Merge pull request #67 from pbs-data-solutions/comments

Add missing comments
pbs-data-solutions · Oct 15, 2024 · d8729b6 · d8729b6
2 parents 823d190 + ff3fcbd
commit d8729b6
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Showing 13 changed files with 119 additions and 5 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "prelude-xml-parser"
-version = "0.7.1"
+version = "0.7.2"
 edition = "2021"
 authors = ["Paul Sanders <[email protected]>"]
 description = "Deserialize Prelude EDC native XML files into Rust stucts."

diff --git a/src/lib.rs b/src/lib.rs
@@ -86,6 +86,9 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///           <entry id="1">
 ///             <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-08-07 08:14:21 -0700" xml:space="preserve">1111 Moon Drive</value>
 ///           </entry>
+///           <comment id="1">
+///             <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-08-07 08:14:21 -0700" xml:space="preserve">Some comment</value>
+///           </comment>
 ///         </field>
 ///       </category>
 ///     </form>
@@ -153,6 +156,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                 .with_timezone(&Utc),
 ///                                 keep_history: true,
 ///                                 entries: None,
+///                                 comments: None,
 ///                             },
 ///                             Field {
 ///                                 name: "company".to_string(),
@@ -180,6 +184,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                     }),
 ///                                     reason: None,
 ///                                 }]),
+///                                 comments: None,
 ///                             },
 ///                             Field {
 ///                                 name: "site_code_name".to_string(),
@@ -244,6 +249,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                         }),
 ///                                     },
 ///                                 ]),
+///                                 comments: None,
 ///                             },
 ///                         ]),
 ///                     },
@@ -264,6 +270,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                 .with_timezone(&Utc),
 ///                                 keep_history: true,
 ///                                 entries: None,
+///                                 comments: None,
 ///                             },
 ///                             Field {
 ///                                 name: "enrollment_open".to_string(),
@@ -291,6 +298,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                     }),
 ///                                     reason: None,
 ///                                 }]),
+///                                 comments: None,
 ///                             },
 ///                             Field {
 ///                                 name: "enrollment_open_date".to_string(),
@@ -304,6 +312,7 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                                 .with_timezone(&Utc),
 ///                                 keep_history: true,
 ///                                 entries: None,
+///                                 comments: None,
 ///                             },
 ///                         ]),
 ///                     },
@@ -375,6 +384,18 @@ pub fn parse_site_native_file(xml_path: &Path) -> Result<SiteNative, Error> {
 ///                             }),
 ///                             reason: None,
 ///                         }]),
+///                         comments: Some(vec![Comment {
+///                             comment_id: "1".to_string(),
+///                             value: Some(Value {
+///                                 by: "Paul Sanders".to_string(),
+///                                 by_unique_id: Some("1681162687395".to_string()),
+///                                 role: "Project Manager".to_string(),
+///                                 when: DateTime::parse_from_rfc3339("2023-08-07T15:14:21Z")
+///                                     .unwrap()
+///                                     .with_timezone(&Utc),
+///                                 value: "Some comment".to_string(),
+///                             }),
+///                         }]),
 ///                     }]),
 ///                 }]),
 ///             }]),
@@ -515,6 +536,7 @@ pub fn parse_subject_native_file(xml_path: &Path) -> Result<SubjectNative, Error
 ///                             }),
 ///                             reason: None,
 ///                         }]),
+///                         comments: None,
 ///                     }]),
 ///                 }]),
 ///             }]),
@@ -583,6 +605,7 @@ pub fn parse_subject_native_file(xml_path: &Path) -> Result<SubjectNative, Error
 ///                             }),
 ///                             reason: None,
 ///                         }]),
+///                         comments: None,
 ///                     }]),
 ///                 }]),
 ///             }]),
@@ -708,6 +731,7 @@ pub fn parse_user_native_file(xml_path: &Path) -> Result<UserNative, Error> {
 ///                                         .with_timezone(&Utc),
 ///                                     keep_history: true,
 ///                                     entries: None,
+///                                     comments: None,
 ///                                 },
 ///                                 Field {
 ///                                     name: "email".to_string(),
@@ -731,6 +755,7 @@ pub fn parse_user_native_file(xml_path: &Path) -> Result<UserNative, Error> {
 ///                                         }),
 ///                                         reason: None,
 ///                                     }]),
+///                                     comments: None,
 ///                                 },
 ///                             ]),
 ///                         },
@@ -771,6 +796,7 @@ pub fn parse_user_native_file(xml_path: &Path) -> Result<UserNative, Error> {
 ///                                             }),
 ///                                         },
 ///                                     ]),
+///                                     comments: None,
 ///                                 },
 ///                             ]),
 ///                         },

diff --git a/src/native/common.rs b/src/native/common.rs
@@ -228,6 +228,51 @@ impl Entry {
     }
 }
 
