---------------------------------------------------------------------------
OptionalImportError Traceback (most recent call last)
Cell In[8], line 3
1 # Directly search for smoking status observations
----> 3 df_observations2 = search.steal_bundles_to_dataframe(
4 resource_type="Observation",
5 request_params={
6 "code": "http://loinc.org|72166-2", # LOINC code for smoking status
7 "_count": 20, # Get more observations since we're not limiting by patient
8 },
9 num_pages=1,
10 fhir_paths=[
11 ("observation_id", "id"),
12 ("patient", "subject.reference"),
13 ("status", "status"),
14 ("code", "code.coding[0].code"),
15 ("code_display", "code.coding[0].display"),
16 ("value", "valueCodeableConcept.coding[0].code"),
17 ("value_display", "valueCodeableConcept.coding[0].display"),
18 ("datetime", "effectiveDateTime"),
19 ],
20 )
22 # Look at the first row of the Observations DataFrame
23 df_observations2.head(15)
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:282, in Pirate.steal_bundles_to_dataframe(self, resource_type, request_params, num_pages, process_function, fhir_paths, build_df_after_query)
251 def steal_bundles_to_dataframe(
252 self,
253 resource_type: str,
(...) 258 build_df_after_query: bool = False,
259 ) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]:
260 """
261 Execute a request, iterates through the result pages, and builds a DataFrame with their
262 information. The DataFrames are either built after each
(...) 280 returned.
281 """
--> 282 return self._query_to_dataframe(self._get_bundles)(
283 resource_type=resource_type,
284 request_params=request_params,
285 num_pages=num_pages,
286 silence_tqdm=False,
287 process_function=process_function,
288 fhir_paths=fhir_paths,
289 build_df_after_query=build_df_after_query,
290 disable_multiprocessing_build=True,
291 always_return_dict=False,
292 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1441, in Pirate._query_to_dataframe.<locals>.wrap(process_function, fhir_paths, build_df_after_query, disable_multiprocessing_build, always_return_dict, *args, **kwargs)
1436 if fhir_paths is not None:
1437 logger.info(
1438 f"The selected process_function {process_function.__name__} will be "
1439 f"overwritten."
1440 )
-> 1441 process_function = self._set_up_fhirpath_function(fhir_paths)
1442 return self._bundles_to_dataframe(
1443 bundles=bundles_function(
1444 *args, **kwargs, tqdm_df_build=not build_df_after_query
(...) 1449 always_return_dict=always_return_dict,
1450 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1349, in Pirate._set_up_fhirpath_function(self, fhir_paths)
1331 if (
1332 re.search(pattern=rf"{token}[\.\[]|[\.\]]{token}$", string=path)
1333 is not None
1334 ):
1335 warnings.warn(
1336 f"You are using the term {token} in of your FHIR path {path}. "
1337 f"Please keep in mind that this token can be used a function according "
(...) 1346 stacklevel=2,
1347 )
1348 compiled_paths = [
-> 1349 (name, fhirpathpy.compile(path=path)) for name, path in fhir_paths_with_name
1350 ]
1351 return partial(parse_fhir_path, compiled_fhir_paths=compiled_paths)
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/util/imports.py:106, in optional_import.<locals>._LazyRaise.__getattr__(self, name)
101 def __getattr__(self, name: str) -> str:
102 """
103 Raise:
104 OptionalImportError: When you call this method.
105 """
--> 106 raise self._exception
[... skipping hidden 1 frame]
Cell In[4], line 2
1 # Instantiate and perform the FHIR search interaction in a single function call
----> 2 df = search.steal_bundles_to_dataframe(
3 resource_type="Patient",
4 request_params={
5 "_count": 10, # Get 10 instances per page
6 "identifier": "https://github.com/synthetichealth/synthea|",
7 },
8 num_pages=1, # Get 1 page (so a total of 10 instances)
9 fhir_paths=[("id", "identifier[0].value"), ("identifiers", "identifier.value")],
10 )
11 df
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:282, in Pirate.steal_bundles_to_dataframe(self, resource_type, request_params, num_pages, process_function, fhir_paths, build_df_after_query)
251 def steal_bundles_to_dataframe(
252 self,
253 resource_type: str,
(...) 258 build_df_after_query: bool = False,
259 ) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]:
260 """
261 Execute a request, iterates through the result pages, and builds a DataFrame with their
262 information. The DataFrames are either built after each
(...) 280 returned.
