diff --git a/.github/workflows/pr-branch-build.yml b/.github/workflows/pr-branch-build.yml index d8a2ecaf..d90eff80 100644 --- a/.github/workflows/pr-branch-build.yml +++ b/.github/workflows/pr-branch-build.yml @@ -11,16 +11,16 @@ jobs: strategy: matrix: - python_version: ["3.8", "3.9", "3.10", "3.11"] + python_version: ["3.9", "3.10", "3.11"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install poetry - run: pipx install poetry==1.5.1 + run: pipx install poetry==1.8.5 - name: Set up Python - uses: actions/setup-python@v4 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python_version }} cache: "poetry" @@ -32,5 +32,5 @@ jobs: poetry build -f sdist poetry build -f wheel - - if: ${{ matrix.python_version == '3.8' }} + - if: ${{ matrix.python_version == '3.9' }} run: poetry run poe doc diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d3bbb4f8..21b281b1 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -10,15 +10,15 @@ jobs: runs-on: ubuntu-latest environment: pypi steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Install poetry - run: pipx install poetry==1.5.1 + run: pipx install poetry==1.8.5 - - name: Set up Python 3.8 - uses: actions/setup-python@v4 + - name: Set up Python 3.9 + uses: actions/setup-python@v5 with: - python-version: "3.8" # pdoc works under this version + python-version: "3.9" # pdoc works under this version cache: "poetry" - run: poetry install diff --git a/CHANGELOG.md b/CHANGELOG.md index d012eea4..bf0bcb4d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,6 +8,19 @@ and this project adheres to _(NOTE: All examples use fictitious data or freely available data sets.)_ +## [1.0.0] - 2024-12-17 + +### Removed + +- Support for Python 3.8 has been dropped, since 3.8 has reached end-of-life: + https://devguide.python.org/versions/ + +### Changed + +- This project now uses `pydantic` v2 instead of v1. +- **BREAKING**: `PagingApiOptions.dict()` has been renamed to + `PagingApiOptions.model_dump()`. + ## [0.36.0] - 2024-11-15 ### Added diff --git a/README.md b/README.md index 0a61bf62..16bc777f 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ # PHC SDK for Python -The phc-sdk-py is a developer kit for interfacing with the [PHC API](https://api.docs.lifeomic.com/) on Python 3.7 and above. +The phc-sdk-py is a developer kit for interfacing with the +[PHC API](https://api.docs.lifeomic.com/) on Python 3.7 and above. ## Project Status @@ -15,7 +16,7 @@ The phc-sdk-py is a developer kit for interfacing with the [PHC API](https://api ### Dependencies -- [Python 3](https://www.python.org/download/releases/3.0/) version >= 3.8 +- [Python 3](https://www.python.org/download/releases/3.0/) version >= 3.9 ### Getting the Source @@ -23,7 +24,10 @@ This project is [hosted on GitHub](https://github.com/lifeomic/phc-sdk-py). ### Usage -A `Session` needs to be created first that stores the token and account information needed to access the PHC API. One can currently using API Key tokens generated from the PHC Account, or OAuth tokens generated using the [CLI](https://github.com/lifeomic/cli). +A `Session` needs to be created first that stores the token and account +information needed to access the PHC API. One can currently using API Key tokens +generated from the PHC Account, or OAuth tokens generated using the +[CLI](https://github.com/lifeomic/cli). ```python from phc import Session @@ -31,7 +35,8 @@ from phc import Session session = Session(token=, account="myaccount") ``` -Once a `Session` is created, you can then access the different parts of the platform. +Once a `Session` is created, you can then access the different parts of the +platform. ```python from phc.services import Accounts @@ -42,18 +47,24 @@ myaccounts = accounts.get_list() ## Contributing -We encourage public contributions! Please review [CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) for details on our code of conduct and development process. +We encourage public contributions! Please review +[CONTRIBUTING.md](CONTRIBUTING.md) and [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md) +for details on our code of conduct and development process. ## License -This project is licensed under the MIT License - see [LICENSE](LICENSE) file for details. +This project is licensed under the MIT License - see [LICENSE](LICENSE) file for +details. ## Authors -See the list of [contributors](https://github.com/lifeomic/phc-sdk-py/contributors) who participate in this project. +See the list of +[contributors](https://github.com/lifeomic/phc-sdk-py/contributors) who +participate in this project. ## Acknowledgements This project is built with the following: -- [aiohttp](https://aiohttp.readthedocs.io/en/stable/) - Asynchronous HTTP Client/Server for asyncio and Python. +- [aiohttp](https://aiohttp.readthedocs.io/en/stable/) - Asynchronous HTTP + Client/Server for asyncio and Python. diff --git a/bin/one-schema.py b/bin/one-schema.py index 8d09abad..db1f1c43 100644 --- a/bin/one-schema.py +++ b/bin/one-schema.py @@ -8,13 +8,13 @@ import boto3 from fire import Fire from datamodel_code_generator import ( + DataModelType, InputFileType, LiteralType, OpenAPIScope, PythonVersion, generate, ) -from datamodel_code_generator import DataModelType def fetch_remote_schema(*, source: str, output: str): @@ -65,7 +65,7 @@ def _generate_data_models(schema_path: str) -> str: OpenAPIScope.Parameters, ], # Format of the types generated. - output_model_type=DataModelType.PydanticBaseModel, + output_model_type=DataModelType.PydanticV2BaseModel, target_python_version=PythonVersion.PY_38, # Copy doc strings into the source code. use_schema_description=True, diff --git a/phc/__init__.py b/phc/__init__.py index fab0ad91..3c972784 100644 --- a/phc/__init__.py +++ b/phc/__init__.py @@ -1,6 +1,7 @@ """ .. include:: ../README.md """ + import nest_asyncio from phc.session import Session from phc.api_response import ApiResponse diff --git a/phc/base_client.py b/phc/base_client.py index ea66e5b1..775ac8af 100644 --- a/phc/base_client.py +++ b/phc/base_client.py @@ -1,4 +1,5 @@ """A Python module for a base PHC web client.""" + import asyncio import platform import sys diff --git a/phc/easy/abstract/paging_api_item.py b/phc/easy/abstract/paging_api_item.py index 8a4b88b4..50da1f07 100644 --- a/phc/easy/abstract/paging_api_item.py +++ b/phc/easy/abstract/paging_api_item.py @@ -17,8 +17,8 @@ class PagingApiOptions(BaseModel): def transform(key, value): return (key, value) - def dict(self): - raw = super().dict() + def model_dump(self): + raw = super().model_dump() def preprocess_value(v): if isinstance(v, Enum): @@ -68,7 +68,7 @@ def params_class() -> type: @classmethod def process_params(cls, params: dict) -> dict: "Validates and transforms the API query parameters" - return cls.params_class()(**params).dict() + return cls.params_class()(**params).model_dump() @staticmethod def transform_results(data_frame: pd.DataFrame, **expand_args): diff --git a/phc/easy/ocr/options/ocr_config_types.py b/phc/easy/ocr/options/ocr_config_types.py index ad2ddb29..627f9024 100644 --- a/phc/easy/ocr/options/ocr_config_types.py +++ b/phc/easy/ocr/options/ocr_config_types.py @@ -125,12 +125,10 @@ class Config(BaseModel): class OcrConfigPayload(BaseModel): - project: constr( - regex=r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}$", + project: str = Field( + pattern=r"^[0-9a-fA-F]{8}-[0-9a-fA-F]{4}-4[0-9a-fA-F]{3}-[89abAB][0-9a-fA-F]{3}-[0-9a-fA-F]{12}$", min_length=36, max_length=36, - ) = Field( - ..., examples=["e97e27d3-f553-432a-bde1-7ae3d3ba5078"], title="Project Id", ) diff --git a/phc/easy/ocr/suggestion.py b/phc/easy/ocr/suggestion.py index 14def13d..42da8773 100644 --- a/phc/easy/ocr/suggestion.py +++ b/phc/easy/ocr/suggestion.py @@ -197,16 +197,19 @@ def expand_nested_array_column(df: pd.DataFrame, key: str, lprefix=""): expanded = pd.concat( df.apply( - lambda x: pd.concat( - [ - pd.DataFrame( - [{"index": x.name, "_item": i, **v} for v in array] - ) - for i, array in enumerate(x[key]) - ] - ) - # pd.concat does not like an empty array so we avoid that situation - if x[key] != [] else pd.DataFrame(), + lambda x: ( + pd.concat( + [ + pd.DataFrame( + [{"index": x.name, "_item": i, **v} for v in array] + ) + for i, array in enumerate(x[key]) + ] + ) + # pd.concat does not like an empty array so we avoid that situation + if x[key] != [] + else pd.DataFrame() + ), axis=1, ).values ).add_prefix(lprefix) diff --git a/phc/easy/omics/gene.py b/phc/easy/omics/gene.py index 8c2d1a60..717ba154 100644 --- a/phc/easy/omics/gene.py +++ b/phc/easy/omics/gene.py @@ -19,9 +19,9 @@ def get_data_frame(search: str = "", auth_args: Auth = Auth.shared()): if "alias" in frame.columns: frame["alias"] = frame.alias.apply( - lambda