use concurrent for the multiple file uploads instead of multiprocess.
This commit is contained in:
parent
6e065e7e25
commit
c724af538b
@ -4,6 +4,7 @@ import requests
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from pydantic import parse_obj_as
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from pydantic import parse_obj_as
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from requests import Response
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from requests import Response
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from mdrsclient.connection import MDRSConnection
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from mdrsclient.exceptions import (
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from mdrsclient.exceptions import (
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BadRequestException,
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BadRequestException,
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ForbiddenException,
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ForbiddenException,
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@ -11,27 +12,28 @@ from mdrsclient.exceptions import (
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UnexpectedException,
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UnexpectedException,
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)
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)
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from mdrsclient.models import DRFStandardizedErrors
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from mdrsclient.models import DRFStandardizedErrors
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from mdrsclient.session import MDRSSession
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class BaseApi(ABC):
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class BaseApi(ABC):
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def __init__(self, session: MDRSSession) -> None:
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connection: MDRSConnection
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self.session = session
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def __init__(self, connection: MDRSConnection) -> None:
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self.connection = connection
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def _get(self, url, *args, **kwargs) -> Response:
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def _get(self, url, *args, **kwargs) -> Response:
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return self.session.get(self.__build_url(url), *args, **kwargs)
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return self.connection.session.get(self.__build_url(url), *args, **kwargs)
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def _post(self, url, *args, **kwargs) -> Response:
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def _post(self, url, *args, **kwargs) -> Response:
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return self.session.post(self.__build_url(url), *args, **kwargs)
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return self.connection.session.post(self.__build_url(url), *args, **kwargs)
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def _put(self, url, *args, **kwargs) -> Response:
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def _put(self, url, *args, **kwargs) -> Response:
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return self.session.put(self.__build_url(url), *args, **kwargs)
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return self.connection.session.put(self.__build_url(url), *args, **kwargs)
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def _delete(self, url, *args, **kwargs) -> Response:
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def _delete(self, url, *args, **kwargs) -> Response:
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return self.session.delete(self.__build_url(url), *args, **kwargs)
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return self.connection.session.delete(self.__build_url(url), *args, **kwargs)
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def _patch(self, url, *args, **kwargs) -> Response:
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def _patch(self, url, *args, **kwargs) -> Response:
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return self.session.patch(self.__build_url(url), *args, **kwargs)
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return self.connection.session.patch(self.__build_url(url), *args, **kwargs)
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def _raise_response_error(self, response: Response) -> None:
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def _raise_response_error(self, response: Response) -> None:
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if response.status_code >= 300:
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if response.status_code >= 300:
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@ -48,4 +50,4 @@ class BaseApi(ABC):
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raise UnexpectedException(errors.errors[0].detail)
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raise UnexpectedException(errors.errors[0].detail)
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def __build_url(self, *args: tuple) -> str:
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def __build_url(self, *args: tuple) -> str:
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return self.session.build_url(*args)
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return self.connection.build_url(*args)
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@ -21,7 +21,7 @@ class FileApi(BaseApi):
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def retrieve(self, id: str) -> File:
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def retrieve(self, id: str) -> File:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + id + "/"
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url = self.ENTRYPOINT + id + "/"
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url)
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response = self._get(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return parse_obj_as(File, response.json())
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return parse_obj_as(File, response.json())
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@ -29,7 +29,7 @@ class FileApi(BaseApi):
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def create(self, folder_id: str, path: str) -> str:
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def create(self, folder_id: str, path: str) -> str:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT
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url = self.ENTRYPOINT
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token_check(self.session)
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token_check(self.connection)
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data = {"folder_id": folder_id}
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data = {"folder_id": folder_id}
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try:
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try:
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with open(path, mode="rb") as fp:
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with open(path, mode="rb") as fp:
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@ -43,7 +43,7 @@ class FileApi(BaseApi):
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def update(self, file: File, path: str | None) -> bool:
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def update(self, file: File, path: str | None) -> bool:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + file.id + "/"
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url = self.ENTRYPOINT + file.id + "/"
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token_check(self.session)
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token_check(self.connection)
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if path is not None:
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if path is not None:
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try:
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try:
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with open(path, mode="rb") as fp:
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with open(path, mode="rb") as fp:
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@ -59,7 +59,7 @@ class FileApi(BaseApi):
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def destroy(self, file: File) -> bool:
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def destroy(self, file: File) -> bool:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + file.id + "/"
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url = self.ENTRYPOINT + file.id + "/"
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token_check(self.session)
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token_check(self.connection)
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response = self._delete(url)
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response = self._delete(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return True
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return True
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@ -68,7 +68,7 @@ class FileApi(BaseApi):
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + file.id + "/move/"
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url = self.ENTRYPOINT + file.id + "/move/"
