Support newer versions of pydantic

pyscicat/model.py

@@ -16,18 +16,18 @@ class DatasetType(str, enum.Enum):
 class MongoQueryable(BaseModel):
     """Many objects in SciCat are mongo queryable"""
 
-    createdBy: Optional[str]
-    updatedBy: Optional[str]
-    updatedAt: Optional[str]
-    createdAt: Optional[str]
+    createdBy: Optional[str] = None
+    updatedBy: Optional[str] = None
+    updatedAt: Optional[str] = None
+    createdAt: Optional[str] = None
 
 
 class Ownable(MongoQueryable):
     """Many objects in SciCat are ownable"""
 
     ownerGroup: str
-    accessGroups: Optional[List[str]]
-    instrumentGroup: Optional[str]
+    accessGroups: Optional[List[str]] = None
+    instrumentGroup: Optional[str] = None
 
 
 class User(BaseModel):
@@ -47,19 +47,19 @@ class Proposal(Ownable):
     """
 
     proposalId: str
-    pi_email: Optional[str]
-    pi_firstname: Optional[str]
-    pi_lastname: Optional[str]
+    pi_email: Optional[str] = None
+    pi_firstname: Optional[str] = None
+    pi_lastname: Optional[str] = None
     email: str
-    firstname: Optional[str]
-    lastname: Optional[str]
-    title: Optional[str]  # required in next backend version
-    abstract: Optional[str]
-    startTime: Optional[str]
-    endTime: Optional[str]
+    firstname: Optional[str] = None
+    lastname: Optional[str] = None
+    title: Optional[str] = None  # required in next backend version
+    abstract: Optional[str] = None
+    startTime: Optional[str] = None
+    endTime: Optional[str] = None
     MeasurementPeriodList: Optional[
         List[dict]
-    ]  # may need updating with the measurement period model
+    ] = None  # may need updating with the measurement period model
 
 
 class Sample(Ownable):
@@ -68,10 +68,10 @@ class Sample(Ownable):
     Raw datasets should be linked to such sample definitions.
     """
 
-    sampleId: Optional[str]
-    owner: Optional[str]
-    description: Optional[str]
-    sampleCharacteristics: Optional[dict]
+    sampleId: Optional[str] = None
+    owner: Optional[str] = None
+    description: Optional[str] = None
+    sampleCharacteristics: Optional[dict] = None
     isPublished: bool = False
 
 
@@ -83,72 +83,72 @@ class Job(MongoQueryable):
     track of analysis jobs e.g. for automated analysis workflows
     """
 
-    id: Optional[str]
+    id: Optional[str] = None
     emailJobInitiator: str
     type: str
-    creationTime: Optional[str]  # not sure yet which ones are optional or not.
-    executionTime: Optional[str]
-    jobParams: Optional[dict]
-    jobStatusMessage: Optional[str]
-    datasetList: Optional[dict]  # documentation says dict, but should maybe be list?
-    jobResultObject: Optional[dict]  # ibid.
+    creationTime: Optional[str] = None  # not sure yet which ones are optional or not.
+    executionTime: Optional[str] = None
+    jobParams: Optional[dict] = None
+    jobStatusMessage: Optional[str] = None
+    datasetList: Optional[dict] = None  # documentation says dict, but should maybe be list?
+    jobResultObject: Optional[dict] = None  # ibid.
 
 
 class Instrument(MongoQueryable):
     """
     Instrument class, most of this is flexibly definable in customMetadata
     """
 
-    pid: Optional[str]
+    pid: Optional[str] = None
     name: str
-    customMetadata: Optional[dict]
+    customMetadata: Optional[dict] = None
 
 
 class Dataset(Ownable):
     """
     A dataset in SciCat, base class for derived and raw datasets
     """
 
-    pid: Optional[str]
-    classification: Optional[str]
+    pid: Optional[str] = None
+    classification: Optional[str] = None
     contactEmail: str
     creationTime: str  # datetime
-    datasetName: Optional[str]
-    description: Optional[str]
-    history: Optional[List[dict]]  # list of foreigh key ids to the Messages table
-    instrumentId: Optional[str]
+    datasetName: Optional[str] = None
+    description: Optional[str] = None
+    history: Optional[List[dict]] = None  # list of foreigh key ids to the Messages table
+    instrumentId: Optional[str] = None
     isPublished: Optional[bool] = False
-    keywords: Optional[List[str]]
-    license: Optional[str]
-    numberOfFiles: Optional[int]
-    numberOfFilesArchived: Optional[int]
-    orcidOfOwner: Optional[str]
-    packedSize: Optional[int]
+    keywords: Optional[List[str]] = None
+    license: Optional[str] = None
+    numberOfFiles: Optional[int] = None
+    numberOfFilesArchived: Optional[int] = None
+    orcidOfOwner: Optional[str] = None
+    packedSize: Optional[int] = None
     owner: str
-    ownerEmail: Optional[str]
-    sharedWith: Optional[List[str]]
-    size: Optional[int]
+    ownerEmail: Optional[str] = None
+    sharedWith: Optional[List[str]] = None
+    size: Optional[int] = None
     sourceFolder: str
-    sourceFolderHost: Optional[str]
-    techniques: Optional[List[dict]]  # with {'pid':pid, 'name': name} as entries
+    sourceFolderHost: Optional[str] = None
+    techniques: Optional[List[dict]] = None  # with {'pid':pid, 'name': name} as entries
     type: DatasetType
-    validationStatus: Optional[str]
-    version: Optional[str]
-    scientificMetadata: Optional[Dict]
+    validationStatus: Optional[str] = None
+    version: Optional[str] = None
+    scientificMetadata: Optional[Dict] = None
 
