Merge pull request #228 from rcpch/eatyourpeas/issue227

trisomy-21-aap

main.py

@@ -10,7 +10,7 @@
 
 # local / rcpch imports
 from rcpchgrowth import chart_functions, constants
-from routers import trisomy_21, turners, uk_who, cdc, utilities
+from routers import trisomy_21, trisomy_21_aap, turners, uk_who, cdc, utilities
 
 
 version='4.2.20'  # this is set by bump version
@@ -40,6 +40,7 @@
 app.include_router(uk_who)
 app.include_router(turners)
 app.include_router(trisomy_21)
+app.include_router(trisomy_21_aap)
 app.include_router(cdc)
 app.include_router(utilities)
 
@@ -77,7 +78,7 @@ def root():
 # This data is only generated once and then is stored and served from file.
 def generate_and_store_chart_data():
     for centile_format in [constants.COLE_TWO_THIRDS_SDS_NINE_CENTILES, constants.THREE_PERCENT_CENTILES, constants.FIVE_PERCENT_CENTILES, constants.EIGHTY_FIVE_PERCENT_CENTILES]:
-        for reference in constants.REFERENCES + [constants.CDC]:
+        for reference in constants.REFERENCES + [constants.CDC] + [constants.TRISOMY_21_AAP]:
             for sex in constants.SEXES:
                 for measurement_method in constants.MEASUREMENT_METHODS:
                     # Don't generate files for Turner's for references we don't have (males or non-height measurements)

