Merge pull request #307 from pbs-data-solutions/user-native

Add function to load user native xml
pbs-data-solutions · Jun 3, 2024 · 68d42c0 · 68d42c0
2 parents b733df7 + 4cb4aff
commit 68d42c0
Show file tree

Hide file tree

Showing 6 changed files with 99 additions and 3 deletions.
diff --git a/prelude_parser/__init__.py b/prelude_parser/__init__.py
@@ -1,9 +1,14 @@
-from prelude_parser._prelude_parser import parse_site_native_file, parse_subject_native_file
+from prelude_parser._prelude_parser import (
+    parse_site_native_file,
+    parse_subject_native_file,
+    parse_user_native_file,
+)
 from prelude_parser.parser import parse_to_classes, parse_to_dict
 
 __all__ = [
     "parse_site_native_file",
     "parse_subject_native_file",
+    "parse_user_native_file",
     "parse_to_classes",
     "parse_to_dict",
 ]
diff --git a/prelude_parser/_prelude_parser.pyi b/prelude_parser/_prelude_parser.pyi
@@ -2,7 +2,11 @@ from __future__ import annotations
 
 from pathlib import Path
 
-from prelude_parser._prelude_parser import SiteNative, SubjectNative  # type: ignore[attr-defined]
+from prelude_parser._prelude_parser import (  # type: ignore[attr-defined]
+    SiteNative,
+    SubjectNative,
+    UserNative,
+)
 from prelude_parser.types import FlatFormInfo
 
 def _parse_flat_file_to_dict(
@@ -13,6 +17,7 @@ def _parse_flat_file_to_pandas_dict(
 ) -> dict[str, FlatFormInfo]: ...
 def parse_site_native_file(xml_file: str | Path) -> SiteNative: ...
 def parse_subject_native_file(xml_file: str | Path) -> SubjectNative: ...
+def parse_user_native_file(xml_file: str | Path) -> UserNative: ...
 
 class FileNotFoundError(Exception):
     pass

diff --git a/src/lib.rs b/src/lib.rs
@@ -6,9 +6,12 @@ use std::fs::read_to_string;
 use std::path::PathBuf;
 
 use chrono::{Datelike, NaiveDate};
-pub use prelude_xml_parser::native::{site_native::SiteNative, subject_native::SubjectNative};
+pub use prelude_xml_parser::native::{
+    site_native::SiteNative, subject_native::SubjectNative, user_native::UserNative,
+};
 use prelude_xml_parser::parse_site_native_file as parse_site_native_file_rs;
 use prelude_xml_parser::parse_subject_native_file as parse_subject_native_file_rs;
+use prelude_xml_parser::parse_user_native_file as parse_user_native_file_rs;
 use pyo3::prelude::*;
 use pyo3::types::{IntoPyDict, PyDict, PyList};
 use roxmltree::Document;
@@ -252,14 +255,27 @@ fn parse_subject_native_file(_py: Python, xml_file: PathBuf) -> PyResult<Subject
     }
 }
 
+#[pyfunction]
+fn parse_user_native_file(_py: Python, xml_file: PathBuf) -> PyResult<UserNative> {
+    match parse_user_native_file_rs(&xml_file) {
+        Ok(native) => Ok(native),
+        Err(e) => Err(ParsingError::new_err(format!(
+            "Error parsing xml file: {:?}",
+            e
+        ))),
+    }
+}
+
 #[pymodule]
 fn _prelude_parser(py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_class::<SiteNative>()?;
     m.add_class::<SubjectNative>()?;
+    m.add_class::<UserNative>()?;
     m.add_function(wrap_pyfunction!(_parse_flat_file_to_dict, m)?)?;
     m.add_function(wrap_pyfunction!(_parse_flat_file_to_pandas_dict, m)?)?;
     m.add_function(wrap_pyfunction!(parse_site_native_file, m)?)?;
     m.add_function(wrap_pyfunction!(parse_subject_native_file, m)?)?;
+    m.add_function(wrap_pyfunction!(parse_user_native_file, m)?)?;
     m.add(
         "FileNotFoundError",
         py.get_type_bound::<FileNotFoundError>(),