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data = {"folder": folder_id}
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data = {"folder": folder_id}
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token_check(self.session)
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token_check(self.connection)
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response = self._post(url, data=data)
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response = self._post(url, data=data)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return True
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return True
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@ -76,7 +76,7 @@ class FileApi(BaseApi):
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def metadata(self, file: File) -> dict:
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def metadata(self, file: File) -> dict:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + file.id + "/metadata/"
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url = self.ENTRYPOINT + file.id + "/metadata/"
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url)
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response = self._get(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return response.json()
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return response.json()
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@ -21,7 +21,7 @@ class FolderApi(BaseApi):
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT
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url = self.ENTRYPOINT
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params = {"path": path, "laboratory_id": laboratory_id}
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params = {"path": path, "laboratory_id": laboratory_id}
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url, params=params)
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response = self._get(url, params=params)
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self._raise_response_error(response)
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self._raise_response_error(response)
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ret: list[FolderSimple] = []
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ret: list[FolderSimple] = []
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@ -32,7 +32,7 @@ class FolderApi(BaseApi):
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def retrieve(self, id: str) -> Folder:
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def retrieve(self, id: str) -> Folder:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + id + "/"
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url = self.ENTRYPOINT + id + "/"
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url)
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response = self._get(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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ret = parse_obj_as(Folder, response.json())
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ret = parse_obj_as(Folder, response.json())
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@ -42,7 +42,7 @@ class FolderApi(BaseApi):
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT
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url = self.ENTRYPOINT
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data = {"name": name, "parent_id": parent_id, "description": "", "template_id": -1}
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data = {"name": name, "parent_id": parent_id, "description": "", "template_id": -1}
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token_check(self.session)
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token_check(self.connection)
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response = self._post(url, data=data)
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response = self._post(url, data=data)
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self._raise_response_error(response)
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self._raise_response_error(response)
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ret = parse_obj_as(FolderCreateResponse, response.json())
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ret = parse_obj_as(FolderCreateResponse, response.json())
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@ -55,7 +55,7 @@ class FolderApi(BaseApi):
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"name": folder.name,
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"name": folder.name,
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"description": folder.description,
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"description": folder.description,
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}
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}
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token_check(self.session)
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token_check(self.connection)
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response = self._put(url, data=data)
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response = self._put(url, data=data)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return True
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return True
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@ -63,7 +63,7 @@ class FolderApi(BaseApi):
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def destroy(self, id: str) -> bool:
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def destroy(self, id: str) -> bool:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + id + "/"
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url = self.ENTRYPOINT + id + "/"
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token_check(self.session)
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token_check(self.connection)
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response = self._delete(url)
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response = self._delete(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return True
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return True
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@ -71,7 +71,7 @@ class FolderApi(BaseApi):
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def metadata(self, id: str) -> dict:
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def metadata(self, id: str) -> dict:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT + id + "/metadata/"
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url = self.ENTRYPOINT + id + "/metadata/"
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url)
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response = self._get(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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return response.json()
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return response.json()
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@ -14,7 +14,7 @@ class LaboratoryApi(BaseApi):
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def list(self) -> Laboratories:
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def list(self) -> Laboratories:
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
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url = self.ENTRYPOINT
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url = self.ENTRYPOINT
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token_check(self.session)
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token_check(self.connection)
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response = self._get(url)
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response = self._get(url)
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self._raise_response_error(response)
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self._raise_response_error(response)
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ret = Laboratories([])
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ret = Laboratories([])
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@ -1,15 +1,15 @@
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from mdrsclient.api.user import UserApi
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from mdrsclient.api.user import UserApi
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from mdrsclient.connection import MDRSConnection
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from mdrsclient.exceptions import UnauthorizedException
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from mdrsclient.exceptions import UnauthorizedException
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from mdrsclient.session import MDRSSession
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def token_check(session: MDRSSession) -> None:
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def token_check(connection: MDRSConnection) -> None:
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if session.token is not None:
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if connection.token is not None:
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if session.token.is_refresh_required:
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if connection.token.is_refresh_required:
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user_api = UserApi(session)
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user_api = UserApi(connection)
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try:
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try:
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session.token = user_api.refresh(session.token)