openapi.json

@@ -438,6 +438,156 @@
                 }
             }
         },
+        "/trisomy-21-aap/calculation": {
+            "post": {
+                "tags": [
+                    "trisomy-21-aap"
+                ],
+                "summary": "Trisomy 21 Aap Calculation",
+                "description": "## Trisomy-21 AAP Centile and SDS Calculations\n\n* These are the 'standard' centiles for US children with trisomy-21. It uses the American Academy of Pediatrics dataset (American Academy of Pediatrics (AAP) Trisomy 21 reference. Zemel BS, Pipan M, Stallings VA, Hall W, Schgadt K, Freedman DS, Thorpe P. Growth Charts for Children with Down Syndrome in the U.S. Pediatrics, 2015).\n* UK users should use the UK Down Syndrome Growth Charts included in the RCPCHGrowth package and provide on a separate endpoint.\n* Returns a single centile/SDS calculation for the selected `measurement_method`.\n* Gestational age correction will be applied automatically if appropriate according to the gestational age at birth data supplied.\n* Available `measurement_method`s are: `height`, `weight`, `bmi`, or `ofc` (OFC = occipitofrontal circumference = 'head circumference').\n* Note that BMI must be precalculated for the `bmi` function.\n* Dates will discard anything after first 'T' in `YYYY-MM-DDTHH:MM:SS.milliseconds+TZ` etc\n* Bone ages are not supported for this reference.\n* Optional events can be passed in as a list of strings - each list is associated with a measurement",
+                "operationId": "trisomy_21_aap_calculation_trisomy_21_aap_calculation_post",
+                "requestBody": {
+                    "content": {
+                        "application/json": {
+                            "schema": {
+                                "$ref": "#/components/schemas/MeasurementRequest",
+                                "examples": [
+                                    {
+                                        "birth_date": "2020-04-12",
+                                        "observation_date": "2028-06-12",
+                                        "observation_value": 115,
+                                        "sex": "female",
+                                        "gestation_weeks": 40,
+                                        "gestation_days": 0,
+                                        "measurement_method": "height",
+                                        "bone_age": 10,
+                                        "bone_age_centile": 98,
+                                        "bone_age_sds": 2.0,
+                                        "bone_age_text": "This bone age is advanced",
+                                        "bone_age_type": "greulich-pyle",
+                                        "events_text": [
+                                            "Growth hormone start",
+                                            "Growth Hormone Deficiency diagnosis"
+                                        ]
+                                    }
+                                ]
+                            }
+                        }
+                    },
+                    "required": true
+                },
+                "responses": {
+                    "200": {
+                        "description": "Successful Response",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "$ref": "#/components/schemas/MeasurementObject"
+                                }
+                            }
+                        }
+                    },
+                    "422": {
+                        "description": "Validation Error",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "$ref": "#/components/schemas/HTTPValidationError"
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        },
+        "/trisomy-21-aap/chart-coordinates": {
+            "post": {
+                "tags": [
+                    "trisomy-21-aap"
+                ],
+                "summary": "Trisomy 21 Aap Chart Coordinates",
+                "description": "## trisomy-21-aap Chart Coordinates data.\n\n* Returns coordinates for constructing the lines of a traditional growth chart, in JSON format\n* Requires a sex ('male' or 'female' lowercase) and a measurement_method ('height', 'weight' ,'bmi', 'ofc')\n* If custom centiles/sds collections (individually or as a collection) are required, accepts a list of float values (up to 15) as centile_format parameter\n* The is_sds boolean flag (default false) specifies if the custom list is of SDS or centiles.\n* In addition to the custom list, \"cole-nine-centiles\" or \"three-percent-centiles\" can be specified which are standard collections.\n* If no centile_format is supplied, \"cole-nine-centiles\" are returned as a default.",
+                "operationId": "trisomy_21_aap_chart_coordinates_trisomy_21_aap_chart_coordinates_post",
+                "requestBody": {
+                    "content": {
+                        "application/json": {
+                            "schema": {
+                                "$ref": "#/components/schemas/ChartCoordinateRequest"
+                            }
+                        }
+                    },
+                    "required": true
+                },
+                "responses": {
+                    "200": {
+                        "description": "Successful Response",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "$ref": "#/components/schemas/Centile_Data"
+                                }
+                            }
+                        }
+                    },
+                    "422": {
+                        "description": "Validation Error",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "$ref": "#/components/schemas/HTTPValidationError"
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        },
+        "/trisomy-21-aap/fictional-child-data": {
+            "post": {
+                "tags": [
+                    "trisomy-21-aap"
+                ],
+                "summary": "Fictional Child Data",
+                "description": "## trisomy-21-aap Fictional Child Data Endpoint\n\n* Generates synthetic data for demonstration or testing purposes",
+                "operationId": "fictional_child_data_trisomy_21_aap_fictional_child_data_post",
+                "requestBody": {
+                    "content": {
+                        "application/json": {
+                            "schema": {
+                                "$ref": "#/components/schemas/FictionalChildRequest"
+                            }
+                        }
+                    },
+                    "required": true
+                },
+                "responses": {
+                    "200": {
+                        "description": "Successful Response",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "items": {
+                                        "$ref": "#/components/schemas/MeasurementObject"
+                                    },
+                                    "type": "array",
+                                    "title": "Response Fictional Child Data Trisomy 21 Aap Fictional Child Data Post"
+                                }
+                            }
+                        }
+                    },
+                    "422": {
+                        "description": "Validation Error",
+                        "content": {
+                            "application/json": {
+                                "schema": {
+                                    "$ref": "#/components/schemas/HTTPValidationError"
+                                }
+                            }
+                        }
+                    }
+                }
+            }
+        },
         "/cdc/calculation": {
             "post": {
                 "tags": [

requirements/common-requirements.txt

@@ -8,4 +8,4 @@ pydantic == 2.*
 
 # rcpch dependencies
 # python package which does the centile and SDS calculations
-rcpchgrowth==4.1.1
+rcpchgrowth==4.2.1

routers/__init__.py

@@ -2,4 +2,5 @@
 from .turner import turners
 from .trisomy21 import trisomy_21
 from .cdc import cdc
+from .trisomy21aap import trisomy_21_aap
 from .utilities import utilities

