diff data_manager/pangolearn_dm.py @ 0:3eac657893fe draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_pangolearn commit 68adfad76cdb5ff13ec9fb49895a3cde2c502514"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/pangolearn_dm.py	Sat Apr 24 20:56:04 2021 +0000
@@ -0,0 +1,154 @@
+#!/usr/bin/env python
+
+import argparse
+import datetime
+import json
+import operator
+import os
+import shutil
+import sys
+import tarfile
+
+import requests
+
+
+def extract_date(tag_str):
+    parts = tag_str.split("_")
+    assert len(parts) < 3, "expected maximum of two parts, got " + str(parts)
+    tag_date = datetime.datetime.strptime(parts[0], "%Y-%m-%d")
+    if len(parts) == 2:
+        version = int(parts[1])
+        assert (
+            version < 24 * 60
+        )  # because the code stores versions as minutes of the day, it can't handle versions > 1440
+        tag_date += datetime.timedelta(minutes=version)
+    return tag_date
+
+
+def get_model_list(
+    existing_release_tags,
+    url="https://api.github.com/repos/cov-lineages/pangoLEARN/releases",
+):
+    response = requests.get(url)
+    if response.status_code == 200:
+        release_list = json.loads(response.text)
+        release_info = [
+            dict(
+                tag_name=e["tag_name"],
+                name=e["name"],
+                date=extract_date(e["tag_name"]),
+                tarball_url=e["tarball_url"],
+            )
+            for e in release_list
+            if e["tag_name"] not in existing_release_tags
+        ]
+        return release_info
+    else:
+        response.raise_for_status()
+
+
+def filter_by_date(existing_release_tags, start_date=None, end_date=None):
+    release_list = get_model_list(existing_release_tags)
+    return [
+        element
+        for element in release_list
+        if not (
+            (end_date is not None and element["date"] > end_date)
+            or (start_date is not None and element["date"] < start_date)
+        )
+    ]
+
+
+def download_and_unpack(url, output_directory):
+    response = requests.get(url)
+    if response.status_code == 200:
+        tmp_filename = url.split("/")[-1]
+        tmpfile = open(tmp_filename, "wb")
+        tmpfile.write(response.content)
+        tmpfile.close()
+        shutil.copy(tmp_filename, "/tmp")
+        tf = tarfile.open(tmp_filename)
+        pl_path = tf.next().name
+        tf.extractall(output_directory)
+        os.unlink(tmp_filename)
+        os.rename(
+            output_directory + "/" + pl_path + "/" + "pangoLEARN",
+            output_directory + "/" + tmp_filename,
+        )
+        shutil.rmtree(output_directory + "/" + pl_path)
+        return tmp_filename
+    else:
+        response.raise_for_status()
+
+
+def parse_date(d):
+    return datetime.datetime.strptime(d, "%Y-%m-%d")
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--testmode", default=False, action="store_true")
+    parser.add_argument("--latest", default=False, action="store_true")
+    parser.add_argument("--start_date", type=parse_date)
+    parser.add_argument("--end_date", type=parse_date)
+    parser.add_argument("--overwrite", default=False, action="store_true")
+    parser.add_argument('--pangolearn_format_version', default="1.0")
+    parser.add_argument("datatable_name")
+    parser.add_argument("galaxy_datamanager_filename")
+    args = parser.parse_args()
+
+    if args.testmode:
+        releases = filter_by_date(start_date=args.start_date, end_date=args.end_date)
+        for release in releases:
+            print(release["tag_name"], release["tarball_url"].split("/")[-1])
+        sys.exit(0)
+
+    with open(args.galaxy_datamanager_filename) as fh:
+        config = json.load(fh)
+
+    output_directory = config.get("output_data", [{}])[0].get("extra_files_path", None)
+    data_manager_dict = {}
+    data_manager_dict["data_tables"] = config.get("data_tables", {})
+    data_manager_dict["data_tables"][args.datatable_name] = data_manager_dict[
+        "data_tables"
+    ].get(args.datatable_name, [])
+
+    # NOTE: the data_manager_dict["data_tables"][args.datatable_name] is not actually populated with the
+    # contents of the existing data table, so the "no-overwrite" logic and the
+    # only-download-what-we-don't-have logic does not in fact work. It is left but unused for now.
+    if not args.overwrite:
+        existing_release_tags = set(
+            [
+                el["value"]
+                for el in data_manager_dict["data_tables"][args.datatable_name]
+            ]
+        )
+    else:
+        existing_release_tags = set()
+    if args.latest:
+        releases = [get_model_list(existing_release_tags)[0]]
+    else:
+        releases = filter_by_date(
+            existing_release_tags, start_date=args.start_date, end_date=args.end_date
+        )
+    releases_to_download = [
+        release
+        for release in releases
+        if release["tag_name"] not in existing_release_tags
+    ]
+    for release in releases_to_download:
+        tag = download_and_unpack(release["tarball_url"], output_directory)
+        data_manager_dict["data_tables"][args.datatable_name].append(
+            dict(
+                value=tag,
+                description=release["name"],
+                format_version=args.pangolearn_format_version,
+                path=output_directory + "/" + tag,
+            )
+        )
+    data_manager_dict["data_tables"][args.datatable_name].sort(
+        key=operator.itemgetter("value"), reverse=True
+    )
+    with open(args.galaxy_datamanager_filename, "w") as fh:
+        json.dump(data_manager_dict, fh, indent=2, sort_keys=True)