prompt: 
  We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  from_json does not correctly convert BulkDataURI's in SQ data elements
  **Describe the bug**
  When a DICOM object contains large data elements in SQ elements and is converted to JSON, those elements are correctly turned into BulkDataURI's. However, when the JSON is converted back to DICOM using from_json, the BulkDataURI's in SQ data elements are not converted back and warnings are thrown.
  
  **Expected behavior**
  The BulkDataURI's in SQ data elements get converted back correctly.
  
  **Steps To Reproduce**
  Take the `waveform_ecg.dcm` in the test data, convert it to JSON, and then convert the JSON to DICOM
  
  **Your environment**
  module       | version
  ------       | -------
  platform     | macOS-10.15.7-x86_64-i386-64bit
  Python       | 3.8.2 (v3.8.2:7b3ab5921f, Feb 24 2020, 17:52:18)  [Clang 6.0 (clang-600.0.57)]
  pydicom      | 2.1.0
  gdcm         | _module not found_
  jpeg_ls      | _module not found_
  numpy        | _module not found_
  PIL          | _module not found_
  
  The problem is in `jsonrep.py` at line 227. I plan on submitting a pull-request today for this.
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  
  --- BEGIN FILE ---
  ```
  ### pydicom/jsonrep.py
  # Copyright 2008-2019 pydicom authors. See LICENSE file for details.
  """Methods for converting Datasets and DataElements to/from json"""
  
  import base64
  from inspect import signature
  import inspect
  from typing import Callable, Optional, Union
  import warnings
  
  from pydicom.tag import BaseTag
  
  # Order of keys is significant!
  JSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)
  
  BINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',
                      'OB or OW', 'US or OW', 'US or SS or OW']
  VRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]
  VRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']
  
  
  def convert_to_python_number(value, vr):
      """Makes sure that values are either ints or floats
      based on their value representation.
  
      .. versionadded:: 1.4
  
      Parameters
      ----------
      value: Union[Union[str, int, float], List[Union[str, int, float]]]
          value of data element
      vr: str
          value representation of data element
  
      Returns
      -------
      Union[Union[str, int, float], List[Union[str, int, float]]]
  
      """
      if value is None:
          return None
      number_type = None
      if vr in VRs_TO_BE_INTS:
          number_type = int
      if vr in VRs_TO_BE_FLOATS:
          number_type = float
      if number_type is not None:
          if isinstance(value, (list, tuple,)):
              value = [number_type(e) for e in value]
          else:
              value = number_type(value)
      return value
  
  
  class JsonDataElementConverter:
      """Handles conversion between JSON struct and :class:`DataElement`.
  
      .. versionadded:: 1.4
      """
  
      def __init__(
          self,
          dataset_class,
          tag,
          vr,
          value,
          value_key,
          bulk_data_uri_handler: Optional[
              Union[
                  Callable[[BaseTag, str, str], object],
                  Callable[[str], object]
              ]
          ] = None
      ):
          """Create a new converter instance.
  
          Parameters
          ----------
          dataset_class : dataset.Dataset derived class
              Class used to create sequence items.
          tag : BaseTag
              The data element tag or int.
          vr : str
              The data element value representation.
          value : list
              The data element's value(s).
          value_key : str or None
              Key of the data element that contains the value
              (options: ``{"Value", "InlineBinary", "BulkDataURI"}``)
          bulk_data_uri_handler: callable or None
              Callable function that accepts either the tag, vr and "BulkDataURI"
              or just the "BulkDataURI" of the JSON
              representation of a data element and returns the actual value of
              that data element (retrieved via DICOMweb WADO-RS)
          """
          self.dataset_class = dataset_class
          self.tag = tag
          self.vr = vr
          self.value = value
          self.value_key = value_key
          if (
              bulk_data_uri_handler and
              len(signature(bulk_data_uri_handler).parameters) == 1
          ):
              def wrapped_bulk_data_handler(tag, vr, value):
                  return bulk_data_uri_handler(value)
              self.bulk_data_element_handler = wrapped_bulk_data_handler
          else:
              self.bulk_data_element_handler = bulk_data_uri_handler
  
      def get_element_values(self):
          """Return a the data element value or list of values.
  
          Returns
          -------
          str or bytes or int or float or dataset_class
          or PersonName or list of any of these types
              The value or value list of the newly created data element.
          """
          from pydicom.dataelem import empty_value_for_VR
          if self.value_key == 'Value':
              if not isinstance(self.value, list):
                  fmt = '"{}" of data element "{}" must be a list.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              if not self.value:
                  return empty_value_for_VR(self.vr)
              element_value = [self.get_regular_element_value(v)
                               for v in self.value]
              if len(element_value) == 1 and self.vr != 'SQ':
                  element_value = element_value[0]
              return convert_to_python_number(element_value, self.vr)
  
          # The value for "InlineBinary" shall be encoded as a base64 encoded
          # string, as shown in PS3.18, Table F.3.1-1, but the example in
          # PS3.18, Annex F.4 shows the string enclosed in a list.
          # We support both variants, as the standard is ambiguous here,
          # and do the same for "BulkDataURI".
          value = self.value
          if isinstance(value, list):
              value = value[0]
  
          if self.value_key == 'InlineBinary':
              if not isinstance(value, (str, bytes)):
                  fmt = '"{}" of data element "{}" must be a bytes-like object.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              return base64.b64decode(value)
  
          if self.value_key == 'BulkDataURI':
              if not isinstance(value, str):
                  fmt = '"{}" of data element "{}" must be a string.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              if self.bulk_data_element_handler is None:
                  warnings.warn(
                      'no bulk data URI handler provided for retrieval '
                      'of value of data element "{}"'.format(self.tag)
                  )
                  return empty_value_for_VR(self.vr, raw=True)
              return self.bulk_data_element_handler(self.tag, self.vr, value)
          return empty_value_for_VR(self.vr)
  
      def get_regular_element_value(self, value):
          """Return a the data element value created from a json "Value" entry.
  
          Parameters
          ----------
          value : str or int or float or dict
              The data element's value from the json entry.
  
          Returns
          -------
          dataset_class or PersonName
          or str or int or float
              A single value of the corresponding :class:`DataElement`.
          """
          if self.vr == 'SQ':
              return self.get_sequence_item(value)
  
          if self.vr == 'PN':
              return self.get_pn_element_value(value)
  
          if self.vr == 'AT':
              try:
                  return int(value, 16)
              except ValueError:
                  warnings.warn('Invalid value "{}" for AT element - '
                                'ignoring it'.format(value))
              return
          return value
  
      def get_sequence_item(self, value):
          """Return a sequence item for the JSON dict `value`.
  
          Parameters
          ----------
          value : dict or None
              The sequence item from the JSON entry.
  
          Returns
          -------
          dataset_class
              The decoded dataset item.
  
          Raises
          ------
          KeyError
              If the "vr" key is missing for a contained element
          """
          ds = self.dataset_class()
          if value:
              for key, val in value.items():
                  if 'vr' not in val:
                      fmt = 'Data element "{}" must have key "vr".'
                      raise KeyError(fmt.format(self.tag))
                  vr = val['vr']
                  unique_value_keys = tuple(
                      set(val.keys()) & set(JSON_VALUE_KEYS)
                  )
                  from pydicom import DataElement
                  from pydicom.dataelem import empty_value_for_VR
                  if not unique_value_keys:
                      # data element with no value
                      elem = DataElement(
                          tag=int(key, 16),
                          value=empty_value_for_VR(vr),
                          VR=vr)
                  else:
                      value_key = unique_value_keys[0]
                      elem = DataElement.from_json(
                          self.dataset_class, key, vr,
                          val[value_key], value_key
                      )
                  ds.add(elem)
          return ds
  
      def get_pn_element_value(self, value):
          """Return PersonName value from JSON value.
  
          Values with VR PN have a special JSON encoding, see the DICOM Standard,
          Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.
  
          Parameters
          ----------
          value : dict
              The person name components in the JSON entry.
  
          Returns
          -------
          PersonName or str
              The decoded PersonName object or an empty string.
          """
          if not isinstance(value, dict):
              # Some DICOMweb services get this wrong, so we
              # workaround the issue and warn the user
              # rather than raising an error.
              warnings.warn(
                  'value of data element "{}" with VR Person Name (PN) '
                  'is not formatted correctly'.format(self.tag)
              )
              return value
          else:
              if 'Phonetic' in value:
                  comps = ['', '', '']
              elif 'Ideographic' in value:
                  comps = ['', '']
              else:
                  comps = ['']
              if 'Alphabetic' in value:
                  comps[0] = value['Alphabetic']
              if 'Ideographic' in value:
                  comps[1] = value['Ideographic']
              if 'Phonetic' in value:
                  comps[2] = value['Phonetic']
              elem_value = '='.join(comps)
              return elem_value
  
  ```
  --- END FILE ---
  
