From 6eea26db6ceadbc0dbdd77288f94cecff0fbc8b6 Mon Sep 17 00:00:00 2001
From: souzadevinicius <souzadevinicius@gmail.com>
Date: Wed, 11 Dec 2024 15:37:21 +0000
Subject: [PATCH] feat(runner.py): new function added: implemented a function
 to download and extract the exomiser runner

this function will handle the preinstallation processes for exomiser runner, and must exist for every different pheval runner ensuring a streamlined setup.
---
 src/pheval_exomiser/runner.py | 72 ++++++++++++++++++++++++++++++++++-
 1 file changed, 70 insertions(+), 2 deletions(-)

diff --git a/src/pheval_exomiser/runner.py b/src/pheval_exomiser/runner.py
index 6a6f862..edf7855 100644
--- a/src/pheval_exomiser/runner.py
+++ b/src/pheval_exomiser/runner.py
@@ -1,13 +1,20 @@
 """Exomiser Runner"""
 
+import os
+import zipfile
 from dataclasses import dataclass
 from pathlib import Path
 
+import requests
 from pheval.runners.runner import PhEvalRunner
 
 from pheval_exomiser.post_process.post_process import post_process_result_format
-from pheval_exomiser.prepare.tool_specific_configuration_options import ExomiserConfigurations
-from pheval_exomiser.prepare.write_application_properties import ExomiserConfigurationFileWriter
+from pheval_exomiser.prepare.tool_specific_configuration_options import (
+    ExomiserConfigurations,
+)
+from pheval_exomiser.prepare.write_application_properties import (
+    ExomiserConfigurationFileWriter,
+)
 from pheval_exomiser.run.run import prepare_batch_files, run_exomiser
 
 
@@ -22,6 +29,67 @@ class ExomiserPhEvalRunner(PhEvalRunner):
     config_file: Path
     version: str
 
+    def install(self, overwrite_existing: bool = False):
+        # Parse configuration options
+        configuration = ExomiserConfigurations.parse_obj(
+            self.input_dir_config.tool_specific_configuration_options
+        )
+        phenotype_version = configuration.application_properties.phenotype_data_version
+
+        # Define filenames and URLs
+        base_url = "https://data.monarchinitiative.org/exomiser"
+        filenames = [
+            f"{phenotype_version}_hg19.zip",
+            f"{phenotype_version}_hg38.zip",
+            f"{phenotype_version}_phenotype.zip",
+        ]
+        urls = [
+            f"{base_url}/{self.version}/exomiser-cli-{self.version}-distribution.zip",
+            *[f"{base_url}/data/{filename}" for filename in filenames],
+        ]
+
+        # Download files
+        os.makedirs("./data/tmp/", exist_ok=True)
+        for url in urls:
+            filename = url.split("/")[-1]
+            full_filename = f"./data/tmp/{filename}"
+
+            if os.path.exists(full_filename) and not overwrite_existing:
+                continue
+
+            response = requests.get(url)
+            response.raise_for_status()  # Raise an error for bad responses
+            with open(full_filename, "wb") as f:
+                f.write(response.content)
+
+        # Check if data directory exists
+        data_dir = f"exomiser-cli-{self.version}/data"
+        if os.path.exists(data_dir) and not overwrite_existing:
+            return
+
+        # Unzip distribution file
+        with zipfile.ZipFile(
+            f"exomiser-cli-{self.version}-distribution.zip", "r"
+        ) as zip_ref:
+            zip_ref.extractall(".")
+
+        # Unzip data files into the appropriate directory
+        os.makedirs(data_dir, exist_ok=True)
+        for filename in filenames:
+            with zipfile.ZipFile(filename, "r") as zip_ref:
+                zip_ref.extractall(data_dir)
+
+        # Update application.properties
+        properties_path = os.path.join(data_dir, "application.properties")
+        with open(properties_path, "a") as prop_file:
+            prop_file.writelines(
+                [
+                    f"exomiser.hg19.data-version={phenotype_version}\n",
+                    f"exomiser.hg38.data-version={phenotype_version}\n",
+                    f"exomiser.phenotype.data-version={phenotype_version}\n",
+                ]
+            )
+
     def prepare(self):
         """prepare"""
         print("preparing")