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connection.token = user_api.refresh(connection.token)
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except UnauthorizedException:
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except UnauthorizedException:
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session.logout()
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connection.logout()
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elif session.token.is_expired:
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elif connection.token.is_expired:
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session.logout()
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connection.logout()
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@ -1,7 +1,7 @@
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import dataclasses
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import dataclasses
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import os
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import os
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from argparse import Namespace, _SubParsersAction
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from argparse import Namespace, _SubParsersAction
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from multiprocessing import Process
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from concurrent.futures import ThreadPoolExecutor
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from pydantic import parse_obj_as
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from pydantic import parse_obj_as
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from pydantic.dataclasses import dataclass
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from pydantic.dataclasses import dataclass
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@ -9,18 +9,18 @@ from pydantic.dataclasses import dataclass
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from mdrsclient.api import FileApi, FolderApi
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from mdrsclient.api import FileApi, FolderApi
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from mdrsclient.commands.base import BaseCommand
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from mdrsclient.commands.base import BaseCommand
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from mdrsclient.commands.utils import (
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from mdrsclient.commands.utils import (
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create_session,
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create_connection,
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find_folder,
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find_folder,
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find_laboratory,
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find_laboratory,
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parse_remote_host_with_path,
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parse_remote_host_with_path,
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)
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)
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from mdrsclient.connection import MDRSConnection
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from mdrsclient.exceptions import (
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from mdrsclient.exceptions import (
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IllegalArgumentException,
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IllegalArgumentException,
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MDRSException,
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MDRSException,
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UnexpectedException,
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UnexpectedException,
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)
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)
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from mdrsclient.models import File, Folder
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from mdrsclient.models import File, Folder
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from mdrsclient.session import MDRSSession
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from mdrsclient.settings import NUMBER_OF_PROCESS
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from mdrsclient.settings import NUMBER_OF_PROCESS
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@ -66,14 +66,14 @@ class FileCommand(BaseCommand):
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local_path = os.path.realpath(args.local_path)
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local_path = os.path.realpath(args.local_path)
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if not os.path.exists(local_path):
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if not os.path.exists(local_path):
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raise IllegalArgumentException(f"File or directory `{args.local_path}` not found.")
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raise IllegalArgumentException(f"File or directory `{args.local_path}` not found.")
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session = create_session(remote)
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connection = create_connection(remote)
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laboratory = find_laboratory(session, laboratory_name)
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laboratory = find_laboratory(connection, laboratory_name)
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folder = find_folder(session, laboratory, path)
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folder = find_folder(connection, laboratory, path)
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upload_files: list[UploadFile] = []
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upload_files: list[UploadFile] = []
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if os.path.isdir(local_path):
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if os.path.isdir(local_path):
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if not args.recursive:
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if not args.recursive:
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raise IllegalArgumentException(f"Cannot upload `{args.local_path}`: Is a directory.")
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raise IllegalArgumentException(f"Cannot upload `{args.local_path}`: Is a directory.")
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folder_api = FolderApi(session)
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folder_api = FolderApi(connection)
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folders: dict[str, Folder] = {}
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folders: dict[str, Folder] = {}
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folders[path] = folder
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folders[path] = folder
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local_basename = os.path.basename(local_path)
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local_basename = os.path.basename(local_path)
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@ -107,7 +107,7 @@ class FileCommand(BaseCommand):
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upload_files.append(UploadFile(folders[dest_folder_path], os.path.join(dirpath, filename)))
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upload_files.append(UploadFile(folders[dest_folder_path], os.path.join(dirpath, filename)))
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else:
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else:
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upload_files.append(UploadFile(folder, local_path))
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upload_files.append(UploadFile(folder, local_path))
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FileCommand._multiple_upload(session, upload_files)
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FileCommand._multiple_upload(connection, upload_files)
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@staticmethod
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@staticmethod
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def download(args: Namespace) -> None:
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def download(args: Namespace) -> None:
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@ -115,16 +115,16 @@ class FileCommand(BaseCommand):
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path = path.rstrip("/")
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path = path.rstrip("/")
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parent_path = os.path.dirname(path)
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parent_path = os.path.dirname(path)
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file_name = os.path.basename(path)
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file_name = os.path.basename(path)
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session = create_session(remote)
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connection = create_connection(remote)
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if not os.path.isdir(args.local_path):
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if not os.path.isdir(args.local_path):
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raise IllegalArgumentException(f"Local directory `{args.local_path}` not found.")
