sapiopycommons 2025.3.6a454__py3-none-any.whl → 2025.3.10a455__py3-none-any.whl

{sapiopycommons-2025.3.6a454.dist-info → sapiopycommons-2025.3.10a455.dist-info}/RECORD

@@ -1,62 +1,59 @@
 sapiopycommons/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/callbacks/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/callbacks/callback_util.py,sha256=pgO3rLAbISs83SH8D-62eSiuaFckKEaJqqAstUawKBY,129944
+sapiopycommons/callbacks/callback_util.py,sha256=2pGr14f_FVCqeF6dsbYP1e4cOsaUTQyQ7XVwZuUkM_k,67952
 sapiopycommons/callbacks/field_builder.py,sha256=p2XacN99MuKk3ite8GAqstUMpixqugul2CsC4gB83-o,38620
 sapiopycommons/chem/IndigoMolecules.py,sha256=slM2y39zZFHc468c366EqR8T-GYJ24UnM9HWAqWFEwQ,3900
-sapiopycommons/chem/Molecules.py,sha256=5PzRyE1s-Z3nfwh3Y4dCNdQOIJGhog08wyZvgTkKwyU,12384
+sapiopycommons/chem/Molecules.py,sha256=9B4sbwbvYs50XHRn0TZiu-D1Oa3pKrI9qE5vNW8zv-U,12464
 sapiopycommons/chem/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/customreport/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/customreport/auto_pagers.py,sha256=9G0yo288ODzpJ5jzdMi8GknB1iWwbK_5_LGuoDUBoA8,13967
 sapiopycommons/customreport/column_builder.py,sha256=0RO53e9rKPZ07C--KcepN6_tpRw_FxF3O9vdG0ilKG8,3014
 sapiopycommons/customreport/custom_report_builder.py,sha256=BlTxZ4t1sfZA2Ciur1EfYvkZxHxJ7ADwYNAe2zwiN0c,7176
 sapiopycommons/customreport/term_builder.py,sha256=PNp71NF1vFxidk5v6uQNi9oQR9KJIk8WfhyntvvZN-U,18573
 sapiopycommons/datatype/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/datatype/attachment_util.py,sha256=_l2swuP8noIGAl4bwzBUEhr6YlN_OVZl3-gi1XqFHYA,3364
-sapiopycommons/datatype/data_fields.py,sha256=C6HpqtEuF0KsxhlBUprfyv1XguaXql3EYWVbh8y-IFU,4064
+sapiopycommons/datatype/data_fields.py,sha256=g8Ib6LH8ikNu9AzeVJs8Z2qS8A-cplACeFU7vYguNEY,4063
 sapiopycommons/datatype/pseudo_data_types.py,sha256=6TG7aJxgmUZ8FQkWBcgmbK5oy7AFFNtKOPpi1w1OOYA,27657
 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
+sapiopycommons/eln/experiment_handler.py,sha256=ZSx0uZy-2OtH_ArHy2OVwoNI3BYQLXSHGBmjviZl1Fw,69283
+sapiopycommons/eln/experiment_report_util.py,sha256=bs9zSUgRo40q2VYtjDCVPsT-D1umdNfl5s4oZrY4uuc,36597
 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=T39veNhvYl6j_uZjIIJ8Mk5Aa7otR5RB-g8XlAdkksA,1421
-sapiopycommons/files/file_bridge.py,sha256=vKbqxPexi15epr_-_qLrEfYoxNxB031mXN92iVtOMqE,9511
-sapiopycommons/files/file_bridge_handler.py,sha256=SEYDIQhSCmjI6qyLdDJE8JVKSd0WYvF7JvAq_Ahp9Do,25503
-sapiopycommons/files/file_data_handler.py,sha256=f96MlkMuQhUCi4oLnzJK5AiuElCp5jLI8_sJkZVwpws,36779
-sapiopycommons/files/file_util.py,sha256=w4Q7zYJb9YaPxrecmT4RT_OOibKMRP0NI1CyoOLfAP4,31747
-sapiopycommons/files/file_validator.py,sha256=ryg22-93csmRO_Pv0ZpWphNkB74xWZnHyJ23K56qLj0,28761
-sapiopycommons/files/file_writer.py,sha256=hACVl0duCjP28gJ1NPljkjagNCLod0ygUlPbvUmRDNM,17605
-sapiopycommons/flowcyto/flow_cyto.py,sha256=vs9WhXXKz3urpjL8QKSk56B-NSmQR3O3x_WFBKoeO10,3227
+sapiopycommons/files/file_bridge.py,sha256=WwCVegk0OGA8eqho8chsOsLlqg1nXctO75zfh-rHF-g,5950
