JAMES - Joint Automatic Measurement and Evaluation System

JAMES 1.10.1 (December 2025)

Overview

JAMES is a web service for creating and interpreting charts of child growth and development. The current version of JAMES

1. provides access to high-quality growth charts used by the Dutch youth health care;
2. screens for abnormal height, weight and head circumference;
3. converts developmental data into the D-score;
4. predicts future growth and development.

JAMES is a RESTful API that runs on a remote host. The system accepts requests from the Dutch Digital Child Health Record System DD-JGZ and other clients using a the Basisdataset JGZ 4.0.0 protocol. Child data are coded according to the JSON data schema 3.0.

Get to know JAMES. Browse the tutorial (in Dutch).

The following sections illustrate how a client can make requests to JAMES using various client languages. In principle, any HTTP client will work with JAMES. The document highlights some applications of the service and provides pointers to relevant background information.

The service aids in monitoring and evaluating childhood growth. JAMES is created and maintained by the Netherlands Organisation for Applied Scientific Research TNO. Please contact Stef van Buuren <stef.vanbuuren at tno.nl> for further information.

Primary JAMES user functionality

Verb	API end point	Description	Maps to james function
POST	/version/{dfm}	Obtain version information	version()
POST	/data/upload/{dfm}	Upload child data	upload_data()
POST	/charts/draw/{ffm}	Draw child data on growth chart	draw_chart()
POST	/charts/list/{dfm}	List available growth charts	list_charts()
POST	/charts/validate/{dfm}	Validate a chart code	validate_chartcode()
POST	/dscore/calculate/{dfm}	Calculate developmental score (D-score)	calculate_dscore()
POST	/ddomain/calculate/{dfm}	Calculate developmental domain scores	calculate_ddomain()
POST	/vwc/select/{dfm}	Select developmental milestones for age	select_vwc()
POST	/vwc/percentiles/{dfm}	Obtain developmental milestone percentiles	percentiles_vwc()
POST	/dcat/calculate/{dfm}	Adaptive testing of milestones	dcat()
POST	/screeners/list/{dfm}	List available growth screeners	list_screeners()
POST	/screeners/apply/{dfm}	Apply growth screeners to child data	apply_screeners()
GET	/site	Request empty site	request_site()
POST	/site/request/{dfm}	Request personalised site	request_site()
POST	/blend/request/{sfm}	Obtain a blend from multiple end points	request_blend()
GET	/{session}/{info}	Extract session details
GET	/{2}/{1}/man	Consult R help	help({1}_{2})

The table lists the defined API end points and the mapping to each end point to the corresponding R function.

The definition of the JAMES endpoints can be found at OpenAPI specification.

Output formats

JAMES is built on top of the OpenCPU API, a powerful and flexible way for online deployment of R functionality. Although it is possible to use JAMES without knowledge of OpenCPU, it is useful to browse the OpenCPU features.

OpenCPU offers multiple output formats out of the box. JAMES supports a subset of these through the /{session}/{info} end point. Here session is a special session code generated by OpenCPU that identifies the server location containing the results of a request. The output format info is one of the following:

{info}	Description
json	Function result as JSON
print	Function result as formatted as print
csv	Function result as comma-separated format
tab	Function result as tab-delimited format
md	Function result as markdown format
svglite	Function result as SVG graph
warnings	Warnings from the R execution
messages	Messages, especially data validation info
console	Console print out, useful for locating errors
stdout	Standard output
info	Overview of JAMES deployment
parent	Parent directory of all OpenCPU session output

In addition, the user can request the function result in a particular form. JAMES distinguishes the following groups of formats.

Format group	Description
dfm	Data format: json, csv, tab, md, print, parent
ffm	Figure format: svglite, print, parent
sfm	System format: json, print, parent

In general, the user can specify the desired format by appending the format name to the URL. See https://www.opencpu.org/api.html#api-formats for examples.

Objective

This document provides a quick introduction into the main JAMES features, and how these can be assessed from R and from the command line.

Target host:  test 

Features

/version: Obtain version information

Let us first check whether JAMES is running. The following code makes a simple request to JAMES to see whether it is alive and to return the version number of the underlying james R package. We illustrate both requests in R and in bash.

R

We first need to install and load packages.

install.packages(c("remotes", "httr", "jsonlite"))
remotes::install_github("growthcharts/jamesclient")
remotes::install_github("growthcharts/jamesdemodata")
remotes::install_github("growthcharts/bdsreader")

library(jamesclient)
library(httr)
library(jsonlite)

The server that hosts JAMES was already defined in the setup block at the top of this document. The host variable is now available for use in all subsequent code chunks.

For bash chunks that need authentication, we use an auth_curl helper function that automatically adds Bearer token when available.

We first illustrate a method that makes two requests to the server. The following commands call the /version/json end point in the JAMES API.

r <- james_post(host = host, path = "version/json")

We added the /json to the pathname to extract the JSON representation of the result of the R function james::version(). The function result is an object of class james_post and consists of various components.

names(r)

 [1] "url"          "status_code"  "headers"      "all_headers"  "cookies"     
 [6] "content"      "date"         "times"        "request"      "handle"      
[11] "request_path" "parsed"       "warnings"     "messages"     "session"     

r$url

[1] "https://james.groeidiagrammen.nl/version/json"

Most of the element are documented in the response object in the httr package. For example, we could use the call httr::status_code(r) to obtain the status code. The function james_post() adds the last five elements:

• r$request_path echoes the endpoint, here /version/json;
• r$parsed is a parsed version of the element r$content. Here it is a list of elements like names of the package, its date, and so on. In case of an error of the server function, we find the error message here;
• r$warnings contain any warnings thrown during execution;
• r$messages contain any messages, e.g. data reading errors;
• r$session (like x008cd0ac82f394) is a unique session code.

The jamesclient::james_post() function wraps the basis workhorse httr::POST() that does the actual server request. For illustration, we may obtain equivalent content by the POST function directly.

auth_token <- Sys.getenv("JAMES_BEARER_TOKEN")
path <- "version/json"
url <- parse_url(host)
url <- modify_url(url, path = file.path(url$path, path), query = "auto_unbox=true")
r <- POST(url, add_headers(accept = "application/json", Authorization = auth_token))
fromJSON(content(r, type = "text", encoding = "UTF-8"))

$package
[1] "james"

$packageVersion
[1] "1.10.1"

$packageDate
[1] "2025-12-17"

$Rversion
[1] "4.5.0"

bash

We use the curl Linux command. If needed, on Ubuntu install curl as

sudo apt update
sudo apt -y install curl

Let’s find out the JAMES version number. We first illustrate a method that makes two requests to the server.

Note: When using the ACC server, authentication is handled automatically via the auth_curl helper function which adds the Bearer token from .bearer file.

