diff --git a/.gitignore b/.gitignore index bf03355..0d39b79 100644 --- a/.gitignore +++ b/.gitignore @@ -75,4 +75,5 @@ dist-ssr *.ntvs* *.njsproj *.sln -*.sw? \ No newline at end of file +*.sw? +backend/src/services/remote/blast_service/align2.py diff --git a/backend/src/services/remote/blast_service/align.py b/backend/src/services/remote/blast_service/align.py index 1bc0216..5cce9e3 100644 --- a/backend/src/services/remote/blast_service/align.py +++ b/backend/src/services/remote/blast_service/align.py @@ -13,8 +13,9 @@ from pathlib import Path from typing import Optional, List, Dict, Any from Bio.Blast import NCBIXML +from services.remote.database_service.xml_to_db import xml_to_db -from src.shared.constants import ( +from shared.constants import ( PROGRAM_STORAGE_DIR_SHARED_BLAST, PROGRAM_STORAGE_DIR_SHARED_DATA_FASTA, ) @@ -152,6 +153,8 @@ def blast_cmdline( logger.error("`blastn` command not found. Is BLAST+ installed and in PATH?") raise + xml_to_db(output_file) + return str(output_file) diff --git a/backend/src/services/remote/blast_service/main.py b/backend/src/services/remote/blast_service/main.py index 36b1084..fe457ac 100644 --- a/backend/src/services/remote/blast_service/main.py +++ b/backend/src/services/remote/blast_service/main.py @@ -8,6 +8,7 @@ from .align import process_single_fasta from .find import process_variants +from services.remote.database_service.json_to_db import json_to_db class BlastService: @@ -30,12 +31,23 @@ def disease_extraction(self, fasta_file: str): try: print(f"Processing file: {fasta_file}") # Perform blast aligning + # +++++++++++++++++++++++++++++++++++++++++++++++++ + # Takes in fasta file and returns json file result_file = process_single_fasta(fasta_file) - + if not result_file: raise Exception("Failed to perform blast aligning") - - + + #++++++++++++++++++++++++++++++++++++++++++++++++ + # Takes in Json file and returns db file + db_file = json_to_db(result_file) + + if not db_file: + raise Exception("Failed to insert data into the database") + + + # +++++++++++++++++++++++++++++++++++++++++++++++++ + # Takes in Json file and returns csv file disease_file = process_variants(result_file) if not disease_file: diff --git a/backend/src/services/remote/database_service/__init__.py b/backend/src/services/remote/database_service/__init__.py new file mode 100644 index 0000000..bacb31b --- /dev/null +++ b/backend/src/services/remote/database_service/__init__.py @@ -0,0 +1,6 @@ +from .xml_to_db import xml_to_db +from .json_to_db import json_to_db + +__all__ = [ + "xml_to_db", +] \ No newline at end of file diff --git a/backend/src/services/remote/database_service/json_to_db.py b/backend/src/services/remote/database_service/json_to_db.py new file mode 100644 index 0000000..202905e --- /dev/null +++ b/backend/src/services/remote/database_service/json_to_db.py @@ -0,0 +1,132 @@ +import sqlite3 +import argparse +from pathlib import Path +import os +import logging +import json + +# Configure logger +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + +# Always use this database file +BASE_OUTPUT_DIR = os.path.join(os.path.expanduser("~"), ".kath", "shared", "data", "blast_results") +DB_FILENAME = "json.db" +SQLITE_DB_FILE = os.path.join(BASE_OUTPUT_DIR, DB_FILENAME) + +def create_database(sqlite_db_file: str): + """ + Create the SQLite database and the variants table if it doesn't exist. + """ + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + cursor.execute(""" + CREATE TABLE IF NOT EXISTS variants ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + file_id INTEGER, + query_id TEXT, + subject_id TEXT, + chromosome TEXT, + position INTEGER, + variation_type TEXT, + reference_allele TEXT, + query_allele TEXT, + query_position INTEGER, + hsp_score REAL, + hsp_evalue REAL, + hsp_identity REAL, + hsp_align_length INTEGER, + hsp_query_start INTEGER, + hsp_subject_start INTEGER, + hsp_strand TEXT, + hsp_gaps INTEGER + ); + """) + conn.commit() + conn.close() + +def