Development

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ROMOPAPI
 Title: ROMOPAPI
-Version: 2.1.1
+Version: 2.2.0
 Authors@R: 
     person("Javier", "Gracia-Tabuenca", , "javier.graciatabuenca@tuni.fi", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

Dockerfile

@@ -22,18 +22,18 @@ RUN apt-get update && apt-get install -y openjdk-8-jdk liblzma-dev libbz2-dev li
 
 # Install renv and restore packages
 ARG ROMOPAPI_BRANCH=main
-ARG BUILD_CACHE_BUSTER=3
+ARG BUILD_CACHE_BUSTER=5
 
 # Install renv and restore packages
 RUN --mount=type=secret,id=build_github_pat \
     cp /usr/local/lib/R/etc/Renviron /tmp/Renviron \
     && echo "GITHUB_PAT=$(cat /run/secrets/build_github_pat)" >> /usr/local/lib/R/etc/Renviron \
     && Rscript -e 'install.packages("remotes")' \
-    && Rscript -e 'remotes::install_github("FINNGEN/ROMOPAPI")' \
+    && Rscript -e 'remotes::install_github("FINNGEN/ROMOPAPI@'$ROMOPAPI_BRANCH'")' \
     && cp /tmp/Renviron /usr/local/lib/R/etc/Renviron;
 
 # Expose the port that the API will run on
-EXPOSE 8585
+EXPOSE 8564
 
 # Run the API server
-CMD ["Rscript", "-e", "ROMOPAPI::runApiServer(host = '0.0.0.0', port = 8585)"] 
+CMD ["Rscript", "-e", "ROMOPAPI::runApiServer(host = '0.0.0.0', port = 8564)"] 

NEWS.md

@@ -1,3 +1,7 @@
+# ROMOPAPI 
+- Added number_of_descendants to concepts with code counts
+- Added conceptId 21600744 to testing data
+
 # ROMOPAPI 2.1.1
 - Added caching concepts with code counts at startup
 

R/getCodeCounts.R

@@ -236,7 +236,8 @@ getCodeCounts <- function(
         dplyr::rename(node_record_counts = record_counts, node_descendant_record_counts = descendant_record_counts)
 
     # - Get concept details
-    conceptsWithCodeCounts <- getConceptsWithCodeCounts_memoise(CDMdbHandler, codeCountsTable = codeCountsTable)
+    conceptsWithCodeCounts <- getConceptsWithCodeCounts_memoise(CDMdbHandler, codeCountsTable = codeCountsTable) |> 
+        dplyr::select(-number_of_descendants)
     concepts <- familyTreeWithMappings |>
         dplyr::distinct(child_concept_id) |>
         dplyr::rename(concept_id = child_concept_id) |>

R/getConceptsWithCodeCounts.R

@@ -47,7 +47,7 @@ getConceptsWithCodeCounts <- function(
     SELECT DISTINCT 
         c.concept_id, 
         c.concept_name, c.domain_id, c.vocabulary_id, c.concept_class_id, c.standard_concept, c.concept_code,
-        cc.record_counts, cc.descendant_record_counts
+        cc.record_counts, cc.descendant_record_counts, cc.number_of_descendants
        FROM @vocabularyDatabaseSchema.concept c
        INNER JOIN @resultsDatabaseSchema.@codeCountsTable cc
        ON c.concept_id = cc.concept_id;"

R/runApiServer.R

@@ -8,7 +8,7 @@
 #' @param cohortTableHandlerConfig Configuration for connecting to the OMOP CDM database.
 #'   If NULL, uses test Eunomia database
 #' @param host Host address to run the API server on. Defaults to "127.0.0.1"
-#' @param port Port number to run the API server on. Defaults to 8585
+#' @param port Port number to run the API server on. Defaults to 8564
 #' @param buildCountsTable Logical indicating whether to build code counts tables. Defaults to FALSE
 #' @param ... Additional arguments passed to plumber::pr_run()
 #'
@@ -33,7 +33,7 @@
 runApiServer <- function(
     cohortTableHandlerConfig = NULL,
     host = "127.0.0.1",
-    port = 8585,
+    port = 8564,
     buildCountsTable = FALSE,
     ...) {
     #

README.md

@@ -26,19 +26,19 @@ library(ROMOPAPI)
 runApiServer()
 ```
 
-This will start the API server on port 8585.
+This will start the API server on port 8564.
 
 #### Testing endpoints
 
-The main endpoint for testing is: http://127.0.0.1:8585/report?conceptId=<concept_id>
+The main endpoint for testing is: http://127.0.0.1:8564/report?conceptId=<concept_id>
 
-For example, http://127.0.0.1:8585/report?conceptId=317009
+For example, http://127.0.0.1:8564/report?conceptId=317009
 
 This will return an HTML report for the concept id 317009.
 
 #### Production endpoints
 
-The main endpoint for production is: http://127.0.0.1:8585/getCodeCounts?conceptId=<concept_id>
+The main endpoint for production is: http://127.0.0.1:8564/getCodeCounts?conceptId=<concept_id>
 
 This will return the code counts for the concept ids 317009.
 
@@ -49,7 +49,7 @@ Separated in 3 tables:
 - `stratified_code_counts`: patient counts by conceptId stratified by gender, year, and age decile
 
 
-See the API documentation for more details: http://127.0.0.1:8585/__docs__/
+See the API documentation for more details: http://127.0.0.1:8564/__docs__/
 
 ### Running the API Server with a custom database
 
@@ -143,7 +143,7 @@ Based on the example output, getCodeCounts returns a list with 3 components:
 Existing docker image is available at: https://hub.docker.com/repository/docker/javiergrata/romopapi/
 
