Improve documentation and cleanup code

ingest/ingest.py

@@ -16,6 +16,7 @@
 
 # round the number to 1 decimal place
 def formatNumber(num):
+    """Convert a value to float and round it to 1 decimal place."""
     num = round(float(num), 1)
     return num
 
@@ -79,24 +80,4 @@ def formatNumber(num):
         for i in range(len(row)):
             # calculate the pH value using the pH index (ph_i) and the pH base
             ph = formatNumber((ph_i * 0.5) + ph_base)
-            # create a nested dictionary for the pH if it doesn't already exist
-            if ph not in d[disinfectant][pathogen][temperature][concentration]:
-                d[disinfectant][pathogen][temperature][concentration][ph] = {}
-
-            # calculate the inactivation log value using the position in the row (m) and the formula (m * 0.5 + 0.5)
-            m = i % 6
-            inactivation_log = formatNumber((m * 0.5) + 0.5)
-            # set the value in the nested dictionary for the pH, concentration, and temperature
-            d[disinfectant][pathogen][temperature][concentration][ph][inactivation_log] = row[i]
-
-            # increment the pH index when 6 values have been processed
-            if m == 5:
-                ph_i = ph_i + 1
-
-        # update the pH base and index values when the concentration is 3.0
-        if concentration == 3.0:
-            ph_base = 8
-            ph_i = 0
-
-# print the dictionary as a JSON string with separators
-print(json.dumps(d, separators=(',', ':')))
+            # create a nested dictionary for the pH if it doesn't already exist

web/src/components/form/Form.svelte

@@ -12,6 +12,10 @@
   let interpolatedResult = "";
   let error = "";
 
+  /**
+   * Handles form submission: calls the calc API with the selected parameters and
+   * updates the displayed results (or error) from the JSON response.
+   */
   async function onSubmit(event: Event) {
     event.preventDefault();
 
@@ -100,26 +104,4 @@
       <option value="2.5">2.5</option>
       <option value="3.0">3.0</option>
     {:else}
-      <option value="1.0">2.0</option>
-      <option value="2.0">3.0</option>
-      <option value="3.0">4.0</option>
-    {/if}
-  </select>
-
-  <br />
-  <button type="submit">Submit</button>
-
-  {#if formulaResult && interpolatedResult}
-    <div class={styles.divider} />
-
-    <p class={styles.result}>Formula result:</p>
-    <p data-cy="result">{formulaResult}</p>
-
-    <p class={styles.result}>Interpolated result:</p>
-    <p data-cy="result">{interpolatedResult}</p>
-  {:else if error}
-    <div class={styles.divider} />
-    <p class={styles.result}>Error:</p>
-    <p data-cy="result">{error}</p>
-  {/if}
-</form>
+      <option value="1.0">2.0</option>

web/src/pages/api/calc.ts

@@ -2,6 +2,10 @@ import { getResults } from "../../utils/inactivation";
 import { parseQueryParams } from "../../utils/parseQueryParams";
 import { validate } from "../../utils/validate";
 
+/**
+ * Astro API route handler: parses query params, validates them, computes CT results,
+ * and returns a JSON response (or an error).
+ */
 export async function get({ params, request }) {
   const queryParams = parseQueryParams(request.url);
   const [validatedParams, error] = validate(queryParams);
@@ -17,4 +21,4 @@ export async function get({ params, request }) {
     status: 200,
     headers: { "Content-Type": "application/json" },
   });
-}
+}

web/src/utils/validate.ts

@@ -1,6 +1,9 @@
 const methodologies = ["round", "interpolate", "formula"] as const;
 export type Methodology = (typeof methodologies)[number];
 
+/**
+ * Check whether the provided value is a supported calculation methodology.
+ */
 function isValidMethodology(methodology: any) {
   if (typeof methodology !== "string") return false;
   return methodologies.includes(methodology as Methodology);
@@ -14,6 +17,9 @@ const disinfectants = [
 ] as const;
 export type Disinfectant = (typeof disinfectants)[number];
 
+/**
+ * Check whether the provided value is a supported disinfectant.
+ */
 function isValidDisinfectant(disinfectant: any) {
   if (typeof disinfectant !== "string") return false;
   return disinfectants.includes(disinfectant as Disinfectant);
@@ -22,21 +28,33 @@ function isValidDisinfectant(disinfectant: any) {
 const pathogens = ["giardia", "virus"] as const;
 export type Pathogen = (typeof pathogens)[number];
 
+/**
+ * Check whether the provided value is a supported pathogen.
+ */
 function isValidPathogen(pathogen: any) {
   if (typeof pathogen !== "string") return false;
   return pathogens.includes(pathogen as Pathogen);
 }
 
+/**
+ * Check whether the provided value is a valid temperature in Celsius.
+ */
 function isValidTemperature(temperature: any) {
   if (typeof temperature !== "number") return false;
   return 0 < temperature && temperature <= 25;
 }
 
+/**
+ * Check whether the provided value is a valid pH.
+ */
 function isValidPh(ph: any) {
   if (typeof ph !== "number") return false;
   return 6 <= ph && ph <= 9;
 }
 
+/**
+ * Check whether the provided value is a valid disinfectant concentration.
+ */
 function isValidConcentration(concentration: any) {
   if (typeof concentration !== "number") return false;
   return 0 < concentration && concentration <= 3;
@@ -45,6 +63,11 @@ function isValidConcentration(concentration: any) {
 // TODO should these be strings?
 const inactivationLogs = [2, 3, 4];
 const giardiaInactivationLogs = [0.5, 1, 1.5, 2, 2.5, 3];
+
+/**
+ * Check whether the provided value is a supported inactivation log value, with an
+ * optional Giardia-specific allowed set.
+ */
 function isValidInactivationLog(inactivationLog: any, isGiardia?: boolean) {
   if (typeof inactivationLog !== "number") return false;
   return (isGiardia ? giardiaInactivationLogs : inactivationLogs).includes(
@@ -91,18 +114,4 @@ export function validate(
     !isValidConcentration(queryParams.concentration)
   )
     return [, `Invalid concentration: ${queryParams.concentration}`];
-
-  if (!isValidInactivationLog(queryParams["inactivation_log"], isGiardia))
-    return [, `Invalid inactivation_log: ${queryParams["inactivation_log"]}`];
-
-  const validatedparams: ValidatedParams = {
-    disinfectant: queryParams.disinfectant as Disinfectant,
-    pathogen: queryParams.pathogen as Pathogen,
-    temperature: Number(queryParams.temperature),
-    ph: Number(queryParams.ph),
-    concentration: Number(queryParams.concentration),
-    inactivationLog: Number(queryParams["inactivation_log"]),
-  };
-
-  return [validatedparams];
-}
+}