+sapiopycommons/files/file_bridge_handler.py,sha256=bt2IfIsxJ4lcJYo_NHvCQ17ZV6C4fSAEa8Zcgixh7B4,14263
+sapiopycommons/files/file_data_handler.py,sha256=SCsjODMJIPEBSsahzXUeOM7CfSCmYwPPoGAM6aOfelo,36743
+sapiopycommons/files/file_util.py,sha256=wbL3rxcFc-t2mXaPWWkoFWYGopvTcQts9Wf-L5GkhT8,29498
+sapiopycommons/files/file_validator.py,sha256=4OvY98ueJWPJdpndwnKv2nqVvLP9S2W7Il_dM0Y0ojo,28709
+sapiopycommons/files/file_writer.py,sha256=96Xl8TTT46Krxe_J8rmmlEMtel4nzZB961f5Yqtl1-I,17616
+sapiopycommons/flowcyto/flow_cyto.py,sha256=YlkKJR_zEHYRuNW0bnTqlTyZeXs0lOaeSCfG2fnfD7E,3227
 sapiopycommons/flowcyto/flowcyto_data.py,sha256=mYKFuLbtpJ-EsQxLGtu4tNHVlygTxKixgJxJqD68F58,2596
 sapiopycommons/general/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/general/accession_service.py,sha256=QeNGd78Zr08ezWpThTuAkxO4bXusEcp5x9jJRZRwliA,13483
-sapiopycommons/general/aliases.py,sha256=alc2R5TOSKbZif3pcGZ706y23Y9F4HQPC-Kj4xJZ_Us,14503
-sapiopycommons/general/audit_log.py,sha256=KQq0PsvukUoE3l6TQb3-vpu5-MbSINpWlnQ9e7jojPg,8743
-sapiopycommons/general/custom_report_util.py,sha256=NwwmejSQLwSbrndEk1gPyFNYk9GZoS7Wrp9ab9moFgw,18014
-sapiopycommons/general/directive_util.py,sha256=7SeQrd2Ye5JHlXZtJZaVGgtaSLdq_Vm9EObuxf44Pz8,3905
-sapiopycommons/general/exceptions.py,sha256=aPlzK1cvxeMU5UsokYlLrIBGltUfJZ7LH8zvLh9DxpI,3233
-sapiopycommons/general/popup_util.py,sha256=HKILegU1uCL_6abNlNL0Wn3xgX2JNa_kJeq7e5CZu6Q,31923
+sapiopycommons/general/accession_service.py,sha256=HYgyOsH_UaoRnoury-c2yTW8SeG4OtjLemdpCzoV4R8,13484
+sapiopycommons/general/aliases.py,sha256=tdDBNWSGx6s39eHJ3n2kscc4xxW3ZYaUfDftct6FmJE,12910
+sapiopycommons/general/audit_log.py,sha256=pvXPfLr4Rw2X52wAXJGsX5fsPllswnCqaFZQ181j_GU,8727
+sapiopycommons/general/custom_report_util.py,sha256=6ZIg_Jl02TYUygfc5xqBoI1srPsSxLyxaJ9jwTolGcM,16671
+sapiopycommons/general/exceptions.py,sha256=GY7fe0qOgoy4kQVn_Pn3tdzHsJZyNIpa6VCChg6tzuM,1813
+sapiopycommons/general/popup_util.py,sha256=L-4qpTemSZdlD6_6oEsDYIzLOCiZgDK6wC6DqUwzOYA,31925
 sapiopycommons/general/sapio_links.py,sha256=o9Z-8y2rz6AI0Cy6tq58ElPge9RBnisGc9NyccbaJxs,2610
 sapiopycommons/general/storage_util.py,sha256=ovmK_jN7v09BoX07XxwShpBUC5WYQOM7dbKV_VeLXJU,8892
 sapiopycommons/general/time_util.py,sha256=jU1urPoZRv6evNucR0-288EyT4PrsDpCr-H1-7BKq9A,12363
-sapiopycommons/multimodal/multimodal.py,sha256=PFaGJPbKvW__tnxb8KkgkJZOKjQdgxF_kGfD5chet1s,6779
+sapiopycommons/multimodal/multimodal.py,sha256=A1QsC8QTPmgZyPr7KtMbPRedn2Ie4WIErodUvQ9otgU,6724
 sapiopycommons/multimodal/multimodal_data.py,sha256=0BeVPr9HaC0hNTF1v1phTIKGruvNnwerHsD994qJKBg,15099
 sapiopycommons/processtracking/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/processtracking/custom_workflow_handler.py,sha256=NY0HboLMI9WX1u7Fwad-KreEyhaHtYBTAmi-fHtZGCg,23509
+sapiopycommons/processtracking/custom_workflow_handler.py,sha256=B8KxQlwlLGkxnEid2jb9igGyGqrtcsBMhcOb9MfnO9E,23465
 sapiopycommons/processtracking/endpoints.py,sha256=w5bziI2xC7450M95rCF8JpRwkoni1kEDibyAux9B12Q,10848
