sapiopycommons 2025.2.12a432__tar.gz → 2025.2.12a433__tar.gz

{sapiopycommons-2025.2.12a432 → sapiopycommons-2025.2.12a433}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.2.12a432
+Version: 2025.2.12a433
 Summary: Official Sapio Python API Utilities Package
 Project-URL: Homepage, https://github.com/sapiosciences
 Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>

{sapiopycommons-2025.2.12a432 → sapiopycommons-2025.2.12a433}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.02.12a432'
+version='2025.02.12a433'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

sapiopycommons-2025.2.12a432/src/sapiopycommons/elain/tool_of_tools.py

@@ -1,632 +0,0 @@
-import base64
-import math
-import re
-from typing import Final, Mapping, Any
-
-from pandas import DataFrame
-from sapiopylib.rest.DataRecordManagerService import DataRecordManager
-from sapiopylib.rest.ELNService import ElnManager
-from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.pojo.DataRecord import DataRecord
-from sapiopylib.rest.pojo.chartdata.DashboardDefinition import GaugeChartDefinition
-from sapiopylib.rest.pojo.chartdata.DashboardEnums import ChartGroupingType, ChartOperationType
-from sapiopylib.rest.pojo.chartdata.DashboardSeries import GaugeChartSeries
-from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition, FieldType
-from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
-from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
-from sapiopylib.rest.pojo.eln.ExperimentEntryCriteria import ElnEntryCriteria, ElnFormEntryUpdateCriteria, \
-    ElnDashboardEntryUpdateCriteria, ElnTextEntryUpdateCriteria
-from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnEntryType, ElnBaseDataType
-from sapiopylib.rest.pojo.eln.eln_headings import ElnExperimentTabAddCriteria, ElnExperimentTab
-from sapiopylib.rest.pojo.eln.field_set import ElnFieldSetInfo
-from sapiopylib.rest.utils.ProtocolUtils import ELNStepFactory
-from sapiopylib.rest.utils.Protocols import ElnEntryStep, ElnExperimentProtocol
-
-from sapiopycommons.callbacks.field_builder import FieldBuilder
-from sapiopycommons.general.aliases import AliasUtil, SapioRecord
-from sapiopycommons.general.exceptions import SapioException
-from sapiopycommons.general.time_util import TimeUtil
-
-CREDENTIALS_HEADER: Final[str] = "SAPIO_APP_API_KEY"
-API_URL_HEADER: Final[str] = "SAPIO_APP_API_URL"
-EXP_ID_HEADER: Final[str] = "EXPERIMENT_ID"
-TAB_PREFIX_HEADER: Final[str] = "TAB_PREFIX"
-
-
-# TODO: There's a lot of duplication between the static functions and the ToT Helper. This should just be one class
-#  that both the tool endpoints and the AI instantiate, or two classes where one is a subclass of the other. Maybe work
-#  on that after the initial implementation is done.
-# FR-47422: Create utility methods to assist the tool of tools.
-def create_tot_headers(url: str, username: str, password: str, experiment_id: int, tab_prefix: str) \
-        -> tuple[str, dict[str, str]]:
-    """
-    Create the headers to be passed to a tool of tools endpoint.
-
-    :param url: The webservice URL of the system to make the changes in.
-    :param username: The username of the user making the changes.
-    :param password: The password of the user making the changes.
-    :param experiment_id: The ID of the experiment to make the changes in.
-    :param tab_prefix: The prefix to use for the tab name that will be created by the tool.
-    :return: The encoded credentials and the headers to be passed to the endpoint.
-    """
-    # Combine the credentials into the format "username:password"
-    credentials: str = f"{username}:{password}"
-    # Encode the credentials to bytes, then encode them using base64,
-    # and finally convert the result back into a string.
