orrisroot
4c9954c1fd
flake8 reported 49 findings and pyright 10, and two of them were real bugs rather than matters of style. The rest were unused imports and four functions over the complexity limit. - Unlock a DOI folder with the id the DOI response carries, rather than an attribute the model does not have, which raised `AttributeError` on every locked DOI folder. - Size the `ls` Size column from the sub-folder on the row rather than from its parent, which pushed the later columns out of line. - Share the path resolution and the destination checks between `cp` and `mv`, and split the recursive download and the `ls` row printing, bringing all four functions under the complexity limit. - Accept a client built without a connection, which `config` and `version` rely on, and report the reason if one is then asked for. - Declare the config protocol's constructor for the type checker alone, so the protocol keeps its guard against being instantiated. - Remove 41 unused imports, and let flake8 accept black's spacing. - Point pyright at the project's own environment, without which it resolved no dependency and reported 124 findings that were not real. - Cover the two fixes and the shared `cp`/`mv` paths with new tests.
252 lines
10 KiB
Python
252 lines
10 KiB
Python
import os
|
|
import re
|
|
from unicodedata import normalize
|
|
|
|
from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
|
|
from mdrsclient.cache import CacheInterface
|
|
from mdrsclient.config import ConfigFile, ConfigInterface
|
|
from mdrsclient.connection import MDRSConnection
|
|
from mdrsclient.exceptions import (
|
|
IllegalArgumentException,
|
|
MissingConfigurationException,
|
|
UnauthorizedException,
|
|
UnexpectedException,
|
|
)
|
|
from mdrsclient.models import File, Folder, Laboratory, Token, User
|
|
from mdrsclient.utils import page_num_from_url
|
|
|
|
|
|
class MdrsService:
|
|
config_class: type[ConfigInterface] = ConfigFile
|
|
|
|
def __init__(self, connection: MDRSConnection | None, config_class: type[ConfigInterface] | None = None):
|
|
self.__connection = connection
|
|
if config_class is not None:
|
|
self.config_class = config_class
|
|
|
|
@property
|
|
def connection(self) -> MDRSConnection:
|
|
"""
|
|
The connection every remote operation goes through.
|
|
|
|
Optional to supply, because `config` and `version` do their work without a remote
|
|
and are reached through the same client. Asking for it when none was given is a
|
|
mistake in the caller, and says so rather than failing later on `None`.
|
|
"""
|
|
if self.__connection is None:
|
|
raise MissingConfigurationException("This operation requires a remote host.")
|
|
return self.__connection
|
|
|
|
@connection.setter
|
|
def connection(self, connection: MDRSConnection | None) -> None:
|
|
# Assignable as it always was: this is a property to check for absence on read,
|
|
# not to make the connection fixed once the client is built.
|
|
self.__connection = connection
|
|
|
|
@classmethod
|
|
def create_connection(
|
|
cls, remote: str, cache: CacheInterface | None = None, config: ConfigInterface | None = None
|
|
) -> MDRSConnection:
|
|
if config is None:
|
|
config = ConfigFile(remote)
|
|
elif config.remote != remote:
|
|
raise IllegalArgumentException("Remote host parameter mismatch.")
|
|
if config.url is None:
|
|
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
|
return MDRSConnection(config.remote, config.url, cache=cache)
|
|
|
|
def login(self, username: str, password: str) -> tuple[Token, User]:
|
|
user_api = UsersApi(self.connection)
|
|
token = user_api.token(username, password)
|
|
self.connection.token = token
|
|
user = user_api.current()
|
|
self.connection.user = user
|
|
return token, user
|
|
|
|
def logout(self) -> None:
|
|
self.connection.logout()
|
|
|
|
def whoami(self) -> User:
|
|
user_api = UsersApi(self.connection)
|
|
return user_api.current()
|
|
|
|
def get_laboratories(self) -> list[Laboratory]:
|
|
laboratory_api = LaboratoriesApi(self.connection)
|
|
labs = laboratory_api.list()
|
|
self.connection.laboratories = labs
|
|
return list(labs)
|
|
|
|
def find_laboratory(self, name: str) -> Laboratory:
|
|
if self.connection.laboratories.empty() or (self.connection.token and self.connection.token.is_expired):
|
|
self.get_laboratories()
|
|
laboratory = self.connection.laboratories.find_by_name(name)
|
|
if laboratory is None:
|
|
raise IllegalArgumentException(f"Laboratory `{name}` not found.")
