sapiopycommons 2025.2.6a421__py3-none-any.whl → 2025.2.7a424__py3-none-any.whl
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- sapiopycommons/callbacks/callback_util.py +363 -1217
- sapiopycommons/chem/Molecules.py +2 -0
- sapiopycommons/datatype/data_fields.py +1 -1
- sapiopycommons/eln/experiment_handler.py +1 -2
- sapiopycommons/eln/experiment_report_util.py +7 -7
- sapiopycommons/files/file_bridge.py +0 -76
- sapiopycommons/files/file_bridge_handler.py +110 -325
- sapiopycommons/files/file_data_handler.py +2 -2
- sapiopycommons/files/file_validator.py +5 -6
- sapiopycommons/flowcyto/flow_cyto.py +1 -1
- sapiopycommons/general/accession_service.py +1 -1
- sapiopycommons/general/aliases.py +27 -40
- sapiopycommons/general/audit_log.py +2 -2
- sapiopycommons/general/custom_report_util.py +1 -24
- sapiopycommons/general/exceptions.py +2 -41
- sapiopycommons/multimodal/multimodal.py +0 -1
- sapiopycommons/processtracking/custom_workflow_handler.py +3 -3
- sapiopycommons/recordmodel/record_handler.py +3 -5
- sapiopycommons/webhook/webhook_handlers.py +55 -445
- {sapiopycommons-2025.2.6a421.dist-info → sapiopycommons-2025.2.7a424.dist-info}/METADATA +1 -1
- {sapiopycommons-2025.2.6a421.dist-info → sapiopycommons-2025.2.7a424.dist-info}/RECORD +23 -27
- sapiopycommons/customreport/auto_pagers.py +0 -270
- sapiopycommons/elain/__init__.py +0 -0
- sapiopycommons/elain/tool_of_tools.py +0 -510
- sapiopycommons/general/directive_util.py +0 -86
- {sapiopycommons-2025.2.6a421.dist-info → sapiopycommons-2025.2.7a424.dist-info}/WHEEL +0 -0
- {sapiopycommons-2025.2.6a421.dist-info → sapiopycommons-2025.2.7a424.dist-info}/licenses/LICENSE +0 -0
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import base64
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import math
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from typing import Final, Mapping, Any
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from pandas import DataFrame
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from sapiopylib.rest.DataRecordManagerService import DataRecordManager
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from sapiopylib.rest.ELNService import ElnManager
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from sapiopylib.rest.User import SapioUser
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from sapiopylib.rest.pojo.DataRecord import DataRecord
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from sapiopylib.rest.pojo.chartdata.DashboardDefinition import GaugeChartDefinition
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from sapiopylib.rest.pojo.chartdata.DashboardEnums import ChartGroupingType, ChartOperationType, ChartType
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from sapiopylib.rest.pojo.chartdata.DashboardSeries import GaugeChartSeries
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from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition, FieldType
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from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
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from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
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from sapiopylib.rest.pojo.eln.ExperimentEntryCriteria import ElnEntryCriteria, ElnFormEntryUpdateCriteria, \
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ElnDashboardEntryUpdateCriteria, AbstractElnEntryUpdateCriteria
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from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnEntryType, ElnBaseDataType
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from sapiopylib.rest.pojo.eln.eln_headings import ElnExperimentTabAddCriteria, ElnExperimentTab
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from sapiopylib.rest.pojo.eln.field_set import ElnFieldSetInfo
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from sapiopylib.rest.utils.ProtocolUtils import ELNStepFactory
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from sapiopylib.rest.utils.Protocols import ElnEntryStep, ElnExperimentProtocol
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from sapiopycommons.callbacks.field_builder import FieldBuilder
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from sapiopycommons.general.exceptions import SapioException
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from sapiopycommons.general.time_util import TimeUtil
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CREDENTIALS_HEADER: Final[str] = "SAPIO_APP_API_KEY"
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API_URL_HEADER: Final[str] = "SAPIO_APP_API_URL"
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EXP_ID_HEADER: Final[str] = "EXPERIMENT_ID"
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TAB_PREFIX_HEADER: Final[str] = "TAB_PREFIX"
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# FR-47422: Create utility methods to assist the tool of tools.
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def create_tot_headers(url: str, username: str, password: str, experiment_id: int, tab_prefix: str) \
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-> tuple[str, dict[str, str]]:
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"""
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Create the headers to be passed to a tool of tools endpoint.
