From dc4896fa0e211c797166f3f48358b1203df6147a Mon Sep 17 00:00:00 2001 From: SanjeevLakhwani Date: Thu, 24 Oct 2024 13:01:08 -0400 Subject: [PATCH 1/5] implemented ingestion --- poetry.lock | 3060 ++++++++++------- pyproject.toml | 1 + .../routers/ingest.py | 79 +- 3 files changed, 1795 insertions(+), 1345 deletions(-) diff --git a/poetry.lock b/poetry.lock index 2ea6d4c..1ab9b69 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.4 and should not be changed by hand. 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"^3.10.0" -content-hash = "a20f6ca06f9aca9773f27d9e2aeac44bccace9bdbd6e6ba889863927198579d6" +content-hash = "8e83dc6e27e9165c440f48c6af4e0d78b39d5dd008d648182238e0705504cf65" diff --git a/pyproject.toml b/pyproject.toml index 5582d14..aadf71a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,6 +13,7 @@ bento-lib = {extras = ["fastapi"], version = "^11.11.2"} jsonschema = "^4.21.1" pydantic-settings = "^2.1.0" asyncpg = "^0.29.0" +pandas = "^2.2.3" [tool.poetry.group.dev.dependencies] aioresponses = "^0.7.6" diff --git a/transcriptomics_data_service/routers/ingest.py b/transcriptomics_data_service/routers/ingest.py index bd2b751..c2274b5 100644 --- a/transcriptomics_data_service/routers/ingest.py +++ b/transcriptomics_data_service/routers/ingest.py @@ -1,7 +1,7 @@ -from fastapi import APIRouter, File, UploadFile, status -import csv +from fastapi import APIRouter, File, HTTPException, Request, UploadFile, status import json from io import StringIO +import pandas as pd from transcriptomics_data_service.db import DatabaseDependency from transcriptomics_data_service.models import ExperimentResult, GeneExpression @@ -26,29 +26,72 @@ async def ingest( ): # Read and process rcm file file_bytes = rcm_file.file.read() - buffer = StringIO(file_bytes.decode("utf-8")) - rcm = {} - for row in csv.DictReader(buffer): - print(row) - rcm[row[GENE_ID_KEY]] = row - # rcm["WASH6P"] would return something like: - # {'GeneID': 'WASH6P', '': '63', ': '0', ...} - # TODO read counts as integers - - experiment_result = ExperimentResult( - experiment_result_id=experiment_result_id, assembly_name=assembly_name, assembly_id=assembly_id - ) - + rcm_df = _load_csv(file_bytes) # Perform the ingestion in a transaction async with db.transaction_connection() as transaction_con: # For each matrix: create ONE row in ExperimentResult + experiment_result = ExperimentResult( + experiment_result_id=experiment_result_id, assembly_name=assembly_name, assembly_id=assembly_id + ) await db.create_experiment_result(experiment_result, transaction_con) - # TODO For EACH cell in the matrix: create one row in GeneExpression - # gene_expressions: list[GeneExpression] - # await db.create_gene_expressions(gene_expressions, transaction_con) + gene_expressions: list[GeneExpression] = [] + for gene_code, row in rcm_df.iterrows(): + + for sample_id, raw_count in row.items(): + gene_expression = GeneExpression( + gene_code=gene_code, + sample_id=sample_id, + experiment_result_id=experiment_result_id, + raw_count=raw_count + ) + gene_expressions.append(gene_expression) + await db.create_gene_expressions(gene_expressions, transaction_con) return +def _load_csv(file_bytes: bytes) -> pd.DataFrame: + buffer = StringIO(file_bytes.decode("utf-8")) + buffer.seek(0) + try: + df = pd.read_csv(buffer, index_col=0, header=0) + + # Check for duplicate values in index column or header + if df.index.duplicated().any(): + raise HTTPException( + status_code=status.HTTP_400_BAD_REQUEST, + detail="Duplicate values found in the Gene ID column." + ) + if df.columns.duplicated().any(): + raise HTTPException( + status_code=status.HTTP_400_BAD_REQUEST, + detail="Duplicate values found in the Sample ID row." + ) + + try: + df = df.applymap(lambda x: int(x) if pd.notna(x) else x) + except ValueError as e: + raise HTTPException( + status_code=status.HTTP_400_BAD_REQUEST, + detail=f"Data type error: Non-integer value found: {e}", + ) + + return df + except pd.errors.ParserError as e: + raise HTTPException( + status_code=status.HTTP_400_BAD_REQUEST, + detail=f"CSV parsing error: {e}", + ) + except ValueError as e: + raise HTTPException( + status_code=status.HTTP_400_BAD_REQUEST, + detail=f"Data type error in CSV: {e}", + ) + except Exception as e: + raise HTTPException( + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, + detail=f"Unexpected error while reading CSV: {e}", + ) + @ingest_router.post("/normalize/{experiment_result_id}") async def normalize( From 805ae24b339f42d75c28f4e7e0dcaeaa0afe8953 Mon Sep 17 00:00:00 2001 From: SanjeevLakhwani Date: Thu, 24 Oct 2024 13:07:40 -0400 Subject: [PATCH 2/5] reformated ingest. --- transcriptomics_data_service/routers/ingest.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/transcriptomics_data_service/routers/ingest.py b/transcriptomics_data_service/routers/ingest.py index c2274b5..63b02bd 100644 --- a/transcriptomics_data_service/routers/ingest.py +++ b/transcriptomics_data_service/routers/ingest.py @@ -43,12 +43,13 @@ async def ingest( gene_code=gene_code, sample_id=sample_id, experiment_result_id=experiment_result_id, - raw_count=raw_count + raw_count=raw_count, ) gene_expressions.append(gene_expression) await db.create_gene_expressions(gene_expressions, transaction_con) return + def _load_csv(file_bytes: bytes) -> pd.DataFrame: buffer = StringIO(file_bytes.decode("utf-8")) buffer.seek(0) @@ -58,13 +59,11 @@ def _load_csv(file_bytes: bytes) -> pd.DataFrame: # Check for duplicate values in index column or header if df.index.duplicated().any(): raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, - detail="Duplicate values found in the Gene ID column." + status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate values found in the Gene ID column." ) if df.columns.duplicated().any(): raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, - detail="Duplicate values found in the Sample ID row." + status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate values found in the Sample ID row." ) try: From 3aae9440182af15e635c83dd0038776e80f0110d Mon Sep 17 00:00:00 2001 From: SanjeevLakhwani Date: Fri, 1 Nov 2024 11:01:26 -0400 Subject: [PATCH 3/5] Code style and comment improvements. --- .../routers/ingest.py | 62 ++++++++----------- 1 file changed, 25 insertions(+), 37 deletions(-) diff --git a/transcriptomics_data_service/routers/ingest.py b/transcriptomics_data_service/routers/ingest.py index 63b02bd..802b786 100644 --- a/transcriptomics_data_service/routers/ingest.py +++ b/transcriptomics_data_service/routers/ingest.py @@ -24,30 +24,31 @@ async def ingest( assembly_id: str, rcm_file: UploadFile = File(...), ): - # Read and process rcm file + # Reading and converting uploaded RCM file to DataFrame file_bytes = rcm_file.file.read() rcm_df = _load_csv(file_bytes) - # Perform the ingestion in a transaction + + # Handling ingestion as a transactional operation async with db.transaction_connection() as transaction_con: - # For each matrix: create ONE row in ExperimentResult experiment_result = ExperimentResult( experiment_result_id=experiment_result_id, assembly_name=assembly_name, assembly_id=assembly_id ) await db.create_experiment_result(experiment_result, transaction_con) - gene_expressions: list[GeneExpression] = [] - for gene_code, row in rcm_df.iterrows(): - - for sample_id, raw_count in row.items(): - gene_expression = GeneExpression( - gene_code=gene_code, - sample_id=sample_id, - experiment_result_id=experiment_result_id, - raw_count=raw_count, - ) - gene_expressions.append(gene_expression) + gene_expressions: list[GeneExpression] = [ + GeneExpression( + gene_code=gene_code, + sample_id=sample_id, + experiment_result_id=experiment_result_id, + raw_count=raw_count, + ) + for gene_code, row in rcm_df.iterrows() + for sample_id, raw_count in row.items() + ] + await db.create_gene_expressions(gene_expressions, transaction_con) - return + + return {"message": "Ingestion completed successfully"} def _load_csv(file_bytes: