Removing H2 jar as internal dependency. Fixes #291

src/pheval/cli_pheval_utils.py

@@ -521,8 +521,15 @@ def benchmark_comparison(
     This is the path where the phenotypic database folder will be written out.""",
     type=Path,
 )
+@click.option(
+    "--h2-jar",
+    required=True,
+    metavar="h2-jar",
+    help="""H2 JAR file. JAR required to run H2 Database. e.g h2.jar""",
+    type=Path,
+)
 def semsim_to_exomiserdb_command(
-    input_file: Path, object_prefix: str, subject_prefix: str, db_path: Path
+    input_file: Path, object_prefix: str, subject_prefix: str, db_path: Path, h2_jar: Path
 ):
     """ingests semsim file into exomiser phenotypic database
 
@@ -531,8 +538,9 @@ def semsim_to_exomiserdb_command(
         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/)
+        h2_jar (Path): H2 JAR file. JAR required to run H2 Database. e.g h2.jar
     """
-    semsim_to_exomiserdb(input_file, object_prefix, subject_prefix, db_path)
+    semsim_to_exomiserdb(input_file, object_prefix, subject_prefix, db_path, h2_jar)
 
 
 @click.command()

src/pheval/infra/exomiserdb.py

@@ -1,6 +1,5 @@
 # -*- coding: cp936 -*-
 import logging as log
-import os
 from pathlib import Path
 
 import jaydebeapi
@@ -15,7 +14,7 @@ class DBConnector:
     def __init__(
         self, jar: Path, driver: str, server: str, database: str, user: str, password: str
     ):
-        self.jar = jar
+        self.jar = str(jar)
         self.driver = driver
         self.server = server
         self.database = database
@@ -61,10 +60,10 @@ def get_cursor(cls) -> jaydebeapi.Cursor:
 
 
 class ExomiserDB:
-    def __init__(self, db_path: Path):
+    def __init__(self, db_path: Path, h2_jar: Path):
         try:
             self.connector = DBConnector(  # noqa
-                jar=os.path.join(os.path.dirname(__file__), "../../../lib/h2-1.4.199.jar"),
+                jar=h2_jar,
                 driver="org.h2.Driver",
                 server=f"jdbc:h2:{db_path}",
                 user="sa",

src/pheval/utils/exomiser.py

@@ -3,14 +3,17 @@
 from pheval.infra.exomiserdb import ExomiserDB
 
 
-def semsim_to_exomiserdb(input_path: Path, object_prefix: str, subject_prefix: str, db_path: Path):
+def semsim_to_exomiserdb(
+    input_path: Path, object_prefix: str, subject_prefix: str, db_path: Path, h2_jar: 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/)
+        h2_jar (Path): H2 JAR file. JAR required to run H2 Database. e.g h2.jar
     """
-    exomiserdb = ExomiserDB(db_path)
+    exomiserdb = ExomiserDB(db_path, h2_jar)
     exomiserdb.import_from_semsim_file(input_path, object_prefix, subject_prefix)

tests/test_exomiser_db_ingestion.py

@@ -7,6 +7,7 @@
 from pheval.utils.exomiser import semsim_to_exomiserdb
 
 PHENO_FOLDER = os.path.abspath("./testdata/phenotype/2302_phenotype")
+H2_JAR = os.path.abspath("./tests/lib/h2-1.4.199.jar")
 
 
 class TestExomiserDBIngestion(unittest.TestCase):
@@ -17,7 +18,7 @@ def tearDown(self):
         _clean_db()
 
     def select_data(self, query: str):
-        edb = ExomiserDB(f"{PHENO_FOLDER}/2302_phenotype_test")
+        edb = ExomiserDB(f"{PHENO_FOLDER}/2302_phenotype_test", H2_JAR)
         with edb.connector as cnn:
             conn = DBConnection(cnn)
             cursor = conn.get_cursor()
@@ -36,6 +37,7 @@ def test_semsim_to_exomiserdb(self):
             object_prefix="MP",
             subject_prefix="HP",
             db_path=f"{PHENO_FOLDER}/2302_phenotype_test",
+            h2_jar=H2_JAR,
         )
         new_res = self.select_data(query)
         self.assertEqual(len(new_res), 9)