routers/trisomy21aap.py

@@ -0,0 +1,198 @@
+"""
+trisomy-21-aap router
+"""
+
+# Standard imports
+import json
+from pathlib import Path
+from typing import List
+from pprint import pprint
+
+# Third party imports
+from schemas.response_schema_classes import Centile_Data, MeasurementObject
+from fastapi import APIRouter, Body, HTTPException
+
+# RCPCH imports
+from rcpchgrowth import (
+    Measurement,
+    constants,
+    generate_fictional_child_data,
+    create_chart,
+)
+from rcpchgrowth.constants.reference_constants import TRISOMY_21_AAP
+from schemas import MeasurementRequest, ChartCoordinateRequest, FictionalChildRequest
+
+# set up the API router
+trisomy_21_aap = APIRouter(
+    prefix="/trisomy-21-aap",
+)
+
+
+@trisomy_21_aap.post("/calculation", tags=["trisomy-21-aap"], response_model=MeasurementObject)
+def trisomy_21_aap_calculation(
+    measurementRequest: MeasurementRequest = Body(
+        ...,
+        examples=[
+            {
+                "birth_date": "2020-04-12",
+                "observation_date": "2028-06-12",
+                "observation_value": 115,
+                "sex": "female",
+                "gestation_weeks": 40,
+                "gestation_days": 0,
+                "measurement_method": "height",
+                "bone_age": 10,
+                "bone_age_centile": 98,
+                "bone_age_sds": 2.0,
+                "bone_age_text": "This bone age is advanced",
+                "bone_age_type": "greulich-pyle",
+                "events_text": [
+                    "Growth hormone start",
+                    "Growth Hormone Deficiency diagnosis",
+                ],
+            }
+        ],
+    )
+):
+    """
+    ## Trisomy-21 AAP Centile and SDS Calculations
+
+    * These are the 'standard' centiles for US children with trisomy-21. It uses the American Academy of Pediatrics dataset (American Academy of Pediatrics (AAP) Trisomy 21 reference. Zemel BS, Pipan M, Stallings VA, Hall W, Schgadt K, Freedman DS, Thorpe P. Growth Charts for Children with Down Syndrome in the U.S. Pediatrics, 2015).
+    * UK users should use the UK Down Syndrome Growth Charts included in the RCPCHGrowth package and provide on a separate endpoint.
+    * Returns a single centile/SDS calculation for the selected `measurement_method`.
+    * Gestational age correction will be applied automatically if appropriate according to the gestational age at birth data supplied.
+    * Available `measurement_method`s are: `height`, `weight`, `bmi`, or `ofc` (OFC = occipitofrontal circumference = 'head circumference').
+    * Note that BMI must be precalculated for the `bmi` function.
+    * Dates will discard anything after first 'T' in `YYYY-MM-DDTHH:MM:SS.milliseconds+TZ` etc
+    * Bone ages are not supported for this reference.
+    * Optional events can be passed in as a list of strings - each list is associated with a measurement
+    """
+    try:
+        calculation = Measurement(
+            reference=constants.TRISOMY_21_AAP,
+            birth_date=measurementRequest.birth_date,
+            gestation_days=measurementRequest.gestation_days,
+            gestation_weeks=measurementRequest.gestation_weeks,
+            measurement_method=measurementRequest.measurement_method,
+            observation_date=measurementRequest.observation_date,
+            observation_value=measurementRequest.observation_value,
+            sex=measurementRequest.sex,
+            bone_age=None,
+            bone_age_centile=None,
+            bone_age_sds=None,
+            bone_age_text=None,
+            bone_age_type=None,
+            events_text=measurementRequest.events_text,
+        ).measurement
+    except ValueError as err:
+        print(err.args)
+        return err.args, 422
+
+    calculation["measurement_calculated_values"]["corrected_centile"] = round(calculation["measurement_calculated_values"]["corrected_centile"],4)
+    calculation["measurement_calculated_values"]["chronological_centile"] = round(calculation["measurement_calculated_values"]["chronological_centile"],4)
+    calculation["plottable_data"]["centile_data"]["corrected_decimal_age_data"]["centile"] = round(calculation["plottable_data"]["centile_data"]["corrected_decimal_age_data"]["centile"],4)
+    calculation["plottable_data"]["centile_data"]["chronological_decimal_age_data"]["centile"] = round(calculation["plottable_data"]["centile_data"]["chronological_decimal_age_data"]["centile"],4)
+    calculation["plottable_data"]["sds_data"]["corrected_decimal_age_data"]["centile"] = round(calculation["plottable_data"]["sds_data"]["corrected_decimal_age_data"]["centile"],4)
+    calculation["plottable_data"]["sds_data"]["chronological_decimal_age_data"]["centile"] = round(calculation["plottable_data"]["sds_data"]["chronological_decimal_age_data"]["centile"],4)
+    return calculation
