sapiopycommons 2024.10.24a342__py3-none-any.whl → 2024.10.29a346__py3-none-any.whl

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