sapiopycommons 2024.11.8a355__py3-none-any.whl → 2024.11.8a359__py3-none-any.whl
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- sapiopycommons/callbacks/callback_util.py +83 -532
- sapiopycommons/chem/IndigoMolecules.py +0 -2
- sapiopycommons/chem/Molecules.py +18 -77
- sapiopycommons/datatype/attachment_util.py +10 -11
- sapiopycommons/eln/experiment_handler.py +70 -272
- sapiopycommons/files/complex_data_loader.py +4 -5
- sapiopycommons/files/file_bridge.py +24 -31
- sapiopycommons/files/file_data_handler.py +5 -2
- sapiopycommons/files/file_util.py +9 -59
- sapiopycommons/files/file_validator.py +6 -92
- sapiopycommons/files/file_writer.py +15 -44
- sapiopycommons/general/aliases.py +6 -207
- sapiopycommons/general/custom_report_util.py +37 -212
- sapiopycommons/general/exceptions.py +8 -21
- sapiopycommons/general/popup_util.py +0 -21
- sapiopycommons/general/time_util.py +2 -8
- sapiopycommons/processtracking/endpoints.py +22 -22
- sapiopycommons/recordmodel/record_handler.py +97 -481
- sapiopycommons/rules/eln_rule_handler.py +25 -34
- sapiopycommons/rules/on_save_rule_handler.py +31 -34
- sapiopycommons/webhook/webhook_handlers.py +42 -201
- {sapiopycommons-2024.11.8a355.dist-info → sapiopycommons-2024.11.8a359.dist-info}/METADATA +2 -4
- sapiopycommons-2024.11.8a359.dist-info/RECORD +38 -0
- sapiopycommons/callbacks/field_builder.py +0 -537
- sapiopycommons/customreport/__init__.py +0 -0
- sapiopycommons/customreport/column_builder.py +0 -60
- sapiopycommons/customreport/custom_report_builder.py +0 -130
- sapiopycommons/customreport/term_builder.py +0 -299
- sapiopycommons/datatype/data_fields.py +0 -61
- sapiopycommons/datatype/pseudo_data_types.py +0 -440
- sapiopycommons/eln/experiment_report_util.py +0 -653
- sapiopycommons/files/file_bridge_handler.py +0 -340
- sapiopycommons/flowcyto/flow_cyto.py +0 -77
- sapiopycommons/flowcyto/flowcyto_data.py +0 -75
- sapiopycommons/general/accession_service.py +0 -375
- sapiopycommons/general/audit_log.py +0 -189
- sapiopycommons/general/sapio_links.py +0 -50
- sapiopycommons/multimodal/multimodal.py +0 -146
- sapiopycommons/multimodal/multimodal_data.py +0 -489
- sapiopycommons/processtracking/custom_workflow_handler.py +0 -406
- sapiopycommons/sftpconnect/__init__.py +0 -0
- sapiopycommons/sftpconnect/sftp_builder.py +0 -69
- sapiopycommons/webhook/webhook_context.py +0 -39
- sapiopycommons/webhook/webservice_handlers.py +0 -67
- sapiopycommons-2024.11.8a355.dist-info/RECORD +0 -59
- {sapiopycommons-2024.11.8a355.dist-info → sapiopycommons-2024.11.8a359.dist-info}/WHEEL +0 -0
- {sapiopycommons-2024.11.8a355.dist-info → sapiopycommons-2024.11.8a359.dist-info}/licenses/LICENSE +0 -0
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@@ -4,21 +4,19 @@ import urllib.parse
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from requests import Response
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from sapiopylib.rest.User import SapioUser
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from sapiopycommons.general.aliases import UserIdentifier, AliasUtil
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from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
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# FR-46064 - Initial port of PyWebhookUtils to sapiopycommons.
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class FileBridge:
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@staticmethod
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def read_file(context:
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def read_file(context: SapioWebhookContext | SapioUser, bridge_name: str, file_path: str,
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base64_decode: bool = True) -> bytes:
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"""
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Read a file from FileBridge.
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:param context: The current webhook context or a user object to send requests from.