  Please first localize the bug based on the issue statement, and then generate *SEARCH/REPLACE* edits to fix the issue.
  
  Every *SEARCH/REPLACE* edit must use this format:
  1. The file path
  2. The start of search block: <<<<<<< SEARCH
  3. A contiguous chunk of lines to search for in the existing source code
  4. The dividing line: =======
  5. The lines to replace into the source code
  6. The end of the replace block: >>>>>>> REPLACE
  
  Here is an example:
  
  ```python
  ### mathweb/flask/app.py
  <<<<<<< SEARCH
  from flask import Flask
  =======
  import math
  from flask import Flask
  >>>>>>> REPLACE
  ```
  
  Please note that the *SEARCH/REPLACE* edit REQUIRES PROPER INDENTATION. If you would like to add the line '        print(x)', you must fully write that out, with all those spaces before the code!
  Wrap the *SEARCH/REPLACE* edit in blocks ```python...```.
  
instance: {"FAIL_TO_PASS": "[\"pydicom/tests/test_json.py::TestBinary::test_bulk_data_reader_is_called_within_SQ\"]", "PASS_TO_PASS": "[\"pydicom/tests/test_json.py::TestPersonName::test_json_pn_from_file\", \"pydicom/tests/test_json.py::TestPersonName::test_pn_components_to_json\", \"pydicom/tests/test_json.py::TestPersonName::test_pn_components_from_json\", \"pydicom/tests/test_json.py::TestPersonName::test_empty_value\", \"pydicom/tests/test_json.py::TestPersonName::test_multi_value_to_json\", \"pydicom/tests/test_json.py::TestPersonName::test_dataelem_from_json\", \"pydicom/tests/test_json.py::TestAT::test_to_json\", \"pydicom/tests/test_json.py::TestAT::test_from_json\", \"pydicom/tests/test_json.py::TestAT::test_invalid_value_in_json\", \"pydicom/tests/test_json.py::TestAT::test_invalid_tag_in_json\", \"pydicom/tests/test_json.py::TestDataSetToJson::test_json_from_dicom_file\", \"pydicom/tests/test_json.py::TestDataSetToJson::test_roundtrip\", \"pydicom/tests/test_json.py::TestDataSetToJson::test_dataset_dumphandler\", \"pydicom/tests/test_json.py::TestDataSetToJson::test_dataelement_dumphandler\", \"pydicom/tests/test_json.py::TestDataSetToJson::test_sort_order\", \"pydicom/tests/test_json.py::TestSequence::test_nested_sequences\", \"pydicom/tests/test_json.py::TestBinary::test_inline_binary\", \"pydicom/tests/test_json.py::TestBinary::test_invalid_inline_binary\", \"pydicom/tests/test_json.py::TestBinary::test_valid_bulkdata_uri\", \"pydicom/tests/test_json.py::TestBinary::test_invalid_bulkdata_uri\", \"pydicom/tests/test_json.py::TestBinary::test_bulk_data_reader_is_called\", \"pydicom/tests/test_json.py::TestBinary::test_bulk_data_reader_is_called_2\"]", "base_commit": "49a3da4a3d9c24d7e8427a25048a1c7d5c4f7724", "created_at": "2020-11-04T21:13:33Z", "environment_setup_commit": "506ecea8f378dc687d5c504788fc78810a190b7a", "hints_text": "", "instance_id": "pydicom__pydicom-1256", "patch": "diff --git a/pydicom/jsonrep.py b/pydicom/jsonrep.py\n--- a/pydicom/jsonrep.py\n+++ b/pydicom/jsonrep.py\n@@ -226,7 +226,8 @@ def get_sequence_item(self, value):\n                     value_key = unique_value_keys[0]\n                     elem = DataElement.from_json(\n                         self.dataset_class, key, vr,\n-                        val[value_key], value_key\n+                        val[value_key], value_key,\n+                        self.bulk_data_element_handler\n                     )\n                 ds.add(elem)\n         return ds\n", "problem_statement": "from_json does not correctly convert BulkDataURI's in SQ data elements\n**Describe the bug**\r\nWhen a DICOM object contains large data elements in SQ elements and is converted to JSON, those elements are correctly turned into BulkDataURI's. However, when the JSON is converted back to DICOM using from_json, the BulkDataURI's in SQ data elements are not converted back and warnings are thrown.\r\n\r\n**Expected behavior**\r\nThe BulkDataURI's in SQ data elements get converted back correctly.\r\n\r\n**Steps To Reproduce**\r\nTake the `waveform_ecg.dcm` in the test data, convert it to JSON, and then convert the JSON to DICOM\r\n\r\n**Your environment**\r\nmodule       | version\r\n------       | -------\r\nplatform     | macOS-10.15.7-x86_64-i386-64bit\r\nPython       | 3.8.2 (v3.8.2:7b3ab5921f, Feb 24 2020, 17:52:18)  [Clang 6.0 (clang-600.0.57)]\r\npydicom      | 2.1.0\r\ngdcm         | _module not found_\r\njpeg_ls      | _module not found_\r\nnumpy        | _module not found_\r\nPIL          | _module not found_\r\n\r\nThe problem is in `jsonrep.py` at line 227. I plan on submitting a pull-request today for this.\n", "repo": "pydicom/pydicom", "test_patch": "diff --git a/pydicom/tests/test_json.py b/pydicom/tests/test_json.py\n--- a/pydicom/tests/test_json.py\n+++ b/pydicom/tests/test_json.py\n@@ -354,3 +354,25 @@ def bulk_data_reader(tag, vr, value):\n         ds = Dataset().from_json(json.dumps(json_data), bulk_data_reader)\n \n         assert b'xyzzy' == ds[0x00091002].value\n+\n+    def test_bulk_data_reader_is_called_within_SQ(self):\n+        def bulk_data_reader(_):\n+            return b'xyzzy'\n+\n+        json_data = {\n+            \"003a0200\": {\n+                \"vr\": \"SQ\", \n+                \"Value\": [\n+                    {\n+                        \"54001010\": {\n+                            \"vr\": \"OW\",\n+                            \"BulkDataURI\": \"https://a.dummy.url\"\n+                        }\n+                    }\n+                ]\n+            }\n+        }\n+\n+        ds = Dataset().from_json(json.dumps(json_data), bulk_data_reader)\n+\n+        assert b'xyzzy' == ds[0x003a0200].value[0][0x54001010].value\n", "version": "2.1"}
parsed_commit_content: {"file_diffs":[{"old_file_content":"# Copyright 2008-2019 pydicom authors. See LICENSE file for details.\n\"\"\"Methods for converting Datasets and DataElements to/from json\"\"\"\n\nimport base64\nfrom inspect import signature\nimport inspect\nfrom typing import Callable, Optional, Union\nimport warnings\n\nfrom pydicom.tag import BaseTag\n\n# Order of keys is significant!\nJSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)\n\nBINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',\n                    'OB or OW', 'US or OW', 'US or SS or OW']\nVRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]\nVRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']\n\n\ndef convert_to_python_number(value, vr):\n    \"\"\"Makes sure that values are either ints or floats\n    based on their value representation.\n\n    .. versionadded:: 1.4\n\n    Parameters\n    ----------\n    value: Union[Union[str, int, float], List[Union[str, int, float]]]\n        value of data element\n    vr: str\n        value representation of data element\n\n    Returns\n    -------\n    Union[Union[str, int, float], List[Union[str, int, float]]]\n\n    \"\"\"\n    if value is None:\n        return None\n    number_type = None\n    if vr in VRs_TO_BE_INTS:\n        number_type = int\n    if vr in VRs_TO_BE_FLOATS:\n        number_type = float\n    if number_type is not None:\n        if isinstance(value, (list, tuple,)):\n            value = [number_type(e) for e in value]\n        else:\n            value = number_type(value)\n    return value\n\n\nclass JsonDataElementConverter:\n    \"\"\"Handles conversion between JSON struct and :class:`DataElement`.\n\n    .. versionadded:: 1.4\n    \"\"\"\n\n    def __init__(\n        self,\n        dataset_class,\n        tag,\n        vr,\n        value,\n        value_key,\n        bulk_data_uri_handler: Optional[\n            Union[\n                Callable[[BaseTag, str, str], object],\n                Callable[[str], object]\n            ]\n        ] = None\n    ):\n        \"\"\"Create a new converter instance.\n\n        Parameters\n        ----------\n        dataset_class : dataset.Dataset derived class\n            Class used to create sequence items.\n        tag : BaseTag\n            The data element tag or int.\n        vr : str\n            The data element value representation.\n        value : list\n            The data element's value(s).\n        value_key : str or None\n            Key of the data element that contains the value\n            (options: ``{\"Value\", \"InlineBinary\", \"BulkDataURI\"}``)\n        bulk_data_uri_handler: callable or None\n            Callable function that accepts either the tag, vr and \"BulkDataURI\"\n            or just the \"BulkDataURI\" of the JSON\n            representation of a data element and returns the actual value of\n            that data element (retrieved via DICOMweb WADO-RS)\n        \"\"\"\n        self.dataset_class = dataset_class\n        self.tag = tag\n        self.vr = vr\n        self.value = value\n        self.value_key = value_key\n        if (\n            bulk_data_uri_handler and\n            len(signature(bulk_data_uri_handler).parameters) == 1\n        ):\n            def wrapped_bulk_data_handler(tag, vr, value):\n                return bulk_data_uri_handler(value)\n            self.bulk_data_element_handler = wrapped_bulk_data_handler\n        else:\n            self.bulk_data_element_handler = bulk_data_uri_handler\n\n    def get_element_values(self):\n        \"\"\"Return a the data element value or list of values.