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Add title to Field calls where necessary #299

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merged 7 commits into from
Dec 3, 2020
Merged

Add title to Field calls where necessary #299

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bcd9d7f
Add field titles where necessary
jjnesbitt Dec 2, 2020
863c8c7
added to jake's changes
satra Dec 2, 2020
75e5de3
Apply suggestions from code review
satra Dec 2, 2020
12200ee
Merge pull request #1 from satra/enh/models
jjnesbitt Dec 2, 2020
064f538
fix tests
satra Dec 2, 2020
812b28e
Fix line length
jjnesbitt Dec 2, 2020
bea4699
Merge pull request #2 from satra/enh/models
jjnesbitt Dec 3, 2020
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172 changes: 119 additions & 53 deletions dandi/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,8 +86,8 @@ def model2graph(model):

AccessType = create_enum(AccessTypeDict)
RoleType = create_enum(RoleTypeDict)
Relation = create_enum(RelationTypeDict)
License = create_enum(LicenseTypeDict)
RelationType = create_enum(RelationTypeDict)
LicenseType = create_enum(LicenseTypeDict)
IdentifierType = create_enum(IdentifierTypeDict)
DigestType = create_enum(DigestTypeDict)

Expand Down Expand Up @@ -125,17 +125,23 @@ def to_dictrepr(__pydantic_cls__: Type[BaseModel]):


class PropertyValue(DandiBaseModel):
maxValue: float = Field(None, nskey="schema")
minValue: float = Field(None, nskey="schema")
unitCode: Union[str, AnyUrl] = Field(None, nskey="schema")
unitText: str = Field(None, nskey="schema")
maxValue: float = Field(None, title="Max Value", nskey="schema")
minValue: float = Field(None, title="Min Value", nskey="schema")
unitCode: Union[str, AnyUrl] = Field(None, title="Unit Code", nskey="schema")
unitText: str = Field(None, title="Unit Text", nskey="schema")
value: Union[str, bool, int, float, List[Union[str, bool, int, float]]] = Field(
None, nskey="schema"
)
valueReference: "PropertyValue" = Field(
None, nskey="schema"
None, title="Value Reference", nskey="schema"
) # Note: recursive (circular or not)
propertyID: Union[IdentifierType, AnyUrl, str] = Field(None, nskey="schema")
propertyID: Union[IdentifierType, AnyUrl, str] = Field(
None,
title="Property ID",
description="A commonly used identifier for"
"the characteristic represented by the property.",
nskey="schema",
)

_ldmeta = {"nskey": "schema"}

Expand Down Expand Up @@ -211,14 +217,21 @@ class ContactPoint(DandiBaseModel):


class Contributor(DandiBaseModel):
identifier: Identifier = Field(None, nskey="schema")
identifier: Identifier = Field(
None,
title="A Common Identifier",
description="Use a common identifier such as ORCID for people or ROR for institutions",
nskey="schema",
)
name: str = Field(None, nskey="schema")
email: EmailStr = Field(None, nskey="schema")
url: AnyUrl = Field(None, nskey="schema")
roleName: List[RoleType] = Field(nskey="schema")
roleName: List[RoleType] = Field(
title="Role", description="Role of the contributor", nskey="schema"
)
includeInCitation: bool = Field(
True,
title="Include contributor in citation",
title="Include Contributor in Citation",
description="A flag to indicate whether a contributor should be included "
"when generating a citation for the item",
nskey="dandi",
Expand All @@ -233,7 +246,9 @@ class Contributor(DandiBaseModel):

class Organization(Contributor):
contactPoint: List[ContactPoint] = Field(
description="Contact for the organization", nskey="schema"
title="Contact Point",
description="Contact for the organization",
nskey="schema",
)
_ldmeta = {
"rdfs:subClassOf": ["schema:Organization", "prov:Organization"],
Expand Down Expand Up @@ -264,9 +279,13 @@ class Software(DandiBaseModel):
class EthicsApproval(DandiBaseModel):
"""Information about ethics committee approval for project"""

identifier: Identifier = Field(nskey="schema")
identifier: Identifier = Field(
nskey="schema", title="Identifier String for Approved Protocol"
)
contactPoint: ContactPoint = Field(
description="Information about the ethics approval committee.", nskey="schema"
title="Contact Point",
description="Information about the ethics approval committee.",
nskey="schema",
)