-    encoded_credentials: str = base64.b64encode(credentials.encode('utf-8')).decode('utf-8')
-    headers: dict[str, str] = {
-        CREDENTIALS_HEADER: f"Basic {encoded_credentials}",
-        API_URL_HEADER: url,
-        EXP_ID_HEADER: str(experiment_id),
-        TAB_PREFIX_HEADER: tab_prefix
-    }
-    return encoded_credentials, headers
-
-
-def create_user_from_tot_headers(headers: Mapping[str, str]) -> SapioUser:
-    """
-    Create a SapioUser object from the headers passed to a tool of tools endpoint.
-
-    :param headers: The headers that were passed to the endpoint.
-    :return: A SapioUser object created from the headers that can be used to communicate with the Sapio server.
-    """
-    headers: dict[str, str] = format_tot_headers(headers)
-    credentials = (base64.b64decode(headers[CREDENTIALS_HEADER.lower()].removeprefix("Basic "))
-                   .decode("utf-8").split(":", 1))
-    return SapioUser(headers[API_URL_HEADER.lower()], username=credentials[0], password=credentials[1])
-
-
-def format_tot_headers(headers: Mapping[str, str]) -> dict[str, str]:
-    """
-    Format the headers passed to a tool of tools endpoint to guarantee that the keys are lowercase.
-
-    :param headers: The headers that were passed to the endpoint.
-    :return: The headers with all keys converted to lowercase. (Conflicting keys will cause one to overwrite the other,
-        but there should not be any conflicting keys in the headers passed to a tool of tools endpoint.)
-    """
-    return {k.lower(): v for k, v in headers.items()}
-
-
-def create_experiment_details_from_data_frame(user: SapioUser,
-                                              exp_id: int,
-                                              entry_name: str,
-                                              tab: ElnExperimentTab,
-                                              df: DataFrame) -> ExperimentEntry | None:
-    """
-    Create an experiment detail entry from a DataFrame.
-
-    :param user: The user to send the request from.
-    :param exp_id: The ID of the experiment to create the entry in.
-    :param entry_name: The name of the entry.
-    :param tab: The tab that the entry should be added to.
-    :param df: The DataFrame to create the entry from.
-    :return: The created entry object.
-    """
-    json_list: list[dict[str, Any]] = []
-    for _, row in df.iterrows():
-        json_list.append(row.to_dict())
-    return create_experiment_details_from_json(user, exp_id, entry_name, tab, json_list)
-
-
-def create_experiment_details_from_json(user: SapioUser,
-                                        exp_id: int,
-                                        entry_name: str,
-                                        tab: ElnExperimentTab,
-                                        json_list: list[dict[str, Any]]) -> ExperimentEntry | None:
-    """
-    Create an experiment detail entry from a list of JSON dictionaries.
-
-    :param user: The user to send the request from.
-    :param exp_id: The ID of the experiment to create the entry in.
-    :param entry_name: The name of the entry.
-    :param tab: The tab that the entry should be added to.
-    :param json_list: The list of JSON dictionaries to create the entry from. Each dictionary is expected to have the
-        same keys.
-    :return: The created entry object.
-    """
-    if not json_list:
-        return None
-
-    # Determine which fields in the JSON can be used to create field definitions.
-    fb = FieldBuilder()
-    fields: list[AbstractVeloxFieldDefinition] = []
-    fields_by_name: dict[str, AbstractVeloxFieldDefinition] = {}
-    for key, value in json_list[0].items():
-        field_name: str = key.replace(" ", "_")
-        if isinstance(value, str):
-            field = fb.string_field(field_name, display_name=key)
-            fields.append(field)
-            fields_by_name[key] = field
-        elif isinstance(value, (int, float)):
-            field = fb.double_field(field_name, display_name=key, precision=3)
-            fields.append(field)
-            fields_by_name[key] = field
-
-    # Extract the valid field values from the JSON.
-    field_maps: list[dict[str, Any]] = []
-    for json_dict in json_list:
-        field_map: dict[str, Any] = {}
-        for key, field in fields_by_name.items():
-            # Watch out for NaN values or other special values.
