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author | Alexander Kabui | 2021-05-15 01:20:46 +0300 |
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committer | GitHub | 2021-05-15 01:20:46 +0300 |
commit | c69b11cffba7547d65ac9812b0118cddad91be0d (patch) | |
tree | bfa55c23f702db5072e8839e44961dd72fd4a9e2 /gn3/fs_helpers.py | |
parent | bcba700bd2835f0a36042d781860b3407519f6d8 (diff) | |
parent | 46a96ec0b89620eed4874ada565a9643ac19a042 (diff) | |
download | genenetwork3-c69b11cffba7547d65ac9812b0118cddad91be0d.tar.gz |
Merge branch 'main' into feature/minor-fixes
Diffstat (limited to 'gn3/fs_helpers.py')
-rw-r--r-- | gn3/fs_helpers.py | 98 |
1 files changed, 98 insertions, 0 deletions
diff --git a/gn3/fs_helpers.py b/gn3/fs_helpers.py new file mode 100644 index 0000000..73f6567 --- /dev/null +++ b/gn3/fs_helpers.py @@ -0,0 +1,98 @@ +"""Procedures that operate on files/ directories""" +import hashlib +import json +import os +import random +import string +import tarfile +import pathlib + +from functools import partial +from typing import Dict +from typing import List +from werkzeug.utils import secure_filename + +import ipfshttpclient + + +def get_hash_of_files(files: List[str]) -> str: + """Given a list of valid of FILES, return their hash as a string""" + md5hash = hashlib.md5() + for file_path in sorted(files): + if not os.path.exists(file_path): + raise FileNotFoundError + with open(file_path, "rb") as file_: + for buf in iter(partial(file_.read, 4096), b''): + md5hash.update(bytearray( + hashlib.md5(buf).hexdigest(), "utf-8")) + return md5hash.hexdigest() + + +def get_dir_hash(directory: str) -> str: + """Return the hash of a DIRECTORY""" + if not os.path.exists(directory): + raise FileNotFoundError + all_files = [ + os.path.join(root, names) for root, _, files in os.walk(directory) + for names in sorted(files) + ] + return get_hash_of_files(all_files) + + +def jsonfile_to_dict(json_file: str) -> Dict: + """Give a JSON_FILE, return a python dict""" + with open(json_file) as _file: + data = json.load(_file) + return data + raise FileNotFoundError + + +def generate_random_n_string(n_length: int) -> str: + """Generate a random string that is N chars long""" + return ''.join( + random.choice(string.ascii_uppercase + string.digits) + for _ in range(n_length)) + + +def extract_uploaded_file(gzipped_file, + target_dir: str, + token: str = "") -> Dict: + """Get the (directory) hash of extracted contents of GZIPPED_FILE; and move +contents to TARGET_DIR/<dir-hash>. + + """ + if not token: + token = (f"{generate_random_n_string(6)}-" + f"{generate_random_n_string(6)}") + tar_target_loc = os.path.join(target_dir, token, + secure_filename(gzipped_file.filename)) + try: + if not os.path.exists(os.path.join(target_dir, token)): + os.mkdir(os.path.join(target_dir, token)) + gzipped_file.save(tar_target_loc) + # Extract to "tar_target_loc/token" + tar = tarfile.open(tar_target_loc) + tar.extractall(path=os.path.join(target_dir, token)) + tar.close() + # pylint: disable=W0703 + except Exception: + return {"status": 128, "error": "gzip failed to unpack file"} + return {"status": 0, "token": token} + + +def cache_ipfs_file(ipfs_file: str, + cache_dir: str, + ipfs_addr: str = "/ip4/127.0.0.1/tcp/5001") -> str: + """Check if a file exists in cache; if it doesn't, cache it. Return the + cached file location + + """ + file_loc = os.path.join(cache_dir, ipfs_file.split("ipfs/")[-1]) + if not os.path.exists(file_loc): + client = ipfshttpclient.connect(ipfs_addr) + client.get(ipfs_file, + target=str( + pathlib.Path + (os.path.join(cache_dir, + ipfs_file.split("ipfs/")[-1])).parent)) + return file_loc |