_ldmeta = {"rdfs:subClassOf": ["schema:Thing", "prov:Entity"], "nskey": "dandi"}
Expand All @@ -281,7 +300,8 @@ class Resource(DandiBaseModel):
description="An identifier of a repository in which the resource is housed",
nskey="dandi",
)
relation: Relation = Field(
relation: RelationType = Field(
title="Relation",
description="Indicates how the resource is related to the dataset",
nskey="dandi",
)
Expand All @@ -303,7 +323,9 @@ class AccessRequirements(DandiBaseModel):
nskey="dandi",
)
email: Optional[EmailStr] = Field(None, nskey="schema")
contactPoint: Optional[ContactPoint] = Field(None, nskey="schema")
contactPoint: Optional[ContactPoint] = Field(
None, title="Contact Point", nskey="schema"
)
description: Optional[str] = Field(
None,
title="Description",
Expand All @@ -326,22 +348,32 @@ class AssetsSummary(DandiBaseModel):
"""Summary over assets contained in a dandiset (published or not)"""

# stats which are not stats
numberOfBytes: int = Field(readOnly=True, sameas="schema:contentSize")
numberOfFiles: int = Field(readOnly=True) # universe
numberOfSubjects: int = Field(readOnly=True) # NWB + BIDS
numberOfSamples: Optional[int] = Field(None, readOnly=True) # more of NWB
numberOfCells: Optional[int] = Field(None, readOnly=True)
numberOfBytes: int = Field(
title="Number of Bytes", readOnly=True, sameas="schema:contentSize"
)
numberOfFiles: int = Field(title="Number of Files", readOnly=True) # universe
numberOfSubjects: int = Field(
title="Number of Subjects", readOnly=True
) # NWB + BIDS
numberOfSamples: Optional[int] = Field(
None, title="Number of Samples", readOnly=True
) # more of NWB
numberOfCells: Optional[int] = Field(None, title="Number of Cells", readOnly=True)

dataStandard: List[StandardsType] = Field(
readOnly=True
title="Data Standard", readOnly=True
) # TODO: types of things NWB, BIDS
# Web UI: icons per each modality?
modality: List[ModalityType] = Field(
readOnly=True
) # TODO: types of things, BIDS etc...
# Web UI: could be an icon with number, which if hovered on show a list?
measurementTechnique: List[MeasurementTechniqueType] = Field(readOnly=True)
variableMeasured: Optional[List[PropertyValue]] = Field(None, readOnly=True)
measurementTechnique: List[MeasurementTechniqueType] = Field(
title="Measurement Technique", readOnly=True
)
variableMeasured: Optional[List[PropertyValue]] = Field(
None, title="Variable Measured", readOnly=True
)

species: List[SpeciesType] = Field(readOnly=True)

Expand All @@ -356,8 +388,8 @@ class Digest(DandiBaseModel):

value: str = Field(nskey="schema")
cryptoType: DigestType = Field(
description="Which cryptographic checksum is used",
title="Cryptographic method used",
description="Which cryptographic checksum is used",
nskey="dandi",
)

Expand All @@ -373,7 +405,10 @@ class BioSample(DandiBaseModel):

