sapiopycommons 2025.9.5a726__py3-none-any.whl → 2025.9.5rc727__py3-none-any.whl

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Files changed (51) hide show
  1. sapiopycommons/ai/tool_of_tools.py +917 -0
  2. sapiopycommons/callbacks/callback_util.py +26 -16
  3. sapiopycommons/eln/experiment_handler.py +12 -5
  4. sapiopycommons/files/assay_plate_reader.py +93 -0
  5. sapiopycommons/files/file_text_converter.py +207 -0
  6. sapiopycommons/flowcyto/flow_cyto.py +2 -24
  7. sapiopycommons/general/accession_service.py +2 -28
  8. sapiopycommons/multimodal/multimodal.py +2 -24
  9. sapiopycommons/recordmodel/record_handler.py +4 -0
  10. sapiopycommons/rules/eln_rule_handler.py +3 -0
  11. sapiopycommons/rules/on_save_rule_handler.py +3 -0
  12. sapiopycommons/webhook/webservice_handlers.py +1 -1
  13. {sapiopycommons-2025.9.5a726.dist-info → sapiopycommons-2025.9.5rc727.dist-info}/METADATA +2 -2
  14. {sapiopycommons-2025.9.5a726.dist-info → sapiopycommons-2025.9.5rc727.dist-info}/RECORD +16 -48
  15. sapiopycommons/ai/converter_service_base.py +0 -132
  16. sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.py +0 -43
  17. sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2.pyi +0 -31
  18. sapiopycommons/ai/protoapi/fielddefinitions/fields_pb2_grpc.py +0 -24
  19. sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2.py +0 -123
  20. sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2.pyi +0 -598
  21. sapiopycommons/ai/protoapi/fielddefinitions/velox_field_def_pb2_grpc.py +0 -24
  22. sapiopycommons/ai/protoapi/plan/converter/converter_pb2.py +0 -51
  23. sapiopycommons/ai/protoapi/plan/converter/converter_pb2.pyi +0 -63
  24. sapiopycommons/ai/protoapi/plan/converter/converter_pb2_grpc.py +0 -149
  25. sapiopycommons/ai/protoapi/plan/item/item_container_pb2.py +0 -55
  26. sapiopycommons/ai/protoapi/plan/item/item_container_pb2.pyi +0 -90
  27. sapiopycommons/ai/protoapi/plan/item/item_container_pb2_grpc.py +0 -24
  28. sapiopycommons/ai/protoapi/plan/script/script_pb2.py +0 -59
  29. sapiopycommons/ai/protoapi/plan/script/script_pb2.pyi +0 -102
  30. sapiopycommons/ai/protoapi/plan/script/script_pb2_grpc.py +0 -153
  31. sapiopycommons/ai/protoapi/plan/step_output_pb2.py +0 -45
  32. sapiopycommons/ai/protoapi/plan/step_output_pb2.pyi +0 -42
  33. sapiopycommons/ai/protoapi/plan/step_output_pb2_grpc.py +0 -24
  34. sapiopycommons/ai/protoapi/plan/step_pb2.py +0 -43
  35. sapiopycommons/ai/protoapi/plan/step_pb2.pyi +0 -43
  36. sapiopycommons/ai/protoapi/plan/step_pb2_grpc.py +0 -24
  37. sapiopycommons/ai/protoapi/plan/tool/entry_pb2.py +0 -41
  38. sapiopycommons/ai/protoapi/plan/tool/entry_pb2.pyi +0 -35
  39. sapiopycommons/ai/protoapi/plan/tool/entry_pb2_grpc.py +0 -24
  40. sapiopycommons/ai/protoapi/plan/tool/tool_pb2.py +0 -75
  41. sapiopycommons/ai/protoapi/plan/tool/tool_pb2.pyi +0 -237
  42. sapiopycommons/ai/protoapi/plan/tool/tool_pb2_grpc.py +0 -154
  43. sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2.py +0 -39
  44. sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2.pyi +0 -32
  45. sapiopycommons/ai/protoapi/session/sapio_conn_info_pb2_grpc.py +0 -24
  46. sapiopycommons/ai/protobuf_utils.py +0 -504
  47. sapiopycommons/ai/server.py +0 -106
  48. sapiopycommons/ai/test_client.py +0 -356
  49. sapiopycommons/ai/tool_service_base.py +0 -951
  50. {sapiopycommons-2025.9.5a726.dist-info → sapiopycommons-2025.9.5rc727.dist-info}/WHEEL +0 -0
  51. {sapiopycommons-2025.9.5a726.dist-info → sapiopycommons-2025.9.5rc727.dist-info}/licenses/LICENSE +0 -0
@@ -1765,8 +1765,11 @@ class CallbackUtil:
1765
1765
  blank_result_handling = BlankResultHandling.REPEAT
1766
1766
  def not_blank_func(r: list[DataRecord]) -> bool:
1767
1767
  return bool(r)
1768
- return self.__send_dialog_blank_results(request, self.callback.show_input_selection_dialog, not_blank_func,
1769
- blank_result_handling, repeat_message, cancel_message)
1768
+ response: list[DataRecord] = self.__send_dialog_blank_results(request,
1769
+ self.callback.show_input_selection_dialog,
1770
+ not_blank_func, blank_result_handling,
1771
+ repeat_message, cancel_message)
1772
+ return self.rec_handler.wrap_models(response, wrapper_type)
1770
1773
 
