Merge pull request #50 from oyurekten/commented-base-isa

All objects that have comments field inherit from CommentedIsaBase.

mars-cli/mars_lib/models/isa_json.py

@@ -18,8 +18,11 @@ class Comment(IsaBase):
     value: Optional[str] = None
 
 
-class OntologySourceReference(IsaBase):
+class CommentedIsaBase(IsaBase):
     comments: List[Comment] = []
+
+
+class OntologySourceReference(CommentedIsaBase):
     description: Optional[str] = None
     file: Optional[str] = None
     name: Optional[str] = None
@@ -45,9 +48,8 @@ class DataTypeEnum(str, Enum):
 DATA_TYPE_VALUES = {item.value for item in DataTypeEnum}
 
 
-class Data(IsaBase):
+class Data(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
-    comments: List[Comment] = []
     name: Optional[str] = None
     type: Optional[DataTypeEnum] = None
 
@@ -58,32 +60,28 @@ def apply_enum(cls, v: str) -> str:
         return v
 
 
-class OntologyAnnotation(IsaBase):
+class OntologyAnnotation(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     annotationValue: Union[Optional[str], Optional[float], Optional[int]] = Field(
         default=None
     )
-    comments: List[Comment] = []
     termAccession: Optional[str] = None
     termSource: Optional[str] = Field(
         description="The abbreviated ontology name. It should correspond to one of the sources as specified in the ontologySourceReference section of the Investigation.",
         default=None,
     )
 
 
-class MaterialAttributeValue(IsaBase):
+# TODO: QUESTION: comments field is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)
+class MaterialAttributeValue(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     category: Optional[MaterialAttribute] = None
     value: Union[str, float, int, OntologyAnnotation, None] = None
     unit: Optional[OntologyAnnotation] = None
-    comments: List[Comment] = Field(
-        default=[]
-    )  # TODO: QUESTION: This is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)
 
 
-class Factor(IsaBase):
+class Factor(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
-    comments: List[Comment] = []
     factorName: Optional[str] = None
     factorType: Optional[OntologyAnnotation] = None
 
@@ -95,24 +93,20 @@ class FactorValue(IsaBase):
     unit: Optional[OntologyAnnotation] = None
 
 
-class Source(IsaBase):
+# TODO: QUESTION: comments field is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)
+class Source(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     characteristics: List[MaterialAttributeValue] = []
     name: Optional[str] = None
-    comments: List[Comment] = Field(
-        default=[]
-    )  # TODO: QUESTION: This is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#source-schema-json)
 
 
-class Sample(IsaBase):
+# TODO: QUESTION: comments field is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#material-attribute-value-schema-json)
+class Sample(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     name: Optional[str] = None
     characteristics: List[MaterialAttributeValue] = []
     factorValues: List[FactorValue] = []
     derivesFrom: List[Source] = []
-    comments: List[Comment] = Field(
-        default=[]
-    )  # TODO: QUESTION: This is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#sample-schema-json)
 
 
 class ProtocolParameter(IsaBase):
@@ -132,9 +126,8 @@ class Component(IsaBase):
     componentType: Optional[OntologyAnnotation] = None
 
 
-class Protocol(IsaBase):
+class Protocol(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
-    comments: List[Comment] = []
     components: List[Component] = []
     description: Optional[str] = None
     name: Optional[str] = None
@@ -152,10 +145,9 @@ class MaterialTypeEnum(str, Enum):
     LIBRARY_NAME = "library name"  # TODO: QUESTION: This is not mentioned in the specs (https://isa-specs.readthedocs.io/en/latest/isajson.html#material-schema-json) but was found in DataHub ISA-JSON and ARC ISA-JSON.
 
 
-class Material(IsaBase):
+class Material(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     characteristics: List[MaterialAttributeValue] = []
-    comments: List[Comment] = []
     name: Optional[str] = None
     type: Optional[str] = None
     derivesFrom: List[Material] = []
@@ -167,9 +159,8 @@ def apply_enum(cls, v: str) -> str:
         return v
 
 
-class Process(IsaBase):
+class Process(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
-    comments: List[Comment] = []
     date: Optional[str] = None
     executesProtocol: Optional[Protocol] = None
     inputs: Optional[Union[List[Source], List[Sample], List[Material], list[Data]]] = []
@@ -189,10 +180,9 @@ class AssayMaterialType(IsaBase):
     otherMaterials: List[Material] = []
 
 
-class Assay(IsaBase):
+class Assay(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     characteristicCategories: List[MaterialAttribute] = []
-    comments: List[Comment] = []
     dataFiles: List[Data] = []
     filename: Optional[str] = None
     materials: Optional[AssayMaterialType] = None
@@ -222,11 +212,10 @@ def detect_target_repo_comments(cls, v: List[Comment]) -> Optional[List[Comment]
                 )
 
 
-class Person(IsaBase):
+class Person(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     address: Optional[str] = None
     affiliation: Optional[str] = None
-    comments: List[Comment] = []
     email: Optional[str] = None
     fax: Optional[str] = None
     firstName: Optional[str] = None
@@ -236,9 +225,8 @@ class Person(IsaBase):
     roles: List[OntologyAnnotation] = []
 
 
-class Publication(IsaBase):
+class Publication(CommentedIsaBase):
     authorList: Optional[str] = None
-    comments: List[Comment] = []
     doi: Optional[str] = None
     pubMedID: Optional[str] = None
     status: Optional[OntologyAnnotation] = None
@@ -256,11 +244,10 @@ class MaterialAttribute(IsaBase):
     characteristicType: Optional[OntologyAnnotation] = None
 
 
-class Study(IsaBase):
+class Study(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
     assays: List[Assay] = []
     characteristicCategories: List[MaterialAttribute] = []
-    comments: List[Comment] = []
     description: Optional[str] = None
     factors: List[Factor] = []
     filename: Optional[str] = None
@@ -277,9 +264,8 @@ class Study(IsaBase):
     unitCategories: List[OntologyAnnotation] = []
 
 
-class Investigation(IsaBase):
+class Investigation(CommentedIsaBase):
     id: Optional[str] = Field(alias="@id", default=None)
-    comments: List[Comment] = []
     description: Optional[str] = None
     filename: Optional[str] = None
     identifier: Optional[str] = None