281 """
--> 282 return self._query_to_dataframe(self._get_bundles)(
283 resource_type=resource_type,
284 request_params=request_params,
285 num_pages=num_pages,
286 silence_tqdm=False,
287 process_function=process_function,
288 fhir_paths=fhir_paths,
289 build_df_after_query=build_df_after_query,
290 disable_multiprocessing_build=True,
291 always_return_dict=False,
292 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1441, in Pirate._query_to_dataframe.<locals>.wrap(process_function, fhir_paths, build_df_after_query, disable_multiprocessing_build, always_return_dict, *args, **kwargs)
1436 if fhir_paths is not None:
1437 logger.info(
1438 f"The selected process_function {process_function.__name__} will be "
1439 f"overwritten."
1440 )
-> 1441 process_function = self._set_up_fhirpath_function(fhir_paths)
1442 return self._bundles_to_dataframe(
1443 bundles=bundles_function(
1444 *args, **kwargs, tqdm_df_build=not build_df_after_query
(...) 1449 always_return_dict=always_return_dict,
1450 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1349, in Pirate._set_up_fhirpath_function(self, fhir_paths)
1331 if (
1332 re.search(pattern=rf"{token}[\.\[]|[\.\]]{token}$", string=path)
1333 is not None
1334 ):
1335 warnings.warn(
1336 f"You are using the term {token} in of your FHIR path {path}. "
1337 f"Please keep in mind that this token can be used a function according "
(...) 1346 stacklevel=2,
1347 )
1348 compiled_paths = [
-> 1349 (name, fhirpathpy.compile(path=path)) for name, path in fhir_paths_with_name
1350 ]
1351 return partial(parse_fhir_path, compiled_fhir_paths=compiled_paths)
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/util/imports.py:106, in optional_import.<locals>._LazyRaise.__getattr__(self, name)
101 def __getattr__(self, name: str) -> str:
102 """
103 Raise:
104 OptionalImportError: When you call this method.
105 """
--> 106 raise self._exception
[... skipping hidden 1 frame]
Cell In[3], line 2
1 # Instantiate and perform the FHIR search interaction in a single function call
----> 2 df = search.steal_bundles_to_dataframe(
3 resource_type="Patient",
4 request_params={
5 "_count": 10, # Get 10 instances per page
6 "identifier": "https://github.com/synthetichealth/synthea|",
7 },
8 num_pages=1, # Get 1 page (so a total of 10 instances)
9 fhir_paths=[
10 ("id", "identifier[0].value"),
11 ("gender", "gender"),
12 ("date_of_birth", "birthDate"),
13 ("marital_status", "maritalStatus.coding[0].code"),
14 ],
15 )
16 df
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:282, in Pirate.steal_bundles_to_dataframe(self, resource_type, request_params, num_pages, process_function, fhir_paths, build_df_after_query)
251 def steal_bundles_to_dataframe(
252 self,
253 resource_type: str,
(...) 258 build_df_after_query: bool = False,
259 ) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]:
260 """
261 Execute a request, iterates through the result pages, and builds a DataFrame with their
262 information. The DataFrames are either built after each
(...) 280 returned.
281 """
--> 282 return self._query_to_dataframe(self._get_bundles)(
283 resource_type=resource_type,
284 request_params=request_params,
285 num_pages=num_pages,
286 silence_tqdm=False,
287 process_function=process_function,
288 fhir_paths=fhir_paths,
289 build_df_after_query=build_df_after_query,
290 disable_multiprocessing_build=True,
291 always_return_dict=False,
292 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1441, in Pirate._query_to_dataframe.<locals>.wrap(process_function, fhir_paths, build_df_after_query, disable_multiprocessing_build, always_return_dict, *args, **kwargs)
1436 if fhir_paths is not None:
1437 logger.info(
1438 f"The selected process_function {process_function.__name__} will be "
1439 f"overwritten."
1440 )
-> 1441 process_function = self._set_up_fhirpath_function(fhir_paths)
1442 return self._bundles_to_dataframe(
1443 bundles=bundles_function(
1444 *args, **kwargs, tqdm_df_build=not build_df_after_query
(...) 1449 always_return_dict=always_return_dict,
1450 )
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/pirate.py:1349, in Pirate._set_up_fhirpath_function(self, fhir_paths)
1331 if (
1332 re.search(pattern=rf"{token}[\.\[]|[\.\]]{token}$", string=path)
1333 is not None
1334 ):
1335 warnings.warn(
1336 f"You are using the term {token} in of your FHIR path {path}. "
1337 f"Please keep in mind that this token can be used a function according "
(...) 1346 stacklevel=2,
1347 )
1348 compiled_paths = [
-> 1349 (name, fhirpathpy.compile(path=path)) for name, path in fhir_paths_with_name
1350 ]
1351 return partial(parse_fhir_path, compiled_fhir_paths=compiled_paths)
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/util/imports.py:106, in optional_import.<locals>._LazyRaise.__getattr__(self, name)
101 def __getattr__(self, name: str) -> str:
102 """
