From 1140d81b81fe67c49c93f3392cb641e26870b52d Mon Sep 17 00:00:00 2001
From: nmercadeb <nmercade147@gmail.com>
Date: Wed, 16 Oct 2024 14:02:35 +0100
Subject: [PATCH 1/6] test union and collapse

---
 R/unionCohorts.R                       |  4 ++-
 tests/testthat/test-collapseCohorts.R  |  1 +
 tests/testthat/test-intersectCohorts.R | 34 +++++++++++++++++++++
 tests/testthat/test-unionCohorts.R     | 42 +++++++++++++++++++++++++-
 4 files changed, 79 insertions(+), 2 deletions(-)

diff --git a/R/unionCohorts.R b/R/unionCohorts.R
index 4264114e..970c7eaf 100644
--- a/R/unionCohorts.R
+++ b/R/unionCohorts.R
@@ -63,9 +63,11 @@ unionCohorts <- function(cohort,
   tmpTable  <- omopgenerics::uniqueTableName()
   unionedCohort <- cohort |>
     dplyr::filter(.data$cohort_definition_id %in% .env$cohortId) |>
+    PatientProfiles::addObservationPeriodId(name = tmpTable) |>
     joinOverlap(name = tmpTable,
-                by = "subject_id",
+                by = c("observation_period_id", "subject_id"),
                 gap = gap) |>
+    dplyr::select(!"observation_period_id") |>
     dplyr::mutate(cohort_definition_id = 1L) |>
     dplyr::relocate(dplyr::all_of(omopgenerics::cohortColumns("cohort"))) |>
     dplyr::compute(name = tmpTable, temporary = FALSE)
diff --git a/tests/testthat/test-collapseCohorts.R b/tests/testthat/test-collapseCohorts.R
index 6d57edcd..6bf612ea 100644
--- a/tests/testthat/test-collapseCohorts.R
+++ b/tests/testthat/test-collapseCohorts.R
@@ -307,5 +307,6 @@ test_that("multiple observation periods", {
   expect_true(nrow(cdm$cohort_1 |>
                      dplyr::collect()) == 2)
 
+  PatientProfiles::mockDisconnect(cdm)
 
 })
diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index c7a7a0d7..b099ae7f 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -591,3 +591,37 @@ test_that("records combined for gap must be in the same observation period", {
 
   PatientProfiles::mockDisconnect(cdm)
 })
+
+test_that("multiple observation periods", {
+  cdm_local <- omock::mockCdmReference() |>
+    omock::mockPerson(n = 4, seed = 1)
+  cdm_local$observation_period <- dplyr::tibble(
+    "observation_period_id" = as.integer(1:7),
+    "person_id" = as.integer(c(1, 1, 1, 2, 2, 3, 4)),
+    "observation_period_start_date" = as.Date(c(
+      "2000-01-01", "2001-01-01", "2003-01-01", "2001-01-01", "2002-01-01",
+      "2000-01-01", "2000-01-01"
+    )),
+    "observation_period_end_date" =as.Date(c(
+      "2000-12-20", "2002-01-01", "2005-01-01", "2001-12-31", "2004-01-01",
+      "2004-01-01", "2003-01-01"
+    )),
+    "period_type_concept_id" = NA_integer_
+  )
+  cdm_local$cohort <- dplyr::tibble(
+    "cohort_definition_id" = as.integer(c(1, 1, 1, 1, 2, 2)),
+    "subject_id" = as.integer(c(1, 1, 1, 2, 2, 1)),
+    "cohort_start_date" = as.Date(c(
+      "2000-01-01", "2000-12-01", "2001-01-01", "2001-01-01", "2002-01-01", "2003-01-01"
+    )),
+    "cohort_end_date" =as.Date(c(
+      "2000-05-20", "2000-12-20", "2001-04-01", "2001-12-30", "2003-01-01", "2004-01-01"
+    ))
+  )
+  cdm <- cdm_local |> copyCdm()
+  cdm$cohort <- cdm$cohort |> omopgenerics::newCohortTable()
+  cdm$cohort <- cdm$cohort |> intersectCohorts(gap = 9999)
+  expect_true(cdm$cohort |> dplyr::tally() |> dplyr::pull(n) == 0)
+
+  PatientProfiles::mockDisconnect(cdm)
+})
diff --git a/tests/testthat/test-unionCohorts.R b/tests/testthat/test-unionCohorts.R
index 1d92588b..30039a59 100644
--- a/tests/testthat/test-unionCohorts.R
+++ b/tests/testthat/test-unionCohorts.R
@@ -4,7 +4,7 @@ test_that("unionCohorts works", {
     omock::mockObservationPeriod(seed = 1) |>
     omock::mockCohort(name = c("cohort1"), numberCohorts = 4, seed = 1)
   cdm <- cdm_local |> copyCdm()
-   # simple example
+  # simple example
   cdm$cohort2 <- unionCohorts(cdm$cohort1, name = "cohort2")
   expect_true(all(
     cdm$cohort2 %>% dplyr::pull("cohort_start_date") %>% sort() ==
@@ -297,3 +297,43 @@ test_that("keep original cohorts", {
 