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:param url: The webservice URL of the system to make the changes in.
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:param username: The username of the user making the changes.
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:param password: The password of the user making the changes.
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:param experiment_id: The ID of the experiment to make the changes in.
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:param tab_prefix: The prefix to use for the tab name that will be created by the tool.
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:return: The encoded credentials and the headers to be passed to the endpoint.
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"""
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# Combine the credentials into the format "username:password"
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credentials: str = f"{username}:{password}"
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# Encode the credentials to bytes, then encode them using base64,
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# and finally convert the result back into a string.
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encoded_credentials: str = base64.b64encode(credentials.encode('utf-8')).decode('utf-8')
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headers: dict[str, str] = {
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CREDENTIALS_HEADER: f"Basic {encoded_credentials}",
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API_URL_HEADER: url,
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EXP_ID_HEADER: str(experiment_id),
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TAB_PREFIX_HEADER: tab_prefix
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}
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return encoded_credentials, headers
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def create_user_from_tot_headers(headers: Mapping[str, str]) -> SapioUser:
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"""
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Create a SapioUser object from the headers passed to a tool of tools endpoint.
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:param headers: The headers that were passed to the endpoint.
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:return: A SapioUser object created from the headers that can be used to communicate with the Sapio server.
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"""
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headers: dict[str, str] = format_tot_headers(headers)
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credentials = (base64.b64decode(headers[CREDENTIALS_HEADER.lower()].removeprefix("Basic "))
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.decode("utf-8").split(":", 1))
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return SapioUser(headers[API_URL_HEADER.lower()], username=credentials[0], password=credentials[1])
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def format_tot_headers(headers: Mapping[str, str]) -> dict[str, str]:
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"""
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Format the headers passed to a tool of tools endpoint to guarantee that the keys are lowercase.
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:param headers: The headers that were passed to the endpoint.
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:return: The headers with all keys converted to lowercase. (Conflicting keys will cause one to overwrite the other,
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but there should not be any conflicting keys in the headers passed to a tool of tools endpoint.)
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"""
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return {k.lower(): v for k, v in headers.items()}
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def create_experiment_details_from_data_frame(user: SapioUser,
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exp_id: int,
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entry_name: str,
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tab: ElnExperimentTab,
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df: DataFrame) -> ExperimentEntry | None:
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"""
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Create an experiment detail entry from a DataFrame.
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:param user: The user to send the request from.
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:param exp_id: The ID of the experiment to create the entry in.
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:param entry_name: The name of the entry.
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:param tab: The tab that the entry should be added to.
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:param df: The DataFrame to create the entry from.
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:return: The created entry object.
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"""
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json_list: list[dict[str, Any]] = []
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for _, row in df.iterrows():
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json_list.append(row.to_dict())
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return create_experiment_details_from_json(user, exp_id, entry_name, tab, json_list)
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def create_experiment_details_from_json(user: SapioUser,
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exp_id: int,
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entry_name: str,
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tab: ElnExperimentTab,
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json_list: list[dict[str, Any]]) -> ExperimentEntry | None:
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"""
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Create an experiment detail entry from a list of JSON dictionaries.
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:param user: The user to send the request from.
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:param exp_id: The ID of the experiment to create the entry in.
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:param entry_name: The name of the entry.
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:param tab: The tab that the entry should be added to.
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:param json_list: The list of JSON dictionaries to create the entry from. Each dictionary is expected to have the
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same keys.
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:return: The created entry object.
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"""
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if not json_list:
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return None
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# Determine which fields in the JSON can be used to create field definitions.
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fb = FieldBuilder()
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fields: list[AbstractVeloxFieldDefinition] = []
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fields_by_name: dict[str, AbstractVeloxFieldDefinition] = {}
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valid_keys: list[str] = []
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display_to_field_name: dict[str, str] = {}
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for key, value in json_list[0].items():
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field_name: str = key.replace(" ", "_")
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display_to_field_name[key] = field_name
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if isinstance(value, str):
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field = fb.string_field(field_name, display_name=key)
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fields.append(field)
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fields_by_name[field_name] = field
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valid_keys.append(key)
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elif isinstance(value, (int, float)):
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field = fb.double_field(field_name, display_name=key, precision=3)
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fields.append(field)
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fields_by_name[field_name] = field
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valid_keys.append(key)
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# Extract the valid field values from the JSON.