\n\n        Returns\n        -------\n        str or bytes or int or float or dataset_class\n        or PersonName or list of any of these types\n            The value or value list of the newly created data element.\n        \"\"\"\n        from pydicom.dataelem import empty_value_for_VR\n        if self.value_key == 'Value':\n            if not isinstance(self.value, list):\n                fmt = '\"{}\" of data element \"{}\" must be a list.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if not self.value:\n                return empty_value_for_VR(self.vr)\n            element_value = [self.get_regular_element_value(v)\n                             for v in self.value]\n            if len(element_value) == 1 and self.vr != 'SQ':\n                element_value = element_value[0]\n            return convert_to_python_number(element_value, self.vr)\n\n        # The value for \"InlineBinary\" shall be encoded as a base64 encoded\n        # string, as shown in PS3.18, Table F.3.1-1, but the example in\n        # PS3.18, Annex F.4 shows the string enclosed in a list.\n        # We support both variants, as the standard is ambiguous here,\n        # and do the same for \"BulkDataURI\".\n        value = self.value\n        if isinstance(value, list):\n            value = value[0]\n\n        if self.value_key == 'InlineBinary':\n            if not isinstance(value, (str, bytes)):\n                fmt = '\"{}\" of data element \"{}\" must be a bytes-like object.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            return base64.b64decode(value)\n\n        if self.value_key == 'BulkDataURI':\n            if not isinstance(value, str):\n                fmt = '\"{}\" of data element \"{}\" must be a string.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if self.bulk_data_element_handler is None:\n                warnings.warn(\n                    'no bulk data URI handler provided for retrieval '\n                    'of value of data element \"{}\"'.format(self.tag)\n                )\n                return empty_value_for_VR(self.vr, raw=True)\n            return self.bulk_data_element_handler(self.tag, self.vr, value)\n        return empty_value_for_VR(self.vr)\n\n    def get_regular_element_value(self, value):\n        \"\"\"Return a the data element value created from a json \"Value\" entry.\n\n        Parameters\n        ----------\n        value : str or int or float or dict\n            The data element's value from the json entry.\n\n        Returns\n        -------\n        dataset_class or PersonName\n        or str or int or float\n            A single value of the corresponding :class:`DataElement`.\n        \"\"\"\n        if self.vr == 'SQ':\n            return self.get_sequence_item(value)\n\n        if self.vr == 'PN':\n            return self.get_pn_element_value(value)\n\n        if self.vr == 'AT':\n            try:\n                return int(value, 16)\n            except ValueError:\n                warnings.warn('Invalid value \"{}\" for AT element - '\n                              'ignoring it'.format(value))\n            return\n        return value\n\n    def get_sequence_item(self, value):\n        \"\"\"Return a sequence item for the JSON dict `value`.\n\n        Parameters\n        ----------\n        value : dict or None\n            The sequence item from the JSON entry.\n\n        Returns\n        -------\n        dataset_class\n            The decoded dataset item.\n\n        Raises\n        ------\n        KeyError\n            If the \"vr\" key is missing for a contained element\n        \"\"\"\n        ds = self.dataset_class()\n        if value:\n            for key, val in value.items():\n                if 'vr' not in val:\n                    fmt = 'Data element \"{}\" must have key \"vr\".'\n                    raise KeyError(fmt.format(self.tag))\n                vr = val['vr']\n                unique_value_keys = tuple(\n                    set(val.keys()) & set(JSON_VALUE_KEYS)\n                )\n                from pydicom import DataElement\n                from pydicom.dataelem import empty_value_for_VR\n                if not unique_value_keys:\n                    # data element with no value\n                    elem = DataElement(\n                        tag=int(key, 16),\n                        value=empty_value_for_VR(vr),\n                        VR=vr)\n                else:\n                    value_key = unique_value_keys[0]\n                    elem = DataElement.from_json(\n                        self.dataset_class, key, vr,\n                        val[value_key], value_key\n                    )\n                ds.add(elem)\n        return ds\n\n    def get_pn_element_value(self, value):\n        \"\"\"Return PersonName value from JSON value.\n\n        Values with VR PN have a special JSON encoding, see the DICOM Standard,\n        Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.\n\n        Parameters\n        ----------\n        value : dict\n            The person name components in the JSON entry.\n\n        Returns\n        -------\n        PersonName or str\n            The decoded PersonName object or an empty string.\n        \"\"\"\n        if not isinstance(value, dict):\n            # Some DICOMweb services get this wrong, so we\n            # workaround the issue and warn the user\n            # rather than raising an error.\n            warnings.warn(\n                'value of data element \"{}\" with VR Person Name (PN) '\n                'is not formatted correctly'.format(self.tag)\n            )\n            return value\n        else:\n            if 'Phonetic' in value:\n                comps = ['', '', '']\n            elif 'Ideographic' in value:\n                comps = ['', '']\n            else:\n                comps = ['']\n            if 'Alphabetic' in value:\n                comps[0] = value['Alphabetic']\n            if 'Ideographic' in value:\n                comps[1] = value['Ideographic']\n            if 'Phonetic' in value:\n                comps[2] = value['Phonetic']\n            elem_value = '='.join(comps)\n            return elem_value\n","new_file_content":"# Copyright 2008-2019 pydicom authors. See LICENSE file for details.\n\"\"\"Methods for converting Datasets and DataElements to/from json\"\"\"\n\nimport base64\nfrom inspect import signature\nimport inspect\nfrom typing import Callable, Optional, Union\nimport warnings\n\nfrom pydicom.tag import BaseTag\n\n# Order of keys is significant!\nJSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)\n\nBINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',\n                    'OB or OW', 'US or OW', 'US or SS or OW']\nVRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]\nVRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']\n\n\ndef convert_to_python_number(value, vr):\n    \"\"\"Makes sure that values are either ints or floats\n    based on their value representation.\n\n    .. versionadded:: 1.4\n\n    Parameters\n    ----------\n    value: Union[Union[str, int, float], List[Union[str, int, float]]]\n        value of data element\n    vr: str\n        value representation of data element\n\n    Returns\n    -------\n    Union[Union[str, int, float], List[Union[str, int, float]]]\n\n    \"\"\"\n    if value is None:\n        return None\n    number_type = None\n    if vr in VRs_TO_BE_INTS:\n        number_type = int\n    if vr in VRs_TO_BE_FLOATS:\n        number_type = float\n    if number_type is not None:\n        if isinstance(value, (list, tuple,)):\n            value = [number_type(e) for e in value]\n        else:\n            value = number_type(value)\n    return value\n\n\nclass JsonDataElementConverter:\n    \"\"\"Handles conversion between JSON struct and :class:`DataElement`.\n\n    .. versionadded:: 1.4\n    \"\"\"\n\n    def __init__(\n        self,\n        dataset_class,\n        tag,\n        vr,\n        value,\n        value_key,\n        bulk_data_uri_handler: Optional[\n            Union[\n                Callable[[BaseTag, str, str], object],\n                Callable[[str], object]\n            ]\n        ] = None\n    ):\n        \"\"\"Create a new converter instance.\n\n        Parameters\n        ----------\n        dataset_class : dataset.Dataset derived class\n            Class used to create sequence items.\n        tag : BaseTag\n            The data element tag or int.\n        vr : str\n            The data element value representation.\n        value : list\n            The data element's value(s).