orrisroot
8ce9e09e69
Decouple CLI commands from internal helper logic and consolidate the core file transfer operations in the service layer to improve library portability. - Make MdrsClient subclass MdrsService to inherit resource resolution. - Remove all deprecated helper methods from BaseCommand. - Move core upload and download logic to a new transfer module. - Refactor all CLI commands to route actions through MdrsClient. - Eliminate circular imports between client and CLI command modules.
225 lines
9.3 KiB
Python
225 lines
9.3 KiB
Python
import os
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import re
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from typing import Any
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from unicodedata import normalize
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from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
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from mdrsclient.cache import CacheInterface
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from mdrsclient.config import ConfigFile
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from mdrsclient.connection import MDRSConnection
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from mdrsclient.exceptions import (
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IllegalArgumentException,
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MissingConfigurationException,
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UnauthorizedException,
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UnexpectedException,
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)
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from mdrsclient.models import File, Folder, Laboratory, Token, User
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from mdrsclient.utils import page_num_from_url
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class MdrsService:
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def __init__(self, connection: MDRSConnection):
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self.connection = connection
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@classmethod
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def create_connection(cls, remote: str, cache: CacheInterface | None = None) -> MDRSConnection:
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config = ConfigFile(remote)
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if config.url is None:
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raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
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return MDRSConnection(config.remote, config.url, cache=cache)
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def login(self, username: str, password: str) -> tuple[Token, User]:
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user_api = UsersApi(self.connection)
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token = user_api.token(username, password)
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self.connection.token = token
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user = user_api.current()
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self.connection.user = user
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return token, user
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def logout(self) -> None:
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self.connection.logout()
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def whoami(self) -> User:
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user_api = UsersApi(self.connection)
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return user_api.current()
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def get_laboratories(self) -> list[Laboratory]:
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laboratory_api = LaboratoriesApi(self.connection)
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labs = laboratory_api.list()
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self.connection.laboratories = labs
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return list(labs)
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def find_laboratory(self, name: str) -> Laboratory:
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if self.connection.laboratories.empty() or (self.connection.token and self.connection.token.is_expired):
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self.get_laboratories()
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laboratory = self.connection.laboratories.find_by_name(name)
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if laboratory is None:
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raise IllegalArgumentException(f"Laboratory `{name}` not found.")
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return laboratory
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def find_folder(self, laboratory: Laboratory, path: str, password: str | None = None) -> Folder:
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folder_api = FoldersApi(self.connection)
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folders = folder_api.list(laboratory.id, normalize("NFC", path))
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if len(folders) != 1:
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raise UnexpectedException(f"Folder `{path}` not found.")
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if folders[0].lock:
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if password is None:
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raise UnauthorizedException(f"Folder `{path}` is locked.")
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folder_api.auth(folders[0].id, password)
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return folder_api.retrieve(folders[0].id)
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def find_files(self, folder_id: str) -> list[File]:
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files_api = FilesApi(self.connection)
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page = 1
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results_file = []
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while page:
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result = files_api.list(folder_id, page)
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results_file.extend(result.results)
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page = 0
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if result.next:
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page = page_num_from_url(result.next)
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return results_file
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@staticmethod
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def is_doi(path_component: str) -> bool:
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return path_component.startswith("10.") and "/" in path_component
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@staticmethod
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def doi_suffix_id(doi: str) -> str:
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doi = doi.rstrip("/")
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slash_pos = doi.find("/")
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if slash_pos == -1:
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return doi
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suffix = doi[slash_pos + 1 :]
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dot_pos = suffix.rfind(".")
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return suffix[dot_pos + 1 :] if dot_pos != -1 else suffix
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@staticmethod
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def split_doi_and_subpath(doi_with_path: str) -> tuple[str, str]:
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first_slash = doi_with_path.find("/")
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if first_slash != -1:
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after_suffix_start = first_slash + 1
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after_first = doi_with_path[after_suffix_start:]
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second_slash = after_first.find("/")
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if second_slash != -1:
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doi_end = after_suffix_start + second_slash
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doi = doi_with_path[:doi_end]
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subpath = doi_with_path[doi_end:]
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if subpath == "/":
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return (doi, "")
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else:
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return (doi, subpath)
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else:
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return (doi_with_path, "")
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else:
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return (doi_with_path, "")
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@classmethod
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def parse_remote_host(cls, path: str) -> str:
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path_array = path.split(":")
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remote_host = path_array[0]
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if len(path_array) == 2 and path_array[1] != "" or len(path_array) > 2:
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raise IllegalArgumentException("Invalid remote host")
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return remote_host
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@classmethod
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def parse_remote_host_with_path(cls, path: str) -> tuple[str, str, str]:
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path = re.sub(r"//+|/\./+|/\.$", "/", path)
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if re.search(r"/\.\./|/\.\.$", path) is not None:
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raise IllegalArgumentException("Path traversal found.")
