sapiopycommons 2025.2.5a415__py3-none-any.whl → 2025.2.6a418__py3-none-any.whl

sapiopycommons/elain/tool_of_tools.py

@@ -1,6 +1,7 @@
 import base64
 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
@@ -8,16 +9,18 @@ from sapiopylib.rest.pojo.DataRecord import DataRecord
 from sapiopylib.rest.pojo.chartdata.DashboardDefinition import GaugeChartDefinition
 from sapiopylib.rest.pojo.chartdata.DashboardEnums import ChartGroupingType, ChartOperationType, ChartType
 from sapiopylib.rest.pojo.chartdata.DashboardSeries import GaugeChartSeries
+from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition
 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, AbstractElnEntryUpdateCriteria
+    ElnDashboardEntryUpdateCriteria, 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
 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.exceptions import SapioException
 from sapiopycommons.general.time_util import TimeUtil
 
@@ -78,6 +81,86 @@ def format_tot_headers(headers: Mapping[str, str]) -> dict[str, str]:
     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] = []
+    valid_keys: list[str] = []
+    display_to_field_name: dict[str, str] = {}
+    for key, value in json_list[0].items():
+        field_name: str = key.replace(" ", "_")
+        display_to_field_name[key] = field_name
+        if isinstance(value, str):
+            fields.append(fb.string_field(field_name, display_name=key))
+            valid_keys.append(key)
+        elif isinstance(value, (int, float)):
+            fields.append(fb.double_field(field_name, display_name=key))
+            valid_keys.append(key)
+
+    # 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 in valid_keys:
+            field_map[display_to_field_name[key]] = json_dict.get(key)
+        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)
+
+
+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
+
+
 class ToolOfToolsHelper:
     """
     A class with helper methods utilized by the Tool of Tools for the creation and updating of experiment tabs that
@@ -213,6 +296,7 @@ class ToolOfToolsHelper:
         # 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.
@@ -227,6 +311,7 @@ class ToolOfToolsHelper:
         # 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,
@@ -238,12 +323,14 @@ class ToolOfToolsHelper:
         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)
 
-        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
-        })
+        # 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:
@@ -409,4 +496,4 @@ class _ElnTextEntryUpdateCriteria(AbstractElnEntryUpdateCriteria):
 
     def to_json(self) -> dict[str, Any]:
         ret = super().to_json()
-        return ret
+        return ret

{sapiopycommons-2025.2.5a415.dist-info → sapiopycommons-2025.2.6a418.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2025.2.5a415
+Version: 2025.2.6a418
 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-2025.2.5a415.dist-info → sapiopycommons-2025.2.6a418.dist-info}/RECORD

@@ -15,7 +15,7 @@ sapiopycommons/datatype/attachment_util.py,sha256=_l2swuP8noIGAl4bwzBUEhr6YlN_OV
 sapiopycommons/datatype/data_fields.py,sha256=C6HpqtEuF0KsxhlBUprfyv1XguaXql3EYWVbh8y-IFU,4064
 sapiopycommons/datatype/pseudo_data_types.py,sha256=6TG7aJxgmUZ8FQkWBcgmbK5oy7AFFNtKOPpi1w1OOYA,27657
 sapiopycommons/elain/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/elain/tool_of_tools.py,sha256=ernAtZMlFtEulnk4hVO3ZM9Yehaf7AzPicjXjVjc-8g,20455
+sapiopycommons/elain/tool_of_tools.py,sha256=zYcvsTqLgVP91vf16FMVIJcQ7Wa58nUDMSfS1B9W47Y,24690
 sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/eln/experiment_handler.py,sha256=8hmR7sawDo9K6iBwB44QSoxlH1M91inor7dfuXQ4LKs,69323
 sapiopycommons/eln/experiment_report_util.py,sha256=EA2Iq8gW17bSEI6lPoHYQQ-fDvG4O28RWOoTPXpOlUw,36640
@@ -57,7 +57,7 @@ sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
 sapiopycommons/webhook/webhook_handlers.py,sha256=M5PMt-j7PpnzUQMUQDTvqwJUyJNxuFtC9wdnk5VRNpI,39703
 sapiopycommons/webhook/webservice_handlers.py,sha256=Y5dHx_UFWFuSqaoPL6Re-fsKYRuxvCWZ8bj6KSZ3jfM,14285
-sapiopycommons-2025.2.5a415.dist-info/METADATA,sha256=KIywfrDTUc15xKeX4-YwuiMiZZSrb4sRjxqzxXKYh80,3142
-sapiopycommons-2025.2.5a415.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.2.5a415.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2025.2.5a415.dist-info/RECORD,,
+sapiopycommons-2025.2.6a418.dist-info/METADATA,sha256=ybJdIh2Y18kYi7HOgROF0yXvJGIX9wSweV5ICol4BWg,3142
+sapiopycommons-2025.2.6a418.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+sapiopycommons-2025.2.6a418.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2025.2.6a418.dist-info/RECORD,,