103 Raise:
104 OptionalImportError: When you call this method.
105 """
--> 106 raise self._exception
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhir_pyrate/util/imports.py:59, in optional_import(module, name, descriptor, allow_namespace_pkg)
57 actual_cmd = f"import {module}"
58 try:
---> 59 the_module = import_module(module)
60 if not allow_namespace_pkg:
61 is_namespace = getattr(the_module, "__file__", None) is None and hasattr(
62 the_module, "__path__"
63 )
File /opt/hostedtoolcache/Python/3.14.3/x64/lib/python3.14/importlib/__init__.py:88, in import_module(name, package)
86 break
87 level += 1
---> 88 return _bootstrap._gcd_import(name[level:], package, level)
File <frozen importlib._bootstrap>:1398, in _gcd_import(name, package, level)
1396 if level > 0:
1397 name = _resolve_name(name, package, level)
-> 1398 return _find_and_load(name, _gcd_import)
File <frozen importlib._bootstrap>:1371, in _find_and_load(name, import_)
1369 module = sys.modules.get(name, _NEEDS_LOADING)
1370 if module is _NEEDS_LOADING:
-> 1371 return _find_and_load_unlocked(name, import_)
1373 # Optimization: only call _bootstrap._lock_unlock_module() if
1374 # module.__spec__._initializing is True.
1375 # NOTE: because of this, initializing must be set *before*
1376 # putting the new module in sys.modules.
1377 _lock_unlock_module(name)
File <frozen importlib._bootstrap>:1342, in _find_and_load_unlocked(name, import_)
1340 parent_spec._uninitialized_submodules.append(child)
1341 try:
-> 1342 module = _load_unlocked(spec)
1343 finally:
1344 if parent_spec:
File <frozen importlib._bootstrap>:938, in _load_unlocked(spec)
935 raise ImportError('missing loader', name=spec.name)
936 # A namespace package so do nothing.
937 else:
--> 938 spec.loader.exec_module(module)
939 except:
940 try:
File <frozen importlib._bootstrap_external>:759, in _LoaderBasics.exec_module(self, module)
756 if code is None:
757 raise ImportError(f'cannot load module {module.__name__!r} when '
758 'get_code() returns None')
--> 759 _bootstrap._call_with_frames_removed(exec, code, module.__dict__)
File <frozen importlib._bootstrap>:491, in _call_with_frames_removed(f, *args, **kwds)
483 def _call_with_frames_removed(f, *args, **kwds):
484 """remove_importlib_frames in import.c will always remove sequences
485 of importlib frames that end with a call to this function
486
(...) 489 module code)
490 """
--> 491 return f(*args, **kwds)
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhirpathpy/__init__.py:2
1 from fhirpathpy.engine.invocations.constants import constants
----> 2 from fhirpathpy.parser import parse
3 from fhirpathpy.engine import do_eval
4 from fhirpathpy.engine.util import arraify, get_data, set_paths
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/fhirpathpy/parser/__init__.py:2
1 import sys
----> 2 from antlr4 import *
3 from antlr4.tree.Tree import ParseTreeWalker
4 from antlr4.error.ErrorListener import ErrorListener
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/antlr4/__init__.py:6
4 from antlr4.StdinStream import StdinStream
5 from antlr4.BufferedTokenStream import TokenStream
----> 6 from antlr4.CommonTokenStream import CommonTokenStream
7 from antlr4.Lexer import Lexer
8 from antlr4.Parser import Parser
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/antlr4/CommonTokenStream.py:33
1 #
2 # Copyright (c) 2012-2017 The ANTLR Project. All rights reserved.
3 # Use of this file is governed by the BSD 3-clause license that
(...) 29 # channel.</p>
30 #/
32 from antlr4.BufferedTokenStream import BufferedTokenStream
---> 33 from antlr4.Lexer import Lexer
34 from antlr4.Token import Token
37 class CommonTokenStream(BufferedTokenStream):
File ~/work/fhir-for-research/fhir-for-research/.venv/lib/python3.14/site-packages/antlr4/Lexer.py:12
1 # Copyright (c) 2012-2017 The ANTLR Project. All rights reserved.
2 # Use of this file is governed by the BSD 3-clause license that
3 # can be found in the LICENSE.txt file in the project root.
(...) 9 # of speed.
10 #/
11 from io import StringIO
---> 12 from typing.io import TextIO
13 import sys
14 from antlr4.CommonTokenFactory import CommonTokenFactory
OptionalImportError: import fhirpathpy (No module named 'typing.io'; 'typing' is not a package).