Update nimads model

Author: adelavega

autonima/coordinates/nimads_models.py

@@ -28,10 +28,12 @@ class Point:
     label_id: Optional[str] = None
     values: List[PointValue] = field(default_factory=list)
     analysis_id: Optional[str] = None
+    id: Optional[str] = None
 
     def to_dict(self) -> dict:
         """Convert to dictionary representation."""
         return {
+            "id": self.id,
             "coordinates": self.coordinates,
             "space": self.space,
             "kind": self.kind,
@@ -155,7 +157,7 @@ def to_dict(self) -> dict:
         }
 
 
-def convert_to_nimads_point(analysis_id: str, point: CoordinatePoint, study_space: Optional[str] = None) -> Point:
+def convert_to_nimads_point(analysis_id: str, point: CoordinatePoint, study_space: Optional[str] = None, point_id: Optional[str] = None) -> Point:
     """Convert a coordinate point to a NiMADS point."""
     # Sanitize the coordinate space
     sanitized_space = sanitize_coordinate_space(point.space, study_space)
@@ -166,7 +168,8 @@ def convert_to_nimads_point(analysis_id: str, point: CoordinatePoint, study_spac
     nimads_point = Point(
         coordinates=sanitized_coordinates,
         space=sanitized_space,
-        analysis_id=analysis_id
+        analysis_id=analysis_id,
+        id=point_id
     )
 
     # Convert point values if they exist
@@ -193,8 +196,9 @@ def convert_to_nimads_analysis(analysis_id: str, analysis: Analysis, study_id: s
     )
 
     # Convert points
-    for point in analysis.points:
-        nimads_point = convert_to_nimads_point(analysis_id, point, study_space)
+    for i, point in enumerate(analysis.points):
+        point_id = f"{analysis_id}_point_{i}"
+        nimads_point = convert_to_nimads_point(analysis_id, point, study_space, point_id)
         nimads_analysis.points.append(nimads_point)
 
     return nimads_analysis
@@ -211,8 +215,11 @@ def convert_to_nimads_study(study_id: str, autonima_study: 'autonima.models.type
         except (ValueError, IndexError):
             pass
 
+    # Use the study's PMID as the study_id if available
+    nimads_study_id = autonima_study.pmid if autonima_study.pmid else study_id
+    
     nimads_study = Study(
-        id=study_id,
+        id=nimads_study_id,
         doi=autonima_study.doi,
         name=autonima_study.title,
         description=autonima_study.abstract,
@@ -227,8 +234,8 @@ def convert_to_nimads_study(study_id: str, autonima_study: 'autonima.models.type
 
     # Convert analyses
     for i, analysis in enumerate(autonima_study.analyses):
-        analysis_id = f"{study_id}_analysis_{i}"
-        nimads_analysis = convert_to_nimads_analysis(analysis_id, analysis, study_id, study_space)
+        analysis_id = f"{nimads_study_id}_analysis_{i}"
+        nimads_analysis = convert_to_nimads_analysis(analysis_id, analysis, nimads_study_id, study_space)
         nimads_study.analyses.append(nimads_analysis)
 
     return nimads_study
@@ -282,8 +289,9 @@ def convert_to_nimads_studyset(studyset_id: str, studies: List['autonima.models.
     )
 
     # Convert studies
-    for i, study in enumerate(studies):
-        study_id = f"study_{i}"
+    for study in studies:
+        # Use the study's PMID as the study_id if available, otherwise generate one
+        study_id = study.pmid if study.pmid else f"study_{len(studyset.studies)}"
         nimads_study = convert_to_nimads_study(study_id, study)
         studyset.studies.append(nimads_study)