sapiopycommons 2024.7.2a279__py3-none-any.whl → 2024.7.3a280__py3-none-any.whl

sapiopycommons/eln/experiment_report_util.py

@@ -0,0 +1,214 @@
+from sapiopylib.rest.User import SapioUser
+from sapiopylib.rest.pojo.CustomReport import (
+    CompositeReportTerm,
+    CompositeTermOperation,
+    CustomReportCriteria,
+    ExplicitJoinDefinition,
+    FieldCompareReportTerm,
+    RawReportTerm,
+    RawTermOperation,
+    ReportColumn,
+)
+from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
+from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
+from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
+
+from sapiopycommons.general.aliases import SapioRecord
+from sapiopycommons.general.custom_report_util import CustomReportUtil
+from sapiopycommons.recordmodel.record_handler import RecordHandler
+
+_NOTEBOOK_ID = "EXPERIMENTID"
+_RECORD_ID = "RECORDID"
+
+
+# FR-46908 - Provide a utility class that holds experiment related custom reports e.g. getting all the experiments
+# that given records were used in or getting all records of a datatype used in given experiments.
+class ExperimentReportUtil:
+    @staticmethod
+    def map_records_to_experiment_ids(
+        context: SapioWebhookContext | SapioUser,
+        records: list[SapioRecord],
+    ) -> dict[SapioRecord, list[int]]:
+        """
+        Return a dictionary mapping each record to a list of ids of experiments that they were used in.
+        If a record wasn't used in any experiments then it will be mapped to an empty list.
+
+        :param context: The current webhook context or a user object to send requests from.
+        :param records: a list of records of the same data type.
+        :return: a dictionary mapping each record to a list of ids of each experiment it was used in.
+        """
+        if not records:
+            return {}
+
+        user: SapioUser = context if isinstance(context, SapioUser) else context.user
+
+        data_type_name = records[0].data_type_name
+
+        record_ids = [record.record_id for record in records]
+
+        rows = ExperimentReportUtil.__get_record_experiment_relation_rows(
+            user, data_type_name, record_ids=record_ids
+        )
+
+        id_to_record: dict[int, SapioRecord] = RecordHandler.map_by_id(records)
+
+        record_to_exps: dict[SapioRecord, set[int]] = {
+            record: set() for record in records
+        }
+
+        for row in rows:
+            record_id: int = row[_RECORD_ID]
+            exp_id: int = row[_NOTEBOOK_ID]
+
+            record = id_to_record[record_id]
+
+            record_to_exps[record].add(exp_id)
+
+        return {record: list(exps) for record, exps in record_to_exps.items()}
+
+    @staticmethod
+    def map_experiments_to_records_of_type(
+        context: SapioWebhookContext | SapioUser,
+        exp_ids: list[int],
+        wrapper_type: type[WrappedType],
+    ) -> dict[int, list[WrappedType]]:
+        """
+        Return a dictionary mapping each experiment id to a list of records of the given type that were used in each experiment.
+        If an experiment didn't use any records of the given type then it will be mapped to an empty list.
+
+        :param context: The current webhook context or a user object to send requests from.
+        :param exp_ids: a list of experiment ids. These are specifically the Notebook Experiment ids which can be found in the title of the experiment.
+        :param wrapper_type: The record model wrapper to use, corresponds to which data type we will query for.
+        :return: a dictionary mapping each experiment id to a list of records of the given type that were used in that experiment.
+        """
+        if not exp_ids:
+            return {}
+
+        user = context if isinstance(context, SapioUser) else context.user
+
+        record_handler = RecordHandler(user)
+
+        data_type_name: str = wrapper_type.get_wrapper_data_type_name()
+
+        rows = ExperimentReportUtil.__get_record_experiment_relation_rows(
+            user, data_type_name, exp_ids=exp_ids
+        )
+
+        record_ids: set[int] = {row[_RECORD_ID] for row in rows}
+
+        records = record_handler.query_models_by_id(wrapper_type, record_ids)
+
+        id_to_record: dict[int, WrappedType] = RecordHandler.map_by_id(records)
+
+        exp_to_records: dict[int, set[SapioRecord]] = {exp: set() for exp in exp_ids}
+
+        for row in rows:
+            record_id: int = row[_RECORD_ID]
+            exp_id: int = row[_NOTEBOOK_ID]
+
+            record = id_to_record[record_id]
+
+            exp_to_records[exp_id].add(record)
+
+        return {exp: list(records) for exp, records in exp_to_records.items()}
+
+    @staticmethod
+    def __get_record_experiment_relation_rows(
+        user: SapioUser,
+        data_type_name: str,
+        record_ids: list[int] | None = None,
+        exp_ids: list[int] | None = None,
+    ) -> list[dict[str, int]]:
+        """
+        Return a list of dicts mapping \"RECORDID\" to the record id and \"EXPERIMENTID\" to the experiment id.
+        At least one of record_ids and exp_ids should be provided.
+        """
+        assert (record_ids or exp_ids)
+
+        if record_ids:
+            rec_ids = [str(record_id) for record_id in record_ids]
+
+            ids_str = "{" + ", ".join(rec_ids) + "}"
+
+            records_term = RawReportTerm(
+                data_type_name, "RECORDID", RawTermOperation.EQUAL_TO_OPERATOR, ids_str
+            )
+
+        else:
+            # Get all records of the given type
+            records_term = RawReportTerm(
+                data_type_name,
+                "RECORDID",
+                RawTermOperation.GREATER_THAN_OR_EQUAL_OPERATOR,
+                "0",
+            )
+
+        if exp_ids:
+            exp_ids = [str(exp_id) for exp_id in exp_ids]
+
+            ids_str = "{" + ", ".join(exp_ids) + "}"
+
+            exp_term = RawReportTerm(
+                "NOTEBOOKEXPERIMENT",
+                "EXPERIMENTID",
+                RawTermOperation.EQUAL_TO_OPERATOR,
+                ids_str,
+            )
+
+        else:
+            # Get all experiments
+            exp_term = RawReportTerm(
+                "NOTEBOOKEXPERIMENT",
+                "EXPERIMENTID",
+                RawTermOperation.GREATER_THAN_OR_EQUAL_OPERATOR,
+                "0",
+            )
+
+        root_term = CompositeReportTerm(
+            records_term, CompositeTermOperation.AND_OPERATOR, exp_term
+        )
+
+        # The columns the resulting dataframe will have
+        column_list = [
+            ReportColumn(data_type_name, "RECORDID", FieldType.LONG),
+            ReportColumn("NOTEBOOKEXPERIMENT", "EXPERIMENTID", FieldType.LONG),
+        ]
+
+        # Join records on the experiment entry records that correspond to them.
+        records_entry_join = FieldCompareReportTerm(
+            data_type_name,
+            "RECORDID",
+            RawTermOperation.EQUAL_TO_OPERATOR,
+            "EXPERIMENTENTRYRECORD",
+            "RECORDID",
+        )
+
+        # Join entry records on the experiment entries they are in.
+        experiment_entry_enb_entry_join = FieldCompareReportTerm(
+            "EXPERIMENTENTRYRECORD",
+            "ENTRYID",
+            RawTermOperation.EQUAL_TO_OPERATOR,
+            "ENBENTRY",
+            "ENTRYID",
+        )
+
+        # Join entries on the experiments they are in.
+        enb_entry_experiment_join = FieldCompareReportTerm(
+            "ENBENTRY",
+            "EXPERIMENTID",
+            RawTermOperation.EQUAL_TO_OPERATOR,
+            "NOTEBOOKEXPERIMENT",
+            "EXPERIMENTID",
+        )
+
+        report_criteria = CustomReportCriteria(
+            column_list,
+            root_term,
+            join_list=[
+                ExplicitJoinDefinition("EXPERIMENTENTRYRECORD", records_entry_join),
+                ExplicitJoinDefinition("ENBENTRY", experiment_entry_enb_entry_join),
+                ExplicitJoinDefinition("NOTEBOOKEXPERIMENT", enb_entry_experiment_join),
+            ],
+        )
+
+        return CustomReportUtil.run_custom_report(user, report_criteria)

