Upgrade boto3 and botocore versions to get UBAM changes (#24)

* Upgrade boto3 and botocore versions to get UBAM changes

* Refactor to address UBAM linting issues

omics/transfer/read_set_upload.py

@@ -53,7 +53,7 @@ def _main(
         )
         upload_id = response["uploadId"]
 
-        if (args["referenceArn"] == "" and args["sourceFileType" != "FASTQ" or "UBAM"]):
+        if (args["referenceArn"] == "") and (args["sourceFileType"] not in ["FASTQ", "UBAM"]):
             raise AttributeError("Unlinked read set file types must specify a reference ARN")
 
         # Add a cleanup if the multipart upload fails at any point.

pyproject.toml

@@ -14,10 +14,10 @@ packages = [{ include = "omics" }]
 
 [tool.poetry.dependencies]
 python = "^3.10"
-s3transfer = "^0.6.0"
-boto3 = "^1.26.133"
-mypy-boto3-omics = "^1.26.133"
-botocore-stubs = "^1.29.130"
+s3transfer = "^0.7.0"
+boto3 = "^1.28.83"
+mypy-boto3-omics = "^1.28.83"
+botocore-stubs = "^1.31.83"
 
 [tool.poetry.group.dev.dependencies]
 black = "^22.8.0"

tests/transfer/unit/test_manager.py

@@ -5,10 +5,7 @@
 from s3transfer.futures import TransferFuture
 from s3transfer.utils import OSUtils
 
-from omics.common.omics_file_types import (
-    ReadSetFileName,
-    ReferenceFileName,
-)
+from omics.common.omics_file_types import ReadSetFileName, ReferenceFileName
 from omics.transfer.manager import TransferManager, _format_local_filename
 from tests.transfer import (
     TEST_CONSTANTS,
@@ -214,7 +211,7 @@ def test_upload_no_reference_with_BAM_file_type_exception(self):
 
         self.stubber.assert_no_pending_responses()
 
-    def test_upload_no_reference_with_BAM_file_type_exception(self):
+    def test_upload_no_reference_with_CRAM_file_type_exception(self):
         with self.assertRaises(AttributeError):
             self.self.transfer_manager.upload_read_set(
                 io.BytesIO(b"some file content1"),
@@ -226,9 +223,8 @@ def test_upload_no_reference_with_BAM_file_type_exception(self):
             ).result()
 
         self.stubber.assert_no_pending_responses()
-    def run_simple_upload(
-        self, files: any, file_type: str = "FASTQ"
-    ) -> TransferFuture:
+
+    def run_simple_upload(self, files: any, file_type: str = "FASTQ") -> TransferFuture:
         return self.transfer_manager.upload_read_set(
             files,
             TEST_CONSTANTS["sequence_store_id"],