   PatientProfiles::mockDisconnect(cdm)
 })
+
+test_that("multiple observation periods", {
+  cdm_local <- omock::mockCdmReference() |>
+    omock::mockPerson(n = 4, seed = 1)
+  cdm_local$observation_period <- dplyr::tibble(
+    "observation_period_id" = as.integer(1:7),
+    "person_id" = as.integer(c(1, 1, 1, 2, 2, 3, 4)),
+    "observation_period_start_date" = as.Date(c(
+      "2000-01-01", "2001-01-01", "2003-01-01", "2001-01-01", "2002-01-01",
+      "2000-01-01", "2000-01-01"
+    )),
+    "observation_period_end_date" =as.Date(c(
+      "2000-12-20", "2002-01-01", "2005-01-01", "2001-12-31", "2004-01-01",
+      "2004-01-01", "2003-01-01"
+    )),
+    "period_type_concept_id" = NA_integer_
+  )
+  cdm_local$cohort <- dplyr::tibble(
+    "cohort_definition_id" = as.integer(c(1, 1, 1, 1, 2, 2)),
+    "subject_id" = as.integer(c(1, 1, 1, 2, 2, 1)),
+    "cohort_start_date" = as.Date(c(
+      "2000-01-01", "2000-12-01", "2001-01-01", "2001-01-01", "2002-01-01", "2003-01-01"
+    )),
+    "cohort_end_date" =as.Date(c(
+      "2000-05-20", "2000-12-20", "2001-04-01", "2001-12-30", "2003-01-01", "2004-01-01"
+    ))
+  )
+  cdm <- cdm_local |> copyCdm()
+  cdm$cohort <- cdm$cohort |> omopgenerics::newCohortTable() |> unionCohorts(gap = 99999)
+  expect_equal(
+    collectCohort(cdm$cohort, 1),
+    dplyr::tibble(
+      "subject_id" = as.integer(c(1, 1, 1, 2, 2)),
+      "cohort_start_date" = as.Date(c("2000-01-01", "2001-01-01", "2003-01-01", "2001-01-01", "2002-01-01")),
+      "cohort_end_date" = as.Date(c("2000-12-20", "2001-04-01", "2004-01-01", "2001-12-30", "2003-01-01"))
+    )
+  )
+
+  PatientProfiles::mockDisconnect(cdm)
+})

From 81c56f806bf6814a37e02a4cc3e9561408b96f36 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Wed, 16 Oct 2024 15:11:19 +0100
Subject: [PATCH 2/6] test intersect