get_next_file_id(sqlite_db_file: str) -> int: + """ + Get the next file_id to use for a new JSON file. + """ + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + cursor.execute("SELECT MAX(file_id) FROM variants") + result = cursor.fetchone() + conn.close() + if result and result[0]: + return result[0] + 1 + else: + return 1 + +def json_to_db(json_file_path: str) -> str: + """ + Parse a JSON file and insert its data into a shared SQLite database. + + Args: + json_file_path: Path to the JSON file. + + Returns: + Path to the shared SQLite database. + """ + # Ensure the output directory exists + os.makedirs(BASE_OUTPUT_DIR, exist_ok=True) + + # Always use the same database file + sqlite_db_file = SQLITE_DB_FILE + + # Create the database if needed + create_database(sqlite_db_file) + + # Determine the file_id for this JSON file + file_id = get_next_file_id(sqlite_db_file) + + # Load the JSON file + with open(json_file_path, "r", encoding="utf-8") as f: + variant_list = json.load(f) + + # Insert data into the database + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + + for variant in variant_list: + cursor.execute(""" + INSERT INTO variants ( + file_id, query_id, subject_id, chromosome, position, variation_type, + reference_allele, query_allele, query_position, hsp_score, hsp_evalue, + hsp_identity, hsp_align_length, hsp_query_start, hsp_subject_start, + hsp_strand, hsp_gaps + ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) + """, ( + file_id, + variant.get("query_id"), + variant.get("subject_id"), + variant.get("chromosome"), + variant.get("position"), + variant.get("variation_type"), + variant.get("reference_allele"), + variant.get("query_allele"), + variant.get("query_position"), + variant.get("hsp_score"), + variant.get("hsp_evalue"), + variant.get("hsp_identity"), + variant.get("hsp_align_length"), + variant.get("hsp_query_start"), + variant.get("hsp_subject_start"), + json.dumps(variant.get("hsp_strand")), # store as JSON string + variant.get("hsp_gaps"), + )) + + conn.commit() + conn.close() + logger.info(f"Inserted variant data from file_id {file_id} into the database: {sqlite_db_file}") + + return sqlite_db_file + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Parse JSON and insert results into a shared SQLite database.") + parser.add_argument("--json", required=True, help="Path to JSON file") + args = parser.parse_args() + + db_path = json_to_db(args.json) + print(f"Database updated at: {db_path}") \ No newline at end of file diff --git a/backend/src/services/remote/database_service/main.py b/backend/src/services/remote/database_service/main.py new file mode 100644 index 0000000..ec90793 --- /dev/null +++ b/backend/src/services/remote/database_service/main.py @@ -0,0 +1,2 @@ +if __name__ == "__main__": + print("Database service module executed directly.") \ No newline at end of file diff --git a/backend/src/services/remote/database_service/xml_to_db.py b/backend/src/services/remote/database_service/xml_to_db.py new file mode 100644 index 0000000..bb563e3 --- /dev/null +++ b/backend/src/services/remote/database_service/xml_to_db.py @@ -0,0 +1,135 @@ +import sqlite3 +import argparse +from pathlib import Path +import os +import logging +from xml.etree import ElementTree as ET + +# Configure logger +logging.basicConfig(level=logging.INFO) +logger = logging.getLogger(__name__) + +# Always use this database file +BASE_OUTPUT_DIR = os.path.join(os.path.expanduser("~"), ".kath", "shared", "data", "blast_results") +DB_FILENAME = "xml.db" +SQLITE_DB_FILE = os.path.join(BASE_OUTPUT_DIR, DB_FILENAME) + +def create_database(sqlite_db_file: str): + """ + Create the SQLite database and the hsps table if it doesn't exist. + """ + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + + # Add file_id column + cursor.execute(""" + CREATE TABLE IF NOT EXISTS hsps ( + id INTEGER PRIMARY KEY AUTOINCREMENT, + file_id INTEGER, + hit_id INTEGER, + hsp_num