sapiopycommons 2024.8.27a312__py3-none-any.whl → 2024.8.28a313__py3-none-any.whl
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- sapiopycommons/callbacks/callback_util.py +35 -277
- sapiopycommons/chem/IndigoMolecules.py +0 -1
- sapiopycommons/chem/Molecules.py +0 -1
- sapiopycommons/files/file_bridge.py +10 -16
- sapiopycommons/files/file_util.py +6 -13
- sapiopycommons/files/file_validator.py +0 -71
- sapiopycommons/general/custom_report_util.py +27 -199
- sapiopycommons/recordmodel/record_handler.py +45 -278
- sapiopycommons/webhook/webhook_handlers.py +1 -58
- {sapiopycommons-2024.8.27a312.dist-info → sapiopycommons-2024.8.28a313.dist-info}/METADATA +2 -4
- {sapiopycommons-2024.8.27a312.dist-info → sapiopycommons-2024.8.28a313.dist-info}/RECORD +13 -18
- sapiopycommons/eln/experiment_report_util.py +0 -214
- sapiopycommons/files/file_bridge_handler.py +0 -318
- sapiopycommons/general/accession_service.py +0 -375
- sapiopycommons/multimodal/multimodal.py +0 -146
- sapiopycommons/multimodal/multimodal_data.py +0 -487
- {sapiopycommons-2024.8.27a312.dist-info → sapiopycommons-2024.8.28a313.dist-info}/WHEEL +0 -0
- {sapiopycommons-2024.8.27a312.dist-info → sapiopycommons-2024.8.28a313.dist-info}/licenses/LICENSE +0 -0
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@@ -4,15 +4,12 @@ from abc import abstractmethod
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from typing import Any
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from sapiopylib.rest.User import SapioUser
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from sapiopylib.rest.pojo.CustomReport import RawReportTerm, RawTermOperation
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from sapiopylib.rest.pojo.datatype.FieldDefinition import VeloxIntegerFieldDefinition, VeloxStringFieldDefinition, \
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AbstractVeloxFieldDefinition
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from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
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from sapiopylib.rest.pojo.webhook.WebhookResult import SapioWebhookResult
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from sapiopycommons.callbacks.callback_util import CallbackUtil
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from sapiopycommons.files.file_data_handler import FileDataHandler, FilterList
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from sapiopycommons.general.custom_report_util import CustomReportUtil
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from sapiopycommons.general.time_util import TimeUtil
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@@ -483,71 +480,3 @@ class ContainsSubstringFromCellRule(RowRule):
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def validate(self, row: dict[str, Any]) -> bool:
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return row.get(self.second) in row.get(self.first)
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class UniqueSystemValueRule(ColumnRule):
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"""
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Requires that every cell in the column has a value that is not already in use in the system for a given data type
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and field name.
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"""
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user: SapioUser
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data_type_name: str
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data_field_name: str
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def __init__(self, context: SapioWebhookContext | SapioUser, header: str, data_type_name: str,
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data_field_name: str):
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"""
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:param context: The current webhook context or a user object to send requests from.
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:param header: The header that this rule acts upon.
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:param data_type_name: The data type name to search on.
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:param data_field_name: The data field name to search on. This is expected to be a string field.
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"""
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self.user = context.user if isinstance(context, SapioWebhookContext) else context
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self.data_type_name = data_type_name
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self.data_field_name = data_field_name
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super().__init__(header, f"This value already exists in the system.")
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def validate(self, rows: list[dict[str, Any]]) -> list[int]:
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file_handler = FileDataHandler(rows)
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values: list[str] = file_handler.get_values_list(self.header)
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# Run a quick report for all records of this type that match these field values.
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term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
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"{" + ",".join(values) + "}")
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results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
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existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
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return file_handler.get_in_list(self.header, existing_values)
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class ExistingSystemValueRule(ColumnRule):
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"""
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Requires that every cell in the column has a value that is already in use in the system for a given data type
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and field name.
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"""
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user: SapioUser
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data_type_name: str
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data_field_name: str
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def __init__(self, context: SapioWebhookContext | SapioUser, header: str, data_type_name: str,
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data_field_name: str):
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"""
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:param context: The current webhook context or a user object to send requests from.
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:param header: The header that this rule acts upon.
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:param data_type_name: The data type name to search on.
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:param data_field_name: The data field name to search on. This is expected to be a string field.