aliases: ",".join(aliases) - if isinstance(aliases, list) - else None + lambda aliases: ( + ",".join(aliases) if isinstance(aliases, list) else None + ) ) # We choose to not expand topCancerDrivers and cancerDrivers since it diff --git a/phc/easy/omics/options/genomic_copy_number_variant.py b/phc/easy/omics/options/genomic_copy_number_variant.py index 85eb88b5..96b162b7 100644 --- a/phc/easy/omics/options/genomic_copy_number_variant.py +++ b/phc/easy/omics/options/genomic_copy_number_variant.py @@ -16,7 +16,7 @@ class GenomicCopyNumberVariantOptions(PagingApiOptions): """Options to pass to `/v1/genomics/copy-numbers`""" - variant_set_ids: List[str] = Field(..., min_items=1) + variant_set_ids: List[str] = Field(..., min_length=1) include: List[GenomicVariantInclude] = [] gene: List[str] = [] interpretation: List[str] = [] diff --git a/phc/easy/omics/options/genomic_expression.py b/phc/easy/omics/options/genomic_expression.py index b7f79c52..9083f59c 100644 --- a/phc/easy/omics/options/genomic_expression.py +++ b/phc/easy/omics/options/genomic_expression.py @@ -5,12 +5,6 @@ from phc.easy.abstract.paging_api_item import PagingApiOptions from phc.easy.omics.options.common import GenomicVariantInclude -EXPRESSION = constr( - regex=r"^(\d+(\.\d+)?\-\d+(\.\d+)?|[\>\<]\=\s?\d+(\.\d+)?|\d+(\.\d+)?:(lte|gte))$" -) - -ORDER_BY = constr(regex=r"^expression(:desc)?$") - MAPPINGS = { "variant_set_ids": "rnaQuantificationSetIds", "outlier_std_dev": "outlierStdDev", @@ -22,11 +16,11 @@ class GenomicExpressionOptions(PagingApiOptions): """Options to pass to `/v1/genomics/expressions`""" - variant_set_ids: List[str] = Field(..., min_items=1) + variant_set_ids: List[str] = Field(..., min_length=1) include: List[GenomicVariantInclude] = [] gene: List[str] = [] - expression: Optional[EXPRESSION] = None - order_by: Optional[ORDER_BY] = None + expression: Optional[str] = Field(None, pattern=r"^(\d+(\.\d+)?-\d+(\.\d+)?|[><]=\s?\d+(\.\d+)?|\d+(\.\d+)?:(lte|gte))$") + order_by: Optional[str] = Field(None, pattern=r"^expression(:desc)?$") in_ckb: Optional[bool] = None # TODO: Fill out allowed options for this parameter outlier_std_dev: Optional[str] = None diff --git a/phc/easy/omics/options/genomic_short_variant.py b/phc/easy/omics/options/genomic_short_variant.py index 88c3bf03..eece25c5 100644 --- a/phc/easy/omics/options/genomic_short_variant.py +++ b/phc/easy/omics/options/genomic_short_variant.py @@ -12,8 +12,8 @@ from pydantic import Field, constr RS_ID = r"^rs(\d+)$" -NUM_DECIMAL_RANGE = constr(regex=r"^\d+(\.\d+)?\-\d+(\.\d+)?$") -NUM_RANGE = constr(regex=r"^(\d+\-\d+|\d+)$") +NUM_DECIMAL_RANGE = constr(pattern=r"^\d+(\.\d+)?\-\d+(\.\d+)?$") +NUM_RANGE = constr(pattern=r"^(\d+\-\d+|\d+)$") MAPPINGS = { "variant_set_ids": "variantSetIds", @@ -68,10 +68,10 @@ class GenomicShortVariantOptions(PagingApiOptions): # - Combined In Silico Prediction # - Individual In Silico Predictors - variant_set_ids: List[str] = Field(..., min_items=1) + variant_set_ids: List[str] = Field(..., min_length=1) include: List[GenomicVariantInclude] = ["vcf"] gene: List[str] = [] - rs_id: List[constr(regex=RS_ID)] = [] + rs_id: List[constr(pattern=RS_ID)] = [] chromosome: List[Chromosome] = [] clinvar_allele_id: List[str] = [] clinvar_disease: List[str] = [] @@ -114,7 +114,7 @@ class GenomicShortVariantOptions(PagingApiOptions): alt_read_depth: List[str] = [] ref_read_depth: List[str] = [] variant_filter: List[str] = [] - in_ckb: Optional[bool] + in_ckb: Optional[bool] = None @staticmethod def transform(key, value): diff --git a/phc/easy/omics/options/genomic_structural_variant.py b/phc/easy/omics/options/genomic_structural_variant.py index 283cb375..1e20cd98 100644 --- a/phc/easy/omics/options/genomic_structural_variant.py +++ b/phc/easy/omics/options/genomic_structural_variant.py @@ -14,7 +14,7 @@ class GenomicStructuralVariantOptions(PagingApiOptions): - variant_set_ids: List[str] = Field(..., min_items=1) + variant_set_ids: List[str] = Field(..., min_length=1) gene: List[str] = [] effect: List[StructuralType] = [] interpretation: List[str] = [] diff --git a/phc/easy/query/__init__.py b/phc/easy/query/__init__.py index e56273de..644f494d 100644 --- a/phc/easy/query/__init__.py +++ b/phc/easy/query/__init__.py @@ -297,9 +297,11 @@ def execute_paging_api( ) results = with_progress( - lambda: (progress if progress is not None else