From 9b9d544ab3c141ba42c6f25ec7f524a2682a42e6 Mon Sep 17 00:00:00 2001 From: Amrit Krishnan Date: Sun, 8 Oct 2023 13:41:10 -0400 Subject: [PATCH] Remove hydra use query api (#491) --- cyclops/query/base.py | 55 +- cyclops/query/configs/config.yaml | 6 - cyclops/query/eicu.py | 15 - cyclops/query/gemini.py | 15 - cyclops/query/mimiciii.py | 15 - cyclops/query/mimiciv.py | 15 - cyclops/query/omop.py | 33 +- cyclops/query/orm.py | 50 +- poetry.lock | 2666 +++++++++++++------------ pyproject.toml | 1 - tests/cyclops/data/test_slicer.py | 7 +- tests/cyclops/query/test_base.py | 7 +- tests/cyclops/query/test_eicu.py | 7 +- tests/cyclops/query/test_interface.py | 7 +- tests/cyclops/query/test_mimiciv.py | 7 +- tests/cyclops/query/test_omop.py | 14 +- tests/cyclops/query/test_ops.py | 7 +- tests/cyclops/query/test_orm.py | 7 +- 18 files changed, 1527 insertions(+), 1407 deletions(-) delete mode 100644 cyclops/query/configs/config.yaml diff --git a/cyclops/query/base.py b/cyclops/query/base.py index 8aa685036..83dd0b9ae 100644 --- a/cyclops/query/base.py +++ b/cyclops/query/base.py @@ -1,25 +1,20 @@ """Base querier class.""" import logging -import os from functools import partial from typing import Any, Callable, Dict, List, Optional -import yaml -from hydra import compose, initialize -from omegaconf import OmegaConf from sqlalchemy import MetaData from sqlalchemy.sql.selectable import Subquery from cyclops.query import ops as qo from cyclops.query.interface import QueryInterface -from cyclops.query.orm import Database +from cyclops.query.orm import Database, DatasetQuerierConfig from cyclops.query.util import ( DBSchema, _to_subquery, get_attr_name, ) -from cyclops.utils.file import join as join_path from cyclops.utils.log import setup_logging @@ -81,9 +76,18 @@ class DatasetQuerier: Parameters ---------- - config_overrides - Override configuration parameters, specified as kwargs. - + database + Name of database. + user + Username for database. + password + Password for database. + dbms + Database management system. + host + Hostname of database. + port + Port of database. Notes ----- @@ -98,26 +102,21 @@ class DatasetQuerier: def __init__( self, - **config_overrides: Dict[str, Any], + database: str, + user: str, + password: str, + dbms: str = "postgresql", + host: str = "localhost", + port: int = 5432, ) -> None: - overrides = [] - if config_overrides: - config_file = join_path(os.path.dirname(__file__), "configs", "config.yaml") - with open(config_file, "r", encoding="utf-8") as file: - config_keys = list(yaml.safe_load(file).keys()) - for key, value in config_overrides.items(): - if key in config_keys: - overrides.append(f"{key}={value}") - else: - overrides.append(f"+{key}={value}") - with initialize( - version_base=None, - config_path="configs", - job_name="DatasetQuerier", - ): - config = compose(config_name="config", overrides=overrides) - LOGGER.debug(OmegaConf.to_yaml(config)) - + config = DatasetQuerierConfig( + database=database, + user=user, + password=password, + dbms=dbms, + host=host, + port=port, + ) self.db = Database(config) if not self.db.is_connected: LOGGER.error("Database is not connected, cannot run queries.") diff --git a/cyclops/query/configs/config.yaml b/cyclops/query/configs/config.yaml deleted file mode 100644 index ead013c95..000000000 --- a/cyclops/query/configs/config.yaml +++ /dev/null @@ -1,6 +0,0 @@ -dbms: "postgresql" -port: 5432 -host: "localhost" -database: "mimiciv-2.0" -user: "postgres" -password: "pwd" diff --git a/cyclops/query/eicu.py b/cyclops/query/eicu.py index a89c05e21..6db1cc2b3 100644 --- a/cyclops/query/eicu.py +++ b/cyclops/query/eicu.py @@ -5,7 +5,6 @@ """ import logging -from typing import Any, Dict from cyclops.query.base import DatasetQuerier from cyclops.utils.log import setup_logging @@ -18,17 +17,3 @@ class EICUQuerier(DatasetQuerier): """EICU dataset querier.""" - - def __init__(self, **config_overrides: Dict[str, Any]) -> None: - """Initialize. - - Parameters - ---------- - **config_overrides - Override configuration parameters, specified as kwargs. - - """ - overrides = {} - if config_overrides: - overrides = config_overrides - super().