feat: switch from attrs to pydantic (#166) (#168)

clinvar_api/client.py

@@ -3,10 +3,10 @@
 import json
 import typing
 
-import attrs
-import cattrs
 from jsonschema import ValidationError
 from logzero import logger
+from pydantic import BaseModel, SecretStr
+from pydantic.config import ConfigDict
 import requests
 
 from clinvar_api import common, exceptions, models, msg, schemas
@@ -21,20 +21,13 @@
 SUFFIX_DRYRUN = "?dry-run=true"
 
 
-def _obfuscate_repr(s):
-    """Helper function for obfustating passwords"""
-    if len(s) < 5:
-        return repr("*" * len(s))
-    else:
-        return repr(s[:5] + "*" * (len(s) - 5))
-
-
-@attrs.define(frozen=True)
-class Config:
+class Config(BaseModel):
     """Configuration for the ``Client`` class."""
 
+    model_config = ConfigDict(frozen=True)
+
     #: Token to use for authentication.
-    auth_token: str = attrs.field(repr=_obfuscate_repr)
+    auth_token: SecretStr
 
     #: Whether to use the test endpoint.
     use_testing: bool = False
@@ -64,10 +57,10 @@ def submit_data(submission_container: models.SubmissionContainer, config: Config
     url = f"{url_prefix}{url_suffix}"
     logger.debug("Will submit to URL %s", url)
     headers = {
-        "SP-API-KEY": config.auth_token,
+        "SP-API-KEY": config.auth_token.get_secret_value(),
     }
 
-    payload = cattrs.unstructure(submission_container.to_msg())
+    payload = submission_container.to_msg().model_dump(mode="json")
     logger.debug("Payload data is %s", json.dumps(payload, indent=2))
     cleaned_payload = common.clean_for_json(payload)
     logger.debug("Cleaned payload data is %s", json.dumps(cleaned_payload, indent=2))
@@ -93,11 +86,11 @@ def submit_data(submission_container: models.SubmissionContainer, config: Config
             logger.info("Server returned '204: No Content', constructing fake created message.")
             return models.Created(id="--NONE--dry-run-result--")
         else:
-            created_msg = common.CONVERTER.structure(response.json(), msg.Created)
+            created_msg = msg.Created.model_validate_json(response.content)
             return models.Created.from_msg(created_msg)
     else:
         logger.warning("API returned an error - %s: %s", response.status_code, response.reason)
-        error_msg = common.CONVERTER.structure(response.json(), msg.Error)
+        error_msg = msg.Error.model_validate_json(response.content)
         error_obj = models.Error.from_msg(error_msg)
         logger.debug("Full server response is %s", response.json())
         if hasattr(error_obj, "errors"):
@@ -108,10 +101,11 @@ def submit_data(submission_container: models.SubmissionContainer, config: Config
             raise exceptions.SubmissionFailed(f"ClinVar submission failed: {error_obj.message}")
 
 
-@attrs.define(frozen=True)
-class RetrieveStatusResult:
+class RetrieveStatusResult(BaseModel):
     """Result type for ``retrieve_status`` function."""
 
+    model_config = ConfigDict(frozen=True)
+
     #: The submission status.
     status: models.SubmissionStatus
     #: A dict mapping file URLs to the parsed ``Sum``.
@@ -132,7 +126,7 @@ def _retrieve_status_summary(
             except ValidationError as e:
                 logger.warning("Response summary validation JSON is invalid: %s", e)
             logger.debug("... done validating status summary response")
-        sr_msg = cattrs.structure(response.json(), msg.SummaryResponse)
+        sr_msg = msg.SummaryResponse.model_validate_json(response.content)
         return models.SummaryResponse.from_msg(sr_msg)
     else:
         raise exceptions.QueryFailed(
@@ -155,17 +149,17 @@ def retrieve_status(
     url_suffix = SUFFIX_DRYRUN if config.use_dryrun else ""
     url = f"{url_prefix}{submission_id}/actions/{url_suffix}"
     headers = {
-        "SP-API-KEY": config.auth_token,
+        "SP-API-KEY": config.auth_token.get_secret_value(),
     }
     logger.debug("Will query URL %s", url)
     response = requests.get(url, headers=headers)
     if response.ok:
         logger.info("API returned OK - %s: %s", response.status_code, response.reason)
         logger.debug("Structuring response ...")
-        status_msg = common.CONVERTER.structure(response.json(), msg.SubmissionStatus)
+        status_msg = msg.SubmissionStatus.model_validate_json(response.content)
         logger.debug(
             "structured response is %s",
-            json.dumps(common.CONVERTER.unstructure(status_msg), indent=2),
+            status_msg.model_dump_json(indent=2),
         )
         logger.debug("... done structuring response")
         status_obj = models.SubmissionStatus.from_msg(status_msg)