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field_maps: list[dict[str, Any]] = []
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for json_dict in json_list:
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field_map: dict[str, Any] = {}
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for key in valid_keys:
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# Watch out for NaN values or other special values.
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val: Any = json_dict.get(key)
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if (fields_by_name[key].data_field_type == FieldType.DOUBLE
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and (not isinstance(val, (int, float))) or (isinstance(val, float) and math.isnan(val))):
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val = None
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field_map[display_to_field_name[key]] = val
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field_maps.append(field_map)
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detail_entry = ElnEntryCriteria(ElnEntryType.Table, entry_name,
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ElnBaseDataType.EXPERIMENT_DETAIL.data_type_name,
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tab_next_entry_order(user, exp_id, tab),
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notebook_experiment_tab_id=tab.tab_id,
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field_definition_list=fields)
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entry = ElnManager(user).add_experiment_entry(exp_id, detail_entry)
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DataRecordManager(user).add_data_records_with_data(entry.data_type_name, field_maps)
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def tab_next_entry_order(user: SapioUser, exp_id: int, tab: ElnExperimentTab) -> int:
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max_order: int = 0
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for step in ElnExperimentProtocol(ElnExperiment(exp_id, "", 0), user).get_sorted_step_list():
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if step.eln_entry.notebook_experiment_tab_id == tab.tab_id and step.eln_entry.order > max_order:
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max_order = step.eln_entry.order
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return max_order + 1
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class ToolOfToolsHelper:
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"""
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A class with helper methods utilized by the Tool of Tools for the creation and updating of experiment tabs that
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track a tool's progress and results.
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"""
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# Contextual info.
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user: SapioUser
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tab_prefix: str
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exp_id: int
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_protocol: ElnExperimentProtocol
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# Tool info.
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name: str
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description: str
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results_data_type: str | None
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# Managers.
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eln_man: ElnManager
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dr_man: DataRecordManager
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# Stuff created by this helper.
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_initialized: bool
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"""Whether a tab for this tool has been initialized."""
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tab: ElnExperimentTab
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"""The tab that contains the tool's entries."""
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description_entry: ElnEntryStep | None
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"""The text entry that displays the description of the tool."""
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description_record: DataRecord | None
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"""The record that stores the description of the tool."""
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progress_entry: ElnEntryStep | None
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"""A hidden entry for tracking the progress of the tool."""
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progress_record: DataRecord | None
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"""The record that stores the progress of the tool."""
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progress_gauge_entry: ElnEntryStep | None
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"""A chart entry that displays the progress of the tool using the hidden progress entry."""
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results_entry: ElnEntryStep | None
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"""An entry for displaying the results of the tool. If None, the tool does not produce result records."""
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def __init__(self, headers: Mapping[str, str], name: str, description: str,
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results_data_type: str | None = None):
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"""
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:param headers: The headers that were passed to the endpoint.
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:param name: The name of the tool.
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:param description: A description of the tool.
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:param results_data_type: The data type name for the results of the tool. If None, the tool does not produce
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result records.
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"""
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headers: dict[str, str] = format_tot_headers(headers)
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self.user = create_user_from_tot_headers(headers)
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self.exp_id = int(headers[EXP_ID_HEADER.lower()])
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self.tab_prefix = headers[TAB_PREFIX_HEADER.lower()]
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# The experiment name and record ID aren't necessary to know.
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self._protocol = ElnExperimentProtocol(ElnExperiment(self.exp_id, "", 0), self.user)
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self.name = name
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self.description = description
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self.results_data_type = results_data_type
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self.eln_man = ElnManager(self.user)
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self.dr_man = DataRecordManager(self.user)
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self._initialized = False
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def initialize_tab(self) -> ElnExperimentTab:
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if self._initialized:
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return self.tab
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self._initialized = True
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# Determine if a previous call to this endpoint already created a tab for these results. If so, grab the entries
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# from that tab.
