sapiopycommons 2025.5.9a518__py3-none-any.whl → 2025.5.12a519__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.


This version of sapiopycommons might be problematic. Click here for more details.

Files changed (54) hide show
  1. sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.py +43 -0
  2. sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2.pyi +31 -0
  3. sapiopycommons/ai/api/fielddefinitions/proto/fields_pb2_grpc.py +24 -0
  4. sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.py +123 -0
  5. sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2.pyi +598 -0
  6. sapiopycommons/ai/api/fielddefinitions/proto/velox_field_def_pb2_grpc.py +24 -0
  7. sapiopycommons/ai/api/plan/proto/step_output_pb2.py +45 -0
  8. sapiopycommons/ai/api/plan/proto/step_output_pb2.pyi +42 -0
  9. sapiopycommons/ai/api/plan/proto/step_output_pb2_grpc.py +24 -0
  10. sapiopycommons/ai/api/plan/proto/step_pb2.py +43 -0
  11. sapiopycommons/ai/api/plan/proto/step_pb2.pyi +43 -0
  12. sapiopycommons/ai/api/plan/proto/step_pb2_grpc.py +24 -0
  13. sapiopycommons/ai/api/plan/script/proto/script_pb2.py +53 -0
  14. sapiopycommons/ai/api/plan/script/proto/script_pb2.pyi +99 -0
  15. sapiopycommons/ai/api/plan/script/proto/script_pb2_grpc.py +153 -0
  16. sapiopycommons/ai/api/plan/tool/proto/entry_pb2.py +57 -0
  17. sapiopycommons/ai/api/plan/tool/proto/entry_pb2.pyi +96 -0
  18. sapiopycommons/ai/api/plan/tool/proto/entry_pb2_grpc.py +24 -0
  19. sapiopycommons/ai/api/plan/tool/proto/tool_pb2.py +67 -0
  20. sapiopycommons/ai/api/plan/tool/proto/tool_pb2.pyi +220 -0
  21. sapiopycommons/ai/api/plan/tool/proto/tool_pb2_grpc.py +154 -0
  22. sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.py +39 -0
  23. sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2.pyi +32 -0
  24. sapiopycommons/ai/api/session/proto/sapio_conn_info_pb2_grpc.py +24 -0
  25. sapiopycommons/ai/protobuf_utils.py +454 -0
  26. sapiopycommons/ai/tool_service_base.py +740 -0
  27. sapiopycommons/callbacks/callback_util.py +64 -116
  28. sapiopycommons/callbacks/field_builder.py +0 -2
  29. sapiopycommons/customreport/auto_pagers.py +1 -2
  30. sapiopycommons/customreport/term_builder.py +1 -1
  31. sapiopycommons/datatype/pseudo_data_types.py +326 -349
  32. sapiopycommons/eln/experiment_handler.py +719 -336
  33. sapiopycommons/eln/plate_designer.py +2 -7
  34. sapiopycommons/files/file_util.py +4 -4
  35. sapiopycommons/general/accession_service.py +2 -2
  36. sapiopycommons/general/aliases.py +1 -4
  37. sapiopycommons/general/html_formatter.py +456 -0
  38. sapiopycommons/general/sapio_links.py +12 -4
  39. sapiopycommons/processtracking/custom_workflow_handler.py +1 -2
  40. sapiopycommons/recordmodel/record_handler.py +27 -357
  41. sapiopycommons/rules/eln_rule_handler.py +1 -8
  42. sapiopycommons/rules/on_save_rule_handler.py +1 -8
  43. sapiopycommons/webhook/webhook_handlers.py +0 -3
  44. sapiopycommons/webhook/webservice_handlers.py +2 -2
  45. {sapiopycommons-2025.5.9a518.dist-info → sapiopycommons-2025.5.12a519.dist-info}/METADATA +2 -2
  46. sapiopycommons-2025.5.12a519.dist-info/RECORD +91 -0
  47. sapiopycommons/ai/tool_of_tools.py +0 -809
  48. sapiopycommons/eln/experiment_cache.py +0 -188
  49. sapiopycommons/eln/experiment_step_factory.py +0 -476
  50. sapiopycommons/eln/step_creation.py +0 -236