__init__(**overrides) diff --git a/cyclops/query/gemini.py b/cyclops/query/gemini.py index dfc8555b6..47e5632b4 100644 --- a/cyclops/query/gemini.py +++ b/cyclops/query/gemini.py @@ -1,7 +1,6 @@ """GEMINI query API.""" import logging -from typing import Any, Dict from sqlalchemy import select from sqlalchemy.sql.expression import union_all @@ -24,20 +23,6 @@ class GEMINIQuerier(DatasetQuerier): """GEMINI dataset querier.""" - def __init__(self, **config_overrides: Dict[str, Any]) -> None: - """Initialize. - - Parameters - ---------- - **config_overrides - Override configuration parameters, specified as kwargs. - - """ - overrides = {} - if config_overrides: - overrides = config_overrides - super().__init__(**overrides) - def ip_admin( self, ) -> QueryInterface: diff --git a/cyclops/query/mimiciii.py b/cyclops/query/mimiciii.py index bfd499dfd..4152468b9 100644 --- a/cyclops/query/mimiciii.py +++ b/cyclops/query/mimiciii.py @@ -5,7 +5,6 @@ """ import logging -from typing import Any, Dict import cyclops.query.ops as qo from cyclops.query.base import DatasetQuerier @@ -21,20 +20,6 @@ class MIMICIIIQuerier(DatasetQuerier): """MIMIC-III dataset querier.""" - def __init__(self, **config_overrides: Dict[str, Any]) -> None: - """Initialize. - - Parameters - ---------- - **config_overrides - Override configuration parameters, specified as kwargs. - - """ - overrides = {} - if config_overrides: - overrides = config_overrides - super().__init__(**overrides) - def diagnoses( self, ) -> QueryInterface: diff --git a/cyclops/query/mimiciv.py b/cyclops/query/mimiciv.py index d270da84a..4fa0293e6 100644 --- a/cyclops/query/mimiciv.py +++ b/cyclops/query/mimiciv.py @@ -5,7 +5,6 @@ """ import logging -from typing import Any, Dict from sqlalchemy import Integer, func, select @@ -24,20 +23,6 @@ class MIMICIVQuerier(DatasetQuerier): """MIMICIV dataset querier.""" - def __init__(self, **config_overrides: Dict[str, Any]) -> None: - """Initialize. - - Parameters - ---------- - **config_overrides - Override configuration parameters, specified as kwargs. - - """ - overrides = {} - if config_overrides: - overrides = config_overrides - super().__init__(**overrides) - def patients( self, ) -> QueryInterface: diff --git a/cyclops/query/omop.py b/cyclops/query/omop.py index 978706996..b3209ce8d 100644 --- a/cyclops/query/omop.py +++ b/cyclops/query/omop.py @@ -1,7 +1,7 @@ """OMOP query API.""" import logging -from typing import Any, Dict, List, Optional, Union +from typing import List, Optional, Union from sqlalchemy.sql.selectable import Subquery @@ -58,24 +58,23 @@ class OMOPQuerier(DatasetQuerier): def __init__( self, - schema_name: str, - **config_overrides: Dict[str, Any], + database: str, + user: str, + password: str, + dbms: str = "postgresql", + host: str = "localhost", + port: int = 5432, + schema_name: str = "omop", ) -> None: - """Initialize. - - Parameters - ---------- - schema_name - Name of database schema. - **config_overrides - Override configuration parameters, specified as kwargs. - - """ + super().__init__( + database=database, + user=user, + password=password, + dbms=dbms, + host=host, + port=port, + ) self.schema_name = schema_name - overrides = {} - if config_overrides: - overrides = config_overrides - super().__init__(**overrides) def map_concept_ids_to_name( self, diff --git a/cyclops/query/orm.py b/cyclops/query/orm.py index 9a19c853a..28ad26781 100644 --- a/cyclops/query/orm.py +++ b/cyclops/query/orm.py @@ -4,14 +4,15 @@ import logging import os import socket +from dataclasses import dataclass from typing import Dict, List, Literal, Optional, Union +from urllib.parse import quote_plus import dask.dataframe as dd import pandas as pd import pyarrow.csv as pv import pyarrow.parquet as pq from datasets import Dataset -from omegaconf import DictConfig from sqlalchemy import MetaData, create_engine, inspect from sqlalchemy.engine.base