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Merge pull request #110 from pbs-data-solutions/json
Add methods to convert native structs to json
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‎src/native/site_native.rs‎

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@@ -2,6 +2,7 @@ use chrono::{DateTime, Utc};
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#[cfg(feature = "python")]
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use pyo3::{
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exceptions::PyValueError,
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prelude::*,
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types::{PyDateTime, PyDict},
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};
@@ -133,6 +134,32 @@ pub struct SiteNative {
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pub sites: Vec<Site>,
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}
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#[cfg(not(feature = "python"))]
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impl SiteNative {
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/// Convert to a JSON string
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///
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/// # Example
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///
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/// ```
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/// use std::path::Path;
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///
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/// use prelude_xml_parser::parse_site_native_file;
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///
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/// let file_path = Path::new("tests/assets/site_native_small.xml");
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/// let native = parse_site_native_file(&file_path).unwrap();
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/// let json = native.to_json().unwrap();
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/// println!("{json}");
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/// let expected = r#"{"sites":[{"name":"Some Site","uniqueId":"1681574834910","numberOfPatients":4,"countOfRandomizedPatients":0,"whenCreated":"2023-04-15T16:08:19Z","creator":"Paul Sanders","numberOfForms":1,"forms":[{"name":"demographic.form.name.site.demographics","lastModified":"2023-04-15T16:08:19Z","whoLastModifiedName":"Paul Sanders","whoLastModifiedRole":"Project Manager","whenCreated":1681574834930,"hasErrors":false,"hasWarnings":false,"locked":false,"user":null,"dateTimeChanged":null,"formTitle":"Site Demographics","formIndex":1,"formGroup":"Demographic","formState":"In-Work","states":[{"value":"form.state.in.work","signer":"Paul Sanders - Project Manager","signerUniqueId":"1681162687395","dateSigned":"2023-04-15T16:08:19Z"}],"categories":[{"name":"Demographics","categoryType":"normal","highestIndex":0,"fields":[{"name":"address","fieldType":"text","dataType":"string","errorCode":"valid","whenCreated":"2023-04-15T16:07:14Z","keepHistory":true,"entries":null,"comments":null},{"name":"company","fieldType":"text","dataType":"string","errorCode":"valid","whenCreated":"2023-04-15T16:07:14Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-04-15T16:08:19Z","value":"Some Company"},"reason":null}],"comments":[{"commentId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-04-15T16:09:02Z","value":"Some Comment"}}]}]}]}]}]}"#;;
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///
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/// assert_eq!(json, expected);
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/// ```
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pub fn to_json(&self) -> serde_json::Result<String> {
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let json = serde_json::to_string(&self)?;
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Ok(json)
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}
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}
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#[cfg(feature = "python")]
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/// Contains the information from the Prelude native site XML.
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#[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
@@ -162,6 +189,12 @@ impl SiteNative {
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dict.set_item("sites", site_dicts)?;
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Ok(dict)
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}
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/// Convert the class instance to a JSON string
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fn to_json(&self) -> PyResult<String> {
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serde_json::to_string(&self)
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.map_err(|_| PyErr::new::<PyValueError, _>("Error converting to JSON"))
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}
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}
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#[cfg(test)]