  51. sapiopycommons/general/data_structure_util.py +0 -115
  52. sapiopycommons-2025.5.9a518.dist-info/RECORD +0 -69
  53. {sapiopycommons-2025.5.9a518.dist-info → sapiopycommons-2025.5.12a519.dist-info}/WHEEL +0 -0
  54. {sapiopycommons-2025.5.9a518.dist-info → sapiopycommons-2025.5.12a519.dist-info}/licenses/LICENSE +0 -0
@@ -167,7 +167,7 @@ class PlateDesignerEntry(ElnEntryStep):
167
167
  self._designer_elements_by_plate = {}
168
168
  self._designer_elements_by_plate.clear()
169
169
  for element in self._designer_elements:
170
- plate_id: int = element.get_field_value(WellElement.PLATE_RECORD_ID__FIELD.field_name)
170
+ plate_id: int = element.get(WellElement.PLATE_RECORD_ID__FIELD)
171
171
  self._designer_elements_by_plate.setdefault(plate_id, []).append(element)
172
172
  return self._designer_elements
173
173
 
@@ -194,8 +194,7 @@ class PlateDesignerEntry(ElnEntryStep):
194
194
  return self._designer_elements_by_plate[plate]
195
195
 
196
196
  def create_well_element(self, sample: RecordModel, plate: RecordModel, location: PlateLocation | None = None,
197
- layer: int = 1, wrapper_type: type[WrappedType] | None = None) \
198
- -> WrappedType | PyRecordModel:
197
+ wrapper_type: type[WrappedType] | None = None) -> WrappedType | PyRecordModel:
199
198
  """
200
199
  Create a new plate designer well element for the input sample and plate. A record model manager store and commit
201
200
  must be called to save this new well element to the server.
@@ -204,7 +203,6 @@ class PlateDesignerEntry(ElnEntryStep):
204
203
  :param plate: The plate that the element is for. Must exist in the system (i.e. have a >0 record ID).
205
204
  :param location: The location of the well element. If not provided, the row and column position fields of the
206
205
  sample will be used.
207
- :param layer: The layer that the well element is on.
208
206
  :param wrapper_type: The record model wrapper to use for the plate designer well element. If not provided, the
209
207
  returned record will be a PyRecordModel instead of a WrappedRecordModel.
210
208
  :return: The newly created PlateDesignerWellElementModel.
@@ -218,8 +216,6 @@ class PlateDesignerEntry(ElnEntryStep):
218
216
  raise SapioException("Sample record must be of type Sample.")
219
217
  if AliasUtil.to_data_type_name(plate) != "Plate":
220
218
  raise SapioException("Plate record must be of type Plate.")
221
- if layer < 1:
222
- raise SapioException("Layer must be greater than 0.")
223
219
 
224
220
  dt: type[WrappedType] | str = wrapper_type if wrapper_type else WellElement.DATA_TYPE_NAME
225
221
  plate_id: int = AliasUtil.to_record_id(plate)
@@ -229,7 +225,6 @@ class PlateDesignerEntry(ElnEntryStep):
229
225
  WellElement.ROW_POSITION__FIELD: location.row_pos if location else sample.get_field_value("RowPosition"),
230
226
  WellElement.COL_POSITION__FIELD: str(location.col_pos) if location else sample.get_field_value("ColPosition"),
231
227
  WellElement.SOURCE_DATA_TYPE_NAME__FIELD: "Sample",
232
- WellElement.LAYER__FIELD: layer,
233
228
  }
234
229
  element = self._rec_handler.add_models_with_data(dt, [fields])[0]
235
230
 
@@ -327,10 +327,10 @@ class FileUtil:
327
327
  :param files: A dictionary of file name to file data as a string or bytes.
328
328
  :return: The bytes for a zip file containing the input files.