diff --git a/tests/assets/user_native.xml b/tests/assets/user_native.xml
@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<export_from_vision_EDC date="02-Jun-2024 06:59 -0500" createdBy="Paul Sanders" role="Project Manager" numberSubjectsProcessed="3">
+
+  <user uniqueId="1691421275437" lastLanguage="" creator="Paul Sanders(1681162687395)" numberOfForms="1">
+    <form name="form.name.demographics" lastModified="2023-08-07 10:15:41 -0500" whoLastModifiedName="Paul Sanders" whoLastModifiedRole="Project Manager" whenCreated="1691421341578" hasErrors="false" hasWarnings="false" locked="false" user="" dateTimeChanged="" formTitle="User Demographics" formIndex="1" formGroup="" formState="In-Work">
+      <state value="form.state.in.work" signer="Paul Sanders - Project Manager" signerUniqueId="1681162687395" dateSigned="2023-08-07 10:15:41 -0500" />
+      <category name="demographics" type="normal" highestIndex="0">
+        <field name="address" type="text" dataType="string" errorCode="undefined" whenCreated="2024-01-12 14:14:09 -0600" keepHistory="true" />
+        <field name="email" type="text" dataType="string" errorCode="undefined" whenCreated="2023-08-07 10:15:41 -0500" keepHistory="true">
+          <entry id="1">
+            <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-08-07 10:15:41 -0500" xml:space="preserve">[email protected]</value>
+          </entry>
+        </field>
+      </category>
+      <category name="Administrative" type="normal" highestIndex="0">
+        <field name="study_assignment" type="text" dataType="" errorCode="undefined" whenCreated="2023-08-07 10:15:41 -0500" keepHistory="true">
+          <entry id="1">
+            <value by="set from calculation" byUniqueId="" role="System" when="2023-08-07 10:15:41 -0500" xml:space="preserve">On 07-Aug-2023 10:15 -0500, Paul Sanders assigned user from another study</value>
+            <reason by="set from calculation" byUniqueId="" role="System" when="2023-08-07 10:15:41 -0500" xml:space="preserve">calculated value</reason>
+          </entry>
+        </field>
+      </category>
+    </form>
+  </user>
+
+  <user uniqueId="1681162687395" lastLanguage="" creator="1609858291483(1609858291483)" numberOfForms="2">
+    <form name="form.name.demographics" lastModified="2023-04-10 16:39:30 -0500" whoLastModifiedName="1609858291483" whoLastModifiedRole="role.administrator" whenCreated="1681162770378" hasErrors="false" hasWarnings="false" locked="false" user="" dateTimeChanged="" formTitle="User Demographics" formIndex="1" formGroup="" formState="In-Work">
+      <state value="form.state.in.work" signer="1609858291483 - Administrator" signerUniqueId="1609858291483" dateSigned="2023-04-10 16:39:30 -0500" />
+      <category name="demographics" type="normal" highestIndex="0">
+        <field name="address" type="text" dataType="string" errorCode="undefined" whenCreated="2023-04-15 10:21:14 -0500" keepHistory="true" />
+        <field name="email" type="text" dataType="string" errorCode="undefined" whenCreated="2023-04-10 16:39:30 -0500" keepHistory="true">
+          <entry id="1">
+            <value by="1609858291483" byUniqueId="1609858291483" role="Administrator" when="2023-04-10 16:39:30 -0500" xml:space="preserve">[email protected]</value>
+          </entry>
+        </field>
+      </category>
+      <category name="Administrative" type="normal" highestIndex="0">
+        <field name="study_assignment" type="text" dataType="" errorCode="undefined" whenCreated="2023-04-10 16:39:30 -0500" keepHistory="true">
+          <entry id="1">
+            <value by="set from calculation" byUniqueId="" role="System" when="2023-04-10 16:39:30 -0500" xml:space="preserve">On 10-Apr-2023 16:39 -0500, 1609858291483 assigned user from another study</value>
+            <reason by="set from calculation" byUniqueId="" role="System" when="2023-04-10 16:39:30 -0500" xml:space="preserve">calculated value</reason>
+          </entry>
+        </field>
+      </category>
+    </form>
+    <form name="training.form.name.checklist" lastModified="" whenCreated="1702998014133" hasErrors="false" hasWarnings="false" locked="false" user="" dateTimeChanged="" formTitle="Training Checklist" formIndex="1" formGroup="Training" formState="New">
+      <state value="form.state.new" signer="System set" signerUniqueId="system" dateSigned="2023-12-19 09:00:14 -0600" />
+      <category name="Training_Modules" type="normal" highestIndex="0">
+        <field name="date(1)" type="setToday" dataType="date" errorCode="undefined" whenCreated="2023-12-19 09:00:15 -0600" keepHistory="true" />
+      </category>
+      <category name="Other_Training_Modules" type="indexed" highestIndex="1">
+        <field name="date_field(1)" type="setToday" dataType="date" errorCode="undefined" whenCreated="2023-12-19 09:00:15 -0600" keepHistory="true" />
+      </category>
+      <category name="21CFR11" type="normal" highestIndex="0" />
+    </form>
+  </user>
+
+</export_from_vision_EDC>
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -33,3 +33,8 @@ def site_native_xml():
 @pytest.fixture
 def subject_native_xml():
     return ASSETS_PATH / "subject_native.xml"
+
+
+@pytest.fixture
+def user_native_xml():
+    return ASSETS_PATH / "user_native.xml"
diff --git a/tests/test_parser.py b/tests/test_parser.py
@@ -7,6 +7,7 @@
     parse_subject_native_file,
     parse_to_classes,
     parse_to_dict,
+    parse_user_native_file,
 )
 from prelude_parser._prelude_parser import FileNotFoundError, InvalidFileTypeError, ParsingError
 
@@ -23,6 +24,12 @@ def test_parse_subject_native(subject_native_xml):
     assert result.patients[0].patient_id == "ABC-001"
 
 
+def test_parse_user_native(user_native_xml):
+    result = parse_user_native_file(user_native_xml)
+
+    assert result.users[0].unique_id == "1691421275437"
+
+
 def test_parse_to_classes(test_file_1):
     result = parse_to_classes(test_file_1)
     assert len(result) == 2