The following bash commands call the /version API end point

source auth_curl.sh
auth_curl -sX POST $(cat .host)/version > resp
cat resp

/ocpu/tmp/x02d1ce3fd59931/R/.val
/ocpu/tmp/x02d1ce3fd59931/R/version
/ocpu/tmp/x02d1ce3fd59931/stdout
/ocpu/tmp/x02d1ce3fd59931/source
/ocpu/tmp/x02d1ce3fd59931/console
/ocpu/tmp/x02d1ce3fd59931/info
/ocpu/tmp/x02d1ce3fd59931/files/DESCRIPTION

The response to the request consists of a set of URLs created on the server, each of which contains details on the response.

The path element following tmp/ is a unique session key. See https://www.opencpu.org/api.html for the interpretation of the OpenCPU API.

The next snippet constructs the URL of a JSON representation of the result and downloads the contents of the URL as a file value1.

source auth_curl.sh
auth_curl -s $(cat .host)$(head -1 resp)/json?auto_unbox=true > value1
cat value1

{
  "package": "james",
  "packageVersion": "1.10.1",
  "packageDate": "2025-12-17",
  "Rversion": "4.5.0"
}

The above sequence makes two requests to the server. The following code compacts both steps into one.

source auth_curl.sh
auth_curl -sX POST $(cat .host)/version/json?auto_unbox=true > value2
cat value2

{
  "package": "james",
  "packageVersion": "1.10.1",
  "packageDate": "2025-12-17",
  "Rversion": "4.5.0"
}

/data/upload: Upload child data

JAMES understands data that conform to the Basisdataset JGZ 4.0.1 coded as JSON according to a JSON schema. This section explains how we create, validate and upload child data to JAMES.

R

Let us assume that we have already have child data in R stored as a data.frame or tibble. Here we copy the longitudinal demo data maria.json from the bdsreader package into the working directory.

success <- file.copy(system.file("examples/maria.json", package = "bdsreader"), 
                     "maria.json", overwrite = TRUE)

The contents of the file is json format, ready for upload:

{
  "OrganisatieCode": 1234,
  "Referentie": "fa308134-069e-49ce-9847-ccdae380ed6f",
  "ClientGegevens": {
    "Elementen": [
      {
        "Bdsnummer": 19,
        "Waarde": "2"
      },
      {
        "Bdsnummer": 20,
        "Waarde": "20181011"
      },
      {
        "Bdsnummer": 82,
        "Waarde": "189"
      },
      {
        "Bdsnummer": 91,
        "Waarde": "2"
      },
      {
        "Bdsnummer": 110,
        "Waarde": "990"
      },
      {
        "Bdsnummer": 238,
        "Waarde": "1670"
      },
      {
        "Bdsnummer": 240,
        "Waarde": "1900"
      }
    ],
    "Groepen": [
      {
        "Elementen": [
          {
            "Bdsnummer": 63,
            "Waarde": "19950704"
          },
          {
            "Bdsnummer": 71
          },
          {
            "Bdsnummer": 62,
            "Waarde": "01"
          }
        ]
      },
      {
        "Elementen": [
          {
            "Bdsnummer": 63,
            "Waarde": "19901202"
          },
          {
            "Bdsnummer": 71
          },
          {
            "Bdsnummer": 62,
            "Waarde": "02"
          }
        ]
      }
    ]
  },
  "Contactmomenten": [
    {
      "Tijdstip": "20181011",
      "Elementen": [
        {
          "Bdsnummer": 245,
          "Waarde": "990"
        }
      ]
    },
    {
      "Tijdstip": "20181111",
      "Elementen": [
        {
          "Bdsnummer": 235,
          "Waarde": "380"
        },
        {
          "Bdsnummer": 245,
          "Waarde": "1250"
        },
        {
          "Bdsnummer": 252,
          "Waarde": "270"
        }
      ]
    },
    {
      "Tijdstip": "20181211",
      "Elementen": [
        {
          "Bdsnummer": 235,
          "Waarde": "435"
        },
        {
          "Bdsnummer": 245,
          "Waarde": "2100"
        },
        {
          "Bdsnummer": 252,
          "Waarde": "305"
        }
      ]
    }
  ]
}

There are four ways to upload the data to JAMES:

1. Upload the file "maria.json";
2. Convert to a string and upload;
3. Convert to a JSON object and upload;
4. Read the JSON file from a URL.

The /data/upload API end point handles these cases as follows:

# Test if Bearer token is still active
if (file.exists(".bearer")) {
  bearer_token <- trimws(readLines(".bearer", n = 1))
  cat("About to test james_post with token length:", nchar(bearer_token), "\n")
}

About to test james_post with token length: 551 

# upload as file
fn <- "maria.json"
r1 <- james_post(host = host, path = "data/upload/json", txt = fn)
status_code(r1)

[1] 201

# upload as string
js <- read_json_js(fn)
r2 <- james_post(host = host, path = "data/upload/json", txt = js)
status_code(r2)

[1] 201

# upload as JSON object
jo <- read_json_jo(fn)
r3 <- james_post(host = host, path = "data/upload/json", txt = jo)
status_code(r3)

[1] 201

# upload as URL
url <- "https://james.groeidiagrammen.nl/ocpu/library/bdsreader/examples/maria.json"
r4 <- james_post(host = host, path = "data/upload/json", txt = url)
status_code(r4)

[1] 201

If the status is 201, the data are uploaded to JAMES and processed. For example, the processed data after file upload is available as an R data frame under element r1$parsed.

r1$parsed

$psn
  id  name        dob       dobm       dobf  src    sex gad ga smo  bw hgtm
1 -1 Maria 2018-10-11 1990-12-02 1995-07-04 1234 female 189 27   1 990  167
  hgtf
1  190

$xyz
      age xname yname zname                  zref       x       y      z
1  0.0849   age   hgt hgt_z nl_2012_hgt_female_27  0.0849 38.0000 -0.158
2  0.1670   age   hgt hgt_z nl_2012_hgt_female_27  0.1670 43.5000  0.047
3  0.0000   age   wgt wgt_z nl_2012_wgt_female_27  0.0000  0.9900  0.190
4  0.0849   age   wgt wgt_z nl_2012_wgt_female_27  0.0849  1.2500 -0.203
5  0.1670   age   wgt wgt_z nl_2012_wgt_female_27  0.1670  2.1000  0.015
6  0.0849   age   hdc hdc_z nl_2012_hdc_female_27  0.0849 27.0000 -0.709
7  0.1670   age   hdc hdc_z nl_2012_hdc_female_27  0.1670 30.5000 -0.913
8  0.0000   age   bmi bmi_z nl_1997_bmi_female_nl  0.0000      NA     NA
9  0.0849   age   bmi bmi_z nl_1997_bmi_female_nl  0.0849  8.6565 -5.719
10 0.1670   age   bmi bmi_z nl_1997_bmi_female_nl  0.1670 11.0979 -3.767
11 0.0000   hgt   wfh wfh_z   nl_2012_wfh_female_      NA  0.9900     NA
12 0.0849   hgt   wfh wfh_z   nl_2012_wfh_female_ 38.0000  1.2500 -0.001
13 0.1670   hgt   wfh wfh_z   nl_2012_wfh_female_ 43.5000  2.1000  0.326