‎src/native/subject_native.rs‎

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@@ -2,6 +2,7 @@ use chrono::{DateTime, Utc};
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#[cfg(feature = "python")]
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use pyo3::{
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exceptions::PyValueError,
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prelude::*,
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types::{PyDateTime, PyDict},
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};
@@ -149,6 +150,31 @@ pub struct SubjectNative {
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pub patients: Vec<Patient>,
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}
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#[cfg(not(feature = "python"))]
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impl SubjectNative {
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/// Convert to a JSON string
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///
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/// # Example
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///
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/// ```
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/// use std::path::Path;
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///
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/// use prelude_xml_parser::parse_subject_native_file;
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///
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/// let file_path = Path::new("tests/assets/subject_native_small.xml");
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/// let native = parse_subject_native_file(&file_path).unwrap();
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/// let expected = r#"{"patients":[{"patientId":"ABC-001","uniqueId":"1681574905819","whenCreated":"2023-04-15T16:09:02Z","creator":"Paul Sanders","siteName":"Some Site","siteUniqueId":"1681574834910","lastLanguage":null,"numberOfForms":6,"forms":[{"name":"day.0.form.name.demographics","lastModified":"2023-04-15T16:09:15Z","whoLastModifiedName":"Paul Sanders","whoLastModifiedRole":"Project Manager","whenCreated":1681574905839,"hasErrors":false,"hasWarnings":false,"locked":false,"user":null,"dateTimeChanged":null,"formTitle":"Demographics","formIndex":1,"formGroup":"Day 0","formState":"In-Work","states":[{"value":"form.state.in.work","signer":"Paul Sanders - Project Manager","signerUniqueId":"1681162687395","dateSigned":"2023-04-15T16:09:02Z"}],"categories":[{"name":"Demographics","categoryType":"normal","highestIndex":0,"fields":[{"name":"breed","fieldType":"combo-box","dataType":"string","errorCode":"valid","whenCreated":"2023-04-15T16:08:26Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-04-15T16:09:02Z","value":"Labrador"},"reason":null}],"comments":[{"commentId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-04-15T16:09:02Z","value":"Some Comment"}}]}]}]}]}]}"#;
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/// let json = native.to_json().unwrap();
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///
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/// assert_eq!(json, expected);
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/// ```
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pub fn to_json(&self) -> serde_json::Result<String> {
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let json = serde_json::to_string(&self)?;
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Ok(json)
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}
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}
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#[cfg(feature = "python")]
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/// Contains the information from the Prelude native subject XML.
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#[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
@@ -178,6 +204,12 @@ impl SubjectNative {
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dict.set_item("patients", patient_dicts)?;
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Ok(dict)
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}
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/// Convert the class instance to a JSON string
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fn to_json(&self) -> PyResult<String> {
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serde_json::to_string(&self)
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.map_err(|_| PyErr::new::<PyValueError, _>("Error converting to JSON"))
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}
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}
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#[cfg(test)]