{sapiopycommons-2024.7.2a279.dist-info → sapiopycommons-2024.7.3a280.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: sapiopycommons
-Version: 2024.7.2a279
+Version: 2024.7.3a280
 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-2024.7.2a279.dist-info → sapiopycommons-2024.7.3a280.dist-info}/RECORD

@@ -8,6 +8,7 @@ sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 sapiopycommons/datatype/attachment_util.py,sha256=YlnMprj5IGBbAZDLG2khS1P7JIYTw_NYfpJAfRZfP3M,3219
 sapiopycommons/eln/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/eln/experiment_handler.py,sha256=v1pG4qtZb8OSNWfKtFo6NjnEkReqnu5R9i_hqWh_xxg,57198
+sapiopycommons/eln/experiment_report_util.py,sha256=FTLw-6SLAMeoWTOO-qhGROE9g54pZdyoQJIhiIzlwGw,7848
 sapiopycommons/eln/plate_designer.py,sha256=FYJfhhNq8hdfuXgDYOYHy6g0m2zNwQXZWF_MTPzElDg,7184
 sapiopycommons/files/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/files/complex_data_loader.py,sha256=XSJOl676mIklJo78v07-70u1b015a5DI4sqZPI3C-Tw,1475
@@ -36,7 +37,7 @@ sapiopycommons/rules/eln_rule_handler.py,sha256=qfkBZtck0KK1i9s9Xe2UZqkzQOgPCzDx
 sapiopycommons/rules/on_save_rule_handler.py,sha256=JY9F30IcHwFVdgPAMQtTYuRastV1jeezhVktyrzNASU,10763
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/webhook/webhook_handlers.py,sha256=ibpBY3Sk3Eij919bIdW0awzlogYoQSWYDDOg--NwsQE,13431
-sapiopycommons-2024.7.2a279.dist-info/METADATA,sha256=HqvQb86znDDaqgF0QLCt6WtNtxF70JgGOiOES7iiXXU,3175
-sapiopycommons-2024.7.2a279.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-sapiopycommons-2024.7.2a279.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2024.7.2a279.dist-info/RECORD,,
+sapiopycommons-2024.7.3a280.dist-info/METADATA,sha256=bdT3mlji7J-b8ayWJrDCel9qHdQUA2qAx3oO4xMFq5k,3175
+sapiopycommons-2024.7.3a280.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+sapiopycommons-2024.7.3a280.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2024.7.3a280.dist-info/RECORD,,