329
329
  """
330
- with io.BytesIO() as zip_buffer:
331
- with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
332
- for file_name, file_data in files.items():
333
- zip_file.writestr(file_name, file_data)
330
+ zip_buffer: io.BytesIO = io.BytesIO()
331
+ with zipfile.ZipFile(zip_buffer, "w", zipfile.ZIP_DEFLATED) as zip_file:
332
+ for file_name, file_data in files.items():
333
+ zip_file.writestr(file_name, file_data)
334
334
  return zip_buffer.getvalue()
335
335
 
336
336
  # Deprecated functions:
@@ -199,7 +199,7 @@ class AccessionRequestId(AbstractAccessionServiceOperator):
199
199
 
200
200
  Properties:
201
201
  numberOfCharacters: Number of characters maximum in the request ID.
202
- accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compatibility patch for converting these to the new preference format.
202
+ accessorName: This is a legacy variable from drum.getNextIdListByMapName(), which allows setting different "accessorName" from old system. We need this for compability patch for converting these to the new preference format.
203
203
  """
204
204
  _num_of_characters: int
205
205
  _accessor_name: str
@@ -341,7 +341,7 @@ class AccessionService:
341
341
  def get_affixed_id_in_batch(self, data_type_name: str, data_field_name: str, num_ids: int, prefix: str | None,
342
342
  suffix: str | None, num_digits: int | None, start_num: int = 1) -> list[str]:
343
343
  """
344
- Get the batch affixed IDs that are maximal in cache and contiguous for a particular datatype.datafield under a given format.
344
+ Get the batch affixed IDs that are maximal in cache and contiguious for a particular datatype.datafield under a given format.
345
345
  :param data_type_name: The datatype name to look for max ID
346
346
  :param data_field_name: The datafield name to look for max ID
347
347
  :param num_ids: The number of IDs to accession.
@@ -7,7 +7,6 @@ from sapiopylib.rest.pojo.datatype.FieldDefinition import FieldType, AbstractVel
7
7
  from sapiopylib.rest.pojo.eln.ElnExperiment import ElnExperiment
8
8
  from sapiopylib.rest.pojo.eln.ExperimentEntry import ExperimentEntry
9
9
  from sapiopylib.rest.pojo.eln.SapioELNEnums import ElnBaseDataType
10
- from sapiopylib.rest.pojo.eln.eln_headings import ElnExperimentTab
11
10
  from sapiopylib.rest.pojo.webhook.WebhookContext import SapioWebhookContext
12
11
  from sapiopylib.rest.utils.Protocols import ElnExperimentProtocol, ElnEntryStep
13
12
  from sapiopylib.rest.utils.recordmodel.PyRecordModel import PyRecordModel, AbstractRecordModel
@@ -220,9 +219,7 @@ class AliasUtil:
220
219
  # noinspection PyTypeChecker
221
220
  fields: FieldMap = record.get_fields()
222
221
  else:
223
- # TI-47593: Copy the record's fields by using the get() method instead of copy_to_dict() so that date
224
- # macros get translated to valid field values.
225
- fields: FieldMap = {f: record.fields.get(f) for f in record.fields}
222
+ fields: FieldMap = record.fields.copy_to_dict()
226
223
  # PR-47457: Only include the record ID if the caller requests it, since including the record ID can break
227
224
  # callbacks in certain circumstances if the record ID is negative.
228
225
  if include_record_id:
@@ -0,0 +1,456 @@
1
+ from __future__ import annotations
2
+
3
+ import re
4
+ from typing import Final
5
+
6
+
7
+ class HtmlFormatter:
8
+ """
9
+ A class for formatting text in HTML with tag classes supported by the client.
10
+ """
11
+ TIMESTAMP_TEXT__CSS_CLASS_NAME: Final[str] = "timestamp-text"
12
+ HEADER_1_TEXT__CSS_CLASS_NAME: Final[str] = "header1-text"
13
+ HEADER_2_TEXT__CSS_CLASS_NAME: Final[str] = "header2-text"
14
+ HEADER_3_TEXT__CSS_CLASS_NAME: Final[str] = "header3-text"
15
+ BODY_TEXT__CSS_CLASS_NAME: Final[str] = "body-text"
16
+ CAPTION_TEXT__CSS_CLASS_NAME: Final[str] = "caption-text"
17
+
18
+ @staticmethod
19
+ def timestamp(text: str) -> str:
20
+ """
21
+ Given a text string, return that same text string HTML formatted using the timestamp CSS class.
