Merge pull request #392 from pbs-data-solutions/to-dict

Add to_dict to native classes

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "prelude-parser"
-version = "0.8.0"
+version = "0.9.0"
 description = "Parses XML files exported from Prelude EDC into formats usable by Python."
 edition = "2021"
 license = "MIT"
@@ -16,7 +16,7 @@ crate-type = ["cdylib"]
 [dependencies]
 anyhow = "1.0.89"
 chrono = "0.4.38"
-prelude-xml-parser = { version = "0.6.1", features = ["python"] }
+prelude-xml-parser = { version = "0.7.0", features = ["python"] }
 pyo3 = { version = "0.22.3", features = ["extension-module"] }
 roxmltree = "0.20.0"
 serde = { version = "1.0.210", features = ["derive"] }

prelude_parser/_prelude_parser.pyi

@@ -11,18 +11,24 @@ class Value:
     role: str
     when: datetime
 
+    def to_dict(self) -> dict: ...
+
 class Reason:
     by: str
     by_unique_id: str | None
     role: str
     when: datetime
     value: str
 
+    def to_dict(self) -> dict: ...
+
 class Entry:
     entry_id: str
     value: Value | None
     reason: Reason | None
 
+    def to_dict(self) -> dict: ...
+
 class Field:
     name: str
     data_type: str | None
@@ -31,17 +37,23 @@ class Field:
     keep_history: bool
     entries: list[Entry] | None
 
+    def to_dict(self) -> dict: ...
+
 class Category:
     name: str
     category_type: str
     highest_index: int
     fields: list[Field] | None
 
+    def to_dict(self) -> dict: ...
+
 class State:
     value: str
     signer: str
     signer_unique_id: str
 
+    def to_dict(self) -> dict: ...
+
 class Form:
     name: str
     last_modified: datetime | None
@@ -60,6 +72,8 @@ class Form:
     states: list[State] | None
     categories: list[Category] | None
 
+    def to_dict(self) -> dict: ...
+
 class Patient:
     patient_id: str
     unique_id: str
@@ -70,6 +84,8 @@ class Patient:
     last_language: str | None
     forms: list[Form] | None
 
+    def to_dict(self) -> dict: ...
+
 class Site:
     name: str
     unique_id: str
@@ -80,22 +96,32 @@ class Site:
     number_of_forms: int
     forms: list[Form] | None
 
+    def to_dict(self) -> dict: ...
+
 class User:
     unique_id: str
     last_language: str | None
     creator: str
     number_of_forms: int
     forms: list[Form] | None
 
+    def to_dict(self) -> dict: ...
+
 class SiteNative:
     sites: list[Site]
 
+    def to_dict(self) -> dict: ...
+
 class SubjectNative:
     patients: list[Patient]
 
+    def to_dict(self) -> dict: ...
+
 class UserNative:
     users: list[User]
 
+    def to_dict(self) -> dict: ...
+
 def _parse_flat_file_to_dict(
     xml_file: str | Path, *, short_names: bool = False
 ) -> dict[str, FlatFormInfo]: ...

tests/test_parser.py

@@ -29,6 +29,13 @@ def test_parse_site_native_string(site_native_xml):
     assert result.sites[0].name == "Some Site"
 
 
+def test_site_native_to_dict(site_native_xml):
+    result = parse_site_native_file(site_native_xml)
+    result_dict = result.to_dict()
+
+    assert result_dict["sites"][0]["name"] == "Some Site"
+
+
 def test_parse_subject_native_file(subject_native_xml):
     result = parse_subject_native_file(subject_native_xml)
 
@@ -43,6 +50,13 @@ def test_parse_subject_native_string(subject_native_xml):
     assert result.patients[0].patient_id == "ABC-001"
 
 
+def test_subject_native_to_dict(subject_native_xml):
+    result = parse_subject_native_file(subject_native_xml)
+    result_dict = result.to_dict()
+
+    assert result_dict["patients"][0]["patient_id"] == "ABC-001"
+
+
 def test_parse_user_native_file(user_native_xml):
     result = parse_user_native_file(user_native_xml)
 
@@ -57,6 +71,13 @@ def test_parse_user_native_string(user_native_xml):
     assert result.users[0].unique_id == "1691421275437"
 
 
+def test_user_native_to_dict(user_native_xml):
+    result = parse_user_native_file(user_native_xml)
+    result_dict = result.to_dict()
+
+    assert result_dict["users"][0]["unique_id"] == "1691421275437"
+
+
 def test_parse_to_classes(test_file_1):
     result = parse_to_classes(test_file_1)
     assert len(result) == 2