tqdm()) - if show_progress - else None, + lambda: ( + (progress if progress is not None else tqdm()) + if show_progress + else None + ), lambda progress: recursive_paging_api_call( path, params=params, @@ -499,21 +501,25 @@ def agg_composite_to_frame(prefix: str, data: dict): ] ) .pipe( - lambda df: df - if len(df) == 0 or display_query is None - # Poor man's way to filter only matching codes (since Elasticsearch - # returns records which will include other codes) - else df[ - df["display"] - .str.lower() - .str.contains(display_query.lower()) - ] + lambda df: ( + df + if len(df) == 0 or display_query is None + # Poor man's way to filter only matching codes (since Elasticsearch + # returns records which will include other codes) + else df[ + df["display"] + .str.lower() + .str.contains(display_query.lower()) + ] + ) ) .pipe( - lambda df: pd.DataFrame() - if len(df) == 0 - else df.sort_values("doc_count", ascending=False).reset_index( - drop=True + lambda df: ( + pd.DataFrame() + if len(df) == 0 + else df.sort_values( + "doc_count", ascending=False + ).reset_index(drop=True) ) ) ) diff --git a/phc/easy/summary/counts.py b/phc/easy/summary/counts.py index 149feeee..080f17b8 100644 --- a/phc/easy/summary/counts.py +++ b/phc/easy/summary/counts.py @@ -22,9 +22,11 @@ def resource_path(): def response_to_items(data): squashed = first(pd.json_normalize(data).to_dict("records")) or {} return lmapcat( - lambda k: [{"summary": k, **v} for v in squashed[k]] - if isinstance(squashed[k], list) - else [], + lambda k: ( + [{"summary": k, **v} for v in squashed[k]] + if isinstance(squashed[k], list) + else [] + ), squashed.keys(), ) diff --git a/phc/easy/summary/item_counts.py b/phc/easy/summary/item_counts.py index 7e675b8e..179c6a40 100644 --- a/phc/easy/summary/item_counts.py +++ b/phc/easy/summary/item_counts.py @@ -18,7 +18,7 @@ def resource_path(): @classmethod def process_params(cls, params: dict) -> dict: - new_params = cls.params_class()(**params).dict() + new_params = cls.params_class()(**params).model_dump() if SummaryClinicalType.has_value(new_params["summary"]): return {**new_params, "summary_type": "clinical"} diff --git a/phc/services/files.py b/phc/services/files.py index d5a736d5..916b1505 100644 --- a/phc/services/files.py +++ b/phc/services/files.py @@ -69,9 +69,11 @@ def upload( res = self._api_call( "uploads", json={ - "name": file_name - if file_name is not None - else os.path.basename(source), + "name": ( + file_name + if file_name is not None + else os.path.basename(source) + ), "datasetId": project_id, "overwrite": overwrite, }, @@ -112,9 +114,11 @@ def upload( res = self._api_call( "files", json={ - "name": file_name - if file_name is not None - else os.path.basename(source), + "name": ( + file_name + if file_name is not None + else os.path.basename(source) + ), "datasetId": project_id, "overwrite": overwrite, }, diff --git a/phc/services/patient_ml.py b/phc/services/patient_ml.py index 2a174ad3..ec8d8afc 100644 --- a/phc/services/patient_ml.py +++ b/phc/services/patient_ml.py @@ -9,11 +9,13 @@ from typing import List, Literal, Optional, Union -from pydantic import BaseModel, Extra, Field +from pydantic import BaseModel, ConfigDict, Field, RootModel class LabelDefinitionBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) id: Optional[str] = None """ UUID uniquely identifying this label. @@ -34,12 +36,16 @@ class LabelDefinition(LabelDefinitionBase): class LabelsDefinitionInput(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) labels: List[LabelDefinitionBase] class LabelsDefinition(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) labels: List[LabelDefinition] maxLabelIndex: int = Field(..., ge=-1, le=255) """ @@ -48,12 +54,16 @@ class LabelsDefinition(BaseModel): class ClassificationProblemInput(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) labelDefinition: LabelsDefinitionInput class ClassificationProblem(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) labelDefinition: LabelsDefinition @@ -62,6 +72,9 @@ class ImageSegmentationArea(BaseModel): A run-length encoded (RLE) 4 channel color image, representing the mask for a single label. """ + model_config = ConfigDict( + extra="forbid", + ) id: str """ The ID of the label this mask is for. @@ -77,6 +90,9 @@ class ImageSegmentationLabelData(BaseModel): A raw image segmentation, in the format LabelStudio