+
+
+@trisomy_21_aap.post("/chart-coordinates", tags=["trisomy-21-aap"], response_model=Centile_Data)
+def trisomy_21_aap_chart_coordinates(chartParams: ChartCoordinateRequest):
+    """
+    ## trisomy-21-aap Chart Coordinates data.
+
+    * Returns coordinates for constructing the lines of a traditional growth chart, in JSON format
+    * Requires a sex ('male' or 'female' lowercase) and a measurement_method ('height', 'weight' ,'bmi', 'ofc')
+    * If custom centiles/sds collections (individually or as a collection) are required, accepts a list of float values (up to 15) as centile_format parameter
+    * The is_sds boolean flag (default false) specifies if the custom list is of SDS or centiles.
+    * In addition to the custom list, "cole-nine-centiles" or "three-percent-centiles" can be specified which are standard collections.
+    * If no centile_format is supplied, "cole-nine-centiles" are returned as a default.
+    \f
+    [
+        "height": [
+            {
+                sds: -1.64,
+                trisomy_21_aap_infants: [.....],
+                trisomy_21_aap_children: [
+                    {
+                        label: 5, `this is the centile
+                        x: 4, `this is the decimal age
+                        y: 91.535  `this is the measurement
+                    }
+                    ....
+                ]
+            }
+        ],
+        ... repeat for weight, bmi, ofc, based on which measurements supplied. If only height data supplied, only height centile data returned
+    ]
+    """
+    chart_data = None
+    if type(chartParams.centile_format) is list:
+        # custom centiles requested - calculate these and return. Do not persist.
+        try:
+            chart_data = create_chart(
+                TRISOMY_21_AAP,
+                chartParams.centile_format,
+                measurement_method=chartParams.measurement_method,
+                sex=chartParams.sex,
+                is_sds=chartParams.is_sds,
+            )
+        except:
+            return HTTPException(
+                status_code=422,
+                detail=f"Error creating {chartParams.sex} {chartParams.measurement_method} trisomy-21-aap chart on the server, using {chartParams.centile_format} centile format.",
+            )
+    else:
+        chart_data_file = Path(
+            f"chart-data/{chartParams.centile_format}-{constants.TRISOMY_21_AAP}-{chartParams.sex}-{chartParams.measurement_method}.json"
+        )
+        if chart_data_file.exists():
+            print(
+                f"Chart data file exists for {chartParams.centile_format}-{constants.TRISOMY_21_AAP}-{chartParams.sex}-{chartParams.measurement_method}."
+            )
+            with open(
+                f"chart-data/{chartParams.centile_format}-{constants.TRISOMY_21_AAP}-{chartParams.sex}-{chartParams.measurement_method}.json",
+                "r",
+            ) as file:
+                chart_data = json.load(file)
+        else:
+            return HTTPException(
+                status_code=422,
+                detail=f"Item not found: chart-data/{chartParams.centile_format}-{constants.TRISOMY_21_AAP}-{chartParams.sex}-{chartParams.measurement_method}.json",
+            )
+    return {"centile_data": chart_data}
+
+
+@trisomy_21_aap.post(
+    "/fictional-child-data", tags=["trisomy-21-aap"], response_model=List[MeasurementObject]
+)
+def fictional_child_data(fictional_child_request: FictionalChildRequest):
+    """
+    ## trisomy-21-aap Fictional Child Data Endpoint
+
+    * Generates synthetic data for demonstration or testing purposes
+    """
+    try:
+        life_course_fictional_child_data = generate_fictional_child_data(
+            measurement_method=fictional_child_request.measurement_method,
+            sex=fictional_child_request.sex,
+            start_chronological_age=fictional_child_request.start_chronological_age,
+            end_age=fictional_child_request.end_age,
+            gestation_weeks=fictional_child_request.gestation_weeks,
+            gestation_days=fictional_child_request.gestation_days,
+            measurement_interval_type=fictional_child_request.measurement_interval_type,
+            measurement_interval_number=fictional_child_request.measurement_interval_number,
+            start_sds=fictional_child_request.start_sds,
+            drift=fictional_child_request.drift,
+            drift_range=fictional_child_request.drift_range,
+            noise=fictional_child_request.noise,
+            noise_range=fictional_child_request.noise_range,
+            reference=constants.TRISOMY_21_AAP,
+        )
+        return life_course_fictional_child_data
+    except:
+        return HTTPException(
+            status_code=422,
+            detail=f"Not possible to create trisomy-21-aap fictional child data.",
+        )