Merge pull request #153 from BIH-CEI/152-phenopacketmapper-does-not-n…

…eed-param-resources-can-take-from-data-model remove resources from PhenopacketMapper init
BIH-CEI · Oct 7, 2024 · ab5ff23 · ab5ff23
2 parents 2c9c2bf + e1c3d09
commit ab5ff23
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Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/notebooks/erdri_cds_definition_in_code.ipynb b/notebooks/erdri_cds_definition_in_code.ipynb
@@ -1436,7 +1436,6 @@
     "\n",
     "mapper = PhenopacketMapper(\n",
     "    data_model=erdri_cds_data_model,\n",
-    "    resources=resources,\n",
     "    id=erdri_cds_data_model.pseudonym,\n",
     "    subject=PhenopacketElement(\n",
     "        phenopacket_element=phenopackets.Individual,\n",

diff --git a/src/phenopacket_mapper/mapping/mapper.py b/src/phenopacket_mapper/mapping/mapper.py
@@ -2,14 +2,13 @@
 
 from phenopackets import Phenopacket
 
-from phenopacket_mapper.data_standards import CodeSystem
 from phenopacket_mapper.data_standards.data_model import DataModel, DataSet, DataField
 from phenopacket_mapper.mapping import PhenopacketElement, map_single
 
 
 class PhenopacketMapper:
 
-    def __init__(self, data_model: DataModel, resources: List[CodeSystem], **kwargs):
+    def __init__(self, data_model: DataModel, **kwargs):
         """Create a PhenopacketMapper, this method is equivalent to the constructor of the `Phenopacket` for the mapping
 
         List fields of the `Phenopacket` constructor in the kwargs to map the data to Phenopackets.
@@ -19,7 +18,7 @@ def __init__(self, data_model: DataModel, resources: List[CodeSystem], **kwargs)
         """
         self.data_model = data_model
         self.elements: Dict[str, Union[PhenopacketElement, DataField]] = {}
-        self.resources = resources
+        self.resources = data_model.resources
         for k, v in kwargs.items():
             setattr(self, k, v)
             self.elements[k] = v