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tab_name: str = f"{self.tab_prefix.strip()} {self.name.strip()}"
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tabs: list[ElnExperimentTab] = self.eln_man.get_tabs_for_experiment(self.exp_id)
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for tab in tabs:
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if tab.tab_name != tab_name:
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continue
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for entry in self._protocol.get_sorted_step_list():
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if entry.eln_entry.notebook_experiment_tab_id != tab.tab_id:
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continue
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dt: str = entry.get_data_type_names()[0] if entry.get_data_type_names() else None
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if (entry.eln_entry.entry_type == ElnEntryType.Form
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and ElnBaseDataType.get_base_type(dt) == ElnBaseDataType.EXPERIMENT_DETAIL
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and not hasattr(self, "progress_entry")):
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self.progress_entry = entry
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self.progress_record = entry.get_records()[0]
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elif (entry.eln_entry.entry_type == ElnEntryType.Dashboard
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and not hasattr(self, "progress_gauge_entry")):
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self.progress_gauge_entry = entry
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elif (entry.eln_entry.entry_type == ElnEntryType.Text
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and not hasattr(self, "description_entry")):
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self.description_entry = entry
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self.description_record = entry.get_records()[0]
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elif (entry.eln_entry.entry_type == ElnEntryType.Table
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and dt == self.results_data_type
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and not hasattr(self, "results_entry")):
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self.results_entry = entry
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if not hasattr(self, "progress_entry"):
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self.progress_entry = None
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self.progress_record = None
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if not hasattr(self, "progress_gauge_entry"):
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self.progress_gauge_entry = None
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if not hasattr(self, "description_entry"):
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self.description_entry = None
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self.description_record = None
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if not hasattr(self, "results_entry"):
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self.results_entry = None
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self.tab = tab
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return tab
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# Otherwise, create the tab for the tool progress and results.
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tab_crit = ElnExperimentTabAddCriteria(tab_name, [])
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tab: ElnExperimentTab = self.eln_man.add_tab_for_experiment(self.exp_id, tab_crit)
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self.tab = tab
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292
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# Create a hidden entry for tracking the progress of the tool.
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field_sets: list[ElnFieldSetInfo] = self.eln_man.get_field_set_info_list()
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progress_field_set: list[ElnFieldSetInfo] = [x for x in field_sets if
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x.field_set_name == "Tool of Tools Progress"]
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if not progress_field_set:
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raise SapioException("Unable to locate the field set for the Tool of Tools progress.")
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progress_entry_crit = ElnEntryCriteria(ElnEntryType.Form, f"ELaiN: {self.name} Progress",
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ElnBaseDataType.EXPERIMENT_DETAIL.data_type_name, 1,
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notebook_experiment_tab_id=tab.tab_id,
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enb_field_set_id=progress_field_set[0].field_set_id)
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progress_entry = ElnEntryStep(self._protocol,
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|
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self.eln_man.add_experiment_entry(self.exp_id, progress_entry_crit))
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self.progress_entry = progress_entry
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|
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self.progress_record = progress_entry.get_records()[0]
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|
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307
|
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# Hide the progress entry.
|
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|
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form_update_crit = ElnFormEntryUpdateCriteria()
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|
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form_update_crit.is_hidden = True
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self.eln_man.update_experiment_entry(self.exp_id, self.progress_entry.get_id(), form_update_crit)
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|
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312
|
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# Create the text entry that displays the description of the tool. Include the timestamp of when the
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# tool started and format the description so that the text isn't too small to read.
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# TODO: Get the UTC offset in seconds from the header once that's being sent.
|
|
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|
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now: str = TimeUtil.now_in_format("%Y-%m-%d %H:%M:%S UTC", "UTC")
|
|
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|
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description: str = f"""<p><span style="color: rgb(35, 111, 161); font-size: 12pt; font-weight:500;">{now}</span>
|
|
317
|
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<br><span style="font-size: 15pt;">{self.description}</span></p>"""
|
|
318
|
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text_entry: ElnEntryStep = ELNStepFactory.create_text_entry(self._protocol, description)
|
|
319
|
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self.description_entry = text_entry
|
|
320
|
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self.description_record = text_entry.get_records()[0]
|
|
321
|
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|
|
322
|
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# Shrink the text entry by one column.
|
|
323
|
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text_update_crit = _ElnTextEntryUpdateCriteria()
|
|
324
|
-
text_update_crit.column_span = 2
|
|
325
|
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self.eln_man.update_experiment_entry(self.exp_id, self.description_entry.get_id(), text_update_crit)
|
|
326
|
-
|
|
327
|
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# Create a gauge entry to display the progress.