1771
1774
  # FR-47690: Deprecated the require_authentication parameter.
1772
1775
  # noinspection PyUnusedLocal
@@ -1812,7 +1815,8 @@ class CallbackUtil:
1812
1815
  return response
1813
1816
 
1814
1817
  def request_file(self, title: str, exts: Iterable[str] | None = None,
1815
- show_image_editor: bool = False, show_camera_button: bool = False) -> tuple[str, bytes]:
1818
+ show_image_editor: bool = False, show_camera_button: bool = False,
1819
+ *, enforce_file_extensions: bool = True) -> tuple[str, bytes]:
1816
1820
  """
1817
1821
  Request a single file from the user.
1818
1822
 
@@ -1822,6 +1826,8 @@ class CallbackUtil:
1822
1826
  :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
1823
1827
  :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
1824
1828
  rather than selecting an existing file.
1829
+ :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
1830
+ enforced. If false, then the user may upload any file type.
1825
1831
  :return: The file name and bytes of the uploaded file.
1826
1832
  """
1827
1833
  # If no extensions were provided, use an empty list for the extensions instead.
@@ -1841,11 +1847,12 @@ class CallbackUtil:
1841
1847
  file_path: str = self.__send_dialog(request, self.callback.show_file_dialog, data_sink=do_consume)
1842
1848
 
1843
1849
  # Verify that each of the file given matches the expected extension(s).
1844
- self.__verify_file(file_path, sink.data, exts)
1850
+ self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
1845
1851
  return file_path, sink.data
1846
1852
 
1847
1853
  def request_files(self, title: str, exts: Iterable[str] | None = None,
1848
- show_image_editor: bool = False, show_camera_button: bool = False) -> dict[str, bytes]:
1854
+ show_image_editor: bool = False, show_camera_button: bool = False,
1855
+ *, enforce_file_extensions: bool = True) -> dict[str, bytes]:
1849
1856
  """
1850
1857
  Request multiple files from the user.
1851
1858
 
@@ -1855,6 +1862,8 @@ class CallbackUtil:
1855
1862
  :param show_image_editor: Whether the user will see an image editor when image is uploaded in this file prompt.
1856
1863
  :param show_camera_button: Whether the user will be able to use camera to take a picture as an upload request,
1857
1864
  rather than selecting an existing file.
1865
+ :param enforce_file_extensions: If true, then the file extensions provided in the exts parameter will be
1866
+ enforced. If false, then the user may upload any file type.
1858
1867
  :return: A dictionary of file name to file bytes for each file the user uploaded.
1859
1868
  """
1860
1869
  # If no extensions were provided, use an empty list for the extensions instead.
@@ -1870,7 +1879,7 @@ class CallbackUtil:
1870
1879
  for file_path in file_paths:
1871
1880
  sink = InMemoryRecordDataSink(self.user)
1872
1881
  sink.consume_client_callback_file_path_data(file_path)
1873
- self.__verify_file(file_path, sink.data, exts)
1882
+ self.__verify_file(file_path, sink.data, exts if enforce_file_extensions else None)
1874
1883
  ret_dict.update({file_path: sink.data})
1875
1884
 
