sapiopycommons 2025.2.5a412__tar.gz → 2025.2.5a415__tar.gz

{sapiopycommons-2025.2.5a412 → sapiopycommons-2025.2.5a415}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.2.5a412
+Version: 2025.2.5a415
 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-2025.2.5a412 → sapiopycommons-2025.2.5a415}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.02.05a412'
+version='2025.02.05a415'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2025.2.5a412 → sapiopycommons-2025.2.5a415}/src/sapiopycommons/elain/tool_of_tools.py

@@ -10,7 +10,8 @@ from sapiopylib.rest.pojo.chartdata.DashboardEnums import ChartGroupingType, Cha
 from sapiopylib.rest.pojo.chartdata.DashboardSeries import GaugeChartSeries
 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
+from sapiopylib.rest.pojo.eln.ExperimentEntryCriteria import ElnEntryCriteria, ElnFormEntryUpdateCriteria, \
+    ElnDashboardEntryUpdateCriteria, ElnTextEntryUpdateCriteria, AbstractElnEntryUpdateCriteria
 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
@@ -18,6 +19,7 @@ from sapiopylib.rest.utils.ProtocolUtils import ELNStepFactory
 from sapiopylib.rest.utils.Protocols import ElnEntryStep, ElnExperimentProtocol
 
 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"
@@ -101,13 +103,15 @@ class ToolOfToolsHelper:
     """Whether a tab for this tool has been initialized."""
     tab: ElnExperimentTab
     """The tab that contains the tool's entries."""
-    description_entry: ElnEntryStep
+    description_entry: ElnEntryStep | None
     """The text entry that displays the description of the tool."""
-    progress_entry: ElnEntryStep
+    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
+    progress_record: DataRecord | None
     """The record that stores the progress of the tool."""
-    progress_gauge_entry: ElnEntryStep
+    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."""
@@ -154,7 +158,7 @@ class ToolOfToolsHelper:
                 if entry.eln_entry.notebook_experiment_tab_id != tab.tab_id:
                     continue
 
-                dt: str = entry.get_data_type_names()[0]
+                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")):
@@ -166,18 +170,21 @@ class ToolOfToolsHelper:
                 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, "result_entry")):
+                      and not hasattr(self, "results_entry")):
                     self.results_entry = entry
 
             if not hasattr(self, "progress_entry"):
-                self.results_entry = None
+                self.progress_entry = None
+                self.progress_record = None
             if not hasattr(self, "progress_gauge_entry"):
-                self.results_entry = None
+                self.progress_gauge_entry = None
             if not hasattr(self, "description_entry"):
-                self.results_entry = None
-            if not hasattr(self, "result_entry"):
+                self.description_entry = None
+                self.description_record = None
+            if not hasattr(self, "results_entry"):
                 self.results_entry = None
 
             self.tab = tab
@@ -204,18 +211,39 @@ class ToolOfToolsHelper:
         self.progress_record = progress_entry.get_records()[0]
 
         # Hide the progress entry.
-        update_crit = ElnFormEntryUpdateCriteria()
-        update_crit.is_hidden = True
-        self.eln_man.update_experiment_entry(self.exp_id, progress_entry.get_id(), update_crit)
+        form_update_crit = ElnFormEntryUpdateCriteria()
+        form_update_crit.is_hidden = True
+
+        # 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><span style="color: rgb(35, 111, 161); font-size: 12pt; font-weight:500;">{now}</span>
+        <br><span style="font-size: 15pt;">{self.description}</span></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
 
         # 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
 
-        # Create the text entry that displays the description of the tool.
-        text_entry: ElnEntryStep = ELNStepFactory.create_text_entry(self._protocol, self.description)
-        self.description_entry = text_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_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:
@@ -227,6 +255,20 @@ class ToolOfToolsHelper:
 
         return tab
 
+    def add_to_description(self, description: str) -> None:
+        """
+        Add to the description entry of the tool.
+
+        :param description: The text to add to the description.
+        """
+        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)
+        update += f"""<p style="padding-top: 10px;"><span style="font-size: 15pt;">{description}</span></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.
@@ -240,6 +282,21 @@ class ToolOfToolsHelper:
         self.progress_record.set_field_value("StatusMsg", status_msg)
         self.dr_man.commit_data_records([self.progress_record])
 
+    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:
         """
@@ -338,3 +395,18 @@ class _GaugeChartDefinition(GaugeChartDefinition):
             "dataFieldName": self.status_field
         }
         return result
+
+
+# TODO: Remove once the ElnTextEntryUpdateCriteria is fixed.
+class _ElnTextEntryUpdateCriteria(AbstractElnEntryUpdateCriteria):
+    """
+    Text Entry Update Data Payload
+    Create this payload object and set the attributes you want to update before sending the request.
+    """
+
+    def __init__(self):
+        super().__init__(ElnEntryType.Text)
+
+    def to_json(self) -> dict[str, Any]:
+        ret = super().to_json()
+        return ret