Merge pull request #114 from ramses-antibiotics/maint/dbplyr2.4

Maint/dbplyr2.4
ramses-antibiotics · Nov 19, 2023 · 586c406 · 586c406
2 parents ebd423f + 0d54256
commit 586c406
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.7.0
+Version: 0.7.1
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -31,7 +31,7 @@ Imports:
     DBI,
     rlang,
     dplyr (>= 1.1.0),
-    dbplyr (>= 2.3.2),
+    dbplyr (>= 2.4.0),
     tidyselect (>= 1.2.0),
     magrittr,
     duckdb (>= 0.4.0),
@@ -59,11 +59,12 @@ Suggests:
     R.utils,
     comorbidity,
     RPostgres,
-    gh (>= 1.3.0)
+    gh (>= 1.3.0),
+    vctrs
 Remotes: 
     ramses-antibiotics/snomedizer
 RdMacros: Rdpack    
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 VignetteBuilder: knitr,rmarkdown
 Collate: 
     'Ramses-deprecated.R'

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,14 @@
 
+# Ramses 0.7.1
+
+*19 November 2023* 
+
+## Changed
+
+- Now requires minimum `dbplyr` v2.4.0.
+- Unit test maintenance required by `dbplyr` v2.4.0.
+
+
 # Ramses 0.7.0
 
 *11 April 2023* 

diff --git a/tests/testthat/test-objects.R b/tests/testthat/test-objects.R
@@ -68,16 +68,14 @@ test_that("Patient..interface_methods DuckDB", {
   expect_equal(capture.output(patient_object)[1],
                "Patient 99999999999 ")
   # COMPUTE 
-  expect_equal(
-    patient_object@record$lazy_query$x$x,
-    structure("patients", class = c("ident", "character"))
-  )
+  expect_is(patient_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(patient_object@record$lazy_query$x$x, "table"), "patients")
+
   patient_object_computed <- compute(patient_object)
+
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            patient_object_computed@record$lazy_query$x
-          ))
+          vctrs::field(patient_object_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -119,16 +117,14 @@ test_that("Patient..interface_methods Postgres", {
   expect_equal(capture.output(patient_object)[1],
                "Patient 99999999999 ")
   # COMPUTE 
-  expect_equal(
-    patient_object@record$lazy_query$x$x,
-    structure("patients", class = c("ident", "character"))
-  )
+  expect_is(patient_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(patient_object@record$lazy_query$x$x, "table"), "patients")
+
   patient_object_computed <- compute(patient_object)
+
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            patient_object_computed@record$lazy_query$x
-          ))
+          vctrs::field(patient_object_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -278,16 +274,16 @@ test_that("MedicationRequest..interface_methods DuckDB", {
   )
 
   # COMPUTE 
+  expect_is(med_req_object@record$lazy_query$x$x, "dbplyr_table_ident")
   expect_equal(
-    med_req_object@record$lazy_query$x$x,
-    structure("drug_prescriptions", class = c("ident", "character"))
+    vctrs::field(med_req_object@record$lazy_query$x$x, "table"),
+    "drug_prescriptions"
   )
+
   med_req_object_computed <- compute(med_req_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            med_req_object_computed@record$lazy_query$x
-          ))
+          vctrs::field(med_req_object_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -381,16 +377,13 @@ test_that("MedicationRequest..interface_methods Postgres", {
   )
 
   # COMPUTE 
-  expect_equal(
-    med_req_object@record$lazy_query$x$x,
-    structure("drug_prescriptions", class = c("ident", "character"))
-  )
+  expect_is(med_req_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(med_req_object@record$lazy_query$x$x, "table"), "drug_prescriptions")
+
   med_req_object_computed <- compute(med_req_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            med_req_object_computed@record$lazy_query$x
-          ))
+          vctrs::field(med_req_object_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -533,38 +526,31 @@ test_that("TherapyEpisode..interface_methods DuckDB", {
   )
 