1876
1885
  return ret_dict
@@ -1887,16 +1896,17 @@ class CallbackUtil:
1887
1896
  """
1888
1897
  if file_path is None or len(file_path) == 0 or file_bytes is None or len(file_bytes) == 0:
1889
1898
  raise SapioUserErrorException("Empty file provided or file unable to be read.")
1890
- if allowed_extensions:
1891
- matches: bool = False
1892
- for ext in allowed_extensions:
1893
- # FR-47690: Changed to a case-insensitive match.
1894
- if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
1895
- matches = True
1896
- break
1897
- if matches is False:
1898
- raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
1899
- + (",".join(allowed_extensions)))
1899
+ if not allowed_extensions:
1900
+ return
1901
+ matches: bool = False
1902
+ for ext in allowed_extensions:
1903
+ # FR-47690: Changed to a case-insensitive match.
1904
+ if file_path.casefold().endswith("." + ext.lstrip(".").casefold()):
1905
+ matches = True
1906
+ break
1907
+ if not matches:
1908
+ raise SapioUserErrorException("Unsupported file type. Expecting the following extension(s): "
1909
+ + (",".join(allowed_extensions)))
1900
1910
 
1901
1911
  def write_file(self, file_name: str, file_data: str | bytes) -> None:
1902
1912
  """
@@ -206,12 +206,11 @@ class ExperimentHandler:
206
206
  else:
207
207
  user = context
208
208
  context = None
209
- if context is not None and context.eln_experiment is not None and experiment is None:
210
- experiment = context.eln_experiment
211
209
  # FR-46495 - Allow the init function of ExperimentHandler to take in an ElnExperiment that is separate from the
212
210
  # context.
213
211
  # CR-37038 - Allow other experiment object types to be provided. Convert them all down to ElnExperiment.
214
- if (context is None or context.eln_experiment is None) and experiment is not None:
212
+ # PR-47793 - Fix cases where both a SapioWebhookContext and an experiment parameter are provided.
213
+ if experiment is not None:
215
214
  eln_manager = DataMgmtServer.get_eln_manager(user)
216
215
  # If this object is already an ElnExperiment, do nothing.
217
216
  if isinstance(experiment, ElnExperiment):
@@ -227,13 +226,19 @@ class ExperimentHandler:
227
226
  raise SapioException(f"No experiment with notebook ID {notebook_id} located in the system.")
228
227
  # If this object is a record, assume it is an experiment record that we can query the system with.
229
228
  else:
230
- record_id: int = AliasUtil.to_record_ids([experiment])[0]
229
+ record_id: int = AliasUtil.to_record_id(experiment)
231
230
  experiment: ElnExperiment = eln_manager.get_eln_experiment_by_record_id(record_id)
232
231
  if not experiment:
233
232
  raise SapioException(f"No experiment with record ID {record_id} located in the system.")
233
+ elif context is not None and context.eln_experiment is not None:
234
+ experiment = context.eln_experiment
235
+
234
236
  if experiment is None:
235
237
  raise SapioException("Cannot initialize ExperimentHandler. No ELN Experiment found in the provided "
236
238
  "parameters.")
239
+ elif not isinstance(experiment, ElnExperiment):
240
+ raise SapioException("Cannot initialize ExperimentHandler. The experiment variable is not an "
241
+ "ElnExperiment!")
237
242
 
