Getting started guide - difficulty making the histogram

[Miriam-S-git]

HI. A very basic learner here. So apologies if I have missed something basic.
I am getting stuck on making the histogram.
" add a chart"

The following command in the command line just continues to generate the csv file and doesn't get to the next step of the histogram. opensafely run run_all --force-run-dependencies

I have pasted all the other commands from the tutorial into the files.

I suspect I have made a basic error. But can't pinpoint what it is.

I've added a screen shot of the end point of the this command when I run it.

Thank you for your help.

[StevenMaude]

Hi @Miriam-S-git 👋

Thanks for your question!

The describe part in your file is at the same level as actions. In fact, the describe part goes under actions, because describe is an action, e.g.

version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  describe:
    run: python:latest python analysis/report.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        cohort: output/descriptive.png

(I had to look for a minute here. The problem here is actually a little bit subtle because there is no error! Your slightly incorrect project.yaml file is still treated as a valid file by the opensafely command! However, when you run opensafely, opensafely doesn't recognise the describe action you just added!)

Please let us know if this change fixes your problem 🙂

Or equally if it doesn't, and we can help you figure this out, so that you can complete the tutorial!

[Miriam-S-git]

Thank you! @StevenMaude

Really helpful and think I also understood a bit more about the levels of the different commands.

I can see the error now and corrected it. I now have a histogram! Yay!