | ### Transformations 23 | 24 | You can insert custom functions that will happen whenever dat reads a row or writes a row to the tabular store. These can be commands that do 25 | 26 | ### Blobs 27 | 28 | ### Leveldown 29 | 30 | ### Listen Hook 31 | -------------------------------------------------------------------------------- /wip/beta-use-cases.md: -------------------------------------------------------------------------------- 1 | # Dat Beta Use Cases 2 | 3 | ## Basics 4 | 5 | - Host a dat 6 | ``` 7 | dat host 8 | ``` 9 | - Add tabular data to a dataset 10 | ``` 11 | dat add ahi_pop.csv -d ahi-population 12 | ``` 13 | - Clone entire history (rows and files) 14 | ``` 15 | dat clone ssh/http/dat://path/to/dat/here 16 | ``` 17 | - Clone specific version 18 | ``` 19 | dat clone ssh/http/dat://path/to/dat/here#ab34d32 20 | ``` 21 | 22 | ## Collaboration 23 | *the action of working with someone(s) to produce or create something.* 24 | 25 | - Clone specific dataset 26 | ``` 27 | dat clone ssh/http/dat://path/to/dat/here/ 28 | ``` 29 | - Clone specific dataset at a specific version 30 | ``` 31 | dat clone ssh/http/dat://path/to/dat/here/#ab34d32 32 | ``` 33 | - Clone and later checkout 34 | ``` 35 | dat clone ssh/http/dat://path/to/dat/here/#ab34d32 36 | dat checkout b2b3413 37 | ``` 38 | - Push a dataset 39 | ``` 40 | dat push 41 | dat push ssh/http/dat://path/to/another/dat/here 42 | ``` 43 | - Pull a version of a dataset (*uses dat.json if no remote supplied*) 44 | ``` 45 | dat pull 46 | dat pull ssh/http/dat://path/to/dat/here 47 | ``` 48 | 49 | - Diff two versions of a dataset 50 | ``` 51 | dat pull ssh://path/to/dat/here/ 52 | dat diff 53 | ``` 54 | 55 | - Merge two versions of a dataset to create one version 56 | ``` 57 | dat merge 58 | ``` 59 | 60 | ## Cooperation 61 | *the process of working together to the same end. assistance.* 62 | 63 | - Filesystem-like interface 64 | - Download full dat from remote 65 | ``` 66 | curl http://path/to/another/dat/here.tar > my-data.tar 67 | ``` 68 | - Download full dat at a particular version 69 | ``` 70 | curl http://path/to/another/dat/here.tar#ab34d32 > my-data.tar 71 | ``` 72 | - Download dataset from remote 73 | ``` 74 | curl http://path/to/another/dat/here/.csv#ab34d32 > my-data.csv 75 | curl http://path/to/another/dat/here/.tar#ab34d32 > my-data.tar 76 | ``` 77 | - Download a file in a dataset at specific version 78 | ``` 79 | curl http://path/to/another/dat/here//.tar#ab34d32 > my-data.tar 80 | ``` 81 | 82 | ## Coordination 83 | *the organization of the different elements of a complex body or activity so as to enable them to work together effectively.* 84 | 85 | - Add without copying (link) 86 | ``` 87 | dat add --link test.csv 88 | ``` 89 | - Expose live data source to people so they can 'dat clone' 90 | - Fork: Clone (perhaps at a specific version), edit, and host 91 | - Pipeline integration hooks 92 | 93 | # Beta Features 94 | 95 | - It's a graph 96 | - Supports merging 97 | - Supports branches 98 | 99 | - It's a log 100 | - Supports checkout 101 | - Supports pull 102 | 103 | - It's streaming 104 | - Supports stream processing jobs 105 | - Individual large files can be streamed 106 | - Replication modules 107 | - Stream data source wrappers (this should be a standalone effort) 108 | 109 | - Data is not stored in the graph, only referenced 110 | - Supports shallow or partial clone --------------------------------------------------------------------------------

Welcome!

Table of Contents

Installation

Downloading

Live syncing data

Hosting a website

Downloading a partial dataset from git

Downloading a dataset from GitHub

Extra Credit: Host your site in Beaker

Extra Credit: Distributing Scientific Data

Extra Credit: Desktop Application

Extra Credit: Import genomic data into Dat with the JavaScript API

Welcome!

Table of Contents

Welcome to my data website!