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raise IllegalArgumentException(f"Local directory `{args.local_path}` not found.")
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local_file = os.path.join(args.local_path, file_name)
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local_file = os.path.join(args.local_path, file_name)
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laboratory = find_laboratory(session, laboratory_name)
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laboratory = find_laboratory(connection, laboratory_name)
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folder = find_folder(session, laboratory, parent_path)
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folder = find_folder(connection, laboratory, parent_path)
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file = folder.find_file(file_name)
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file = folder.find_file(file_name)
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if file is None:
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if file is None:
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raise IllegalArgumentException(f"File `{file_name}` not found.")
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raise IllegalArgumentException(f"File `{file_name}` not found.")
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r = session.get(session.build_url("v2/" + file.download_url), stream=True)
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r = connection.session.get(connection.build_url("v2/" + file.download_url), stream=True)
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try:
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try:
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with open(local_file, "wb") as f:
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with open(local_file, "wb") as f:
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for chunk in r.iter_content(chunk_size=4096):
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for chunk in r.iter_content(chunk_size=4096):
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@ -151,17 +151,17 @@ class FileCommand(BaseCommand):
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else:
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else:
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dest_dirpath = os.path.dirname(dest_path)
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dest_dirpath = os.path.dirname(dest_path)
|
||||||
dest_filename = os.path.basename(dest_path)
|
dest_filename = os.path.basename(dest_path)
|
||||||
session = create_session(src_remote)
|
connection = create_connection(src_remote)
|
||||||
laboratory = find_laboratory(session, src_laboratory_name)
|
laboratory = find_laboratory(connection, src_laboratory_name)
|
||||||
src_folder = find_folder(session, laboratory, src_dirpath)
|
src_folder = find_folder(connection, laboratory, src_dirpath)
|
||||||
dest_folder = find_folder(session, laboratory, dest_dirpath)
|
dest_folder = find_folder(connection, laboratory, dest_dirpath)
|
||||||
src_file = src_folder.find_file(src_filename)
|
src_file = src_folder.find_file(src_filename)
|
||||||
if src_file is None:
|
if src_file is None:
|
||||||
raise IllegalArgumentException(f"File `{src_filename}` not found.")
|
raise IllegalArgumentException(f"File `{src_filename}` not found.")
|
||||||
dest_file = dest_folder.find_file(dest_filename)
|
dest_file = dest_folder.find_file(dest_filename)
|
||||||
if dest_file is not None:
|
if dest_file is not None:
|
||||||
raise IllegalArgumentException(f"File `{dest_filename}` already exists.")
|
raise IllegalArgumentException(f"File `{dest_filename}` already exists.")
|
||||||
file_api = FileApi(session)
|
file_api = FileApi(connection)
|
||||||
if src_folder.id != dest_folder.id:
|
if src_folder.id != dest_folder.id:
|
||||||
file_api.move(src_file, dest_folder.id)
|
file_api.move(src_file, dest_folder.id)
|
||||||
if dest_filename != src_filename:
|
if dest_filename != src_filename:
|
||||||
@ -175,13 +175,13 @@ class FileCommand(BaseCommand):
|
|||||||
path = path.rstrip("/")
|
path = path.rstrip("/")
|
||||||
parent_path = os.path.dirname(path)
|
parent_path = os.path.dirname(path)
|
||||||
file_name = os.path.basename(path)
|
file_name = os.path.basename(path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, parent_path)
|
folder = find_folder(connection, laboratory, parent_path)
|
||||||
file = folder.find_file(file_name)
|
file = folder.find_file(file_name)
|
||||||
if file is None:
|
if file is None:
|
||||||
raise IllegalArgumentException(f"File `{file_name}` not found.")
|
raise IllegalArgumentException(f"File `{file_name}` not found.")
