sapiopycommons 2024.11.7a354__py3-none-any.whl → 2024.11.8a359__py3-none-any.whl

sapiopycommons/files/file_bridge_handler.py

@@ -1,340 +0,0 @@
-from __future__ import annotations
-
-from abc import abstractmethod, ABC
-from weakref import WeakValueDictionary
-
-from sapiopylib.rest.User import SapioUser
-
-from sapiopycommons.files.file_bridge import FileBridge
-from sapiopycommons.general.aliases import AliasUtil, UserIdentifier
-
-
-class FileBridgeHandler:
-    """
-    The FileBridgeHandler provides caching of the results of file bridge endpoint calls while also containing quality
-    of life functions for common file bridge actions.
-    """
-    user: SapioUser
-    __bridge: str
-    __file_cache: dict[str, bytes]
-    """A cache of file paths to file bytes."""
-    __files: dict[str, File]
-    """A cache of file paths to File objects."""
-    __dir_cache: dict[str, list[str]]
-    """A cache of directory file paths to the names of the files or nested directories within it."""
-    __directories: dict[str, Directory]
-    """A cache of directory file paths to Directory objects."""
-
-    __instances: WeakValueDictionary[str, FileBridgeHandler] = WeakValueDictionary()
-    __initialized: bool
-
-    def __new__(cls, context: UserIdentifier, bridge_name: str):
-        """
-        :param context: The current webhook context or a user object to send requests from.
-        """
-        user = AliasUtil.to_sapio_user(context)
-        key = f"{user.__hash__()}:{bridge_name}"
-        obj = cls.__instances.get(key)
-        if not obj:
-            obj = object.__new__(cls)
-            obj.__initialized = False
-            cls.__instances[key] = obj
-        return obj
-
-    def __init__(self, context: UserIdentifier, bridge_name: str):
-        """
-        :param context: The current webhook context or a user object to send requests from.
-        :param bridge_name: The name of the bridge to communicate with. This is the "connection name" in the
-            file bridge configurations.
-        """
-        if self.__initialized:
-            return
-        self.__initialized = True
-
-        self.user = AliasUtil.to_sapio_user(context)
-        self.__bridge = bridge_name
-        self.__file_cache = {}
-        self.__files = {}
-        self.__dir_cache = {}
-        self.__directories = {}
-
-    @property
-    def connection_name(self) -> str:
-        return self.__bridge
-
-    def clear_caches(self) -> None:
-        """
-        Clear the file and directory caches of this handler.
-        """
-        self.__file_cache.clear()
-        self.__files.clear()
-        self.__dir_cache.clear()
-        self.__directories.clear()
-
-    def read_file(self, file_path: str, base64_decode: bool = True) -> bytes:
-        """
-        Read a file from FileBridge. The bytes of the given file will be cached so that any subsequent reads of this
-        file will not make an additional webservice call.
-
-        :param file_path: The path to read the file from.
-        :param base64_decode: If true, base64 decode the file. Files are by default base64 encoded when retrieved from
-            FileBridge.
-        :return: The bytes of the file.
-        """
-        if file_path in self.__file_cache:
-            return self.__file_cache[file_path]
-        file_bytes: bytes = FileBridge.read_file(self.user, self.__bridge, file_path, base64_decode)
-        self.__file_cache[file_path] = file_bytes
-        return file_bytes
-
-    def write_file(self, file_path: str, file_data: bytes | str) -> None:
-        """
-        Write a file to FileBridge. The bytes of the given file will be cached so that any subsequent reads of this
-        file will not make an additional webservice call.
-
-        :param file_path: The path to write the file to. If a file already exists at the given path then the file is
-            overwritten.
-        :param file_data: A string or bytes of the file to be written.
-        """
-        FileBridge.write_file(self.user, self.__bridge, file_path, file_data)
-        self.__file_cache[file_path] = file_data if isinstance(file_data, bytes) else file_data.encode()
-
-        # Find the directory path to this file and the name of the file. Add the file name to the cached list of
-        # files for the directory, assuming we have this directory cached and the file isn't already in it.
-        last_slash: int = file_path.rfind("/")
-        dir_path: str = file_path[:last_slash]
-        file_name: str = file_path[last_slash + 1:]
-        if dir_path in self.__dir_cache and file_path not in self.__dir_cache[dir_path]:
-            self.__dir_cache[dir_path].append(file_name)
-
-    def delete_file(self, file_path: str) -> None:
-        """
-        Delete an existing file in FileBridge. If this file is in the cache, it will also be deleted from the cache.
-
-        :param file_path: The path to the file to delete.