|
|
328
|
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gauge_entry: ElnEntryStep = self._create_gauge_chart(self._protocol, progress_entry,
|
|
329
|
-
f"{self.name} Progress", "Progress", "StatusMsg")
|
|
330
|
-
self.progress_gauge_entry = gauge_entry
|
|
331
|
-
|
|
332
|
-
# Make sure the gauge entry isn't too big and stick it to the right of the text entry.
|
|
333
|
-
dash_update_crit = ElnDashboardEntryUpdateCriteria()
|
|
334
|
-
dash_update_crit.entry_height = 250
|
|
335
|
-
dash_update_crit.column_span = 2
|
|
336
|
-
dash_update_crit.column_order = 2
|
|
337
|
-
self.eln_man.update_experiment_entry(self.exp_id, self.progress_gauge_entry.get_id(), dash_update_crit)
|
|
338
|
-
|
|
339
|
-
# TODO: Bulk updates aren't working?
|
|
340
|
-
# self.eln_man.update_experiment_entries(self.exp_id, {
|
|
341
|
-
# self.progress_entry.get_id(): form_update_crit,
|
|
342
|
-
# self.progress_gauge_entry.get_id(): dash_update_crit,
|
|
343
|
-
# self.description_entry.get_id(): text_update_crit
|
|
344
|
-
# })
|
|
345
|
-
|
|
346
|
-
# Create a results entry if this tool produces result records.
|
|
347
|
-
if self.results_data_type:
|
|
348
|
-
results_entry = ELNStepFactory.create_table_step(self._protocol, f"{self.name} Results",
|
|
349
|
-
self.results_data_type)
|
|
350
|
-
self.results_entry = results_entry
|
|
351
|
-
else:
|
|
352
|
-
self.results_entry = None
|
|
353
|
-
|
|
354
|
-
return tab
|
|
355
|
-
|
|
356
|
-
def add_to_description(self, description: str) -> None:
|
|
357
|
-
"""
|
|
358
|
-
Add to the description entry of the tool.
|
|
359
|
-
|
|
360
|
-
:param description: The text to add to the description.
|
|
361
|
-
"""
|
|
362
|
-
if not self._initialized:
|
|
363
|
-
raise SapioException("The tab for this tool has not been initialized.")
|
|
364
|
-
field: str = ElnBaseDataType.get_text_entry_data_field_name()
|
|
365
|
-
update: str = self.description_record.get_field_value(field)
|
|
366
|
-
update += f"""<p style="padding-top: 10px;"><span style="font-size: 15pt;">{description}</span></p>"""
|
|
367
|
-
self.description_record.set_field_value(field, update)
|
|
368
|
-
self.dr_man.commit_data_records([self.description_record])
|
|
369
|
-
|
|
370
|
-
def update_progress(self, progress: float, status_msg: str | None = None) -> None:
|
|
371
|
-
"""
|
|
372
|
-
Updates the progress of the tool.
|
|
373
|
-
|
|
374
|
-
:param progress: A value between 0 and 100 representing the progress of the tool.
|
|
375
|
-
:param status_msg: A status message to display to the user alongside the progress gauge.
|
|
376
|
-
"""
|
|
377
|
-
if not self._initialized:
|
|
378
|
-
raise SapioException("The tab for this tool has not been initialized.")
|
|
379
|
-
self.progress_record.set_field_value("Progress", progress)
|
|
380
|
-
self.progress_record.set_field_value("StatusMsg", status_msg)
|
|
381
|
-
self.dr_man.commit_data_records([self.progress_record])
|
|
382
|
-
|
|
383
|
-
def add_results_bar_chart(self, x_axis: str, y_axis: str) -> ExperimentEntry:
|
|
384
|
-
"""
|
|
385
|
-
Create a bar chart entry for the results of the tool.
|
|
386
|
-
|
|
387
|
-
:param x_axis: The data field to use for the x-axis of the chart.
|
|
388
|
-
:param y_axis: The data field to use for the y-axis of the chart.
|
|
389
|
-
:return: The newly created chart entry.
|
|
390
|
-
"""
|
|
391
|
-
if not self._initialized:
|
|
392
|
-
raise SapioException("The tab for this tool has not been initialized.")
|
|
393
|
-
if not self.results_entry:
|
|
394
|
-
raise SapioException("This tool does not produce result records.")
