sapiopycommons 2025.2.20a441__tar.gz → 2025.2.20a443__tar.gz

{sapiopycommons-2025.2.20a441 → sapiopycommons-2025.2.20a443}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.2.20a441
+Version: 2025.2.20a443
 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-2025.2.20a441 → sapiopycommons-2025.2.20a443}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "sapiopycommons"
-version='2025.02.20a441'
+version='2025.02.20a443'
 authors = [
     { name="Jonathan Steck", email="jsteck@sapiosciences.com" },
     { name="Yechen Qiao", email="yqiao@sapiosciences.com" },

{sapiopycommons-2025.2.20a441 → sapiopycommons-2025.2.20a443}/src/sapiopycommons/ai/tool_of_tools.py

@@ -2,7 +2,7 @@ import base64
 import io
 import math
 import re
-from typing import Final, Mapping, Any
+from typing import Final, Mapping, Any, cast
 
 import requests
 from pandas import DataFrame
@@ -18,7 +18,8 @@ from sapiopylib.rest.pojo.chartdata.DashboardEnums import ChartGroupingType, Cha
 from sapiopylib.rest.pojo.chartdata.DashboardSeries import GaugeChartSeries
 from sapiopylib.rest.pojo.datatype.DataType import DataTypeDefinition
 from sapiopylib.rest.pojo.datatype.DataTypeLayout import DataTypeLayout, TableLayout
-from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition, FieldType
+from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition, FieldType, \
+    VeloxStringFieldDefinition
 from sapiopylib.rest.pojo.eln.ElnEntryPosition import ElnEntryPosition
 from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
 from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
@@ -310,17 +311,39 @@ class AiHelper:
         # Determine which fields in the JSON can be used to create field definitions.
         fb = FieldBuilder()
         fields: list[AbstractVeloxFieldDefinition] = []
-        fields_by_name: dict[str, AbstractVeloxFieldDefinition] = {}
+        fields_by_json_key: dict[str, AbstractVeloxFieldDefinition] = {}
+        string_field_lengths: dict[str, int] = {}
         for key, value in json_list[0].items():
-            field_name: str = key.replace(" ", "_")
+            # The field name is the JSON key name, but with spaces and dashes replaced by underscores and with a leading
+            # underscore added if the field name starts with a number.
+            field_name: str = key.strip()
+            if " " in field_name:
+                field_name = field_name.replace(" ", "_")
+            if "-" in field_name:
+                field_name = field_name.replace("-", "_")
+            if field_name[0].isnumeric():
+                field_name = "_" + field_name
+
             if isinstance(value, str):
                 field = fb.string_field(field_name, display_name=key)
                 fields.append(field)
-                fields_by_name[key] = field
+                fields_by_json_key[key] = field
+                string_field_lengths[key] = 100
             elif isinstance(value, (int, float)):
                 field = fb.double_field(field_name, display_name=key, precision=3)
                 fields.append(field)
-                fields_by_name[key] = field
+                fields_by_json_key[key] = field
+
+        # Determine the max length of each string field.
+        for values in json_list:
+            for key in string_field_lengths:
+                length: int = len(values.get(key)) if values.get(key) else 0
+                string_field_lengths[key] = max(string_field_lengths[key], length)
+
+        # Update the max length of each string field.
+        for key in string_field_lengths:
+            field = cast(VeloxStringFieldDefinition, fields_by_json_key[key])
+            field.max_length = string_field_lengths[key]
 
         # Sort the JSON list if requested.
         if sort_field and sort_direction != SortDirection.NONE:
@@ -340,7 +363,7 @@ class AiHelper:
         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():
+            for key, field in fields_by_json_key.items():
                 # Watch out for NaN values or other special values in numeric columns.
                 val: Any = json_dict.get(key)
                 if (field.data_field_type == FieldType.DOUBLE
@@ -497,14 +520,14 @@ class AiHelper:
             with io.BytesIO(image) as bytes_io:
                 self.dr_man.set_record_image(record, bytes_io)
 
-    def create_bar_chart(self, entry_name: str, source_entry: ExperimentEntry, tab: ElnExperimentTab,
+    def create_bar_chart(self, entry_name: str, tab: ElnExperimentTab, source_entry: ExperimentEntry,
                          x_axis: str, y_axis: str) -> ExperimentEntry:
         """
         Create a bar chart in the experiment based on the contents of the given source entry.
 
         :param entry_name: The name of the bar chart.
-        :param source_entry: The source entry to base the bar chart on.
         :param tab: The tab to create the bar chart in.
+        :param source_entry: The source entry to base the bar chart on.
         :param x_axis: The field to use for the x-axis.
         :param y_axis: The field to use for the y-axis.
         :return: The newly created bar chart entry.
@@ -676,13 +699,6 @@ class ToolOfToolsHelper:
         dash_update_crit.column_span = 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.helper.protocol, f"{self.name} Results",