-            val: Any = json_dict.get(key)
-            if (field.data_field_type == FieldType.DOUBLE
-                    and (not isinstance(val, (int, float))) or (isinstance(val, float) and math.isnan(val))):
-                val = None
-            field_map[field.data_field_name] = val
-        field_maps.append(field_map)
-
-    detail_entry = ElnEntryCriteria(ElnEntryType.Table, entry_name,
-                                    ElnBaseDataType.EXPERIMENT_DETAIL.data_type_name,
-                                    tab_next_entry_order(user, exp_id, tab),
-                                    notebook_experiment_tab_id=tab.tab_id,
-                                    field_definition_list=fields)
-    entry = ElnManager(user).add_experiment_entry(exp_id, detail_entry)
-    DataRecordManager(user).add_data_records_with_data(entry.data_type_name, field_maps)
-    return entry
-
-
-def tab_next_entry_order(user: SapioUser, exp_id: int, tab: ElnExperimentTab) -> int:
-    max_order: int = 0
-    for step in ElnExperimentProtocol(ElnExperiment(exp_id, "", 0), user).get_sorted_step_list():
-        if step.eln_entry.notebook_experiment_tab_id == tab.tab_id and step.eln_entry.order > max_order:
-            max_order = step.eln_entry.order
-    return max_order + 1
-
-
-def set_text_entry(timestamp: str, description: str, text_entry: ExperimentEntry, exp_id: int, user: SapioUser,
-                   auto_format: bool = True) -> None:
-    """
-    Set the text of a text entry.
-
-    :param timestamp: The timestamp to display at the top of the text entry.
-    :param description: The description to display in the text entry.
-    :param text_entry: The text entry to set the text of.
-    :param exp_id: The ID of the experiment that the text entry is in.
-    :param user: The user to send the request from.
-    :param auto_format: Whether to automatically format the text to be added.
-    """
-    if auto_format:
-        timestamp = HtmlFormatter.timestamp(timestamp)
-        description = HtmlFormatter.body(description)
-    description: str = f"<p>{timestamp}<br>{description}</p>"
-    protocol = ElnExperimentProtocol(ElnExperiment(exp_id, "", 0), user)
-    step = ElnEntryStep(protocol, text_entry)
-    text_record: DataRecord = step.get_records()[0]
-    text_record.set_field_value(ElnBaseDataType.get_text_entry_data_field_name(), description)
-    DataRecordManager(user).commit_data_records([text_record])
-
-
-def add_to_text_entry(description: str, text_entry: ExperimentEntry, exp_id: int, user: SapioUser,
-                      auto_format: bool = True) -> None:
-    """
-    Add to the text of a text entry.
-
-    :param description: The text to add to the text entry.
-    :param text_entry: The text entry to add the text to.
-    :param exp_id: The ID of the experiment that the text entry is in.
-    :param user: The user to send the request from.
-    :param auto_format: Whether to automatically format the text to be added.
-    """
-    protocol = ElnExperimentProtocol(ElnExperiment(exp_id, "", 0), user)
-    step = ElnEntryStep(protocol, text_entry)
-    text_record: DataRecord = step.get_records()[0]
-    update: str = text_record.get_field_value(ElnBaseDataType.get_text_entry_data_field_name())
-    if auto_format:
-        description = HtmlFormatter.body(description)
-    update += f"<p style=\"padding-top: 10px;\">{description}</p>"
-    text_record.set_field_value(ElnBaseDataType.get_text_entry_data_field_name(), update)
-    DataRecordManager(user).commit_data_records([text_record])
-
-
-class HtmlFormatter:
-    """
-    A class for formatting text in HTML with classes supported by the client.
