diff --git a/Dockerfile b/Dockerfile index 8253cef..92a16b0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -27,12 +27,19 @@ COPY app/ ./app/ # Copy built frontend from GitHub Actions build COPY ui/dist ./ui/dist -# Expose port -EXPOSE 8000 +# Create startup script that properly handles runtime PORT variable +RUN echo '#!/bin/sh\n\ +PORT="${PORT:-8080}"\n\ +echo "Starting server on port $PORT"\n\ +exec /app/.venv/bin/uvicorn app.main:app --host 0.0.0.0 --port "$PORT"' > /app/start.sh && \ + chmod +x /app/start.sh + +# Expose port 8080 (Cloud Run default) +EXPOSE 8080 # Health check HEALTHCHECK --interval=30s --timeout=30s --start-period=5s --retries=3 \ - CMD curl -f http://localhost:8000/ || exit 1 + CMD curl -f http://localhost:${PORT:-8080}/ || exit 1 # Run the application -CMD ["/app/.venv/bin/uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"] +CMD ["/app/start.sh"] diff --git a/app/config.py b/app/config.py index 583ab31..3fd8866 100644 --- a/app/config.py +++ b/app/config.py @@ -12,18 +12,29 @@ class DevelopmentConfig(BaseConfig): CORS_ORIGINS = [ "http://localhost:3000", "http://localhost:5173", # Vite dev server + "http://localhost:5174", # Vite dev server "http://127.0.0.1:5173", # Vite dev server alternative + "http://127.0.0.1:5174", # Vite dev server alternative "http://localhost:4173", # Vite preview server "http://127.0.0.1:4173", # Vite preview server alternative + "http://localhost:8080", # Docker local + "http://localhost:8000", # Alternative local ] class ProductionConfig(BaseConfig): DEBUG = False - CORS_ORIGINS = [""] + # For Cloud Run, you need to add your actual domain + CORS_ORIGINS = ( + os.getenv("CORS_ORIGINS", "").split(",") if os.getenv("CORS_ORIGINS") else ["*"] + ) def get_config(): + # Check for DEBUG env var first, then APP_ENV + if os.getenv("DEBUG", "").lower() == "true": + return DevelopmentConfig + env = os.getenv("APP_ENV", "development") if env == "production": return ProductionConfig diff --git a/app/controllers/hello.py b/app/controllers/hello.py deleted file mode 100644 index e69de29..0000000 diff --git a/app/main.py b/app/main.py index a9751f6..62fb1a8 100644 --- a/app/main.py +++ b/app/main.py @@ -6,8 +6,6 @@ from starlette.exceptions import HTTPException as StarletteHTTPException from starlette.responses import JSONResponse from app.config import get_config -from app.routers.pathways import router as pathways_router -from app.routers.umap_router import router from app.routers import gsea from app.scripts.prepare_gene_lists import generate_all_library_gene_lists @@ -45,8 +43,6 @@ # Include routers app.include_router(gsea.router, prefix="/api", tags=["GSEA"]) -app.include_router(pathways_router) -app.include_router(router, prefix="/umap") # Mount static files for the React app diff --git a/app/models/__init__.py b/app/models/__init__.py index e69de29..4df7914 100644 --- a/app/models/__init__.py +++ b/app/models/__init__.py @@ -0,0 +1,3 @@ +from app.models.gsea import Gene, GseaJsonRequest + +__all__ = ["Gene", "GseaJsonRequest"] diff --git a/app/models/gsea.py b/app/models/gsea.py new file mode 100644 index 0000000..e8ec94c --- /dev/null +++ b/app/models/gsea.py @@ -0,0 +1,24 @@ +from pydantic import BaseModel, Field, field_validator +from typing import List + + +class Gene(BaseModel): + """Individual gene with symbol and score.""" + + symbol: str = Field(..., description="Gene symbol (e.g., 'BRCA1', 'TP53')") + globalScore: float = Field(..., description="Gene score for ranking") + + +class GseaJsonRequest(BaseModel): + """Request model for JSON-based GSEA endpoint.""" + + genes: List[Gene] = Field( + ..., min_length=1, description="List of genes with symbols and scores" + ) + + @field_validator("genes") + @classmethod + def validate_genes_not_empty(cls, v): + if not v or len(v) == 0: + raise ValueError("Genes list cannot be empty") + return v diff --git a/app/routers/__init__.py b/app/routers/__init__.py index e69de29..3c10ace 100644 --- a/app/routers/__init__.py +++ b/app/routers/__init__.py @@ -0,0 +1,5 @@ +"""API routers for the Pathways API.""" + +from app.routers import gsea + +__all__ = ["gsea"] diff --git a/app/routers/gsea.py b/app/routers/gsea.py index 8c73437..611ae4e 100644 --- a/app/routers/gsea.py +++ b/app/routers/gsea.py @@ -1,6 +1,8 @@ from fastapi import APIRouter, UploadFile, File, Query, HTTPException from typing import Literal -from app.services.gsea import run_gsea, available_gmt_files +from app.services.gsea import run_gsea_from_dataframe, available_gmt_files +from app.models.gsea import GseaJsonRequest +from app.utils.gsea_utils import validate_gsea_dataframe, handle_gsea_error import tempfile import pandas as pd import os @@ -8,46 +10,119 @@ router = APIRouter() + @router.get("/gsea/libraries") async def list_gmt_files(): """List available GMT libraries.""" return list(available_gmt_files().keys()) -@router.post("/gsea") -async def gsea_endpoint( - tsv_file: UploadFile = File(..., description="TSV file containing at least 2 columns: 'symbol' and 'globalScore'"), +@router.post("/gsea/analyze/file") +async def analyze_gsea_from_file( + tsv_file: UploadFile = File( + ..., + description="TSV file containing at least 2 columns: 'symbol' and 'globalScore'", + ), gmt_name: str = Query(..., description="GMT library name (without .gmt extension)"), analysis_direction: Literal["one_sided_positive", "one_sided_negative", "two_sided"] = Query( default="one_sided_positive", description="Analysis direction: 'one_sided_positive' filters NES > 0, 'one_sided_negative' filters NES < 0, 'two_sided' returns all results" - ) + ), ): + """ + Run GSEA analysis from uploaded TSV file. + + Upload a TSV file with gene symbols and scores to perform Gene Set Enrichment Analysis. + + Example: + POST /api/gsea/analyze/file?gmt_name=Reactome/ReactomePathways_2025 + Content-Type: multipart/form-data + Body: file=your_data.tsv + """ # Validate file extension if not tsv_file.filename.endswith(".tsv"): raise HTTPException(status_code=400, detail="File must be .tsv format") - # Save to temp file + # Read and validate file with tempfile.NamedTemporaryFile(delete=False, suffix=".tsv") as tmp: content = await tsv_file.read() tmp.write(content) tsv_path = tmp.name - # Validate TSV structure try: - df = pd.read_csv(tsv_path, sep="\t", nrows=1) # read first row - if not {"symbol", "globalScore"}.issubset(df.columns) and not {0, 1}.issubset(df.columns): - raise ValueError("TSV must contain 'symbol' and 'globalScore' columns (or two unnamed columns).") - except Exception as e: - os.unlink(tsv_path) - raise HTTPException(status_code=400, detail=f"Invalid TSV format: {str(e)}") + # Load and validate DataFrame + df = pd.read_csv(tsv_path, sep="\t") + df = validate_gsea_dataframe(df) - # Run GSEA - try: - res_df, missing_stats = run_gsea(input_tsv=tsv_path, gmt_name=gmt_name) + # Run GSEA + res_df, input_overlap = run_gsea_from_dataframe(df, gmt_name) + + except HTTPException: + raise + except Exception as e: + raise handle_gsea_error(e) finally: # Clean up temp file - os.unlink(tsv_path) + if os.path.exists(tsv_path): + os.unlink(tsv_path) + + # Filter by NES based on analysis direction + if analysis_direction == "one_sided_positive": + res_df = res_df[res_df["NES"] > 0].copy() + elif analysis_direction == "one_sided_negative": + res_df = res_df[res_df["NES"] < 0].copy() + + # Replace NaN/Inf with JSON-safe values + res_df = res_df.replace([np.inf, -np.inf], None) + res_df = res_df.where(pd.notna(res_df), None) + + return { + "results": res_df.to_dict(orient="records"), + "input_overlap": input_overlap, + } + + +@router.post("/gsea/analyze/json") +async def analyze_gsea_from_json( + request: GseaJsonRequest, + gmt_name: str = Query(..., description="GMT library name (without .gmt extension)"), + analysis_direction: Literal["one_sided_positive", "one_sided_negative", "two_sided"] = Query( + default="one_sided_positive", + description="Analysis direction: 'one_sided_positive' filters NES > 0, 'one_sided_negative' filters NES < 0, 'two_sided' returns all results" + ), +): + """ + Run GSEA analysis from JSON payload. + + Send gene data as JSON to perform Gene Set Enrichment Analysis. + + Example: + POST /api/gsea/analyze/json?gmt_name=Reactome/ReactomePathways_2025 + Content-Type: application/json + Body: { + "genes": [ + {"symbol": "BRCA1", "globalScore": 0.95}, + {"symbol": "TP53", "globalScore": 0.87} + ] + } + """ + try: + # Convert request to DataFrame + genes_data = [ + {"symbol": g.symbol, "globalScore": g.globalScore} for g in request.genes + ] + df = pd.DataFrame(genes_data) + + # Validate DataFrame (should already be valid via Pydantic, but double-check) + df = validate_gsea_dataframe(df) + + # Run GSEA directly (no file I/O needed!) + res_df, input_overlap = run_gsea_from_dataframe(df, gmt_name) + + except HTTPException: + raise + except Exception as e: + raise handle_gsea_error(e) # Filter by NES based on analysis direction if analysis_direction == "one_sided_positive": @@ -61,5 +136,5 @@ async def gsea_endpoint( return { "results": res_df.to_dict(orient="records"), - "input_overlap": missing_stats, + "input_overlap": input_overlap, } diff --git a/app/routers/pathways.py b/app/routers/pathways.py deleted file mode 100644 index f9d241c..0000000 --- a/app/routers/pathways.py +++ /dev/null @@ -1,53 +0,0 @@ -from typing import Any -from fastapi import APIRouter, HTTPException, UploadFile, File, Form -from pathlib import Path - -from app.services.gsea import available_gmt_files, run_gsea - -router = APIRouter(prefix="/pathways", tags=["pathways"]) - - -@router.get("/available", response_model=list[str]) -async def list_libraries(): - """ - Return available GMT libraries under data/gmt (subfolders). - Example: ["Reactome/reactome2022", "GO/go2022"] - """ - try: - return list(available_gmt_files().keys()) - except Exception as e: - raise HTTPException(status_code=500, detail=str(e)) - - -@router.post("/gsea", response_model=list[dict[str, Any]]) -async def run_gsea_endpoint( - gmt_name: str = Form(..., description="Library name, e.g. Reactome/reactome2022"), - processes: int = Form(4, description="Number of CPU processes"), - file: UploadFile = File(..., description="TSV file with 'symbol' and 'globalScore'") -): - """ - Run GSEA on an uploaded input file using a chosen GMT library. - """ - tmp_path = Path(f"/tmp/{file.filename}") - try: - # Save uploaded file to a temporary path - with tmp_path.open("wb") as f: - f.write(await file.read()) - - res_df, _missing_stats = run_gsea( - input_tsv=tmp_path, - gmt_name=gmt_name, - processes=processes, - ) - - # Return as JSON records - return res_df.to_dict(orient="records") - - except ValueError as e: - raise HTTPException(status_code=400, detail=str(e)) - except Exception as e: - raise HTTPException(status_code=500, detail=str(e)) - finally: - # Clean up temp file - if tmp_path.exists(): - tmp_path.unlink() diff --git a/app/routers/umap_router.py b/app/routers/umap_router.py deleted file mode 100644 index 160998a..0000000 --- a/app/routers/umap_router.py +++ /dev/null @@ -1,71 +0,0 @@ -import os -import pandas as pd -from fastapi import APIRouter, Query, HTTPException -from fastapi.responses import HTMLResponse -from app.services.umap_service import perform_umap_clustering_api - -router = APIRouter() - -@router.get("/run", response_class=HTMLResponse) -def run_umap( - disease_id: str = Query(..., description="The disease ID (e.g., 'EFO_0000094')"), - library: str = Query(..., description="The library name (e.g., 'open_targets')"), - n_neighbors: int = Query(10), - min_dist: float = Query(0.5), - min_cluster_size: int = Query(12), - umap_dimensions: int = Query(2) -): - try: - # Run UMAP & clustering - output_file = perform_umap_clustering_api( - disease_id=disease_id, - library=library, - n_neighbors=n_neighbors, - min_dist=min_dist, - min_cluster_size=min_cluster_size, - umap_dimensions=umap_dimensions - ) - - # Read TSV into a DataFrame - df = pd.read_csv(output_file, sep='\t') - - # Convert to HTML table (with some basic styling) - html = df.to_html(index=False, classes="table table-bordered table-striped") - - # Wrap in a basic HTML template - html_template = f""" - - - UMAP Clustering Results - - - -

UMAP Clustering Results for {disease_id}