The session details, including the uploaded data, will remain available for a limited time. After 30 minutes the session is wiped. The session key is your entrance to the resource within the 30-minute window. The key can be retrieved as r1$session. For example, to see the result of the file upload session in markdown use

(session <- r1$session)

[1] "x0080817caab740"

resp <- james_get(host = host, path = file.path(session, "md"))
# Handle both text and parsed responses
if (is.character(resp$parsed)) {
  cat(resp$parsed)
} else {
  print(resp$parsed)
}

  * **psn**:

    -------------------------------------------------------------------------------
     id   name       dob          dobm         dobf      src    dnr    sex     gad
    ---- ------- ------------ ------------ ------------ ------ ----- -------- -----
     -1   Maria   2018-10-11   1990-12-02   1995-07-04   1234   NA    female   189
    -------------------------------------------------------------------------------

    Table: Table continues below

    -----------------------------------------------------------------------------------
     ga   smo   bw    hgtm   hgtf   agem   etn   pc4   blbf   blbm   eduf   edum   par
    ---- ----- ----- ------ ------ ------ ----- ----- ------ ------ ------ ------ -----
     27    1    990   167    190     NA    NA    NA     NA     NA     NA     NA    NA
    -----------------------------------------------------------------------------------

  * **xyz**:

    ----------------------------------------------------------------------------------
      age     xname   yname   zname           zref              x        y       z
    -------- ------- ------- ------- ----------------------- -------- ------- --------
     0.0849    age     hgt    hgt_z   nl_2012_hgt_female_27   0.0849    38     -0.158

     0.167     age     hgt    hgt_z   nl_2012_hgt_female_27   0.167    43.5    0.047

       0       age     wgt    wgt_z   nl_2012_wgt_female_27     0      0.99     0.19

     0.0849    age     wgt    wgt_z   nl_2012_wgt_female_27   0.0849   1.25    -0.203

     0.167     age     wgt    wgt_z   nl_2012_wgt_female_27   0.167     2.1    0.015

     0.0849    age     hdc    hdc_z   nl_2012_hdc_female_27   0.0849    27     -0.709

     0.167     age     hdc    hdc_z   nl_2012_hdc_female_27   0.167    30.5    -0.913

       0       age     bmi    bmi_z   nl_1997_bmi_female_nl     0       NA       NA

     0.0849    age     bmi    bmi_z   nl_1997_bmi_female_nl   0.0849   8.657   -5.719

     0.167     age     bmi    bmi_z   nl_1997_bmi_female_nl   0.167    11.1    -3.767

       0       hgt     wfh    wfh_z    nl_2012_wfh_female_      NA     0.99      NA

     0.0849    hgt     wfh    wfh_z    nl_2012_wfh_female_      38     1.25    -0.001

     0.167     hgt     wfh    wfh_z    nl_2012_wfh_female_     43.5     2.1    0.326
    ----------------------------------------------------------------------------------


<!-- end of list -->

Troubleshooting data upload: JAMES executes checks on the conversion and ranges of the data. To gain efficiency, it does not automatically validate the input data against the specified JSON schema. JAMES writes diagnostic, sometimes cryptic, messages to the directory {session}/messages if it finds a problem. The user can rerun the data upload with two additional flags that request extra diagnostic output.

Example: Suppose we compromise the data by removing the required "clientDetails" and the optional "nestedDetails" sections. The mangled input data look like:

{"Format":"3.0","organisationCode":12345,"reference":"Maria's mangled data","clientMeasurements":[{"bdsNumber":235,"values":[{"date":"20181111","value":380},{"date":"20181211","value":435}]}]}

Everything appears normal if we read this data by the default:

fn <- "maria-mangled.json"
r5 <- james_post(host = host, path = "data/upload/json", txt = fn)

Warning in readLines(con): incomplete final line found on 'maria-mangled.json'

r5$parsed

$psn
  id                 name   src
1 -1 Maria's mangled data 12345

$xyz
  xname yname zname            zref  y
1   age   hgt hgt_z nl_1997_hgt__nl 38

If we upload with the additional validate = TRUE flag, JAMES runs the validation of the uploaded JSON against the JSON schema:

r6 <- james_post(host = host, path = "data/upload/json", txt = fn, validate = TRUE)
mess <- james_get(host = host, path = file.path(r6$session, "messages"))
# Handle both text and parsed responses
if (is.character(mess$parsed)) {
  cat(mess$parsed)
} else {
  print(mess$parsed)
}

which indicates that the required JSON element "clientDetails" is missing. We inactivated the code chunk above because it may occasionally give the error “JAMES API request failed [400] child process has died In call: tryCatch()” when validate = TRUE. This is a known, not yet resolved issue.

We may drill down further by setting the intermediate = TRUE flag. This writes five JSON files that document the data flow into {session}/files/{*}.json.

For example, we can ask for the input data as read by JAMES by

r7 <- james_post(host = host, path = "data/upload/json", txt = fn, validate = TRUE, intermediate = TRUE)

Warning in readLines(con): incomplete final line found on 'maria-mangled.json'

url <- file.path(host, r7$session, "files/input.json")
url

[1] "https://james.groeidiagrammen.nl/x0f44485bd7b11c/files/input.json"

With browseURL(url) we may view the file contents in the browser. The files directory contains five JSON files:

1. files/input.json: the JSON input data;
2. files/bds.json: a data frame with info per BDS number;
3. files/ddi.json: result of recoding BDS into GSED item names;
4. files/psn.json: known fixed child covariates;
5. files/xy.json: time-varying variables.

Inspection of these files may uncover any problems with JAMES’s understanding of the data. If needed, study the underlying R source code at https://raw.githubusercontent.com/growthcharts/bdsreader/master/R/read_bds.R.

