75 update rd cdm redcap (#80)

* Add rd-cdm as a submodule

* updatte

* iupdate

* update

* delete

* Re-added rd-cdm submodule in submodules/rd-cdm

* updated data model

* fixing errors

* update

* removed Phenopacket Element for now

Author: aslgraefe

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "submodules/phenopacket_mapper"]
 	path = submodules/phenopacket_mapper
 	url = https://github.com/BIH-CEI/phenopacket_mapper
+[submodule "submodules/rd-cdm"]
+	path = submodules/rd-cdm
+	url = https://github.com/BIH-CEI/rd-cdm

src/rarelink/pipelines/redcap_phenopacket_pipeline/phenopacket_pipeline.py

@@ -2,7 +2,7 @@
 from typing import Union, List
 from phenopackets.schema.v2 import Phenopacket
 import phenopackets
-from phenopacket_mapper.mapping.mapper import PhenopacketMapper, PhenopacketElement
+from phenopacket_mapper.mapping.mapper import PhenopacketMapper
 from rarelink.preprocessing.preprocess_redcap_for_phenopackets import preprocess_redcap_for_phenopackets
 from rarelink.rarelink_cdm import RARELINK_CDM_V2_0_0
 from rarelink.preprocessing import preprocess_redcap_for_phenopackets

src/rarelink/rarelink_cdm/rarelink_cdm.py

@@ -1,5 +1,11 @@
 from phenopacket_mapper.data_standards.code import CodeSystem
-from phenopacket_mapper.data_standards.code_system import NCBITaxon, GENO, SO, ICD10CM, SNOMED_CT, ICD11, HL7FHIR, GA4GH, ISO3166, ICF, MONDO, ORDO, OMIM, LOINC, HGVS, HGNC, HPO
+from phenopacket_mapper.data_standards.code_system import NCBITaxon, GENO, SO, ICD10CM, SNOMED_CT, ICD11, HL7FHIR, GA4GH, ISO3166, ICF, MONDO, ORDO, OMIM, LOINC, HGVS, HGNC, HPO, UO, NCIT
+
+ECO = CodeSystem(
+        name='Evidence & Conclusion Ontology', 
+        namespace_prefix='ECO', 
+        url='https://www.evidenceontology.org/'
+    )
 
 
 class RareLink_CDM_v2_0_0_Resources:
@@ -9,6 +15,7 @@ class RareLink_CDM_v2_0_0_Resources:
 
     __version__ = '2.0.0'
     """
+    
     @property
     def NCBITaxon(self):
         return NCBITaxon.set_version("2024-07-03")
@@ -60,6 +67,15 @@ def HGNC(self):
 
     def HPO(self):
         return HPO.set_version("2024-08-13")
+    
+    def ECO(self):
+        return ECO.set_version("2024-07-19")
+    
+    def UO(self):
+        return UO.set_version("2024-09-12")
+    
+    def NCIT(self):
+        return NCIT.set_version("24.04e")
 
 
 RARELINK_CDM_V2_0_0_RESOURCES = RareLink_CDM_v2_0_0_Resources()