- {html} - - - """ - return HTMLResponse(content=html_template) - - except Exception as e: - raise HTTPException(status_code=500, detail=str(e)) diff --git a/app/services/__init__.py b/app/services/__init__.py index e69de29..943a13f 100644 --- a/app/services/__init__.py +++ b/app/services/__init__.py @@ -0,0 +1,15 @@ +"""Service layer for the Pathways API.""" + +from app.services.gsea import ( + available_gmt_files, + run_gsea, + run_gsea_from_dataframe, + load_custom_gmt, +) + +__all__ = [ + "available_gmt_files", + "run_gsea", + "run_gsea_from_dataframe", + "load_custom_gmt", +] diff --git a/app/services/gsea.py b/app/services/gsea.py index 9ba2c9e..66e51b4 100644 --- a/app/services/gsea.py +++ b/app/services/gsea.py @@ -16,20 +16,21 @@ def get_approved_symbols_from_gcs(): """ # Initialize GCS filesystem fs = gcsfs.GCSFileSystem() - + # Define the GCS path to the target directory gcs_path = "open-targets-pre-data-releases/25.09/output/target/" - + # Read all parquet files in the directory as a single dataset # This is much more efficient than downloading individual files df = pd.read_parquet(gcs_path, filesystem=fs, columns=["approvedSymbol"]) - + # Extract unique approved symbols (excluding NaN values) approved_symbols = set(df["approvedSymbol"].dropna().astype(str)) - + return approved_symbols + def load_custom_gmt(path): p = Path(path) with p.open("r") as f: @@ -39,6 +40,7 @@ def load_custom_gmt(path): if (parts := line.strip().split("\t")) and len(parts) > MIN_GENE_COL_IDX } + def available_gmt_files(): """ Return available GMT libraries as: @@ -62,14 +64,24 @@ def available_gmt_files(): } return libraries -def run_gsea(input_tsv=None, gmt_name=None, processes=4): - """ - Run GSEA using a chosen GMT library and its hierarchy (if present). - Pathway size is computed from the GMT (total genes in the pathway). - Ensure 'Number of input genes' and 'Pathway size' are integers (no .0). + +def run_gsea_from_dataframe( + df: pd.DataFrame, gmt_name: str, processes: int = 4 +) -> tuple[pd.DataFrame, dict]: """ - input_tsv = Path(input_tsv) + Run GSEA using a DataFrame directly (no file required). + + Args: + df: DataFrame with 'symbol' and 'globalScore' columns, already validated + gmt_name: Name of GMT library to use + processes: Number of CPU processes + Returns: + Tuple of (DataFrame with GSEA results, overlap_stats dict) + + Raises: + ValueError: If gmt_name is invalid or DataFrame is missing required columns + """ gmt_files = available_gmt_files() if not gmt_name or gmt_name not in gmt_files: msg = "Invalid gmt_name. Choose from: " + str(list(gmt_files.keys())) @@ -107,16 +119,9 @@ def run_gsea(input_tsv=None, gmt_name=None, processes=4): # if no braces, map Term itself as ID id_to_genes[term] = genes - # --- Load input file safely --- - df = pd.read_csv(input_tsv, sep="\t") - - # Allow unnamed columns (0,1) and rename to expected headers - if set(df.columns) == set(range(len(df.columns))): - df = df.rename(columns={0: "symbol", 1: "globalScore"}) - + # Ensure DataFrame is properly formatted if not {"symbol", "globalScore"}.issubset(df.columns): - msg = "Input file must contain 'symbol' and 'globalScore' columns." - raise ValueError(msg) + raise ValueError("DataFrame must contain 'symbol' and 'globalScore' columns.") # Keep only required columns df = df[["symbol", "globalScore"]].copy() @@ -170,7 +175,9 @@ def run_gsea(input_tsv=None, gmt_name=None, processes=4): if contains_braces: term_series = res_df["Term"] res_df["ID"] = term_series.str.extract(r"\{([^}]+)\}", expand=False).fillna("") - res_df["Term"] = term_series.str.replace(r"\s*\{[^}]+\}", "", regex=True).str.strip() + res_df["Term"] = term_series.str.replace( + r"\s*\{[^}]+\}", "", regex=True + ).str.strip() else: res_df["ID"] = res_df["Term"] # use Term as ID directly @@ -261,3 +268,33 @@ def safe_int_col(df_, col_name): return res_df, overlap_stats + +def run_gsea(input_tsv=None, gmt_name=None, processes=4): + """ + Run GSEA from a TSV file path (backward compatible). + + Args: + input_tsv: Path to TSV file with 'symbol' and 'globalScore' columns + gmt_name: Name of GMT library to use + processes: Number of CPU processes + + Returns: + Tuple of (DataFrame with GSEA results, overlap_stats dict) + + Raises: + ValueError: If gmt_name is invalid or file is missing required columns + """ + if not input_tsv: + raise ValueError("input_tsv parameter is required") + + input_tsv = Path(input_tsv) + + # Load input file + df = pd.read_csv(input_tsv, sep="\t") + + # Handle unnamed columns (legacy support) + if set(df.columns) == set(range(len(df.columns))): + df = df.rename(columns={0: "symbol", 1: "globalScore"}) + + # Validate and run GSEA using the DataFrame-based function + return run_gsea_from_dataframe(df, gmt_name, processes) diff --git a/app/services/pathways_service.py b/app/services/pathways_service.py deleted file mode 100644 index dcc025e..0000000 --- a/app/services/pathways_service.py +++ /dev/null @@ -1,41 +0,0 @@ -from typing import Any, List, Optional - -from pyspark.sql import DataFrame, Row -from pyspark.sql.functions import col - -from app.utils.spark import get_spark_session - -BASE_PATH = "data/table_view" - -def fetch_pathways( - disease_id: str, - library: str, - fdr_lt: Optional[float] = None, - hide_leading_edge: bool = False, -) -> List[dict[str, Any]]: - """ - Load the parquet partition for `library`/`disease_id`, - apply optional filters, drop `diseaseId` and optional columns, - and return as list of dicts. - """ - spark = get_spark_session() - path = f"{BASE_PATH}/{library}/diseaseId={disease_id}" - - # Read the partition - df: DataFrame = spark.read.parquet(path) - - # --- ALWAYS DROP the partition column so it doesn't appear in output --- - if "diseaseId" in df.columns: - df = df.drop("diseaseId") - - # Optional filtering - if fdr_lt is not None: - df = df.filter(col("FDR") < fdr_lt) - - # Optional column drop - if hide_leading_edge and "Leading edge genes" in df.columns: - df = df.drop("Leading edge genes") - - # Collect and convert each Row to a native dict - rows: list[Row] = df.collect() - return [row.asDict(recursive=True) for row in rows] diff --git a/app/services/umap_service.py b/app/services/umap_service.py