Use external concept counts #1136
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…s not already exist. Skip results datamode test if SKIP_DB_TESTS is TRUE.
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Only minor changes suggested - add when ready.
A possible change if you want would be to make the CD concept counts table here identical to the fields needed in the achilles table - before I go and check @ablack3 @cebarboza, are they substantially different?
R/RunDiagnostics.R
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| conceptCountsTable <- "#concept_counts" | ||
| } | ||
| } else { | ||
| if (conceptCountsTable == "#concept_counts") { |
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This should probably be substr(conceptCountsTable, 1, 1) == "#" as otherwise #my_temp_table will render as work_database_schema.#my_temp_table which will crash on some systems
R/RunDiagnostics.R
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| snakeCaseToCamelCase = TRUE, | ||
| tempEmulationSchema = getOption("sqlRenderTempEmulationSchena") | ||
| ) | ||
| if (!identical(vocabVersion, vocabVersionExternalConceptCountsTable[1,1])) { |
tests/testthat/test-other.R
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| if (dbms == "sqlite") { | ||
| # Creating externalConceptCounts | ||
| sql_lite_path <- file.path(test_path(), databaseFile) | ||
| connectionDetails <- createConnectionDetails(dbms= "sqlite", server = sql_lite_path) |
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We may want to build tests out for real databases but this can likely wait - I think adding a pre-computed counts table should speed up the other unit tests
The achilles table we would like to use has "concept_id", "record_count", "descendant_record_count", and we would like to add "person_count" and "descendant_person_count" so we could use those column names. |
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We are adding two parameters that depend on each other: Let's list out the expected behavior:
I'm wondering if we could do this with just one parameter, the cohortCountsTable. if it exists we use it and if not we recreate it. |
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@cebarboza @ablack3 I'm going to release 3.3.0 today for the HADES wide lock file so this will make its way in to a 3.4.0 release whenever it becomes ready |
Moving this PR to the OHDSI organization so we can run all the tests in github actions.