The validate and intermediate flag are useful for development and debugging. In production, we recommend leaving them at their default value (FALSE) and monitor any messages written to {session}/messages.

bash

We start from child data in the file maria.json that we wish to process with JAMES. For testing purposes, you may change the values, but keep the general structure intact. The following commands upload the file and process the data.

curl -sF 'txt=@maria.json' -D headers \
  -H "accept: text/json" \
  -H "Authorization: Bearer $(cat .bearer)" \
  $(cat .host)/data/upload/json | head

{
  "psn": [
    {
      "id": -1,
      "name": "Maria",
      "dob": "2018-10-11",
      "dobm": "1990-12-02",
      "dobf": "1995-07-04",
      "src": "1234",
      "sex": "female",

Alternatively, we may read the file into a JSON string, and upload as follows:

JS=$(jq '.' maria.json | jq -sR '.')
curl -s $(cat .host)/data/upload/json \
  -H "Authorization: Bearer $(cat .bearer)" \
  -d "txt=$JS" | head

{
  "psn": [
    {
      "id": -1,
      "name": "Maria",
      "dob": "2018-10-11",
      "dobm": "1990-12-02",
      "dobf": "1995-07-04",
      "src": "1234",
      "sex": "female",

Finally, if the data are located at a URL, use

URL=https://james.groeidiagrammen.nl/ocpu/library/bdsreader/examples/maria.json
curl -s $(cat .host)/data/upload/json \
  -H "Authorization: Bearer $(cat .bearer)" \
  -d "txt='$URL'" | head

{
  "psn": [
    {
      "id": -1,
      "name": "Maria",
      "dob": "2018-10-11",
      "dobm": "1990-12-02",
      "dobf": "1995-07-04",
      "src": "1234",
      "sex": "female",

/charts/draw: Draw child data on growth chart

R

Maria is a preterm born at 27 weeks of gestational age. We already uploaded her data. We may now plot her growth data on the A4 chart for preterms as follows:

r5 <- james_post(host = host, 
                 path = "/charts/draw/svglite", 
                 session = r1$session,
                 chartcode = "PMAAN27", selector = "chartcode",
                 query = list(height = 29.7/2.54, width = 21/2.54))
writeLines(r5$parsed, con = filename_chart1)

Maria’s growth plotted on preterm chart, 0-15 months

Alternatively, we may upload data for a new child Laura and plot the data in one step:

fn <- system.file("extdata/bds_v3.0/smocc/Laura_S.json", package = "jamesdemodata")
r6 <- james_post(host = host,
                 path = "/charts/draw/svglite", txt = fn, 
                 chartcode = "NMBA", selector = "chartcode",
                 query = list(height = 29.7/2.54, width = 21/2.54))
writeLines(r6$parsed, con = filename_chart2)

For A4 sized charts, we recommend to generate the plot with query arguments list(height = 29.7/2.54, width = 21/2.54), as illustrated above. If you want to change the chart’s size in your HTML, use the out.width knitr chunk option, e.g. set out.width="500px". This gives the following output.

Laura’s growth plotted on chart for Dutch girls, 0-4 years

JAMES features a built-in prediction module based on curve matching. Suppose we want to predict Laura’s height at the 3y9m when Laura is 2 years old. The following chart plots 25 matches to Laura as grey curves. The variation between the grey curves at age 3y9m indicates the likely variation in the prediction. The blue line indicates Laura’s predicted height at age 3y9m.

r7 <- james_post(host = host, 
                 path = "/charts/draw/svglite", txt = fn, 
                 chartcode = "NMBH", dnr = "2-4",
                 lo = 2.0, hi = 3.75, nmatch = 25,
                 show_future = TRUE, show_realized = TRUE,
                 query = list(height = 18/2.54, width = 18/2.54))
writeLines(r7$parsed, con = filename_chart3)

For square charts, use query arguments list(height = 18/2.54, width = 18/2.54) to generate the plot. In order to get the same age units as the previous chart, calculate out.width as 500/21*18 = "429px".

Predict Laura’s future height at the age of 3y9m.

bash

Upload maria.json and draw the height data on the default chart to produce an SVG file. Specify the proper width and height query parameters.

source auth_curl.sh
auth_curl -sX 'POST' $(cat .host)'/charts/draw/svglite?width=7.09&height=7.09' \
-H 'accept: image/*' \
-F 'txt=@maria.json;type=application/json' > maria1.svg

We need to set chartcode and selector parameters to choose a different chart.

source auth_curl.sh
auth_curl -sX 'POST' $(cat .host)'/charts/draw/svglite?width=8.27&height=11.69' \
-H 'accept: image/*' \
-F "chartcode='PMAAN27'" \
-F "selector='chartcode'" \
-F 'txt=@maria.json;type=application/json' > maria2.svg

An alternative is to read the data from a URL, and use the application/json protocol to specify parameters.

source auth_curl.sh

BASE_URL=$(cat .host | sed 's|/modules/james$||')
auth_curl -sX 'POST' \
$(cat .host)'/charts/draw/svglite?width=8.27&height=11.69' \
-H 'accept: image/*' \
-H 'Content-Type: application/json' \
-d '{
"txt": "'$BASE_URL'/ocpu/library/jamesdemodata/extdata/bds_v3.0/smocc/Laura_S.json",
"chartcode" : "NMBA",
"selector" : "chartcode"}' > laura.svg

/charts/list: List available growth charts

R

JAMES contains a wide variety of built-in growth charts. Each chart has a unique chartcode. A typical chart code looks like NJAA. We obtain the full list of chart codes as

r <- james_post(host = host, path = "charts/list/json")
charts <- r$parsed

The charts object is a data frame with 478 rows (charts) and the following variables:

names(charts)

[1] "chartgrp"   "chartcode"  "population" "sex"        "design"    
[6] "side"       "language"   "week"      

JAMES contains charts for various child populations. There are charts for Down syndrome (DS), Hindustan (HS), Moroccan (MA), Dutch (NL)), preterm (PT) and Turkish (TU) children living in the Netherlands and the WHO Growth Standards (WHOblue, WHOpink). These charts contain references for height (hgt), weight (wgt), head circumference (hdc), weight-for-height (wfh), body mass index (bmi) and D-score (dsc), as well as combined charts with multiple references on A4 format (front, back, -hdc).

The most important index variables are population and side:

with(charts, table(population, side))

          side
population -hdc back bmi dsc front hdc hgt wfh wgt
   DS         0    6   2   0     6   6   6   4   2
   HS         4    2   2   0     6   2   6   4   2
   MA         0    6   2   0     6   6   6   4   2
   NL         2    8   2   4     8   8   8   4   4
   PT         0   24   0  48    48  24  48   0  48
   TU         0    6   2   0     6   6   6   4   2
   WHOblue    0    0   0  26     2   1   2   1   1
   WHOpink    0    0   0  26     2   1   2   1   1

The URL {host}/site (see below) displays the currently active chart code as a field in the left sidebar.

bash

Restrict the listing to the WHO references:

source auth_curl.sh
auth_curl -sX 'POST' \
$(cat .host)'/charts/list/json' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{
"chartgrp": "who"
}'

/charts/validate: Validate chart codes

R

The /charts/validate end point attempt to find one or more user-specified chart codes. For example, the following cocde checkc five chart codes:

r <- james_post(host = host, 
                path = "charts/validate/json", 
                chartcode = c("NMAW", "NJAb", "PJAAN23", "PJAAN25", "dummy"))
r$parsed