import Engine from sqlalchemy.orm import sessionmaker @@ -43,11 +44,40 @@ def _get_db_url( user: str, pwd: str, host: str, - port: str, + port: int, database: str, ) -> str: """Combine to make Database URL string.""" - return f"{dbms}://{user}:{pwd}@{host}:{port}/{database}" + return f"{dbms}://{user}:{quote_plus(pwd)}@{host}:{str(port)}/{database}" + + +@dataclass +class DatasetQuerierConfig: + """Configuration for the dataset querier. + + Attributes + ---------- + dbms + Database management system. + host + Hostname of database. + port + Port of database. + database + Name of database. + user + Username for database. + password + Password for database. + + """ + + database: str + user: str + password: str + dbms: str = "postgresql" + host: str = "localhost" + port: int = 5432 class Database: @@ -55,20 +85,20 @@ class Database: Attributes ---------- - config: argparse.Namespace - Configuration stored in object. - engine: sqlalchemy.engine.base.Engine + config + Configuration stored in a dataclass. + engine SQL extraction engine. - inspector: sqlalchemy.engine.reflection.Inspector + inspector Module for schema inspection. - session: sqlalchemy.orm.session.Session + session Session for ORM. - is_connected: bool + is_connected Whether the database is setup, connected and ready to run queries. """ - def __init__(self, config: DictConfig) -> None: + def __init__(self, config: DatasetQuerierConfig) -> None: """Instantiate. Parameters diff --git a/poetry.lock b/poetry.lock index 0069e8060..9c286b3a8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -399,17 +399,22 @@ tests = ["pytest"] [[package]] name = "arrow" -version = "1.2.3" +version = "1.3.0" description = "Better dates & times for Python" optional = false -python-versions = ">=3.6" +python-versions = ">=3.8" files = [ - {file = "arrow-1.2.3-py3-none-any.whl", hash = "sha256:5a49ab92e3b7b71d96cd6bfcc4df14efefc9dfa96ea19045815914a6ab6b1fe2"}, - {file = "arrow-1.2.3.tar.gz", hash = "sha256:3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1"}, + {file = "arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80"}, + {file = "arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85"}, ] [package.dependencies] python-dateutil = ">=2.7.0" +types-python-dateutil = ">=2.8.10" + +[package.extras] +doc = ["doc8", "sphinx (>=7.0.0)", "sphinx-autobuild", 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["category-encoders", "kaleido", "pillow", "plotly", "pybtex", "pydanti [metadata] lock-version = "2.0" python-versions = ">=3.9, <3.12" -content-hash = "f2196dd09e7b73ebc30f14411aaeaaad2810aeb45b43c02ab3adfc07589728f4" +content-hash = "688e2237cb83046f383cf5f56c058af20d36f0532b9c3472e5019237a6fe9182" diff --git a/pyproject.toml b/pyproject.toml index 5e2d29f93..9bc1f3452 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -42,7 +42,6 @@ pillow = { version = "^9.5.0", optional = true } [tool.poetry.group.query.dependencies] psycopg2 = "^2.9.5" -hydra-core = "^1.2.0" SQLAlchemy = "^1.4.32, <2.0" [tool.poetry.group.models.dependencies] diff --git a/tests/cyclops/data/test_slicer.py b/tests/cyclops/data/test_slicer.py index 35f6f7d3c..e9995e66a 100644 --- a/tests/cyclops/data/test_slicer.py +++ b/tests/cyclops/data/test_slicer.py @@ -24,7 +24,12 @@ from cyclops.query.omop import OMOPQuerier -SYNTHEA = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") +SYNTHEA = OMOPQuerier( + database="synthea_integration_test", + user="postgres", + password="pwd", + schema_name="cdm_synthea10", +) def visits_table() -> pd.DataFrame: diff --git a/tests/cyclops/query/test_base.py b/tests/cyclops/query/test_base.py index 888ff30dc..797b0c10a 100644 --- a/tests/cyclops/query/test_base.py +++ b/tests/cyclops/query/test_base.py @@ -8,7 +8,12 @@ @pytest.mark.integration_test() def test_dataset_querier(): """Test base querier methods using OMOPQuerier.""" - querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") + querier = OMOPQuerier( + database="synthea_integration_test", + schema_name="cdm_synthea10", + user="postgres", + password="pwd", + ) assert