import os from concurrent.futures import ThreadPoolExecutor from typing import Any from unicodedata import normalize from pydantic.dataclasses import dataclass from mdrsclient.api import FilesApi, FoldersApi from mdrsclient.exceptions import IllegalArgumentException, UnexpectedException from mdrsclient.models import File, Folder, Laboratory from mdrsclient.models.file import find_file from mdrsclient.settings import CONCURRENT @dataclass(frozen=True) class UploadFileInfo: folder: Folder files: list[File] path: str @dataclass(frozen=True) class DownloadFileInfo: file: File path: str @dataclass class DownloadContext: isSkipIfExists: bool files: list[DownloadFileInfo] class Uploader: def __init__(self, client: Any) -> None: self.client = client def upload( self, local_path: str, remote_path: str, is_recursive: bool = False, is_skip_if_exists: bool = False ) -> None: remote, laboratory_name, r_path = self.client.parse_remote_host_with_path(remote_path) l_path = os.path.abspath(local_path) if not os.path.exists(l_path): raise IllegalArgumentException(f"File or directory `{local_path}` not found.") laboratory = self.client.find_laboratory(laboratory_name) folder = self.client.find_folder(laboratory, r_path) files = self.client.find_files(folder.id) if os.path.isdir(l_path): if not is_recursive: raise IllegalArgumentException(f"Cannot upload `{local_path}`: Is a directory.") infos = self.__collect_directory_uploads(laboratory, r_path, l_path, folder, files) else: infos = [UploadFileInfo(folder, files, l_path)] if not self.__multiple_upload(infos, is_skip_if_exists): # One file failing is worth reporting on its own line, and worth the caller # hearing about: a batch that lost files is not a batch that succeeded. raise UnexpectedException("Some files failed to upload.") def __collect_directory_uploads( self, laboratory: Laboratory, r_path: str, l_path: str, folder: Folder, files: list[File] ) -> list[UploadFileInfo]: """Mirror a local directory tree on the remote, and list the files to send into it.""" infos: list[UploadFileInfo] = [] folder_api = FoldersApi(self.client.connection) folder_map: dict[str, Folder] = {} folder_map[r_path] = folder files_map: dict[str, list[File]] = {} files_map[r_path] = files l_basename = os.path.basename(l_path) for dirpath, _, filenames in os.walk(l_path, followlinks=True): sub = l_basename if dirpath == l_path else os.path.join(l_basename, os.path.relpath(dirpath, l_path)) d_dirname = os.path.join(r_path, sub) d_basename = os.path.basename(d_dirname) # prepare destination parent path d_parent_dirname = os.path.dirname(d_dirname) if folder_map.get(d_parent_dirname) is None: parent_folder = self.client.find_folder(laboratory, d_parent_dirname) folder_map[d_parent_dirname] = parent_folder parent_files = self.client.find_files(parent_folder.id) files_map[d_parent_dirname] = parent_files # prepare destination path if folder_map.get(d_dirname) is None: d_folder = folder_map[d_parent_dirname].find_sub_folder(d_basename) if d_folder is None: d_folder_id = folder_api.create(normalize("NFC", d_basename), folder_map[d_parent_dirname].id) else: d_folder_id = d_folder.id print(d_dirname) folder_map[d_dirname] = folder_api.retrieve(d_folder_id) files_map[d_dirname] = self.client.find_files(d_folder_id) if d_folder is None: folder_map[d_parent_dirname].sub_folders.append(folder_map[d_dirname]) # register upload file list for filename in filenames: infos.append( UploadFileInfo(folder_map[d_dirname], files_map[d_dirname], os.path.join(dirpath, filename)) ) return infos def __multiple_upload(self, infos: list[UploadFileInfo], is_skip_if_exists: bool) -> bool: """Send every file, and report whether all of them arrived.""" file_api = FilesApi(self.client.connection) with ThreadPoolExecutor(max_workers=CONCURRENT) as pool: results = pool.map(lambda x: self.__multiple_upload_worker(file_api, x, is_skip_if_exists), infos) # Consumed inside the block: the results are what carry each worker's verdict. return all(list(results)) def __multiple_upload_worker(self, file_api: FilesApi, info: UploadFileInfo, is_skip_if_exists: bool) -> bool: basename = os.path.basename(info.path) file = find_file(info.files, basename) try: if file is None: file_api.create(info.folder.id, info.path) elif not is_skip_if_exists or file.size != os.path.getsize(info.path): file_api.update(file, info.path) print(os.path.join(info.folder.path, basename)) except Exception as e: # Everything, not just the exceptions the API layer raises: the batch verdict # is read now that the results are consumed, and a file vanishing between the # walk and the upload would otherwise end the whole run with a traceback and # throw away what every other file did. print(f"Failed: {info.path}: {e}") return False return True class Downloader: def __init__(self, client: Any) -> None: self.client = client def download( self, remote_path: str, local_path: str, is_recursive: bool = False, is_skip_if_exists: bool = False, password: str | None = None, excludes: list[str] | None = None, ) -> None: if not self.__download(remote_path, local_path, is_recursive, is_skip_if_exists, password, excludes): # Every failure has already been printed against the file it belongs to. # This is what makes the command as a whole end in failure. raise UnexpectedException("Some files failed to download.") def __download( self, remote_path: str, local_path: str, is_recursive: bool, is_skip_if_exists: bool, password: str | None, excludes: list[str] | None, ) -> bool: """Fetch what the remote path names, and report whether every file arrived.""" excludes_clean = excludes or [] # Detect DOI path: "remote:10.xxxx/prefix.ID[/optional/sub/path]" path_component = remote_path.split(":", 1)[1] if ":" in remote_path else "" if self.client.is_doi(path_component): remote, doi, subpath = self.client.parse_doi_remote_host(remote_path) l_dirname = os.path.realpath(local_path) if not os.path.isdir(l_dirname): raise IllegalArgumentException(f"Local directory `{local_path}` not found.") doi_folder, laboratory = self.client.find_folder_by_doi(doi, password) subpath_clean = subpath.rstrip("/") if not subpath_clean: folder = doi_folder is_folder = True else: r_dirname = os.path.dirname(subpath_clean) r_basename = os.path.basename(subpath_clean) abs_path = doi_folder.path.rstrip("/") + r_dirname r_parent_folder = self.client.find_folder(laboratory, abs_path, password) r_parent_files = self.client.find_files(r_parent_folder.id) file = find_file(r_parent_files, r_basename) if file is not None: if self.