deleted file mode 100644 index 0256b64..0000000 --- a/app/services/umap_service.py +++ /dev/null @@ -1,102 +0,0 @@ -import os -import pandas as pd -import numpy as np -import umap -import hdbscan -from scipy.spatial.distance import pdist, squareform -from fastapi.responses import FileResponse # optional - - -def poincare_dist(u, v): - norm_u = np.linalg.norm(u) - norm_v = np.linalg.norm(v) - norm_diff = np.linalg.norm(u - v) - denom = (1 - norm_u ** 2) * (1 - norm_v ** 2) - if denom <= 0: - return float('inf') - argument = 1 + 2 * (norm_diff ** 2) / denom - argument = max(argument, 1.0) - return np.arccosh(argument) - - -def compute_poincare_distance_matrix(embedding_matrix): - return squareform(pdist(embedding_matrix, metric=poincare_dist)) - - -def perform_umap_clustering_api( - disease_id: str, - library: str, - n_neighbors: int = 10, - min_dist: float = 0.5, - min_cluster_size: int = 12, - umap_dimensions: int = 2, - base_data_dir: str = "data/umap_dynamic" -) -> str: - """ - Perform UMAP and HDBSCAN clustering on embeddings andmetadata for a given disease_id and library. - Returns path to the resulting TSV file. - """ - - # Ensure folder uses 'diseaseId=' prefix - folder_name = disease_id - if not disease_id.startswith("diseaseId="): - folder_name = f"diseaseId={disease_id}" - - # Updated paths include the library directory - coordinates_parquet_dir = os.path.join(base_data_dir, "target_embeddings", library, folder_name) - metadata_parquet_dir = os.path.join(base_data_dir, "target_metadata", library, folder_name) - output_dir = os.path.join(base_data_dir, "output", library, folder_name) - - # Load parquet datasets from directories - metadata = pd.read_parquet(metadata_parquet_dir).query("geneticScore.notnull()") - coords_df = pd.read_parquet(coordinates_parquet_dir) - - # Prepare coordinates - coords_df = coords_df.rename(columns={coords_df.columns[0]: 'approvedSymbol'}) - coord_columns = coords_df.columns[1:] - coords_df[coord_columns] = coords_df[coord_columns].astype(float) - - # Merge embeddings with metadata - merged_df = pd.merge(metadata, coords_df, on='approvedSymbol', how='inner') - - # Validate embedding norms (Poincaré ball condition) - embedding_matrix = merged_df[coord_columns].values - norms = np.linalg.norm(embedding_matrix, axis=1) - if np.any(norms >= 1): - raise ValueError("Some embeddings lie outside the Poincaré ball (norm >= 1).") - - # Compute Poincaré distances - distance_matrix = compute_poincare_distance_matrix(embedding_matrix) - - # UMAP dimensionality reduction - reducer = umap.UMAP( - n_neighbors=n_neighbors, - min_dist=min_dist, - n_components=umap_dimensions, - metric='precomputed', - random_state=42 - ) - embedding_umap = reducer.fit_transform(distance_matrix) - - # HDBSCAN clustering - clusterer = hdbscan.HDBSCAN( - min_cluster_size=min_cluster_size, - min_samples=1, - metric='precomputed' - ) - cluster_labels = clusterer.fit_predict(distance_matrix) - - # Append UMAP and cluster labels - for dim in range(umap_dimensions): - merged_df[f'UMAP {dim+1}'] = embedding_umap[:, dim] - merged_df['cluster'] = cluster_labels - - # Drop original embedding columns - output_df = merged_df.drop(columns=coord_columns) - - # Save result to TSV - os.makedirs(output_dir, exist_ok=True) - output_file = os.path.join(output_dir, f"{disease_id}_clusters.tsv") - output_df.to_csv(output_file, sep='\t', index=False) - - return output_file \ No newline at end of file diff --git a/app/utils/__init__.py b/app/utils/__init__.py index e69de29..1245e14 100644 --- a/app/utils/__init__.py +++ b/app/utils/__init__.py @@ -0,0 +1,5 @@ +"""Utility functions for the Pathways API.""" + +from app.utils.gsea_utils import validate_gsea_dataframe, handle_gsea_error + +__all__ = ["validate_gsea_dataframe", "handle_gsea_error"] diff --git a/app/utils/gsea_utils.py b/app/utils/gsea_utils.py new file mode 100644 index 0000000..0de35f4 --- /dev/null +++ b/app/utils/gsea_utils.py @@ -0,0 +1,67 @@ +from fastapi import HTTPException +import pandas as pd + + +def validate_gsea_dataframe(df: pd.DataFrame) -> pd.DataFrame: + """ + Validate and normalize a DataFrame for GSEA analysis. + + Args: + df: Input DataFrame to validate + + Returns: + Normalized DataFrame with 'symbol' and 'globalScore' columns, sorted by score + + Raises: + HTTPException: If validation fails + """ + # Handle unnamed columns (legacy support) + if set(df.columns) == set(range(len(df.columns))): + df = df.rename(columns={0: "symbol", 1: "globalScore"}) + + # Validate required columns + if not {"symbol", "globalScore"}.issubset(df.columns): + raise HTTPException( + status_code=400, + detail="Input must contain 'symbol' and 'globalScore' columns", + ) + + # Extract only required columns and sort + df = df[["symbol", "globalScore"]].copy() + df = df.sort_values("globalScore", ascending=False) + + return df + + +def handle_gsea_error(error: Exception) -> HTTPException: + """ + Convert GSEA analysis errors into user-friendly HTTP exceptions. + + Args: + error: The exception that occurred during GSEA analysis + + Returns: + HTTPException with appropriate status code and message + """ + error_str = str(error).lower() + + if isinstance(error, ValueError): + if any(keyword in error_str for keyword in ["nan", "solver cannot continue"]): + return HTTPException( + status_code=400, + detail=( + "GSEA analysis failed. This usually means the gene symbols in your input " + "don't match any pathways in the selected GMT library. Please verify that " + "your input contains valid gene symbols (e.g., 'BRCA1', 'TP53', 'EGFR') " + "rather than disease names or other identifiers." + ), + ) + else: + return HTTPException( + status_code=400, detail=f"GSEA analysis error: {str(error)}" + ) + else: + return HTTPException( + status_code=500, + detail=f"Unexpected error during GSEA analysis: {str(error)}", + ) diff --git a/app/utils/spark.py b/app/utils/spark.py deleted file mode 100644 index 8f27533..0000000 --- a/app/utils/spark.py +++ /dev/null @@ -1,15 +0,0 @@ -from pyspark.sql import SparkSession - -_spark = None - -def get_spark_session() -> SparkSession: - global _spark - if _spark is None: - _spark = ( - SparkSession - .builder - .appName("PathwaysAPI") - .config("spark.ui.showConsoleProgress", "false") - .getOrCreate() - ) - return _spark diff --git a/app/utils/xml_parser.py b/app/utils/xml_parser.py deleted file mode 100644 index a15b82e..0000000 --- a/app/utils/xml_parser.py +++ /dev/null @@ -1,11 +0,0 @@ -import xml.etree.ElementTree as ET - - -def xml_to_plain_text(xml_string): - try: - root = ET.fromstring(xml_string) - plain_text = "".join(root.itertext()) - return plain_text.strip() - except ET.ParseError as e: - print(f"Error al analizar el XML: {e}") - return None diff --git a/dev.sh b/dev.sh new file mode 100644 index 0000000..241c68c --- /dev/null +++ b/dev.sh @@ -0,0 +1,57 @@ +#!