len(querier.list_tables()) == 69 assert len(querier.list_schemas()) == 4 assert len(querier.list_tables(schema_name="cdm_synthea10")) == 43 diff --git a/tests/cyclops/query/test_eicu.py b/tests/cyclops/query/test_eicu.py index f6154f76a..42c490e59 100644 --- a/tests/cyclops/query/test_eicu.py +++ b/tests/cyclops/query/test_eicu.py @@ -8,7 +8,12 @@ @pytest.mark.integration_test() def test_eicu_querier(): """Test EICUQuerier on eICU-CRD.""" - querier = EICUQuerier(database="eicu") + querier = EICUQuerier( + database="eicu", + user="postgres", + password="pwd", + ) + patients = querier.eicu_crd.patient().run(limit=10) assert len(patients) == 10 assert "age" in patients diff --git a/tests/cyclops/query/test_interface.py b/tests/cyclops/query/test_interface.py index 51bd5a671..3cca1d5a8 100644 --- a/tests/cyclops/query/test_interface.py +++ b/tests/cyclops/query/test_interface.py @@ -45,7 +45,12 @@ def test_query_interface( @pytest.mark.integration_test() def test_query_interface_integration(): """Test QueryInterface with OMOPQuerier.""" - synthea = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") + synthea = OMOPQuerier( + database="synthea_integration_test", + schema_name="cdm_synthea10", + user="postgres", + password="pwd", + ) visits = synthea.visit_occurrence() assert isinstance(visits, QueryInterface) visits_pd_df = visits.run() diff --git a/tests/cyclops/query/test_mimiciv.py b/tests/cyclops/query/test_mimiciv.py index 77422d85c..8b356849b 100644 --- a/tests/cyclops/query/test_mimiciv.py +++ b/tests/cyclops/query/test_mimiciv.py @@ -8,7 +8,12 @@ @pytest.mark.integration_test() def test_mimiciv_querier(): """Test MIMICQuerier on MIMICIV-2.0.""" - querier = MIMICIVQuerier() + querier = MIMICIVQuerier( + database="mimiciv-2.0", + user="postgres", + password="pwd", + ) + patients = querier.patients().run(limit=10) assert len(patients) == 10 assert "anchor_year_difference" in patients diff --git a/tests/cyclops/query/test_omop.py b/tests/cyclops/query/test_omop.py index f8d23e094..8995e37a5 100644 --- a/tests/cyclops/query/test_omop.py +++ b/tests/cyclops/query/test_omop.py @@ -9,7 +9,12 @@ @pytest.mark.integration_test() def test_omop_querier_synthea(): """Test OMOPQuerier on synthea data.""" - querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") + querier = OMOPQuerier( + database="synthea_integration_test", + schema_name="cdm_synthea10", + user="postgres", + password="pwd", + ) ops = qo.Sequential( qo.ConditionEquals("gender_source_value", "M"), qo.Rename({"race_source_value": "race"}), @@ -36,6 +41,11 @@ def test_omop_querier_synthea(): @pytest.mark.integration_test() def test_omop_querier_mimiciii(): """Test OMOPQuerier on MIMICIII data.""" - querier = OMOPQuerier("omop", database="mimiciii") + querier = OMOPQuerier( + database="mimiciii", + schema_name="omop", + user="postgres", + password="pwd", + ) visits = querier.visit_occurrence().run() assert len(visits) == 58976 diff --git a/tests/cyclops/query/test_ops.py b/tests/cyclops/query/test_ops.py index c6bc0f89b..8fa645a5f 100644 --- a/tests/cyclops/query/test_ops.py +++ b/tests/cyclops/query/test_ops.py @@ -50,7 +50,12 @@ from cyclops.query.util import process_column -QUERIER = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") +QUERIER = OMOPQuerier( + database="synthea_integration_test", + user="postgres", + password="pwd", + schema_name="cdm_synthea10", +) @pytest.fixture() diff --git a/tests/cyclops/query/test_orm.py b/tests/cyclops/query/test_orm.py index cc417da22..1b6691d59 100644 --- a/tests/cyclops/query/test_orm.py +++ b/tests/cyclops/query/test_orm.py @@ -11,7 +11,12 @@ @pytest.mark.integration_test() def test_omop_querier(): """Test ORM using OMOPQuerier.""" - querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test") + querier = OMOPQuerier( + database="synthea_integration_test", + schema_name="cdm_synthea10", + user="postgres", + password="pwd", + ) assert querier is not None db_ = querier.db visits_query = querier.visit_occurrence().query