-    """
-    TIMESTAMP_TEXT__CSS_CLASS_NAME: Final[str] = "timestamp-text"
-    HEADER_1_TEXT__CSS_CLASS_NAME: Final[str] = "header1-text"
-    HEADER_2_TEXT__CSS_CLASS_NAME: Final[str] = "header2-text"
-    HEADER_3_TEXT__CSS_CLASS_NAME: Final[str] = "header3-text"
-    BODY_TEXT__CSS_CLASS_NAME: Final[str] = "body-text"
-    CAPTION_TEXT__CSS_CLASS_NAME: Final[str] = "caption-text"
-
-    @staticmethod
-    def timestamp(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the timestamp CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.TIMESTAMP_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def header_1(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the header 1 CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.HEADER_1_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def header_2(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the header 2 CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.HEADER_2_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def header_3(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the header 3 CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.HEADER_3_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def body(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the body CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.BODY_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def caption(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted using the caption CSS class.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return f"<span class=\"{HtmlFormatter.CAPTION_TEXT__CSS_CLASS_NAME}\">{text}</span>"
-
-    @staticmethod
-    def replace_newlines(text: str) -> str:
-        """
-        Given a text string, return that same text string HTML formatted with newlines replaced by HTML line breaks.
-
-        :param text: The text to format.
-        :return: The HTML formatted text.
-        """
-        return re.sub("\r?\n", "<br>", text)
-
-
-class ToolOfToolsHelper:
-    """
-    A class with helper methods utilized by the Tool of Tools for the creation and updating of experiment tabs that
-    track a tool's progress and results.
-    """
-    # Contextual info.
-    user: SapioUser
-    tab_prefix: str
-    exp_id: int
-    _protocol: ElnExperimentProtocol
-
-    # Tool info.
-    name: str
-    description: str
-    results_data_type: str | None
-
-    # Managers.
-    eln_man: ElnManager
-    dr_man: DataRecordManager
-
-    # Stuff created by this helper.
-    _initialized: bool
-    """Whether a tab for this tool has been initialized."""
-    tab: ElnExperimentTab
-    """The tab that contains the tool's entries."""
-    description_entry: ElnEntryStep | None
-    """The text entry that displays the description of the tool."""
-    description_record: DataRecord | None
-    """The record that stores the description of the tool."""
-    progress_entry: ElnEntryStep | None
-    """A hidden entry for tracking the progress of the tool."""
-    progress_record: DataRecord | None
-    """The record that stores the progress of the tool."""
-    progress_gauge_entry: ElnEntryStep | None
-    """A chart entry that displays the progress of the tool using the hidden progress entry."""
-    results_entry: ElnEntryStep | None
-    """An entry for displaying the results of the tool. If None, the tool does not produce result records."""
-
-    def __init__(self, headers: Mapping[str, str], name: str, description: str,
-                 results_data_type: str | None = None):
-        """
-        :param headers: The headers that were passed to the endpoint.
-        :param name: The name of the tool.
-        :param description: A description of the tool.
-        :param results_data_type: The data type name for the results of the tool. If None, the tool does not produce
-            result records.
-        """
-        headers: dict[str, str] = format_tot_headers(headers)
-        self.user = create_user_from_tot_headers(headers)
-        self.exp_id = int(headers[EXP_ID_HEADER.lower()])
-        self.tab_prefix = headers[TAB_PREFIX_HEADER.lower()]
-        # The experiment name and record ID aren't necessary to know.
-        self._protocol = ElnExperimentProtocol(ElnExperiment(self.exp_id, "", 0), self.user)
-
-        self.name = name
-        self.description = description
-        self.results_data_type = results_data_type
-
-        self.eln_man = ElnManager(self.user)
-        self.dr_man = DataRecordManager(self.user)
-
-        self._initialized = False
-
-    def initialize_tab(self) -> ElnExperimentTab:
-        if self._initialized:
-            return self.tab
-        self._initialized = True
-
-        # Determine if a previous call to this endpoint already created a tab for these results. If so, grab the entries
-        # from that tab.
