aind-data-transfer-service 1.17.2__tar.gz → 1.18.0__tar.gz

{aind_data_transfer_service-1.17.2/src/aind_data_transfer_service.egg-info → aind_data_transfer_service-1.18.0}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: aind-data-transfer-service
-Version: 1.17.2
+Version: 1.18.0
 Summary: Service that handles requests to upload data to the cloud
 Author: Allen Institute for Neural Dynamics
 License: MIT
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: aind-data-schema-models<1.0.0,>=0.3.2
+Requires-Dist: aind-data-schema-models>=0.3.2
 Requires-Dist: email-validator
 Requires-Dist: pydantic>=2.0
 Requires-Dist: pydantic-settings>=2.0
@@ -23,9 +23,7 @@ Provides-Extra: docs
 Requires-Dist: Sphinx; extra == "docs"
 Requires-Dist: furo; extra == "docs"
 Provides-Extra: server
-Requires-Dist: aind-data-schema<2.0,>=1.0.0; extra == "server"
-Requires-Dist: aind-data-transfer-models==0.17.0; extra == "server"
-Requires-Dist: aind-metadata-mapper>=0.23.0; extra == "server"
+Requires-Dist: aind-data-schema==2.0.0; extra == "server"
 Requires-Dist: boto3; extra == "server"
 Requires-Dist: boto3-stubs[ssm]; extra == "server"
 Requires-Dist: fastapi>=0.115.13; extra == "server"

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "aind-data-transfer-service"
 description = "Service that handles requests to upload data to the cloud"
 license = {text = "MIT"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 authors = [
     {name = "Allen Institute for Neural Dynamics"}
 ]
@@ -17,7 +17,7 @@ readme = "README.md"
 dynamic = ["version"]
 
 dependencies = [
-    'aind-data-schema-models>=0.3.2,<1.0.0',
+    'aind-data-schema-models>=0.3.2',
     'email-validator',
     'pydantic>=2.0',
     'pydantic-settings>=2.0',
@@ -39,9 +39,7 @@ docs = [
 ]
 
 server = [
-    'aind-data-schema>=1.0.0,<2.0',
-    'aind-data-transfer-models==0.17.0',
-    'aind-metadata-mapper>=0.23.0',
+    'aind-data-schema==2.0.0',
     'boto3',
     'boto3-stubs[ssm]',
     'fastapi>=0.115.13', 

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/src/aind_data_transfer_service/__init__.py

@@ -1,7 +1,8 @@
 """Init package"""
+
 import os
 
-__version__ = "1.17.2"
+__version__ = "1.18.0"
 
 # Global constants
 OPEN_DATA_BUCKET_NAME = os.getenv("OPEN_DATA_BUCKET_NAME", "open")

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/src/aind_data_transfer_service/configs/csv_handler.py

@@ -7,8 +7,8 @@ from datetime import datetime
 from typing import Any, Dict
 
 from aind_data_schema_models.modalities import Modality
-from aind_data_schema_models.platforms import Platform
 
+from aind_data_transfer_service.configs.platforms_v1 import Platform
 from aind_data_transfer_service.models.core import Task, UploadJobConfigsV2
 
 DATETIME_PATTERN2 = re.compile(
@@ -147,13 +147,18 @@ def map_csv_row_to_job(row: dict) -> UploadJobConfigsV2:
         "gather_preliminary_metadata": metadata_task,
         "check_s3_folder_exists": check_s3_folder_exists_task,
         "modality_transformation_settings": modality_tasks,
-        "codeocean_pipeline_settings": None
-        if codeocean_tasks == dict()
-        else codeocean_tasks,
+        "codeocean_pipeline_settings": (
+            None if codeocean_tasks == dict() else codeocean_tasks
+        ),
     }
+    platform = (
+        None
+        if job_configs.get("platform") is None
+        else Platform.from_abbreviation(job_configs["platform"])
+    )
     job_configs.update(
         {
-            "platform": Platform.from_abbreviation(job_configs["platform"]),
+            "platform": platform,
             "modalities": [
                 Modality.from_abbreviation(m) for m in modality_tasks.keys()
             ],

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/src/aind_data_transfer_service/configs/job_upload_template.py

@@ -5,13 +5,14 @@ from io import BytesIO
 from typing import Any, ClassVar, Dict, List
 
 from aind_data_schema_models.modalities import Modality
-from aind_data_schema_models.platforms import Platform
 from openpyxl import Workbook
 from openpyxl.styles import Font
 from openpyxl.utils import get_column_letter
 from openpyxl.worksheet.datavalidation import DataValidation
 from pydantic import BaseModel
 