[1]  TRUE FALSE FALSE  TRUE FALSE

bash

Check five chart codes:

source auth_curl.sh
auth_curl -sX 'POST' \
$(cat .host)'/charts/validate/json' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{
"chartcode": [
"NMAW",
"NJAB",
"PJAAN23",
"PJAAN25", 
"dummy"
]
}'

[true, true, false, true, false]

/dscore/calculate: Calculate D-score

R

The D-score is a developmental score that is used to assess the development of children. The /dscore/calculate end point calculates the D-score for a child based on the uploaded data. The D-score is a continuous measure of child development, and it is calculated based on the child’s age and developmental milestones.

fn <- system.file("extdata/bds_v3.0/smocc/Laura_S.json", package = "jamesdemodata")
r <- james_post(host = host, path = "dscore/calculate/json", output = "table", txt = fn)
r

JAMES request:
  Path    : dscore/calculate/json
  Status  : 201
  Session : x0bcb6aed73d385

Parsed response:
'data.frame':   20 obs. of  6 variables:
 $ n  : int  0 5 3 5 10 12 11 10 9 10 ...
 $ a  : num  NA 0.101 0.159 0.235 0.485 ...
 $ p  : num  NA 0.6 0.667 0.6 0.5 ...
 $ d  : num  NA 15.7 18 20.9 25.9 ...
 $ sem: num  NA 3.29 3.83 3.32 2.65 ...
 $ daz: num  NA -0.11 -0.182 -0.334 -1.919 ...

head(r$parsed)

   n      a      p     d    sem    daz
1  0     NA     NA    NA     NA     NA
2  5 0.1013 0.6000 15.68 3.2945 -0.110
3  3 0.1588 0.6667 18.01 3.8258 -0.182
4  5 0.2355 0.6000 20.93 3.3205 -0.334
5 10 0.4846 0.5000 25.89 2.6506 -1.919
6 12 0.7529 0.9167 44.58 3.2903  0.674

The D-score is found in column y and the DAZ is in column z.

bash

/ddomain/calculate: Calculate domain scores

R

The D-score is a one-number summary measure of child development. The /ddomain/calculate end point breaks down the D-score into two or more domains.

fn <- system.file("extdata/bds_v3.0/smocc/Laura_S.json", package = "jamesdemodata")
r <- james_post(host = host, path = "ddomain/calculate/json", output = "table", txt = fn)
r

JAMES request:
  Path    : ddomain/calculate/json
  Status  : 201
  Session : x0bf44c1b3e77a5

Parsed response:
List of 6
 $ dscore    :'data.frame': 20 obs. of  6 variables:
  ..$ n  : int [1:20] 0 5 3 5 10 12 11 10 9 10 ...
  ..$ a  : num [1:20] NA 0.101 0.159 0.235 0.485 ...
  ..$ p  : num [1:20] NA 0.6 0.667 0.6 0.5 ...
  ..$ d  : num [1:20] NA 15.7 18 20.9 25.9 ...
  ..$ sem: num [1:20] NA 3.29 3.83 3.32 2.65 ...
  ..$ daz: num [1:20] NA -0.11 -0.182 -0.334 -1.919 ...
 $ grossmotor:'data.frame': 20 obs. of  2 variables:
  ..$ a: num [1:20] 0 0.101 0.159 0.235 0.485 ...
  ..$ n: int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
 $ finemotor :'data.frame': 20 obs. of  2 variables:
  ..$ a: num [1:20] 0 0.101 0.159 0.235 0.485 ...
  ..$ n: int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
 $ language  :'data.frame': 20 obs. of  2 variables:
  ..$ a: num [1:20] 0 0.101 0.159 0.235 0.485 ...
  ..$ n: int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
 $ cognitive :'data.frame': 20 obs. of  2 variables:
  ..$ a: num [1:20] 0 0.101 0.159 0.235 0.485 ...
  ..$ n: int [1:20] 0 0 0 0 0 0 0 0 0 0 ...
 $ social    :'data.frame': 20 obs. of  2 variables:
  ..$ a: num [1:20] 0 0.101 0.159 0.235 0.485 ...
  ..$ n: int [1:20] 0 0 0 0 0 0 0 0 0 0 ...

head(r$parsed)

$dscore
    n      a      p     d    sem    daz
1   0     NA     NA    NA     NA     NA
2   5 0.1013 0.6000 15.68 3.2945 -0.110
3   3 0.1588 0.6667 18.01 3.8258 -0.182
4   5 0.2355 0.6000 20.93 3.3205 -0.334
5  10 0.4846 0.5000 25.89 2.6506 -1.919
6  12 0.7529 0.9167 44.58 3.2903  0.674
7  11 1.0212 0.9091 51.59 3.2715  0.550
8  10 1.2512 0.8000 54.82 2.9505  0.013
9   9 1.5387 0.6667 57.08 2.9298 -0.691
10 10 2.0397 1.0000 70.72 3.6740  1.377
11  0     NA     NA    NA     NA     NA
12  0     NA     NA    NA     NA     NA
13  0     NA     NA    NA     NA     NA
14  0     NA     NA    NA     NA     NA
15  0     NA     NA    NA     NA     NA
16  0     NA     NA    NA     NA     NA
17  0     NA     NA    NA     NA     NA
18  0     NA     NA    NA     NA     NA
19  0     NA     NA    NA     NA     NA
20  0     NA     NA    NA     NA     NA

$grossmotor
        a n
1  0.0000 0
2  0.1013 0
3  0.1588 0
4  0.2355 0
5  0.4846 0
6  0.7529 0
7  1.0212 0
8  1.2512 0
9  1.5387 0
10 2.0397 0
11 0.0000 0
12 0.1013 0
13 0.1588 0
14 0.2355 0
15 0.4846 0
16 0.7529 0
17 1.0212 0
18 1.2512 0
19 1.5387 0
20 2.0397 0

$finemotor
        a n
1  0.0000 0
2  0.1013 0
3  0.1588 0
4  0.2355 0
5  0.4846 0
6  0.7529 0
7  1.0212 0
8  1.2512 0
9  1.5387 0
10 2.0397 0
11 0.0000 0
12 0.1013 0
13 0.1588 0
14 0.2355 0
15 0.4846 0
16 0.7529 0
17 1.0212 0
18 1.2512 0
19 1.5387 0
20 2.0397 0

$language
        a n
1  0.0000 0
2  0.1013 0
3  0.1588 0
4  0.2355 0
5  0.4846 0
6  0.7529 0
7  1.0212 0
8  1.2512 0
9  1.5387 0
10 2.0397 0
11 0.0000 0
12 0.1013 0
13 0.1588 0
14 0.2355 0
15 0.4846 0
16 0.7529 0
17 1.0212 0
18 1.2512 0
19 1.5387 0
20 2.0397 0

