Performant Uploads with TUS

Overview
Creative Commons License: CC-BY Questions:
Objectives:
  • Setup TUSd

  • Configure Galaxy to use it to process uploads

Requirements:
Time estimation: 30 minutes
Supporting Materials:
Published: Mar 1, 2022
Last modification: Jan 31, 2024
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
purl PURL: https://gxy.io/GTN:T00024
rating Rating: 5.0 (0 recent ratings, 1 all time)
version Revision: 42

Here you’ll learn to setup TUS an open source resumable file upload server to process uploads for Galaxy. We use an external process here to offload the main Galaxy processes for more important work and not impact the entire system during periods of heavy uploading.

Agenda
  1. TUS and Galaxy
    1. Installing and Configuring
    2. Check it works
Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

  1. Step 1
    ansible-galaxy
  2. Step 2
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon

TUS and Galaxy

To allow your user to upload via TUS, you will need to:

  • configure Galaxy to know where the files are uploaded.
  • install TUSd
  • configure Nginx to proxy TUSd

Installing and Configuring

Hands-on: Setting up ftp upload with Ansible
  1. In your playbook directory, add the galaxyproject.tusd role to your requirements.yml

    --- a/requirements.yml
    +++ b/requirements.yml
    @@ -14,3 +14,6 @@
     # gxadmin (used in cleanup, and later monitoring.)
     - src: galaxyproject.gxadmin
       version: 0.0.12
    +# TUS (uploads)
    +- name: galaxyproject.tusd
    +  version: 0.0.1
       
    

    If you haven’t worked with diffs before, this can be something quite new or different.

    If we have two files, let’s say a grocery list, in two files. We’ll call them ‘a’ and ‘b’.

    Input: Old
    $ cat old
    🍎
    🍐
    🍊
    🍋
    🍒
    🥑
    Output: New
    $ cat new
    🍎
    🍐
    🍊
    🍋
    🍍
    🥑

    We can see that they have some different entries. We’ve removed 🍒 because they’re awful, and replaced them with an 🍍

    Diff lets us compare these files

    $ diff old new
    5c5
    < 🍒
    ---
    > 🍍

    Here we see that 🍒 is only in a, and 🍍 is only in b. But otherwise the files are identical.

    There are a couple different formats to diffs, one is the ‘unified diff’

    $ diff -U2 old new
    --- old 2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:06:36.340962616 +0100
    @@ -3,4 +3,4 @@
    🍊
    🍋
    -🍒
    +🍍
    🥑

    This is basically what you see in the training materials which gives you a lot of context about the changes:

    • --- old is the ‘old’ file in our view
    • +++ new is the ‘new’ file
    • @@ these lines tell us where the change occurs and how many lines are added or removed.
    • Lines starting with a - are removed from our ‘new’ file
    • Lines with a + have been added.

    So when you go to apply these diffs to your files in the training:

    1. Ignore the header
    2. Remove lines starting with - from your file
    3. Add lines starting with + to your file

    The other lines (🍊/🍋 and 🥑) above just provide “context”, they help you know where a change belongs in a file, but should not be edited when you’re making the above change. Given the above diff, you would find a line with a 🍒, and replace it with a 🍍

    Added & Removed Lines

    Removals are very easy to spot, we just have removed lines

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:10:14.370722802 +0100
    @@ -4,3 +4,2 @@
    🍋
    🍒
    -🥑

    And additions likewise are very easy, just add a new line, between the other lines in your file.

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ new 2022-02-16 14:11:11.422135393 +0100
    @@ -1,3 +1,4 @@
    🍎
    +🍍
    🍐
    🍊

    Completely new files

    Completely new files look a bit different, there the “old” file is /dev/null, the empty file in a Linux machine.

    $ diff -U2 /dev/null old
    --- /dev/null 2022-02-15 11:47:16.100000270 +0100
    +++ old 2022-02-16 14:06:19.697132568 +0100
    @@ -0,0 +1,6 @@
    +🍎
    +🍐
    +🍊
    +🍋
    +🍒
    +🥑

    And removed files are similar, except with the new file being /dev/null

    --- old	2022-02-16 14:06:19.697132568 +0100
    +++ /dev/null 2022-02-15 11:47:16.100000270 +0100
    @@ -1,6 +0,0 @@
    -🍎
    -🍐
    -🍊
    -🍋
    -🍒
    -🥑