-        tab_name: str = f"{self.tab_prefix.strip()} {self.name.strip()}"
-        tabs: list[ElnExperimentTab] = self.eln_man.get_tabs_for_experiment(self.exp_id)
-        for tab in tabs:
-            if tab.tab_name != tab_name:
-                continue
-
-            for entry in self._protocol.get_sorted_step_list():
-                if entry.eln_entry.notebook_experiment_tab_id != tab.tab_id:
-                    continue
-
-                dt: str = entry.get_data_type_names()[0] if entry.get_data_type_names() else None
-                if (entry.eln_entry.entry_type == ElnEntryType.Form
-                        and ElnBaseDataType.get_base_type(dt) == ElnBaseDataType.EXPERIMENT_DETAIL
-                        and not hasattr(self, "progress_entry")):
-                    self.progress_entry = entry
-                    self.progress_record = entry.get_records()[0]
-                elif (entry.eln_entry.entry_type == ElnEntryType.Dashboard
-                      and not hasattr(self, "progress_gauge_entry")):
-                    self.progress_gauge_entry = entry
-                elif (entry.eln_entry.entry_type == ElnEntryType.Text
-                      and not hasattr(self, "description_entry")):
-                    self.description_entry = entry
-                    self.description_record = entry.get_records()[0]
-                elif (entry.eln_entry.entry_type == ElnEntryType.Table
-                      and dt == self.results_data_type
-                      and not hasattr(self, "results_entry")):
-                    self.results_entry = entry
-
-            if not hasattr(self, "progress_entry"):
-                self.progress_entry = None
-                self.progress_record = None
-            if not hasattr(self, "progress_gauge_entry"):
-                self.progress_gauge_entry = None
-            if not hasattr(self, "description_entry"):
-                self.description_entry = None
-                self.description_record = None
-            if not hasattr(self, "results_entry"):
-                self.results_entry = None
-
-            self.tab = tab
-            return tab
-
-        # Otherwise, create the tab for the tool progress and results.
-        tab_crit = ElnExperimentTabAddCriteria(tab_name, [])
-        tab: ElnExperimentTab = self.eln_man.add_tab_for_experiment(self.exp_id, tab_crit)
-        self.tab = tab
-
-        # Create a hidden entry for tracking the progress of the tool.
-        field_sets: list[ElnFieldSetInfo] = self.eln_man.get_field_set_info_list()
-        progress_field_set: list[ElnFieldSetInfo] = [x for x in field_sets if
-                                                     x.field_set_name == "Tool of Tools Progress"]
-        if not progress_field_set:
-            raise SapioException("Unable to locate the field set for the Tool of Tools progress.")
-        progress_entry_crit = ElnEntryCriteria(ElnEntryType.Form, f"ELaiN: {self.name} Progress",
-                                               ElnBaseDataType.EXPERIMENT_DETAIL.data_type_name, 1,
-                                               notebook_experiment_tab_id=tab.tab_id,
-                                               enb_field_set_id=progress_field_set[0].field_set_id)
-        progress_entry = ElnEntryStep(self._protocol,
-                                      self.eln_man.add_experiment_entry(self.exp_id, progress_entry_crit))
-        self.progress_entry = progress_entry
-        self.progress_record = progress_entry.get_records()[0]
-
-        # Hide the progress entry.
-        form_update_crit = ElnFormEntryUpdateCriteria()
-        form_update_crit.is_hidden = True
-        self.eln_man.update_experiment_entry(self.exp_id, self.progress_entry.get_id(), form_update_crit)
-
-        # Create the text entry that displays the description of the tool. Include the timestamp of when the
-        # tool started and format the description so that the text isn't too small to read.
-        # TODO: Get the UTC offset in seconds from the header once that's being sent.
-        now: str = TimeUtil.now_in_format("%Y-%m-%d %H:%M:%S UTC", "UTC")
-        description: str = f"<p>{HtmlFormatter.timestamp(now)}<br>{HtmlFormatter.body(self.description)}</p>"
-        text_entry: ElnEntryStep = ELNStepFactory.create_text_entry(self._protocol, description)
-        self.description_entry = text_entry
-        self.description_record = text_entry.get_records()[0]
-
-        # Shrink the text entry by one column.
-        text_update_crit = ElnTextEntryUpdateCriteria()
-        text_update_crit.column_span = 2
-        self.eln_man.update_experiment_entry(self.exp_id, self.description_entry.get_id(), text_update_crit)
-
-        # Create a gauge entry to display the progress.