$cognitive
        a n
1  0.0000 0
2  0.1013 0
3  0.1588 0
4  0.2355 0
5  0.4846 0
6  0.7529 0
7  1.0212 0
8  1.2512 0
9  1.5387 0
10 2.0397 0
11 0.0000 0
12 0.1013 0
13 0.1588 0
14 0.2355 0
15 0.4846 0
16 0.7529 0
17 1.0212 0
18 1.2512 0
19 1.5387 0
20 2.0397 0

$social
        a n
1  0.0000 0
2  0.1013 0
3  0.1588 0
4  0.2355 0
5  0.4846 0
6  0.7529 0
7  1.0212 0
8  1.2512 0
9  1.5387 0
10 2.0397 0
11 0.0000 0
12 0.1013 0
13 0.1588 0
14 0.2355 0
15 0.4846 0
16 0.7529 0
17 1.0212 0
18 1.2512 0
19 1.5387 0
20 2.0397 0

The D-score is found in column y and the DAZ is in column z.

bash

/vwc/select: Select Van Wiechen development milestones based on D-score and age

R

The Van Wiechenonderzoek is a Dutch screening tool used to track a child’s development from birth to age 4.5. It includes 75 milestones across three areas: fine motor skills, gross motor skills, and communication. The /vwc/select end point suggest the most fitting milestones for a child based on the uploaded data.

fn <- system.file("extdata/bds_v3.0/smocc/Laura_S.json", package = "jamesdemodata")
r <- james_post(host = host, path = "vwc/select/json", output = "table", txt = fn, percentiles = TRUE)
r$url

[1] "https://james.groeidiagrammen.nl/vwc/select/json"

r$parsed

[1] "ddifmd027" "ddigmm073" "ddifmd023" "ddicmm050" "ddicmm047" "ddigmd074"

bash

To be added

/vwc/percentiles: Select Van Wiechen development milestones with detailed cut-off information

R

It is also possible to obtain a table of age and D-score percentiles for a selection of milestones. This can be done either directly using the vwc argument, or indirectly from uploaded child data.

r <- james_post(
  host = host,
  path = "vwc/percentiles/json",
  output = "table",
  vwc = "ddifmd018"
)
r$parsed

       item      D2     D10  D50     D90     D98      A2     A10     A50
1 ddifmd018 52.1101 55.6762 60.3 64.9238 68.4899 13.9437 16.4593 20.4204
      A90     A98
1 25.3019 29.7694

bash

To be added

/dcat/calculate: Calculate next milestone item

R

The DCAT allows users to performa adapative testing using either ddi or gs1 items.

The following snippet uploads child data and requests the next item to be tested based on the gs1 instrument, the default.

fn <- system.file("examples", "example_v3.1.json", package = "bdsreader")
r <- james_post(host = host, path = "dcat/calculate/json", txt = fn)
r$parsed

[1] "gs1lgc112"

By specifying the instrument we can specify whether we want to include ddi or gs1 (or even both). In the case of only ddi items, we must additionally specify a key that supports the ddi instrument.

fn <- system.file("examples", "example_v3.1.json", package = "bdsreader")
r <- james_post(
  host = host,
  path = "dcat/calculate/json",
  txt = fn,
  instrument = "ddi",
  key = "gsed2406"
)
r$parsed

[1] "ddifmd023"

bash

To be added

/screeners/list: List available growth screeners

R

JAMES implements several screening algorithms. The /screeners/list end point provides detailed information on each of these.

r <- james_post(
  host = host,
  path = "/screeners/list/json",
  session = r1$session
)
names(r$parsed)
with(r$parsed, table(yname, Categorie))

There are currently different codes. Codes ending in 31, e.g., 1031 or 2031 indicate normal growth, whereas code ending in 41, 42 and so on, signal that - according to the guidelines - the child should be referred for further investigation.

bash

We get the details for the guidelines for head circumference as

source auth_curl.sh
auth_curl -sX 'POST' \
$(cat .host)'/screeners/list/json' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{"ynames": "hdc"}'

/screeners/apply: Apply growth screeners to child data

R

The /screeners/apply end point applies standard screeners to the child data. Invoke the screeners by

r <- james_post(
  host = host,
  path = "/screeners/apply/json",
  session = r1$session
)
r$parsed

  Categorie CategorieOmschrijving Code
1      1000                Lengte 1031
2      2000               Gewicht 2031
3      3000           Hoofdomtrek 3031
                                                                                                               CodeOmschrijving
1 Het advies volgens de JGZ-richtlijn lengtegroei is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen.
2 Het advies volgens de JGZ-richtlijn overgewicht is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen.
3                                                               In principe geen verwijzing nodig, naar eigen inzicht handelen.
  Versie Leeftijd
1 1.24.0    0.167
2 1.24.0    0.167
3 1.24.0    0.167

The procedure

1. calculates, per outcome, the intervals between the most recent measurement and all earlier measurements;
2. tests whether any of those intervals produces a signal according the screening algorithm;
3. reports the most recent non-standard signal that indicate abnormal growth.

In the example, all returned codes (1031, 2031, 3031) end in “31”, which signals normal growth. The full table of return codes and messages can be obtained by the /screeners/list end point (see above).

There are several possibilities to visualise and integrate multiple evaluations per curve performed in step 2 into one advice. Before May 2023, JAMES returned an advice for each combination of time point and outcome, but that table presented a lot of output that was difficult to act one. Since May 2023, JAMES reports only one signal per curve.

bash

source auth_curl.sh
auth_curl -sX 'POST' \
$(cat .host)'/screeners/apply/json' \
-H 'accept: application/json' \
-H 'Content-Type: multipart/form-data' \
-F 'txt=@maria.json;type=application/json'

[
  {
    "Categorie": 1000,
    "CategorieOmschrijving": "Lengte",
    "Code": 1031,
    "CodeOmschrijving": "Het advies volgens de JGZ-richtlijn lengtegroei is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen.",
    "Versie": "1.24.0",
    "Leeftijd": 0.167
  },
  {
    "Categorie": 2000,
    "CategorieOmschrijving": "Gewicht",
    "Code": 2031,
    "CodeOmschrijving": "Het advies volgens de JGZ-richtlijn overgewicht is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen.",
    "Versie": "1.24.0",
    "Leeftijd": 0.167
  },
  {
    "Categorie": 3000,
    "CategorieOmschrijving": "Hoofdomtrek",
    "Code": 3031,
    "CodeOmschrijving": "In principe geen verwijzing nodig, naar eigen inzicht handelen.",
    "Versie": "1.24.0",
    "Leeftijd": 0.167
  }
]

/site: Request an empty site

R

The /site end point provides interactive site containing all charts, but without child data. This end point is primarily useful to obtain a quick overview of the available charts.

browseURL(file.path(host, "site"))

bash

/site/request: Request personalised site

R

The /site/request end point creates an URL to a personalised, interactive site containing all charts.

r <- james_post(
  host = host,
  path = "/site/request/json",
  sitehost = host,
  txt = js
)
r$parsed

[1] "https://james.groeidiagrammen.nl/site?session=x0bce05b69f1b3f"

Run the command and paste the generated URL in the address field of your browser. The starting chart is chosen by JAMES and depends on the age of the child.