|
|
395
|
-
return ELNStepFactory.create_bar_chart_step(self._protocol, self.results_entry, f"{self.name} Results Chart",
|
|
396
|
-
x_axis, y_axis)[0].eln_entry
|
|
397
|
-
|
|
398
|
-
def add_attachment_entry(self, file_name: str, file_data: str | bytes, entry_name: str,
|
|
399
|
-
tab: ElnExperimentTab | None = None) -> ExperimentEntry:
|
|
400
|
-
"""
|
|
401
|
-
Add a new attachment entry to the experiment with the provided attachment data.
|
|
402
|
-
|
|
403
|
-
:param file_name: The name of the attachment.
|
|
404
|
-
:param file_data: The data of the attachment. This can be a string or bytes.
|
|
405
|
-
:param entry_name: Name of the attachment entry to create in the experiment.
|
|
406
|
-
:param tab: The tab where the attachment will be added. If not provided, the tab initialized by this helper
|
|
407
|
-
will be used.
|
|
408
|
-
:return: The created entry object.
|
|
409
|
-
"""
|
|
410
|
-
# Check if the tab has been initialized or a tab has been provided.
|
|
411
|
-
if not self._initialized and tab is None:
|
|
412
|
-
raise SapioException("The tab for this tool has not been initialized. Either initialize a tab for this "
|
|
413
|
-
"tool or provide the tab to this function to add the attachment entry to.")
|
|
414
|
-
tab_id: int = self.tab.tab_id if tab is None else tab.tab_id
|
|
415
|
-
|
|
416
|
-
# Encode the file contents in base64.
|
|
417
|
-
if isinstance(file_data, str):
|
|
418
|
-
file_data: bytes = file_data.encode("utf-8")
|
|
419
|
-
base64_encoded: str = base64.b64encode(file_data).decode("utf-8")
|
|
420
|
-
|
|
421
|
-
# Crete an attachment entry with the provided data.
|
|
422
|
-
attachment_entry = self.eln_man.add_experiment_entry(
|
|
423
|
-
self.exp_id,
|
|
424
|
-
ElnEntryCriteria(ElnEntryType.Attachment, entry_name, "Attachment", order=2,
|
|
425
|
-
notebook_experiment_tab_id=tab_id, attachment_file_name=file_name,
|
|
426
|
-
attachment_data_base64=base64_encoded)
|
|
427
|
-
)
|
|
428
|
-
|
|
429
|
-
# Return the entry object for further use.
|
|
430
|
-
return attachment_entry
|
|
431
|
-
|
|
432
|
-
def add_attachment_entry_from_file_system(self, file_path: str, entry_name: str,
|
|
433
|
-
tab: ElnExperimentTab | None = None) -> ExperimentEntry:
|
|
434
|
-
"""
|
|
435
|
-
Add a new attachment entry to the experiment with the provided file path to a file in the file system.
|
|
436
|
-
|
|
437
|
-
:param file_path: The path to a file in the system to attach to the experiment.
|
|
438
|
-
:param entry_name: Name of the attachment entry to create in the experiment.
|
|
439
|
-
:param tab: The tab where the attachment will be added. If not provided, the tab initialized by this helper
|
|
440
|
-
will be used.
|
|
441
|
-
:return: The created entry object.
|
|
442
|
-
"""
|
|
443
|
-
# Check if the tab has been initialized or a tab has been provided.
|
|
444
|
-
# This is redundant with the same check in the add_attachment_entry function, but it's duplicated here as to
|
|
445
|
-
# not read the provided file and then find out we can't do anything with it anyway.
|
|
446
|
-
if not self._initialized and tab is None:
|
|
447
|
-
raise SapioException("The tab for this tool has not been initialized. Either initialize a tab for this "
|
|
448
|
-
"tool or provide the tab to this function to add the attachment entry to.")
|
|
449
|
-
|
|
450
|
-
with open(file_path, 'rb') as f:
|
|
451
|
-
file_contents: bytes = f.read()
|
|
452
|
-
return self.add_attachment_entry(file_path, file_contents, entry_name, tab)
|
|
453
|
-
|
|
454
|
-
# TODO: Remove this once pylib has a gauge chart function in ElnStepFactory.
|
|
455
|
-
@staticmethod
|
|
456
|
-
def _create_gauge_chart(protocol: ElnExperimentProtocol, data_source_step: ElnEntryStep, step_name: str,
|
|
457
|
-
field_name: str, status_field: str, group_by_field_name: str = "DataRecordName") \
|
|
458
|
-
-> ElnEntryStep:
|
|
459
|
-
"""
|
|
460
|
-
Create a gauge chart step in the experiment protocol.