‎src/native/user_native.rs‎

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@@ -1,7 +1,7 @@
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use serde::{Deserialize, Serialize};
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#[cfg(feature = "python")]
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use pyo3::{prelude::*, types::PyDict};
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use pyo3::{exceptions::PyValueError, prelude::*, types::PyDict};
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pub use crate::native::{
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common::{Category, Comment, Entry, Field, Form, Reason, State, Value},
@@ -102,6 +102,31 @@ pub struct UserNative {
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pub users: Vec<User>,
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}
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#[cfg(not(feature = "python"))]
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impl UserNative {
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/// Convert to a JSON string
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///
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/// # Example
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///
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/// ```
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/// use std::path::Path;
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///
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/// use prelude_xml_parser::parse_user_native_file;
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///
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/// let file_path = Path::new("tests/assets/user_native_small.xml");
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/// let native = parse_user_native_file(&file_path).unwrap();
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/// let expected = r#"{"users":[{"uniqueId":"1691421275437","lastLanguage":null,"creator":"Paul Sanders(1681162687395)","numberOfForms":1,"forms":[{"name":"form.name.demographics","lastModified":"2023-08-07T15:15:41Z","whoLastModifiedName":"Paul Sanders","whoLastModifiedRole":"Project Manager","whenCreated":1691421341578,"hasErrors":false,"hasWarnings":false,"locked":false,"user":null,"dateTimeChanged":null,"formTitle":"User Demographics","formIndex":1,"formGroup":null,"formState":"In-Work","states":[{"value":"form.state.in.work","signer":"Paul Sanders - Project Manager","signerUniqueId":"1681162687395","dateSigned":"2023-08-07T15:15:41Z"}],"categories":[{"name":"demographics","categoryType":"normal","highestIndex":0,"fields":[{"name":"address","fieldType":"text","dataType":"string","errorCode":"undefined","whenCreated":"2024-01-12T20:14:09Z","keepHistory":true,"entries":null,"comments":null},{"name":"email","fieldType":"text","dataType":"string","errorCode":"undefined","whenCreated":"2023-08-07T15:15:41Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-08-07T15:15:41Z","value":"[email protected]"},"reason":null}],"comments":[{"commentId":"1","value":{"by":"Paul Sanders","byUniqueId":"1681162687395","role":"Project Manager","when":"2023-04-15T16:09:02Z","value":"Some Comment"}}]}]},{"name":"Administrative","categoryType":"normal","highestIndex":0,"fields":[{"name":"study_assignment","fieldType":"text","dataType":null,"errorCode":"undefined","whenCreated":"2023-08-07T15:15:41Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"set from calculation","byUniqueId":null,"role":"System","when":"2023-08-07T15:15:41Z","value":"On 07-Aug-2023 10:15 -0500, Paul Sanders assigned user from another study"},"reason":{"by":"set from calculation","byUniqueId":null,"role":"System","when":"2023-08-07T15:15:41Z","value":"calculated value"}}],"comments":null}]}]}]},{"uniqueId":"1681162687395","lastLanguage":null,"creator":"1609858291483(1609858291483)","numberOfForms":2,"forms":[{"name":"form.name.demographics","lastModified":"2023-04-10T21:39:30Z","whoLastModifiedName":"1609858291483","whoLastModifiedRole":"role.administrator","whenCreated":1681162770378,"hasErrors":false,"hasWarnings":false,"locked":false,"user":null,"dateTimeChanged":null,"formTitle":"User Demographics","formIndex":1,"formGroup":null,"formState":"In-Work","states":[{"value":"form.state.in.work","signer":"1609858291483 - Administrator","signerUniqueId":"1609858291483","dateSigned":"2023-04-10T21:39:30Z"}],"categories":[{"name":"demographics","categoryType":"normal","highestIndex":0,"fields":[{"name":"address","fieldType":"text","dataType":"string","errorCode":"undefined","whenCreated":"2023-04-15T15:21:14Z","keepHistory":true,"entries":null,"comments":null},{"name":"email","fieldType":"text","dataType":"string","errorCode":"undefined","whenCreated":"2023-04-10T21:39:30Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"1609858291483","byUniqueId":"1609858291483","role":"Administrator","when":"2023-04-10T21:39:30Z","value":"[email protected]"},"reason":null}],"comments":null}]},{"name":"Administrative","categoryType":"normal","highestIndex":0,"fields":[{"name":"study_assignment","fieldType":"text","dataType":null,"errorCode":"undefined","whenCreated":"2023-04-10T21:39:30Z","keepHistory":true,"entries":[{"entryId":"1","value":{"by":"set from calculation","byUniqueId":null,"role":"System","when":"2023-04-10T21:39:30Z","value":"On 10-Apr-2023 16:39 -0500, 1609858291483 assigned user from another study"},"reason":{"by":"set from calculation","byUniqueId":null,"role":"System","when":"2023-04-10T21:39:30Z","value":"calculated value"}}],"comments":null}]}]},{"name":"training.form.name.checklist","lastModified":null,"whoLastModifiedName":null,"whoLastModifiedRole":null,"whenCreated":1702998014133,"hasErrors":false,"hasWarnings":false,"locked":false,"user":null,"dateTimeChanged":null,"formTitle":"Training Checklist","formIndex":1,"formGroup":"Training","formState":"New","states":[{"value":"form.state.new","signer":"System set","signerUniqueId":"system","dateSigned":"2023-12-19T15:00:14Z"}],"categories":[{"name":"Training_Modules","categoryType":"normal","highestIndex":0,"fields":[{"name":"date(1)","fieldType":"setToday","dataType":"date","errorCode":"undefined","whenCreated":"2023-12-19T15:00:15Z","keepHistory":true,"entries":null,"comments":null}]},{"name":"Other_Training_Modules","categoryType":"indexed","highestIndex":1,"fields":[{"name":"date_field(1)","fieldType":"setToday","dataType":"date","errorCode":"undefined","whenCreated":"2023-12-19T15:00:15Z","keepHistory":true,"entries":null,"comments":null}]},{"name":"21CFR11","categoryType":"normal","highestIndex":0,"fields":null}]}]}]}"#;
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/// let json = native.to_json().unwrap();
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///
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/// assert_eq!(json, expected);
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/// ```
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pub fn to_json(&self) -> serde_json::Result<String> {
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let json = serde_json::to_string(&self)?;
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Ok(json)
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}
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}
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#[cfg(feature = "python")]
106131
/// Contains the information from the Prelude native user XML.
107132
#[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
@@ -131,6 +156,12 @@ impl UserNative {
131156
dict.set_item("users", user_dicts)?;
132157
Ok(dict)
133158
}
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160+
/// Convert the class instance to a JSON string
161+
fn to_json(&self) -> PyResult<String> {
162+
serde_json::to_string(&self)
163+
.map_err(|_| PyErr::new::<PyValueError, _>("Error converting to JSON"))
164+
}
134165
}
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136167
#[cfg(test)]

