fix: updates parsing of modality (#72)

src/aind_data_transfer_service/configs/job_configs.py

@@ -10,11 +10,12 @@
 from aind_data_schema.models.modalities import Modality
 from aind_data_schema.models.platforms import Platform
 from pydantic import (
+    ConfigDict,
     Field,
     PrivateAttr,
     SecretStr,
     ValidationInfo,
-    field_validator, ConfigDict,
+    field_validator,
 )
 from pydantic_settings import BaseSettings
 
@@ -77,7 +78,7 @@ def parse_modality_string(
         if unable to do so."""
         if isinstance(input_modality, str):
             modality_abbreviation = cls._MODALITY_MAP.get(
-                input_modality.upper()
+                input_modality.upper().replace("-", "_")
             )
             if modality_abbreviation is None:
                 raise AttributeError(f"Unknown Modality: {input_modality}")
@@ -105,7 +106,9 @@ class BasicUploadJobConfigs(BaseSettings):
     """Configuration for the basic upload job"""
 
     # Allow users to pass in extra fields
-    model_config = ConfigDict(extra='allow',)
+    model_config = ConfigDict(
+        extra="allow",
+    )
 
     # Need some way to extract abbreviations. Maybe a public method can be
     # added to the Platform class

tests/resources/sample_alt_modality_case.csv

@@ -0,0 +1,4 @@
+modality0, modality0.source, modality1, modality1.source, s3-bucket, subject-id, platform, acq-datetime
+ecephys, dir/data_set_1, ,, some_bucket, 123454, ecephys, 2020-10-10 14:10:10
+behavior-videos, dir/data_set_2, MRI, dir/data_set_3, some_bucket2, 123456, BEHAVIOR, 10/13/2020 1:10:10 PM
+behavior-videos, dir/data_set_2, BEHAVIOR_VIDEOS, dir/data_set_3, some_bucket2, 123456, BEHAVIOR, 10/13/2020 1:10:10 PM

tests/test_configs.py

@@ -18,6 +18,7 @@
 
 RESOURCES_DIR = Path(os.path.dirname(os.path.realpath(__file__))) / "resources"
 SAMPLE_FILE = RESOURCES_DIR / "sample.csv"
+SAMPLE_ALT_MODALITY_CASE_FILE = RESOURCES_DIR / "sample_alt_modality_case.csv"
 
 
 class TestJobConfigs(unittest.TestCase):
@@ -171,6 +172,42 @@ def test_parse_csv_file(self):
             ),
         )
 
+    def test_parse_alt_csv_file(self):
+        """Tests that the jobs can be parsed from a csv file correctly where
+        the modalities are lower case."""
+
+        jobs = []
+
+        with open(SAMPLE_ALT_MODALITY_CASE_FILE, newline="") as csvfile:
+            reader = csv.DictReader(csvfile, skipinitialspace=True)
+            for row in reader:
+                jobs.append(
+                    BasicUploadJobConfigs.from_csv_row(
+                        row, aws_param_store_name="/some/param/store"
+                    )
+                )
+
+        modality_outputs = []
+        for job in jobs:
+            job_s3_prefix = job.s3_prefix
+            for modality in job.modalities:
+                modality_outputs.append(
+                    (
+                        job_s3_prefix,
+                        modality.default_output_folder_name,
+                        modality.number_id,
+                    )
+                )
+        expected_modality_outputs = [
+            ("ecephys_123454_2020-10-10_14-10-10", "ecephys", None),
+            ("behavior_123456_2020-10-13_13-10-10", "behavior-videos", None),
+            ("behavior_123456_2020-10-13_13-10-10", "MRI", None),
+            ("behavior_123456_2020-10-13_13-10-10", "behavior-videos", None),
+            ("behavior_123456_2020-10-13_13-10-10", "behavior-videos1", 1),
+        ]
+        self.assertEqual(self.expected_job_configs, jobs)
+        self.assertEqual(expected_modality_outputs, modality_outputs)
+
     def test_malformed_platform(self):
         """Tests that an error is raised if an unknown platform is used"""