INTEGER, + bit_score REAL, + score INTEGER, + evalue REAL, + query_from INTEGER, + query_to INTEGER, + hit_from INTEGER, + hit_to INTEGER, + query_frame INTEGER, + hit_frame INTEGER, + identity INTEGER, + positive INTEGER, + gaps INTEGER, + align_len INTEGER, + qseq TEXT, + hseq TEXT, + midline TEXT + ); + """) + + conn.commit() + conn.close() + +def get_next_file_id(sqlite_db_file: str) -> int: + """ + Get the next file_id to use for a new XML file. + """ + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + cursor.execute("SELECT MAX(file_id) FROM hsps") + result = cursor.fetchone() + conn.close() + if result and result[0]: + return result[0] + 1 + else: + return 1 + +def xml_to_db(xml_file_path: str) -> str: + """ + Parse a BLAST XML file and insert its data into a shared SQLite database. + + Args: + xml_file_path: Path to the BLAST XML file. + + Returns: + Path to the shared SQLite database. + """ + # Ensure the output directory exists + os.makedirs(BASE_OUTPUT_DIR, exist_ok=True) + + # Always use the same database file + sqlite_db_file = SQLITE_DB_FILE + + # Create the database if needed + create_database(sqlite_db_file) + + # Determine the file_id for this XML file + file_id = get_next_file_id(sqlite_db_file) + + # Parse the XML file + tree = ET.parse(xml_file_path) + root = tree.getroot() + + # Insert data into the database + conn = sqlite3.connect(sqlite_db_file) + cursor = conn.cursor() + + for hsp in root.findall(".//Hsp"): + hsp_num = int(hsp.findtext("Hsp_num")) + bit_score = float(hsp.findtext("Hsp_bit-score")) + score = int(hsp.findtext("Hsp_score")) + evalue = float(hsp.findtext("Hsp_evalue")) + query_from = int(hsp.findtext("Hsp_query-from")) + query_to = int(hsp.findtext("Hsp_query-to")) + hit_from = int(hsp.findtext("Hsp_hit-from")) + hit_to = int(hsp.findtext("Hsp_hit-to")) + query_frame = int(hsp.findtext("Hsp_query-frame")) + hit_frame = int(hsp.findtext("Hsp_hit-frame")) + identity = int(hsp.findtext("Hsp_identity")) + positive = int(hsp.findtext("Hsp_positive")) + gaps = int(hsp.findtext("Hsp_gaps")) + align_len = int(hsp.findtext("Hsp_align-len")) + qseq = hsp.findtext("Hsp_qseq") + hseq = hsp.findtext("Hsp_hseq") + midline = hsp.findtext("Hsp_midline") + + cursor.execute(""" + INSERT INTO hsps (file_id, hit_id, hsp_num, bit_score, score, evalue, query_from, query_to, hit_from, hit_to, + query_frame, hit_frame, identity, positive, gaps, align_len, qseq, hseq, midline) + VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) + """, (file_id, None, hsp_num, bit_score, score, evalue, query_from, query_to, hit_from, hit_to, + query_frame, hit_frame, identity, positive, gaps, align_len, qseq, hseq, midline)) + + conn.commit() + conn.close() + logger.info(f"Inserted HSP data from file_id {file_id} into the database: {sqlite_db_file}") + + return sqlite_db_file + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Parse BLAST XML and insert results into a shared SQLite database.") + parser.add_argument("--xml", required=True, help="Path to BLAST XML file") + args = parser.parse_args() + + db_path = xml_to_db(args.xml) + print(f"Database updated at: {db_path}") \ No newline at end of file diff --git a/backend/src/services/remote/fasta_service/downloader.py b/backend/src/services/remote/fasta_service/downloader.py index 4e8ea62..af17dca 100644 --- a/backend/src/services/remote/fasta_service/downloader.py +++ b/backend/src/services/remote/fasta_service/downloader.py @@ -13,7 +13,7 @@ from Bio import Entrez from dotenv import load_dotenv -from src.utils.logger import get_logger +from utils.logger import get_logger from services.utils.script_setup import ( EnvSetup, FolderSetup, diff --git a/backend/src/services/utils/script_setup.py b/backend/src/services/utils/script_setup.py index 4586f92..85a2cf9 100644 --- a/backend/src/services/utils/script_setup.py +++ b/backend/src/services/utils/script_setup.py @@ -2,7 +2,7 @@ import os from pathlib import Path from Bio import Entrez -from src.shared.constants import * +from shared.constants import * from utils.logger import get_logger diff --git a/frontend/src/components/cards/DiseaseOptionCard.tsx b/frontend/src/components/cards/DiseaseOptionCard.tsx index 76b9e23..0f94d7b 100644 --- a/frontend/src/components/cards/DiseaseOptionCard.tsx +++ b/frontend/src/components/cards/DiseaseOptionCard.tsx @@ -10,9 +10,9 @@ import { Stack, CircularProgress, } from '@mui/material'; -import DiseaseModal from '@/components/modals/DiseaseModal'; import ScienceIcon from '@mui/icons-material/Science'; import VisibilityIcon from '@mui/icons-material/Visibility'; +import TableModal from '@/components/modals/tableModal'; export default function DiseaseOptionCard(): JSX.Element { const [fastaFilePath, setFastaFilePath] = useState(''); @@ -20,13 +20,9 @@ export default function DiseaseOptionCard(): JSX.Element { status: string; result_file: string; }>(); - const [geneticDiseaseData, setGeneticDiseaseData] = useState<{ - clinicalSignificance: string; - disease: string; - }[]>([]); - const [showModal, setShowModal] = useState(false); const [isExtracting, setIsExtracting] = useState(false); + const [tableData, setTableData] = useState([]); const theme = useTheme(); @@ -81,46 +77,15 @@ export default function DiseaseOptionCard(): JSX.Element { } try { - const diseaseData = - await window.pywebview.api.disease_service.get_disease_data( - extractionResult.result_file - ); - - if (!diseaseData || diseaseData.length === 0) { - // TODO UNCOMMENT - // alert('No disease data found.'); - setGeneticDiseaseData([ - { - clinicalSignificance: 'Pathogenic', - disease: 'Type 1 Diabetes Mellitus', - }, - { - clinicalSignificance: 'Likely Pathogenic', - disease: 'Maturity-Onset Diabetes of the Young (MODY)', - }, - { - clinicalSignificance: 'Benign', - disease: 'Gestational Diabetes', - }, - { - clinicalSignificance: 'Uncertain Significance', - disease: 'Latent Autoimmune Diabetes in Adults (LADA)', - }, - { - clinicalSignificance: 'Likely Benign', - disease: 'Prediabetes', - }, - ]); - } else { - setGeneticDiseaseData(diseaseData.map((item: any) => ({ - clinicalSignificance: item.clinical_significance, - disease: item.disease_name, - }))); - } + // Fetch your table data from your backend or API + // Example: fetch from Flask API or your backend endpoint + const res = await fetch('http://localhost:5000/api/variants'); // Adjust URL as needed + const data = await res.json(); + setTableData(data); setShowModal(true); } catch (error) { - console.error('Failed to fetch disease data:', error); - alert('Failed to fetch disease data.'); + console.error('Failed to fetch table data:', error); + alert('Failed to fetch table data.'); } }; @@ -226,11 +191,13 @@ export default function DiseaseOptionCard(): JSX.Element { )} {showModal && ( - setShowModal(false)} + data={tableData} + title="All Variants" /> )} ); -} +} \ No newline at end of file diff --git a/frontend/src/components/modals/tableModal.tsx b/frontend/src/components/modals/tableModal.tsx new file mode 100644 index 0000000..b327c08 --- /dev/null +++ b/frontend/src/components/modals/tableModal.tsx @@ -0,0 +1,93 @@ +import React from 'react'; +import { + Dialog, + DialogTitle, + DialogContent, + IconButton, + Table, + TableBody, + TableCell, + TableContainer, + TableHead, + TableRow, + Paper +} from '@mui/material'; +import CloseIcon from '@mui/icons-material/Close'; + +interface TableModalProps { + open: boolean; + onClose: () => void; + data: any[]; + title?: string; +} + +const tableModal: React.FC = ({ open, onClose, data, title }) => { + if (!data || data.length === 0) return null; + const columns = Object.keys(data[0]); + + return ( + + + {title || 'Database Table'} + + + + + + + + + + {columns.map((col) => ( + + {col} + + ))} + + + + {data.map((row, i) => ( + + {columns.map((col) => ( + + {String(row[col])} + + ))} + + ))} + +
+ + + + ); +}; + +export default tableModal; \ No newline at end of file