Release 2026.2.2

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "mavedb"
-version = "2026.2.1"
+version = "2026.2.2"
 description = "API for MaveDB, the database of Multiplexed Assays of Variant Effect."
 license = "AGPL-3.0-only"
 readme = "README.md"
@@ -35,7 +35,7 @@ numpy = "~1.26"
 httpx = "~0.26.0"
 pandas = ">=2.2.0,<3.0.0"
 pydantic = "~2.10.0"
-python-dotenv = "~0.20.0"
+python-dotenv = "^1.2"
 python-json-logger = "~2.0.7"
 SQLAlchemy = "~2.0.29"
 ga4gh-va-spec = "~0.4.2"
@@ -58,7 +58,7 @@ pyathena = { version = "~3.14.1", optional = true }
 psycopg2 = { version = "~2.9.3", optional = true }
 python-jose = { extras = ["cryptography"], version = "~3.5.0", optional = true }
 python-multipart = { version = "~0.0.22", optional = true }
-requests = { version = "~2.32.2", optional = true }
+requests = { version = "^2.33", optional = true }
 starlette = { version = "~0.49.0", optional = true }
 starlette-context = { version = "^0.3.6", optional = true }
 slack-sdk = { version = "~3.21.3", optional = true }

src/mavedb/__init__.py

@@ -6,7 +6,7 @@
 logger = module_logging.getLogger(__name__)
 
 __project__ = "mavedb-api"
-__version__ = "2026.2.1"
+__version__ = "2026.2.2"
 
 logger.info(f"MaveDB {__version__}")
 

src/mavedb/lib/clingen/services.py

@@ -276,70 +276,3 @@ def _existing_jwt(self) -> Optional[str]:
 
         logger.debug(msg="Found existing but expired Genboree JWT.", extra=logging_context())
         return None
-
-
-def get_allele_registry_associations(
-    content_submissions: list[str], submission_response: list[Union[ClinGenAllele, ClinGenSubmissionError]]
-) -> dict[str, str]:
-    """
-    Links HGVS strings and ClinGen Canonoical Allele IDs (CAIDs) given a list of both.
-
-    Args:
-        content_submissions (list[str]): A list of HGVS strings to check for associations in the ClinGen Allele Registry.
-        submission_response (list[ClinGenAllele]): The response from the ClinGen Allele Registry submission,
-                                                    which contains the registered alleles and their associated CAIDs.
-
-    Returns:
-        dict[str, str]: A dictionary mapping HGVS strings to their corresponding ClinGen Allele Registry IDs (CAIDs).
-                        The keys are the HGVS strings, and the values are the CAIDs assigned by the ClinGen Allele Registry.
-                        If no associations are found, an empty dictionary is returned.
-    """
-    save_to_logging_context(
-        {
-            "num_hgvs_strings_to_associate": len(content_submissions),
-            "num_car_alleles_to_associate": len(submission_response),
-        }
-    )
-
-    if not content_submissions or not submission_response:
-        logger.warning(
-            msg="No content submissions or submission response provided for ClinGen Allele Registry association.",
-            extra=logging_context(),
-        )
-        return {}
-    else:
-        logger.info(
-            msg="Attempting to associate ClinGen Allele Registry allees with MaveDB HGVS strings.",
-            extra=logging_context(),
-        )
-
-    allele_registry_associations: dict[str, str] = {}
-    for registration in submission_response:
-        if "errorType" in registration:
-            logger.warning(
-                msg=f"Skipping errored ClinGen Allele Registry HGVS {registration.get('hgvs', 'unknown')} ({registration.get('errorType', 'unknown')}): {registration.get('message', 'unknown error message')}",
-                extra=logging_context(),
-            )
-            continue
-
-        # Extract the CAID from the URL (e.g., "http://reg.test.genome.network/allele/CA2513066" -> "CA2513066")
-        caid = registration["@id"].split("/")[-1]
-        alleles = (
-            registration.get("genomicAlleles", [])
-            + registration.get("transcriptAlleles", [])
-            + registration.get("aminoAcidAlleles", [])
-        )
-
-        for allele in alleles:
-            for hgvs_string in content_submissions:
-                if hgvs_string in allele["hgvs"]:
-                    allele_registry_associations[hgvs_string] = caid
-                    logger.debug(
-                        msg=f"Found allele registry association for HGVS string '{hgvs_string}': {caid}",
-                        extra=logging_context(),
-                    )
-                    break
-
-    save_to_logging_context({"num_hgvs_strings_associated_with_caid": len(allele_registry_associations)})
-    logger.info(msg="Done associating ClinGen Allele Registry responses.", extra=logging_context())
-    return allele_registry_associations

src/mavedb/lib/types/clingen.py

@@ -1,6 +1,6 @@
 from typing import Any, Literal, Optional, TypedDict
 
-from typing_extensions import NotRequired, TypeGuard
+from typing_extensions import NotRequired
 
 # See: https://ldh.genome.network/docs/ldh/submit.html#content-submission-body
 
@@ -164,7 +164,3 @@ class ClinGenAlleleDefinition(TypedDict):
         "position": str,
     },
 )
-
-
-def is_car_submission_error(err: ClinGenAllele | ClinGenSubmissionError) -> TypeGuard[ClinGenSubmissionError]:
-    return "errorType" in err and "hgvs" in err

src/mavedb/lib/utils.py

@@ -1,7 +1,7 @@
 import logging
-import requests
 import time
 
+import requests
 
 logger = logging.getLogger(__name__)
 
@@ -11,11 +11,22 @@ def request_with_backoff(
 ) -> requests.Response:
     attempt = 0
     while attempt <= backoff_limit:
-        logger.debug(f"Attempting request to {url}. This is attempt {attempt+1}.")
+        logger.debug(f"Attempting request to {url}. This is attempt {attempt + 1}.")
         try:
             response = requests.request(method=method, url=url, **kwargs)
             response.raise_for_status()
             return response
+        except requests.exceptions.HTTPError as exc:
+            status = exc.response.status_code if exc.response is not None else None
+            # 429 means rate-limited — retrying with backoff is the correct response.
+            # Other 4xx errors are client mistakes that won't improve on retry.
+            if status is not None and status != 429 and status < 500:
+                raise
+            logger.warning(f"Request to {url} failed with status {status}.", exc_info=exc)
+            backoff_time = backoff_wait * (2**attempt)
+            attempt += 1
+            logger.info(f"Retrying request to {url} in {backoff_wait} seconds.")
+            time.sleep(backoff_time)
         except requests.exceptions.RequestException as exc:
             logger.warning(f"Request to {url} failed.", exc_info=exc)
             backoff_time = backoff_wait * (2**attempt)