|
|
461
|
-
"""
|
|
462
|
-
if not data_source_step.get_data_type_names():
|
|
463
|
-
raise ValueError("The data source step did not declare a data type name.")
|
|
464
|
-
data_type_name: str = data_source_step.get_data_type_names()[0]
|
|
465
|
-
series = GaugeChartSeries(data_type_name, field_name)
|
|
466
|
-
series.operation_type = ChartOperationType.VALUE
|
|
467
|
-
chart = _GaugeChartDefinition()
|
|
468
|
-
chart.main_data_type_name = data_type_name
|
|
469
|
-
chart.status_field = status_field
|
|
470
|
-
chart.minimum_value = 0.
|
|
471
|
-
chart.maximum_value = 100.
|
|
472
|
-
chart.series_list = [series]
|
|
473
|
-
chart.grouping_type = ChartGroupingType.GROUP_BY_FIELD
|
|
474
|
-
chart.grouping_type_data_type_name = data_type_name
|
|
475
|
-
chart.grouping_type_data_field_name = group_by_field_name
|
|
476
|
-
dashboard, step = ELNStepFactory._create_dashboard_step_from_chart(chart, data_source_step, protocol, step_name)
|
|
477
|
-
protocol.invalidate()
|
|
478
|
-
return step
|
|
479
|
-
|
|
480
|
-
|
|
481
|
-
# TODO: This is only here because the get_chart_type function in pylib is wrong. Remove this once pylib is fixed.
|
|
482
|
-
# Also using this to set the new status field setting.
|
|
483
|
-
class _GaugeChartDefinition(GaugeChartDefinition):
|
|
484
|
-
status_field: str
|
|
485
|
-
|
|
486
|
-
def get_chart_type(self) -> ChartType:
|
|
487
|
-
return ChartType.GAUGE_CHART
|
|
488
|
-
|
|
489
|
-
def to_json(self) -> dict[str, Any]:
|
|
490
|
-
result = super().to_json()
|
|
491
|
-
result["statusValueField"] = {
|
|
492
|
-
"dataTypeName": self.main_data_type_name,
|
|
493
|
-
"dataFieldName": self.status_field
|
|
494
|
-
}
|
|
495
|
-
return result
|
|
496
|
-
|
|
497
|
-
|
|
498
|
-
# TODO: Remove once the ElnTextEntryUpdateCriteria is fixed.
|
|
499
|
-
class _ElnTextEntryUpdateCriteria(AbstractElnEntryUpdateCriteria):
|
|
500
|
-
"""
|
|
501
|
-
Text Entry Update Data Payload
|
|
502
|
-
Create this payload object and set the attributes you want to update before sending the request.
|
|
503
|
-
"""
|
|
504
|
-
|
|
505
|
-
def __init__(self):
|
|
506
|
-
super().__init__(ElnEntryType.Text)
|
|
507
|
-
|
|
508
|
-
def to_json(self) -> dict[str, Any]:
|
|
509
|
-
ret = super().to_json()
|
|
510
|
-
return ret
|
|
@@ -1,86 +0,0 @@
|
|
|
1
|
-
from typing import Iterable, cast
|
|
2
|
-
|
|
3
|
-
from sapiopylib.rest.User import SapioUser
|
|
4
|
-
from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, CustomReport
|
|
5
|
-
from sapiopylib.rest.pojo.webhook.WebhookDirective import HomePageDirective, FormDirective, TableDirective, \
|
|
6
|
-
CustomReportDirective, ElnExperimentDirective, ExperimentEntryDirective
|
|
7
|
-
|
|
8
|
-
from sapiopycommons.general.aliases import SapioRecord, AliasUtil, ExperimentIdentifier, ExperimentEntryIdentifier, \
|
|
9
|
-
UserIdentifier
|
|
10
|
-
from sapiopycommons.general.custom_report_util import CustomReportUtil
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
# FR-47392: Create a DirectiveUtil class to simplify the creation of directives.
|
|
14
|
-
class DirectiveUtil:
|
|
15
|
-
"""
|
|
16
|
-
DirectiveUtil is a class for creating webhook directives. The utility functions reduce the provided variables
|
|
17
|
-
down to the exact type that the directives require, removing the need for the caller to handle the conversion.