 sapiopycommons/recordmodel/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-sapiopycommons/recordmodel/record_handler.py,sha256=47VNr3CfL51myaySGZ8yElNJrljcbHaxEfx0V9xPGog,64945
+sapiopycommons/recordmodel/record_handler.py,sha256=5kCO5zsSg0kp3uYpgw1vf0WLHw30pMNC_6Bn3G7iQkI,64796
 sapiopycommons/rules/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/rules/eln_rule_handler.py,sha256=JYzDA_14D2nLnlqwbpIxVOrfKWzbOS27AYf4TQfGr4Q,10469
 sapiopycommons/rules/on_save_rule_handler.py,sha256=Rkqvph20RbNq6m-RF4fbvCP-YfD2CZYBM2iTr3nl0eY,10236
-sapiopycommons/samples/aliquot.py,sha256=mWOJUqaQh0t3HklNuGdmuV7D5zzXs6fpLwtDdM6_XTo,3018
 sapiopycommons/sftpconnect/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/sftpconnect/sftp_builder.py,sha256=lFK3FeXk-sFLefW0hqY8WGUQDeYiGaT6yDACzT_zFgQ,3015
 sapiopycommons/webhook/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 sapiopycommons/webhook/webhook_context.py,sha256=D793uLsb1691SalaPnBUk3rOSxn_hYLhdvkaIxjNXss,1909
-sapiopycommons/webhook/webhook_handlers.py,sha256=L0HetSm43NvA5KyW3xbLpGFh2DbAaeZJVtXIEl2fvV8,39689
+sapiopycommons/webhook/webhook_handlers.py,sha256=MdsVK4bHffkMNmNWl0_qvu-5Lz8-qGu4Ryi7lZO1BZs,18586
 sapiopycommons/webhook/webservice_handlers.py,sha256=Y5dHx_UFWFuSqaoPL6Re-fsKYRuxvCWZ8bj6KSZ3jfM,14285
-sapiopycommons-2025.3.6a454.dist-info/METADATA,sha256=UQJNjRiyoGl3P7wvigJMyHe0b57qzLLg7CMysfzp6so,3142
-sapiopycommons-2025.3.6a454.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-sapiopycommons-2025.3.6a454.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
-sapiopycommons-2025.3.6a454.dist-info/RECORD,,
+sapiopycommons-2025.3.10a455.dist-info/METADATA,sha256=PYodInpHx8Ia7h-pIQalBtai4RLvP1s4xqSSFgnTrWg,3143
+sapiopycommons-2025.3.10a455.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+sapiopycommons-2025.3.10a455.dist-info/licenses/LICENSE,sha256=HyVuytGSiAUQ6ErWBHTqt1iSGHhLmlC8fO7jTCuR8dU,16725
+sapiopycommons-2025.3.10a455.dist-info/RECORD,,

sapiopycommons/customreport/auto_pagers.py

@@ -1,270 +0,0 @@
-from abc import ABC
-from copy import copy
-from queue import Queue
-
-from sapiopylib.rest.CustomReportService import CustomReportManager
-from sapiopylib.rest.DataMgmtService import DataMgmtServer
-from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, CustomReport, RawReportTerm, ReportColumn
-from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType
-from sapiopylib.rest.utils.autopaging import SapioPyAutoPager, PagerResultCriteriaType, _default_report_page_size, \
-    _default_record_page_size
-from sapiopylib.rest.utils.recordmodel.RecordModelWrapper import WrappedType
-
-from sapiopycommons.general.aliases import FieldValue, UserIdentifier, AliasUtil, RecordModel
-from sapiopycommons.general.custom_report_util import CustomReportUtil
-from sapiopycommons.general.exceptions import SapioException
-from sapiopycommons.recordmodel.record_handler import RecordHandler
-
-
-# FR-47389: Create auto pagers for running custom/system/quick reports that return dictionaries or records for each row.
