Merge pull request #546 from pbs-data-solutions/prelude-xml-parser

Bump prelude-xml-parser

Author: sanders41

Cargo.lock

@@ -16,8 +16,8 @@ crate-type = ["cdylib"]
 [dependencies]
 anyhow = "1.0.99"
 chrono = "0.4.41"
-prelude-xml-parser = { version = "0.8.3", features = ["python"] }
-pyo3 = { version = "0.25.1", features = ["extension-module"] }
+prelude-xml-parser = { version = "0.9.0", features = ["python"] }
+pyo3 = { version = "0.26.0", features = ["extension-module"] }
 roxmltree = "0.20.0"
 serde = { version = "1.0.219", features = ["derive"] }
 serde-xml-rs = "0.8.1"

Cargo.toml

@@ -11,15 +11,15 @@ class Value:
     by: str
     by_unique_id: str | None
     role: str
-    when: datetime
+    when: datetime | None
 
     def to_dict(self) -> dict: ...
 
 class Reason:
     by: str
     by_unique_id: str | None
     role: str
-    when: datetime
+    when: datetime | None
     value: str
 
     def to_dict(self) -> dict: ...
@@ -41,7 +41,7 @@ class Field:
     name: str
     data_type: str | None
     error_code: str
-    when_created: datetime
+    when_created: datetime | None
     keep_history: bool
     entries: list[Entry] | None
     comments: list[Comment] | None
@@ -86,7 +86,7 @@ class Form:
 class Patient:
     patient_id: str
     unique_id: str
-    when_created: datetime
+    when_created: datetime | None
     creator: str
     site_name: str
     site_unique_id: str
@@ -100,7 +100,7 @@ class Site:
     unique_id: str
     number_of_patients: int
     count_of_randomized_patients: int
-    when_created: datetime
+    when_created: datetime | None
     creator: str
     number_of_forms: int
     forms: list[Form] | None

prelude_parser/_prelude_parser.pyi

@@ -42,14 +42,15 @@ def test_site_native_to_json(site_native_small_xml):
 
     assert (
         result_json
-        == '{"site":[{"name":"Some Site","uniqueId":"1681574834910","numberOfPatients":4,"countOfRandomizedPatients":0,"whenCreated":"2023-04-15T16:08:19Z","creator":"Paul Sanders","numberOfForms":1,"form":[{"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":"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"}}]}]}]}]}]}'
+        == '{"sites":[{"name":"Some Site","uniqueId":"1681574834910","numberOfPatients":4,"countOfRandomizedPatients":0,"whenCreated":"2023-04-15T16:08:19Z","creator":"Paul Sanders","numberOfForms":1,"form":[{"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":"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"}}]}]}]}]}]}'
     )
 
 
 def test_parse_subject_native_file(subject_native_xml):
     result = parse_subject_native_file(subject_native_xml)
 
     assert result.patients[0].patient_id == "ABC-001"
+    assert result.patients[0].forms is not None
 
 
 def test_parse_subject_native_string(subject_native_xml):