Merge pull request #137 from AllenNeuralDynamics/release-v0.17.0

Release v0.17.0

pyproject.toml

@@ -17,9 +17,10 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    "aind-data-schema==0.36.0",
-    "aind-data-schema-models==0.1.7",
+    "aind-data-schema==1.0.0",
+    "aind-data-schema-models>=0.3.2",
     "pydantic-settings>=2.0",
+    "pydantic<2.9"
 ]
 
 [project.optional-dependencies]
@@ -40,6 +41,7 @@ all = [
     "aind-metadata-mapper[mesoscope]",
     "aind-metadata-mapper[openephys]",
     "aind-metadata-mapper[dynamicrouting]",
+    "aind-metadata-mapper[u19]",
 ]
 
 bergamo = [
@@ -70,6 +72,10 @@ dynamicrouting = [
     "pyyaml >= 6.0.0",
 ]
 
+u19 = [
+    "pandas >= 2.2.2",
+]
+
 [tool.setuptools.packages.find]
 where = ["src"]
 

src/aind_metadata_mapper/__init__.py

@@ -1,3 +1,3 @@
 """Init package"""
 
-__version__ = "0.16.1"
+__version__ = "0.17.0"

src/aind_metadata_mapper/bergamo/session.py

@@ -1069,7 +1069,7 @@ def run_job(self) -> JobResponse:  # noqa: C901
                     )
                 ),
             )  # from Jon's script - seconds
-
+            wavelength = self.job_settings.photostim_laser_wavelength
             stim_epoch_photostim = StimulusEpoch(
                 stimulus_start_time=stream_start_time,
                 stimulus_end_time=stream_end_time,  # datetime,
@@ -1079,15 +1079,17 @@ def run_job(self) -> JobResponse:  # noqa: C901
                 stimulus_parameters=[photostim],
                 # opticalBCI class to be added in future
                 stimulus_device_names=self.job_settings.stimulus_device_names,
-                light_source_config=LaserConfig(
-                    # from rig json
-                    name=self.job_settings.photostim_laser_name,
-                    wavelength=self.job_settings.photostim_laser_wavelength,
-                    # user set value
-                    excitation_power=np.nanmean(group_powers),
-                    # from tiff header,
-                    excitation_power_unit=PowerUnit.PERCENT,
-                ),
+                light_source_config=[
+                    LaserConfig(
+                        # from rig json
+                        name=self.job_settings.photostim_laser_name,
+                        wavelength=wavelength,
+                        # user set value
+                        excitation_power=np.nanmean(group_powers),
+                        # from tiff header,
+                        excitation_power_unit=PowerUnit.PERCENT,
+                    )
+                ],
                 output_parameters={
                     "tiff_files": tiff_list,
                     "tiff_stem": tiff_stem,

src/aind_metadata_mapper/dynamic_routing/neuropixels_rig.py

@@ -77,6 +77,6 @@ def update_modification_date(
             modification_date = date.today()
 
         extracted_source.rig_id = (
-            f"{room_id}_{rig_name}_{modification_date.strftime('%y%m%d')}"
+            f"{room_id}_{rig_name}_{modification_date.strftime('%Y%m%d')}"
         )
         extracted_source.modification_date = modification_date

src/aind_metadata_mapper/models.py

@@ -1,7 +1,7 @@
 """Module to define models for Gather Metadata Job"""
 
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import List, Literal, Optional, Union
 
 from aind_data_schema.core.processing import PipelineProcess
 from aind_data_schema_models.modalities import Modality
@@ -106,6 +106,7 @@ class MetadataSettings(BaseJobSettings):
 class JobSettings(BaseJobSettings):
     """Fields needed to gather all metadata"""
 
+    job_settings_name: Literal["GatherMetadata"] = "GatherMetadata"
     metadata_service_domain: Optional[str] = None
     subject_settings: Optional[SubjectSettings] = None
     session_settings: Optional[SessionSettings] = None

src/aind_metadata_mapper/open_ephys/utils/behavior_utils.py

@@ -730,9 +730,9 @@ def fix_omitted_end_frame(stim_pres_table: pd.DataFrame) -> pd.DataFrame:
         stim_pres_table[stim_pres_table["omitted"]]["start_frame"]
         + median_stim_frame_duration
     )
-    stim_pres_table.loc[
-        stim_pres_table["omitted"], "end_frame"
-    ] = omitted_end_frames
+    stim_pres_table.loc[stim_pres_table["omitted"], "end_frame"] = (
+        omitted_end_frames
+    )
 
     stim_dtypes = stim_pres_table.dtypes.to_dict()
     stim_dtypes["start_frame"] = int
@@ -796,9 +796,9 @@ def compute_is_sham_change(
                 if np.array_equal(
                     active_images, stim_image_names[passive_block_mask].values
                 ):
-                    stim_df.loc[
-                        passive_block_mask, "is_sham_change"
-                    ] = stim_df[active_block_mask]["is_sham_change"].values
+                    stim_df.loc[passive_block_mask, "is_sham_change"] = (
+                        stim_df[active_block_mask]["is_sham_change"].values
+                    )
 
     return stim_df.sort_index()
 

src/aind_metadata_mapper/u19/__init__.py

@@ -0,0 +1 @@
+"""Init u19 package"""

src/aind_metadata_mapper/u19/models.py

@@ -0,0 +1,37 @@
+"""Defines Job Settings for U19 ETL"""
+
+from pathlib import Path
+from typing import List, Literal, Optional
+
+from pydantic import Field
+from pydantic_settings import BaseSettings
+
+
+class JobSettings(BaseSettings):
+    """Data that needs to be input by user."""
+
+    job_settings_name: Literal["U19"] = "U19"
+    tissue_sheet_path: Path
+    tissue_sheet_names: List[str]
+    output_directory: Optional[Path] = Field(
+        default=None,
+        description=(
+            "Directory where to save the json file to. If None, then json"
+            " contents will be returned in the Response message."
+        ),
+    )
+    experimenter_full_name: List[str]
+    subject_to_ingest: str = Field(
+        default=None,
+        description=(
+            "subject ID to ingest. If None,"
+            " then all subjects in spreadsheet will be ingested."
+        ),
+    )
+    procedures_download_link: str = Field(
+        description="Link to download the relevant procedures "
+        "from metadata service",
+    )
+    allow_validation_errors: bool = Field(
+        False, description="Whether or not to allow validation errors."
+    )