|
|
return laboratory
|
|
|
|
def find_folder(self, laboratory: Laboratory, path: str, password: str | None = None) -> Folder:
|
|
folder_api = FoldersApi(self.connection)
|
|
folders = folder_api.list(laboratory.id, normalize("NFC", path))
|
|
if len(folders) != 1:
|
|
raise UnexpectedException(f"Folder `{path}` not found.")
|
|
if folders[0].lock:
|
|
if password is None:
|
|
raise UnauthorizedException(f"Folder `{path}` is locked.")
|
|
folder_api.auth(folders[0].id, password)
|
|
return folder_api.retrieve(folders[0].id)
|
|
|
|
def find_files(self, folder_id: str) -> list[File]:
|
|
files_api = FilesApi(self.connection)
|
|
page = 1
|
|
results_file = []
|
|
while page:
|
|
result = files_api.list(folder_id, page)
|
|
results_file.extend(result.results)
|
|
page = 0
|
|
if result.next:
|
|
page = page_num_from_url(result.next)
|
|
return results_file
|
|
|
|
@staticmethod
|
|
def is_doi(path_component: str) -> bool:
|
|
return path_component.startswith("10.") and "/" in path_component
|
|
|
|
@staticmethod
|
|
def doi_suffix_id(doi: str) -> str:
|
|
doi = doi.rstrip("/")
|
|
slash_pos = doi.find("/")
|
|
if slash_pos == -1:
|
|
return doi
|
|
suffix = doi[slash_pos + 1 :]
|
|
dot_pos = suffix.rfind(".")
|
|
return suffix[dot_pos + 1 :] if dot_pos != -1 else suffix
|
|
|
|
@staticmethod
|
|
def split_doi_and_subpath(doi_with_path: str) -> tuple[str, str]:
|
|
first_slash = doi_with_path.find("/")
|
|
if first_slash != -1:
|
|
after_suffix_start = first_slash + 1
|
|
after_first = doi_with_path[after_suffix_start:]
|
|
second_slash = after_first.find("/")
|
|
if second_slash != -1:
|
|
doi_end = after_suffix_start + second_slash
|
|
doi = doi_with_path[:doi_end]
|
|
subpath = doi_with_path[doi_end:]
|
|
if subpath == "/":
|
|
return (doi, "")
|
|
else:
|
|
return (doi, subpath)
|
|
else:
|
|
return (doi_with_path, "")
|
|
else:
|
|
return (doi_with_path, "")
|
|
|
|
@classmethod
|
|
def parse_remote_host(cls, path: str) -> str:
|
|
path_array = path.split(":")
|
|
remote_host = path_array[0]
|
|
if len(path_array) == 2 and path_array[1] != "" or len(path_array) > 2:
|
|
raise IllegalArgumentException("Invalid remote host")
|
|
return remote_host
|
|
|
|
@classmethod
|
|
def parse_remote_host_with_path(cls, path: str) -> tuple[str, str, str]:
|
|
path = re.sub(r"//+|/\./+|/\.$", "/", path)
|
|
if re.search(r"/\.\./|/\.\.$", path) is not None:
|
|
raise IllegalArgumentException("Path traversal found.")
|
|
path_array = path.split(":")
|
|
if len(path_array) != 2:
|
|
raise IllegalArgumentException("Invalid remote host.")
|
|
remote_host = path_array[0]
|
|
folder_array = path_array[1].split("/")
|
|
is_absolute_path = folder_array[0] == ""
|
|
if not is_absolute_path:
|
|
raise IllegalArgumentException("Must be absolute paths.")