-        gauge_entry: ElnEntryStep = self._create_gauge_chart(self._protocol, progress_entry,
-                                                             f"{self.name} Progress", "Progress", "StatusMsg")
-        self.progress_gauge_entry = gauge_entry
-
-        # Make sure the gauge entry isn't too big and stick it to the right of the text entry.
-        dash_update_crit = ElnDashboardEntryUpdateCriteria()
-        dash_update_crit.entry_height = 250
-        dash_update_crit.column_span = 2
-        dash_update_crit.column_order = 2
-        self.eln_man.update_experiment_entry(self.exp_id, self.progress_gauge_entry.get_id(), dash_update_crit)
-
-        # TODO: Bulk updates aren't working?
-        # self.eln_man.update_experiment_entries(self.exp_id, {
-        #     self.progress_entry.get_id(): form_update_crit,
-        #     self.progress_gauge_entry.get_id(): dash_update_crit,
-        #     self.description_entry.get_id(): text_update_crit
-        # })
-
-        # Create a results entry if this tool produces result records.
-        if self.results_data_type:
-            results_entry = ELNStepFactory.create_table_step(self._protocol, f"{self.name} Results",
-                                                             self.results_data_type)
-            self.results_entry = results_entry
-        else:
-            self.results_entry = None
-
-        return tab
-
-    def add_to_description(self, description: str, auto_format: bool = True) -> None:
-        """
-        Add to the description entry of the tool.
-
-        :param description: The text to add to the description.
-        :param auto_format: Whether to automatically format the text to be added.
-        """
-        if not self._initialized:
-            raise SapioException("The tab for this tool has not been initialized.")
-        field: str = ElnBaseDataType.get_text_entry_data_field_name()
-        update: str = self.description_record.get_field_value(field)
-        if auto_format:
-            description = HtmlFormatter.body(description)
-        update += f"<p style=\"padding-top: 10px;\">{description}</p>"
-        self.description_record.set_field_value(field, update)
-        self.dr_man.commit_data_records([self.description_record])
-
-    def update_progress(self, progress: float, status_msg: str | None = None) -> None:
-        """
-        Updates the progress of the tool.
-
-        :param progress: A value between 0 and 100 representing the progress of the tool.
-        :param status_msg: A status message to display to the user alongside the progress gauge.
-        """
-        if not self._initialized:
-            raise SapioException("The tab for this tool has not been initialized.")
-        self.progress_record.set_field_value("Progress", progress)
-        self.progress_record.set_field_value("StatusMsg", status_msg)
-        self.dr_man.commit_data_records([self.progress_record])
-
-    def add_results(self, results: list[SapioRecord]) -> None:
-        """
-        Add the results of the tool to the results entry.
-
-        :param results: The result records to add to the results entry.
-        """
-        if not self._initialized:
-            raise SapioException("The tab for this tool has not been initialized.")
-        self.results_entry.add_records(AliasUtil.to_data_records(results))
-
-    def add_results_bar_chart(self, x_axis: str, y_axis: str) -> ExperimentEntry:
-        """
-        Create a bar chart entry for the results of the tool.
-
-        :param x_axis: The data field to use for the x-axis of the chart.
-        :param y_axis: The data field to use for the y-axis of the chart.
-        :return: The newly created chart entry.
-        """
-        if not self._initialized:
-            raise SapioException("The tab for this tool has not been initialized.")
-        if not self.results_entry:
-            raise SapioException("This tool does not produce result records.")
-        return ELNStepFactory.create_bar_chart_step(self._protocol, self.results_entry, f"{self.name} Results Chart",
-                                                    x_axis, y_axis)[0].eln_entry
-
-    def add_attachment_entry(self, file_name: str, file_data: str | bytes, entry_name: str,
-                             tab: ElnExperimentTab | None = None) -> ExperimentEntry:
-        """
-        Add a new attachment entry to the experiment with the provided attachment data.
-
-        :param file_name: The name of the attachment.
-        :param file_data: The data of the attachment. This can be a string or bytes.
-        :param entry_name: Name of the attachment entry to create in the experiment.
