Source code for galaxy.managers.remote_files

import hashlib
import logging
from operator import itemgetter
from typing import (
    Optional,
    Set,
    Tuple,
)

from galaxy import exceptions
from galaxy.files import (
    ConfiguredFileSources,
    FileSourcePath,
    ProvidesFileSourcesUserContext,
)
from galaxy.files.sources import (
    FilesSourceOptions,
    PluginKind,
)
from galaxy.managers.context import ProvidesUserContext
from galaxy.schema.remote_files import (
    AnyRemoteFilesListResponse,
    CreatedEntryResponse,
    CreateEntryPayload,
    RemoteFilesDisableMode,
    RemoteFilesFormat,
    RemoteFilesTarget,
)
from galaxy.structured_app import MinimalManagerApp
from galaxy.util import (
    jstree,
    smart_str,
)

log = logging.getLogger(__name__)


[docs]class RemoteFilesManager:
    """
    Interface/service object for interacting with remote files.
    """

[docs]    def __init__(self, app: MinimalManagerApp):
        self._app = app

[docs]    def index(
        self,
        user_ctx: ProvidesUserContext,
        target: str,
        format: Optional[RemoteFilesFormat],
        recursive: Optional[bool],
        disable: Optional[RemoteFilesDisableMode],
        writeable: Optional[bool] = False,
        limit: Optional[int] = None,
        offset: Optional[int] = None,
        query: Optional[str] = None,
        sort_by: Optional[str] = None,
    ) -> Tuple[AnyRemoteFilesListResponse, int]:
        """Returns a list of remote files and directories available to the user and the total count of them."""

        user_file_source_context = ProvidesFileSourcesUserContext(user_ctx)
        default_recursive = False
        default_format = RemoteFilesFormat.uri

        if "://" in target:
            uri = target
        elif target == RemoteFilesTarget.userdir:
            uri = "gxuserimport://"
            default_format = RemoteFilesFormat.flat
            default_recursive = True
        elif target == RemoteFilesTarget.importdir:
            uri = "gximport://"
            default_format = RemoteFilesFormat.flat
            default_recursive = True
        elif target in [RemoteFilesTarget.ftpdir, "ftp"]:  # legacy, allow both
            uri = "gxftp://"
            default_format = RemoteFilesFormat.flat
            default_recursive = True
        else:
            raise exceptions.RequestParameterInvalidException(f"Invalid target parameter supplied [{target}]")

        if format is None:
            format = default_format

        if recursive is None:
            recursive = default_recursive

        self._file_sources.validate_uri_root(uri, user_context=user_file_source_context)

        file_source_path = self._file_sources.get_file_source_path(uri)
        file_source = file_source_path.file_source

        opts = FilesSourceOptions()
        opts.writeable = writeable or False
        try:
            index, count = file_source.list(
                file_source_path.path,
                recursive=recursive,
                user_context=user_file_source_context,
                opts=opts,
                limit=limit,
                offset=offset,
                query=query,
                sort_by=sort_by,
            )
        except exceptions.MessageException:
            log.warning(self._get_error_message(file_source_path), exc_info=True)
            raise
        except Exception:
            message = self._get_error_message(file_source_path)
            log.warning(message, exc_info=True)
            raise exceptions.InternalServerError(message)
        if format == RemoteFilesFormat.flat:
            # rip out directories, ensure sorted by path
            index = [i for i in index if i["class"] == "File"]
            index = sorted(index, key=itemgetter("path"))
        elif format == RemoteFilesFormat.jstree:
            if disable is None:
                disable = RemoteFilesDisableMode.folders

            jstree_paths = []
            for ent in index:
                path = ent["path"]
                path_hash = hashlib.sha1(smart_str(path)).hexdigest()
                if ent["class"] == "Directory":
                    path_type = "folder"
                    disabled = True if disable == RemoteFilesDisableMode.folders else False
                else:
                    path_type = "file"
                    disabled = True if disable == RemoteFilesDisableMode.files else False

                jstree_paths.append(
                    jstree.Path(
                        path,
                        path_hash,
                        {"type": path_type, "state": {"disabled": disabled}, "li_attr": {"full_path": path}},
                    )
                )
            userdir_jstree = jstree.JSTree(jstree_paths)
            index = userdir_jstree.jsonData()

        return index, count

    def _get_error_message(self, file_source_path: FileSourcePath) -> str:
        return f"Problem listing file source path {file_source_path.file_source.get_uri_root()}{file_source_path.path}"

[docs]    def get_files_source_plugins(
        self,
        user_context: ProvidesUserContext,
        browsable_only: Optional[bool] = True,
        include_kind: Optional[Set[PluginKind]] = None,
        exclude_kind: Optional[Set[PluginKind]] = None,
    ):
        """Display plugin information for each of the gxfiles:// URI targets available."""
        user_file_source_context = ProvidesFileSourcesUserContext(user_context)
        browsable_only = True if browsable_only is None else browsable_only
        plugins_dict = self._file_sources.plugins_to_dict(
            user_context=user_file_source_context,
            browsable_only=browsable_only,
            include_kind=include_kind,
            exclude_kind=exclude_kind,
        )
        return plugins_dict

    @property
    def _file_sources(self) -> ConfiguredFileSources:
        return self._app.file_sources

[docs]    def create_entry(self, user_ctx: ProvidesUserContext, entry_data: CreateEntryPayload) -> CreatedEntryResponse:
        """Create an entry (directory or record) in a remote files location."""
        target = entry_data.target
        user_file_source_context = ProvidesFileSourcesUserContext(user_ctx)
        self._file_sources.validate_uri_root(target, user_context=user_file_source_context)
        file_source_path = self._file_sources.get_file_source_path(target)
        file_source = file_source_path.file_source
        try:
            result = file_source.create_entry(entry_data.dict(), user_context=user_file_source_context)
        except exceptions.MessageException:
            log.warning(f"Problem creating entry {entry_data.name} in file source {entry_data.target}", exc_info=True)
            raise
        except Exception:
            message = f"Problem creating entry {entry_data.name} in file source {entry_data.target}"
            log.warning(message, exc_info=True)
            raise exceptions.InternalServerError(message)
        return CreatedEntryResponse(
            name=result["name"],
            uri=result["uri"],
            external_link=result.get("external_link", None),
        )