Update to JAMES 1.7.1

growthcharts · Feb 10, 2025 · 961c093 · 961c093
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: james
 Type: Package
 Title: Joint Automatic Measurement and Evaluation System
-Version: 1.7.0.9000
+Version: 1.7.1
 Authors@R: c(person("Stef", "van Buuren", email = "[email protected]", role = c("cre", "aut")), 
              person("Arjan", "Huizing", email = "[email protected]", role = "aut"))
 Maintainer: Stef van Buuren <[email protected]>
@@ -16,7 +16,7 @@ Depends:
     R (>= 2.10),
     svglite (>= 2.1.3.9000)
 Imports: 
-    bdsreader (>= 0.27.0),
+    bdsreader (>= 0.28.0),
     chartbox (>= 1.16.0),
     chartcatalog (>= 1.16.0),
     chartplotter (>= 0.35.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# james 1.7.1 (Feb 2025)
+
+- Resolves a bug in the de-duplication of parental data in BDS field 63. The `bdsreader 0.28.0` package now returns the correct data for these cases. See <https://github.com/growthcharts/bdsreader/issues/10>.
+
 # james 1.7.0 (Nov 2024)
 
 - Adds a target height indicator to height charts for ages 1–21 years and 0–21 years. The target height is calculated using the mid-parental height method described by Hermanussen and Cole (2004). This indicator is plotted at the age of 20.5 years and includes the 95% target height range. The calculation requires the heights of both biological parents (preferred) but can also be performed using only the mother’s height. The target height is adjusted based on the child’s sex and the population standard used for comparison. In the JAMES interface, the target height is automatically recalculated when the user selects a different population.

diff --git a/README.Rmd b/README.Rmd
@@ -4,9 +4,6 @@ output: github_document
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-<!-- badges: start -->
-[![R-CMD-check](https://github.com/growthcharts/james/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/growthcharts/james/actions/workflows/R-CMD-check.yaml)
-<!-- badges: end -->
 
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
@@ -49,7 +46,7 @@ The service aids in monitoring and evaluating childhood growth. JAMES is created
 
 The table lists the defined API end points and the mapping to each end point to the corresponding R function. 
 
-The current OpenAPI definition of JAMES is at <https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. Note that this definition may evolve over time.
+The OpenAPI definition of JAMES is at <https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. The API is currently frozen at version 1.5.4. The API is subject to change in future versions.
 
 ## Resources
 
@@ -58,7 +55,7 @@ The current OpenAPI definition of JAMES is at <https://app.swaggerhub.com/apis/s
 | Description                                           | Status                                  |
 |:------------------------------------------------------|:----------------------------------------|
 | [Example requests](https://james.groeidiagrammen.nl) | current |
-| [OpenAPI specification](https://app.swaggerhub.com/apis-docs/stefvanbuuren/james) | current     |
+| [OpenAPI specification](https://app.swaggerhub.com/apis-docs/stefvanbuuren/james/1.5.4) | current     |
 | [Source files](https://github.com/growthcharts) | current |
 | [JSON data schema 3.0](https://github.com/growthcharts/bdsreader/blob/master/inst/schemas/bds_v3.0.json) | current |
 | [JAMES issue tracker](https://github.com/growthcharts/james/issues) | current |

diff --git a/README.md b/README.md
@@ -1,9 +1,5 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
-<!-- badges: start -->
-
-[![R-CMD-check](https://github.com/growthcharts/james/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/growthcharts/james/actions/workflows/R-CMD-check.yaml)
-<!-- badges: end -->
 
 ## Overview
 
@@ -48,9 +44,10 @@ at tno.nl\> for further information.
 The table lists the defined API end points and the mapping to each end
 point to the corresponding R function.
 
-The current OpenAPI definition of JAMES is at
-<https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. Note that
-this definition may evolve over time.
+The OpenAPI definition of JAMES is at
+<https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. The API is
+currently frozen at version 1.5.4. The API is subject to change in
+future versions.
 
 ## Resources
 
@@ -59,7 +56,7 @@ this definition may evolve over time.
 | Description | Status |
 |:---|:---|
 | [Example requests](https://james.groeidiagrammen.nl) | current |
-| [OpenAPI specification](https://app.swaggerhub.com/apis-docs/stefvanbuuren/james) | current |
+| [OpenAPI specification](https://app.swaggerhub.com/apis-docs/stefvanbuuren/james/1.5.4) | current |
 | [Source files](https://github.com/growthcharts) | current |
 | [JSON data schema 3.0](https://github.com/growthcharts/bdsreader/blob/master/inst/schemas/bds_v3.0.json) | current |
 | [JAMES issue tracker](https://github.com/growthcharts/james/issues) | current |

diff --git a/inst/www/index.html b/inst/www/index.html
@@ -221,7 +221,7 @@
       <div class="col-sm-9 graph" id="plotcontainer">
         <div id="plotDiv"></div>
         <div id="textDiv">
-          <h5 id="version" class="highlight-background">JAMES 1.6.4 (20240512), &copy; TNO 2024</h5>
+          <h5 id="version" class="highlight-background">JAMES 1.7.1 (20250210), &copy; TNO 2024</h5>
           <p id="rq1-session" class="highlight-background"></p>
           <p id="rq1-console" class="preserve-whitespace"></p>
           <p id="rq1-warnings" class="preserve-whitespace"></p>