\n        value_key : str or None\n            Key of the data element that contains the value\n            (options: ``{\"Value\", \"InlineBinary\", \"BulkDataURI\"}``)\n        bulk_data_uri_handler: callable or None\n            Callable function that accepts either the tag, vr and \"BulkDataURI\"\n            or just the \"BulkDataURI\" of the JSON\n            representation of a data element and returns the actual value of\n            that data element (retrieved via DICOMweb WADO-RS)\n        \"\"\"\n        self.dataset_class = dataset_class\n        self.tag = tag\n        self.vr = vr\n        self.value = value\n        self.value_key = value_key\n        if (\n            bulk_data_uri_handler and\n            len(signature(bulk_data_uri_handler).parameters) == 1\n        ):\n            def wrapped_bulk_data_handler(tag, vr, value):\n                return bulk_data_uri_handler(value)\n            self.bulk_data_element_handler = wrapped_bulk_data_handler\n        else:\n            self.bulk_data_element_handler = bulk_data_uri_handler\n\n    def get_element_values(self):\n        \"\"\"Return a the data element value or list of values.\n\n        Returns\n        -------\n        str or bytes or int or float or dataset_class\n        or PersonName or list of any of these types\n            The value or value list of the newly created data element.\n        \"\"\"\n        from pydicom.dataelem import empty_value_for_VR\n        if self.value_key == 'Value':\n            if not isinstance(self.value, list):\n                fmt = '\"{}\" of data element \"{}\" must be a list.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if not self.value:\n                return empty_value_for_VR(self.vr)\n            element_value = [self.get_regular_element_value(v)\n                             for v in self.value]\n            if len(element_value) == 1 and self.vr != 'SQ':\n                element_value = element_value[0]\n            return convert_to_python_number(element_value, self.vr)\n\n        # The value for \"InlineBinary\" shall be encoded as a base64 encoded\n        # string, as shown in PS3.18, Table F.3.1-1, but the example in\n        # PS3.18, Annex F.4 shows the string enclosed in a list.\n        # We support both variants, as the standard is ambiguous here,\n        # and do the same for \"BulkDataURI\".\n        value = self.value\n        if isinstance(value, list):\n            value = value[0]\n\n        if self.value_key == 'InlineBinary':\n            if not isinstance(value, (str, bytes)):\n                fmt = '\"{}\" of data element \"{}\" must be a bytes-like object.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            return base64.b64decode(value)\n\n        if self.value_key == 'BulkDataURI':\n            if not isinstance(value, str):\n                fmt = '\"{}\" of data element \"{}\" must be a string.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if self.bulk_data_element_handler is None:\n                warnings.warn(\n                    'no bulk data URI handler provided for retrieval '\n                    'of value of data element \"{}\"'.format(self.tag)\n                )\n                return empty_value_for_VR(self.vr, raw=True)\n            return self.bulk_data_element_handler(self.tag, self.vr, value)\n        return empty_value_for_VR(self.vr)\n\n    def get_regular_element_value(self, value):\n        \"\"\"Return a the data element value created from a json \"Value\" entry.\n\n        Parameters\n        ----------\n        value : str or int or float or dict\n            The data element's value from the json entry.\n\n        Returns\n        -------\n        dataset_class or PersonName\n        or str or int or float\n            A single value of the corresponding :class:`DataElement`.\n        \"\"\"\n        if self.vr == 'SQ':\n            return self.get_sequence_item(value)\n\n        if self.vr == 'PN':\n            return self.get_pn_element_value(value)\n\n        if self.vr == 'AT':\n            try:\n                return int(value, 16)\n            except ValueError:\n                warnings.warn('Invalid value \"{}\" for AT element - '\n                              'ignoring it'.format(value))\n            return\n        return value\n\n    def get_sequence_item(self, value):\n        \"\"\"Return a sequence item for the JSON dict `value`.\n\n        Parameters\n        ----------\n        value : dict or None\n            The sequence item from the JSON entry.\n\n        Returns\n        -------\n        dataset_class\n            The decoded dataset item.\n\n        Raises\n        ------\n        KeyError\n            If the \"vr\" key is missing for a contained element\n        \"\"\"\n        ds = self.dataset_class()\n        if value:\n            for key, val in value.items():\n                if 'vr' not in val:\n                    fmt = 'Data element \"{}\" must have key \"vr\".'\n                    raise KeyError(fmt.format(self.tag))\n                vr = val['vr']\n                unique_value_keys = tuple(\n                    set(val.keys()) & set(JSON_VALUE_KEYS)\n                )\n                from pydicom import DataElement\n                from pydicom.dataelem import empty_value_for_VR\n                if not unique_value_keys:\n                    # data element with no value\n                    elem = DataElement(\n                        tag=int(key, 16),\n                        value=empty_value_for_VR(vr),\n                        VR=vr)\n                else:\n                    value_key = unique_value_keys[0]\n                    elem = DataElement.from_json(\n                        self.dataset_class, key, vr,\n                        val[value_key], value_key,\n                        self.bulk_data_element_handler\n                    )\n                ds.add(elem)\n        return ds\n\n    def get_pn_element_value(self, value):\n        \"\"\"Return PersonName value from JSON value.\n\n        Values with VR PN have a special JSON encoding, see the DICOM Standard,\n        Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.\n\n        Parameters\n        ----------\n        value : dict\n            The person name components in the JSON entry.\n\n        Returns\n        -------\n        PersonName or str\n            The decoded PersonName object or an empty string.\n        \"\"\"\n        if not isinstance(value, dict):\n            # Some DICOMweb services get this wrong, so we\n            # workaround the issue and warn the user\n            # rather than raising an error.\n            warnings.warn(\n                'value of data element \"{}\" with VR Person Name (PN) '\n                'is not formatted correctly'.format(self.tag)\n            )\n            return value\n        else:\n            if 'Phonetic' in value:\n                comps = ['', '', '']\n            elif 'Ideographic' in value:\n                comps = ['', '']\n            else:\n                comps = ['']\n            if 'Alphabetic' in value:\n                comps[0] = value['Alphabetic']\n            if 'Ideographic' in value:\n                comps[1] = value['Ideographic']\n            if 'Phonetic' in value:\n                comps[2] = value['Phonetic']\n            elem_value = '='.join(comps)\n            return elem_value\n","header":{"file":{"path":"pydicom/jsonrep.py"},"misc_line":null},"index_line":null,"is_binary_file":false,"binary_line":null,"minus_file":{"path":"a/pydicom/jsonrep.py"},"plus_file":{"path":"b/pydicom/jsonrep.py"},"hunks":[{"descriptor":{"old_range":{"start":226,"length":7},"new_range":{"start":226,"length":8},"section":"def get_sequence_item(self, value):"},"line_group":{"all_lines":[{"content":"                    value_key = unique_value_keys[0]","type":"context"},{"content":"                    elem = DataElement.from_json(","type":"context"},{"content":"                        self.dataset_class, key, vr,","type":"context"},{"content":"                        val[value_key], value_key","type":"deleted"},{"content":"                        val[value_key], value_key,","type":"added"},{"content":"                        self.bulk_data_element_handler","type":"added"},{"content":"                    )","type":"context"},{"content":"                ds.add(elem)","type":"context"},{"content":"        return ds","type":"context"},{"content":"","type":"context"}]},"modified_entities":[],"added_entities":[],"deleted_entities":[]}]}],"old_commit_hash":"49a3da4a3d9c24d7e8427a25048a1c7d5c4f7724","new_commit_hash":"0e803d7dc54ec8d3d134400ed54d5447818fb78f","commit_message":"ensured that the bulk_data_uri_handler is called","commit_date":"2020-11-04T15:10:28-06:00","metadata":{}}
problem_statement: from_json does not correctly convert BulkDataURI's in SQ data elements
  **Describe the bug**
  When a DICOM object contains large data elements in SQ elements and is converted to JSON, those elements are correctly turned into BulkDataURI's. However, when the JSON is converted back to DICOM using from_json, the BulkDataURI's in SQ data elements are not converted back and warnings are thrown.
  