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:param bridge_name: The name of the bridge to use.
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file bridge configurations.
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:param bridge_name: The name of the bridge to use.
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:param file_path: The path to read the file from.
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:param base64_decode: If true, base64 decode the file. Files are by default base64 encoded when retrieved from
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FileBridge.
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params = {
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'Filepath': f"bridge://{bridge_name}/{file_path}"
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}
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user: SapioUser =
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user: SapioUser = context if isinstance(context, SapioUser) else context.user
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response = user.get(sub_path, params)
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return ret_val
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@staticmethod
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def write_file(context:
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def write_file(context: SapioWebhookContext | SapioUser, bridge_name: str, file_path: str,
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file_data: bytes | str) -> None:
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"""
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Write a file to FileBridge.
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:param context: The current webhook context or a user object to send requests from.
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:param bridge_name: The name of the bridge to use.
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file bridge configurations.
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:param bridge_name: The name of the bridge to use.
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:param file_path: The path to write the file to. If a file already exists at the given path then the file is
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overwritten.
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:param file_data: A string or bytes of the file to be written.
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params = {
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'Filepath': f"bridge://{bridge_name}/{file_path}"
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}
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user: SapioUser =
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with io.
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user: SapioUser = context if isinstance(context, SapioUser) else context.user
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with io.StringIO(file_data) if isinstance(file_data, str) else io.BytesIO(file_data) as data_stream:
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response = user.post_data_stream(sub_path, params=params, data_stream=data_stream)
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@staticmethod
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def list_directory(context:
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def list_directory(context: SapioWebhookContext | SapioUser, bridge_name: str,
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file_path: str | None = "") -> list[str]:
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"""
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List the contents of a FileBridge directory.
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:param bridge_name: The name of the bridge to use.
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file bridge configurations.
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:param bridge_name: The name of the bridge to use.
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:param file_path: The path to read the directory from.
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:return: A list of
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:return: A list of name of files and folders in the directory.
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"""
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sub_path = '/ext/filebridge/listDirectory'
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params = {
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'Filepath': f"bridge://{bridge_name}/{file_path}"
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}
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user: SapioUser =
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user: SapioUser = context if isinstance(context, SapioUser) else context.user
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response: Response = user.get(sub_path, params=params)
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response_body: list[str] = response.json()
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path_length = len(f"bridge://{bridge_name}/")
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return [urllib.parse.unquote(value
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return [urllib.parse.unquote(value[path_length:]) for value in response_body]
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@staticmethod
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def create_directory(context:
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def create_directory(context: SapioWebhookContext | SapioUser, bridge_name: str, file_path: str) -> None:
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"""
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file bridge configurations.
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:param bridge_name: The name of the bridge to use.
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:param file_path: The path to create the directory at. If a directory already exists at the given path then an
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exception is raised.
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"""
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'Filepath': f"bridge://{bridge_name}/{file_path}"
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user: SapioUser = context if isinstance(context, SapioUser) else context.user
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response = user.post(sub_path, params=params)
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@staticmethod
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def delete_file(context:
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def delete_file(context: SapioWebhookContext | SapioUser, bridge_name: str, file_path: str) -> None:
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"""
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file bridge configurations.
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:param bridge_name: The name of the bridge to use.
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:param file_path: The path to the file to delete.
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"""
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'Filepath': f"bridge://{bridge_name}/{file_path}"
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response = user.
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response = user.post(sub_path, params=params)
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def delete_directory(context: SapioWebhookContext | SapioUser, bridge_name: str, file_path: str) -> None:
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"""
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response = user.