bytes) -> pd.DataFrame: @@ -56,39 +57,26 @@ def _load_csv(file_bytes: bytes) -> pd.DataFrame: try: df = pd.read_csv(buffer, index_col=0, header=0) - # Check for duplicate values in index column or header + # Validating for unique Gene and Sample IDs if df.index.duplicated().any(): - raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate values found in the Gene ID column." - ) + raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate Gene IDs detected.") if df.columns.duplicated().any(): - raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate values found in the Sample ID row." - ) + raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate Sample IDs detected.") + # Ensuring raw count values are integers, otherwise flagging an error try: - df = df.applymap(lambda x: int(x) if pd.notna(x) else x) + df = df.applymap(lambda x: int(x) if pd.notna(x) else None) except ValueError as e: - raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, - detail=f"Data type error: Non-integer value found: {e}", - ) + raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Invalid non-integer value found: {e}") return df except pd.errors.ParserError as e: - raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, - detail=f"CSV parsing error: {e}", - ) + raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Error parsing CSV: {e}") except ValueError as e: - raise HTTPException( - status_code=status.HTTP_400_BAD_REQUEST, - detail=f"Data type error in CSV: {e}", - ) + raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Value error in CSV data: {e}") except Exception as e: raise HTTPException( - status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, - detail=f"Unexpected error while reading CSV: {e}", + status_code=status.HTTP_500_INTERNAL_SERVER_ERROR, detail=f"Unexpected error while reading CSV: {e}" ) From ebcb8de07d320374d0c06470c970ce737c915e26 Mon Sep 17 00:00:00 2001 From: SanjeevLakhwani Date: Fri, 1 Nov 2024 11:07:04 -0400 Subject: [PATCH 4/5] Added informative comment --- transcriptomics_data_service/routers/ingest.py | 1 + 1 file changed, 1 insertion(+) diff --git a/transcriptomics_data_service/routers/ingest.py b/transcriptomics_data_service/routers/ingest.py index 802b786..ef0ea07 100644 --- a/transcriptomics_data_service/routers/ingest.py +++ b/transcriptomics_data_service/routers/ingest.py @@ -67,6 +67,7 @@ def _load_csv(file_bytes: bytes) -> pd.DataFrame: try: df = df.applymap(lambda x: int(x) if pd.notna(x) else None) except ValueError as e: + # HTTPException is terminal, it cannot get caught by any other try/catch block raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Invalid non-integer value found: {e}") return df From 5793eec7b980c82ab3c5590ebfec258676f5e1e3 Mon Sep 17 00:00:00 2001 From: SanjeevLakhwani Date: Fri, 1 Nov 2024 11:24:53 -0400 Subject: [PATCH 5/5] Corrected error handling --- transcriptomics_data_service/routers/ingest.py | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/transcriptomics_data_service/routers/ingest.py b/transcriptomics_data_service/routers/ingest.py index ef0ea07..0211f8f 100644 --- a/transcriptomics_data_service/routers/ingest.py +++ b/transcriptomics_data_service/routers/ingest.py @@ -63,14 +63,10 @@ def _load_csv(file_bytes: bytes) -> pd.DataFrame: if df.columns.duplicated().any(): raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="Duplicate Sample IDs detected.") - # Ensuring raw count values are integers, otherwise flagging an error - try: - df = df.applymap(lambda x: int(x) if pd.notna(x) else None) - except ValueError as e: - # HTTPException is terminal, it cannot get caught by any other try/catch block - raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Invalid non-integer value found: {e}") - + # Ensuring raw count values are integers + df = df.applymap(lambda x: int(x) if pd.notna(x) else None) return df + except pd.errors.ParserError as e: raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=f"Error parsing CSV: {e}") except ValueError as e: