From a66cd4c40dc33f6a1176970b02defe98cd9848c2 Mon Sep 17 00:00:00 2001
From: jtyoung84 <104453205+jtyoung84@users.noreply.github.com>
Date: Mon, 5 Feb 2024 17:44:43 -0800
Subject: [PATCH] fix: updates parsing of modality (#72)

---
 .../configs/job_configs.py                    |  9 +++--
 tests/resources/sample_alt_modality_case.csv  |  4 ++
 tests/test_configs.py                         | 37 +++++++++++++++++++
 3 files changed, 47 insertions(+), 3 deletions(-)
 create mode 100644 tests/resources/sample_alt_modality_case.csv

diff --git a/src/aind_data_transfer_service/configs/job_configs.py b/src/aind_data_transfer_service/configs/job_configs.py
index 881267a..776ed5e 100644
--- a/src/aind_data_transfer_service/configs/job_configs.py
+++ b/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
diff --git a/tests/resources/sample_alt_modality_case.csv b/tests/resources/sample_alt_modality_case.csv
new file mode 100644
index 0000000..b23dcad
--- /dev/null
+++ b/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
diff --git a/tests/test_configs.py b/tests/test_configs.py
index 39652b0..deda2c0 100644
--- a/tests/test_configs.py
+++ b/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"""