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from sapiopycommons.general.aliases import SapioRecord
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FilterList = Iterable[int] | range | Callable[[int, dict[str, Any]], bool] | None
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"""A FilterList is an object used to determine if a row in the file data should be skipped over. This can take the
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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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|
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AbstractVeloxFieldDefinition
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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
|
|
13
|
-
from sapiopycommons.general.aliases import UserIdentifier, AliasUtil
|
|
14
|
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from sapiopycommons.general.custom_report_util import CustomReportUtil
|
|
15
|
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from sapiopycommons.general.exceptions import SapioUserCancelledException
|
|
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|
|
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14
|
|
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18
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|
|
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@@ -80,10 +77,10 @@ class FileValidator:
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|
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79
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|
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def build_violation_report(self, context:
|
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|
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def build_violation_report(self, context: SapioWebhookResult | SapioUser,
|
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rule_violations: dict[int, list[ValidationRule]]) -> None:
|
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"""
|
|
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|
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|
|
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|
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Build a simple report of any rule violations in the file to display to the user as a table dialog.
|
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|
88
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|
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|
|
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|
|
@@ -121,24 +118,9 @@ class FileValidator:
|
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"Reason": violation.reason[:2000]
|
|
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})
|
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|
|
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|
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|
|
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|
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|
|
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|
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def validate_and_report_errors(self, context: UserIdentifier) -> None:
|
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|
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"""
|
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Validate the file. If any rule violations are found, display a simple report of any rule violations in the file
|
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to the user as a table dialog and throw a SapioUserCancelled exception after the user acknowledges the dialog
|
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to end the webhook interaction.
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|
|
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Shorthand for calling validate_file() and then build_violation_report() if there are any errors.
|
|
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|
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|
|
136
|
-
:param context: The current webhook context or a user object to send requests from.
|
|
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|
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"""
|
|
138
|
-
violations = self.validate_file()
|
|
139
|
-
if violations:
|
|
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|
-
self.build_violation_report(context, violations)
|
|
141
|
-
raise SapioUserCancelledException()
|
|
121
|
+
callback_util = CallbackUtil(context)
|
|
122
|
+
callback_util.table_dialog("Errors", "The following rule violations were encountered in the provided file.",
|
|
123
|
+
columns, rows)
|
|
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124
|
|
|
143
125
|
|
|
144
126
|
class ValidationRule:
|
|
@@ -498,71 +480,3 @@ class ContainsSubstringFromCellRule(RowRule):
|
|
|
498
480
|
|
|
499
481
|
def validate(self, row: dict[str, Any]) -> bool:
|
|
500
482
|
return row.get(self.second) in row.get(self.first)
|
|
501
|
-
|
|
502
|
-
|
|
503
|
-
class UniqueSystemValueRule(ColumnRule):
|
|
504
|
-
"""
|
|
505
|
-
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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|
-
"""
|
|
508
|
-
user: SapioUser
|
|
509
|
-
data_type_name: str
|
|
510
|
-
data_field_name: str
|
|
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|
-
|
|
512
|
-
def __init__(self, context: UserIdentifier, header: str, data_type_name: str,
|
|
513
|
-
data_field_name: str):
|
|
514
|
-
"""
|
|
515
|
-
:param context: The current webhook context or a user object to send requests from.
|
|
516
|
-
:param header: The header that this rule acts upon.
|
|
517
|
-
:param data_type_name: The data type name to search on.
|
|
518
|
-
:param data_field_name: The data field name to search on. This is expected to be a string field.
|
|
519
|
-
"""
|
|
520
|
-
self.user = AliasUtil.to_sapio_user(context)
|
|
521
|
-
self.data_type_name = data_type_name
|
|
522
|
-
self.data_field_name = data_field_name
|
|
523
|
-
super().__init__(header, f"This value already exists in the system.")
|
|
524
|
-
|
|
525
|
-
def validate(self, rows: list[dict[str, Any]]) -> list[int]:
|
|
526
|
-
file_handler = FileDataHandler(rows)
|
|
527
|
-
values: list[str] = file_handler.get_values_list(self.header)
|
|
528
|
-
|
|
529
|
-
# Run a quick report for all records of this type that match these field values.
|
|
530
|
-
term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
|
|
531
|
-
"{" + ",".join(values) + "}")
|
|
532
|
-
results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
|
|
533
|
-
existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
|
|
534
|
-
return file_handler.get_in_list(self.header, existing_values)
|
|
535
|
-
|
|
536
|
-
|
|
537
|
-
class ExistingSystemValueRule(ColumnRule):
|
|
538
|
-
"""
|
|
539
|
-
Requires that every cell in the column has a value that is already in use in the system for a given data type
|
|
540
|
-
and field name.