/bin/bash + +# Local development script for pathways-api + +echo "🚀 Starting Pathways API local development environment..." + +# Function to cleanup on exit +cleanup() { + echo "🛑 Stopping services..." + docker-compose down + exit +} + +# Set trap to cleanup on script exit +trap cleanup EXIT INT TERM + +# Check if running in Docker mode or local mode +if [ "$1" = "docker" ]; then + echo "📦 Running in Docker mode..." + + # Build and run with docker-compose + docker-compose build + docker-compose up -d + + echo "✅ API running at http://localhost:8080" + echo "📝 Logs: docker-compose logs -f pathways-api" + + # Wait for services + docker-compose logs -f + +elif [ "$1" = "local" ]; then + echo "💻 Running in local development mode..." + + # Start backend + echo "🔧 Starting backend..." + cd /Users/carlos_cruz/projects/ot/pathways-api + PORT=8080 uvicorn app.main:app --reload --host 0.0.0.0 --port 8080 & + BACKEND_PID=$! + + # Start frontend + echo "🎨 Starting frontend..." + cd ui + npm run dev & + FRONTEND_PID=$! + + echo "✅ Backend running at http://localhost:8080" + echo "✅ Frontend running at http://localhost:5173" + + # Wait for both processes + wait $BACKEND_PID $FRONTEND_PID + +else + echo "Usage: $0 [docker|local]" + echo " docker - Run everything in Docker" + echo " local - Run backend and frontend locally" + exit 1 +fi diff --git a/docker-compose.yml b/docker-compose.yml index f1ab0e1..7d6547c 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -6,16 +6,18 @@ services: context: . dockerfile: Dockerfile ports: - - "8000:8000" + - "8080:8080" environment: - - DEBUG=false - - CORS_ORIGINS=http://localhost:3000,http://localhost:8000 + - PORT=8080 + - DEBUG=true + - APP_ENV=development + - CORS_ORIGINS=http://localhost:3000,http://localhost:5173,http://127.0.0.1:5173,http://localhost:8080 volumes: # Mount data directory for development - ./app/data:/app/app/data:ro restart: unless-stopped healthcheck: - test: [ "CMD", "curl", "-f", "http://localhost:8000/" ] + test: [ "CMD", "curl", "-f", "http://localhost:8080/" ] interval: 30s timeout: 10s retries: 3 diff --git a/pyproject.toml b/pyproject.toml index c9477ff..c0e9357 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,19 +1,10 @@ [project] name = "pathways-api" version = "0.1.0" -description = "Pathways API for Open Targets - A comprehensive API for pathway analysis and visualization" -readme = "README.md" +description = "FastAPI service for pathway analysis (GSEA) for Open Targets" authors = [{ name = "Open Targets", email = "contact@opentargets.org" }] -license = { text = "Apache-2.0" } -keywords = ["pathways", "bioinformatics", "api", "open-targets", "gsea", "umap"] -classifiers = [ - "Development Status :: 4 - Beta", - "Intended Audience :: Science/Research", - "License :: OSI Approved :: Apache Software License", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.12", - "Topic :: Scientific/Engineering :: Bio-Informatics", -] +readme = "README.md" + requires-python = ">=3.12" dependencies = [ @@ -24,34 +15,11 @@ dependencies = [ "uvicorn>=0.32.0", "blitzgsea>=1.3.54", "pandas>=2.2.3", - "umap>=0.1.1", - "hdbscan>=0.8.40", "numpy>=1.26.4", "google-cloud-storage>=3.4.1", "pyarrow>=22.0.0", "gcsfs>=2025.9.0", ] -[build-system] -requires = ["hatchling"] -build-backend = "hatchling.build" - -[tool.hatch.build.targets.wheel] -packages = ["app"] - [dependency-groups] -lint = ["ruff>=0.7.1"] -dev = [ - "pytest>=7.0.0", - "pytest-asyncio>=0.21.0", - "httpx>=0.24.0", -] - -[tool.ruff] -target-version = "py312" -line-length = 88 -select = ["E", "F", "W", "C90", "I", "N", "UP", "YTT", "S", "BLE", "FBT", "B", "A", "COM", "C4", "DTZ", "T10", "EM", "EXE", "FA", "ISC", "ICN", "G", "INP", "PIE", "T20", "PYI", "PT", "Q", "RSE", "RET", "SLF", "SIM", "TID", "TCH", "ARG", "PTH", "ERA", "PD", "PGH", "PL", "TRY", "FLY", "NPY", "AIR", "PERF", "FURB", "LOG", "RUF"] -ignore = ["E501", "S101", "S104", "S105", "S106", "S107"] - -[tool.ruff.per-file-ignores] -"__init__.py" = ["F401"] +lint = ["ruff>=0.7.1"] \ No newline at end of file diff --git a/ui/.env.development b/ui/.env.development new file mode 100644 index 0000000..e8b2023 --- /dev/null +++ b/ui/.env.development @@ -0,0 +1,2 @@ +# Add a .env file for local development +VITE_API_URL=http://localhost:8000 diff --git a/ui/.env.production b/ui/.env.production new file mode 100644 index 0000000..460e575 --- /dev/null +++ b/ui/.env.production @@ -0,0 +1 @@ +VITE_API_URL=http://localhost:8080 diff --git a/ui/index.html b/ui/index.html index e4b78ea..53b3037 100644 --- a/ui/index.html +++ b/ui/index.html @@ -1,13 +1,16 @@ - - - - - Vite + React + TS - - -
- - - + + + + + + Vite + React + TS + + + +
