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Refactor test files#1133

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ablack3 wants to merge 25 commits intoOHDSI:v3.3.0_branchOHDSI/CohortDiagnostics:v3.3.0_branchfrom darwin-eu-dev:refactor_test_filesdarwin-eu-dev/CohortDiagnostics:refactor_test_filesCopy head branch name to clipboard

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Commits on Jun 12, 2024

• add option to use Achilles for concept counts

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Commits on Sep 13, 2024

• Merge branch 'achilles_concept_counts' into v3.3.0

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• refactor setup test file to more easily allow for running tests on one or multiple databases.

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• switch to base pipe in tests to avoid loading dplyr when running tests

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• fix database names in setup test file

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Commits on Sep 15, 2024

• import and re-export getCohortCounts from CohortGenerator.

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• remove unused parameter. inline the checkIfCohortInstatiated function. remove the internal getCohortCounts function since we have it from CohortGenerator.

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• remove redundant min cell count supression. Don't assume we have write access to the cdm schema by default.

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• use "achillesDatabaseSchema" for the location of the achilles tables. Don't assume we can write to cdmDatabaseSchema.

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• rename the file runDiagnostics to executeDiagnostics to match the main function it contains.

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• remove redundant parameter instantiatedCohorts. All cohorts in cohortDefinitionSet are instantiated and have records at this point in the program exectution.

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• refactor makeDataExportable and remove the enforceMinCellValueInDataframe function.

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• add parameter to getResultsDataModelSpecification to return just the specification for one table from the results data model.

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• move has data to private.R

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• remove sql files we no longer need.

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• use achilles_database_schema for the location of the achilles tables.

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• update documentation

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• create the concept table in executeDiagnostics

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• update setup test file.

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Commits on Sep 16, 2024

• add parameter for workDatabaseSchema where concept counts table can be created and will persist. Also fix the callingArgsJson. see OHDSI#1070

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Commits on Sep 17, 2024

• refactor againstCdm test file to use loop over databases

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• fix sql errors

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• export the createConceptCounts table

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• undo pipe switch just to reduce the files changed.

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• fix setup file

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