diff --git a/.gitignore b/.gitignore index 7b6caf3..0edf355 100644 --- a/.gitignore +++ b/.gitignore @@ -160,3 +160,9 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. .idea/ + +# vscode +.vscode/ + +# tds-db +pg_data diff --git a/README.md b/README.md index 848a7ff..24d7c20 100644 --- a/README.md +++ b/README.md @@ -14,6 +14,8 @@ The `--build` argument forces the image to be rebuilt. Be sure to use it if you You can now interact with the API by querying `localhost:5000/{endpoint}` +For the OpenAPI browser interface, go to `localhost:5000/docs`. + ## Endpoints * /service-info diff --git a/docker-compose.yaml b/docker-compose.yaml index 4656fb9..415f4ba 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -3,10 +3,11 @@ services: tds: build: . + container_name: tds depends_on: - tds-db environment: - - DATABASE_URI=postgres://reference-db:5432 + - DATABASE_URI=postgres://tds_user:tds_password@tds-db:5432/tds_db - CORS_ORIGINS="*" - BENTO_AUTHZ_SERVICE_URL="" ports: @@ -14,6 +15,7 @@ services: tds-db: image: postgres:16 + container_name: tds-db volumes: - ./pg_data:/var/lib/postgresql/data environment: @@ -22,3 +24,10 @@ services: - POSTGRES_DB=tds_db expose: - 5432 + + adminer: + image: adminer:4.8.1 + container_name: adminer + restart: unless-stopped + ports: + - 8080:8080 diff --git a/poetry.lock b/poetry.lock index 2a8bb59..2ea6d4c 100644 --- 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.logger import LoggerDependency +from .models import GeneExpression + + +SCHEMA_PATH = Path(__file__).parent / "sql" / "schema.sql" + + +class Database(PgAsyncDatabase): + def __init__(self, config: Config, logger: logging.Logger): + self._config = config + self.logger = logger + super().__init__(config.database_uri, SCHEMA_PATH) + + async def insert_gene_expression(self, expression: GeneExpression): + query = """ + INSERT INTO gene_expressions (gene_code, sample_id, experiment_result_id, raw_count, tpm_count, tmm_count) + VALUES ($1, $2, $3, $4, $5, $6) + """ + await self.execute( + query, + expression.gene_code, + expression.sample_id, + expression.experiment_result_id, + expression.raw_count, + expression.tpm_count, + expression.tmm_count, + ) + + async def fetch_expressions(self): + conn: asyncpg.Connection + query = "SELECT * FROM gene_expressions" + async with self.connect() as conn: + res = await conn.fetch(query) + return res + + @asynccontextmanager + async def transaction(self): + conn = await self.get_connection() + trx = await conn.transaction() + try: + yield + await trx.commit() + except Exception as e: + await trx.rollback() + raise e + + +@lru_cache() +def get_db(config: ConfigDependency, logger: LoggerDependency) -> Database: + return Database(config, logger) + + +DatabaseDependency = Annotated[Database, Depends(get_db)] diff --git a/transcriptomics_data_service/main.py b/transcriptomics_data_service/main.py index cf149fc..8f9d35d 100644 --- a/transcriptomics_data_service/main.py +++ b/transcriptomics_data_service/main.py @@ -1,4 +1,9 @@ +from contextlib import asynccontextmanager from bento_lib.apps.fastapi import BentoFastAPI +from fastapi import FastAPI + +from transcriptomics_data_service.db import get_db +from transcriptomics_data_service.routers.expressions import expression_router from . import __version__ from .config import get_config @@ -15,6 +20,16 @@ config_for_setup = get_config() logger_for_setup = get_logger(config_for_setup) + +@asynccontextmanager +async def lifespan(_app: FastAPI): + db = get_db(config_for_setup, logger_for_setup) + + await db.close() + + yield + + app = BentoFastAPI( authz_middleware=None, config=config_for_setup, @@ -22,4 +37,7 @@ bento_extra_service_info=BENTO_SERVICE_INFO, service_type=SERVICE_TYPE, version=__version__, + lifespan=lifespan, ) + +app.include_router(expression_router) diff --git a/transcriptomics_data_service/models.py b/transcriptomics_data_service/models.py new file mode 100644 index 0000000..3774b0a --- /dev/null +++ b/transcriptomics_data_service/models.py @@ -0,0 +1,21 @@ +from pydantic import BaseModel + +__all__ = [ + "ExperimentResult", + "GeneExpression", +] + + +class ExperimentResult(BaseModel): + experiment_result_id: str + assembly_id: str | None = None + assembly_name: str | None = None + + +class GeneExpression(BaseModel): + gene_code: str + sample_id: str + experiment_result_id: str + raw_count: int + tpm_count: float | None = None + tmm_count: float | None = None diff --git a/transcriptomics_data_service/routers/__init__.py b/transcriptomics_data_service/routers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/transcriptomics_data_service/routers/expressions.py b/transcriptomics_data_service/routers/expressions.py new file mode 100644 index 0000000..b2d5feb --- /dev/null +++ b/transcriptomics_data_service/routers/expressions.py @@ -0,0 +1,12 @@ +from fastapi import APIRouter, status + +from transcriptomics_data_service.db import DatabaseDependency + +__all__ = ["expression_router"] + +expression_router = APIRouter(prefix="/expressions") + + +@expression_router.get("", status_code=status.HTTP_200_OK) +async def expressions_list(db: DatabaseDependency): + return await db.fetch_expressions() diff --git a/transcriptomics_data_service/sql/schema.sql b/transcriptomics_data_service/sql/schema.sql new file mode 100644 index 0000000..120c0ac --- /dev/null +++ b/transcriptomics_data_service/sql/schema.sql @@ -0,0 +1,19 @@ +CREATE TABLE IF NOT EXISTS experiment_results ( + experiment_result_id VARCHAR(31) NOT NULL PRIMARY KEY, + assembly_id VARCHAR(63), + assembly_name VARCHAR(63) +); + +CREATE TABLE IF NOT EXISTS gene_expressions ( + gene_code VARCHAR(31) NOT NULL, + sample_id VARCHAR(31) NOT NULL, + experiment_result_id VARCHAR(31) NOT NULL REFERENCES experiment_results ON DELETE CASCADE, + raw_count INTEGER NOT NULL, + tpm_count FLOAT, + tmm_count FLOAT, + PRIMARY KEY (gene_code, sample_id, experiment_result_id) +); + +CREATE INDEX idx_gene_code ON gene_expressions(gene_code); +CREATE INDEX idx_sample_id ON gene_expressions(sample_id); +CREATE INDEX idx_experiment_result_id ON gene_expressions(experiment_result_id);