diff --git a/qmd/deploy_JAMES.qmd b/qmd/deploy_JAMES.qmd
@@ -47,6 +47,10 @@ james:::update_version_files("inst/www/index.html",
                              "DESCRIPTION")
 ```
 
+### Update swaggerhub
+
+- Free accounts no longer exist at SwaggerHub, but the last published version 1.5.4 is still current
+
 ### Next steps
 
 -   Check `renv::status` and commit changes to `renv.lock`

diff --git a/renv.lock b/renv.lock
@@ -114,13 +114,13 @@
     },
     "bdsreader": {
       "Package": "bdsreader",
-      "Version": "0.27.0",
+      "Version": "0.28.0",
       "Source": "GitHub",
       "RemoteType": "github",
       "RemoteHost": "api.github.com",
       "RemoteRepo": "bdsreader",
       "RemoteUsername": "growthcharts",
-      "RemoteSha": "1922fe4de7d0c88510c5c816ad95e0421d41e912",
+      "RemoteSha": "66c2f7681c1f0d541e96420d0e706b96f759d2d8",
       "Requirements": [
         "R",
         "centile",
@@ -135,7 +135,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "7db20a6b4fcfccbcf2755308b104b596"
+      "Hash": "83cc76563eb26c8f28d9394037f8863b"
     },
     "bit": {
       "Package": "bit",
@@ -209,7 +209,7 @@
         "rlang",
         "stats"
       ],
-      "Hash": "55b1286555aecb30e3bbd8f358f03827"
+      "Hash": "463edb6f808b2ca61e1e796f0caead9e"
     },
     "chartbox": {
       "Package": "chartbox",
@@ -225,7 +225,7 @@
         "chartcatalog",
         "grDevices"
       ],
-      "Hash": "7fa19665c957394c2e256e46f1f49f50"
+      "Hash": "d42a83a50e03a07964f9bc9ead383690"
     },
     "chartcatalog": {
       "Package": "chartcatalog",
@@ -239,7 +239,7 @@
       "Requirements": [
         "R"
       ],
-      "Hash": "447851fc436200d71e29cb43b9b4cda9"
+      "Hash": "356e61513f0978f6d542aeffb4099771"
     },
     "chartplotter": {
       "Package": "chartplotter",
@@ -268,7 +268,7 @@
         "tidyr",
         "utils"
       ],
-      "Hash": "b5452e4bed3e83f68e85e3bfcc86576b"
+      "Hash": "01759a339519a213005eb57ce6f51324"
     },
     "cli": {
       "Package": "cli",
@@ -326,13 +326,13 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "6.0.1",
+      "Version": "6.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "e8ba62486230951fcd2b881c5be23f96"
+      "Hash": "8dd23d308c751efdf675124aad4bf5d7"
     },
     "curvematching": {
       "Package": "curvematching",
@@ -372,7 +372,7 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "503704dd61e356a2c7b9bed8ad8a28c8"
+      "Hash": "f5f5bf5564d87a169ceec57d8db835da"
     },
     "dplyr": {
       "Package": "dplyr",
@@ -415,7 +415,7 @@
         "stringi",
         "tidyr"
       ],
-      "Hash": "dd4d21b799b1d3e9ec61cd3fb377acc8"
+      "Hash": "10e0509fd9221f34974c7d18e552bdcd"
     },
     "fansi": {
       "Package": "fansi",
@@ -486,7 +486,7 @@
         "tidyr",
         "tidyselect"
       ],
-      "Hash": "a2cdec830fb65389baf346e1abca3c22"
+      "Hash": "f47ae4c1a545c9f76dcbcbd2112d4bc2"
     },
     "hms": {
       "Package": "hms",
@@ -736,13 +736,13 @@
     },
     "openssl": {
       "Package": "openssl",
-      "Version": "2.2.2",
+      "Version": "2.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "askpass"
       ],
-      "Hash": "d413e0fef796c9401a4419485f709ca1"
+      "Hash": "37a7f0abce0349f5950ce49f38c7626b"
     },
     "pillar": {
       "Package": "pillar",
@@ -845,14 +845,14 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.1.4",
+      "Version": "1.1.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
+      "Hash": "724dcc1490cd7071ee75ca2994a5446e"
     },
     "stringi": {
       "Package": "stringi",
@@ -901,7 +901,7 @@
         "rlang",
         "systemfonts"
       ],
-      "Hash": "30d61b1c821549fcd29805fa07ea9170"
+      "Hash": "47571abc37c9bfc3120f1ec20e8f38cd"
     },
     "sys": {
       "Package": "sys",

diff --git a/vignettes/articles/getting_started.Rmd b/vignettes/articles/getting_started.Rmd
@@ -1,6 +1,6 @@
 ---
 title: JAMES - Joint Automatic Measurement and Evaluation System
-subtitle: JAMES 1.7.0 (Nov 2024)
+subtitle: JAMES 1.7.1 (February 2025)
 author: Stef van Buuren, Arjan Huizing (TNO Child Health)
 output:
   html_document:
@@ -52,7 +52,7 @@ The service aids in monitoring and evaluating childhood growth. JAMES is created
 
 The table lists the defined API end points and the mapping to each end point to the corresponding R function. 
 
-The current OpenAPI definition of JAMES is at <https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. Note that this definition may evolve over time.
+The OpenAPI definition of JAMES is at <https://app.swaggerhub.com/apis/stefvanbuuren/james/1.5.4>. The API is currently frozen at version 1.5.4. The API is subject to change in future versions.
 
 ### Output formats
 
@@ -168,7 +168,7 @@ The following `bash` commands call the `/version` API end point
 
 ```{bash}
 curl -sX 'GET' \
-  'http://localhost:8080/version' \
+   $(cat .host)/version \
   -H 'accept: text/json'
   
 curl -sX POST $(cat .host)/version > resp