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Document results data model for modules #167

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merged 39 commits into from
Sep 30, 2024
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Aims to address #143 through the following changes:

  • Add a getResultsDataModelSpecification function to the StrategusModule base class. Each module then implements this method to provide the results data model specification so that we can construct the full results data model for all modules in Strategus.
  • Add extras/DocumentResultsDataModel.R to construct SQL used to document the results data model. At the moment this full results model is kept in the extras folder. We might consider exposing this as a package function so we can version the results data model for a given release of Strategus as described by @schuemie on our recent HADES Strategus WG call.
  • Update the package using usethis::use_pkgdown_github_pages() to add a new GHA workflow .github/workflows/pkgdown.yaml to automatically document the package using pkgdown when publishing to the main branch.
  • Extended the .github/workflows/pkgdown.yaml workflow to include the steps to run SchemaSpy on a PG instance set up during the GHA workflow to document the results data model. Credit to https://blog.devops.dev/generate-db-documentation-and-deploy-in-github-4ef7a3132401.

Additional work required:

  • Currently the SchemaSpy documentation is minimal - more work is required to add proper table descriptions and in some cases column descriptions. Details for this are found in extras/rdms/schema_meta.xml
  • I need to add additional navigation to the Strategus documentation pages to link to the results data model documentation produced by SchemaSpy.
  • Site documentation will come from the gh-pages branch of this repo so when Strategus v1.0 is released, I need to update the repo configuration.

@anthonysena anthonysena linked an issue Sep 18, 2024 that may be closed by this pull request
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codecov bot commented Sep 20, 2024

Codecov Report

Attention: Patch coverage is 89.39394% with 7 lines in your changes missing coverage. Please review.

Project coverage is 90.89%. Comparing base (46f97a0) to head (e7c7506).
Report is 2 commits behind head on v1.0-main.

Files with missing lines Patch % Lines
R/Module-CohortIncidence.R 50.00% 5 Missing ⚠️
R/Module-Characterization.R 77.77% 2 Missing ⚠️
Additional details and impacted files
@@              Coverage Diff              @@
##           v1.0-main     #167      +/-   ##
=============================================
+ Coverage      90.12%   90.89%   +0.77%     
=============================================
  Files             14       14              
  Lines           1752     1802      +50     
=============================================
+ Hits            1579     1638      +59     
+ Misses           173      164       -9     
Flag Coverage Δ
90.89% <89.39%> (?)

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@anthonysena anthonysena merged commit fc2c9d1 into v1.0-main Sep 30, 2024
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anthonysena added a commit that referenced this pull request Oct 7, 2024
* Add functions to expose rdms for each module and test
* Create full data model SQL
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Document results data model for modules
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