|
|
18
|
-
"""
|
|
19
|
-
user: SapioUser
|
|
20
|
-
|
|
21
|
-
def __init__(self, context: UserIdentifier):
|
|
22
|
-
"""
|
|
23
|
-
:param context: The current webhook context or a user object to send requests from.
|
|
24
|
-
"""
|
|
25
|
-
self.user = AliasUtil.to_sapio_user(context)
|
|
26
|
-
|
|
27
|
-
@staticmethod
|
|
28
|
-
def homepage() -> HomePageDirective:
|
|
29
|
-
"""
|
|
30
|
-
:return: A directive that sends the user back to their home page.
|
|
31
|
-
"""
|
|
32
|
-
return HomePageDirective()
|
|
33
|
-
|
|
34
|
-
@staticmethod
|
|
35
|
-
def record_form(record: SapioRecord) -> FormDirective:
|
|
36
|
-
"""
|
|
37
|
-
:param record: A record in the system.
|
|
38
|
-
:return: A directive that sends the user to a specific data record form.
|
|
39
|
-
"""
|
|
40
|
-
return FormDirective(AliasUtil.to_data_record(record))
|
|
41
|
-
|
|
42
|
-
@staticmethod
|
|
43
|
-
def record_table(records: Iterable[SapioRecord]) -> TableDirective:
|
|
44
|
-
"""
|
|
45
|
-
:param records: A list of records in the system.
|
|
46
|
-
:return: A directive that sends the user to a table of data records.
|
|
47
|
-
"""
|
|
48
|
-
return TableDirective(AliasUtil.to_data_records(records))
|
|
49
|
-
|
|
50
|
-
@staticmethod
|
|
51
|
-
def record_adaptive(records: Iterable[SapioRecord]) -> TableDirective | FormDirective:
|
|
52
|
-
"""
|
|
53
|
-
:param records: A list of records in the system.
|
|
54
|
-
:return: A directive that sends the user to a table of data records if there are multiple records,
|
|
55
|
-
or a directive that sends the user to a specific data record form if there is only one record.
|
|
56
|
-
"""
|
|
57
|
-
records: list[SapioRecord] = list(records)
|
|
58
|
-
if len(records) == 1:
|
|
59
|
-
return DirectiveUtil.record_form(records[0])
|
|
60
|
-
return DirectiveUtil.record_table(records)
|
|
61
|
-
|
|
62
|
-
def custom_report(self, report: CustomReport | CustomReportCriteria | str) -> CustomReportDirective:
|
|
63
|
-
"""
|
|
64
|
-
:param report: A custom report, the criteria for a custom report, or the name of a system report.
|
|
65
|
-
:return: A directive that sends the user to the results of the provided custom report.
|
|
66
|
-
"""
|
|
67
|
-
if isinstance(report, str):
|
|
68
|
-
report: CustomReport = CustomReportUtil.get_system_report_criteria(self.user, report)
|
|
69
|
-
return CustomReportDirective(cast(CustomReport, report))
|
|
70
|
-
|
|
71
|
-
@staticmethod
|
|
72
|
-
def eln_experiment(experiment: ExperimentIdentifier) -> ElnExperimentDirective:
|
|
73
|
-
"""
|
|
74
|
-
:param experiment: An identifier for an experiment.
|
|
75
|
-
:return: A directive that sends the user to the ELN experiment.
|
|
76
|
-
"""
|
|
77
|
-
return ElnExperimentDirective(AliasUtil.to_notebook_id(experiment))
|
|
78
|
-
|
|
79
|
-
@staticmethod
|
|
80
|
-
def eln_entry(experiment: ExperimentIdentifier, entry: ExperimentEntryIdentifier) -> ExperimentEntryDirective:
|
|
81
|
-
"""
|
|
82
|
-
:param experiment: An identifier for an experiment.
|
|
83
|
-
:param entry: An identifier for an entry in the experiment.
|
|
84
|
-
:return: A directive that sends the user to the provided experiment entry within its ELN experiment.
|
|
85
|
-
"""
|
|
86
|
-
return ExperimentEntryDirective(AliasUtil.to_notebook_id(experiment), AliasUtil.to_entry_id(entry))
|
|
File without changes
|
{sapiopycommons-2025.2.6a421.dist-info → sapiopycommons-2025.2.7a424.dist-info}/licenses/LICENSE
RENAMED
|
File without changes
|