On some systems, the above command may fail with the browser error [400] Couldn't connect to server [localhost]. An alternative is to break the request into two steps. First, we create a session by uploading the child data, and then we use that session to create the URL to the personalised site.

We start by uploading data to JAMES and het r$session. After that, we can use either site\request or manual construction of the URL to the site:

fn <- system.file("examples/maria.json", package = "bdsreader")
r <- james_post(host = host, path = "data/upload/json", txt = fn)

# URL construction by /site/request
site1 <- james_post(
  host = host,
  path = "site/request/json",
  sitehost = host,
  session = r$session,
  upload = FALSE
)
site1

JAMES request:
  Path    : site/request/json
  Status  : 201
  Session : x0a61571200eb53

Parsed response:
[1] "https://james.groeidiagrammen.nl/site?session=x074bbb1a8eaf59"

# Or manual URL construction
parsed_host <- httr::parse_url(host)
combined_path <- paste(parsed_host$path, "site", sep = "/")
combined_path <- gsub("//+", "/", combined_path)
site2 <- httr::modify_url(
  url = host,
  path = combined_path,
  query = list(session = r$session)
)
site2

[1] "https://james.groeidiagrammen.nl/site?session=x074bbb1a8eaf59"

Paste the generated URL in the address field of your browser. The initial page shown depends on the child’s age. This two-step approach also works for remote servers. In practice, use the two-step approach is stabler and more reliable.

bash

source auth_curl.sh
auth_curl -sX 'POST' \
$(cat .host)'/site/request/json' \
-H 'accept: application/json' \
-H 'Content-Type: multipart/form-data' \
-F "sitehost='$(cat .host)'" \
-F 'txt=@maria.json;type=application/json'

["https://james.groeidiagrammen.nl/site?session=x034ad79b7bdaf3"]

/blend/request: Obtain a blend from multiple end points

R

The /blend/request end point returns the results of multiple end points, and thus functions as a one-stop shop. However, currently it does not support graphics output, so use /{session}/{info}/svglite or /charts/draw/svglite for the charts.

fn <- system.file(
  "extdata",
  "bds_v3.0",
  "smocc",
  "Laura_S.json",
  package = "jamesdemodata",
  mustWork = TRUE
)
r <- james_post(
  host = host,
  path = "/blend/request/json",
  sitehost = host,
  txt = fn
)
r

JAMES request:
  Path    : /blend/request/json
  Status  : 201
  Session : x03db7668844ee1

Parsed response:
List of 6
 $ txt      : chr "{\"Format\": \"3.0\",\"organisationCode\": 0,\"reference\": \"Laura S\",\"clientDetails\": [{\"bdsNumber\": 19,"| __truncated__
 $ session  : chr "x0e6f6609e5e4bc"
 $ site     : chr "https://james.groeidiagrammen.nl/site?session=x0e6f6609e5e4bc"
 $ child    :'data.frame':  1 obs. of  12 variables:
  ..$ id  : int -1
  ..$ name: chr "Laura S"
  ..$ dob : chr "1989-01-21"
  ..$ dobm: chr "1961-07-22"
  ..$ src : chr "0"
  ..$ sex : chr "female"
  ..$ gad : int 276
  ..$ ga  : int 39
  ..$ smo : int 0
  ..$ bw  : int 2950
  ..$ hgtm: int 164
  ..$ hgtf: int 179
 $ time     :'data.frame':  58 obs. of  8 variables:
  ..$ age  : num [1:58] 0 0.101 0.159 0.235 0.485 ...
  ..$ xname: chr [1:58] "age" "age" "age" "age" ...
  ..$ yname: chr [1:58] "hgt" "hgt" "hgt" "hgt" ...
  ..$ zname: chr [1:58] "hgt_z" "hgt_z" "hgt_z" "hgt_z" ...
  ..$ zref : chr [1:58] "nl_1997_hgt_female_nl" "nl_1997_hgt_female_nl" "nl_1997_hgt_female_nl" "nl_1997_hgt_female_nl" ...
  ..$ x    : num [1:58] 0 0.101 0.159 0.235 0.485 ...
  ..$ y    : num [1:58] 48 53.5 56 59.5 65.5 71.5 75 80 84 90 ...
  ..$ z    : num [1:58] -1.515 -0.499 -0.261 0.163 -0.259 ...
 $ screeners:'data.frame':  3 obs. of  6 variables:
  ..$ Categorie            : int [1:3] 1000 2000 3000
  ..$ CategorieOmschrijving: chr [1:3] "Lengte" "Gewicht" "Hoofdomtrek"
  ..$ Code                 : int [1:3] 1031 2075 3021
  ..$ CodeOmschrijving     : chr [1:3] "Het advies volgens de JGZ-richtlijn lengtegroei is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen." "Het advies volgens de JGZ-richtlijn ondergewicht is als volgt: Sterke gewichtsafname (-1 SD), advies: Is er spr"| __truncated__ "De richtlijn hoofdomtrek is bedoeld voor kinderen tot 1 jaar."
  ..$ Versie               : chr [1:3] "1.24.0" "1.24.0" "1.24.0"
  ..$ Leeftijd             : num [1:3] 2.04 2.04 2.04

names(r$parsed)

[1] "txt"       "session"   "site"      "child"     "time"      "screeners"

The two-step approach is:

resp1 <- james_post(host = host, path = "data/upload/json", txt = fn)
resp2 <- james_post(
  host = host,
  path = "blend/request/json",
  session = resp1$session
)
names(resp2$parsed)

[1] "txt"       "session"   "site"      "child"     "time"      "screeners"

# browseURL(resp2$parsed$site)

bash

Note: This example requires OpenCPU library access and may not work on ACC server.

source auth_curl.sh

BASE_URL=$(cat .host)
auth_curl -sX 'POST' \
$(cat .host)'/blend/request/json' \
-H 'accept: application/json' \
-H 'Content-Type: application/json' \
-d '{
"txt": "https://james.groeidiagrammen.nl/ocpu/library/bdsreader/examples/Laura_S.json",
"sitehost": "'$(cat .host)'",
"blend": "standard"
}'

