social factors (#536)

* remove Lookup smoking status mapping

* add source primary Id

* simplify name and move order so mapper and mapping work

* change common functions and fix date filtering

* update mock and fix tests, TODO is legacy

* add source primaryId for alcohol plugin

* Use the correct Id for history

* fix data spec

* update logic to identify correct rows to keep and eliminate edge case

* inner join removes unmapped data tidy up other logic

* inner join to remove redunant mapping and tidy up code

* fix select

* fix case for GH to work

* add suggested name changes to add clarity

Author: emgm06

test/uclh/test_observation_mapping.R

@@ -6,10 +6,46 @@ source(here("test/uclh/mapping_expectations.R"))
 source(here("test/uclh/utils.R"))
 
 test_that("smoking table is valid", {
-  mapping <- omop_plugins$observation$smoking_Patient$mapping(mock_project$conns$caboodle)
-  expect_concept_matches_spec(mapping, value_as_concept_id, omop_spec$observation)
-  # TODO Smoking has a local SNOMED code in the mock data, this should be fixed
-  # expect_valid_omop_mapping(mapping,SmokingStatus,value_as_concept_id)
+  mapping <- omop_plugins$observation$smoking$mapping(mock_project$conns$caboodle, trim = FALSE)
+  expect_valid_omop_mapping(mapping, SmokingStatus, value_as_concept_id)
+
+  # smoking value_as_concept_id are non-standard
+  mapping |>
+    pull(standard_concept) |>
+    expect_all_na()
+})
+
+test_that("social factors keep correct rows", {
+  source(here::here("mapping/UCLH/epic_common/social_factors_common.R"), local = TRUE)
+  # Given that there are two VisitIds in SocialFactorsFactX
+  # WHEN both Ids are populated
+  # THEN check row relates to the same patient
+
+  valid_mapping_pdk <- 91L
+  invalid_row_Id <- 165L
+
+  social_factors <- fetch_social_factors_for_cohort(mock_project$conns, mock_project$cohort)
+
+  social_factors |>
+    pull(PatientPersistentId) |>
+    expect_setequal(valid_mapping_pdk)
+
+  invalid_factors <- tbl(mock_project$conns$caboodle, "SocialFactorsFactX") |>
+    filter(SocialFactorsId == invalid_row_Id)
+
+  # expect the invalid row to not exist after running common function
+  social_factors |>
+    inner_join(collect(invalid_factors), join_by(SocialFactorsId)) |>
+    expect_no_rows()
+
+  # expect the invalid row to link to two patients in the raw table
+  invalid_factors |>
+    select(VisitId, HistoryVisitId) |>
+    pivot_longer(everything()) |>
+    left_join(tbl(mock_project$conns$caboodle, "Encounter"), join_by(value == VisitId)) |>
+    distinct(PatientPersistentId) |>
+    collect() |>
+    expect_row_count(2L)
 })
 
 test_that("observation Observation mapping has correct types", {