+#[cfg(not(feature = "python"))]
+#[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
+#[serde(rename_all = "camelCase")]
+pub struct Comment {
+    #[serde(alias = "id")]
+    pub comment_id: String,
+    pub value: Option<Value>,
+}
+
+#[cfg(feature = "python")]
+#[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
+#[serde(rename_all = "camelCase")]
+#[pyclass(get_all)]
+pub struct Comment {
+    #[serde(alias = "id")]
+    pub comment_id: String,
+    pub value: Option<Value>,
+}
+
+#[cfg(feature = "python")]
+#[pymethods]
+impl Comment {
+    #[getter]
+    fn comment_id(&self) -> PyResult<String> {
+        Ok(self.comment_id.clone())
+    }
+
+    #[getter]
+    fn value(&self) -> PyResult<Option<Value>> {
+        Ok(self.value.clone())
+    }
+
+    pub fn to_dict<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyDict>> {
+        let dict = PyDict::new_bound(py);
+        dict.set_item("comment_id", &self.comment_id)?;
+        if let Some(value) = &self.value {
+            dict.set_item("value", value.to_dict(py)?)?;
+        } else {
+            dict.set_item("value", py.None())?;
+        }
+
+        Ok(dict)
+    }
+}
+
 #[cfg(not(feature = "python"))]
 #[derive(Clone, Debug, Deserialize, Serialize, PartialEq)]
 #[serde(rename_all = "camelCase")]
@@ -248,6 +293,9 @@ pub struct Field {
 
     #[serde(alias = "entry")]
     pub entries: Option<Vec<Entry>>,
+
+    #[serde(alias = "comment")]
+    pub comments: Option<Vec<Comment>>,
 }
 
 #[cfg(feature = "python")]
@@ -272,6 +320,9 @@ pub struct Field {
 
     #[serde(alias = "entry")]
     pub entries: Option<Vec<Entry>>,
+
+    #[serde(alias = "comment")]
+    pub comments: Option<Vec<Comment>>,
 }
 
 #[cfg(feature = "python")]
@@ -312,6 +363,11 @@ impl Field {
         Ok(self.entries.clone())
     }
 
+    #[getter]
+    fn comments(&self) -> PyResult<Option<Vec<Comment>>> {
+        Ok(self.comments.clone())
+    }
+
     pub fn to_dict<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyDict>> {
         let dict = PyDict::new_bound(py);
         dict.set_item("name", &self.name)?;
@@ -332,6 +388,17 @@ impl Field {
             dict.set_item("entries", py.None())?;
         }
 
+        let mut comment_dicts = Vec::new();
+        if let Some(comments) = &self.comments {
+            for comment in comments {
+                let comment_dict = comment.to_dict(py)?;
+                comment_dicts.push(comment_dict.to_object(py));
+            }
+            dict.set_item("comments", comment_dicts)?;
+        } else {
+            dict.set_item("comments", py.None())?;
+        }
+
         Ok(dict)
     }
 }

diff --git a/src/native/site_native.rs b/src/native/site_native.rs
@@ -9,7 +9,7 @@ use pyo3::{
 use serde::{Deserialize, Serialize};
 
 pub use crate::native::{
-    common::{Category, Entry, Field, Form, Reason, State, Value},
+    common::{Category, Comment, Entry, Field, Form, Reason, State, Value},
     deserializers::{
         default_datetime_none, default_string_none, deserialize_empty_string_as_none,
         deserialize_empty_string_as_none_datetime,