  **Expected behavior**
  The BulkDataURI's in SQ data elements get converted back correctly.
  
  **Steps To Reproduce**
  Take the `waveform_ecg.dcm` in the test data, convert it to JSON, and then convert the JSON to DICOM
  
  **Your environment**
  module       | version
  ------       | -------
  platform     | macOS-10.15.7-x86_64-i386-64bit
  Python       | 3.8.2 (v3.8.2:7b3ab5921f, Feb 24 2020, 17:52:18)  [Clang 6.0 (clang-600.0.57)]
  pydicom      | 2.1.0
  gdcm         | _module not found_
  jpeg_ls      | _module not found_
  numpy        | _module not found_
  PIL          | _module not found_
  
  The problem is in `jsonrep.py` at line 227. I plan on submitting a pull-request today for this.
  
patch: diff --git a/pydicom/jsonrep.py b/pydicom/jsonrep.py
  --- a/pydicom/jsonrep.py
  +++ b/pydicom/jsonrep.py
  @@ -226,7 +226,8 @@ def get_sequence_item(self, value):
                       value_key = unique_value_keys[0]
                       elem = DataElement.from_json(
                           self.dataset_class, key, vr,
  -                        val[value_key], value_key
  +                        val[value_key], value_key,
  +                        self.bulk_data_element_handler
                       )
                   ds.add(elem)
           return ds
   