238
243
  return user, context, experiment
239
244
 
@@ -1425,7 +1430,9 @@ class ExperimentHandler:
1425
1430
  :return: The map of options for the input step.
1426
1431
  """
1427
1432
  step: ElnEntryStep = self.get_step(step)
1428
- if step not in self._step_options:
1433
+ # PR-47796: Fix the get_step_options function making a webservice query every time it is called instead of
1434
+ # properly checking its cache of entry options.
1435
+ if step.get_id() not in self._step_options:
1429
1436
  self._step_options.update(ExperimentReportUtil.get_experiment_entry_options(self.user,
1430
1437
  self.get_all_steps()))
1431
1438
  return self._step_options[step.get_id()]
@@ -0,0 +1,93 @@
1
+ import base64
2
+ import dataclasses
3
+ from typing import Any
4
+
5
+ from databind.core.dataclasses import dataclass
6
+ from databind.json import loads
7
+ from sapiopylib.rest.utils.singletons import SapioContextManager
8
+
9
+
10
+ @dataclasses.dataclass
11
+ class ProcessAssayPlateRequest:
12
+ """
13
+ A request to process the results of assay plate reader with a configuration set in Sapio.
14
+
15
+ Attributes:
16
+ num_rows (int): The number of rows in the plate.
17
+ num_columns (int): The number of columns in the plate.
18
+ plate_ids_in_context (list[str]): List of plate IDs that are in context for this request.
19
+ filename (str): The name of the file containing the assay data.
20
+ file_data (bytes): The binary content of the file.
21
+ plate_reader_config_name (str): The name of the plate reader configuration to use.
22
+ """
23
+ num_rows: int
24
+ num_columns: int
25
+ plate_ids_in_context: list[str] | None
26
+ filename: str
27
+ file_data: bytes
28
+ plate_reader_config_name: str
29
+
30
+ def to_json(self) -> dict[str, Any]:
31
+ return {
32
+ "numRows": self.num_rows,
33
+ "numCols": self.num_columns,
34
+ "plateIdsInContext": self.plate_ids_in_context,
35
+ "fileName": self.filename,
36
+ "fileDataBase64": base64.b64encode(self.file_data).decode('utf-8'),
37
+ "plateReaderName": self.plate_reader_config_name
38
+ }
39
+
40
+
41
+ @dataclass
42
+ class AssayPlateResultIdent:
43
+ plateId: str
44
+ channelIdOrBlock: str
45
+ kineticAssaySeconds: float | None
46
+
47
+
48
+ @dataclass
49
+ class AssayResultDatum:
50
+ """
51
+ Describes the data received from an assay plate reader.
52
+ Most of the time, the data is a single value, but sometimes it can be multiple values, especially for kinetic data.
53
+ """
54
+ DEFAULT_PROPERTY_NAME: str = "read"
55
+ rowPosition: str
56
+ columnPosition: str
57
+ valueByPropertyName: dict[str, float]
58
+ textValueByPropertyName: dict[str, str]
59
+
60
+
61
+ @dataclass
62
+ class AssayPlateResult:
63
+ """
64
+ Assay plate load result for a single plate in a file. A file can have more than one of this result if it has multiple plate of data in a single file.
65
+ """
66
+ resultIdent: AssayPlateResultIdent
67
+ numRows: int
68
+ numColumns: int
69
+ resultDatum: list[AssayResultDatum]
70
+
71
+
72
+ @dataclass
73
+ class AssayFileLoadResult:
74
+ """
75
+ The entire top-level file loading result for an assay plate reader file.
76
+ """
77
+ filename: str
78
+ plateResultList: list[AssayPlateResult]
79
+
80
+
81
+ class AssayPlateReader(SapioContextManager):
82
+ """
83
+ This class contains services for Sapio Assay Plate Reader.
84
+ """
85
+
86
+ def process_plate_reader_data(self, request: ProcessAssayPlateRequest) -> AssayFileLoadResult:
87
+ """
88
+ Processes the assay plate reader data using provided request into a structured result using configuration defined in Sapio.