|
|
541
|
-
"""
|
|
542
|
-
user: SapioUser
|
|
543
|
-
data_type_name: str
|
|
544
|
-
data_field_name: str
|
|
545
|
-
|
|
546
|
-
def __init__(self, context: UserIdentifier, header: str, data_type_name: str,
|
|
547
|
-
data_field_name: str):
|
|
548
|
-
"""
|
|
549
|
-
:param context: The current webhook context or a user object to send requests from.
|
|
550
|
-
:param header: The header that this rule acts upon.
|
|
551
|
-
:param data_type_name: The data type name to search on.
|
|
552
|
-
:param data_field_name: The data field name to search on. This is expected to be a string field.
|
|
553
|
-
"""
|
|
554
|
-
self.user = AliasUtil.to_sapio_user(context)
|
|
555
|
-
self.data_type_name = data_type_name
|
|
556
|
-
self.data_field_name = data_field_name
|
|
557
|
-
super().__init__(header, f"This value doesn't exist in the system.")
|
|
558
|
-
|
|
559
|
-
def validate(self, rows: list[dict[str, Any]]) -> list[int]:
|
|
560
|
-
file_handler = FileDataHandler(rows)
|
|
561
|
-
values: list[str] = file_handler.get_values_list(self.header)
|
|
562
|
-
|
|
563
|
-
# Run a quick report for all records of this type that match these field values.
|
|
564
|
-
term = RawReportTerm(self.data_type_name, self.data_field_name, RawTermOperation.EQUAL_TO_OPERATOR,
|
|
565
|
-
"{" + ",".join(values) + "}")
|
|
566
|
-
results: list[dict[str, Any]] = CustomReportUtil.run_quick_report(self.user, term)
|
|
567
|
-
existing_values: list[Any] = [x.get(self.data_field_name) for x in results]
|
|
568
|
-
return file_handler.get_not_in_list(self.header, existing_values)
|
|
@@ -1,6 +1,5 @@
|
|
|
1
1
|
from __future__ import annotations
|
|
2
2
|
|
|
3
|
-
import warnings
|
|
4
3
|
from abc import abstractmethod
|
|
5
4
|
from enum import Enum
|
|
6
5
|
from typing import Any
|
|
@@ -19,7 +18,7 @@ class FileWriter:
|
|
|
19
18
|
body: list[list[Any]]
|
|
20
19
|
delimiter: str
|
|
21
20
|
line_break: str
|
|
22
|
-
column_definitions:
|
|
21
|
+
column_definitions: list[ColumnDef]
|
|
23
22
|
|
|
24
23
|
def __init__(self, headers: list[str], delimiter: str = ",", line_break: str = "\r\n"):
|
|
25
24
|
"""
|
|
@@ -31,7 +30,7 @@ class FileWriter:
|
|
|
31
30
|
self.delimiter = delimiter
|
|
32
31
|
self.line_break = line_break
|
|
33
32
|
self.body = []
|
|
34
|
-
self.column_definitions =
|
|
33
|
+
self.column_definitions = []
|
|
35
34
|
|
|
36
35
|
def add_row_list(self, row: list[Any]) -> None:
|
|
37
36
|
"""
|
|
@@ -66,49 +65,21 @@ class FileWriter:
|
|
|
66
65
|
new_row.append(row.get(header, ""))
|
|
67
66
|
self.body.append(new_row)
|
|
68
67
|
|
|
69
|
-
def
|
|
68
|
+
def add_column_definitions(self, column_defs: list[ColumnDef]) -> None:
|
|
70
69
|
"""
|
|
71
|
-
Add
|
|
70
|
+
Add new column definitions to this FileWriter. Column definitions are evaluated in the order they are added,
|
|
71
|
+
meaning that they map to the header with the equivalent index. Before the file is built, the number of column
|
|
72
|
+
definitions must equal the number of headers if any column definition is provided.
|
|
72
73
|
|
|
73
|
-
ColumnDefs are only used if the build_file function is provided with a list of RowBundles.
|
|
74
|
-
have a column definition if this is the case.