-        :param tab: The tab where the attachment will be added. If not provided, the tab initialized by this helper
-            will be used.
-        :return: The created entry object.
-        """
-        # Check if the tab has been initialized or a tab has been provided.
-        if not self._initialized and tab is None:
-            raise SapioException("The tab for this tool has not been initialized. Either initialize a tab for this "
-                                 "tool or provide the tab to this function to add the attachment entry to.")
-        tab_id: int = self.tab.tab_id if tab is None else tab.tab_id
-
-        # Encode the file contents in base64.
-        if isinstance(file_data, str):
-            file_data: bytes = file_data.encode("utf-8")
-        base64_encoded: str = base64.b64encode(file_data).decode("utf-8")
-
-        # Crete an attachment entry with the provided data.
-        attachment_entry = self.eln_man.add_experiment_entry(
-            self.exp_id,
-            ElnEntryCriteria(ElnEntryType.Attachment, entry_name, "Attachment", order=2,
-                             notebook_experiment_tab_id=tab_id, attachment_file_name=file_name,
-                             attachment_data_base64=base64_encoded)
-        )
-
-        # Return the entry object for further use.
-        return attachment_entry
-
-    def add_attachment_entry_from_file_system(self, file_path: str, entry_name: str,
-                                              tab: ElnExperimentTab | None = None) -> ExperimentEntry:
-        """
-        Add a new attachment entry to the experiment with the provided file path to a file in the file system.
-
-        :param file_path: The path to a file in the system to attach to the experiment.
-        :param entry_name: Name of the attachment entry to create in the experiment.
-        :param tab: The tab where the attachment will be added. If not provided, the tab initialized by this helper
-            will be used.
-        :return: The created entry object.
-        """
-        # Check if the tab has been initialized or a tab has been provided.
-        # This is redundant with the same check in the add_attachment_entry function, but it's duplicated here as to
-        # not read the provided file and then find out we can't do anything with it anyway.
-        if not self._initialized and tab is None:
-            raise SapioException("The tab for this tool has not been initialized. Either initialize a tab for this "
-                                 "tool or provide the tab to this function to add the attachment entry to.")
-
-        with open(file_path, 'rb') as f:
-            file_contents: bytes = f.read()
-            return self.add_attachment_entry(file_path, file_contents, entry_name, tab)
-
-    # TODO: Remove this once pylib's gauge chart definition is up to date.
-    @staticmethod
-    def _create_gauge_chart(protocol: ElnExperimentProtocol, data_source_step: ElnEntryStep, step_name: str,
-                            field_name: str, status_field: str, group_by_field_name: str = "DataRecordName") \
-            -> ElnEntryStep:
-        """
-        Create a gauge chart step in the experiment protocol.
-        """
-        if not data_source_step.get_data_type_names():
-            raise ValueError("The data source step did not declare a data type name.")
-        data_type_name: str = data_source_step.get_data_type_names()[0]
-        series = GaugeChartSeries(data_type_name, field_name)
-        series.operation_type = ChartOperationType.VALUE
-        chart = _GaugeChartDefinition()
-        chart.main_data_type_name = data_type_name
-        chart.status_field = status_field
-        chart.minimum_value = 0.
-        chart.maximum_value = 100.
-        chart.series_list = [series]
-        chart.grouping_type = ChartGroupingType.GROUP_BY_FIELD
-        chart.grouping_type_data_type_name = data_type_name
-        chart.grouping_type_data_field_name = group_by_field_name
-        dashboard, step = ELNStepFactory._create_dashboard_step_from_chart(chart, data_source_step, protocol, step_name,
-                                                                           None)
-        protocol.invalidate()
-        return step
-
-
-# TODO: Using this to set the new status field setting.
-class _GaugeChartDefinition(GaugeChartDefinition):
-    status_field: str
-
-    def to_json(self) -> dict[str, Any]:
-        result = super().to_json()
-        result["statusValueField"] = {
-            "dataTypeName": self.main_data_type_name,
-            "dataFieldName": self.status_field
-        }
-        return result