bugfix: update view code params to take constant not constants

.github/workflows/test.yml

@@ -76,14 +76,23 @@ jobs:
       - name: Run install goal
         env:
           R_KEEP_PKG_SOURCE: yes
-          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
         run: |
           mvn --batch-mode install \
+          -pl '!site,!benchmark'
+        timeout-minutes: 60
+
+      - name: Run SonarCloud analysis
+        # Secrets are not available for pull requests from forks.
+        if: env.SONAR_TOKEN != ''
+        env:
+          SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
+        run: |
+          mvn --batch-mode \
           org.sonarsource.scanner.maven:sonar-maven-plugin:sonar \
           -Dsonar.projectKey=aehrc_pathling -Dsonar.organization=aehrc \
           -Dsonar.host.url=https://sonarcloud.io \
           -pl '!site,!benchmark'
-        timeout-minutes: 60
+        timeout-minutes: 10
 
       - name: Upload test artifacts
         if: always()

lib/R/R/view.R

@@ -20,7 +20,7 @@
 #' @param ds The DataSource object containing the data to be queried.
 #' @param resource A string representing the type of FHIR resource that the view is based upon, e.g. 'Patient' or 'Observation'.
 #' @param select A list of columns and nested selects to include in the view. Each element should be a list with appropriate structure.
-#' @param constants An optional list of constants that can be used in FHIRPath expressions.
+#' @param constant An optional list of constants that can be used in FHIRPath expressions.
 #' @param where An optional list of FHIRPath expressions that can be used to filter the view.
 #' @param json An optional JSON string representing the view definition, as an alternative to providing the parameters as R objects.
 #' @return A Spark DataFrame containing the results of the view.
@@ -66,7 +66,7 @@
 #'   )
 #' )
 #' }
-ds_view <- function(ds, resource, select = NULL, constants = NULL, where = NULL, json = NULL) {
+ds_view <- function(ds, resource, select = NULL, constant = NULL, where = NULL, json = NULL) {
   jquery <- j_invoke(ds, "view", as.character(resource))
 
   if (!is.null(json)) {
@@ -83,8 +83,8 @@ ds_view <- function(ds, resource, select = NULL, constants = NULL, where = NULL,
       query$select <- select
     }
 
-    if (!is.null(constants)) {
-      query$constants <- constants
+    if (!is.null(constant)) {
+      query$constant <- constant
     }
 
     if (!is.null(where)) {

lib/R/tests/testthat/test-view.R

@@ -100,3 +100,35 @@ test_that("test SOF view with components", {
   expect_equal(colnames(sof_result), colnames(ResultRow))
   expect_equal(sof_result %>% sdf_collect(), ResultRow)
 })
+
+
+# test SOF view with constants
+test_that("test SOF view with constants", {
+  # expectations
+  ResultRow <- tibble::tibble(
+    id = c("8ee183e2-b3c0-4151-be94-b945d6aa8c6d"),
+    family_name = c("Krajcik437")
+  )
+
+  # actuals
+  sof_result <- ds_view(
+    test_data_source(),
+    resource = "Patient",
+    constant = list(
+      list(name = "filter_id", valueUuid = "8ee183e2-b3c0-4151-be94-b945d6aa8c6d")
+    ),
+    select = list(
+      list(
+        column = list(
+          list(path = "id", name = "id"),
+          list(path = "name.first().family", name = "family_name")
+        )
+      )
+    ),
+    where = list(
+      list(path = "id = %filter_id")
+    )
+  )
+  expect_equal(colnames(sof_result), colnames(ResultRow))
+  expect_equal(sof_result %>% sdf_collect(), ResultRow)
+})

lib/python/pathling/datasource.py

@@ -72,7 +72,7 @@ def view(
         self,
         resource: Optional[str] = None,
         select: Optional[Sequence[Dict]] = None,
-        constants: Optional[Sequence[Dict]] = None,
+        constant: Optional[Sequence[Dict]] = None,
         where: Optional[Sequence[Dict]] = None,
         json: Optional[str] = None,
     ) -> DataFrame:
@@ -82,7 +82,7 @@ def view(
         :param resource: The FHIR resource that the view is based upon, e.g. 'Patient' or
                'Observation'.
         :param select: A list of columns and nested selects to include in the view.
-        :param constants: A list of constants that can be used in FHIRPath expressions.
+        :param constant: A list of constants that can be used in FHIRPath expressions.
         :param where: A list of FHIRPath expressions that can be used to filter the view.
         :param json: A JSON string representing the view definition, as an alternative to providing
                the parameters as Python objects.
@@ -96,7 +96,7 @@ def view(
             args = locals()
             query = {
                 key: args[key]
-                for key in ["resource", "select", "constants", "where"]
+                for key in ["resource", "select", "constant", "where"]
                 if args[key] is not None
             }
             query_json = dumps(query)

lib/python/tests/test_view.py

@@ -47,6 +47,30 @@ def test_view_on_ndjson(ndjson_test_data_dir, pathling_ctx):
     ]
 
 
+def test_view_with_constants(ndjson_test_data_dir, pathling_ctx):
+    """Reproduces #2574: view with constants fails to resolve constant references in where clause."""
+
+    data_source = pathling_ctx.read.ndjson(ndjson_test_data_dir)
+    result = data_source.view(
+        resource="Patient",
+        constant=[
+            {"name": "filter_id", "valueUuid": "8ee183e2-b3c0-4151-be94-b945d6aa8c6d"}
+        ],
+        select=[
+            {
+                "column": [
+                    {"path": "id", "name": "id"},
+                    {"path": "name.first().family", "name": "family_name"},
+                ]
+            }
+        ],
+        where=[{"path": "id = %filter_id"}],
+    )
+    assert result.collect() == [
+        ResultRow("8ee183e2-b3c0-4151-be94-b945d6aa8c6d", "Krajcik437"),
+    ]
+
+
 ConditionCodingRow = Row("id", "code_text", "system", "code", "display")