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fix_filepath.py
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fix_filepath.py
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# This fixes an error where the projectdirs component of the path was
# for some reason changed to a symlink.
from pyscicat.client import from_credentials
from pyscicat.model import RawDataset, DerivedDataset
from dotenv import load_dotenv
import os
from pathlib import Path
load_dotenv()
SCICAT_URL = os.getenv("SCICAT_URL")
USERNAME = os.getenv("USERNAME")
INGEST_USER = os.getenv("INGEST_USER")
PASSWORD = os.getenv("PASSWORD")
assert type(SCICAT_URL) == str and len(SCICAT_URL) != 0
assert type(USERNAME) == str and len(USERNAME) != 0
assert type(PASSWORD) == str and len(PASSWORD) != 0
assert type(INGEST_USER) == str and len(INGEST_USER) != 0
client = from_credentials(SCICAT_URL, USERNAME, PASSWORD)
datasets = client.datasets_get_many()
for dataset in datasets:
path_array = list(Path(dataset["sourceFolder"]).parts)
path_array[3] = "projectdirs"
actualPath = os.path.join(*path_array)
dataset["sourceFolder"] = actualPath
if (dataset["type"] == "raw"):
dataset = RawDataset(**dataset)
elif dataset["type"] == "derived":
dataset = DerivedDataset(**dataset)
client.update_dataset(dataset, dataset.pid)