89
+ """
90
+ payload = request.to_json()
91
+ response = self.user.plugin_post("assayplatereader/process", payload=payload)
92
+ self.user.raise_for_status(response)
93
+ return loads(response.text, AssayFileLoadResult)
@@ -0,0 +1,207 @@
1
+ import io
2
+ import os
3
+ import tempfile
4
+ from enum import Enum, auto
5
+
6
+ class FileType(Enum):
7
+ """Supported file types for conversion."""
8
+ TXT = auto()
9
+ MD = auto()
10
+ CSV = auto()
11
+ DOC = auto()
12
+ DOCX = auto()
13
+ XLS = auto()
14
+ XLSX = auto()
15
+ PPT = auto()
16
+ PPTX = auto()
17
+ PDF = auto()
18
+ UNKNOWN = auto()
19
+
20
+
21
+ class FileToTextConverter:
22
+ """
23
+ A class for converting various file types to raw text.
24
+ """
25
+ @staticmethod
26
+ def mime_type_to_enum(mime_type: str) -> FileType:
27
+ """
28
+ Converts a MIME type to a FileType enum.
29
+
30
+ :param mime_type: The MIME type string to convert.
31
+ :return: The corresponding FileType enum, or UNKNOWN if not recognized.
32
+ """
33
+ if not mime_type or not mime_type.strip():
34
+ return FileType.UNKNOWN
35
+
36
+ mime_map = {
37
+ "text/plain": FileType.TXT,
38
+ "text/markdown": FileType.MD,
39
+ "text/csv": FileType.CSV,
40
+ "application/msword": FileType.DOC,
41
+ "application/vnd.openxmlformats-officedocument.wordprocessingml.document": FileType.DOCX,
42
+ "application/vnd.ms-excel": FileType.XLS,
43
+ "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet": FileType.XLSX,
44
+ "application/vnd.ms-powerpoint": FileType.PPT,
45
+ "application/vnd.openxmlformats-officedocument.presentationml.presentation": FileType.PPTX,
46
+ "application/pdf": FileType.PDF,
47
+ }
48
+ return mime_map.get(mime_type, FileType.UNKNOWN)
49
+
50
+ @staticmethod
51
+ def file_extension_to_enum(file_path: str) -> FileType:
52
+ """
53
+ Converts a file path or extension to a FileType enum.
54
+
55
+ :param file_path: The file path or extension to convert.
56
+ :return: The corresponding FileType enum, or UNKNOWN if not recognized.
57
+ """
58
+ if not file_path or not file_path.strip():
59
+ return FileType.UNKNOWN
60
+
61
+ # Extract the file extension, removing the leading dot and making it lowercase
62
+ file_extension = os.path.splitext(file_path)[1].lstrip('.').lower()
63
+
64
+ ext_map = {
65
+ "txt": FileType.TXT,
66
+ "md": FileType.MD,
67
+ "csv": FileType.CSV,
68
+ "doc": FileType.DOC,
69
+ "docx": FileType.DOCX,
70
+ "xls": FileType.XLS,
71
+ "xlsx": FileType.XLSX,
72
+ "ppt": FileType.PPT,
73
+ "pptx": FileType.PPTX,
74
+ "pdf": FileType.PDF,
75
+ }
76
+ return ext_map.get(file_extension, FileType.UNKNOWN)
77
+
78
+ @classmethod
79
+ def parse_file(cls, file_type: FileType, file_bytes: bytes) -> str | None:
80
+ """
81
+ Parses file bytes based on the FileType and returns the text content.
82
+
83
+ :param file_type: The type of the file to parse.
84
+ :param file_bytes: The raw bytes of the file to parse.
85
+ :return: The text content of the file, or None if the file type is not supported or parsing fails.
86
+ """
87
+ if file_type is None or file_bytes is None:
88
+ return None
89
+ if not file_bytes:
90
+ return ""
91
+
92
+ # Dispatch to the correct parser method
93
+ parser_map = {
94
+ FileType.TXT: cls._parse_plain_text,
95
+ FileType.MD: cls._parse_plain_text,
96
+ FileType.CSV: cls._parse_plain_text,
97
+ FileType.DOC: cls._parse_doc,
98
+ FileType.DOCX: cls._parse_docx,
99
+ FileType.XLS: cls._parse_xls,
100
+ FileType.XLSX: cls._parse_xlsx,
101
+ FileType.PPT: cls._parse_ppt,
102
+ FileType.PPTX: cls._parse_pptx,
103
+ FileType.PDF: cls._parse_pdf,