-        """
-        FileBridge.delete_file(self.user, self.__bridge, file_path)
-        if file_path in self.__file_cache:
-            self.__file_cache.pop(file_path)
-        if file_path in self.__files:
-            self.__files.pop(file_path)
-
-    def list_directory(self, file_path: str) -> list[str]:
-        """
-        List the contents of a FileBridge directory. The contents of this directory will be cached so that any
-        subsequent lists of this directory will not make an additional webservice call.
-
-        :param file_path: The path to read the directory from.
-        :return: A list of names of files and folders in the directory.
-        """
-        if file_path in self.__dir_cache:
-            return self.__dir_cache[file_path]
-        files: list[str] = FileBridge.list_directory(self.user, self.__bridge, file_path)
-        self.__dir_cache[file_path] = files
-        return files
-
-    def create_directory(self, file_path: str) -> None:
-        """
-        Create a new directory in FileBridge. This new directory will be added to the cache as empty so that listing
-        the same directory does not make an additional webservice call.
-
-        :param file_path: The path to create the directory at. If a directory already exists at the given path then an
-            exception is raised.
-        """
-        FileBridge.create_directory(self.user, self.__bridge, file_path)
-        # This directory was just created, so we know it's empty.
-        self.__dir_cache[file_path] = []
-
-    def delete_directory(self, file_path: str) -> None:
-        """
-        Delete an existing directory in FileBridge. If this directory is in the cache, it will also be deleted
-        from the cache.
-
-        :param file_path: The path to the directory to delete.
-        """
-        FileBridge.delete_directory(self.user, self.__bridge, file_path)
-        if file_path in self.__dir_cache:
-            self.__dir_cache.pop(file_path)
-        if file_path in self.__directories:
-            self.__directories.pop(file_path)
-
-    def is_file(self, file_path: str) -> bool:
-        """
-        Determine if the given file path points to a file or a directory. This is achieved by trying to call
-        list_directory on the given file path. If an exception is thrown, that's because the function was called
-        on a file. If no exception is thrown, then we know that this is a directory, and we have now also cached
-        the contents of that directory if it wasn't cached already.
-
-        :param file_path: A file path.
-        :return: True if the file path points to a file. False if it points to a directory.
-        """
-        try:
-            self.list_directory(file_path)
-            return False
-        except Exception:
-            return True
-
-    def move_file(self, move_from: str, move_to: str, old_name: str, new_name: str | None = None) -> None:
-        """
-        Move a file from one location to another within File Bridge. This is done be reading the file into memory,
-        writing a copy of the file in the new location, then deleting the original file.
-
-        :param move_from: The path to the current location of the file.
-        :param move_to: The path to move the file to.
-        :param old_name: The current name of the file.
-        :param new_name: The name that the file should have after it is moved. if this is not provided, then the new
-            name will be the same as the old name.
-        """
-        if not new_name:
-            new_name = old_name
-
-        # Read the file into memory.
-        file_bytes: bytes = self.read_file(move_from + "/" + old_name)
-        # Write the file into the new location.
-        self.write_file(move_to + "/" + new_name, file_bytes)
-        # Delete the file from the old location. We do this last in case the write call fails.
-        self.delete_file(move_from + "/" + old_name)
-
-    def get_file_object(self, file_path: str) -> File:
-        """
-        Get a File object from a file path. This object can be used to get the contents of the file at this path
-        and traverse up the file hierarchy to the directory that the file is contained within.
-
-        There is no guarantee that this file actually exists within the current file bridge connection when it is
-        constructed. If the file doesn't exist, then retrieving its contents will fail.
-
-        :param file_path: A file path.
-        :return: A File object constructed form the given file path.
-        """
-        if file_path in self.__files:
-            return self.__files[file_path]
-        file = File(self, file_path)
-        self.__files[file_path] = file
-        return file
-
-    def get_directory_object(self, file_path: str) -> Directory | None:
-        """
-        Get a Directory object from a file path. This object can be used to traverse up and down the file hierarchy
-        by going up to the parent directory that this directory is contained within or going down to the contents of
-        this directory.
-
-        There is no guarantee that this directory actually exists within the current file bridge connection when it is
-        constructed. If the directory doesn't exist, then retrieving its contents will fail.
-
-        :param file_path: A file path.
-        :return: A Directory object constructed form the given file path.
-        """
-        if file_path is None:
-            return None
-        if file_path in self.__directories:
-            return self.__directories[file_path]
-        directory = Directory(self, file_path)
-        self.__directories[file_path] = directory
-        return directory
-
-
-class FileBridgeObject(ABC):
-    """
-    A FileBridgeObject is either a file or a directory that is contained within file bridge. Every object has a
-    name and a parent directory that it is contained within (unless the object is located in the bridge root, in
-    which case the parent is None). From the name and the parent, a path can be constructed to that object.