|
||||||
file_api = FileApi(session)
|
file_api = FileApi(connection)
|
||||||
file_api.destroy(file)
|
file_api.destroy(file)
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
@ -190,42 +190,31 @@ class FileCommand(BaseCommand):
|
|||||||
path = path.rstrip("/")
|
path = path.rstrip("/")
|
||||||
parent_path = os.path.dirname(path)
|
parent_path = os.path.dirname(path)
|
||||||
file_name = os.path.basename(path)
|
file_name = os.path.basename(path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, parent_path)
|
folder = find_folder(connection, laboratory, parent_path)
|
||||||
file = folder.find_file(file_name)
|
file = folder.find_file(file_name)
|
||||||
if file is None:
|
if file is None:
|
||||||
raise IllegalArgumentException(f"File `{file_name}` not found.")
|
raise IllegalArgumentException(f"File `{file_name}` not found.")
|
||||||
file_api = FileApi(session)
|
file_api = FileApi(connection)
|
||||||
metadata = file_api.metadata(file)
|
metadata = file_api.metadata(file)
|
||||||
print(metadata)
|
print(metadata)
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def _multiple_upload(session: MDRSSession, upload_files: list[UploadFile]) -> None:
|
def _multiple_upload(connection: MDRSConnection, upload_files: list[UploadFile]) -> None:
|
||||||
processes: list[Process] = []
|
file_api = FileApi(connection)
|
||||||
for idx in range(NUMBER_OF_PROCESS):
|
with ThreadPoolExecutor(max_workers=NUMBER_OF_PROCESS) as pool:
|
||||||
processes.append(
|
pool.map(lambda x: FileCommand._multiple_upload_worker(file_api, x), upload_files)
|
||||||
Process(
|
|
||||||
target=FileCommand._multiple_upload_worker,
|
|
||||||
args=(session, upload_files, idx, NUMBER_OF_PROCESS),
|
|
||||||
)
|
|
||||||
)
|
|
||||||
for process in processes:
|
|
||||||
process.start()
|
|
||||||
for process in processes:
|
|
||||||
process.join()
|
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def _multiple_upload_worker(session: MDRSSession, upload_files: list[UploadFile], idx: int, num_proc: int) -> None:
|
def _multiple_upload_worker(file_api: FileApi, upload_file: UploadFile) -> None:
|
||||||
file_api = FileApi(session)
|
file_name = os.path.basename(upload_file.path)
|
||||||
for upload_file in upload_files[idx::num_proc]:
|
file = next((x for x in upload_file.folder.files if x.name == file_name), None)
|
||||||
file_name = os.path.basename(upload_file.path)
|
try:
|
||||||
file = next((x for x in upload_file.folder.files if x.name == file_name), None)
|
if file is None:
|
||||||
try:
|
file_api.create(upload_file.folder.id, upload_file.path)
|
||||||
if file is None:
|
else:
|
||||||
file_api.create(upload_file.folder.id, upload_file.path)
|
file_api.update(file, upload_file.path)
|
||||||
else:
|
pass
|
||||||
file_api.update(file, upload_file.path)
|
except MDRSException as e:
|
||||||
pass
|
print(f"API Error: {e}")
|
||||||
except MDRSException as e:
|
|
||||||
print(f"API Error: {e}")
|
|
||||||
|
@ -4,7 +4,7 @@ from argparse import Namespace, _SubParsersAction
|
|||||||
from mdrsclient.api import FolderApi
|
from mdrsclient.api import FolderApi
|
||||||
from mdrsclient.commands.base import BaseCommand
|
from mdrsclient.commands.base import BaseCommand
|
||||||
from mdrsclient.commands.utils import (
|
from mdrsclient.commands.utils import (
|
||||||
create_session,
|
create_connection,
|
||||||
find_folder,
|
find_folder,
|
||||||
find_laboratory,
|
find_laboratory,
|
||||||
parse_remote_host_with_path,
|
parse_remote_host_with_path,
|
||||||
@ -34,9 +34,9 @@ class FolderCommand(BaseCommand):
|
|||||||
@staticmethod
|
@staticmethod
|
||||||
def list(args: Namespace) -> None:
|
def list(args: Namespace) -> None:
|
||||||
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, path)
|
folder = find_folder(connection, laboratory, path)
|
||||||
label = {
|
label = {
|
||||||
"type": "Type",
|
"type": "Type",
|
||||||
"acl": "Access",
|
"acl": "Access",
|
||||||
@ -49,7 +49,7 @@ class FolderCommand(BaseCommand):
|
|||||||
for key in label.keys():
|
for key in label.keys():
|
||||||
length[key] = len(label[key])
|
length[key] = len(label[key])