+ + + + \ No newline at end of file diff --git a/ui/package-lock.json b/ui/package-lock.json index dbbcba2..ed13c38 100644 --- a/ui/package-lock.json +++ b/ui/package-lock.json @@ -19,9 +19,11 @@ "@mui/icons-material": "^7.2.0", "@mui/material": "^7.2.0", "@reactflow/background": "^11.3.14", + "@types/d3": "^7.4.3", "@types/dagre": "^0.7.53", "@types/plotly.js": "^3.0.3", "@types/react-plotly.js": "^2.6.3", + "d3": "^7.9.0", "dagre": "^0.8.5", "graphql": "^16.11.0", "plotly.js-dist": "^3.0.3", @@ -3667,6 +3669,47 @@ "node": ">=0.12" } }, + "node_modules/d3": { + "version": "7.9.0", + "resolved": "https://registry.npmjs.org/d3/-/d3-7.9.0.tgz", + "integrity": "sha512-e1U46jVP+w7Iut8Jt8ri1YsPOvFpg46k+K8TpCb0P+zjCkjkPnV7WzfDJzMHy1LnA+wj5pLT1wjO901gLXeEhA==", + "license": "ISC", + "dependencies": { + "d3-array": "3", + "d3-axis": "3", + "d3-brush": "3", + "d3-chord": "3", + "d3-color": "3", + "d3-contour": "4", + "d3-delaunay": "6", + "d3-dispatch": "3", + "d3-drag": "3", + "d3-dsv": "3", + "d3-ease": "3", + "d3-fetch": "3", + "d3-force": "3", + "d3-format": "3", + "d3-geo": "3", + "d3-hierarchy": "3", + "d3-interpolate": "3", + "d3-path": "3", + "d3-polygon": "3", + "d3-quadtree": "3", + "d3-random": "3", + "d3-scale": "4", + "d3-scale-chromatic": "3", + "d3-selection": "3", + "d3-shape": "3", + "d3-time": "3", + "d3-time-format": "4", + "d3-timer": "3", + "d3-transition": "3", + "d3-zoom": "3" + }, + "engines": { + "node": ">=12" + } + }, "node_modules/d3-array": { "version": "1.2.4", "resolved": "https://registry.npmjs.org/d3-array/-/d3-array-1.2.4.tgz", @@ -3674,6 +3717,43 @@ "license": "BSD-3-Clause", "peer": true }, + "node_modules/d3-axis": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/d3-axis/-/d3-axis-3.0.0.tgz", + "integrity": "sha512-IH5tgjV4jE/GhHkRV0HiVYPDtvfjHQlQfJHs0usq7M30XcSBvOotpmH1IgkcXsO/5gEQZD43B//fc7SRT5S+xw==", + "license": "ISC", + "engines": { + "node": ">=12" + } + }, + "node_modules/d3-brush": { + "version": "3.0.0", + "resolved": "https://registry.npmjs.org/d3-brush/-/d3-brush-3.0.0.tgz", + "integrity": "sha512-ALnjWlVYkXsVIGlOsuWH1+3udkYFI48Ljihfnh8FZPF2QS9o+PzGLBslO0PjzVoHLZ2KCVgAM8NVkXPJB2aNnQ==", + "license": "ISC", + "dependencies": { + "d3-dispatch": "1 - 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3" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-hierarchy": { + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/d3-hierarchy/-/d3-hierarchy-3.1.2.tgz", + "integrity": "sha512-FX/9frcub54beBdugHjDCdikxThEqjnR93Qt7PvQTOHxyiNCAlvMrHhclk3cD5VeAaq9fxmfRp+CnWw9rEMBuA==", + "license": "ISC", + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-path": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/d3-path/-/d3-path-3.1.0.tgz", + "integrity": "sha512-p3KP5HCf/bvjBSSKuXid6Zqijx7wIfNW+J/maPs+iwR35at5JCbLUT0LzF1cnjbCHWhqzQTIN2Jpe8pRebIEFQ==", + "license": "ISC", + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-quadtree": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/d3-quadtree/-/d3-quadtree-3.0.1.tgz", + "integrity": "sha512-04xDrxQTDTCFwP5H6hRhsRcb9xxv2RzkcsygFzmkSIOJy3PeRJP7sNk3VRIbKXcog561P9oU0/rVH6vDROAgUw==", + "license": "ISC", + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-shape": { + "version": "3.2.0", + "resolved": "https://registry.npmjs.org/d3-shape/-/d3-shape-3.2.0.tgz", + "integrity": "sha512-SaLBuwGm3MOViRq2ABk3eLoxwZELpH6zhl3FbAoJ7Vm1gofKx6El1Ib5z23NUEhF9AsGl7y+dzLe5Cw2AArGTA==", + "license": "ISC", + "dependencies": { + "d3-path": "^3.1.0" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-time": { + "version": "3.1.0", + "resolved": "https://registry.npmjs.org/d3-time/-/d3-time-3.1.0.tgz", + "integrity": "sha512-VqKjzBLejbSMT4IgbmVgDjpkYrNWUYJnbCGo874u7MMKIWsILRX+OpX/gTk8MqjpT1A/c6HY2dCA77ZN0lkQ2Q==", + "license": "ISC", + "dependencies": { + "d3-array": "2 - 3" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/d3/node_modules/d3-time-format": { + "version": "4.1.0", + "resolved": "https://registry.npmjs.org/d3-time-format/-/d3-time-format-4.1.0.tgz", + "integrity": "sha512-dJxPBlzC7NugB2PDLwo9Q8JiTR3M3e4/XANkreKSUxF8vvXKqm1Yfq4Q5dl8budlunRVlUUaDUgFt7eA8D6NLg==", + "license": "ISC", + "dependencies": { + "d3-time": "1 - 3" + }, + "engines": { + "node": ">=12" + } + }, "node_modules/dagre": { "version": "0.8.5", "resolved": "https://registry.npmjs.org/dagre/-/dagre-0.8.5.tgz", @@ -3942,6 +4293,15 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/delaunator": { + "version": "5.0.1", + "resolved": "https://registry.npmjs.org/delaunator/-/delaunator-5.0.1.tgz", + "integrity": "sha512-8nvh+XBe96aCESrGOqMp/84b13H9cdKbG5P2ejQCh4d4sK9RL4371qou9drQjMhvnPmhWl5hnmqbEE0fXr9Xnw==", + "license": "ISC", + "dependencies": { + "robust-predicates": "^3.0.2" + } + }, "node_modules/detect-kerning": { "version": "2.1.2", "resolved": "https://registry.npmjs.org/detect-kerning/-/detect-kerning-2.1.2.tgz", @@ -5247,6 +5607,15 @@ "node": "^14.17.0 || ^16.13.0 || >=18.0.0" } }, + "node_modules/internmap": { + "version": "2.0.3", + "resolved": "https://registry.npmjs.org/internmap/-/internmap-2.0.3.tgz", + "integrity": "sha512-5Hh7Y1wQbvY5ooGgPbDaL5iYLAPzMTUrjMulskHLH6wnv/A+1q5rgEaiuqEjB+oxGXIVZs1FF+R/KPN3ZSQYYg==", + "license": "ISC", + "engines": { + "node": ">=12" + } + }, "node_modules/is-arrayish": { "version": "0.2.1", "resolved": "https://registry.npmjs.org/is-arrayish/-/is-arrayish-0.2.1.tgz", @@ -6708,6 +7077,12 @@ "license": "MIT", "peer": true }, + "node_modules/robust-predicates": { + "version": "3.0.2", + "resolved": "https://registry.npmjs.org/robust-predicates/-/robust-predicates-3.0.2.tgz", + "integrity": "sha512-IXgzBWvWQwE6PrDI05OvmXUIruQTcoMDzRsOd5CDvHCVLcLHMTSYvOK5Cm46kWqlV3yAbuSpBZdJ5oP5OUoStg==", + "license": "Unlicense" + }, "node_modules/rollup": { "version": "4.46.2", "resolved": "https://registry.npmjs.org/rollup/-/rollup-4.46.2.tgz", @@ -6776,8 +7151,7 @@ "version": "1.3.3", "resolved": "https://registry.npmjs.org/rw/-/rw-1.3.3.tgz", "integrity": "sha512-PdhdWy89SiZogBLaw42zdeqtRJ//zFd2PgQavcICDUgJT5oW10QCRKbJ6bg4r0/UY2M6BWd5tkxuGFRvCkgfHQ==", - "license": "BSD-3-Clause", - "peer": true + "license": "BSD-3-Clause" }, "node_modules/safe-buffer": { "version": "5.2.1", @@ -6804,8 +7178,7 @@ "version": "2.1.2", "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz", "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==", - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/sax": { "version": "1.4.1", diff --git a/ui/package.json b/ui/package.json index f78631a..59a99b8 100644 --- a/ui/package.json +++ b/ui/package.json @@ -21,9 +21,11 @@ "@mui/icons-material": "^7.2.0", "@mui/material": "^7.2.0", "@reactflow/background": "^11.3.14", + "@types/d3": "^7.4.3", "@types/dagre": "^0.7.53", "@types/plotly.js": "^3.0.3", "@types/react-plotly.js": "^2.6.3", + "d3": "^7.9.0", "dagre": "^0.8.5", "graphql": "^16.11.0", "plotly.js-dist": "^3.0.3", diff --git a/ui/src/components/flame-graph/D3SunburstChart.tsx