provides. """ + model_config = ConfigDict( + extra="forbid", + ) labelType: Literal["imgSeg"] projectId: str """ @@ -93,22 +109,26 @@ class ImageSegmentationLabelData(BaseModel): areas: List[ImageSegmentationArea] -class LabelFileData(BaseModel): - __root__: ImageSegmentationLabelData +class LabelFileData(RootModel[ImageSegmentationLabelData]): + root: ImageSegmentationLabelData class Tag(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) name: str value: str -class Tags(BaseModel): - __root__: List[Tag] +class Tags(RootModel[List[Tag]]): + root: List[Tag] class LabelBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) isConfirmed: Optional[bool] = None """ A confirmed label is believed to be correct and may be used during training and evaluation. @@ -129,6 +149,9 @@ class Mask(BaseModel): The fileId of an image containing per-pixel labels """ + model_config = ConfigDict( + extra="forbid", + ) fileId: str @@ -148,12 +171,14 @@ class ImageClassificationLabel(LabelBase): """ -class Label(BaseModel): - __root__: Union[ImageSegmentationLabel, ImageClassificationLabel] +class Label(RootModel[Union[ImageSegmentationLabel, ImageClassificationLabel]]): + root: Union[ImageSegmentationLabel, ImageClassificationLabel] class ExampleBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) id: str updatedAt: float """ @@ -162,7 +187,9 @@ class ExampleBase(BaseModel): class Image(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) fileId: str @@ -178,8 +205,10 @@ class ImageClassificationExample(ExampleBase): label: Optional[ImageClassificationLabel] = None -class Example(BaseModel): - __root__: Union[ImageSegmentationExample, ImageClassificationExample] +class Example( + RootModel[Union[ImageSegmentationExample, ImageClassificationExample]] +): + root: Union[ImageSegmentationExample, ImageClassificationExample] class FhirCodesFilter(BaseModel): @@ -187,23 +216,30 @@ class FhirCodesFilter(BaseModel): Used to find FHIR resources containing a type code that equals any value in the codes array """ + model_config = ConfigDict( + extra="forbid", + ) filterType: Literal["FhirCodesFilter"] - codes: List[str] = Field(..., max_items=10, min_items=1) + codes: List[str] = Field(..., max_length=10, min_length=1) class CategoricalParameterSpace(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) type: Literal["categorical"] name: str values: List[str] -class NumericScale(BaseModel): - __root__: Literal["auto", "linear", "log", "reverseLog"] +class NumericScale(RootModel[Literal["auto", "linear", "log", "reverseLog"]]): + root: Literal["auto", "linear", "log", "reverseLog"] class NumericParameterSpace(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) name: str min: float max: float @@ -218,20 +254,30 @@ class IntegerParameterSpace(NumericParameterSpace): type: Literal["integer"] -class ParameterSpace(BaseModel): - __root__: Union[ +class ParameterSpace( + RootModel[ + Union[ + CategoricalParameterSpace, + ContinuousParameterSpace, + IntegerParameterSpace, + ] + ] +): + root: Union[ CategoricalParameterSpace, ContinuousParameterSpace, IntegerParameterSpace, ] -class OptimizationDirection(BaseModel): - __root__: Literal["minimize", "maximize"] +class OptimizationDirection(RootModel[Literal["minimize", "maximize"]]): + root: Literal["minimize", "maximize"] class OptimizationObjective(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) direction: OptimizationDirection metric: str @@ -241,16 +287,21 @@ class MetricDefinition(BaseModel): Camel-cased mirror of https://docs.aws.amazon.com/sagemaker/latest/APIReference/API_MetricDefinition.html. """ + model_config = ConfigDict( + extra="forbid", + ) name: str regex: str class TuningJobTrainingApproach(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) type: Literal["tuningJob"] trainingImage: str = Field( ..., - regex="^[0-9]+\\.dkr.ecr.[-a-z0-9]+\\.amazonaws\\.com\\/[-_a-zA-Z0-9]+:[-_a-zA-Z0-9]+$", + pattern="^[0-9]+\\.dkr.ecr.[-a-z0-9]+\\.amazonaws\\.com\\/[-_a-zA-Z0-9]+:[-_a-zA-Z0-9]+$", ) """ An aws ecr image uri of the form .dkr.ecr..amazonaws.com/: @@ -274,15 +325,17 @@ class TuningJobTrainingApproach(BaseModel): """ -class TrainingApproach(BaseModel): - __root__: TuningJobTrainingApproach +class TrainingApproach(RootModel[TuningJobTrainingApproach]): + root: TuningJobTrainingApproach class DeployApproachBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) inferenceImage: str = Field( ..., - regex="^[0-9]+\\.dkr.ecr.