 
 class RawDataset(Dataset):
     """
     Raw datasets from which derived datasets are... derived.
     """
 
-    principalInvestigator: Optional[str]
-    creationLocation: Optional[str]
+    principalInvestigator: Optional[str] = None
+    creationLocation: Optional[str] = None
     type: DatasetType = DatasetType.raw
-    dataFormat: Optional[str]
-    endTime: Optional[str]  # datetime
-    sampleId: Optional[str]
-    proposalId: Optional[str]
+    dataFormat: Optional[str] = None
+    endTime: Optional[str] = None  # datetime
+    sampleId: Optional[str] = None
+    proposalId: Optional[str] = None
 
 
 class DerivedDataset(Dataset):
@@ -159,8 +159,8 @@ class DerivedDataset(Dataset):
     investigator: str
     inputDatasets: List[str]
     usedSoftware: List[str]
-    jobParameters: Optional[dict]
-    jobLogData: Optional[str]
+    jobParameters: Optional[dict] = None
+    jobLogData: Optional[str] = None
     type: DatasetType = DatasetType.derived
 
 
@@ -173,8 +173,8 @@ class DataFile(MongoQueryable):
 
     path: str
     size: int
-    time: Optional[str]
-    chk: Optional[str]
+    time: Optional[str] = None
+    chk: Optional[str] = None
     uid: Optional[str] = None
     gid: Optional[str] = None
     perm: Optional[str] = None
@@ -185,13 +185,13 @@ class Datablock(Ownable):
     A Datablock maps between a Dataset and contains DataFiles
     """
 
-    id: Optional[str]
+    id: Optional[str] = None
     # archiveId: str = None  listed in catamel model, but comes back invalid?
     size: int
-    packedSize: Optional[int]
-    chkAlg: Optional[int]
+    packedSize: Optional[int] = None
+    chkAlg: Optional[int] = None
     version: str = None
-    instrumentGroup: Optional[str]
+    instrumentGroup: Optional[str] = None
     dataFileList: List[DataFile]
     datasetId: str
 
@@ -201,10 +201,10 @@ class OrigDatablock(Ownable):
     An Original Datablock maps between a Dataset and contains DataFiles
     """
 
-    id: Optional[str]
+    id: Optional[str] = None
     # archiveId: str = None  listed in catamel model, but comes back invalid?
     size: int
-    instrumentGroup: Optional[str]
+    instrumentGroup: Optional[str] = None
     dataFileList: List[DataFile]
     datasetId: str
 
@@ -214,9 +214,9 @@ class Attachment(Ownable):
     Attachments can be any base64 encoded string...thumbnails are attachments
     """
 
-    id: Optional[str]
+    id: Optional[str] = None
     thumbnail: str
-    caption: Optional[str]
+    caption: Optional[str] = None
     datasetId: str
 
 
@@ -231,17 +231,17 @@ class PublishedData:
     publisher: str
     publicationYear: int
     title: str
-    url: Optional[str]
+    url: Optional[str] = None
     abstract: str
     dataDescription: str
     resourceType: str
-    numberOfFiles: Optional[int]
-    sizeOfArchive: Optional[int]
+    numberOfFiles: Optional[int] = None
+    sizeOfArchive: Optional[int] = None
     pidArray: List[str]
     authors: List[str]
     registeredTime: str
     status: str
-    thumbnail: Optional[str]
+    thumbnail: Optional[str] = None
     createdBy: str
     updatedBy: str
     createdAt: str

tests/test_pyscicat/test_client.py

@@ -140,7 +140,7 @@ def test_scicat_ingest():
         data_file = DataFile(path="/foo/bar", size=42)
         data_block = Datablock(
             size=42,
-            version=1,
+            version="1",
             datasetId=dataset_id,
             dataFileList=[data_file],
             **ownable.dict()

tests/tests_integration/tests_integration.py

@@ -25,8 +25,7 @@
 
 
 def test_client():
-
-    assert type(sci_clie) == ScicatClient
+    assert type(sci_clie) == ScicatClient  # noqa: E721
 
 
 def test_upload_dataset():