22
+
23
+ :param text: The text to format.
24
+ :return: The HTML formatted text.
25
+ """
26
+ return f'<span class="{HtmlFormatter.TIMESTAMP_TEXT__CSS_CLASS_NAME}">{text}</span>'
27
+
28
+ @staticmethod
29
+ def header_1(text: str) -> str:
30
+ """
31
+ Given a text string, return that same text string HTML formatted using the header 1 CSS class.
32
+
33
+ :param text: The text to format.
34
+ :return: The HTML formatted text.
35
+ """
36
+ return f'<span class="{HtmlFormatter.HEADER_1_TEXT__CSS_CLASS_NAME}">{text}</span>'
37
+
38
+ @staticmethod
39
+ def header_2(text: str) -> str:
40
+ """
41
+ Given a text string, return that same text string HTML formatted using the header 2 CSS class.
42
+
43
+ :param text: The text to format.
44
+ :return: The HTML formatted text.
45
+ """
46
+ return f'<span class="{HtmlFormatter.HEADER_2_TEXT__CSS_CLASS_NAME}">{text}</span>'
47
+
48
+ @staticmethod
49
+ def header_3(text: str) -> str:
50
+ """
51
+ Given a text string, return that same text string HTML formatted using the header 3 CSS class.
52
+
53
+ :param text: The text to format.
54
+ :return: The HTML formatted text.
55
+ """
56
+ return f'<span class="{HtmlFormatter.HEADER_3_TEXT__CSS_CLASS_NAME}">{text}</span>'
57
+
58
+ @staticmethod
59
+ def body(text: str) -> str:
60
+ """
61
+ Given a text string, return that same text string HTML formatted using the body text CSS class.
62
+
63
+ :param text: The text to format.
64
+ :return: The HTML formatted text.
65
+ """
66
+ return f'<span class="{HtmlFormatter.BODY_TEXT__CSS_CLASS_NAME}">{text}</span>'
67
+
68
+ @staticmethod
69
+ def caption(text: str) -> str:
70
+ """
71
+ Given a text string, return that same text string HTML formatted using the caption text CSS class.
72
+
73
+ :param text: The text to format.
74
+ :return: The HTML formatted text.
75
+ """
76
+ return f'<span class="{HtmlFormatter.CAPTION_TEXT__CSS_CLASS_NAME}">{text}</span>'
77
+
78
+ @staticmethod
79
+ def replace_newlines(text: str) -> str:
80
+ """
81
+ Given a text string, return that same text string HTML formatted with newlines replaced by HTML line breaks.
82
+
83
+ :param text: The text to format.
84
+ :return: The HTML formatted text.
85
+ """
86
+ return re.sub("\r?\n", "<br>", text)
87
+
88
+ @staticmethod
89
+ def scrub_html(text: str) -> str:
90
+ """
91
+ Given a string that contains HTML, return that same string with all HTML removed.
92
+
93
+ :param text: The HTML string to scrub.
94
+ :return: The scrubbed text.
95
+ """
96
+ if not text:
97
+ return ""
98
+
99
+ from bs4 import BeautifulSoup
100
+ return BeautifulSoup(text, "html.parser").get_text()
101
+
102
+ @staticmethod
103
+ def scrub_markdown(text: str) -> str:
104
+ """
105
+ Given a string that contains markdown, return that same string with all markdown removed.
106
+
107
+ :param text: The markdown string to scrub.
108
+ :return: The scrubbed text.