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"""
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self.user = context.user if isinstance(context, SapioWebhookContext) else context
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self.data_type_name = data_type_name
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self.data_field_name = data_field_name
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super().__init__(header, f"This value doesn't exist in the system.")
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def validate(self, rows: list[dict[str, Any]]) -> list[int]:
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file_handler = FileDataHandler(rows)
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values: list[str] = file_handler.get_values_list(self.header)
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# Run a quick report for all records of this type that match these field values.
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term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
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"{" + ",".join(values) + "}")
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results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
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existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
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return file_handler.get_not_in_list(self.header, existing_values)
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@@ -3,7 +3,7 @@ from typing import Any
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from sapiopylib.rest.DataMgmtService import DataMgmtServer
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from sapiopylib.rest.User import SapioUser
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from sapiopylib.rest.pojo.CustomReport import ReportColumn, CustomReport
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from sapiopylib.rest.pojo.CustomReport import ReportColumn, CustomReport
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from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
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@@ -13,9 +13,7 @@ class CustomReportUtil:
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def run_system_report(context: SapioWebhookContext | SapioUser,
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report_name: str,
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filters: dict[str, Iterable[Any]] | None = None,
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page_limit: int | None = None,
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page_size: int | None = None,
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page_number: int | None = None) -> list[dict[str, Any]]:
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page_limit: int | None = None) -> list[dict[str, Any]]:
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"""
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Run a system report and return the results of that report as a list of dictionaries for the values of each
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column in each row.
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filter on. Only those headers that both the filters and the custom report share will take effect. That is,
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any filters that have a header name that isn't in the custom report will be ignored.
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:param page_limit: The maximum number of pages to query. If None, exhausts all possible pages.
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:param page_size: The size of each page of results in the search. If None, the page size is set by the server.
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:param page_number: The page number to start the search from, If None, starts on the first page.
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:return: The results of the report listed row by row, mapping each cell to the header it is under. The header
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values in the dicts are the data field names of the columns.
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If two columns in the search have the same data field name but differing data type names, then the
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dictionary key to the value in the column will be "DataTypeName.DataFieldName". For example, if you
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had a Sample column with a data field name of Identifier and a Request column with the same data field name,
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then the dictionary keys for these columns would be Sample.Identifier and Request.Identifier respectively.
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"""
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results
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results = CustomReportUtil.__exhaust_system_report(context, report_name, page_limit)
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columns: list[ReportColumn] = results[0]
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rows: list[list[Any]] = results[1]
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return CustomReportUtil.__process_results(rows, columns, filters)
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:param context: The current webhook context or a user object to send requests from.
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:param report_criteria: The custom report criteria to run.
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:param filters: If provided, filter the results of the report using the given mapping of headers to values to
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filter on. Only those headers that both the filters and the custom report share will take effect. That is,
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any filters that have a header name that isn't in the custom report will be ignored.
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Note that this parameter is only provided for parity with the other run report functions. If you need to
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filter the results of a search, it would likely be more beneficial to have just added a new term to the
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input report criteria that corresponds to the filter.
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:param page_limit: The maximum number of pages to query. If None, exhausts all possible pages.
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:param page_size: The size of each page of results in the search. If None, uses the value from the given report
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criteria. If not None, overwrites the value from the given report criteria.
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criteria. If not None, overwrites the value from the given report criteria.
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"""
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columns: list[ReportColumn] = results[0]
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return CustomReportUtil.__process_results(rows, columns, filters)
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@staticmethod
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"""
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the data record manager allows, but still simpler than a full-blown custom report. The columns that are returned
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in a quick search are every visible field from the data type that corresponds to the given report term. (Fields
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which are not marked as visible in the data designer will be excluded.)
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@staticmethod
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def __exhaust_custom_report(context: SapioWebhookContext | SapioUser,
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page_number: int | None) \
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174
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-> tuple[list[ReportColumn], list[list[Any]]]:
|
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175
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-
"""
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176
|
-
Given a custom report, iterate over every page of the report and collect the results
|
|
177
|
-
until there are no remaining pages.