-    """
-    _handler: FileBridgeHandler
-    name: str
-    parent: Directory | None
-
-    def __init__(self, handler: FileBridgeHandler, file_path: str):
-        self._handler = handler
-
-        name, root = split_path(file_path)
-        self.name = name
-        self.parent = handler.get_directory_object(root)
-
-    @abstractmethod
-    def is_file(self) -> bool:
-        """
-        :return: True if this object is a file. False if it is a directory.
-        """
-        pass
-
-    def get_path(self) -> str:
-        """
-        :return: The file path that leads to this object.
-        """
-        if self.parent is None:
-            return self.name
-        return self.parent.get_path() + "/" + self.name
-
-
-class File(FileBridgeObject):
-    def __init__(self, handler: FileBridgeHandler, file_path: str):
-        """
-        :param handler: A FileBridgeHandler for the connection that this file came from.
-        :param file_path: The path to this file.
-        """
-        super().__init__(handler, file_path)
-
-    @property
-    def contents(self) -> bytes:
-        """
-        :return: The bytes of this file.
-            This pulls from the cache of this object's related FileBridgeHandler.
-        """
-        return self._handler.read_file(self.get_path())
-
-    def is_file(self) -> bool:
-        return True
-
-
-class Directory(FileBridgeObject):
-    def __init__(self, handler: FileBridgeHandler, file_path: str):
-        """
-        :param handler: A FileBridgeHandler for the connection that this directory came from.
-        :param file_path: The path to this directory.
-        """
-        super().__init__(handler, file_path)
-
-    @property
-    def contents(self) -> dict[str, FileBridgeObject]:
-        """
-        :return: A dictionary of object names to the objects (Files or Directories) contained within this Directory.
-            This pulls from the cache of this object's related FileBridgeHandler.
-        """
-        contents: dict[str, FileBridgeObject] = {}
-        path: str = self.get_path()
-        for name in self._handler.list_directory(path):
-            file_path: str = path + "/" + name
-            if self._handler.is_file(file_path):
-                contents[name] = self._handler.get_file_object(file_path)
-            else:
-                contents[name] = self._handler.get_directory_object(file_path)
-        return contents
-
-    def is_file(self) -> bool:
-        return False
-
-    def get_files(self) -> dict[str, File]:
-        """
-        :return: A mapping of file name to File for every file in this Directory.
-            This pulls from the cache of this object's related FileBridgeHandler.
-        """
-        return {x: y for x, y in self.contents.items() if y.is_file()}
-
-    def get_directories(self) -> dict[str, Directory]:
-        """
-        :return: A mapping of directory name to Directory for every directory in this Directory.
-            This pulls from the cache of this object's related FileBridgeHandler.
-        """
-        return {x: y for x, y in self.contents.items() if not y.is_file()}
-
-
-def split_path(file_path: str) -> tuple[str, str]:
-    """
-    :param file_path: A file path where directories are separated the "/" characters.
-    :return: A tuple of two strings that splits the path on its last slash. The first string is the name of the
-        file/directory at the given file path and the second string is the location to that file.
-    """
-    last_slash: int = file_path.rfind("/")
-    if last_slash == -1:
-        return file_path, None
-    return file_path[last_slash + 1:], file_path[:last_slash]

sapiopycommons/flowcyto/flow_cyto.py

@@ -1,77 +0,0 @@
-from __future__ import annotations
-
-from weakref import WeakValueDictionary
-
-from sapiopylib.rest.User import SapioUser
-from databind.json import dumps
-
-from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
-    ComputeFlowStatisticsInputJson
-
-
-class FlowCytoManager:
-    """
-    This manager includes flow cytometry analysis tools that would require FlowCyto license to use.
-    """
-    _user: SapioUser
-
-    __instances: WeakValueDictionary[SapioUser, FlowCytoManager] = WeakValueDictionary()
-    __initialized: bool
-
-    def __new__(cls, user: SapioUser):
-        """
-        Observes singleton pattern per record model manager object.
-
-        :param user: The user that will make the webservice request to the application.
-        """
-        obj = cls.__instances.get(user)
-        if not obj:
-            obj = object.__new__(cls)
-            obj.__initialized = False
-            cls.__instances[user] = obj
-        return obj
-
-    def __init__(self, user: SapioUser):
-        if self.__initialized:
-            return
-        self._user = user
-        self.__initialized = True
-
-    def create_flowjo_workspace(self, workspace_input: FlowJoWorkspaceInputJson) -> int:
-        """
-        Create FlowJo Workspace and return the workspace record ID of workspace root record,
-        after successful creation.