{
  "txt": "https://james.groeidiagrammen.nl/ocpu/library/bdsreader/examples/Laura_S.json",
  "session": "x06c45ded90d372",
  "site": "https://james.groeidiagrammen.nl/site?session=x06c45ded90d372",
  "child": [
    {
      "id": -1,
      "name": "Laura S",
      "dob": "1989-01-21",
      "dobm": "1961-07-22",
      "src": "0",
      "sex": "female",
      "gad": 276,
      "ga": 39,
      "smo": 0,
      "bw": 2950,
      "hgtm": 164,
      "hgtf": 179
    }
  ],
  "time": [
    {
      "age": 0,
      "xname": "age",
      "yname": "hgt",
      "zname": "hgt_z",
      "zref": "nl_1997_hgt_female_nl",
      "x": 0,
      "y": 48,
      "z": -1.515
    },
    {
      "age": 0.1013,
      "xname": "age",
      "yname": "hgt",
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      "zref": "ph_2023_dsc_female_40",
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    {
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    {
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      "zref": "nl_1997_wfh_female_nla",
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      "zref": "nl_1997_wfh_female_nla",
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  ],
  "screeners": [
    {
      "Categorie": 1000,
      "CategorieOmschrijving": "Lengte",
      "Code": 1031,
      "CodeOmschrijving": "Het advies volgens de JGZ-richtlijn lengtegroei is als volgt: In principe geen verwijzing nodig, naar eigen inzicht handelen.",
      "Versie": "1.24.0",
      "Leeftijd": 2.0397
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    {
      "Categorie": 2000,
      "CategorieOmschrijving": "Gewicht",
      "Code": 2075,
      "CodeOmschrijving": "Het advies volgens de JGZ-richtlijn ondergewicht is als volgt: Sterke gewichtsafname (-1 SD), advies: Is er sprake van een afwijkende voedingstoestand en/of klachten of symptomen die kunnen wijzen op onderliggende ziekte of problemen? Indien ja, Verwijzen naar kinderarts. Indien nee, dan is er in principe geen verwijzing nodig. Naar eigen inzicht handelen.",
      "Versie": "1.24.0",
      "Leeftijd": 2.0397
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    {
      "Categorie": 3000,
      "CategorieOmschrijving": "Hoofdomtrek",
      "Code": 3021,
      "CodeOmschrijving": "De richtlijn hoofdomtrek is bedoeld voor kinderen tot 1 jaar.",
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}

Authentication

Overview

JAMES supports both open and authenticated access depending on the deployment environment:

• Test server (https://james.groeidiagrammen.nl): Open access, no authentication required
• ACC and PROD server : Requires Bearer token authentication

This document uses authentication throughout for compatibility with the ACC server. The authentication mechanism is handled behind the scenes but uses a simple convention that makes it easy to switch between different deployment environments.

Authentication Conventions

The authentication system in this document uses several files and environment variables:

File/Variable	Purpose	Location
apikey-acc.txt	Stores your API key for the ACC server	vignettes/articles/
.bearer	Stores the authentication token obtained from the API	vignettes/articles/ (generated)
.host	Stores the current server URL	vignettes/articles/ (generated)
JAMES_BEARER_TOKEN	Environment variable containing “Bearer {token}”	R session (set automatically)
authenticate-acc.sh	Script to obtain Bearer token from API key	vignettes/articles/
auth_curl.sh	Helper function that adds authentication to curl commands	vignettes/articles/

Note: The .bearer and .host files are temporary and are created when rendering this document. Add apikey-acc.txt, .bearer, and .host to your .gitignore to prevent accidentally committing sensitive information.

How to Set Up Authentication

To use the ACC server (or any authenticated JAMES instance), follow these steps:

1. Obtain an API Key

Contact the JAMES administrator to obtain an API key for the ACC environment. Save this key in a file named apikey-acc.txt (or apikey-prod.txt) in the vignettes/articles/ directory:

echo "your-api-key-here" > vignettes/articles/apikey-acc.txt

2. Authenticate to Get Bearer Token

Run the authentication script to obtain a Bearer token:

cd vignettes/articles
./authenticate-acc.sh

This script: 1. Reads your API key from apikey-acc.txt 2. Sends it to the ACC authentication endpoint 3. Saves the returned Bearer token to .bearer 4. Returns exit code 0 on success, 1 on failure

The Bearer token is typically valid for a limited time (e.g., 24 hours). Re-run the script when the token expires.

3. Use Authentication in Your Code

For R code: The setup chunk automatically loads the Bearer token into the JAMES_BEARER_TOKEN environment variable, which is used by jamesclient functions:

# Token is automatically loaded from .bearer file
# jamesclient functions automatically use JAMES_BEARER_TOKEN
r <- james_post(host = host, path = "version/json")

For bash code: Use the auth_curl helper function instead of curl:

source auth_curl.sh

# Instead of: curl -X POST https://server/endpoint
# Use:
auth_curl -sX POST $(cat .host)/endpoint

The auth_curl function automatically adds the Authorization: Bearer {token} header if the .bearer file exists.

Manual Authentication

If you prefer to handle authentication manually without the helper scripts:

In R:

# Read the bearer token
bearer_token <- trimws(readLines(".bearer", n = 1))

# Add to requests
library(httr2)
resp <- request(paste0(host, "/version/json")) |>
  req_headers(Authorization = paste("Bearer", bearer_token)) |>
  req_perform()

In bash:

# Read the bearer token
TOKEN=$(cat .bearer)

# Add to curl requests
curl -sX POST https://server/endpoint \
  -H "Authorization: Bearer $TOKEN"

Switching Between Servers

To switch between different JAMES servers (test, acc, dev), change the target_host variable in the {r host} setup chunk at the beginning of this document:

target_host <- "dev"   # localhost for development
target_host <- "test"  # No authentication needed
target_host <- "acc"   # Requires authentication
target_host <- "prod"  # Requires authentication

The document will automatically:

1. Set the appropriate server URL in host variable
2. Create the .host file for bash chunks
3. Load authentication tokens if available
4. Use authenticated requests when needed

Troubleshooting Authentication

401 Unauthorized errors:

• Token may have expired - re-run ./authenticate-acc.sh
• Check that .bearer file exists and is not empty
• Verify JAMES_BEARER_TOKEN is set: Sys.getenv("JAMES_BEARER_TOKEN")
• The jamesclient::james_post() and jamesclient::james_get() functions rely on JAMES_BEARER_TOKEN for authentication

Token not found:

• Ensure apikey-acc.txt exists and contains your API key
• Check that you’re running commands from vignettes/articles/ directory
• Verify authenticate-acc.sh has execute permissions: chmod +x authenticate-acc.sh

Connection timeout:

• Check your network connection
• Verify the ACC server URL is correct
• Check if you’re behind a proxy that requires configuration

Resources

Internal

Description	Status
Tutorial (Dutch)	open
Changelog	open
OpenAPI specification	open
JSON data schema 3.0	open
Source files	open
JAMES issue tracker	open

External

Description	Status
JAMES demo	current
Basisdataset JGZ	current
OpenCPU API	current