diff --git a/...apshots/prelude_xml_parser__native__site_native__tests__deserialize_site_native_json.snap b/...apshots/prelude_xml_parser__native__site_native__tests__deserialize_site_native_json.snap
@@ -42,6 +42,7 @@ sites:
                 whenCreated: "2023-04-15T16:07:14Z"
                 keepHistory: true
                 entries: ~
+                comments: ~
               - name: company
                 fieldType: text
                 dataType: string
@@ -57,6 +58,7 @@ sites:
                       when: "2023-04-15T16:08:19Z"
                       value: Some Company
                     reason: ~
+                comments: ~
               - name: site_code_name
                 fieldType: hidden
                 dataType: string
@@ -90,6 +92,7 @@ sites:
                       role: System
                       when: "2023-04-15T16:07:24Z"
                       value: calculated value
+                comments: ~
           - name: Enrollment
             categoryType: normal
             highestIndex: 0
@@ -101,6 +104,7 @@ sites:
                 whenCreated: "2023-04-15T16:07:14Z"
                 keepHistory: true
                 entries: ~
+                comments: ~
               - name: enrollment_open
                 fieldType: radio
                 dataType: string
@@ -116,13 +120,15 @@ sites:
                       when: "2023-04-15T16:08:19Z"
                       value: "Yes"
                     reason: ~
+                comments: ~
               - name: enrollment_open_date
                 fieldType: popUpCalendar
                 dataType: date
                 errorCode: valid
                 whenCreated: "2023-04-15T16:07:14Z"
                 keepHistory: true
                 entries: ~
+                comments: ~
   - name: Artemis
     uniqueId: "1691420994591"
     numberOfPatients: 0
@@ -170,3 +176,4 @@ sites:
                       when: "2023-08-07T15:14:21Z"
                       value: 1111 Moon Drive
                     reason: ~
+                comments: ~
diff --git a/...s/prelude_xml_parser__native__subject_native__tests__deserialize_subject_native_json.snap b/...s/prelude_xml_parser__native__subject_native__tests__deserialize_subject_native_json.snap
@@ -51,6 +51,7 @@ patients:
                       when: "2023-04-15T16:09:02Z"
                       value: Labrador
                     reason: ~
+                comments: ~
   - patientId: DEF-002
     uniqueId: "1681574905820"
     whenCreated: "2023-04-16T16:10:02Z"
@@ -99,3 +100,4 @@ patients:
                       when: "2023-04-15T16:09:02Z"
                       value: Labrador
                     reason: ~
+                comments: ~
diff --git a/...apshots/prelude_xml_parser__native__user_native__tests__deserialize_user_native_json.snap b/...apshots/prelude_xml_parser__native__user_native__tests__deserialize_user_native_json.snap
@@ -39,6 +39,7 @@ users:
                 whenCreated: "2024-01-12T20:14:09Z"
                 keepHistory: true
                 entries: ~
+                comments: ~
               - name: email
                 fieldType: text
                 dataType: string
@@ -54,6 +55,7 @@ users:
                       when: "2023-08-07T15:15:41Z"
                       value: jazz@artemis.com
                     reason: ~
+                comments: ~
           - name: Administrative
             categoryType: normal
             highestIndex: 0
@@ -78,3 +80,4 @@ users:
                       role: System
                       when: "2023-08-07T15:15:41Z"
                       value: calculated value
+                comments: ~
diff --git a/src/native/subject_native.rs b/src/native/subject_native.rs
@@ -12,7 +12,7 @@ use crate::native::deserializers::to_py_datetime;
 use serde::{Deserialize, Serialize};
 
 pub use crate::native::{
-    common::{Category, Entry, Field, Form, Reason, State, Value},
+    common::{Category, Comment, Entry, Field, Form, Reason, State, Value},
     deserializers::{
         default_datetime_none, default_string_none, deserialize_empty_string_as_none,
         deserialize_empty_string_as_none_datetime,

diff --git a/src/native/user_native.rs b/src/native/user_native.rs
@@ -4,7 +4,7 @@ use serde::{Deserialize, Serialize};
 use pyo3::{prelude::*, types::PyDict};
 
 pub use crate::native::{
-    common::{Category, Entry, Field, Form, Reason, State, Value},
+    common::{Category, Comment, Entry, Field, Form, Reason, State, Value},
     deserializers::{
         default_datetime_none, default_string_none, deserialize_empty_string_as_none,
         deserialize_empty_string_as_none_datetime,

diff --git a/tests/assets/site_native.xml b/tests/assets/site_native.xml
@@ -10,6 +10,9 @@
           <entry id="1">
             <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:08:19 -0400" xml:space="preserve">Some Company</value>
           </entry>
+          <comment id="1">
+            <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Some Comment</value>
+          </comment>
         </field>
         <field name="site_code_name" type="hidden" dataType="string" errorCode="valid" whenCreated="2023-04-15 11:07:14 -0500" keepHistory="true">
           <entry id="1">

diff --git a/tests/assets/subject_native.xml b/tests/assets/subject_native.xml
@@ -9,6 +9,9 @@
           <entry id="1">
             <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Labrador</value>
           </entry>
+          <comment id="1">
+            <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Some Comment</value>
+          </comment>
         </field>
         <field name="dob" type="popUpCalendar" dataType="date" errorCode="valid" whenCreated="2023-04-15 12:08:26 -0400" keepHistory="true">
           <entry id="1">

diff --git a/tests/assets/user_native.xml b/tests/assets/user_native.xml
@@ -10,6 +10,9 @@
           <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>
+          <comment id="1">
+            <value by="Paul Sanders" byUniqueId="1681162687395" role="Project Manager" when="2023-04-15 12:09:02 -0400" xml:space="preserve">Some Comment</value>
+          </comment>
         </field>
       </category>
       <category name="Administrative" type="normal" highestIndex="0">