104
+ }
105
+
106
+ parser_func = parser_map.get(file_type)
107
+
108
+ if parser_func:
109
+ return parser_func(file_bytes)
110
+
111
+ return None
112
+
113
+ @staticmethod
114
+ def _parse_plain_text(file_bytes: bytes) -> str:
115
+ return file_bytes.decode('utf-8')
116
+
117
+ @staticmethod
118
+ def _run_textract(file_bytes: bytes, extension: str) -> str:
119
+ """
120
+ Helper to run textract on in-memory bytes by writing to a temp file.
121
+ Note: textract may require external system dependencies.
122
+ """
123
+ import textract
124
+ with tempfile.NamedTemporaryFile(suffix=f".{extension}", delete=True) as temp_file:
125
+ temp_file.write(file_bytes)
126
+ temp_file.flush() # Ensure all bytes are written to disk
127
+ text = textract.process(temp_file.name).decode('utf-8')
128
+ return text
129
+
130
+ @classmethod
131
+ def _parse_doc(cls, file_bytes: bytes) -> str:
132
+ return cls._run_textract(file_bytes, 'doc')
133
+
134
+ @staticmethod
135
+ def _parse_docx(file_bytes: bytes) -> str:
136
+ import docx
137
+ with io.BytesIO(file_bytes) as stream:
138
+ document = docx.Document(stream)
139
+ return "\n".join(para.text for para in document.paragraphs if para.text.strip())
140
+
141
+ @staticmethod
142
+ def _parse_xls(file_bytes: bytes) -> str:
143
+ import xlrd
144
+ workbook = xlrd.open_workbook(file_contents=file_bytes)
145
+ text_parts = []
146
+ for sheet in workbook.sheets():
147
+ text_parts.append(f"Sheet: {sheet.name}\n")
148
+ for row_idx in range(sheet.nrows):
149
+ row_cells = []
150
+ for col_idx in range(sheet.ncols):
151
+ cell_text = str(sheet.cell_value(row_idx, col_idx))
152
+ if cell_text.strip():
153
+ row_cells.append(cell_text + "\t")
154
+ if row_cells:
155
+ text_parts.append("".join(row_cells))
156
+ text_parts.append("\n")
157
+ text_parts.append("\n")
158
+ return "".join(text_parts)
159
+
160
+ @staticmethod
161
+ def _parse_xlsx(file_bytes: bytes) -> str:
162
+ import openpyxl
163
+ with io.BytesIO(file_bytes) as stream:
164
+ workbook = openpyxl.load_workbook(stream, read_only=True)
165
+ text_parts = []
166
+ for sheet in workbook.worksheets:
167
+ text_parts.append(f"Sheet: {sheet.title}\n")
168
+ for row in sheet.iter_rows():
169
+ row_cells = []
170
+ for cell in row:
171
+ cell_text = str(cell.value) if cell.value is not None else ""
172
+ if cell_text.strip():
173
+ row_cells.append(cell_text + "\t")
174
+ if row_cells:
175
+ text_parts.append("".join(row_cells))
176
+ text_parts.append("\n")
177
+ text_parts.append("\n")
178
+ return "".join(text_parts)
179
+
180
+ @classmethod
181
+ def _parse_ppt(cls, file_bytes: bytes) -> str:
182
+ return cls._run_textract(file_bytes, 'ppt')
183
+
184
+ @staticmethod
185
+ def _parse_pptx(file_bytes: bytes) -> str:
186
+ import pptx
187
+ with io.BytesIO(file_bytes) as stream:
188
+ presentation = pptx.Presentation(stream)
189
+ text_parts = []
190
+ for slide in presentation.slides:
191
+ for shape in slide.shapes:
192
+ if shape.has_text_frame:
193
+ text = shape.text_frame.text
194
+ if text and text.strip():
195
+ text_parts.append(text)
196
+ return "\n".join(text_parts)
197
+
198
+ @staticmethod
199
+ def _parse_pdf(file_bytes: bytes) -> str:
200
+ """Parses a PDF file's bytes and extracts text using PyMuPDF."""
201
+ import pymupdf
202
+ text_parts = []
203
+ with io.BytesIO(file_bytes) as stream:
204
+ with pymupdf.open(stream=stream) as doc:
205
+ for page in doc:
206
+ text_parts.append(page.get_text())
207
+ return "\n".join(text_parts)
@@ -4,38 +4,16 @@ from weakref import WeakValueDictionary
4
4
 