   # COMPUTE 
-  expect_equal(
-    therapy_object@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
-  )
+  expect_is(therapy_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object@record$lazy_query$x$x, "table"),
+               "drug_therapy_episodes")
   therapy_object_computed <- compute(therapy_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    therapy_object_multi@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
+          vctrs::field(therapy_object_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(therapy_object_multi@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object_multi@record$lazy_query$x$x, "table"), 
+               "drug_therapy_episodes")
   therapy_object_multi_computed <- compute(therapy_object_multi)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_multi_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    therapy_object_multi4@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
+          vctrs::field(therapy_object_multi_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(therapy_object_multi4@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object_multi4@record$lazy_query$x$x, "table"), 
+               "drug_therapy_episodes")
   therapy_object_multi_computed4 <- compute(therapy_object_multi4)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_multi_computed4@record$lazy_query$x
-          ))
+          vctrs::field(therapy_object_multi_computed4@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -699,38 +685,28 @@ test_that("TherapyEpisode..interface_methods Postgres", {
   )
 
   # COMPUTE 
-  expect_equal(
-    therapy_object@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
-  )
+  expect_is(therapy_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object@record$lazy_query$x$x, "table"), "drug_therapy_episodes")
   therapy_object_computed <- compute(therapy_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    therapy_object_multi@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
+          vctrs::field(therapy_object_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(therapy_object_multi@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object_multi@record$lazy_query$x$x, "table"), "drug_therapy_episodes")
   therapy_object_multi_computed <- compute(therapy_object_multi)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_multi_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    therapy_object_multi4@record$lazy_query$x$x,
-    structure("drug_therapy_episodes", class = c("ident", "character"))
+          vctrs::field(therapy_object_multi_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(therapy_object_multi4@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(therapy_object_multi4@record$lazy_query$x$x, "table"), "drug_therapy_episodes")
   therapy_object_multi_computed4 <- compute(therapy_object_multi4)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            therapy_object_multi_computed4@record$lazy_query$x
-          ))
+          vctrs::field(therapy_object_multi_computed4@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -898,38 +874,28 @@ test_that("Encounter..interface_methods DuckDB", {
   )
 
   # COMPUTE 
-  expect_equal(
-    encounter_object@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
-  )
+  expect_is(encounter_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_computed <- compute(encounter_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    encounter_object_multi@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
+          vctrs::field(encounter_object_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(encounter_object_multi@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object_multi@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_multi_computed <- compute(encounter_object_multi)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_multi_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    encounter_object_multi5@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
+          vctrs::field(encounter_object_multi_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(encounter_object_multi5@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object_multi5@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_multi5_computed <- compute(encounter_object_multi5)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_multi5_computed@record$lazy_query$x
-          ))
+          vctrs::field(encounter_object_multi5_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT
@@ -1071,38 +1037,28 @@ test_that("Encounter..interface_methods Postgres", {
   )
 
   # COMPUTE 
-  expect_equal(
-    encounter_object@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
-  )
+  expect_is(encounter_object@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_computed <- compute(encounter_object)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    encounter_object_multi@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
+          vctrs::field(encounter_object_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(encounter_object_multi@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object_multi@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_multi_computed <- compute(encounter_object_multi)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_multi_computed@record$lazy_query$x
-          ))
-  )
-  expect_equal(
-    encounter_object_multi5@record$lazy_query$x$x,
-    structure("inpatient_episodes", class = c("ident", "character"))
+          vctrs::field(encounter_object_multi_computed@record$lazy_query$x, "table"))
   )
+
+  expect_is(encounter_object_multi5@record$lazy_query$x$x, "dbplyr_table_ident")
+  expect_equal(vctrs::field(encounter_object_multi5@record$lazy_query$x$x, "table"), "inpatient_episodes")
   encounter_object_multi5_computed <- compute(encounter_object_multi5)
   expect_true(
     grepl("^dbplyr_", 
-          as.character(
-            encounter_object_multi5_computed@record$lazy_query$x
-          ))
+          vctrs::field(encounter_object_multi5_computed@record$lazy_query$x, "table"))
   )
 
   # COLLECT