|
||||||
for sub_folder in folder.sub_folders:
|
for sub_folder in folder.sub_folders:
|
||||||
sub_laboratory = session.laboratories.find_by_id(sub_folder.lab_id)
|
sub_laboratory = connection.laboratories.find_by_id(sub_folder.lab_id)
|
||||||
sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
|
sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
|
||||||
length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
|
length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
|
||||||
length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
|
length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
|
||||||
@ -71,7 +71,7 @@ class FolderCommand(BaseCommand):
|
|||||||
print("-" * len(header.expandtabs()))
|
print("-" * len(header.expandtabs()))
|
||||||
|
|
||||||
for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
|
for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
|
||||||
sub_laboratory = session.laboratories.find_by_id(sub_folder.lab_id)
|
sub_laboratory = connection.laboratories.find_by_id(sub_folder.lab_id)
|
||||||
sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
|
sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
|
||||||
print(
|
print(
|
||||||
f"{'[d]':{length['type']}}\t{sub_folder.access_level_name:{length['acl']}}\t"
|
f"{'[d]':{length['type']}}\t{sub_folder.access_level_name:{length['acl']}}\t"
|
||||||
@ -91,27 +91,27 @@ class FolderCommand(BaseCommand):
|
|||||||
path = path.rstrip("/")
|
path = path.rstrip("/")
|
||||||
parent_path = os.path.dirname(path)
|
parent_path = os.path.dirname(path)
|
||||||
folder_name = os.path.basename(path)
|
folder_name = os.path.basename(path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, parent_path)
|
folder = find_folder(connection, laboratory, parent_path)
|
||||||
folder_api = FolderApi(session)
|
folder_api = FolderApi(connection)
|
||||||
folder_api.create(folder_name, folder.id)
|
folder_api.create(folder_name, folder.id)
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def rmdir(args: Namespace) -> None:
|
def rmdir(args: Namespace) -> None:
|
||||||
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, path)
|
folder = find_folder(connection, laboratory, path)
|
||||||
folder_api = FolderApi(session)
|
folder_api = FolderApi(connection)
|
||||||
folder_api.destroy(folder.id)
|
folder_api.destroy(folder.id)
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def metadata(args: Namespace) -> None:
|
def metadata(args: Namespace) -> None:
|
||||||
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
(remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory = find_laboratory(session, laboratory_name)
|
laboratory = find_laboratory(connection, laboratory_name)
|
||||||
folder = find_folder(session, laboratory, path)
|
folder = find_folder(connection, laboratory, path)
|
||||||
folder_api = FolderApi(session)
|
folder_api = FolderApi(connection)
|
||||||
metadata = folder_api.metadata(folder.id)
|
metadata = folder_api.metadata(folder.id)
|
||||||
print(metadata)
|
print(metadata)
|
||||||
|
@ -2,7 +2,7 @@ from argparse import Namespace, _SubParsersAction
|
|||||||
|
|
||||||
from mdrsclient.api import LaboratoryApi
|
from mdrsclient.api import LaboratoryApi
|
||||||
from mdrsclient.commands.base import BaseCommand
|
from mdrsclient.commands.base import BaseCommand
|
||||||
from mdrsclient.commands.utils import create_session, parse_remote_host
|
from mdrsclient.commands.utils import create_connection, parse_remote_host
|
||||||
|
|
||||||
|
|
||||||
class LaboratoryCommand(BaseCommand):
|
class LaboratoryCommand(BaseCommand):
|
||||||
@ -16,10 +16,10 @@ class LaboratoryCommand(BaseCommand):
|
|||||||
@staticmethod
|
@staticmethod
|
||||||
def list(args: Namespace) -> None:
|
def list(args: Namespace) -> None:
|
||||||
remote = parse_remote_host(args.remote)
|
remote = parse_remote_host(args.remote)
|
||||||
session = create_session(remote)
|
connection = create_connection(remote)
|
||||||
laboratory_api = LaboratoryApi(session)
|
laboratory_api = LaboratoryApi(connection)
|
||||||
laboratories = laboratory_api.list()
|