---
 R/intersectCohorts.R                   |  8 ++++++--
 tests/testthat/test-intersectCohorts.R | 23 +++++++++++++++--------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/R/intersectCohorts.R b/R/intersectCohorts.R
index 94fd92e3..57e01de6 100644
--- a/R/intersectCohorts.R
+++ b/R/intersectCohorts.R
@@ -131,8 +131,12 @@ intersectCohorts <- function(cohort,
     dplyr::compute(name = tblName, temporary = FALSE)
   if (cohortOut |> dplyr::tally() |> dplyr::pull("n") > 0) {
     cohortOut <- cohortOut %>%
-      dplyr::compute(name = tblName, temporary = FALSE) |>
-      joinOverlap(name = tblName, gap = gap)
+      PatientProfiles::addObservationPeriodId(name = tblName) |>
+      joinOverlap(
+        name = tblName, gap = gap,
+        by = c("observation_period_id", "cohort_definition_id", "subject_id")
+      ) |>
+      dplyr::select(!"observation_period_id")
   }
 
   # attributes
diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index b099ae7f..85f55559 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -608,20 +608,27 @@ test_that("multiple observation periods", {
     )),
     "period_type_concept_id" = NA_integer_
   )
-  cdm_local$cohort <- dplyr::tibble(
-    "cohort_definition_id" = as.integer(c(1, 1, 1, 1, 2, 2)),
-    "subject_id" = as.integer(c(1, 1, 1, 2, 2, 1)),
+  cdm_local$cohort1 <- dplyr::tibble(
+    "cohort_definition_id" = as.integer(c(1, 2, 1, 2)),
+    "subject_id" = as.integer(c(1, 1, 1, 1)),
     "cohort_start_date" = as.Date(c(
-      "2000-01-01", "2000-12-01", "2001-01-01", "2001-01-01", "2002-01-01", "2003-01-01"
+      "2000-01-01", "2000-12-01", "2001-01-01", "2001-01-01"
     )),
     "cohort_end_date" =as.Date(c(
-      "2000-05-20", "2000-12-20", "2001-04-01", "2001-12-30", "2003-01-01", "2004-01-01"
+      "2000-12-20", "2000-12-20", "2001-04-01", "2001-12-30"
     ))
   )
   cdm <- cdm_local |> copyCdm()
-  cdm$cohort <- cdm$cohort |> omopgenerics::newCohortTable()
-  cdm$cohort <- cdm$cohort |> intersectCohorts(gap = 9999)
-  expect_true(cdm$cohort |> dplyr::tally() |> dplyr::pull(n) == 0)
+  cdm$cohort1 <- cdm$cohort1 |> omopgenerics::newCohortTable()
+  cdm$cohort1 <- cdm$cohort1 |> intersectCohorts(gap = 9999)
+  expect_equal(
+    collectCohort(cdm$cohort1, 1),
+    dplyr::tibble(
+      "subject_id" = as.integer(c(1, 1)),
+      "cohort_start_date" = as.Date(c("2001-01-01", "2001-12-30")),
+      "cohort_end_date" = as.Date(c("2000-01-01", "2000-12-20"))
+    )
+  )
 
   PatientProfiles::mockDisconnect(cdm)
 })

From 592b1e993c9a857e861f094e6eaeadef8884a87b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Wed, 16 Oct 2024 15:17:38 +0100
Subject: [PATCH 3/6] checks

---
 tests/testthat/test-intersectCohorts.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index 85f55559..1428d54b 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -625,8 +625,8 @@ test_that("multiple observation periods", {
     collectCohort(cdm$cohort1, 1),
     dplyr::tibble(
       "subject_id" = as.integer(c(1, 1)),
-      "cohort_start_date" = as.Date(c("2001-01-01", "2001-12-30")),
-      "cohort_end_date" = as.Date(c("2000-01-01", "2000-12-20"))
+      "cohort_start_date" = as.Date(c("2000-01-01", "2001-01-01")),
+      "cohort_end_date" = as.Date(c("2000-12-20", "2001-12-30"))
     )
   )
 

From 319240370c15ab007fe5e5ea5ec51bfaf300cbde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Wed, 16 Oct 2024 17:24:05 +0100
Subject: [PATCH 4/6] Update test-intersectCohorts.R