5
5
  from databind.json import dumps
6
6
  from sapiopylib.rest.User import SapioUser
7
+ from sapiopylib.rest.utils.singletons import SapioContextManager
7
8
 
8
9
  from sapiopycommons.flowcyto.flowcyto_data import FlowJoWorkspaceInputJson, UploadFCSInputJson, \
9
10
  ComputeFlowStatisticsInputJson
10
11
 
11
12
 
12
- class FlowCytoManager:
13
+ class FlowCytoManager(SapioContextManager):
13
14
  """
14
15
  This manager includes flow cytometry analysis tools that would require FlowCyto license to use.
15
16
  """
16
- _user: SapioUser
17
-
18
- __instances: WeakValueDictionary[SapioUser, FlowCytoManager] = WeakValueDictionary()
19
- __initialized: bool
20
-
21
- def __new__(cls, user: SapioUser):
22
- """
23
- Observes singleton pattern per record model manager object.
24
-
25
- :param user: The user that will make the webservice request to the application.
26
- """
27
- obj = cls.__instances.get(user)
28
- if not obj:
29
- obj = object.__new__(cls)
30
- obj.__initialized = False
31
- cls.__instances[user] = obj
32
- return obj
33
-
34
- def __init__(self, user: SapioUser):
35
- if self.__initialized:
36
- return
37
- self._user = user
38
- self.__initialized = True
39
17
 
40
18
  def create_flowjo_workspace(self, workspace_input: FlowJoWorkspaceInputJson) -> int:
41
19
  """
@@ -5,6 +5,7 @@ from typing import Any
5
5
  from weakref import WeakValueDictionary
6
6
 
7
7
  from sapiopylib.rest.User import SapioUser
8
+ from sapiopylib.rest.utils.singletons import SapioContextManager
8
9
 
9
10
  _STR_JAVA_TYPE = "java.lang.String"
10
11
  _INT_JAVA_TYPE = "java.lang.Integer"
@@ -274,37 +275,10 @@ class AccessionServiceDescriptor:
274
275
  }
275
276
 
276
277
 
277
- class AccessionService:
278
+ class AccessionService(SapioContextManager):
278
279
  """
279
280
  Provides Sapio Foundations Accession Service functionalities.
280
281
  """
281
- _user: SapioUser
282
-
283
- __instances: WeakValueDictionary[SapioUser, AccessionService] = WeakValueDictionary()
284
- __initialized: bool
285
-
286
- @property
287
- def user(self) -> SapioUser:
288
- return self._user
289
-
290
- def __new__(cls, user: SapioUser):
291
- """
292
- Observes singleton pattern per record model manager object.
293
-
294
- :param user: The user that will make the webservice request to the application.
295
- """
296
- obj = cls.__instances.get(user)
297
- if not obj:
298
- obj = object.__new__(cls)
299
- obj.__initialized = False
300
- cls.__instances[user] = obj
301
- return obj
302
-
303
- def __init__(self, user: SapioUser):
304
- if self.__initialized:
305
- return
306
- self._user = user
307
- self.__initialized = True
308
282
 
309
283
  def accession_with_config(self, data_type_name: str, data_field_name: str, num_ids: int) -> list[str]:
310
284
  """
@@ -7,35 +7,13 @@ from weakref import WeakValueDictionary
7
7
  from databind.json import dumps, loads
8
8
  from sapiopylib.rest.User import SapioUser
9
9
  from sapiopylib.rest.pojo.DataRecord import DataRecord
10
+ from sapiopylib.rest.utils.singletons import SapioContextManager
10
11
 
