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Merge pull request #215 from monarch-initiative/214-new-method-for-se…
…msim-ingestion New method for semsim ingestion
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| # -*- coding: cp936 -*- | ||
| import logging as log | ||
| import os | ||
| from pathlib import Path | ||
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| import jaydebeapi | ||
| import polars as pl | ||
| from tqdm import tqdm | ||
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| info_log = log.getLogger("info") | ||
| info_debug = log.getLogger("debug") | ||
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| class DBConnector: | ||
| def __init__( | ||
| self, jar: Path, driver: str, server: str, database: str, user: str, password: str | ||
| ): | ||
| self.jar = jar | ||
| self.driver = driver | ||
| self.server = server | ||
| self.database = database | ||
| self.user = user | ||
| self.password = password | ||
| self.dbconn = None | ||
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| def create_connection(self) -> jaydebeapi.Connection: | ||
| """creates h2 database connection""" | ||
| return jaydebeapi.connect( | ||
| self.driver, | ||
| f"{self.server}{self.database}", | ||
| [self.user, self.password], | ||
| self.jar, | ||
| ) | ||
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| def __enter__(self) -> jaydebeapi.Connection: | ||
| self.dbconn = self.create_connection() | ||
| return self.dbconn | ||
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| def __exit__(self, *other): | ||
| self.dbconn.close() | ||
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| class DBConnection: | ||
| connection = None | ||
|
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| def __init__(self, connection): | ||
| DBConnection.connection = connection | ||
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| @classmethod | ||
| def get_connection(cls) -> jaydebeapi.Connection: | ||
| """Creates return new Singleton database connection""" | ||
| return DBConnection.connection | ||
|
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| def close(self): | ||
| return self.connection.close() | ||
|
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| @classmethod | ||
| def get_cursor(cls) -> jaydebeapi.Cursor: | ||
| connection = cls.get_connection() | ||
| return connection.cursor() | ||
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| class ExomiserDB: | ||
| def __init__(self, db_path: Path): | ||
| try: | ||
| self.connector = DBConnector( # noqa | ||
| jar=os.path.join(os.path.dirname(__file__), "../../../lib/h2-1.4.199.jar"), | ||
| driver="org.h2.Driver", | ||
| server=f"jdbc:h2:{db_path}", | ||
| user="sa", | ||
| password="", | ||
| database="", | ||
| ) | ||
| except Exception as e: | ||
| print("An exception occurred", e) | ||
|
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| def import_from_semsim_file(self, input_file: Path, subject_prefix: str, object_prefix: str): | ||
| """imports semsim tsv profile into exomiser phenotype database | ||
| Args: | ||
| input_file (Path): semsim profile | ||
| subject_prefix (str): Subject Prefix. e.g HP | ||
| object_prefix (str): Object Prefix. e.g MP | ||
| """ | ||
| with self.connector as cnn: | ||
| conn = DBConnection(cnn) | ||
| reader = pl.read_csv_batched(input_file, separator="\t") | ||
| batch_length = 5 | ||
| batches = reader.next_batches(batch_length) | ||
| cursor = conn.get_cursor() | ||
| # # TODO: Refactor this | ||
| with open(input_file, "r") as f: | ||
| total = sum(1 for line in f) | ||
| pbar = tqdm(total=total - 1) | ||
| mapping_id = 1 | ||
| while batches: | ||
| input_data = pl.concat(batches) | ||
| sql = _semsim2h2(input_data, object_prefix, subject_prefix, mapping_id=mapping_id) | ||
| cursor.execute(sql) | ||
| len_input_data = len(input_data) | ||
| mapping_id += len_input_data | ||
| pbar.update(len_input_data) | ||
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| batches = reader.next_batches(batch_length) | ||
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| def _format_row(mapping_id, data): | ||
| """format row in a exomiser database way | ||
| Args: | ||
| mapping_id (_type_): row sequencial id | ||
| data (_type_): row data | ||
| """ | ||
| # TODO:Improve string escaping. Replace this code with parametrised query | ||
| return f"""({mapping_id}, '{data['subject_id']}', '{data['subject_label'].replace("'", "")}', '{data['object_id']}', '{data['object_label'].replace("'", "")}', {data['jaccard_similarity']}, {data['ancestor_information_content']}, {data['phenodigm_score']}, '{data['ancestor_id'].split(",")[0]}', '{data['ancestor_label'].replace("'", "")}')""" # noqa | ||
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| def _semsim2h2( | ||
| input_data: pl.DataFrame, subject_prefix: str, object_prefix: str, mapping_id=1 | ||
| ) -> None: | ||
| """This function is responsible for generate sql insertion query for each semsim profile row | ||
| Args: | ||
| input_data (pl.DataFrame): input data. (e.g. semantic similarity profile file) | ||
| subject_prefix (str): subject prefix. (e.g HP) | ||
| object_prefix (str): object prefix. (e.g MP) | ||
| mapping_id (int, optional): MAPPING_ID. | ||
| """ | ||
| sql = "" | ||
| if mapping_id == 1: | ||
| sql += f"TRUNCATE TABLE EXOMISER.{subject_prefix}_{object_prefix}_MAPPINGS;\n" | ||
|
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| object_id = ( | ||
| f"{object_prefix}_ID_HIT" if subject_prefix == object_prefix else f"{object_prefix}_ID" | ||
| ) | ||
| object_term = ( | ||
| f"{object_prefix}_HIT_TERM" if subject_prefix == object_prefix else f"{object_prefix}_TERM" | ||
| ) | ||
| sql += f"""INSERT INTO EXOMISER.{subject_prefix}_{object_prefix}_MAPPINGS | ||
| (MAPPING_ID, {subject_prefix}_ID, {subject_prefix}_TERM, {object_id}, {object_term}, SIMJ, IC, SCORE, LCS_ID, LCS_TERM) | ||
| VALUES""" | ||
| rows = [ | ||
| _format_row(data=frame, mapping_id=mapping_id + jdx) | ||
| for jdx, frame in enumerate(input_data.iter_rows(named=True)) | ||
| ] | ||
| sql += ",\n".join(rows) + ";" | ||
| return sql |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| from pathlib import Path | ||
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| from pheval.infra.exomiserdb import ExomiserDB | ||
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| def semsim_to_exomiserdb(input_path: Path, object_prefix: str, subject_prefix: str, db_path: Path): | ||
| """ingests semsim file into exomiser phenotypic database | ||
| Args: | ||
| input_path (Path): semsim input file. e.g phenio-plus-hp-mp.0.semsimian.tsv | ||
| object_prefix (str): object prefix. e.g. MP | ||
| subject_prefix (str): subject prefix e.g HP | ||
| db_path (Path): Exomiser Phenotypic Database Folder Path. (e.g. /exomiser_folder/2209_phenotype/2209_phenotype/) | ||
| """ | ||
| exomiserdb = ExomiserDB(db_path) | ||
| exomiserdb.import_from_semsim_file(input_path, object_prefix, subject_prefix) |
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