laboratories = laboratory_api.list()
|
||||||
session.laboratories = laboratories
|
connection.laboratories = laboratories
|
||||||
label = {"id": "ID", "name": "Name", "pi_name": "PI", "full_name": "Laboratory"}
|
label = {"id": "ID", "name": "Name", "pi_name": "PI", "full_name": "Laboratory"}
|
||||||
length: dict[str, int] = {}
|
length: dict[str, int] = {}
|
||||||
for key in label.keys():
|
for key in label.keys():
|
||||||
|
@ -5,8 +5,8 @@ from mdrsclient.api import UserApi
|
|||||||
from mdrsclient.commands.base import BaseCommand
|
from mdrsclient.commands.base import BaseCommand
|
||||||
from mdrsclient.commands.utils import parse_remote_host
|
from mdrsclient.commands.utils import parse_remote_host
|
||||||
from mdrsclient.config import ConfigFile
|
from mdrsclient.config import ConfigFile
|
||||||
|
from mdrsclient.connection import MDRSConnection
|
||||||
from mdrsclient.exceptions import MissingConfigurationException
|
from mdrsclient.exceptions import MissingConfigurationException
|
||||||
from mdrsclient.session import MDRSSession
|
|
||||||
|
|
||||||
|
|
||||||
class UserCommand(BaseCommand):
|
class UserCommand(BaseCommand):
|
||||||
@ -31,13 +31,13 @@ class UserCommand(BaseCommand):
|
|||||||
config = ConfigFile(remote)
|
config = ConfigFile(remote)
|
||||||
if config.url is None:
|
if config.url is None:
|
||||||
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
||||||
session = MDRSSession(config.remote, config.url)
|
connection = MDRSConnection(config.remote, config.url)
|
||||||
username = input("Username: ").strip()
|
username = input("Username: ").strip()
|
||||||
password = getpass.getpass("Password: ").strip()
|
password = getpass.getpass("Password: ").strip()
|
||||||
user_api = UserApi(session)
|
user_api = UserApi(connection)
|
||||||
(user, token) = user_api.auth(username, password)
|
(user, token) = user_api.auth(username, password)
|
||||||
session.user = user
|
connection.user = user
|
||||||
session.token = token
|
connection.token = token
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def logout(args: Namespace) -> None:
|
def logout(args: Namespace) -> None:
|
||||||
@ -45,8 +45,8 @@ class UserCommand(BaseCommand):
|
|||||||
config = ConfigFile(remote)
|
config = ConfigFile(remote)
|
||||||
if config.url is None:
|
if config.url is None:
|
||||||
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
||||||
session = MDRSSession(config.remote, config.url)
|
connection = MDRSConnection(config.remote, config.url)
|
||||||
session.logout()
|
connection.logout()
|
||||||
|
|
||||||
@staticmethod
|
@staticmethod
|
||||||
def whoami(args: Namespace) -> None:
|
def whoami(args: Namespace) -> None:
|
||||||
@ -54,8 +54,8 @@ class UserCommand(BaseCommand):
|
|||||||
config = ConfigFile(remote)
|
config = ConfigFile(remote)
|
||||||
if config.url is None:
|
if config.url is None:
|
||||||
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
||||||
session = MDRSSession(config.remote, config.url)
|
connection = MDRSConnection(config.remote, config.url)
|
||||||
if session.token is not None and session.token.is_expired:
|
if connection.token is not None and connection.token.is_expired:
|
||||||
session.logout()
|
connection.logout()
|
||||||
username = session.user.username if session.user is not None else "(Anonymous)"
|
username = connection.user.username if connection.user is not None else "(Anonymous)"
|
||||||
print(username)
|
print(username)
|
||||||
|
@ -2,6 +2,7 @@ import re
|
|||||||
|
|
||||||
from mdrsclient.api import FolderApi, LaboratoryApi
|
from mdrsclient.api import FolderApi, LaboratoryApi
|
||||||
from mdrsclient.config import ConfigFile
|
from mdrsclient.config import ConfigFile
|
||||||
|
from mdrsclient.connection import MDRSConnection
|
||||||
from mdrsclient.exceptions import (
|
from mdrsclient.exceptions import (
|
||||||
IllegalArgumentException,
|
IllegalArgumentException,
|
||||||
MissingConfigurationException,
|
MissingConfigurationException,
|
||||||
@ -9,28 +10,27 @@ from mdrsclient.exceptions import (
|
|||||||
UnexpectedException,
|
UnexpectedException,
|
||||||
)
|