  
file_context: {"pydicom/jsonrep.py": "# Copyright 2008-2019 pydicom authors. See LICENSE file for details.\n\"\"\"Methods for converting Datasets and DataElements to/from json\"\"\"\n\nimport base64\nfrom inspect import signature\nimport inspect\nfrom typing import Callable, Optional, Union\nimport warnings\n\nfrom pydicom.tag import BaseTag\n\n# Order of keys is significant!\nJSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)\n\nBINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',\n                    'OB or OW', 'US or OW', 'US or SS or OW']\nVRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]\nVRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']\n\n\ndef convert_to_python_number(value, vr):\n    \"\"\"Makes sure that values are either ints or floats\n    based on their value representation.\n\n    .. versionadded:: 1.4\n\n    Parameters\n    ----------\n    value: Union[Union[str, int, float], List[Union[str, int, float]]]\n        value of data element\n    vr: str\n        value representation of data element\n\n    Returns\n    -------\n    Union[Union[str, int, float], List[Union[str, int, float]]]\n\n    \"\"\"\n    if value is None:\n        return None\n    number_type = None\n    if vr in VRs_TO_BE_INTS:\n        number_type = int\n    if vr in VRs_TO_BE_FLOATS:\n        number_type = float\n    if number_type is not None:\n        if isinstance(value, (list, tuple,)):\n            value = [number_type(e) for e in value]\n        else:\n            value = number_type(value)\n    return value\n\n\nclass JsonDataElementConverter:\n    \"\"\"Handles conversion between JSON struct and :class:`DataElement`.\n\n    .. versionadded:: 1.4\n    \"\"\"\n\n    def __init__(\n        self,\n        dataset_class,\n        tag,\n        vr,\n        value,\n        value_key,\n        bulk_data_uri_handler: Optional[\n            Union[\n                Callable[[BaseTag, str, str], object],\n                Callable[[str], object]\n            ]\n        ] = None\n    ):\n        \"\"\"Create a new converter instance.\n\n        Parameters\n        ----------\n        dataset_class : dataset.Dataset derived class\n            Class used to create sequence items.\n        tag : BaseTag\n            The data element tag or int.\n        vr : str\n            The data element value representation.\n        value : list\n            The data element's value(s).\n        value_key : str or None\n            Key of the data element that contains the value\n            (options: ``{\"Value\", \"InlineBinary\", \"BulkDataURI\"}``)\n        bulk_data_uri_handler: callable or None\n            Callable function that accepts either the tag, vr and \"BulkDataURI\"\n            or just the \"BulkDataURI\" of the JSON\n            representation of a data element and returns the actual value of\n            that data element (retrieved via DICOMweb WADO-RS)\n        \"\"\"\n        self.dataset_class = dataset_class\n        self.tag = tag\n        self.vr = vr\n        self.value = value\n        self.value_key = value_key\n        if (\n            bulk_data_uri_handler and\n            len(signature(bulk_data_uri_handler).parameters) == 1\n        ):\n            def wrapped_bulk_data_handler(tag, vr, value):\n                return bulk_data_uri_handler(value)\n            self.bulk_data_element_handler = wrapped_bulk_data_handler\n        else:\n            self.bulk_data_element_handler = bulk_data_uri_handler\n\n    def get_element_values(self):\n        \"\"\"Return a the data element value or list of values.\n\n        Returns\n        -------\n        str or bytes or int or float or dataset_class\n        or PersonName or list of any of these types\n            The value or value list of the newly created data element.\n        \"\"\"\n        from pydicom.dataelem import empty_value_for_VR\n        if self.value_key == 'Value':\n            if not isinstance(self.value, list):\n                fmt = '\"{}\" of data element \"{}\" must be a list.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if not self.value:\n                return empty_value_for_VR(self.vr)\n            element_value = [self.get_regular_element_value(v)\n                             for v in self.value]\n            if len(element_value) == 1 and self.vr != 'SQ':\n                element_value = element_value[0]\n            return convert_to_python_number(element_value, self.vr)\n\n        # The value for \"InlineBinary\" shall be encoded as a base64 encoded\n        # string, as shown in PS3.18, Table F.3.1-1, but the example in\n        # PS3.18, Annex F.4 shows the string enclosed in a list.\n        # We support both variants, as the standard is ambiguous here,\n        # and do the same for \"BulkDataURI\".\n        value = self.value\n        if isinstance(value, list):\n            value = value[0]\n\n        if self.value_key == 'InlineBinary':\n            if not isinstance(value, (str, bytes)):\n                fmt = '\"{}\" of data element \"{}\" must be a bytes-like object.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            return base64.b64decode(value)\n\n        if self.value_key == 'BulkDataURI':\n            if not isinstance(value, str):\n                fmt = '\"{}\" of data element \"{}\" must be a string.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if self.bulk_data_element_handler is None:\n                warnings.warn(\n                    'no bulk data URI handler provided for retrieval '\n                    'of value of data element \"{}\"'.format(self.tag)\n                )\n                return empty_value_for_VR(self.vr, raw=True)\n            return self.bulk_data_element_handler(self.tag, self.vr, value)\n        return empty_value_for_VR(self.vr)\n\n    def get_regular_element_value(self, value):\n        \"\"\"Return a the data element value created from a json \"Value\" entry.\n\n        Parameters\n        ----------\n        value : str or int or float or dict\n            The data element's value from the json entry.\n\n        Returns\n        -------\n        dataset_class or PersonName\n        or str or int or float\n            A single value of the corresponding :class:`DataElement`.\n        \"\"\"\n        if self.vr == 'SQ':\n            return self.get_sequence_item(value)\n\n        if self.vr == 'PN':\n            return self.get_pn_element_value(value)\n\n        if self.vr == 'AT':\n            try:\n                return int(value, 16)\n            except ValueError:\n                warnings.warn('Invalid value \"{}\" for AT element - '\n                              'ignoring it'.format(value))\n            return\n        return value\n\n    def get_sequence_item(self, value):\n        \"\"\"Return a sequence item for the JSON dict `value`.\n\n        Parameters\n        ----------\n        value : dict or None\n            The sequence item from the JSON entry.\n\n        Returns\n        -------\n        dataset_class\n            The decoded dataset item.\n\n        Raises\n        ------\n        KeyError\n            If the \"vr\" key is missing for a contained element\n        \"\"\"\n        ds = self.dataset_class()\n        if value:\n            for key, val in value.items():\n                if 'vr' not in val:\n                    fmt = 'Data element \"{}\" must have key \"vr\".'\n                    raise KeyError(fmt.format(self.tag))\n                vr = val['vr']\n                unique_value_keys = tuple(\n                    set(val.keys()) & set(JSON_VALUE_KEYS)\n                )\n                from pydicom import DataElement\n                from pydicom.dataelem import empty_value_for_VR\n                if not unique_value_keys:\n                    # data element with no value\n                    elem = DataElement(\n                        tag=int(key, 16),\n                        value=empty_value_for_VR(vr),\n                        VR=vr)\n                else:\n                    value_key = unique_value_keys[0]\n                    elem = DataElement.from_json(\n                        self.dataset_class, key, vr,\n                        val[value_key], value_key\n                    )\n                ds.add(elem)\n        return ds\n\n    def get_pn_element_value(self, value):\n        \"\"\"Return PersonName value from JSON value.\n\n        Values with VR PN have a special JSON encoding, see the DICOM Standard,\n        Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.\n\n        Parameters\n        ----------\n        value : dict\n            The person name components in the JSON entry.\n\n        Returns\n        -------\n        PersonName or str\n            The decoded PersonName object or an empty string.\n        \"\"\"\n        if not isinstance(value, dict):\n            # Some DICOMweb services get this wrong, so we\n            # workaround the issue and warn the user\n            # rather than raising an error.\n            warnings.warn(\n                'value of data element \"{}\" with VR Person Name (PN) '\n                'is not formatted correctly'.format(self.tag)\n            )\n            return value\n        else:\n            if 'Phonetic' in value:\n                comps = ['', '', '']\n            elif 'Ideographic' in value:\n                comps = ['', '']\n            else:\n                comps = ['']\n            if 'Alphabetic' in value:\n                comps[0] = value['Alphabetic']\n            if 'Ideographic' in value:\n                comps[1] = value['Ideographic']\n            if 'Phonetic' in value:\n                comps[2] = value['Phonetic']\n            elem_value = '='.join(comps)\n            return elem_value\n"}
filelevel_patches: {"pydicom/jsonrep.py": "@@ -226,7 +226,8 @@ def get_sequence_item(self, value):\n                     value_key = unique_value_keys[0]\n                     elem = DataElement.from_json(\n                         self.dataset_class, key, vr,\n-                        val[value_key], value_key\n+                        val[value_key], value_key,\n+                        self.bulk_data_element_handler\n                     )\n                 ds.add(elem)\n         return ds"}
messages.content: 
  We are currently solving the following issue within our repository. Here is the issue text:
  --- BEGIN ISSUE ---
  from_json does not correctly convert BulkDataURI's in SQ data elements
  **Describe the bug**
  When a DICOM object contains large data elements in SQ elements and is converted to JSON, those elements are correctly turned into BulkDataURI's. However, when the JSON is converted back to DICOM using from_json, the BulkDataURI's in SQ data elements are not converted back and warnings are thrown.
  