109
+ """
110
+ if not text:
111
+ return ""
112
+
113
+ # --- Remove Headers ---
114
+ # Level 1-6 headers (# to ######)
115
+ text = re.sub(r"^#{1,6}\s*(.*)$", r"\1", text, flags=re.MULTILINE).strip()
116
+
117
+ # --- Remove Emphasis ---
118
+ # Bold (**text** or __text__)
119
+ text = re.sub(r"\*\*(.*?)\*\*", r"\1", text)
120
+ text = re.sub(r"__(.*?)__", r"\1", text)
121
+
122
+ # Italic (*text* or _text_)
123
+ text = re.sub(r"\*(.*?)\*", r"\1", text)
124
+ text = re.sub(r"_(.*?)_", r"\1", text)
125
+
126
+ # --- Remove Strikethrough ---
127
+ # Strikethrough (~~text~~)
128
+ text = re.sub(r"~~(.*?)~~", r"\1", text)
129
+
130
+ # --- Remove Links ---
131
+ # Links ([text](url))
132
+ text = re.sub(r"\[(.*?)]\((.*?)\)", r"\1", text)
133
+
134
+ # --- Remove Images ---
135
+ # Images (![alt text](url))
136
+ text = re.sub(r"!\\[(.*?)\\]\\((.*?)\\)", "", text) # remove the entire image tag
137
+
138
+ # --- Remove Code ---
139
+ # Inline code (`code`)
140
+ text = re.sub(r"`(.*?)`", r"\1", text)
141
+
142
+ # Code blocks (```code```)
143
+ text = re.sub(r"```.*?```", "", text, flags=re.DOTALL) # multiline code blocks
144
+
145
+ # --- Remove Lists ---
146
+ # Unordered lists (* item, - item, + item)
147
+ text = re.sub(r"(?m)^[*\-+]\s+", "", text)
148
+
149
+ # Ordered lists (1. item)
150
+ text = re.sub(r"(?m)^\d+\.\s+", "", text)
151
+
152
+ # --- Remove Blockquotes ---
153
+ # Blockquotes (> text)
154
+ text = re.sub(r"(?m)^>\s+", "", text)
155
+
156
+ # --- Remove Horizontal Rules ---
157
+ # Horizontal rules (---, ***, ___)
158
+ text = re.sub(r"(?m)^[-_*]{3,}\s*$", "", text) # Remove horizontal rules
159
+
160
+ # --- Remove HTML tags (basic)---
161
+ # This is a very simple HTML tag removal, it does not handle nested tags or attributes properly.
162
+ text = re.sub(r"<[^>]*>", "", text)
163
+
164
+ # --- Remove escaped characters ---
165
+ text = re.sub(r"\\([!\"#$%&'()*+,./:;<=>?@\\[]^_`{|}~-])", r"\1", text)
166
+
167
+ return text
168
+
169
+ @staticmethod
170
+ def convert_markdown_to_html(text: str) -> str:
171
+ """
172
+ Given a markdown string, convert it to HTML and return the HTML string.
173
+
174
+ :param text: The markdown string to convert.
175
+ :return: The HTML string.
176
+ """
177
+ if not text:
178
+ return ""
179
+
180
+ # Replace newlines with break tags and tabs with em spaces.
181
+ text = text.replace("\r\n", "<br>").replace("\n", "<br>").replace("\t", "&emsp;")
182
+
183
+ # Format code blocks to maintain indentation.
184
+ text = HtmlFormatter.format_code_blocks(text, "<br>")
185
+
186
+ # Convert any other markdown to HTML.
187
+ text = HtmlFormatter._convert_markdown_by_line(text)
188
+
189
+ return text
190
+
191
+ @staticmethod
192
+ def format_code_blocks(text: str, newline: str = "\n") -> str:
193
+ """
194
+ Locate each markdown code block in the given text and format it with HTML code and preformatting tags
195
+ to maintain indentation and add language-specific syntax highlighting.
196
+
197
+ :param text: The text to format.
198
+ :param newline: The newline character to expect in the input text.
199
+ :return: The formatted text.
200
+ """
201
+ # Extract all the code blocks from the text
202
+ code_blocks = HtmlFormatter.extract_code_blocks(text, newline)
203
+ if not code_blocks:
204
+ return text
205
+
206
+ # Iterate through the code blocks, adding them to the text with the <pre><code> </code></pre>
207
+ # so that indentation is preserved.
208
+ current_index = 0
209
+ formatted = []
210
+ for code_block in code_blocks:
211
+ formatted.append(text[current_index:code_block.start_index])
212
+ formatted.append(code_block.to_html())
213
+ current_index = code_block.end_index
214
+ # Append the rest of the text after the last code block.
215
+ formatted.append(text[current_index:])
216
+ return "".join(formatted)
217
+
218
+ @staticmethod
219
+ def sanitize_code_blocks(text: str, newline: str = "\n") -> str:
220
+ """
221
+ Given the input text, remove all code blocks while leaving all other text unchanged.