)
|
||||||
from mdrsclient.models import Folder, Laboratory
|
from mdrsclient.models import Folder, Laboratory
|
||||||
from mdrsclient.session import MDRSSession
|
|
||||||
|
|
||||||
|
|
||||||
def create_session(remote: str) -> MDRSSession:
|
def create_connection(remote: str) -> MDRSConnection:
|
||||||
config = ConfigFile(remote)
|
config = ConfigFile(remote)
|
||||||
if config.url is None:
|
if config.url is None:
|
||||||
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
|
||||||
return MDRSSession(config.remote, config.url)
|
return MDRSConnection(config.remote, config.url)
|
||||||
|
|
||||||
|
|
||||||
def find_laboratory(session: MDRSSession, laboratory_name: str) -> Laboratory:
|
def find_laboratory(connection: MDRSConnection, laboratory_name: str) -> Laboratory:
|
||||||
if session.laboratories.empty() or session.token is not None and session.token.is_expired:
|
if connection.laboratories.empty() or connection.token is not None and connection.token.is_expired:
|
||||||
laboratory_api = LaboratoryApi(session)
|
laboratory_api = LaboratoryApi(connection)
|
||||||
session.laboratories = laboratory_api.list()
|
connection.laboratories = laboratory_api.list()
|
||||||
laboratory = session.laboratories.find_by_name(laboratory_name)
|
laboratory = connection.laboratories.find_by_name(laboratory_name)
|
||||||
if laboratory is None:
|
if laboratory is None:
|
||||||
raise IllegalArgumentException(f"Laboratory `{laboratory_name}` not found.")
|
raise IllegalArgumentException(f"Laboratory `{laboratory_name}` not found.")
|
||||||
return laboratory
|
return laboratory
|
||||||
|
|
||||||
|
|
||||||
def find_folder(session: MDRSSession, laboratory: Laboratory, path: str) -> Folder:
|
def find_folder(connection: MDRSConnection, laboratory: Laboratory, path: str) -> Folder:
|
||||||
folder_api = FolderApi(session)
|
folder_api = FolderApi(connection)
|
||||||
folders = folder_api.list(laboratory.id, path)
|
folders = folder_api.list(laboratory.id, path)
|
||||||
if len(folders) != 1:
|
if len(folders) != 1:
|
||||||
raise UnexpectedException(f"Folder `{path}` not found.")
|
raise UnexpectedException(f"Folder `{path}` not found.")
|
||||||
|
@ -5,13 +5,15 @@ from mdrsclient.exceptions import MissingConfigurationException
|
|||||||
from mdrsclient.models import Laboratories, Token, User
|
from mdrsclient.models import Laboratories, Token, User
|
||||||
|
|
||||||
|
|
||||||
class MDRSSession(requests.Session):
|
class MDRSConnection:
|
||||||
url: str
|
url: str
|
||||||
|
session: requests.Session
|
||||||
__cache: CacheFile
|
__cache: CacheFile
|
||||||
|
|
||||||
def __init__(self, remote: str, url: str) -> None:
|
def __init__(self, remote: str, url: str) -> None:
|
||||||
super().__init__()
|
super().__init__()
|
||||||
self.url = url
|
self.url = url
|
||||||
|
self.session = requests.Session()
|
||||||
self.__cache = CacheFile(remote)
|
self.__cache = CacheFile(remote)
|
||||||
self.__prepare_headers()
|
self.__prepare_headers()
|
||||||
|
|
||||||
@ -25,7 +27,7 @@ class MDRSSession(requests.Session):
|
|||||||
def logout(self) -> None:
|
def logout(self) -> None:
|
||||||
del self.__cache.user
|
del self.__cache.user
|
||||||
del self.__cache.token
|
del self.__cache.token
|
||||||
self.headers.update({"Authorization": ""})
|
self.session.headers.update({"Authorization": ""})
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def user(self) -> User | None:
|
def user(self) -> User | None:
|
||||||
@ -53,6 +55,6 @@ class MDRSSession(requests.Session):
|
|||||||
self.__cache.laboratories = laboratories
|
self.__cache.laboratories = laboratories
|
||||||
|
|
||||||
def __prepare_headers(self) -> None:
|
def __prepare_headers(self) -> None:
|
||||||
self.headers.update({"accept": "application/json"})
|
self.session.headers.update({"accept": "application/json"})
|
||||||
if self.token is not None:
|
if self.token is not None:
|
||||||
self.headers.update({"Authorization": f"Bearer {self.token.access}"})
|
self.session.headers.update({"Authorization": f"Bearer {self.token.access}"})
|
Loading…
Reference in New Issue
Block a user