diff data_manager/data_manager_fetch_pharokka_db.py @ 0:97f310b8e308 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pharokka_database_fetcher/ commit 31e99045208605780b3fe4b89a999137adcabe13

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_pharokka_db.py	Thu Apr 20 07:51:43 2023 +0000
@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import subprocess
+import sys
+from datetime import datetime
+
+
+def main():
+    # Parse Command Line
+    parser = argparse.ArgumentParser(description="Create data manager JSON.")
+    parser.add_argument("--out", dest="output", action="store", help="JSON filename")
+    parser.add_argument("--version", dest="version", action="store", help="Version of the DB")
+    parser.add_argument(
+        "--test",
+        action="store_true",
+        help="option to test the script with an lighted database",
+    )
+
+    args = parser.parse_args()
+
+    # the output file of a DM is a json containing args that can be used by the DM
+    # most tools mainly use these args to find the extra_files_path for the DM, which can be used
+    # to store the DB data
+    with open(args.output) as fh:
+        params = json.load(fh)
+
+    workdir = params["output_data"][0]["extra_files_path"]
+    os.mkdir(workdir)
+
+    time = datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
+    db_value = "db_from_{0}".format(time)
+    db_path = os.path.join(workdir, db_value)
+
+    # create DB
+    if args.test:  # the test only checks that the pharokka download script is available and copies the test DB
+
+        # check if install_databases.py is there
+        command_args = ["install_databases.py", "-h"]
+        proc = subprocess.Popen(args=command_args, shell=False)
+        return_code = proc.wait()
+        if return_code:
+            print("Error downloading Pharokka database.", file=sys.stderr)
+            sys.exit(return_code)
+
+        # copy the test DB
+        test_db_path = os.path.join(os.path.dirname(os.path.realpath(__file__)), "subset_pharokka_db")
+        command_args = ["cp", "-r", test_db_path, db_path]
+    else:
+        command_args = ["install_databases.py", "-o", db_path]
+
+    proc = subprocess.Popen(args=command_args, shell=False)
+    return_code = proc.wait()
+    if return_code:
+        print("Error downloading Pharokka database.", file=sys.stderr)
+        sys.exit(return_code)
+
+    # Update Data Manager JSON and write to file
+    data_manager_entry = {
+        "data_tables": {
+            "pharokka_db": {
+                "value": db_value,
+                "dbkey": db_value,
+                "version": args.version,
+                "name": f"Pharokka DB version {args.version} downloaded at {datetime.now()}",
+                "path": db_path,
+            }
+        }
+    }
+
+    with open(os.path.join(args.output), "w+") as fh:
+        json.dump(data_manager_entry, fh, sort_keys=True)
+
+
+if __name__ == "__main__":
+    main()