 ```
-docker run -p 8585:8585 javiergrata/romopapi
+docker run -p 8564:8564 javiergrata/romopapi
 ```
 
 ## Build the docker image
@@ -163,7 +163,7 @@ docker build --secret id=build_github_pat,src=GITHUBPAT.txt --build-arg ROMOPAPI
 ## Run the docker container
 
 ```
-docker run -p 8585:8585 romopapi
+docker run -p 8564:8564 romopapi
 ```
 
 

inst/plumber/plumber.R

@@ -58,7 +58,7 @@ function() {
 function() {
   concepts <- getConceptsWithCodeCounts_memoise(CDMdbHandler = CDMdbHandler)
   concepts <- concepts |>
-    dplyr::select(concept_id, concept_name, vocabulary_id, concept_code)
+    dplyr::select(concept_id, concept_name, vocabulary_id, concept_code, number_of_descendants)
   return(concepts)
 }
 

inst/sql/sql_server/createCodeCountsTable.sql

@@ -3,7 +3,8 @@ DROP TABLE IF EXISTS @resultsDatabaseSchema.@codeCountsTable;
 CREATE TABLE @resultsDatabaseSchema.@codeCountsTable (
   concept_id int,
   record_counts int,
-  descendant_record_counts int
+  descendant_record_counts int,
+  number_of_descendants int
 );
 
 INSERT INTO @resultsDatabaseSchema.@codeCountsTable 
@@ -57,7 +58,8 @@ descendant_counts AS (
     SELECT 
         ca.ancestor_concept_id AS concept_id,
         COALESCE(cc.record_counts, 0) AS record_counts,
-        SUM(COALESCE(cctosum.record_counts, 0)) AS descendant_record_counts
+        SUM(COALESCE(cctosum.record_counts, 0)) AS descendant_record_counts,
+        COUNT(*) AS number_of_descendants
     FROM
         temp_concept_ancestor ca 
     INNER JOIN
@@ -77,6 +79,7 @@ descendant_counts AS (
 SELECT 
     CAST(ccd.concept_id AS BIGINT) AS concept_id,
     CAST(ccd.record_counts AS BIGINT) AS record_counts,
-    CAST(ccd.descendant_record_counts AS BIGINT) AS descendant_record_counts
+    CAST(ccd.descendant_record_counts AS BIGINT) AS descendant_record_counts,
+    CAST(ccd.number_of_descendants AS BIGINT) AS number_of_descendants
 FROM
     descendant_counts ccd;

inst/testdata/data/createTestingData.R

@@ -9,10 +9,13 @@ conceptIds <- c(
     45596282, # ICD10: Asthma
     21601855, # ATC level 4: C10AA (Statins)
     320136, # Big graph, parent of Asthma snomed concept (Disorders of the respiratory system)
-    4024567# biger
+    4024567,# biger
+    21600744 # bug in plot
 )
 
 CDMdbHandler <- HadesExtras_createCDMdbHandlerFromList(test_cohortTableHandlerConfig, loadConnectionChecksLevel = "basicChecks")
+# uncomment to create code counts tables
+createCodeCountsTables(CDMdbHandler)
 helper_createSqliteDatabaseFromDatabase(
     CDMdbHandler,
     conceptIds = conceptIds,

tests/testmanual/manualtest-runApiServer.R

@@ -7,4 +7,4 @@ ROMOPAPI::runApiServer(
   buildCountsTable = FALSE
 )
 
-# http://127.0.0.1:8585/__docs__/
+# http://127.0.0.1:8564/__docs__/

tests/testthat/test-createCodeCountsTable.R

@@ -113,7 +113,8 @@ test_that("createCodeCountsTables works", {
     expect_equal(c(
       "concept_id",
       "record_counts",
-      "descendant_record_counts"
+      "descendant_record_counts",
+      "number_of_descendants"
     ))
 
   # check that descendant_record_counts is greater than or equal to record_counts
@@ -129,4 +130,27 @@ test_that("createCodeCountsTables works", {
     dplyr::count() |>
     dplyr::pull(n) |>
     expect_equal(code_counts |> dplyr::count() |> dplyr::pull(n))
+
+  # check that number_of_descendants is greater than or equal to 1
+  code_counts |>
+    dplyr::filter(number_of_descendants < 1) |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_equal(0)
+
+  # check that all with record_counts = descendant_record_counts have  number_of_descendants = 1
+  code_counts |>
+    dplyr::filter(record_counts == descendant_record_counts) |>
+    dplyr::filter(number_of_descendants != 1) |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_equal(0)
+
+  # check that all with number_of_descendants > 1 have record_counts > descendant_record_counts
+  code_counts |>
+    dplyr::filter(number_of_descendants > 1) |>
+    dplyr::filter(record_counts > descendant_record_counts) |>
+    dplyr::count() |>
+    dplyr::pull(n) |>
+    expect_equal(0)
 })

tests/testthat/test-getConceptsWithCodeCounts.R

@@ -18,7 +18,7 @@ test_that("getConceptsWithCodeCounts works", {
   # Check column names match expected structure
   expected_columns <- c("concept_id", "concept_name", "domain_id", "vocabulary_id", 
                        "concept_class_id", "standard_concept", "concept_code", 
-                       "record_counts", "descendant_record_counts")
+                       "record_counts", "descendant_record_counts", "number_of_descendants")
 
   result |>
     colnames() |>