Merge pull request #151 from BIH-CEI/150-bug-tuple-list-fields

150 bug tuple list fields

res/test_data/erdri/output/patient0.json

@@ -13,15 +13,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient1.json

@@ -15,15 +15,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ICD9:781"
+          "id": "ICD9:781 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ICD9:781"
+        "id": "ICD9:781 ()"
       }
     }
   ]

res/test_data/erdri/output/patient2.json

@@ -13,15 +13,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient3.json

@@ -13,15 +13,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient4.json

@@ -11,15 +11,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient5.json

@@ -11,15 +11,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient6.json

@@ -13,15 +13,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient7.json

@@ -13,15 +13,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

res/test_data/erdri/output/patient8.json

@@ -15,15 +15,15 @@
     {
       "diagnosis": {
         "disease": {
-          "id": "ORPHA:206638"
+          "id": "ORPHA:206638 ()"
         }
       }
     }
   ],
   "diseases": [
     {
       "term": {
-        "id": "ORPHA:206638"
+        "id": "ORPHA:206638 ()"
       }
     }
   ]

src/phenopacket_mapper/data_standards/__init__.py

@@ -9,7 +9,7 @@
 
 __all__ = [
     "Coding", "CodeableConcept",
-    "DataModel", "DataField", "DataModelInstance", "DataFieldValue",
+    "DataModel", "DataField", "DataModelInstance", "DataFieldValue", "DataSet",
     "data_models",
     "CodeSystem",
     "SNOMED_CT", "HPO", "MONDO", "OMIM", "ORDO", "LOINC",

src/phenopacket_mapper/data_standards/code_system.py

@@ -58,13 +58,13 @@ def __contains__(self, item):
 GENO = CodeSystem(
     name='GENO: The Genotype Ontology', 
     namespace_prefix='GENO', 
-    url='http://www.genoontology.org/'
+    url='https://www.genoontology.org/'
 )
 
 SO = CodeSystem(
     name='Sequence types and features ontology', 
     namespace_prefix='SO',
-    url='http://www.sequenceontology.org/'
+    url='https://www.sequenceontology.org/'
 )
 
 ICD9 = CodeSystem(
@@ -128,12 +128,12 @@ def __contains__(self, item):
 MONDO = CodeSystem(
     name="Monarch Disease Ontology",
     namespace_prefix="MONDO",
-    url="http://purl.obolibrary.org/obo/mondo.owl"
+    url="https://purl.obolibrary.org/obo/mondo.owl"
 )
 ORDO = CodeSystem(
     name="Orphanet Rare Disease Ontology",
     namespace_prefix="ORPHA",
-    url="http://www.orpha.net/",
+    url="https://www.orpha.net/",
     synonyms=['ORDO']
 )
 OMIM = CodeSystem(
@@ -149,7 +149,7 @@ def __contains__(self, item):
 HGVS = CodeSystem(
     name="Human Genome Variation Society",
     namespace_prefix="HGVS",
-    url="http://varnomen.hgvs.org/"
+    url="https://varnomen.hgvs.org/"
 )
 HGNC = CodeSystem(
     name="HUGO Gene Nomenclature Committee",
@@ -159,14 +159,14 @@ def __contains__(self, item):
 HPO = CodeSystem(
     name="Human Phenotype Ontology",
     namespace_prefix="HP",
-    url="http://www.human-phenotype-ontology.org",
-    iri_prefix="http://purl.obolibrary.org/obo/HP_",
+    url="https://www.human-phenotype-ontology.org",
+    iri_prefix="https://purl.obolibrary.org/obo/HP_",
     synonyms=["HPO"]
 )
 UO = CodeSystem(
     name="Units of Measurement Ontology",
     namespace_prefix="UO",
-    url="http://www.ontobee.org/ontology/UO"
+    url="https://www.ontobee.org/ontology/UO"
 )
 NCIT = CodeSystem(
     name = "NCI Thesaurus OBO Edition",

src/phenopacket_mapper/data_standards/data_model.py

@@ -151,7 +151,7 @@ class DataModel:
     :ivar resources: List of `CodeSystem` objects
     """
     data_model_name: str = field()
-    fields: Tuple[DataField] = field()
+    fields: Tuple[DataField, ...] = field()
     resources: List[CodeSystem] = field(default_factory=list)
 
     def __post_init__(self):
@@ -166,8 +166,8 @@ def __getattr__(self, var_name: str) -> DataField:
 
     def __str__(self):
         ret = f"DataModel(name={self.data_model_name}\n"
-        for field in self.fields:
-            ret += f"\t{str(field)}\n"
+        for _field in self.fields:
+            ret += f"\t{str(_field)}\n"
         ret += "---\n"
         for res in self.resources:
             ret += f"\t{str(res)}\n"
@@ -399,11 +399,12 @@ def data_frame(self) -> pd.DataFrame:
         for instance in self.data:
             for f in self.data_model.fields:
                 field_id = f.id
+                value: Any = None
                 try:
                     dfv: DataFieldValue = getattr(instance, field_id)
                     value = dfv.value
                 except AttributeError:
-                    value = None
+                    pass
                 finally:
                     data_dict[field_id].append(value)
         return pd.DataFrame(data_dict, columns=column_names)

src/phenopacket_mapper/data_standards/data_models/__init__.py

@@ -1,6 +1,5 @@
 """Selection of rare disease specific data models"""
-from .rarelink_datamodel import RARELINK_DATA_MODEL
 from .erdri_cds import ERDRI_CDS
 from phenopacket_mapper.utils.parsing.parse_data_type import parse_data_type
 
-__all__ = ["RARELINK_DATA_MODEL", "ERDRI_CDS", "parse_data_type"]
+__all__ = ["ERDRI_CDS", "parse_data_type"]

src/phenopacket_mapper/data_standards/data_models/erdri_cds.py

@@ -1,9 +1,9 @@
 from phenopacket_mapper.data_standards.data_model import DataModel, DataField
-
-ERDRI_CDS = DataModel(
-    data_model_name="ERDRI_CDS",
-    resources=[],
-    fields=[
-        # TODO: Implement fields
-    ]
-)
+ERDRI_CDS = None
+# ERDRI_CDS = DataModel(
+#     data_model_name="ERDRI_CDS",
+#     resources=[],
+#     fields=[
+#         # TODO: Implement fields
+#     ]
+# )