Performant Uploads with TUS
Marius van den Beek
Helena Rasche
Lucille DelisleOverviewQuestions:Objectives:
Requirements:
Setup TUSd
Configure Galaxy to use it to process uploads
- Galaxy Server administration
- Ansible: slides slides - tutorial hands-on
- Galaxy Installation with Ansible: slides slides - tutorial hands-on
Time estimation: 30 minutesSupporting Materials:Last modification: Sep 28, 2022
Questions:
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
Comment: Galaxy Admin Training PathThe 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.
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
In your playbook directory, add the
galaxyproject.tusdrole to yourrequirements.yml--- a/requirements.yml +++ b/requirements.yml @@ -12,3 +12,5 @@ version: 0.3.0 - src: usegalaxy_eu.certbot version: 0.1.5 +- name: galaxyproject.tusd + version: 0.0.1If 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’.
Old $ cat old
🍎
🍐
🍊
🍋
🍒
🥑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:
--- oldis the ‘old’ file in our view+++ newis 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:
- Ignore the header
- Remove lines starting with - from your file
- 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 @@
-🍎
-🍐
-🍊
-🍋
-🍒
-🥑Install the role with:
Input: Bashansible-galaxy install -p roles -r requirements.ymlConfigure it in your group variables
--- a/group_vars/galaxyservers.yml +++ b/group_vars/galaxyservers.yml @@ -60,6 +60,8 @@ galaxy_config: allow_user_impersonation: true # Tool security outputs_to_working_directory: true + # TUS + tus_upload_store: /data/tus gravity: galaxy_root: "{{ galaxy_root }}/server" app_server: gunicorn @@ -139,3 +141,16 @@ 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-nginx.pem + +# TUS +galaxy_tusd_port: 1080 +tusd_instances: + - name: main + user: "{{ galaxy_user.name }}" + group: "galaxy" + args: + - "-host=localhost" + - "-port={{ galaxy_tusd_port }}" + - "-upload-dir={{ galaxy_config.galaxy.tus_upload_store }}" + - "-hooks-http=https://{{ inventory_hostname }}/api/upload/hooks" + - "-hooks-http-forward-headers=X-Api-Key,Cookie"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!Add to the end of your Galaxy playbook
--- a/galaxy.yml +++ b/galaxy.yml @@ -19,3 +19,4 @@ become: true become_user: "{{ galaxy_user.name }}" - galaxyproject.nginx + - galaxyproject.tusdRun the playbook
Input: Bashansible-playbook galaxy.yml
Congratulations, you’ve set up TUS for Galaxy.
Check it works
Hands-on: Check that it works.
SSH into your machine
Check the active status of tusd by
systemctl status tusd-main.Upload a small file! (Pasted text will not pass via TUS)
Check the directory
/data/tus/has been created and it’s contentsInput: Bashsudo tree /data/tus/You’ll see files in that directory, a file that’s been uploaded and an ‘info’ file which contains metadata about the upload.
1.sh
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
gitto track your progress, remember to add your changes and commit with a good commit message!
Key points
Use TUS to make uploads more efficient, especially for large uploads over unstable connections.
Frequently Asked Questions
Have questions about this tutorial? Check out the FAQ page for the Galaxy Server administration topic to see if your question is listed there. If not, please ask your question on the GTN Gitter Channel or the Galaxy Help ForumFeedback
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Citing this Tutorial
- Marius van den Beek, Helena Rasche, Lucille Delisle, 2022 Performant Uploads with TUS (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/admin/tutorials/tus/tutorial.html Online; accessed TODAY
- Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012
Congratulations on successfully completing this tutorial!@misc{admin-tus, author = "Marius van den Beek and Helena Rasche and Lucille Delisle", title = "Performant Uploads with TUS (Galaxy Training Materials)", year = "2022", month = "09", day = "28" url = "\url{https://training.galaxyproject.org/training-material/topics/admin/tutorials/tus/tutorial.html}", note = "[Online; accessed TODAY]" } @article{Batut_2018, doi = {10.1016/j.cels.2018.05.012}, url = {https://doi.org/10.1016%2Fj.cels.2018.05.012}, year = 2018, month = {jun}, publisher = {Elsevier {BV}}, volume = {6}, number = {6}, pages = {752--758.e1}, author = {B{\'{e}}r{\'{e}}nice Batut and Saskia Hiltemann and Andrea Bagnacani and Dannon Baker and Vivek Bhardwaj and Clemens Blank and Anthony Bretaudeau and Loraine Brillet-Gu{\'{e}}guen and Martin {\v{C}}ech and John Chilton and Dave Clements and Olivia Doppelt-Azeroual and Anika Erxleben and Mallory Ann Freeberg and Simon Gladman and Youri Hoogstrate and Hans-Rudolf Hotz and Torsten Houwaart and Pratik Jagtap and Delphine Larivi{\`{e}}re and Gildas Le Corguill{\'{e}} and Thomas Manke and Fabien Mareuil and Fidel Ram{\'{\i}}rez and Devon Ryan and Florian Christoph Sigloch and Nicola Soranzo and Joachim Wolff and Pavankumar Videm and Markus Wolfien and Aisanjiang Wubuli and Dilmurat Yusuf and James Taylor and Rolf Backofen and Anton Nekrutenko and Björn Grüning}, title = {Community-Driven Data Analysis Training for Biology}, journal = {Cell Systems} }