|
|
del folder_array[0]
|
|
if len(folder_array) == 0:
|
|
laboratory = ""
|
|
folder = ""
|
|
else:
|
|
laboratory = folder_array.pop(0)
|
|
folder = "/" + "/".join(folder_array)
|
|
return (remote_host, laboratory, folder)
|
|
|
|
@classmethod
|
|
def parse_doi_remote_host(cls, path: str) -> tuple[str, str, str]:
|
|
parts = path.split(":", 1)
|
|
if len(parts) != 2:
|
|
raise IllegalArgumentException("remote_path must be in the form 'remote:10.xxxx/prefix.ID'")
|
|
remote, doi_with_path = parts
|
|
if not cls.is_doi(doi_with_path):
|
|
raise IllegalArgumentException(f"Path `{doi_with_path}` does not look like a DOI.")
|
|
doi, subpath = cls.split_doi_and_subpath(doi_with_path)
|
|
return (remote, doi, subpath)
|
|
|
|
def find_folder_by_doi(self, doi: str, password: str | None = None) -> tuple[Folder, Laboratory]:
|
|
doi_clean = doi.rstrip("/")
|
|
doi_id = self.doi_suffix_id(doi_clean)
|
|
doi_api = DoiApi(self.connection)
|
|
doi_resp = doi_api.retrieve(doi_id)
|
|
|
|
returned_doi = doi_resp.doi.rstrip("/")
|
|
if returned_doi.lower() != doi_clean.lower():
|
|
raise IllegalArgumentException(
|
|
f"DOI mismatch: requested `{doi_clean}` but server returned `{returned_doi}`."
|
|
)
|
|
|
|
folder_api = FoldersApi(self.connection)
|
|
folder = folder_api.retrieve(doi_resp.folder_id)
|
|
|
|
if folder.lock:
|
|
if password is None:
|
|
raise UnauthorizedException(f"Folder for DOI `{doi_clean}` is locked.")
|
|
folder_api.auth(doi_resp.folder_id, password)
|
|
|
|
lab_api = LaboratoriesApi(self.connection)
|
|
labs = lab_api.list()
|
|
lab = labs.find_by_id(folder.laboratory_id)
|
|
if lab is None:
|
|
raise UnexpectedException(f"Laboratory with id {folder.laboratory_id} not found.")
|
|
|
|
self.connection.laboratories = labs
|
|
return (folder, lab)
|
|
|
|
def resolve_folder(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory]:
|
|
path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
|
|
if self.is_doi(path_component):
|
|
remote, doi, subpath = self.parse_doi_remote_host(remote_path)
|
|
doi_folder, laboratory = self.find_folder_by_doi(doi, password)
|
|
if not subpath:
|
|
return (doi_folder, laboratory)
|
|
else:
|
|
abs_path = doi_folder.path.rstrip("/") + subpath
|
|
folder = self.find_folder(laboratory, abs_path, password)
|
|
return (folder, laboratory)
|
|
else:
|
|
remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
|
|
laboratory = self.find_laboratory(laboratory_name)
|
|
folder = self.find_folder(laboratory, r_path, password)
|
|
return (folder, laboratory)
|
|
|
|
def resolve_file(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory, str]:
|
|
path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
|
|
if self.is_doi(path_component):
|
|
remote, doi, subpath = self.parse_doi_remote_host(remote_path)
|
|
doi_folder, laboratory = self.find_folder_by_doi(doi, password)
|
|
subpath_clean = subpath.rstrip("/")
|
|
if not subpath_clean:
|
|
raise IllegalArgumentException("DOI path must point to a file, not a folder.")
|
|
r_dirname = os.path.dirname(subpath_clean)
|
|
r_basename = os.path.basename(subpath_clean)
|
|
abs_path = doi_folder.path.rstrip("/") + r_dirname
|
|
parent_folder = self.find_folder(laboratory, abs_path, password)
|
|
return (parent_folder, laboratory, r_basename)
|
|
else:
|
|
remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
|
|
r_path = r_path.rstrip("/")
|
|
r_dirname = os.path.dirname(r_path)
|
|
r_basename = os.path.basename(r_path)
|
|
laboratory = self.find_laboratory(laboratory_name)
|
|
parent_folder = self.find_folder(laboratory, r_dirname, password)
|
|
return (parent_folder, laboratory, r_basename)
|