---
 tests/testthat/test-intersectCohorts.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index 1428d54b..53de670b 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -457,8 +457,6 @@ test_that("codelist", {
       "drug_exposure_start_date" = as.Date(.data$drug_exposure_start_date, origin = "2010-01-01"),
       "drug_exposure_end_date" = as.Date(.data$drug_exposure_end_date, origin = "2010-01-01")
     )
-  cdm_local$observation_period <- cdm_local$observation_period|>
-    dplyr::mutate(observation_period_start_date = as.Date("1990-01-01"), observation_period_end_date = as.Date("2020-01-01"))
 
   cdm <- cdm_local |> copyCdm()
 

From 412bffaebc45ab3db42e149893a1c000cdf4b10c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Wed, 16 Oct 2024 17:24:30 +0100
Subject: [PATCH 5/6] Update test-intersectCohorts.R

---
 tests/testthat/test-intersectCohorts.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index 53de670b..cacda5f4 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -434,7 +434,7 @@ test_that("codelist", {
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(n = 3) |>
     omock::mockObservationPeriod() |>
-    omock::mockCohort()
+    omock::mockCohort(seed = 1)
   cdm_local$concept <- dplyr::tibble(
     "concept_id" = c(1, 2, 3),
     "concept_name" = c("my concept 1", "my concept 2", "my concept 3"),
@@ -457,6 +457,8 @@ test_that("codelist", {
       "drug_exposure_start_date" = as.Date(.data$drug_exposure_start_date, origin = "2010-01-01"),
       "drug_exposure_end_date" = as.Date(.data$drug_exposure_end_date, origin = "2010-01-01")
     )
+  cdm_local$observation_period <- cdm_local$observation_period |>
+    dplyr::mutate(observation_period_start_date = as.Date("1990-01-01"), observation_period_end_date = as.Date("2020-01-01"))
 
   cdm <- cdm_local |> copyCdm()
 

From 167fbc2c72a249ecb4d95082198197fc1fdc463f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?N=C3=BAria=20Mercad=C3=A9-Besora?=
 <61558739+nmercadeb@users.noreply.github.com>
Date: Wed, 16 Oct 2024 20:48:44 +0100
Subject: [PATCH 6/6] checks

---
 R/mockCohortConstructor.R              | 2 +-
 tests/testthat/test-intersectCohorts.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/mockCohortConstructor.R b/R/mockCohortConstructor.R
index 3a9e1a40..f62b425e 100644
--- a/R/mockCohortConstructor.R
+++ b/R/mockCohortConstructor.R
@@ -56,7 +56,7 @@ mockCohortConstructor <- function(nPerson = 10,
   }
 
   if (!is.null(conceptIdClass) && !is.null(conceptId)) {
-    cdm <- cdm |> omock::mockConcepts(conceptSet = conceptId, domain = conceptIdClass)
+    cdm <- cdm |> omock::mockConcepts(conceptSet = conceptId, domain = conceptIdClass, seed = seed)
   }
 
   if (drugExposure) {
diff --git a/tests/testthat/test-intersectCohorts.R b/tests/testthat/test-intersectCohorts.R
index cacda5f4..dd57cd3f 100644
--- a/tests/testthat/test-intersectCohorts.R
+++ b/tests/testthat/test-intersectCohorts.R
@@ -458,7 +458,7 @@ test_that("codelist", {
       "drug_exposure_end_date" = as.Date(.data$drug_exposure_end_date, origin = "2010-01-01")
     )
   cdm_local$observation_period <- cdm_local$observation_period |>
-    dplyr::mutate(observation_period_start_date = as.Date("1990-01-01"), observation_period_end_date = as.Date("2020-01-01"))
+    dplyr::mutate(observation_period_start_date = as.Date("1980-01-01"), observation_period_end_date = as.Date("2020-01-01"))
 
   cdm <- cdm_local |> copyCdm()