222
+ For use in any location where we don't want to display code (because it's scary).
223
+
224
+ :param text: The text to sanitize.
225
+ :param newline: The newline character to expect in the input text.
226
+ :return: The sanitized text.
227
+ """
228
+ code_blocks = HtmlFormatter.extract_code_blocks(text, newline)
229
+
230
+ if not code_blocks:
231
+ return text
232
+
233
+ current_index = 0
234
+ formatted_text = []
235
+
236
+ for block in code_blocks:
237
+ formatted_text.append(text[current_index: block.start_index])
238
+ current_index = block.end_index
239
+
240
+ formatted_text.append(text[current_index:])
241
+
242
+ return "".join(formatted_text)
243
+
244
+ @staticmethod
245
+ def extract_code_blocks(text: str, newline: str = "\n") -> list[CodeBlock]:
246
+ """
247
+ Extract all code blocks from the given response.
248
+
249
+ :param text: The text to extract the code blocks from.
250
+ :param newline: The newline character to expect in the input text.
251
+ :return: A list of code blocks.
252
+ """
253
+ code: list[CodeBlock] = []
254
+ current_index = 0
255
+ while current_index < len(text):
256
+ code_block = HtmlFormatter.next_code_block(text, current_index, newline)
257
+ if code_block is None:
258
+ break
259
+ code.append(code_block)
260
+ current_index = code_block.end_index
261
+ return code
262
+
263
+ @staticmethod
264
+ def next_code_block(text: str, start_index: int, newline: str = "\n") -> CodeBlock | None:
265
+ """
266
+ Extract the next code block from the given response, starting at the given index.
267
+
268
+ :param text: The text to extract the code block from.
269
+ :param start_index: The index to start searching for the code block at.
270
+ :param newline: The newline character to expect in the input text.
271
+ :return: The extracted code block. Null if no code block is found after the start index.
272
+ """
273
+ # Find the start of the next code block.
274
+ start_tag = text.find("```", start_index)
275
+ if start_tag == -1:
276
+ return None
277
+
278
+ # Extract the language from the starting tag of the code block.
279
+ first_line = text.find(newline, start_tag)
280
+ if first_line == -1:
281
+ return None
282
+ language = text[start_tag + 3:first_line].strip()
283
+ first_line += len(newline)
284
+
285
+ # Find the end of the code block.
286
+ code: str
287
+ end_tag = text.find("```", first_line)
288
+ # If there is no end to the code block, just return the rest of the text as a code block.
289
+ if end_tag == -1:
290
+ end_tag = len(text)
291
+ code = text[first_line:end_tag]
292
+ else:
293
+ code = text[first_line:end_tag]
294
+ end_tag += 3
295
+ return CodeBlock(code, language, start_tag, end_tag)
296
+
297
+ @staticmethod
298
+ def _convert_markdown_by_line(text: str) -> str:
299
+ """
300
+ Convert markdown to HTML for each line in the given markdown text. Line breaks are expected to be represented
301
+ by break tags already.
302
+
303
+ :param text: The markdown text to convert.
304
+ :return: The HTML text.
305
+ """
306
+ html = []
307
+ lines = text.split("<br>")
308
+
309
+ in_unordered_list = False
310
+ in_ordered_list = False
311
+
312
+ for line in lines:
313
+ # Skip code blocks, as these have already been formatted.
314
+ # Also skip empty lines.