[-a-z0-9]+\\.amazonaws\\.com\\/[-_a-zA-Z0-9]+:[-_a-zA-Z0-9]+$", + pattern="^[0-9]+\\.dkr.ecr.[-a-z0-9]+\\.amazonaws\\.com\\/[-_a-zA-Z0-9]+:[-_a-zA-Z0-9]+$", ) """ An aws ecr image uri of the form .dkr.ecr..amazonaws.com/: @@ -297,18 +350,22 @@ class CloudDeployApproach(DeployApproachBase): type: Literal["cloud"] -class DeployApproach(BaseModel): - __root__: Union[EdgeDeployApproach, CloudDeployApproach] +class DeployApproach(RootModel[Union[EdgeDeployApproach, CloudDeployApproach]]): + root: Union[EdgeDeployApproach, CloudDeployApproach] class DatasetConfigBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) name: str description: str class ModelConfigBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) name: str description: str trainingApproach: TrainingApproach @@ -336,7 +393,9 @@ class ModelConfig(ModelConfigBase): class Metric(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) name: str """ The name of the metric e.g. "Cross Entopy Loss", "Accuracy", "F1 Macro", etc. @@ -356,12 +415,14 @@ class Metric(BaseModel): """ -class ApprovalChoice(BaseModel): - __root__: Literal["approved", "rejected"] +class ApprovalChoice(RootModel[Literal["approved", "rejected"]]): + root: Literal["approved", "rejected"] class ApprovalDecisionInput(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) description: Optional[str] = None """ Reasoning, justification, or other notes to associate with the decision. @@ -385,12 +446,16 @@ class UserApprovalDecision(ApprovalDecisionBase): user: str -class ApprovalDecision(BaseModel): - __root__: Union[SystemApprovalDecision, UserApprovalDecision] +class ApprovalDecision( + RootModel[Union[SystemApprovalDecision, UserApprovalDecision]] +): + root: Union[SystemApprovalDecision, UserApprovalDecision] class RunMetrics(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) challenger: List[Metric] """ Metrics about how the model version trained in this run (the challenger) performed on this run's test set. @@ -406,6 +471,9 @@ class Parameter(BaseModel): A hyperparameter value. The values themselves are represented as strings. """ + model_config = ConfigDict( + extra="forbid", + ) name: str value: str @@ -415,6 +483,9 @@ class LogEvent(BaseModel): An event logged by some component of a model run, as well as metadata about the log event. """ + model_config = ConfigDict( + extra="forbid", + ) type: Literal["logEntry"] timestamp: float """ @@ -431,7 +502,9 @@ class LogEvent(BaseModel): class ImageSegmentationPredictionRequest(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) predictionType: Literal["imgSeg"] """ The type of prediction requested. This must be the same as the problem type in your model config. @@ -443,7 +516,9 @@ class ImageSegmentationPredictionRequest(BaseModel): class ImageClassificationPredictionRequest(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) predictionType: Literal["imgClf"] """ The type of prediction requested. This must be the same as the problem type in your model config. @@ -454,14 +529,23 @@ class ImageClassificationPredictionRequest(BaseModel): """ -class PredictionRequest(BaseModel): - __root__: Union[ +class PredictionRequest( + RootModel[ + Union[ + ImageSegmentationPredictionRequest, + ImageClassificationPredictionRequest, + ] + ] +): + root: Union[ ImageSegmentationPredictionRequest, ImageClassificationPredictionRequest ] class ImageClassificationPrediction(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) index: int """ The index of a classification label. @@ -477,7 +561,9 @@ class ImageClassificationPrediction(BaseModel): class ImageClassificationPredictionResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) predictionType: Literal["imgClf"] predictions: List[ImageClassificationPrediction] """ @@ -485,27 +571,35 @@ class ImageClassificationPredictionResponse(BaseModel): """ -class PredictionResponse(BaseModel): - __root__: ImageClassificationPredictionResponse +class PredictionResponse(RootModel[ImageClassificationPredictionResponse]): + root: ImageClassificationPredictionResponse class CreateModelResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) model: ModelConfig class GetModelsResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) models: List[ModelConfig] class UpdateModelResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) model: ModelConfig class DeleteModelResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) id: str """ The id of the model that was deleted. @@ -513,12 +607,16 @@ class DeleteModelResponse(BaseModel): class GetModelResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) model: Optional[ModelConfig] = None class CreateRunResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) runId: str """ The id of the newly created run. Can be used to fetch data about the run. @@ -526,7 +624,9 @@ class CreateRunResponse(BaseModel): class GetModelArtifactResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) url: str @@ -546,7 +646,9 @@ class GetModelLogsParams(BaseModel): class GetModelLogsResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) events: List[LogEvent] marker: Optional[str] = None """ @@ -555,12 +657,16 @@ class GetModelLogsResponse(BaseModel): class CreateApprovalDecisionResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) approvalDecision: UserApprovalDecision class DeleteDatasetResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) id: str """ The id of the dataset that was deleted. @@ -580,7 +686,9 @@ class GetDatasetExamplesParams(BaseModel): class GetDatasetExamplesResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) examples: List[Example] marker: Optional[str] = None """ @@ -594,17 +702,23 @@ class GetDatasetExampleParams(BaseModel): class GetDatasetExampleResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) example: Optional[Example] = None class GetDatasetLabelFileResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) labelData: Optional[LabelFileData] = None class PutDatasetLabelFileResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) fileId: str """ The id of the file-service file the label file was saved to. @@ -612,7 +726,9 @@ class PutDatasetLabelFileResponse(BaseModel): class ImageSegmentationProblemBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) problemType: Literal["imgSeg"] trainingDataFilter: FhirCodesFilter """ @@ -633,7 +749,9 @@ class ImageSegmentationProblem( class ImageClassificationProblemBase(BaseModel): - + model_config = ConfigDict( + extra="allow", + ) problemType: Literal["imgClf"] trainingDataFilter: FhirCodesFilter """ @@ -653,14 +771,18 @@ class ImageClassificationProblem( pass -class MlProblemDefinitionInput(BaseModel): - __root__: Union[ - ImageSegmentationProblemInput, ImageClassificationProblemInput +class MlProblemDefinitionInput( + RootModel[ + Union[ImageSegmentationProblemInput, ImageClassificationProblemInput] ] +): + root: Union[ImageSegmentationProblemInput, ImageClassificationProblemInput] -class MlProblemDefinition(BaseModel): - __root__: Union[ImageSegmentationProblem, ImageClassificationProblem] +class MlProblemDefinition( + RootModel[Union[ImageSegmentationProblem, ImageClassificationProblem]] +): + root: Union[ImageSegmentationProblem, ImageClassificationProblem] class DatasetConfigInput(DatasetConfigBase): @@ -677,7 +799,9 @@ class DatasetConfig(DatasetConfigBase): class ModelRun(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) id: str """ UUID uniquely identifying this model run. @@ -736,32 +860,44 @@ class ModelRun(BaseModel): class GetRunsResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) runs: List[ModelRun] class GetRunResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) run: Optional[ModelRun] = None class CreateDatasetResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) dataset: DatasetConfig class GetDatasetsResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) datasets: List[DatasetConfig] class UpdateDatasetResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) dataset: DatasetConfig class GetDatasetResponse(BaseModel): - + model_config = ConfigDict( + extra="forbid", + ) dataset: Optional[DatasetConfig] = None diff --git a/phc/util/patient_filter_query_builder.py b/phc/util/patient_filter_query_builder.py index c232d2d9..5cfe9b67 100644 --- a/phc/util/patient_filter_query_builder.py +++ b/phc/util/patient_filter_query_builder.py @@ -1,6 +1,7 @@ """ Query builder class to make subject search queries. """ + from abc import abstractmethod @@ -39,9 +40,9 @@ def __global_handler(self, *args, **kwargs): for value in values: components.append({"operator": operator, "value": value}) - self.component_body[ - self.__global_handler.