-class _DictReportPagerBase(SapioPyAutoPager[CustomReportCriteria, dict[str, FieldValue]], ABC):
-    """
-    A base class for automatically paging through a report and returning the results as a list of dictionaries.
-    """
-    _columns: list[ReportColumn]
-    _report_man: CustomReportManager
-
-    def __init__(self, user: UserIdentifier, first_page_criteria: CustomReportCriteria):
-        self._columns = first_page_criteria.column_list
-        super().__init__(AliasUtil.to_sapio_user(user), first_page_criteria)
-        self._report_man = DataMgmtServer.get_custom_report_manager(self.user)
-
-    def get_all_at_once(self) -> list[dict[str, FieldValue]]:
-        """
-        Get the results of all pages. Be cautious of client memory usage.
-        """
-        if self.has_iterated:
-            raise BrokenPipeError("Cannot use this method if the iterator has already been used.")
-        return [x for x in self]
-
-    def default_first_page_criteria(self) -> PagerResultCriteriaType:
-        raise ValueError("Cannot generate a default first page criteria for custom reports.")
-
-    def get_next_page_result(self) -> tuple[CustomReportCriteria | None, Queue[dict[str, FieldValue]]]:
-        report: CustomReport = self._report_man.run_custom_report(self.next_page_criteria)
-        queue: Queue[dict[str, FieldValue]] = Queue()
-        for row in _process_results(report.result_table, self._columns):
-            queue.put(row)
-        if report.has_next_page:
-            next_page_criteria = copy(self.next_page_criteria)
-            next_page_criteria.page_number += 1
-            return next_page_criteria, queue
-        else:
-            return None, queue
-
-
-class CustomReportDictAutoPager(_DictReportPagerBase):
-    """
-    A class that automatically pages through a custom report and returns the results as a list of dictionaries.
-    """
-    def __init__(self, user: UserIdentifier, report_criteria: CustomReportCriteria,
-                 page_number: int = 0, page_size: int = _default_report_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_criteria: The custom report criteria to run.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        first_page_criteria: CustomReportCriteria = copy(report_criteria)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria)
-
-
-class SystemReportDictAutoPager(_DictReportPagerBase):
-    """
-    A class that automatically pages through a system report and returns the results as a list of dictionaries.
-
-    System reports are also known as predefined searches in the system and must be defined in the data designer for
-    a specific data type. That is, saved searches created by users cannot be run using this function.
-    """
-    def __init__(self, user: UserIdentifier, report_name: str,
-                 page_number: int = 0, page_size: int = _default_report_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_name: The name of the system report to run.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        first_page_criteria: CustomReportCriteria = CustomReportUtil.get_system_report_criteria(user, report_name)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria)
-
-
-class QuickReportDictAutoPager(_DictReportPagerBase):
-    """
-    A class that automatically pages through a quick report and returns the results as a list of dictionaries.
-    """
-    def __init__(self, user: UserIdentifier, report_term: RawReportTerm,
-                 page_number: int = 0, page_size: int = _default_report_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_term: The raw report term to use for the quick report.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        first_page_criteria: CustomReportCriteria = CustomReportUtil.get_quick_report_criteria(user, report_term)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria)
-
-
-class _RecordReportPagerBase(SapioPyAutoPager[CustomReportCriteria, WrappedType], ABC):
-    """
-    A base class for automatically paging through a report and returning the results as a list of records.