  **Expected behavior**
  The BulkDataURI's in SQ data elements get converted back correctly.
  
  **Steps To Reproduce**
  Take the `waveform_ecg.dcm` in the test data, convert it to JSON, and then convert the JSON to DICOM
  
  **Your environment**
  module       | version
  ------       | -------
  platform     | macOS-10.15.7-x86_64-i386-64bit
  Python       | 3.8.2 (v3.8.2:7b3ab5921f, Feb 24 2020, 17:52:18)  [Clang 6.0 (clang-600.0.57)]
  pydicom      | 2.1.0
  gdcm         | _module not found_
  jpeg_ls      | _module not found_
  numpy        | _module not found_
  PIL          | _module not found_
  
  The problem is in `jsonrep.py` at line 227. I plan on submitting a pull-request today for this.
  
  --- END ISSUE ---
  
  Below are some code segments, each from a relevant file. One or more of these files may contain bugs.
  
  --- BEGIN FILE ---
  ```
  ### pydicom/jsonrep.py
  # Copyright 2008-2019 pydicom authors. See LICENSE file for details.
  """Methods for converting Datasets and DataElements to/from json"""
  
  import base64
  from inspect import signature
  import inspect
  from typing import Callable, Optional, Union
  import warnings
  
  from pydicom.tag import BaseTag
  
  # Order of keys is significant!
  JSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)
  
  BINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',
                      'OB or OW', 'US or OW', 'US or SS or OW']
  VRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]
  VRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']
  
  
  def convert_to_python_number(value, vr):
      """Makes sure that values are either ints or floats
      based on their value representation.
  
      .. versionadded:: 1.4
  
      Parameters
      ----------
      value: Union[Union[str, int, float], List[Union[str, int, float]]]
          value of data element
      vr: str
          value representation of data element
  
      Returns
      -------
      Union[Union[str, int, float], List[Union[str, int, float]]]
  
      """
      if value is None:
          return None
      number_type = None
      if vr in VRs_TO_BE_INTS:
          number_type = int
      if vr in VRs_TO_BE_FLOATS:
          number_type = float
      if number_type is not None:
          if isinstance(value, (list, tuple,)):
              value = [number_type(e) for e in value]
          else:
              value = number_type(value)
      return value
  
  
  class JsonDataElementConverter:
      """Handles conversion between JSON struct and :class:`DataElement`.
  
      .. versionadded:: 1.4
      """
  
      def __init__(
          self,
          dataset_class,
          tag,
          vr,
          value,
          value_key,
          bulk_data_uri_handler: Optional[
              Union[
                  Callable[[BaseTag, str, str], object],
                  Callable[[str], object]
              ]
          ] = None
      ):
          """Create a new converter instance.
  
          Parameters
          ----------
          dataset_class : dataset.Dataset derived class
              Class used to create sequence items.
          tag : BaseTag
              The data element tag or int.
          vr : str
              The data element value representation.
          value : list
              The data element's value(s).
          value_key : str or None
              Key of the data element that contains the value
              (options: ``{"Value", "InlineBinary", "BulkDataURI"}``)
          bulk_data_uri_handler: callable or None
              Callable function that accepts either the tag, vr and "BulkDataURI"
              or just the "BulkDataURI" of the JSON
              representation of a data element and returns the actual value of
              that data element (retrieved via DICOMweb WADO-RS)
          """
          self.dataset_class = dataset_class
          self.tag = tag
          self.vr = vr
          self.value = value
          self.value_key = value_key
          if (
              bulk_data_uri_handler and
              len(signature(bulk_data_uri_handler).parameters) == 1
          ):
              def wrapped_bulk_data_handler(tag, vr, value):
                  return bulk_data_uri_handler(value)
              self.bulk_data_element_handler = wrapped_bulk_data_handler
          else:
              self.bulk_data_element_handler = bulk_data_uri_handler
  
      def get_element_values(self):
          """Return a the data element value or list of values.
  
          Returns
          -------
          str or bytes or int or float or dataset_class
          or PersonName or list of any of these types
              The value or value list of the newly created data element.
          """
          from pydicom.dataelem import empty_value_for_VR
          if self.value_key == 'Value':
              if not isinstance(self.value, list):
                  fmt = '"{}" of data element "{}" must be a list.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              if not self.value:
                  return empty_value_for_VR(self.vr)
              element_value = [self.get_regular_element_value(v)
                               for v in self.value]
              if len(element_value) == 1 and self.vr != 'SQ':
                  element_value = element_value[0]
              return convert_to_python_number(element_value, self.vr)
  
          # The value for "InlineBinary" shall be encoded as a base64 encoded
          # string, as shown in PS3.18, Table F.3.1-1, but the example in
          # PS3.18, Annex F.4 shows the string enclosed in a list.
          # We support both variants, as the standard is ambiguous here,
          # and do the same for "BulkDataURI".
          value = self.value
          if isinstance(value, list):
              value = value[0]
  
          if self.value_key == 'InlineBinary':
              if not isinstance(value, (str, bytes)):
                  fmt = '"{}" of data element "{}" must be a bytes-like object.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              return base64.b64decode(value)
  
          if self.value_key == 'BulkDataURI':
              if not isinstance(value, str):
                  fmt = '"{}" of data element "{}" must be a string.'
                  raise TypeError(fmt.format(self.value_key, self.tag))
              if self.bulk_data_element_handler is None:
                  warnings.warn(
                      'no bulk data URI handler provided for retrieval '
                      'of value of data element "{}"'.format(self.tag)
                  )
                  return empty_value_for_VR(self.vr, raw=True)
              return self.bulk_data_element_handler(self.tag, self.vr, value)
          return empty_value_for_VR(self.vr)
  
      def get_regular_element_value(self, value):
          """Return a the data element value created from a json "Value" entry.
  
          Parameters
          ----------
          value : str or int or float or dict
              The data element's value from the json entry.
  
          Returns
          -------
          dataset_class or PersonName
          or str or int or float
              A single value of the corresponding :class:`DataElement`.
          """
          if self.vr == 'SQ':
              return self.get_sequence_item(value)
  
          if self.vr == 'PN':
              return self.get_pn_element_value(value)
  
          if self.vr == 'AT':
              try:
                  return int(value, 16)
              except ValueError:
                  warnings.warn('Invalid value "{}" for AT element - '
                                'ignoring it'.format(value))
              return
          return value
  
      def get_sequence_item(self, value):
          """Return a sequence item for the JSON dict `value`.
  
          Parameters
          ----------
          value : dict or None
              The sequence item from the JSON entry.
  
          Returns
          -------
          dataset_class
              The decoded dataset item.
  
          Raises
          ------
          KeyError
              If the "vr" key is missing for a contained element
          """
          ds = self.dataset_class()
          if value:
              for key, val in value.items():
                  if 'vr' not in val:
                      fmt = 'Data element "{}" must have key "vr".'
                      raise KeyError(fmt.format(self.tag))
                  vr = val['vr']
                  unique_value_keys = tuple(
                      set(val.keys()) & set(JSON_VALUE_KEYS)
                  )
                  from pydicom import DataElement
                  from pydicom.dataelem import empty_value_for_VR
                  if not unique_value_keys:
                      # data element with no value
                      elem = DataElement(
                          tag=int(key, 16),
                          value=empty_value_for_VR(vr),
                          VR=vr)
                  else:
                      value_key = unique_value_keys[0]
                      elem = DataElement.from_json(
                          self.dataset_class, key, vr,
                          val[value_key], value_key
                      )
                  ds.add(elem)
          return ds
  
      def get_pn_element_value(self, value):
          """Return PersonName value from JSON value.
  
          Values with VR PN have a special JSON encoding, see the DICOM Standard,
          Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.
  
          Parameters
          ----------
          value : dict
              The person name components in the JSON entry.
  
          Returns
          -------
          PersonName or str
              The decoded PersonName object or an empty string.
          """
          if not isinstance(value, dict):
              # Some DICOMweb services get this wrong, so we
              # workaround the issue and warn the user
              # rather than raising an error.
              warnings.warn(
                  'value of data element "{}" with VR Person Name (PN) '
                  'is not formatted correctly'.format(self.tag)
              )
              return value
          else:
              if 'Phonetic' in value:
                  comps = ['', '', '']
              elif 'Ideographic' in value:
                  comps = ['', '']
              else:
                  comps = ['']
              if 'Alphabetic' in value:
                  comps[0] = value['Alphabetic']
              if 'Ideographic' in value:
                  comps[1] = value['Ideographic']
              if 'Phonetic' in value:
                  comps[2] = value['Phonetic']
              elem_value = '='.join(comps)
              return elem_value
  
  ```
  --- END FILE ---
  