__check_excludes(excludes_clean, laboratory, r_parent_folder, file): return True context = DownloadContext(is_skip_if_exists, []) l_path = os.path.join(l_dirname, r_basename) context.files.append(DownloadFileInfo(file, l_path)) return self.__multiple_download(context) else: folder_simple = r_parent_folder.find_sub_folder(r_basename) if folder_simple is None: raise IllegalArgumentException(f"File or folder `{subpath_clean}` not found.") folder = FoldersApi(self.client.connection).retrieve(folder_simple.id) is_folder = True # For a DOI target the whole folder is the download target. if not is_recursive: # Non-recursive: download only the files at the top level of the DOI folder. files = self.client.find_files(folder.id) context = DownloadContext(is_skip_if_exists, []) for file in files: if self.__check_excludes(excludes_clean, laboratory, folder, file): continue l_path = os.path.join(l_dirname, file.name) context.files.append(DownloadFileInfo(file, l_path)) return self.__multiple_download(context) folder_api = FoldersApi(self.client.connection) return self.__multiple_download_pickup_recursive_files( folder_api, laboratory, folder.id, l_dirname, excludes_clean, is_skip_if_exists ) remote, laboratory_name, r_path = self.client.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) l_dirname = os.path.realpath(local_path) if not os.path.isdir(l_dirname): raise IllegalArgumentException(f"Local directory `{local_path}` not found.") laboratory = self.client.find_laboratory(laboratory_name) r_parent_folder = self.client.find_folder(laboratory, r_dirname, password) r_parent_files = self.client.find_files(r_parent_folder.id) file = find_file(r_parent_files, r_basename) if file is not None: if self.__check_excludes(excludes_clean, laboratory, r_parent_folder, file): return True context = DownloadContext(is_skip_if_exists, []) l_path = os.path.join(l_dirname, r_basename) context.files.append(DownloadFileInfo(file, l_path)) return self.__multiple_download(context) else: folder = r_parent_folder.find_sub_folder(r_basename) if folder is None: raise IllegalArgumentException(f"File or folder `{r_path}` not found.") if not is_recursive: raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.") folder_api = FoldersApi(self.client.connection) return self.__multiple_download_pickup_recursive_files( folder_api, laboratory, folder.id, l_dirname, excludes_clean, is_skip_if_exists ) def __multiple_download_pickup_recursive_files( self, folder_api: FoldersApi, laboratory: Laboratory, folder_id: str, basedir: str, excludes: list[str], is_skip_if_exists: bool, ) -> bool: context = DownloadContext(is_skip_if_exists, []) try: folder = folder_api.retrieve(folder_id) files = self.client.find_files(folder.id) except Exception as e: print(f"Failed: {basedir}: {e}") return False dirname = os.path.join(basedir, folder.name) if self.__check_excludes(excludes, laboratory, folder, None): return True try: # `exist_ok` rather than a prior check: two workers can reach the same parent. os.makedirs(dirname, exist_ok=True) except OSError as e: # One folder the client cannot make locally is not a reason to abandon its # siblings, which is what this walk now promises. print(f"Failed: {dirname}: {e}") return False print(dirname) for file in files: if self.__check_excludes(excludes, laboratory, folder, file): continue path = os.path.join(dirname, file.name) context.files.append(DownloadFileInfo(file, path)) succeeded = self.__multiple_download(context) # A folder that lost a file is still a folder whose sub-folders the user asked # for, so the walk carries on and the verdict is collected for the caller. for sub_folder in folder.sub_folders: if not self.__multiple_download_pickup_recursive_files( folder_api, laboratory, sub_folder.id, dirname, excludes, is_skip_if_exists ): succeeded = False return succeeded def __multiple_download(self, context: DownloadContext) -> bool: """Fetch every file in the batch, and report whether all of them arrived.""" file_api = FilesApi(self.client.connection) with ThreadPoolExecutor(max_workers=CONCURRENT) as pool: results = pool.map( lambda x: self.__multiple_download_worker(file_api, x, context.isSkipIfExists), context.files ) # Consumed inside the block, and in full: every worker's verdict counts, not # just the first refusal. return all(list(results)) def __multiple_download_worker(self, file_api: FilesApi, info: DownloadFileInfo, is_skip_if_exists: bool) -> bool: if not is_skip_if_exists or not os.path.exists(info.path) or info.file.size != os.path.getsize(info.path): try: file_api.download(info.file, info.path) except Exception as e: # Nothing to clear up: a failed transfer writes only to its own scratch # file beside the destination, and removes that itself. print(f"Failed: {info.path}: {e}") return False print(info.path) return True def __check_excludes(self, excludes: list[str], laboratory: Laboratory, folder: Folder, file: File | None) -> bool: path = f"/{laboratory.name}{folder.path}{file.name if file is not None else ''}".rstrip("/").lower() return path in excludes