(temporary) Creates 2 databases, uses one of them in json file creation.#23
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(temporary) Creates 2 databases, uses one of them in json file creation.#23
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KajusC
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May 21, 2025
| import sqlite3 | ||
| from typing import List, Dict, Any | ||
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| BASE_OUTPUT_DIR = os.path.join(os.path.expanduser("~"), ".kath", "shared", "data", "blast_results") |
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Use constants from constants.py
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| #++++++++++++++++++++++++++++++++++++++++++++++++ | ||
| # Takes in Json file and returns db file | ||
| db_file = json_to_db(result_file) |
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what for db_file is used? If you dont use for anything, dont apply for anything
| logger = logging.getLogger(__name__) | ||
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| # Always use this database file | ||
| BASE_OUTPUT_DIR = os.path.join(os.path.expanduser("~"), ".kath", "shared", "data", "blast_results") |
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should be from constants.py
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| 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) |
| *.sln | ||
| *.sw? No newline at end of file | ||
| *.sw? | ||
| backend/src/services/remote/blast_service/align2.py |
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Why is this here? Remove it
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| from shared.constants import ( | ||
| PROGRAM_STORAGE_DIR_SHARED_BLAST, | ||
| PROGRAM_STORAGE_DIR_SHARED_DATA_FASTA, | ||
| ) |
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Suggested change
| from shared.constants import ( | |
| PROGRAM_STORAGE_DIR_SHARED_BLAST, | |
| PROGRAM_STORAGE_DIR_SHARED_DATA_FASTA, | |
| ) | |
| from shared import PROGRAM_STORAGE_DIR_SHARED_BLAST, PROGRAM_STORAGE_DIR_SHARED_DATA_FASTA |
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| import os | ||
| import sqlite3 |
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Imports at the middle of a file? Relocate to the top of the file where imports should be
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| import os | ||
| import sqlite3 | ||
| from typing import List, Dict, Any |
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Duplicate from typing, remove it
| from dotenv import load_dotenv | ||
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| from src.utils.logger import get_logger | ||
| from utils.logger import get_logger |
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Suggested change
| from utils.logger import get_logger | |
| from utils import get_logger |
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