b/ui/src/components/flame-graph/D3SunburstChart.tsx new file mode 100644 index 0000000..6801c74 --- /dev/null +++ b/ui/src/components/flame-graph/D3SunburstChart.tsx @@ -0,0 +1,322 @@ +import React, { useEffect, useRef, useMemo } from "react"; +import * as d3 from "d3"; +import { Box } from "@mui/material"; +import type { Pathway } from "../../lib/api"; +import { buildPathwayHierarchy, getEffectiveRootPathways } from "../../utils/pathwayHierarchy"; +import { + PRIORITISATION_COLORS, + mapToPrioritizationColor, + ROOT_NODE_COLORS +} from "../../utils/colorPalettes"; + +interface D3SunburstChartProps { + pathways: Pathway[]; + maxPathways: number; + orientation: "h" | "v"; + branchvalues: "total" | "remainder"; +} + +interface D3Node extends d3.HierarchyNode { + data: { + id: string; + name: string; + pathway?: Pathway; + pValue?: number; + fdr?: number; + nes?: number; + geneCount?: number; + genes?: string[]; + type: "root" | "pathway"; + }; +} + +const D3SunburstChart: React.FC = ({ + pathways, + maxPathways, + orientation, + branchvalues, +}) => { + const svgRef = useRef(null); + const containerRef = useRef(null); + + // Convert pathway data to D3 hierarchy format + const hierarchyData = useMemo(() => { + if (pathways.length === 0) return null; + + const limitedPathways = pathways.slice(0, maxPathways); + const { pathwayMap, childrenMap } = buildPathwayHierarchy(limitedPathways); + const rootPathways = getEffectiveRootPathways(limitedPathways); + + // Collect all NES values for color scaling + const allNESValues: number[] = []; + limitedPathways.forEach((pathway) => { + const nes = pathway["NES"] || pathway["nes"] || 0; + allNESValues.push(nes); + }); + + const maxNES = Math.max(...allNESValues); + const minNES = Math.min(...allNESValues); + + // Helper function to create node data + const createNodeData = (pathway: Pathway, type: "root" | "pathway") => { + const pValue = pathway["p-value"] || pathway["p_value"] || pathway["pvalue"]; + const fdr = pathway["FDR"] || pathway["fdr"]; + const nes = pathway["NES"] || pathway["nes"]; + const genes = pathway["Leading edge genes"] || pathway["genes"] || []; + const geneCount = Array.isArray(genes) + ? genes.length + : typeof genes === "string" + ? genes.split(",").length + : 0; + + // Calculate value based on significance (more significant = larger) + const significance = 1 / (pValue || 1); + const value = Math.max(1, Math.log(significance) * 5); + + return { + id: pathway["ID"] || pathway["id"] || "", + name: pathway["Pathway"] || pathway["pathway"] || "", + pathway, + pValue, + fdr, + nes, + geneCount, + genes: Array.isArray(genes) + ? genes + : typeof genes === "string" + ? genes.split(",").map((g: string) => g.trim()) + : [], + type, + value, + color: type === "root" + ? ROOT_NODE_COLORS.primary + : mapToPrioritizationColor(nes || 0, minNES, maxNES) + }; + }; + + // Build hierarchy structure + const buildHierarchy = (parentId: string, processedIds: Set): any[] => { + const children = childrenMap.get(parentId) || []; + return children + .filter(childId => !processedIds.has(childId)) + .map(childId => { + processedIds.add(childId); + const pathway = pathwayMap.get(childId); + if (!pathway) return null; + + const nodeData = createNodeData(pathway, "pathway"); + const childNodes = buildHierarchy(childId, processedIds); + + return { + ...nodeData, + children: childNodes.length > 0 ? childNodes : undefined + }; + }) + .filter(Boolean); + }; + + // Create root node + const rootNodeData = { + id: "root", + name: "All Pathways", + type: "root" as const, + value: limitedPathways.length, + color: ROOT_NODE_COLORS.primary, + children: rootPathways.map(pathway => { + const pathwayId = pathway["ID"] || pathway["id"] || ""; + const nodeData = createNodeData(pathway, "pathway"); + const processedIds = new Set(); + processedIds.add(pathwayId); + + const childNodes = buildHierarchy(pathwayId, processedIds); + + return { + ...nodeData, + children: childNodes.length > 0 ? childNodes : undefined + }; + }) + }; + + return rootNodeData; + }, [pathways, maxPathways]); + + // D3 rendering function + const renderSunburst = () => { + if (!hierarchyData || !svgRef.current || !containerRef.current) return; + + const container = containerRef.current; + const svg = d3.select(svgRef.current); + + // Clear previous content + svg.selectAll("*").remove(); + + const width = container.clientWidth; + const height = 700; + const radius = Math.min(width, height) / 2 - 10; + + // Set up SVG + svg + .attr("width", width) + .attr("height", height) + .style("background-color", "white"); + + // Create main group + const g = svg + .append("g") + .attr("transform", `translate(${width / 2},${height / 2})`); + + // Create partition layout + const partition = d3.partition() + .size([2 * Math.PI, radius]); + + // Create arc generator + const arc = d3.arc() + .startAngle(d => d.x0) + .endAngle(d => d.x1) + .padAngle(d => Math.min((d.x1 - d.x0) / 2, 0.005)) + .padRadius(radius / 2) + .innerRadius(d => d.y0) + .outerRadius(d => d.y1 - 1); + + // Create hierarchy + const root = d3.hierarchy(hierarchyData) + .sum(d => d.value) + .sort((a, b) => (b.value || 0) - (a.value || 0)); + + const nodes = partition(root).descendants().filter(d => d.x1 - d.x0 > 0.005); + + // Create arcs + const arcs = g + .selectAll(".arc") + .data(nodes) + .enter() + .append("path") + .attr("class", "arc") + .attr("d", arc) + .style("fill", d => d.data.color) + .style("cursor", "pointer") + .style("opacity", 0) + .on("mouseover", function(event, d) { + // Highlight current path + const sequenceArray = d.ancestors().reverse(); + + // Fade all arcs + arcs.transition().duration(300).style("opacity", 0.3); + + // Highlight current path + arcs + .filter(d => sequenceArray.indexOf(d) >= 0) + .transition() + .duration(300) + .style("opacity", 1); + + // Show tooltip (you can implement this based on your tooltip system) + showTooltip(event, d); + }) + .on("mouseleave", function() { + // Reset all arcs + arcs.transition().duration(300).style("opacity", 1); + hideTooltip(); + }) + .on("click", function(event, d) { + // Handle click events if needed + console.log("Clicked:", d.data); + }); + + // Animate arcs + arcs + .transition() + .delay((d, i) => i * 20) + .style("opacity", 1); + + // Add labels for larger arcs + const labels = g + .selectAll(".label") + .data(nodes.filter(d => d.x1 - d.x0 > 0.1 && d.y1 - d.y0 > 10)) + .enter() + .append("text") + .attr("class", "label") + .attr("transform", d => { + const x = (d.x0 + d.x1) / 2 * 180 / Math.PI; + const y = (d.y0 + d.y1) / 2; + return `rotate(${x - 90}) translate(${y},0) rotate(${x < 180 ? 