‎tests/assets/site_native_small.xml‎

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@@ -0,0 +1,21 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<export_from_vision_EDC date="01-Jun-2024 18:17 -0500" createdBy="Paul Sanders" role="Project Manager" numberSubjectsProcessed="2">
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<site name="Some Site" uniqueId="1681574834910" numberOfPatients="4" countOfRandomizedPatients="0" whenCreated="2023-04-15 12:08:19 -0400" creator="Paul Sanders" numberOfForms="1">
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<form name="demographic.form.name.site.demographics" lastModified="2023-04-15 12:08:19 -0400" whoLastModifiedName="Paul Sanders" whoLastModifiedRole="Project Manager" whenCreated="1681574834930" hasErrors="false" hasWarnings="false" locked="false" user="" dateTimeChanged="" formTitle="Site Demographics" formIndex="1" formGroup="Demographic" formState="In-Work">
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<state value="form.state.in.work" signer="Paul Sanders - Project Manager" signerUniqueId="1681162687395" dateSigned="2023-04-15 12:08:19 -0400" />
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<category name="Demographics" type="normal" highestIndex="0">
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<field name="address" type="text" dataType="string" errorCode="valid" whenCreated="2023-04-15 11:07:14 -0500" keepHistory="true" />
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<field name="company" type="text" dataType="string" errorCode="valid" whenCreated="2023-04-15 11:07:14 -0500" keepHistory="true">
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<entry id="1">
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<value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:08:19 -0400" xml:space="preserve">Some Company</value>
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</entry>
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<comment id="1">
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<value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Some Comment</value>
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</comment>
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</field>
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</category>
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</form>
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</site>
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</export_from_vision_EDC>

‎tests/assets/subject_native_small.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<export_from_vision_EDC date="30-May-2024 10:35 -0500" createdBy="Paul Sanders" role="Project Manager" numberSubjectsProcessed="4">
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<patient patientId="ABC-001" uniqueId="1681574905819" whenCreated="2023-04-15 12:09:02 -0400" creator="Paul Sanders" siteName="Some Site" siteUniqueId="1681574834910" lastLanguage="" numberOfForms="6">
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<form name="day.0.form.name.demographics" lastModified="2023-04-15 12:09:15 -0400" whoLastModifiedName="Paul Sanders" whoLastModifiedRole="Project Manager" whenCreated="1681574905839" hasErrors="false" hasWarnings="false" locked="false" user="" dateTimeChanged="" formTitle="Demographics" formIndex="1" formGroup="Day 0" formState="In-Work">
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<state value="form.state.in.work" signer="Paul Sanders - Project Manager" signerUniqueId="1681162687395" dateSigned="2023-04-15 12:09:02 -0400" />
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<category name="Demographics" type="normal" highestIndex="0">
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<field name="breed" type="combo-box" dataType="string" errorCode="valid" whenCreated="2023-04-15 12:08:26 -0400" keepHistory="true">
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<entry id="1">
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<value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Labrador</value>
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</entry>
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<comment id="1">
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<value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Some Comment</value>
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</comment>
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</field>
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</category>
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</form>
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</patient>
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</export_from_vision_EDC>

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