Galaxy Monitoring with Reports

Author(s) orcid logoNate Coraor avatar Nate Coraororcid logoBjörn Grüning avatar Björn Grüningorcid logoSimon Gladman avatar Simon Gladmanorcid logoHelena Rasche avatar Helena Rasche
Reviewers Saskia Hiltemann avatarSimon Gladman avatarMartin Čech avatarGianmauro Cuccuru avatarHelena Rasche avatarLucille Delisle avatarNate Coraor avatarMarius van den Beek avatarYvan Le Bras avatarNicola Soranzo avatarBérénice Batut avatarBjörn Grüning avatarAnthony Bretaudeau avatarArmin Dadras avatar
Overview
Creative Commons License: CC-BY Questions:

  • How to monitor a Galaxy service with the Reports application?

Objectives:

  • Setup and start the Galaxy reports app.

Requirements:
Time estimation: 30 minutes
Supporting Materials:
Published: Jan 31, 2019
Last modification: Apr 8, 2025
License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MIT
PURL: https://gxy.io/GTN:T00018
Rating: 5.0 (0 recent ratings, 3 all time)
Revision: 43

The reports application gives some pre-configured analytics screens. These are very easy to setup and can help with debugging issues in Galaxy.

Agenda
  1. Setting up Reports
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

Setting up Reports

The reports application is included with the Galaxy codebase and this tutorial assumes you’ve already done all of the setup required for Galaxy, systemd, uWSGI, and NGINX.

Hands On: Setup Reports

  1. First we add a basic configuration of the Reports app to the playbook templates. Create templates/galaxy/config/ folder, if it doesn’t exist, and create templates/galaxy/config/reports.yml with the following contents:

    --- /dev/null
+++ b/templates/galaxy/config/reports.yml
@@ -0,0 +1,4 @@
+reports:
+    database_connection: "{{ galaxy_config.galaxy.database_connection }}"
+    file_path: "{{ galaxy_config.galaxy.file_path }}"
+    template_cache_path: "{{ galaxy_mutable_data_dir }}/compiled_templates/reports/"

    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’.

    Code In: Old
    $ cat old
    🍎
    🍐
    🍊
    🍋
    🍒
    🥑
    Code Out: 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. In your galaxyservers group variables file, tell the playbook to deploy the reports configuration file, and gravity to manage reports:

    --- a/group_vars/galaxyservers.yml
+++ b/group_vars/galaxyservers.yml
@@ -151,6 +151,11 @@ galaxy_config:
         pools:
           - job-handlers
           - workflow-schedulers
+    reports:
+      enable: true
+      url_prefix: /reports
+      bind: "unix:{{ galaxy_mutable_config_dir }}/reports.sock"
+      config_file: "{{ galaxy_config_dir }}/reports.yml"
    
 galaxy_job_config_file: "{{ galaxy_config_dir }}/galaxy.yml"
    
@@ -171,6 +176,8 @@ galaxy_config_templates:
     dest: "{{ galaxy_config.galaxy.dependency_resolvers_config_file }}"
   - src: templates/galaxy/config/job_resource_params_conf.xml.j2
     dest: "{{ galaxy_config.galaxy.job_resource_params_file }}"
+  - src: templates/galaxy/config/reports.yml
+    dest: "{{ galaxy_config.gravity.reports.config_file }}"
    
 galaxy_extra_dirs:
   - /data

  3. Then we need to tell NGINX it should serve our Reports app under <server_url>/reports url. Edit your templates/nginx/galaxy.j2 file, and within the server block, add a block for proxying the reports application. It should look like:

    --- a/templates/nginx/galaxy.j2
+++ b/templates/nginx/galaxy.j2
@@ -103,4 +103,10 @@ server {
 		proxy_set_header Upgrade $http_upgrade;
 		proxy_set_header Connection "upgrade";
 	}
+
+	location /reports/ {
+		proxy_pass http://{{ galaxy_config.gravity.reports.bind }}:/;
+		proxy_set_header X-Forwarded-Host $host;
+		proxy_set_header X-Forwarded-Proto $scheme;
+	}
 }

  4. Run the playbook:

    Code In: Bash
    ansible-playbook galaxy.yml

  5. The reports application should be available, under /reports

Comment: Insecure!

But notice that your Reports server is not secured! Check out the External Authentication tutorial for information on securing Reports.

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 Galaxy Monitoring with Reports'

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