11
12
  from sapiopycommons.general.exceptions import SapioException
12
13
  from sapiopycommons.multimodal.multimodal_data import *
13
14
 
14
15
 
15
- class MultiModalManager:
16
- _user: SapioUser
17
-
18
- __instances: WeakValueDictionary[SapioUser, MultiModalManager] = WeakValueDictionary()
19
- __initialized: bool
20
-
21
- def __new__(cls, user: SapioUser):
22
- """
23
- Observes singleton pattern per record model manager object.
24
-
25
- :param user: The user that will make the webservice request to the application.
26
- """
27
- obj = cls.__instances.get(user)
28
- if not obj:
29
- obj = object.__new__(cls)
30
- obj.__initialized = False
31
- cls.__instances[user] = obj
32
- return obj
33
-
34
- def __init__(self, user:SapioUser):
35
- if self.__initialized:
36
- return
37
- self._user = user
38
- self.__initialized = True
16
+ class MultiModalManager(SapioContextManager):
39
17
 
40
18
  def load_image_data(self, request: ImageDataRequestPojo) -> list[str]:
41
19
  """
@@ -100,6 +100,10 @@ class RecordHandler:
100
100
  PyRecordModel instead of a WrappedRecordModel.
101
101
  :return: The record model for the input.
102
102
  """
103
+ # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType]. The type hints
104
+ # say this shouldn't be done anyway, but using this as a safeguard against user error.
105
+ if isinstance(wrapper_type, str):
106
+ wrapper_type = None
103
107
  if wrapper_type is not None:
104
108
  self.__verify_data_type(record, wrapper_type)
105
109
  if isinstance(record, PyRecordModel):
@@ -184,4 +184,7 @@ class ElnRuleHandler:
184
184
  instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
185
185
  """
186
186
  dt: str = AliasUtil.to_data_type_name(wrapper_type)
187
+ # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType].
188
+ if isinstance(wrapper_type, str):
189
+ wrapper_type = None
187
190
  return self._rec_handler.wrap_models(self.get_records(dt, entry), wrapper_type)
@@ -180,4 +180,7 @@ class OnSaveRuleHandler:
180
180
  instead of a model wrapper, then the returned records will be PyRecordModels instead of WrappedRecordModels.
181
181
  """
182
182
  dt: str = AliasUtil.to_data_type_name(wrapper_type)
183
+ # PR-47792: Set the wrapper_type to None if a str was provided instead of a type[WrappedType].
184
+ if isinstance(wrapper_type, str):
185
+ wrapper_type = None
183
186
  return self._rec_handler.wrap_models(self.get_records(dt, record_id), wrapper_type)
@@ -140,7 +140,7 @@ class AbstractWebserviceHandler(AbstractWebhookHandler):
140
140
  # Get the login credentials from the headers.
141
141
  auth: str = headers.get("Authorization")
142
142
  if auth and auth.startswith("Basic "):
143
- credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":", 1)
143
+ credentials: list[str] = b64decode(auth.split("Basic ")[1]).decode().split(":")
144
144
  user = self.basic_auth(url, credentials[0], credentials[1])
145
145
  elif auth and auth.startswith("Bearer "):
146
146
  user = self.bearer_token_auth(url, auth.split("Bearer ")[1])
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: sapiopycommons
3
- Version: 2025.9.5a726
3
+ Version: 2025.9.5rc727
4
4
  Summary: Official Sapio Python API Utilities Package
5
5
  Project-URL: Homepage, https://github.com/sapiosciences
6
6
  Author-email: Jonathan Steck <jsteck@sapiosciences.com>, Yechen Qiao <yqiao@sapiosciences.com>
@@ -17,7 +17,7 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
17
17
  Classifier: Topic :: Software Development :: Libraries :: Python Modules
18
18
  Requires-Python: >=3.10
19
19
  Requires-Dist: databind>=4.5
20
- Requires-Dist: sapiopylib>=2025.4.17.264
20
+ Requires-Dist: sapiopylib>=2025.7.31a279
21
21
  Description-Content-Type: text/markdown
22
22
 
23
23