+from aind_data_transfer_service.configs.platforms_v1 import Platform
+
 
 class JobUploadTemplate(BaseModel):
     """Class to configure and create xlsx job upload template"""

aind_data_transfer_service-1.18.0/src/aind_data_transfer_service/configs/platforms_v1.py

@@ -0,0 +1,177 @@
+"""Platforms"""
+
+from typing import Literal, Union
+
+from pydantic import BaseModel, ConfigDict, Field
+from typing_extensions import Annotated
+
+
+class _PlatformModel(BaseModel):
+    """Base model for platform"""
+
+    model_config = ConfigDict(frozen=True)
+    name: str
+    abbreviation: str
+
+
+class _Behavior(_PlatformModel):
+    """Model behavior"""
+
+    name: Literal["Behavior platform"] = "Behavior platform"
+    abbreviation: Literal["behavior"] = "behavior"
+
+
+class _Confocal(_PlatformModel):
+    """Model confocal"""
+
+    name: Literal["Confocal microscopy platform"] = (
+        "Confocal microscopy platform"
+    )
+    abbreviation: Literal["confocal"] = "confocal"
+
+
+class _Ecephys(_PlatformModel):
+    """Model ecephys"""
+
+    name: Literal["Electrophysiology platform"] = "Electrophysiology platform"
+    abbreviation: Literal["ecephys"] = "ecephys"
+
+
+class _Exaspim(_PlatformModel):
+    """Model exaSPIM"""
+
+    name: Literal["ExaSPIM platform"] = "ExaSPIM platform"
+    abbreviation: Literal["exaSPIM"] = "exaSPIM"
+
+
+class _Fip(_PlatformModel):
+    """Model FIP"""
+
+    name: Literal["Frame-projected independent-fiber photometry platform"] = (
+        "Frame-projected independent-fiber photometry platform"
+    )
+    abbreviation: Literal["FIP"] = "FIP"
+
+
+class _Hcr(_PlatformModel):
+    """Model HCR"""
+
+    name: Literal["Hybridization chain reaction platform"] = (
+        "Hybridization chain reaction platform"
+    )
+    abbreviation: Literal["HCR"] = "HCR"
+
+
+class _Hsfp(_PlatformModel):
+    """Model HSFP"""
+
+    name: Literal["Hyperspectral fiber photometry platform"] = (
+        "Hyperspectral fiber photometry platform"
+    )
+    abbreviation: Literal["HSFP"] = "HSFP"
+
+
+class _Isi(_PlatformModel):
+    """Model ISI"""
+
+    name: Literal["Intrinsic signal imaging platform"] = (
+        "Intrinsic signal imaging platform"
+    )
+    abbreviation: Literal["ISI"] = "ISI"
+
+
+class _Merfish(_PlatformModel):
+    """Model MERFISH"""
+
+    name: Literal["MERFISH platform"] = "MERFISH platform"
+    abbreviation: Literal["MERFISH"] = "MERFISH"
+
+
+class _Mri(_PlatformModel):
+    """Model MRI"""
+
+    name: Literal["Magnetic resonance imaging platform"] = (
+        "Magnetic resonance imaging platform"
+    )
+    abbreviation: Literal["MRI"] = "MRI"
+
+
+class _Mesospim(_PlatformModel):
+    """Model mesoSPIM"""
+
+    name: Literal["MesoSPIM platform"] = "MesoSPIM platform"
+    abbreviation: Literal["mesoSPIM"] = "mesoSPIM"
+
+
+class _Motor_Observatory(_PlatformModel):
+    """Model motor-observatory"""
+
+    name: Literal["Motor observatory platform"] = "Motor observatory platform"
+    abbreviation: Literal["motor-observatory"] = "motor-observatory"
+
+
+class _Multiplane_Ophys(_PlatformModel):
+    """Model multiplane-ophys"""
+
+    name: Literal["Multiplane optical physiology platform"] = (
+        "Multiplane optical physiology platform"
+    )
+    abbreviation: Literal["multiplane-ophys"] = "multiplane-ophys"
+
+
+class _Slap2(_PlatformModel):
+    """Model SLAP2"""
+
+    name: Literal["SLAP2 platform"] = "SLAP2 platform"
+    abbreviation: Literal["SLAP2"] = "SLAP2"
+
+
+class _Single_Plane_Ophys(_PlatformModel):
+    """Model single-plane-ophys"""
+
+    name: Literal["Single-plane optical physiology platform"] = (
+        "Single-plane optical physiology platform"
+    )
+    abbreviation: Literal["single-plane-ophys"] = "single-plane-ophys"
+
+
+class _Smartspim(_PlatformModel):
+    """Model SmartSPIM"""
+
+    name: Literal["SmartSPIM platform"] = "SmartSPIM platform"
+    abbreviation: Literal["SmartSPIM"] = "SmartSPIM"
+
+
+class Platform:
+    """Platforms"""
+
+    BEHAVIOR = _Behavior()
+    CONFOCAL = _Confocal()
+    ECEPHYS = _Ecephys()
+    EXASPIM = _Exaspim()
+    FIP = _Fip()
+    HCR = _Hcr()
+    HSFP = _Hsfp()
+    ISI = _Isi()
+    MERFISH = _Merfish()
+    MRI = _Mri()
+    MESOSPIM = _Mesospim()
+    MOTOR_OBSERVATORY = _Motor_Observatory()
+    MULTIPLANE_OPHYS = _Multiplane_Ophys()
+    SLAP2 = _Slap2()
+    SINGLE_PLANE_OPHYS = _Single_Plane_Ophys()
+    SMARTSPIM = _Smartspim()
+
+    ALL = tuple(_PlatformModel.__subclasses__())
+
+    ONE_OF = Annotated[
+        Union[tuple(_PlatformModel.__subclasses__())],
+        Field(discriminator="name"),
+    ]
+
+    abbreviation_map = {m().abbreviation: m() for m in ALL}
+
+    @classmethod
+    def from_abbreviation(cls, abbreviation: str):
+        """Get platform from abbreviation"""
+        return cls.abbreviation_map.get(abbreviation, None)