315
+ if "</code></pre>" in line or not line.strip():
316
+ html.append(line + "<br>")
317
+ continue
318
+ processed_line = HtmlFormatter._process_line(line.strip())
319
+
320
+ # Handle headings
321
+ if processed_line.startswith("# "):
322
+ HtmlFormatter._close_lists(html, in_unordered_list, in_ordered_list)
323
+ in_unordered_list = False
324
+ in_ordered_list = False
325
+ html.append(HtmlFormatter.header_1(processed_line[2:].strip()) + "<br>")
326
+ elif processed_line.startswith("## "):
327
+ HtmlFormatter._close_lists(html, in_unordered_list, in_ordered_list)
328
+ in_unordered_list = False
329
+ in_ordered_list = False
330
+ html.append(HtmlFormatter.header_2(processed_line[3:].strip()) + "<br>")
331
+ elif processed_line.startswith("### "):
332
+ HtmlFormatter._close_lists(html, in_unordered_list, in_ordered_list)
333
+ in_unordered_list = False
334
+ in_ordered_list = False
335
+ html.append(HtmlFormatter.header_3(processed_line[4:].strip()) + "<br>")
336
+ # Handle unordered lists
337
+ elif processed_line.startswith("* "):
338
+ if not in_unordered_list:
339
+ HtmlFormatter._close_lists(html, False, in_ordered_list) # Close any previous ordered list.
340
+ in_ordered_list = False
341
+ html.append("<ul>")
342
+ in_unordered_list = True
343
+ html.append("<li>" + HtmlFormatter.body(processed_line[2:].strip()) + "</li>")
344
+ # Handle ordered lists
345
+ elif re.match(r"^\d+\. .*", processed_line): # Matches "1. text"
346
+ if not in_ordered_list:
347
+ HtmlFormatter._close_lists(html, in_unordered_list, False) # Close any previous unordered list.
348
+ in_unordered_list = False
349
+ html.append("<ol>")
350
+ in_ordered_list = True
351
+ html.append(
352
+ "<li>" + HtmlFormatter.body(processed_line[processed_line.find('.') + 2:].strip()) + "</li>")
353
+
354
+ # Handle regular paragraphs
355
+ else:
356
+ HtmlFormatter._close_lists(html, in_unordered_list, in_ordered_list)
357
+ in_unordered_list = False
358
+ in_ordered_list = False
359
+ html.append(HtmlFormatter.body(processed_line.strip()) + "<br>")
360
+
361
+ # Close any open lists at the end
362
+ HtmlFormatter._close_lists(html, in_unordered_list, in_ordered_list)
363
+
364
+ return "".join(html)
365
+
366
+ @staticmethod
367
+ def _close_lists(text: list, in_unordered_list: bool, in_ordered_list: bool):
368
+ """
369
+ Close any open unordered or ordered lists in the given HTML string.
370
+
371
+ :param text: The HTML string to append to.
372
+ :param in_unordered_list: Whether an unordered list is currently open.
373
+ :param in_ordered_list: Whether an ordered list is currently open.
374
+ """
375
+ if in_unordered_list:
376
+ text.append("</ul>")
377
+ if in_ordered_list:
378
+ text.append("</ol>")
379
+
380
+ @staticmethod
381
+ def _process_line(line: str) -> str:
382
+ """
383
+ Process a single line of markdown text and convert it to HTML.
384
+
385
+ :param line: The line of markdown text to process.
386
+ :return: The HTML formatted line.
387
+ """
388
+ # Bold: **text**
389
+ line = re.sub(r"\*\*(.*?)\*\*", r"<strong>\1</strong>", line)
390
+
391
+ # Italic: *text*
392
+ line = re.sub(r"\*(.*?)\*", r"<em>\1</em>", line)
393
+
394
+ # Code: `text`
395
+ line = re.sub(r"`(.*?)`", r"<code>\1</code>", line)
396
+
397
+ return line
398
+
399
+
400
+ class CodeBlock:
401
+ """
402
+ A class representing a code block extracted from a response.
403
+ """
404
+ def __init__(self, code: str, language: str, start_index: int, end_index: int):
405
+ """
406
+ :param code: The text of the code block.
407
+ :param language: The language of the code block.
408
+ :param start_index: The index of the first character of the code block in the original response.
409
+ :param end_index: The index after the last character of the code block in the original response.
410
+ """
411
+ if code is None:
412
+ raise ValueError("Code cannot be None")
413
+ if language is None:
414
+ language = ""
415
+ if start_index < 0 or end_index < 0 or start_index > end_index:
416
+ raise ValueError("Invalid start or end index")
417
+
418
+ # Replace em spaces within code blocks with quadruple spaces and break tags with newlines.
419
+ # Code editors that the code is copy/pasted into might not recognize em spaces as valid indentation,
420
+ # and the library that adds the language-specific syntax highlighting expects newlines instead of break
421
+ # tags.