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path_array = path.split(":")
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if len(path_array) != 2:
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raise IllegalArgumentException("Invalid remote host.")
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remote_host = path_array[0]
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folder_array = path_array[1].split("/")
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is_absolute_path = folder_array[0] == ""
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if not is_absolute_path:
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raise IllegalArgumentException("Must be absolute paths.")
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del folder_array[0]
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if len(folder_array) == 0:
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laboratory = ""
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folder = ""
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else:
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laboratory = folder_array.pop(0)
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folder = "/" + "/".join(folder_array)
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return (remote_host, laboratory, folder)
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@classmethod
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def parse_doi_remote_host(cls, path: str) -> tuple[str, str, str]:
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parts = path.split(":", 1)
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if len(parts) != 2:
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raise IllegalArgumentException("remote_path must be in the form 'remote:10.xxxx/prefix.ID'")
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remote, doi_with_path = parts
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if not cls.is_doi(doi_with_path):
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raise IllegalArgumentException(f"Path `{doi_with_path}` does not look like a DOI.")
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doi, subpath = cls.split_doi_and_subpath(doi_with_path)
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return (remote, doi, subpath)
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def find_folder_by_doi(self, doi: str, password: str | None = None) -> tuple[Folder, Laboratory]:
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doi_clean = doi.rstrip("/")
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doi_id = self.doi_suffix_id(doi_clean)
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doi_api = DoiApi(self.connection)
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doi_resp = doi_api.retrieve(doi_id)
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returned_doi = doi_resp.doi.rstrip("/")
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if returned_doi.lower() != doi_clean.lower():
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raise IllegalArgumentException(
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f"DOI mismatch: requested `{doi_clean}` but server returned `{returned_doi}`."
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)
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folder_api = FoldersApi(self.connection)
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folder = folder_api.retrieve(doi_resp.folder_id)
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if folder.lock:
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if password is None:
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raise UnauthorizedException(f"Folder for DOI `{doi_clean}` is locked.")
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folder_api.auth(doi_resp.folder.id, password)
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lab_api = LaboratoriesApi(self.connection)
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labs = lab_api.list()
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lab = labs.find_by_id(folder.laboratory_id)
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if lab is None:
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raise UnexpectedException(f"Laboratory with id {folder.laboratory_id} not found.")
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self.connection.laboratories = labs
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return (folder, lab)
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def resolve_folder(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory]:
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path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
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if self.is_doi(path_component):
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remote, doi, subpath = self.parse_doi_remote_host(remote_path)
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doi_folder, laboratory = self.find_folder_by_doi(doi, password)
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if not subpath:
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return (doi_folder, laboratory)
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else:
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abs_path = doi_folder.path.rstrip("/") + subpath
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folder = self.find_folder(laboratory, abs_path, password)
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return (folder, laboratory)
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else:
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remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
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laboratory = self.find_laboratory(laboratory_name)
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folder = self.find_folder(laboratory, r_path, password)
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return (folder, laboratory)
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def resolve_file(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory, str]:
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path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
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if self.is_doi(path_component):
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remote, doi, subpath = self.parse_doi_remote_host(remote_path)
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doi_folder, laboratory = self.find_folder_by_doi(doi, password)
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subpath_clean = subpath.rstrip("/")
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if not subpath_clean:
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raise IllegalArgumentException("DOI path must point to a file, not a folder.")
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r_dirname = os.path.dirname(subpath_clean)
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r_basename = os.path.basename(subpath_clean)
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abs_path = doi_folder.path.rstrip("/") + r_dirname
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parent_folder = self.find_folder(laboratory, abs_path, password)
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return (parent_folder, laboratory, r_basename)
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else:
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remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
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r_path = r_path.rstrip("/")
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r_dirname = os.path.dirname(r_path)
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r_basename = os.path.basename(r_path)
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laboratory = self.find_laboratory(laboratory_name)
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parent_folder = self.find_folder(laboratory, r_dirname, password)
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return (parent_folder, laboratory, r_basename)
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