-    """
-    _columns: list[ReportColumn]
-    _wrapper: type[WrappedType]
-    _data_type: str
-    _rec_handler: RecordHandler
-    _report_man: CustomReportManager
-
-    def __init__(self, user: UserIdentifier, first_page_criteria: CustomReportCriteria, wrapper_type: type[WrappedType]):
-        self._columns = first_page_criteria.column_list
-        self._wrapper = wrapper_type
-        self._data_type = wrapper_type.get_wrapper_data_type_name()
-        self._rec_handler = RecordHandler(user)
-        super().__init__(AliasUtil.to_sapio_user(user), first_page_criteria)
-        self._report_man = DataMgmtServer.get_custom_report_manager(self.user)
-
-    def get_all_at_once(self) -> list[RecordModel]:
-        """
-        Get the results of all pages. Be cautious of client memory usage.
-        """
-        if self.has_iterated:
-            raise BrokenPipeError("Cannot use this method if the iterator has already been used.")
-        return [x for x in self]
-
-    def default_first_page_criteria(self) -> PagerResultCriteriaType:
-        raise ValueError("Cannot generate a default first page criteria for custom reports.")
-
-    def get_next_page_result(self) -> tuple[CustomReportCriteria | None, Queue[WrappedType]]:
-        report: CustomReport = self._report_man.run_custom_report(self.next_page_criteria)
-        queue: Queue[WrappedType] = Queue()
-        id_index: int = -1
-        for i, column in enumerate(self._columns):
-            if column.data_type_name == self._data_type and column.data_field_name == "RecordId":
-                id_index = i
-                break
-        if id_index == -1:
-            raise SapioException(f"This report does not contain a Record ID column for the given record model type "
-                                 f"{self._data_type}.")
-        ids: list[int] = [row[id_index] for row in report.result_table]
-        for row in self._rec_handler.query_models_by_id(self._wrapper, ids, page_size=report.page_size):
-            queue.put(row)
-        if report.has_next_page:
-            next_page_criteria = copy(self.next_page_criteria)
-            next_page_criteria.page_number += 1
-            return next_page_criteria, queue
-        else:
-            return None, queue
-
-
-class CustomReportRecordAutoPager(_RecordReportPagerBase):
-    """
-    A class that automatically pages through a custom report and returns the results as a list of records.
-    """
-    def __init__(self, user: UserIdentifier, report_criteria: CustomReportCriteria, wrapper_type: type[WrappedType],
-                 page_number: int = 0, page_size: int = _default_record_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_criteria: The custom report criteria to run.
-        :param wrapper_type: The record model wrapper type to use for the records.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        first_page_criteria: CustomReportCriteria = copy(report_criteria)
-        _add_record_id_column(first_page_criteria, wrapper_type)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria, wrapper_type)
-
-
-class SystemReportRecordAutoPager(_RecordReportPagerBase):
-    """
-    A class that automatically pages through a system report and returns the results as a list of records.
-
-    System reports are also known as predefined searches in the system and must be defined in the data designer for
-    a specific data type. That is, saved searches created by users cannot be run using this function.
-    """
-    def __init__(self, user: UserIdentifier, report_name: str, wrapper_type: type[WrappedType],
-                 page_number: int = 0, page_size: int = _default_record_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_name: The name of the system report to run.
-        :param wrapper_type: The record model wrapper type to use for the records.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        first_page_criteria: CustomReportCriteria = CustomReportUtil.get_system_report_criteria(user, report_name)
-        _add_record_id_column(first_page_criteria, wrapper_type)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria, wrapper_type)
-
-
-class QuickReportRecordAutoPager(_RecordReportPagerBase):
-    """
-    A class that automatically pages through a quick report and returns the results as a list of records.
-    """
-    def __init__(self, user: UserIdentifier, report_term: RawReportTerm, wrapper_type: type[WrappedType],
-                 page_number: int = 0, page_size: int = _default_record_page_size):
-        """
-        :param user: The current webhook context or a user object to send requests from.
-        :param report_term: The raw report term to use for the quick report.
-        :param wrapper_type: The record model wrapper type to use for the records.
-        :param page_number: The page number to start on. The first page is page 0.
-        :param page_size: The number of results to return per page.
-        """
-        if report_term.data_type_name != wrapper_type.get_wrapper_data_type_name():
-            raise SapioException("The data type name of the report term must match the data type name of the wrapper type.")
-        first_page_criteria: CustomReportCriteria = CustomReportUtil.get_quick_report_criteria(user, report_term)
-        first_page_criteria.page_number = page_number
-        first_page_criteria.page_size = page_size
-        super().__init__(user, first_page_criteria, wrapper_type)
-
-
-def _add_record_id_column(report: CustomReportCriteria, wrapper_type: type[WrappedType]) -> None:
-    """
-    Given a custom report criteria, ensure that the report contains a Record ID column for the given record model's
-    data type. Add one if it is missing.