clinvar_api/common.py

@@ -1,29 +1,4 @@
-import datetime
 import typing
-import uuid
-
-import cattr
-import dateutil.parser
-
-
-def _setup_converter() -> cattr.Converter:
-    """Setup ``cattr`` converter for UUID and datetime."""
-    result = cattr.Converter()
-    result.register_structure_hook(uuid.UUID, lambda d, _: uuid.UUID(d))
-    result.register_unstructure_hook(uuid.UUID, str)
-    result.register_structure_hook(datetime.datetime, lambda d, _: dateutil.parser.parse(d))
-    result.register_unstructure_hook(
-        datetime.datetime,
-        lambda obj: obj.replace(tzinfo=datetime.timezone.utc)
-        .astimezone()
-        .replace(microsecond=0)
-        .isoformat(),
-    )
-    return result
-
-
-#: cattr Converter to use
-CONVERTER = _setup_converter()
 
 
 def clean_for_json(

clinvar_api/models/query_response.py

@@ -3,23 +3,26 @@
 import datetime
 import typing
 
-import attrs
+from pydantic import BaseModel
+from pydantic.config import ConfigDict
 
 from clinvar_api import msg
 from clinvar_api.msg import ErrorCode
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusFile:
+class SubmissionStatusFile(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     url: str
 
     @classmethod
     def from_msg(cls, other: msg.SubmissionStatusFile):
         return SubmissionStatusFile(url=other.url)
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusObjectContent:
+class SubmissionStatusObjectContent(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     #: Processing status
     clinvar_processing_status: str
     #: Release status
@@ -33,8 +36,9 @@ def from_msg(cls, other: msg.SubmissionStatusObjectContent):
         )
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusObject:
+class SubmissionStatusObject(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     #: Optional object accession.
     accession: typing.Optional[str]
     #: Object content.
@@ -51,8 +55,9 @@ def from_msg(cls, other: msg.SubmissionStatusObject):
         )
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusResponseMessage:
+class SubmissionStatusResponseMessage(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     #: The error code.
     error_code: typing.Optional[ErrorCode]
     #: The message severity.
@@ -67,8 +72,9 @@ def from_msg(cls, other: msg.SubmissionStatusResponseMessage):
         )
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusResponse:
+class SubmissionStatusResponse(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     #: Status, one of "processing", "processed", "error",
     status: str
     #: Files in the response.
@@ -92,8 +98,9 @@ def from_msg(cls, other: msg.SubmissionStatusResponse):
         )
 
 
-@attrs.define(frozen=True)
-class SubmissionStatusActions:
+class SubmissionStatusActions(BaseModel):
+    model_config = ConfigDict(frozen=True)
+
     #: Identifier of the submission
     id: str
     #: Entries in ``actions[*].responses``, only one entry per the docs.
@@ -116,10 +123,11 @@ def from_msg(cls, other: msg.SubmissionStatusActions):
         )
 
 
-@attrs.define(frozen=True)
-class SubmissionStatus:
+class SubmissionStatus(BaseModel):
     """Internal submission status."""
 
+    model_config = ConfigDict(frozen=True)
+
     #: The list of actions (one element only by the docs).
     actions: typing.List[SubmissionStatusActions]