|
|
74
|
+
ColumnDefs are only used if the build_file function is provided with a list of RowBundles.
|
|
75
75
|
|
|
76
76
|
Custom column definitions can be created by defining a class that extends ColumnDef and implements the print
|
|
77
77
|
method.
|
|
78
78
|
|
|
79
|
-
:param
|
|
79
|
+
:param column_defs: A list of column definitions to be used to construct the file when build_file is
|
|
80
80
|
called.
|
|
81
|
-
:param header: The header that this column definition is for. If a header is provided that isn't in the headers
|
|
82
|
-
list, the header is appended to the end of the list.
|
|
83
81
|
"""
|
|
84
|
-
|
|
85
|
-
self.headers.append(header)
|
|
86
|
-
self.column_definitions[header] = column_def
|
|
87
|
-
|
|
88
|
-
def add_column_definitions(self, column_defs: dict[str, ColumnDef]) -> None:
|
|
89
|
-
"""
|
|
90
|
-
Add new column definitions to this FileWriter.
|
|
91
|
-
|
|
92
|
-
ColumnDefs are only used if the build_file function is provided with a list of RowBundles. Every header must
|
|
93
|
-
have a column definition if this is the case.
|
|
94
|
-
|
|
95
|
-
Custom column definitions can be created by defining a class that extends ColumnDef and implements the print
|
|
96
|
-
method.
|
|
97
|
-
|
|
98
|
-
:param column_defs: A dictionary of header names to column definitions to be used to construct the file when
|
|
99
|
-
build_file is called.
|
|
100
|
-
"""
|
|
101
|
-
# For backwards compatibility purposes, if column definitions are provided as a list,
|
|
102
|
-
# add them in order of appearance of the headers. This will only work if the headers are defined first, though.
|
|
103
|
-
if isinstance(column_defs, list):
|
|
104
|
-
warnings.warn("Adding column definitions is no longer expected as a list. Continuing to provide a list to "
|
|
105
|
-
"this function may result in undesirable behavior.", UserWarning)
|
|
106
|
-
if not self.headers:
|
|
107
|
-
raise SapioException("No headers provided to FileWriter before the column definitions were added.")
|
|
108
|
-
for header, column_def in zip(self.headers, column_defs):
|
|
109
|
-
self.column_definitions[header] = column_def
|
|
110
|
-
for header, column_def in column_defs.items():
|
|
111
|
-
self.add_column_definition(header, column_def)
|
|
82
|
+
self.column_definitions.extend(column_defs)
|
|
112
83
|
|
|
113
84
|
def build_file(self, rows: list[RowBundle] | None = None, sorter=None, reverse: bool = False) -> str:
|
|
114
85
|
"""
|
|
@@ -129,10 +100,11 @@ class FileWriter:
|
|
|
129
100
|
"""
|
|
130
101
|
# If any column definitions have been provided, the number of column definitions and headers must be equal.
|
|
131
102
|
if self.column_definitions:
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
103
|
+
def_count: int = len(self.column_definitions)
|
|
104
|
+
header_count: int = len(self.headers)
|
|
105
|
+
if def_count != header_count:
|
|
106
|
+
raise SapioException(f"FileWriter has {def_count} column definitions defined but {header_count} "
|
|
107
|
+
f"headers. The number of column definitions must equal the number of headers.")
|
|
136
108
|
# If any RowBundles have been provided, there must be column definitions for mapping them to the file.
|
|
137
109
|
elif rows:
|
|
138
110
|
raise SapioException(f"FileWriter was given RowBundles but contains no column definitions for mapping "
|
|
@@ -158,8 +130,7 @@ class FileWriter:
|
|
|
158
130
|
rows.sort(key=lambda x: x.index)
|
|
159
131
|
for row in rows:
|
|
160
132
|
new_row: list[Any] = []
|
|
161
|
-
for
|
|
162
|
-
column = self.column_definitions[header]
|
|
133
|
+
for column in self.column_definitions:
|
|
163
134
|
if column.may_skip and row.may_skip:
|
|
164
135
|
new_row.append("")
|
|
165
136
|
else:
|