-    """
-    dt: str = wrapper_type.get_wrapper_data_type_name()
-    # Ensure that the root data type is the one we're looking for.
-    report.root_data_type = dt
-    # Enforce that the given custom report has a record ID column.
-    if not any([x.data_type_name == dt and x.data_field_name == "RecordId" for x in report.column_list]):
-        report.column_list.append(ReportColumn(dt, "RecordId", FieldType.LONG))
-
-
-def _process_results(rows: list[list[FieldValue]], columns: list[ReportColumn]) -> list[dict[str, FieldValue]]:
-    """
-    Given the results of a report as a list of row values and the report's columns, combine these lists to
-    result in a singular list of dictionaries for each row in the results.
-    """
-    # It may be the case that two columns have the same data field name but differing data type names.
-    # If this occurs, then we need to be able to differentiate these columns in the resulting dictionary.
-    prepend_dt: set[str] = set()
-    encountered_names: list[str] = []
-    for column in columns:
-        field_name: str = column.data_field_name
-        if field_name in encountered_names:
-            prepend_dt.add(field_name)
-        else:
-            encountered_names.append(field_name)
-
-    ret: list[dict[str, FieldValue]] = []
-    for row in rows:
-        row_data: dict[str, FieldValue] = {}
-        filter_row: bool = False
-        for value, column in zip(row, columns):
-            header: str = column.data_field_name
-            # If two columns share the same data field name, prepend the data type name of the column to the
-            # data field name.
-            if header in prepend_dt:
-                header = column.data_type_name + "." + header
-            row_data.update({header: value})
-        if filter_row is False:
-            ret.append(row_data)
-    return ret

sapiopycommons/general/directive_util.py

@@ -1,86 +0,0 @@
-from typing import Iterable, cast
-
-from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.pojo.CustomReport import CustomReportCriteria, CustomReport
-from sapiopylib.rest.pojo.webhook.WebhookDirective import HomePageDirective, FormDirective, TableDirective, \
-    CustomReportDirective, ElnExperimentDirective, ExperimentEntryDirective
-
-from sapiopycommons.general.aliases import SapioRecord, AliasUtil, ExperimentIdentifier, ExperimentEntryIdentifier, \
-    UserIdentifier
-from sapiopycommons.general.custom_report_util import CustomReportUtil
-
-
-# FR-47392: Create a DirectiveUtil class to simplify the creation of directives.
-class DirectiveUtil:
-    """
-    DirectiveUtil is a class for creating webhook directives. The utility functions reduce the provided variables
-    down to the exact type that the directives require, removing the need for the caller to handle the conversion.
-    """
-    user: SapioUser
-
-    def __init__(self, context: UserIdentifier):
-        """
-        :param context: The current webhook context or a user object to send requests from.
-        """
-        self.user = AliasUtil.to_sapio_user(context)
-
-    @staticmethod
-    def homepage() -> HomePageDirective:
-        """
-        :return: A directive that sends the user back to their home page.
-        """
-        return HomePageDirective()
-
-    @staticmethod
-    def record_form(record: SapioRecord) -> FormDirective:
-        """
-        :param record: A record in the system.
-        :return: A directive that sends the user to a specific data record form.
-        """
-        return FormDirective(AliasUtil.to_data_record(record))
-
-    @staticmethod
-    def record_table(records: Iterable[SapioRecord]) -> TableDirective:
-        """
-        :param records: A list of records in the system.
-        :return: A directive that sends the user to a table of data records.
-        """
-        return TableDirective(AliasUtil.to_data_records(records))
-
-    @staticmethod
-    def record_adaptive(records: Iterable[SapioRecord]) -> TableDirective | FormDirective:
-        """
-        :param records: A list of records in the system.
-        :return: A directive that sends the user to a table of data records if there are multiple records,
-            or a directive that sends the user to a specific data record form if there is only one record.
-        """
-        records: list[SapioRecord] = list(records)
-        if len(records) == 1:
-            return DirectiveUtil.record_form(records[0])
-        return DirectiveUtil.record_table(records)
-
-    def custom_report(self, report: CustomReport | CustomReportCriteria | str) -> CustomReportDirective:
-        """
-        :param report: A custom report, the criteria for a custom report, or the name of a system report.
