Merge pull request #162 from BIH-CEI/120-rename-phenopacketelement-to…

…-phenopacketbuildingblock

120 rename phenopacketelement to phenopacketbuildingblock

notebooks/erdri_cds_definition_in_code.ipynb

@@ -1416,7 +1416,7 @@
     "import phenopackets\n",
     "\n",
     "from phenopacket_mapper import PhenopacketMapper\n",
-    "from phenopacket_mapper.mapping import PhenopacketElement"
+    "from phenopacket_mapper.mapping import PhenopacketBuildingBlock"
    ],
    "metadata": {
     "collapsed": false,
@@ -1437,35 +1437,35 @@
     "mapper = PhenopacketMapper(\n",
     "    data_model=erdri_cds_data_model,\n",
     "    id=erdri_cds_data_model.pseudonym,\n",
-    "    subject=PhenopacketElement(\n",
+    "    subject=PhenopacketBuildingBlock(\n",
     "        phenopacket_element=phenopackets.Individual,\n",
     "        id=erdri_cds_data_model.pseudonym,\n",
     "        date_of_birth=erdri_cds_data_model.date_of_birth,\n",
-    "        vital_status=PhenopacketElement(\n",
+    "        vital_status=PhenopacketBuildingBlock(\n",
     "            phenopacket_element=phenopackets.VitalStatus,\n",
     "            status=erdri_cds_data_model.patient_s_status,\n",
-    "            time_of_death=PhenopacketElement(\n",
+    "            time_of_death=PhenopacketBuildingBlock(\n",
     "                phenopacket_element=phenopackets.TimeElement,\n",
     "                timestamp=erdri_cds_data_model.date_of_death\n",
     "            )\n",
     "        ),\n",
     "        sex=erdri_cds_data_model.sex,\n",
     "    ),\n",
     "    diseases=[\n",
-    "        PhenopacketElement(\n",
+    "        PhenopacketBuildingBlock(\n",
     "            phenopacket_element=phenopackets.Disease,\n",
     "            term=erdri_cds_data_model.diagnosis_of_the_rare_disease,\n",
     "            # TODO: preprocess to remove the strings\n",
-    "            # onset=PhenopacketElement(\n",
+    "            # onset=PhenopacketBuildingBlock(\n",
     "            #     phenopacket_element=phenopackets.TimeElement,\n",
     "            #     timestamp=erdri_cds_data_model.age_at_diagnosis\n",
     "            # )\n",
     "        )\n",
     "    ],\n",
     "    interpretations=[\n",
-    "        PhenopacketElement(\n",
+    "        PhenopacketBuildingBlock(\n",
     "            phenopacket_element=phenopackets.Interpretation,\n",
-    "            diagnosis=PhenopacketElement(\n",
+    "            diagnosis=PhenopacketBuildingBlock(\n",
     "                phenopacket_element=phenopackets.Diagnosis,\n",
     "                disease=erdri_cds_data_model.diagnosis_of_the_rare_disease,\n",
     "            )\n",

src/phenopacket_mapper/mapping/__init__.py

@@ -1,11 +1,11 @@
 """This module facilitates the mapping from a local data model to the phenopacket schema"""
 
-from .phenopacket_element import PhenopacketElement, map_single
+from .phenopacket_building_block import PhenopacketBuildingBlock, map_single
 from .mapper import PhenopacketMapper
 
 __all__ = [
     'map_single',
-    'PhenopacketElement',
+    'PhenopacketBuildingBlock',
     'PhenopacketMapper',
 
 ]

src/phenopacket_mapper/mapping/mapper.py

@@ -3,7 +3,7 @@
 from phenopackets import Phenopacket
 
 from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField
-from phenopacket_mapper.mapping import PhenopacketElement, map_single
+from phenopacket_mapper.mapping import PhenopacketBuildingBlock, map_single
 
 
 class PhenopacketMapper:
@@ -17,7 +17,7 @@ def __init__(self, data_model: DataModel, **kwargs):
         :param kwargs: The elements to map the data to Phenopackets
         """
         self.data_model = data_model
-        self.elements: Dict[str, Union[PhenopacketElement, DataField]] = {}
+        self.elements: Dict[str, Union[PhenopacketBuildingBlock, DataField]] = {}
         self.resources = data_model.resources
         for k, v in kwargs.items():
             setattr(self, k, v)
@@ -30,14 +30,14 @@ def __post_init__(self):
         for e in self.elements.values():
             self.check_data_fields_in_model(e)
 
-    def check_data_fields_in_model(self, element: Union[PhenopacketElement, DataField]):
+    def check_data_fields_in_model(self, element: Union[PhenopacketBuildingBlock, DataField]):
         if isinstance(element, DataField):
             field = element
             if field not in self.data_model:
                 raise AttributeError(f"The mapping definition contains an invalid field. "
                                      f"{field} is not in the data model underlying the passed data set."
                                      f" (The data model includes the fields: {self.data_model.get_field_ids()})")
-        elif isinstance(element, PhenopacketElement):
+        elif isinstance(element, PhenopacketBuildingBlock):
             for key, ee in element.elements.items():
                 self.check_data_fields_in_model(ee)
 

src/phenopacket_mapper/mapping/phenopacket_element.py → src/phenopacket_mapper/mapping/phenopacket_building_block.py

@@ -6,7 +6,7 @@
 from phenopacket_mapper.data_standards import DataModelInstance, DataField, DataFieldValue, Coding
 
 
-class PhenopacketElement:
+class PhenopacketBuildingBlock:
 
     def __init__(self, phenopacket_element, **kwargs):
         """Mapping equivalent to the constructor of a Phenopacket element (e.g., Individual) for the mapping
@@ -17,7 +17,7 @@ def __init__(self, phenopacket_element, **kwargs):
         :param kwargs: The elements to map the data to Phenopackets
         """
         self.phenopacket_element = phenopacket_element
-        self.elements: Dict[str, Union[PhenopacketElement, DataField]] = {}
+        self.elements: Dict[str, Union[PhenopacketBuildingBlock, DataField]] = {}
         for k, v in kwargs.items():
             setattr(self, k, v)
             self.elements[k] = v
@@ -30,7 +30,7 @@ def map(self, instance: DataModelInstance):
         >>> data_field = DataField("pseudonym", str)
         >>> data_model = DataModel("Example data model", [data_field], [])
         >>> inst = DataModelInstance(0, data_model, [DataFieldValue(0, data_field, "example_pseudonym")])
-        >>> individual = PhenopacketElement(phenopackets.Individual, id=data_field).map(inst)
+        >>> individual = PhenopacketBuildingBlock(phenopackets.Individual, id=data_field).map(inst)
         >>> individual.id
         'example_pseudonym'
 
@@ -64,6 +64,6 @@ def map_single(key, e, instance, kwargs):
             pass
     elif isinstance(e, list):
         kwargs[key] = [v.map(instance) for v in e]
-    elif isinstance(e, PhenopacketElement):
+    elif isinstance(e, PhenopacketBuildingBlock):
         phenopacket_element = e
         kwargs[key] = phenopacket_element.map(instance)