__func__.func_name - ] = components + self.component_body[self.__global_handler.__func__.func_name] = ( + components + ) return self def to_dict(self): @@ -102,9 +103,9 @@ def to_dict(self): component_values.append(value.to_dict()) component_body_dict["components"] = component_values else: - component_body_dict[ - "components" - ] = value_or_values.to_dict() + component_body_dict["components"] = ( + value_or_values.to_dict() + ) else: component_body_dict[key] = value_or_values return component_body_dict diff --git a/poetry.lock b/poetry.lock index 223422ed..0d9bfa48 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,114 +1,99 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.5 and should not be changed by hand. 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"d1a3bd1b6dc4b9a9d27f49e4ffa744ccf3b7ff63b5b7db958efc7fc4768b316c" diff --git a/poetry.toml b/poetry.toml new file mode 100644 index 00000000..5fcef8cd --- /dev/null +++ b/poetry.toml @@ -0,0 +1,3 @@ +[virtualenvs] +in-project = true +prefer-active-python = true diff --git a/pyproject.toml b/pyproject.toml index 3174aa7b..11f6a0e5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "phc" -version = "0.36.0" +version = "1.0.0" description = "Python SDK for the LifeOmic platform" authors = ["LifeOmic "] license = "MIT" @@ -16,14 +16,15 @@ classifiers = [ "Natural Language :: English", "Programming Language :: Python", "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Utilities", ] [tool.poetry.dependencies] -python = "^3.8" +python = "^3.9" aiohttp = ">3.5.3,<4.0.0" backoff = ">=1.10.0,<2.0.0" nest-asyncio = ">=1.5.6,<2.0.0" @@ -32,23 +33,24 @@ pandas = ">=1.3.5,<2.0.0" funcy = ">=2.0,<3.0.0" lenses = ">=1.1.0,<2.0.0" toolz = ">=0.12.0,<1.0.0" -pydantic = ">=1.10.2,<2.0.0" +pydantic = "^2.9.2" python-pmap = ">=2.0.0,<3.0.0" fastparquet = ">=0.8.1,<1.0.0" +numpy = "<2.0.0" [tool.poetry.group.dev.dependencies] -pre-commit = "2.21.0" -black = "24.3.0" -flake8 = "5.0.4" -pdoc3 = "0.10.0" -twine = "4.0.2" -pytest = "7.4.0" -pytest-watch = "4.2.0" -click = "8.0.2" -boto3 = "1.26.158" -fire = "0.5.0" -typing-extensions = "4.6.3" -datamodel-code-generator = "0.21.1" +pre-commit = "^2.21.0" +black = "^24.3.0" +flake8 = "^5.0.4" +pdoc3 = "^0.10.0" +twine = "^4.0.2" +pytest = "^7.4.0" +pytest-watch = "^4.2.0" +click = "^8.0.2" +boto3 = "^1.26.158" +fire = "^0.5.0" +typing-extensions = "^4.12.2" +datamodel-code-generator = "^0.26.4" poethepoet = "^0.21.1" [build-system] diff --git a/service-schemas/patient-ml-service.json b/service-schemas/patient-ml-service.json index cec10f32..4feae904 100644 --- a/service-schemas/patient-ml-service.json +++ b/service-schemas/patient-ml-service.json @@ -3,7 +3,7 @@ "info": { "title": "Patient ML", "description": "Enables training, evaluating, and deploying Machine Learning models on your data stored in the LifeOmic Platform.", - "version": "234" + "version": "238" }, "components": { "schemas": { diff --git a/tests/test_option_genomic_expression.py b/tests/test_option_genomic_expression.py index 48f4762c..dd11e579 100644 --- a/tests/test_option_genomic_expression.py +++ b/tests/test_option_genomic_expression.py @@ -7,20 +7,20 @@ def test_genomic_expression_option(): result = GenomicExpressionOptions( variant_set_ids=variant_set_ids, expression="1-2" - ).dict() + ).model_dump() assert result.get("expression") == "1-2" result = GenomicExpressionOptions( variant_set_ids=variant_set_ids, expression=">= 1.2" - ).dict() + ).model_dump() assert result.get("expression") == "1.2:gte" result = GenomicExpressionOptions( variant_set_ids=variant_set_ids, expression="<=1.2" - ).dict() + ).model_dump() assert result.get("expression") == "1.2:lte" result = GenomicExpressionOptions( variant_set_ids=variant_set_ids, expression="1.2:lte" - ).dict() + ).model_dump() assert result.get("expression") == "1.2:lte" diff --git a/tests/test_option_genomic_short_variant.py b/tests/test_option_genomic_short_variant.py index 3d4d28b0..5bbd10da 100644 --- a/tests/test_option_genomic_short_variant.py +++ b/tests/test_option_genomic_short_variant.py @@ -29,7 +29,7 @@ def test_transforms_cosmic_min_count(): def test_min_allele_frequency_range(): result = GenomicShortVariantOptions( variant_set_ids=[str(uuid4())], min_allele_frequency="0.0002-0.1" - ).dict() + ).model_dump() assert result.get("minAlleleFrequency") == "0.0002-0.1"