sapiopycommons 2025.2.11a431__tar.gz → 2025.2.12a432__tar.gz

{sapiopycommons-2025.2.11a431 → sapiopycommons-2025.2.12a432}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.2.11a431
+Version: 2025.2.12a432
 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-2025.2.11a431 → sapiopycommons-2025.2.12a432}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.02.11a431'
+version='2025.02.12a432'
 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

@@ -0,0 +1,632 @@
+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