-        :param workspace_input: the request data payload.
-        :return: The new workspace record ID.
-        """
-        payload = dumps(workspace_input, FlowJoWorkspaceInputJson)
-        response = self._user.plugin_post("flowcyto/workspace", payload=payload, is_payload_plain_text=True)
-        self._user.raise_for_status(response)
-        return int(response.json())
-
-    def upload_fcs_for_sample(self, upload_input: UploadFCSInputJson) -> int:
-        """
-        Upload FCS file as root of the sample FCS.
-        :param upload_input: The request data payload
-        :return: The root FCS file uploaded under sample.
-        """
-        payload = dumps(upload_input, UploadFCSInputJson)
-        response = self._user.plugin_post("flowcyto/fcs", payload=payload, is_payload_plain_text=True)
-        self._user.raise_for_status(response)
-        return int(response.json())
-
-    def compute_statistics(self, stat_compute_input: ComputeFlowStatisticsInputJson) -> list[int]:
-        """
-        Requests to compute flow cytometry statistics.
-        The children are of type FCSStatistic.
-        If the FCS files have not been evaluated yet,
-        then the lazy evaluation will be performed immediately prior to computing statistics, which can take longer.
-        If any new statistics are computed as children of FCS, they will be returned in the result record id list.
-        Note: if input has multiple FCS files, the client should try to get parent FCS file from each record to figure out which one is for which FCS.
-        :param stat_compute_input:
-        :return:
-        """
-        payload = dumps(stat_compute_input, ComputeFlowStatisticsInputJson)
-        response = self._user.plugin_post("flowcyto/statistics", payload=payload, is_payload_plain_text=True)
-        self._user.raise_for_status(response)
-        return list(response.json())

sapiopycommons/flowcyto/flowcyto_data.py

@@ -1,75 +0,0 @@
-import base64
-from enum import Enum
-
-from databind.core.dataclasses import dataclass
-
-
-class ChannelStatisticType(Enum):
-    """
-    All supported channel statistics type.
-    """
-    MEAN = "(Mean) MFI"
-    MEDIAN = "(Median) MFI"
-    STD_EV = "Std. Dev."
-    COEFFICIENT_OF_VARIATION = "CV"
-
-    display_name: str
-
-    def __init__(self, display_name: str):
-        self.display_name = display_name
-
-
-@dataclass
-class ChannelStatisticsParameterJSON:
-    channelNameList: list[str]
-    statisticsType: ChannelStatisticType
-
-    def __init__(self, channel_name_list: list[str], stat_type: ChannelStatisticType):
-        self.channelNameList = channel_name_list
-        self.statisticsType = stat_type
-
-
-@dataclass
-class ComputeFlowStatisticsInputJson:
-    fcsFileRecordIdList: list[int]
-    statisticsParameterList: list[ChannelStatisticsParameterJSON]
-
-    def __init__(self, fcs_file_record_id_list: list[int], statistics_parameter_list: list[ChannelStatisticsParameterJSON]):
-        self.fcsFileRecordIdList = fcs_file_record_id_list
-        self.statisticsParameterList = statistics_parameter_list
-
-
-@dataclass
-class FlowJoWorkspaceInputJson:
-    filePath: str
-    base64Data: str
-
-    def __init__(self, filePath: str, file_data: bytes):
-        self.filePath = filePath
-        self.base64Data = base64.b64encode(file_data).decode('utf-8')
-
-
-@dataclass
-class UploadFCSInputJson:
-    """
-    Request to upload new FCS file
-    Attributes:
-        filePath: The file name of the FCS file to be uploaded. For FlowJo workspace, this is important to match the file in group (via file names).
-        attachmentDataType: the attachment data type that contains already-uploaded FCS data.
-        attachmentRecordId: the attachment record ID that contains already-uploaded FCS data.
-        associatedRecordDataType: the "parent" association for the FCS. Can either be a workspace or a sample record.
-        associatedRecordId: the "parent" association for the FCS. Can either be a workspace or a sample record.
-    """
-    filePath: str
-    attachmentDataType: str
-    attachmentRecordId: int
-    associatedRecordDataType: str
-    associatedRecordId: int
-
-    def __init__(self, associated_record_data_type: str, associated_record_id: int,
-                 file_path: str, attachment_data_type: str, attachment_record_id: int):
-        self.filePath = file_path
-        self.attachmentDataType = attachment_data_type
-        self.attachmentRecordId = attachment_record_id
-        self.associatedRecordDataType = associated_record_data_type
-        self.associatedRecordId = associated_record_id