  2. Install the role with:

    Input: Bash
    ansible-galaxy install -p roles -r requirements.yml
    
  3. Configure it in your group variables

    --- a/group_vars/galaxyservers.yml
    +++ b/group_vars/galaxyservers.yml
    @@ -70,6 +70,9 @@ galaxy_config:
         # Tool security
         outputs_to_working_directory: true
         new_user_dataset_access_role_default_private: true # Make datasets private by default
    +    # TUS
    +    galaxy_infrastructure_url: "https://{{ inventory_hostname }}"
    +    tus_upload_store: "{{ galaxy_tus_upload_store }}"
       gravity:
         process_manager: systemd
         galaxy_root: "{{ galaxy_root }}/server"
    @@ -90,6 +93,10 @@ galaxy_config:
         celery:
           concurrency: 2
           loglevel: DEBUG
    +    tusd:
    +      enable: true
    +      tusd_path: /usr/local/sbin/tusd
    +      upload_dir: "{{ galaxy_tus_upload_store }}"
         handlers:
           handler:
             processes: 2
    @@ -159,3 +166,7 @@ nginx_conf_http:
     nginx_ssl_role: usegalaxy_eu.certbot
     nginx_conf_ssl_certificate: /etc/ssl/certs/fullchain.pem
     nginx_conf_ssl_certificate_key: /etc/ssl/user/privkey-www-data.pem
    +
    +# TUS
    +galaxy_tusd_port: 1080
    +galaxy_tus_upload_store: /data/tus
       
    
  4. We proxy the service next to Galaxy. As it resides “under” the Galaxy path, clients will send cookies and authentication headers to TUS, which it can use to process the uploads before telling Galaxy when they’re done.

    --- a/templates/nginx/galaxy.j2
    +++ b/templates/nginx/galaxy.j2
    @@ -28,6 +28,22 @@ server {
     		proxy_set_header Upgrade $http_upgrade;
     	}
        
    +	location /api/upload/resumable_upload {
    +		# Disable request and response buffering
    +		proxy_request_buffering     off;
    +		proxy_buffering             off;
    +		proxy_http_version          1.1;
    +
    +		# Add X-Forwarded-* headers
    +		proxy_set_header X-Forwarded-Host   $host;
    +		proxy_set_header X-Forwarded-Proto  $scheme;
    +
    +		proxy_set_header Upgrade            $http_upgrade;
    +		proxy_set_header Connection         "upgrade";
    +		client_max_body_size        0;
    +		proxy_pass http://localhost:{{ galaxy_tusd_port }}/files;
    +	}
    +
     	# Static files can be more efficiently served by Nginx. Why send the
     	# request to Gunicorn which should be spending its time doing more useful
     	# things like serving Galaxy!
       
    
  5. Add to the end of your Galaxy playbook

    --- a/galaxy.yml
    +++ b/galaxy.yml
    @@ -30,6 +30,7 @@
             name: ['tmpreaper']
           when: ansible_os_family == 'Debian'
       roles:
    +    - galaxyproject.tusd
         - galaxyproject.galaxy
         - role: galaxyproject.miniconda
           become: true
       
    
  6. Run the playbook

    Input: Bash
    ansible-playbook galaxy.yml
    

Congratulations, you’ve set up TUS for Galaxy.

Check it works

Hands-on: Check that it works.
  1. SSH into your machine

  2. Check the active status of tusd by systemctl status galaxy-tusd.

  3. Upload a small file! (Pasted text will not pass via TUS)

  4. Check the directory /data/tus/ has been created and it’s contents

    Input: Bash
    sudo tree /data/tus/
    
  5. You’ll see files in that directory, a file that’s been uploaded and an ‘info’ file which contains metadata about the upload.

Hands-on: Time to git commit

It’s time to commit your work! Check the status with

git status

Add your changed files with

git add ... # any files you see that are changed

And then commit it!

git commit -m 'Finished Performant Uploads with TUS'

Comment: Got lost along the way?

If you missed any steps, you can compare against the reference files, or see what changed since the previous tutorial.

If you’re using git to track your progress, remember to add your changes and commit with a good commit message!

Comment: Galaxy Admin Training Path

The yearly Galaxy Admin Training follows a specific ordering of tutorials. Use this timeline to help keep track of where you are in Galaxy Admin Training.

  1. Step 1
    ansible-galaxy
  2. Step 2
    backup-cleanup
  3. Step 3
    customization
  4. Step 4
    tus
  5. Step 5
    cvmfs
  6. Step 6
    apptainer
  7. Step 7
    tool-management
  8. Step 8
    reference-genomes
  9. Step 9
    data-library
  10. Step 10
    dev/bioblend-api
  11. Step 11
    connect-to-compute-cluster
  12. Step 12
    job-destinations
  13. Step 13
    pulsar
  14. Step 14
    celery
  15. Step 15
    gxadmin
  16. Step 16
    reports
  17. Step 17
    monitoring
  18. Step 18
    tiaas
  19. Step 19
    sentry
  20. Step 20
    ftp
  21. Step 21
    beacon