0 : 180})`; + }) + .attr("text-anchor", "middle") + .attr("dy", "0.35em") + .style("font-size", "12px") + .style("font-family", "Arial, sans-serif") + .style("fill", "#333") + .text(d => d.data.name.length > 15 ? d.data.name.substring(0, 15) + "..." : d.data.name) + .style("opacity", 0) + .transition() + .delay((d, i) => i * 20 + 200) + .style("opacity", 1); + }; + + // Tooltip functions + const showTooltip = (event: MouseEvent, d: D3Node) => { + const tooltip = d3.select("body") + .append("div") + .attr("class", "sunburst-tooltip") + .style("position", "absolute") + .style("background", "rgba(0, 0, 0, 0.8)") + .style("color", "white") + .style("padding", "8px") + .style("border-radius", "4px") + .style("font-size", "12px") + .style("pointer-events", "none") + .style("z-index", "1000"); + + const content = ` +
${d.data.name}
+ ${d.data.type === "pathway" ? ` +
NES: ${d.data.nes?.toFixed(3) || "N/A"}
+
P-value: ${d.data.pValue?.toExponential(2) || "N/A"}
+
FDR: ${d.data.fdr?.toExponential(2) || "N/A"}
+
Genes: ${d.data.geneCount || 0}
+ ` : ""} + `; + + tooltip.html(content); + + tooltip + .style("left", (event.pageX + 10) + "px") + .style("top", (event.pageY - 10) + "px"); + }; + + const hideTooltip = () => { + d3.selectAll(".sunburst-tooltip").remove(); + }; + + // Render on mount and when data changes + useEffect(() => { + renderSunburst(); + }, [hierarchyData]); + + // Handle resize + useEffect(() => { + const handleResize = () => { + renderSunburst(); + }; + + window.addEventListener("resize", handleResize); + return () => window.removeEventListener("resize", handleResize); + }, [hierarchyData]); + + if (pathways.length === 0) { + return null; + } + + return ( + +
+ +
+
+ ); +}; + +export default D3SunburstChart; diff --git a/ui/src/components/flame-graph/PathwaysFlameGraph.tsx b/ui/src/components/flame-graph/PathwaysFlameGraph.tsx index 4ed4618..2c896d7 100644 --- a/ui/src/components/flame-graph/PathwaysFlameGraph.tsx +++ b/ui/src/components/flame-graph/PathwaysFlameGraph.tsx @@ -3,10 +3,12 @@ import { Box, Tabs, Tab, Typography, Button } from "@mui/material"; import { DonutLarge as SunburstIcon, ShowChart as BarChartIcon, + DonutLarge as D3SunburstIcon, } from "@mui/icons-material"; import type { Pathway } from "../../lib/api"; import FlameGraphHeader from "./FlameGraphHeader"; import SunburstChart from "./SunburstChart"; +import D3SunburstChart from "./D3SunburstChart"; import HorizontalFlameChart from "./HorizontalFlameChart"; import FlameGraphSettings from "./FlameGraphSettings"; import PathwayFilter, { type PathwayFilters } from "./PathwayFilter"; @@ -233,7 +235,12 @@ const PathwaysFlameGraph: React.FC = ({ > } - label="Sunburst" + label="Plotly Sunburst" + iconPosition="start" + /> + } + label="D3 Sunburst" iconPosition="start" /> = ({ minHeight: "500px", }} > - {/* Sunburst Chart */} + {/* Plotly Sunburst Chart */} {activeTab === 0 && ( = ({ )} - {/* Horizontal Flame Graph Chart */} + {/* D3 Sunburst Chart */} {activeTab === 1 && ( + + + + )} + + {/* Horizontal Flame Graph Chart */} + {activeTab === 2 && ( { + // For production (when served from the same domain) + if (window.location.hostname !== 'localhost' && window.location.hostname !== '127.0.0.1') { + return ''; // Use relative URLs in production + } + + // For local development + return import.meta.env.VITE_API_URL || 'http://localhost:8000'; +}; + +const API_BASE_URL = getApiBaseUrl(); export type Pathway = Record; @@ -65,12 +75,12 @@ class ApiClient { } } - // GSEA endpoint + // GSEA endpoint - file upload async runGsea(params: GseaParams): Promise> { const formData = new FormData(); formData.append('tsv_file', params.tsv_file); - return this.request(`/api/gsea?gmt_name=${encodeURIComponent(params.gmt_name)}`, { + return this.request(`/api/gsea/analyze/file?gmt_name=${encodeURIComponent(params.gmt_name)}`, { method: 'POST', body: formData, headers: {}, // Let the browser set the Content-Type for FormData diff --git a/ui/src/pages/Pathways.tsx b/ui/src/pages/Pathways.tsx index cd12dc0..8987599 100644 --- a/ui/src/pages/Pathways.tsx +++ b/ui/src/pages/Pathways.tsx @@ -9,15 +9,19 @@ import { MenuItem, Button, Alert, + Switch, + FormControlLabel, } from "@mui/material"; import { CloudUpload } from "@mui/icons-material"; import { useGsea, useGmtLibraries } from "../hooks/useApi"; import PathwaysResults from "../components/PathwaysResults"; +import { mockPathwayData } from "../data/mockPathwayData"; const Pathways: React.FC = () => { const [selectedFile, setSelectedFile] = useState(null); const [library, setLibrary] = useState(""); const [fileError, setFileError] = useState(""); + const [testMode, setTestMode] = useState(false); const { data: gmtLibraries, @@ -32,7 +36,10 @@ const Pathways: React.FC = () => { execute: runGsea, } = useGsea(); - console.log({pathways}); + // Use mock data in test mode, otherwise use real data + const displayPathways = testMode ? mockPathwayData : pathways; + const displayLoading = testMode ? false : loading; + const displayError = testMode ? null : error; // Set default library when libraries are loaded React.useEffect(() => { @@ -91,7 +98,7 @@ const Pathways: React.FC = () => { value={library} label="GMT Library" onChange={(e) => setLibrary(e.target.value)} - disabled={librariesLoading} + disabled={librariesLoading || testMode} > {gmtLibraries?.map((lib) => ( @@ -115,6 +122,7 @@ const Pathways: React.FC = () => { id="tsv-file-upload" type="file" onChange={handleFileSelect} + disabled={testMode} /> + setTestMode(e.target.checked)} + /> + } + label="Test Mode (Use Mock Data)" + sx={{ mb: 2 }} + /> - + ); }; diff --git a/uv.lock b/uv.lock index 1f81303..d205c37 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