identifier: Identifier = Field(nskey="schema")
assayType: Optional[List[AssayType]] = Field(
None, description="OBI based identifier for the assay(s) used", nskey="dandi"
None,
title="Assay Type",
description="OBI based identifier for the assay(s) used",
nskey="dandi",
)
anatomy: Optional[List[Anatomy]] = Field(
None,
Expand All @@ -384,7 +419,10 @@ class BioSample(DandiBaseModel):
None, description="Identifier for the strain of the sample", nskey="dandi"
)
cellLine: Optional[Identifier] = Field(
None, description="Cell line associated with the sample", nskey="dandi"
None,
title="Cell Line",
description="Cell line associated with the sample",
nskey="dandi",
)
vendor: Optional[Organization] = Field(None, nskey="dandi")
age: Optional[PropertyValue] = Field(
Expand Down Expand Up @@ -437,13 +475,13 @@ class Activity(DandiBaseModel):
description="A description of the item.",
nskey="schema",
)
startDate: Optional[date] = Field(None, nskey="schema")
endDate: Optional[date] = Field(None, nskey="schema")
startDate: Optional[date] = Field(None, title="Start Date", nskey="schema")
endDate: Optional[date] = Field(None, title="End Date", nskey="schema")

isPartOf: Optional["Activity"] = Field(None, nskey="schema")
hasPart: Optional["Activity"] = Field(None, nskey="schema")
isPartOf: Optional["Activity"] = Field(None, title="Is Part Of", nskey="schema")
hasPart: Optional["Activity"] = Field(None, title="Has Part", nskey="schema")
wasAssociatedWith: Optional[Union[Person, Organization, Software]] = Field(
None, nskey="prov"
None, title="Was Associated With", nskey="prov"
)

_ldmeta = {"rdfs:subClassOf": ["prov:Activity", "schema:Thing"], "nskey": "dandi"}
Expand All @@ -457,7 +495,9 @@ class Project(Activity):


class CommonModel(DandiBaseModel):
schemaVersion: str = Field(default="1.0.0-rc1", readOnly=True, nskey="schema")
schemaVersion: str = Field(
default="1.0.0-rc1", title="Schema Version", readOnly=True, nskey="schema"
)
identifier: Identifier = Field(readOnly=True, nskey="schema")
name: Optional[str] = Field(
None,
Expand All @@ -480,16 +520,23 @@ class CommonModel(DandiBaseModel):
)
about: Optional[List[Union[Disorder, Anatomy, Identifier]]] = Field(
None,
title="Subject matter",
title="Subject Matter",
description="The subject matter of the content, such as disorders, brain anatomy.",
nskey="schema",
)
studyTarget: Optional[List[Union[str, AnyUrl]]] = Field(
None, title="What the study is related to", nskey="dandi"
None,
title="Study Target",
description="What the study is related to",
nskey="dandi",
)
license: List[LicenseType] = Field(
title="License", description="License of item.", nskey="schema"
)
protocol: Optional[List[str]] = Field(None, nskey="dandi")
ethicsApproval: Optional[List[EthicsApproval]] = Field(None, nskey="dandi")
license: List[License] = Field(nskey="schema")
ethicsApproval: Optional[List[EthicsApproval]] = Field(
None, title="Ethics Approval", nskey="dandi"
)
keywords: Optional[List[str]] = Field(
None,
title="Keywords",
Expand All @@ -503,6 +550,7 @@ class CommonModel(DandiBaseModel):

# Linking to this dandiset or the larger thing
access: List[AccessRequirements] = Field(
title="Access Type",
default_factory=lambda: [AccessRequirements(status=AccessType.Open)],
nskey="dandi",
)
Expand All @@ -515,10 +563,12 @@ class CommonModel(DandiBaseModel):
description="location of the item",
nskey="dandi",
)
relatedResource: Optional[List[Resource]] = Field(None, nskey="dandi")
relatedResource: Optional[List[Resource]] = Field(
None, title="Related Resource", nskey="dandi"
)

wasGeneratedBy: Optional[Union[Activity, AnyUrl]] = Field(
None, readOnly=True, nskey="prov"
None, title="Was Generated By", readOnly=True, nskey="prov"
)


Expand Down Expand Up @@ -558,14 +608,20 @@ def check_data(cls, values):
citation: str = Field(readOnly=True, nskey="schema")

# From assets
assetsSummary: AssetsSummary = Field(readOnly=True, nskey="dandi")
assetsSummary: AssetsSummary = Field(
title="Assets Summary", readOnly=True, nskey="dandi"
)

# From server (requested by users even for drafts)
manifestLocation: List[AnyUrl] = Field(readOnly=True, nskey="dandi")
manifestLocation: List[AnyUrl] = Field(
title="Manifest Location", readOnly=True, nskey="dandi"
)

# On publish
version: str = Field(readOnly=True, nskey="schema")
doi: Optional[Union[str, AnyUrl]] = Field(None, readOnly=True, nskey="dandi")
doi: Optional[Union[str, AnyUrl]] = Field(
None, title="DOI", readOnly=True, nskey="dandi"
)

_ldmeta = {
"rdfs:subClassOf": ["schema:Dataset", "prov:Entity"],
Expand All @@ -576,11 +632,12 @@ def check_data(cls, values):

class PublishedDandiMeta(DandiMeta):
publishedBy: AnyUrl = Field(
title="Published By",
description="The URL should contain the provenance of the publishing process.",
readOnly=True,
nskey="dandi",
) # TODO: formalize "publish" activity to at least the Actor
datePublished: date = Field(readOnly=True, nskey="schema")
datePublished: date = Field(title="Date Published", readOnly=True, nskey="schema")


class AssetMeta(CommonModel):
Expand All @@ -591,34 +648,42 @@ class AssetMeta(CommonModel):

# Overrides CommonModel.license
# TODO: https://github.com/NeurodataWithoutBorders/nwb-schema/issues/320
license: Optional[List[License]] = Field(None, nskey="schema")
license: Optional[List[LicenseType]] = Field(
None, title="License", description="License of item", nskey="schema"
)

contentSize: str = Field(nskey="schema")
encodingFormat: Union[str, AnyUrl] = Field(nskey="schema")
contentSize: str = Field(title="Content Size", nskey="schema")
encodingFormat: Union[str, AnyUrl] = Field(
title="File Encoding Format", nskey="schema"
)
digest: Digest = Field(nskey="dandi")

path: str = Field(None, nskey="dandi")

# this is from C2M2 level 1 - using EDAM vocabularies - in our case we would
# need to come up with things for neurophys
# TODO: waiting on input <https://github.com/dandi/dandi-cli/pull/226>
dataType: Optional[AnyUrl] = Field(None, nskey="dandi")
dataType: Optional[AnyUrl] = Field(None, title="Data Type", nskey="dandi")

sameAs: Optional[List[AnyUrl]] = Field(None, nskey="schema")
sameAs: Optional[List[AnyUrl]] = Field(None, title="Same As", nskey="schema")

# TODO
modality: Optional[List[ModalityType]] = Field(None, readOnly=True, nskey="dandi")
measurementTechnique: Optional[List[MeasurementTechniqueType]] = Field(
None, readOnly=True, nskey="schema"
None, title="Measurement Technique", readOnly=True, nskey="schema"
)
variableMeasured: Optional[List[PropertyValue]] = Field(
None, readOnly=True, nskey="schema"
None, title="Variable Measured", readOnly=True, nskey="schema"
)

wasDerivedFrom: Optional[List[BioSample]] = Field(None, nskey="prov")
wasDerivedFrom: Optional[List[BioSample]] = Field(
None, title="Was Derived From", nskey="prov"
)

# on publish or set by server
contentUrl: Optional[List[AnyUrl]] = Field(None, readOnly=True, nskey="schema")
contentUrl: Optional[List[AnyUrl]] = Field(
None, title="Content URL", readOnly=True, nskey="schema"
)

_ldmeta = {
"rdfs:subClassOf": ["schema:CreativeWork", "prov:Entity"],
Expand All @@ -629,8 +694,9 @@ class AssetMeta(CommonModel):

class PublishedAssetMeta(AssetMeta):
publishedBy: AnyUrl = Field(
title="Published By",
description="The URL should contain the provenance of the publishing process.",
readOnly=True,
nskey="dandi",
) # TODO: formalize "publish" activity to at least the Actor
datePublished: date = Field(readOnly=True, nskey="schema")
datePublished: date = Field(title="Date Published", readOnly=True, nskey="schema")
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