-        :return: A directive that sends the user to the results of the provided custom report.
-        """
-        if isinstance(report, str):
-            report: CustomReport = CustomReportUtil.get_system_report_criteria(self.user, report)
-        return CustomReportDirective(cast(CustomReport, report))
-
-    @staticmethod
-    def eln_experiment(experiment: ExperimentIdentifier) -> ElnExperimentDirective:
-        """
-        :param experiment: An identifier for an experiment.
-        :return: A directive that sends the user to the ELN experiment.
-        """
-        return ElnExperimentDirective(AliasUtil.to_notebook_id(experiment))
-
-    @staticmethod
-    def eln_entry(experiment: ExperimentIdentifier, entry: ExperimentEntryIdentifier) -> ExperimentEntryDirective:
-        """
-        :param experiment: An identifier for an experiment.
-        :param entry: An identifier for an entry in the experiment.
-        :return: A directive that sends the user to the provided experiment entry within its ELN experiment.
-        """
-        return ExperimentEntryDirective(AliasUtil.to_notebook_id(experiment), AliasUtil.to_entry_id(entry))

sapiopycommons/samples/aliquot.py

@@ -1,48 +0,0 @@
-from sapiopycommons.general.aliases import SapioRecord
-from sapiopylib.rest.User import SapioUser
-from sapiopylib.rest.utils.MultiMap import SetMultimap
-
-# FR-47421 Added module
-
-def create_aliquot_for_samples(parent_sample_to_num_aliquots_map: dict[SapioRecord, int], user: SapioUser) -> SetMultimap[SapioRecord, int]:
-    """"
-    Ask server to create aliquot records for provided sample parent records.
-    :param parent_sample_to_num_aliquots_map: The dictionary containing (parent sample record) -> (number of aliquots to create) mapping.
-    :return: The dictionary containing (parent sample record) -> (list of new aliquot record ids) mapping.
-    """
-    # throw error if at least one record id is blank
-    has_negative_record_ids = any([record.record_id < 0 for record in parent_sample_to_num_aliquots_map.keys()])
-    if has_negative_record_ids:
-        raise ValueError("At least one record requested for aliquot has a negative record ID. "
-                         "You should have stored record model changes first.")
-    has_blank_record_ids = any([record.record_id is None for record in parent_sample_to_num_aliquots_map.keys()])
-    if has_blank_record_ids:
-        raise ValueError("At least one record requested for aliquot does not currently have a record ID.")
-    record_id_to_sapio_record_map = {record.record_id: record for record in parent_sample_to_num_aliquots_map.keys()}
-    parent_record_id_to_num_aliquots_map = {record.record_id: num_aliquots for record, num_aliquots in parent_sample_to_num_aliquots_map.items()}
-    aliquot_result: SetMultimap[int, int] = create_aliquot_for_samples_record_ids(parent_record_id_to_num_aliquots_map, user)
-    ret: SetMultimap[SapioRecord, int] = SetMultimap()
-    for parent_record_id in aliquot_result.keys():
-        parent_record = record_id_to_sapio_record_map[parent_record_id]
-        for aliquot_record_id in aliquot_result.get(parent_record_id):
-            ret.put(parent_record, aliquot_record_id)
-    return ret
-
-
-def create_aliquot_for_samples_record_ids(parent_record_id_to_num_aliquots_map: dict[int, int], user: SapioUser) -> SetMultimap[int, int]:
-    """
-    Ask the server to create aliquot records for the provided sample record IDs.
-    :param sample_record_id_list: The dictionary containing (parent sample record id) -> (number of aliquots to create) mapping.
-    :return: The dictionary containing (parent sample record id) -> (list of new aliquot record ids) mapping.
-    """
-    if not parent_record_id_to_num_aliquots_map:
-        return SetMultimap()
-    endpoint_path = 'sample/aliquot'
-    response = user.plugin_put(endpoint_path, payload=parent_record_id_to_num_aliquots_map)
-    user.raise_for_status(response)
-    response_map: dict[int, list[int]] = response.json()
-    ret: SetMultimap[int, int] = SetMultimap()
-    for parent_record_id, aliquot_record_ids in response_map.items():
-        for aliquot_record_id in aliquot_record_ids:
-            ret.put(int(parent_record_id), int(aliquot_record_id))
-    return ret