422
+ if "<br>" in code:
423
+ code = code.replace("<br>", "\n")
424
+ if "&emsp;" in code:
425
+ code = code.replace("&emsp;", " ")
426
+ # We don't want mixed whitespace, so replace all tabs with quad spaces.
427
+ if "\t" in code:
428
+ code = code.replace("\t", " ")
429
+
430
+ self.code = code
431
+ self.language = language.strip()
432
+ self.start_index = start_index
433
+ self.end_index = end_index
434
+
435
+ def to_html(self) -> str:
436
+ """
437
+ :return: The HTML representation of this code block.
438
+ """
439
+ start_tag: str
440
+ if self.language:
441
+ lang_class = f'class="language-{self.language}"'
442
+ start_tag = f"<pre {lang_class}><code {lang_class}>"
443
+ else:
444
+ start_tag = "<pre><code>"
445
+ end_tag = "</code></pre>"
446
+
447
+ return start_tag + self.code + end_tag
448
+
449
+ def to_markdown(self) -> str:
450
+ """
451
+ :return: The markdown representation of this code block.
452
+ """
453
+ start_tag = f"```{self.language}\n"
454
+ end_tag = "```" if self.code.endswith("\n") else "\n```"
455
+
456
+ return start_tag + self.code + end_tag
@@ -10,7 +10,8 @@ class SapioNavigationLinker:
10
10
  Given a URL to a system's webservice API (example: https://company.exemplareln.com/webservice/api), construct
11
11
  URLs for navigation links to various locations in the system.
12
12
  """
13
- base_url: str
13
+ client_url: str
14
+ webservice_url: str
14
15
 
15
16
  def __init__(self, url: str | SapioUser | SapioWebhookContext):
16
17
  """
@@ -21,7 +22,14 @@ class SapioNavigationLinker:
21
22
  url = url.user.url
22
23
  elif isinstance(url, SapioUser):
23
24
  url = url.url
24
- self.base_url = url.rstrip("/").replace('webservice/api', 'veloxClient')
25
+ self.webservice_url = url.rstrip("/")
26
+ self.client_url = url.rstrip("/").replace('webservice/api', 'veloxClient')
27
+
28
+ def homepage(self) -> str:
29
+ """
30
+ :return: A URL for navigating to the system's homepage.
31
+ """
32
+ return self.client_url + "/#view=homepage"
25
33
 
26
34
  def data_record(self, record_identifier: RecordIdentifier, data_type_name: DataTypeIdentifier | None = None) -> str:
27
35
  """
@@ -39,7 +47,7 @@ class SapioNavigationLinker:
39
47
  if not data_type_name:
40
48
  raise SapioException("Unable to create a data record link without a data type name. "
41
49
  "Only a record ID was provided.")
42
- return self.base_url + f"/#dataType={data_type_name};recordId={record_id};view=dataRecord"
50
+ return self.client_url + f"/#dataType={data_type_name};recordId={record_id};view=dataRecord"
43
51
 
44
52
  def experiment(self, experiment: ExperimentIdentifier) -> str:
45
53
  """
@@ -47,4 +55,4 @@ class SapioNavigationLinker:
47
55
  object, experiment protocol, or a notebook ID.
48
56
  :return: A URL for navigating to the input experiment.
49
57
  """
50
- return self.base_url + f"/#notebookExperimentId={AliasUtil.to_notebook_id(experiment)};view=eln"
58
+ return self.client_url + f"/#notebookExperimentId={AliasUtil.to_notebook_id(experiment)};view=eln"
@@ -105,8 +105,7 @@ class QueueItemHandler:
105
105
  """
106
106
  self.user = AliasUtil.to_sapio_user(context)
107
107
  self.rec_handler = RecordHandler(self.user)
108
- # PR-47565: Only initialize a ProcessQueueContext if the given context object has context_data.
109
- if isinstance(context, SapioWebhookContext) and context.context_data:
108
+ if isinstance(context, SapioWebhookContext):
110
109
  self.context = ProcessQueueContext(context)
111
110
  else:
112
111
  self.context = None