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authorBonfaceKilz2021-02-16 22:17:41 +0300
committerBonfaceKilz2021-02-16 22:19:31 +0300
commit0a70905e5b16e372bea9fd3e13a16fbd9152a416 (patch)
treea13894ad650e64c7a86a26c7d5ae1a198565c0aa /gn3/file_utils.py
parent53d81e0d9f66f09b63e5b36bd33c79e8bc930215 (diff)
downloadgenenetwork3-0a70905e5b16e372bea9fd3e13a16fbd9152a416.tar.gz
Add procedure for uploading gzipped file
* gn3/file_utils.py (extract_uploaded_file): New procedure. * tests/unit/test_file_utils.py: Test cases for ^^. * tests/unit/upload-data.tar.gz: New test data.
Diffstat (limited to 'gn3/file_utils.py')
-rw-r--r--gn3/file_utils.py29
1 files changed, 29 insertions, 0 deletions
diff --git a/gn3/file_utils.py b/gn3/file_utils.py
index a6929e1..d9301bb 100644
--- a/gn3/file_utils.py
+++ b/gn3/file_utils.py
@@ -2,9 +2,12 @@
import hashlib
import json
import os
+import shutil
+import tarfile
from functools import partial
from typing import Dict
+from werkzeug.utils import secure_filename
from gn3.settings import APP_DEFAULTS
@@ -46,3 +49,29 @@ def jsonfile_to_dict(json_file: str) -> Dict:
data = json.load(_file)
return data
raise FileNotFoundError
+
+
+def extract_uploaded_file(gzipped_file, target_dir: str) -> Dict:
+ """Get the (directory) hash of extracted contents of GZIPPED_FILE; and move
+contents to TARGET_DIR/<dir-hash>.
+
+ """
+ tar_target_loc = os.path.join(target_dir,
+ secure_filename(gzipped_file.filename))
+ gzipped_file.save(tar_target_loc)
+ try:
+ # Extract to "tar_target_loc/tempdir"
+ tar = tarfile.open(tar_target_loc)
+ tar.extractall(
+ path=os.path.join(target_dir, "tempdir"))
+ tar.close()
+ # pylint: disable=W0703
+ except Exception:
+ return {"status": 128, "error": "gzip failed to unpack file"}
+ dir_hash = get_dir_hash(tar_target_loc)
+ if os.path.exists(os.path.join(target_dir, dir_hash)):
+ shutil.rmtree(os.path.join(target_dir, 'tempdir'))
+ else:
+ os.rename(os.path.join(target_dir, "tempdir"),
+ os.path.join(target_dir, dir_hash))
+ return {"status": 0, "token": dir_hash}