diff data_manager/data_manager_fetch_motus_db.py @ 0:0370fe3cf518 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/ commit f42263c2875a78500f141027803a38606ecb0f14

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_fetch_motus_db.py	Thu Oct 10 11:00:40 2024 +0000
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+
+import argparse
+import json
+import os
+import shutil
+import subprocess
+import sys
+import tarfile
+from datetime import datetime
+
+import wget
+
+version_mapping = {
+    "3.1.0": "https://zenodo.org/records/7778108/files/db_mOTU_v3.1.0.tar.gz",
+    "3.0.1": "https://zenodo.org/records/5140350/files/db_mOTU_v3.0.1.tar.gz",
+    "3.0.0": "https://zenodo.org/records/5012106/files/db_mOTU_v3.0.0.tar.gz",
+}
+
+
+def download_untar_store(url, tmp_path, dest_path):
+    """
+    Download a tar.gz file containing one folder,
+    extract that folder and move the content inside dest_path
+    """
+
+    extract_path = os.path.join(tmp_path, "extract")
+
+    os.makedirs(tmp_path, exist_ok=True)
+
+    # download data
+    filename = wget.download(url, out=tmp_path)
+    tarfile_path = os.path.join(tmp_path, filename)
+    tar = tarfile.open(tarfile_path)
+    tar.extractall(extract_path)
+
+    if len(list(os.listdir(extract_path))) > 1:
+        print("More then one folder in zipped file, aborting !")
+    else:
+        for folder in os.listdir(extract_path):
+            folder_path = os.path.join(extract_path, folder)
+
+            print(f"Copy data to {dest_path}")
+            shutil.copytree(folder_path, dest_path)
+            print("Done !")
+
+    shutil.rmtree(tmp_path)
+
+
+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)
+    tmp_path = os.path.join(workdir, "tmp")
+    url = version_mapping[args.version]
+
+    # create DB
+    if args.test:  # the test only checks that the pharokka download script is available
+
+        # check if link is there
+        command_args = ["wget", "--spider", url]
+        proc = subprocess.Popen(args=command_args, shell=False)
+        return_code = proc.wait()
+        if return_code:
+            print("Error downloading motus database.", file=sys.stderr)
+            sys.exit(return_code)
+
+        # copy the test DB
+        # TODO ones available: https://github.com/motu-tool/mOTUs/issues/121
+        test_db_path = os.path.join(
+            os.path.dirname(os.path.realpath(__file__)), "motus_test_DB_non_functional"
+        )
+        command_args = ["cp", "-r", test_db_path, db_path]
+        proc = subprocess.Popen(args=command_args, shell=False)
+        return_code = proc.wait()
+        if return_code:
+            print("Error copying motus database.", file=sys.stderr)
+            sys.exit(return_code)
+
+    else:
+
+        # download data
+        download_untar_store(url, tmp_path, db_path)
+
+    # Update Data Manager JSON and write to file
+    data_manager_entry = {
+        "data_tables": {
+            "motus_db_versioned": {
+                "value": db_value,
+                "version": args.version,
+                "name": f"mOTUs 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()