|
|
178
|
-
"""
|
|
179
|
-
user: SapioUser = context if isinstance(context, SapioUser) else context.user
|
|
180
|
-
report_man = DataMgmtServer.get_custom_report_manager(user)
|
|
181
|
-
|
|
182
|
-
result = None
|
|
183
|
-
if page_size is not None:
|
|
184
|
-
report.page_size = page_size
|
|
185
|
-
if page_number is not None:
|
|
186
|
-
report.page_number = page_number
|
|
187
|
-
has_next_page: bool = True
|
|
188
|
-
rows: list[list[Any]] = []
|
|
189
|
-
cur_page: int = 1
|
|
190
|
-
while has_next_page and (not page_limit or cur_page <= page_limit):
|
|
191
|
-
result = report_man.run_custom_report(report)
|
|
192
|
-
report.page_size = result.page_size
|
|
193
|
-
report.page_number = result.page_number
|
|
194
|
-
has_next_page = result.has_next_page
|
|
195
|
-
rows.extend(result.result_table)
|
|
196
|
-
cur_page += 1
|
|
197
|
-
return result.column_list, rows
|
|
198
|
-
|
|
199
|
-
@staticmethod
|
|
200
|
-
def __exhaust_quick_report(context: SapioWebhookContext | SapioUser,
|
|
201
|
-
report_term: RawReportTerm,
|
|
202
|
-
page_limit: int | None,
|
|
203
|
-
page_size: int | None,
|
|
204
|
-
page_number: int | None) \
|
|
205
|
-
-> tuple[list[ReportColumn], list[list[Any]]]:
|
|
206
|
-
"""
|
|
207
|
-
Given a quick report, iterate over every page of the report and collect the results
|
|
208
|
-
until there are no remaining pages.
|
|
209
|
-
"""
|
|
210
|
-
user: SapioUser = context if isinstance(context, SapioUser) else context.user
|
|
211
|
-
report_man = DataMgmtServer.get_custom_report_manager(user)
|
|
212
|
-
|
|
213
|
-
result = None
|
|
214
|
-
has_next_page: bool = True
|
|
215
|
-
rows: list[list[Any]] = []
|
|
216
|
-
cur_page: int = 1
|
|
217
|
-
while has_next_page and (not page_limit or cur_page <= page_limit):
|
|
218
|
-
result = report_man.run_quick_report(report_term, page_size, page_number)
|
|
219
|
-
page_size = result.page_size
|
|
220
|
-
page_number = result.page_number
|
|
221
|
-
has_next_page = result.has_next_page
|
|
222
|
-
rows.extend(result.result_table)
|
|
223
|
-
cur_page += 1
|
|
224
|
-
return result.column_list, rows
|
|
225
|
-
|
|
226
|
-
@staticmethod
|
|
227
|
-
def __process_results(rows: list[list[Any]], columns: list[ReportColumn],
|
|
228
|
-
filters: dict[str, Iterable[Any]] | None) -> list[dict[str, Any]]:
|
|
229
|
-
"""
|
|
230
|
-
Given the results of a report as a list of row values and the report's columns, combine these lists to
|
|
231
|
-
result in a singular list of dictionaries for each row in the results.
|
|
232
|
-
|
|
233
|
-
If any filter criteria has been provided, also use that to filter the row.
|
|
234
|
-
"""
|
|
235
|
-
# It may be the case that two columns have the same data field name but differing data type names.
|
|
236
|
-
# If this occurs, then we need to be able to differentiate these columns in the resulting dictionary.
|
|
237
|
-
prepend_dt: set[str] = set()
|
|
238
|
-
encountered_names: list[str] = []
|
|
239
|
-
for column in columns:
|
|
240
|
-
field_name: str = column.data_field_name
|
|
241
|
-
if field_name in encountered_names:
|
|
242
|
-
prepend_dt.add(field_name)
|
|
243
|
-
else:
|
|
244
|
-
encountered_names.append(field_name)
|
|
245
|
-
|
|
246
|
-
ret: list[dict[str, Any]] = []
|
|
247
|
-
for row in rows:
|
|
248
|
-
row_data: dict[str, Any] = {}
|
|
249
|
-
filter_row: bool = False
|
|
250
|
-
for value, column in zip(row, columns):
|
|
251
|
-
header: str = column.data_field_name
|
|
252
|
-
# If two columns share the same data field name, prepend the data type name of the column to the
|
|
253
|
-
# data field name.
|
|
254
|
-
if header in prepend_dt:
|
|
255
|
-
header = column.data_type_name + "." + header
|
|
256
|
-
if filters is not None and header in filters and value not in filters.get(header):
|
|
257
|
-
filter_row = True
|
|
258
|
-
break
|
|
259
|
-
row_data.update({header: value})
|
|
260
|
-
if filter_row is False:
|
|
261
|
-
ret.append(row_data)
|
|
262
|
-
return ret
|
|
90
|
+
return report.column_list, rows
|