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/src/aind_data_transfer_service/log_handler.py

@@ -17,9 +17,9 @@ class LoggingConfigs(BaseSettings):
     loki_uri: Optional[str] = Field(
         default=None, description="URI of Loki logging server."
     )
-    log_level: Literal[
-        "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"
-    ] = Field(default="INFO", description="Log level")
+    log_level: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = (
+        Field(default="DEBUG", description="Log level")
+    )
 
     @property
     def app_name(self):

{aind_data_transfer_service-1.17.2 → aind_data_transfer_service-1.18.0}/src/aind_data_transfer_service/models/core.py

@@ -8,7 +8,6 @@ from typing import Any, Dict, List, Literal, Optional, Set, Union
 
 from aind_data_schema_models.data_name_patterns import build_data_name
 from aind_data_schema_models.modalities import Modality
-from aind_data_schema_models.platforms import Platform
 from pydantic import (
     BaseModel,
     ConfigDict,
@@ -21,6 +20,8 @@ from pydantic import (
 )
 from pydantic_settings import BaseSettings
 
+from aind_data_transfer_service.configs.platforms_v1 import Platform
+
 _validation_context: ContextVar[Union[Dict[str, Any], None]] = ContextVar(
     "_validation_context", default=None
 )
@@ -163,8 +164,13 @@ class UploadJobConfigsV2(BaseSettings):
     project_name: str = Field(
         ..., description="Name of project", title="Project Name"
     )
-    platform: Platform.ONE_OF = Field(
-        ..., description="Platform", title="Platform"
+    platform: Optional[Platform.ONE_OF] = Field(
+        default=None,
+        title="Platform",
+        description=(
+            "Legacy field required for aind-data-schema v1. Will be removed"
+            " in future versions."
+        ),
     )
     modalities: List[Modality.ONE_OF] = Field(
         ...,
@@ -190,11 +196,26 @@ class UploadJobConfigsV2(BaseSettings):
     @computed_field
     def s3_prefix(self) -> str:
         """Construct s3_prefix from configs."""
+        if self.platform is not None:
+            label = f"{self.platform.abbreviation}_{self.subject_id}"
+        else:
+            label = self.subject_id
         return build_data_name(
-            label=f"{self.platform.abbreviation}_{self.subject_id}",
+            label=label,
             creation_datetime=self.acq_datetime,
         )
 
+    @field_validator("platform", mode="before")
+    def validate_platform(cls, v):
+        """
+        For backwards compatibility, allow a user to input an
+        aind-data-schema-model platform and then convert it.
+        """
+        if type(v).__module__ == "aind_data_schema_models.platforms":
+            return v.model_dump()
+        else:
+            return v
+
     @field_validator("job_type", "project_name", mode="before")
     def validate_with_context(cls, v: str, info: ValidationInfo) -> str:
         """