No output issue when generating measures #590
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I am following the tutorial on my local machine trying to generate sample code for trends in hospitalisations and deaths using OpenSAFELY. I have been going through the Measures tutorial as this appears the most appropriate way to go about getting monthly values. Using the tutorial as my example, and copying the code into my repository here, I have some difficulty getting the code to actually run locally. Specifically, I am currently getting the following error message: => generate_measures Did you mean to match one of these files instead? log file: metadata/generate_measures.log I may assume the issue is because it is expecting the files to exist to write to, but as this is the first time running the code it is not the case. It might be something else of course and I am probably being a dingbat here. Any suggestions would be most welcome. |
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Replies: 2 comments 2 replies
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@markagreen: 👋 It looks like the specified paths under The project runs for me without error if I amend these lines of the generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csvTo highlight the changes: generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-02-01 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
- cohort: output/input_*.csv.gz
+ cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
- measure_csv: output/measure_*.csv
+ measure_csv: output/measures/measure_*.csvI think that should get your project working, but if not, let us know! 😃 |
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Hi - thank you Steven - i thought it would be something simple, although when I update for these changes I still get the same error which either means it is a local issue on my computer (if it works with you) or I am missing something very simple again. Feels like it is searching for the csv's. No outputs found matching patterns: |
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Maybe try running: This will ensure both actions run from scratch, instead of using previous outputs1. Otherwise, you may find that the result of the "successful" but incorrect Footnotes
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Magic! That works - thank you :D |
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Hi - thank you Steven - i thought it would be something simple, although when I update for these changes I still get the same error which either means it is a local issue on my computer (if it works with you) or I am missing something very simple again. Feels like it is searching for the csv's.
No outputs found matching patterns:
- output/measures/measure_*.csv