  Please first localize the bug based on the issue statement, and then generate *SEARCH/REPLACE* edits to fix the issue.
  
  Every *SEARCH/REPLACE* edit must use this format:
  1. The file path
  2. The start of search block: <<<<<<< SEARCH
  3. A contiguous chunk of lines to search for in the existing source code
  4. The dividing line: =======
  5. The lines to replace into the source code
  6. The end of the replace block: >>>>>>> REPLACE
  
  Here is an example:
  
  ```python
  ### mathweb/flask/app.py
  <<<<<<< SEARCH
  from flask import Flask
  =======
  import math
  from flask import Flask
  >>>>>>> REPLACE
  ```
  
  Please note that the *SEARCH/REPLACE* edit REQUIRES PROPER INDENTATION. If you would like to add the line '        print(x)', you must fully write that out, with all those spaces before the code!
  Wrap the *SEARCH/REPLACE* edit in blocks ```python...```.
  
messages.role: user
verification_info: {"file_context": {"pydicom/jsonrep.py": "# Copyright 2008-2019 pydicom authors. See LICENSE file for details.\n\"\"\"Methods for converting Datasets and DataElements to/from json\"\"\"\n\nimport base64\nfrom inspect import signature\nimport inspect\nfrom typing import Callable, Optional, Union\nimport warnings\n\nfrom pydicom.tag import BaseTag\n\n# Order of keys is significant!\nJSON_VALUE_KEYS = ('Value', 'BulkDataURI', 'InlineBinary',)\n\nBINARY_VR_VALUES = ['OW', 'OB', 'OD', 'OF', 'OL', 'UN',\n                    'OB or OW', 'US or OW', 'US or SS or OW']\nVRs_TO_BE_FLOATS = ['DS', 'FL', 'FD', ]\nVRs_TO_BE_INTS = ['IS', 'SL', 'SS', 'UL', 'US', 'US or SS']\n\n\ndef convert_to_python_number(value, vr):\n    \"\"\"Makes sure that values are either ints or floats\n    based on their value representation.\n\n    .. versionadded:: 1.4\n\n    Parameters\n    ----------\n    value: Union[Union[str, int, float], List[Union[str, int, float]]]\n        value of data element\n    vr: str\n        value representation of data element\n\n    Returns\n    -------\n    Union[Union[str, int, float], List[Union[str, int, float]]]\n\n    \"\"\"\n    if value is None:\n        return None\n    number_type = None\n    if vr in VRs_TO_BE_INTS:\n        number_type = int\n    if vr in VRs_TO_BE_FLOATS:\n        number_type = float\n    if number_type is not None:\n        if isinstance(value, (list, tuple,)):\n            value = [number_type(e) for e in value]\n        else:\n            value = number_type(value)\n    return value\n\n\nclass JsonDataElementConverter:\n    \"\"\"Handles conversion between JSON struct and :class:`DataElement`.\n\n    .. versionadded:: 1.4\n    \"\"\"\n\n    def __init__(\n        self,\n        dataset_class,\n        tag,\n        vr,\n        value,\n        value_key,\n        bulk_data_uri_handler: Optional[\n            Union[\n                Callable[[BaseTag, str, str], object],\n                Callable[[str], object]\n            ]\n        ] = None\n    ):\n        \"\"\"Create a new converter instance.\n\n        Parameters\n        ----------\n        dataset_class : dataset.Dataset derived class\n            Class used to create sequence items.\n        tag : BaseTag\n            The data element tag or int.\n        vr : str\n            The data element value representation.\n        value : list\n            The data element's value(s).\n        value_key : str or None\n            Key of the data element that contains the value\n            (options: ``{\"Value\", \"InlineBinary\", \"BulkDataURI\"}``)\n        bulk_data_uri_handler: callable or None\n            Callable function that accepts either the tag, vr and \"BulkDataURI\"\n            or just the \"BulkDataURI\" of the JSON\n            representation of a data element and returns the actual value of\n            that data element (retrieved via DICOMweb WADO-RS)\n        \"\"\"\n        self.dataset_class = dataset_class\n        self.tag = tag\n        self.vr = vr\n        self.value = value\n        self.value_key = value_key\n        if (\n            bulk_data_uri_handler and\n            len(signature(bulk_data_uri_handler).parameters) == 1\n        ):\n            def wrapped_bulk_data_handler(tag, vr, value):\n                return bulk_data_uri_handler(value)\n            self.bulk_data_element_handler = wrapped_bulk_data_handler\n        else:\n            self.bulk_data_element_handler = bulk_data_uri_handler\n\n    def get_element_values(self):\n        \"\"\"Return a the data element value or list of values.\n\n        Returns\n        -------\n        str or bytes or int or float or dataset_class\n        or PersonName or list of any of these types\n            The value or value list of the newly created data element.\n        \"\"\"\n        from pydicom.dataelem import empty_value_for_VR\n        if self.value_key == 'Value':\n            if not isinstance(self.value, list):\n                fmt = '\"{}\" of data element \"{}\" must be a list.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if not self.value:\n                return empty_value_for_VR(self.vr)\n            element_value = [self.get_regular_element_value(v)\n                             for v in self.value]\n            if len(element_value) == 1 and self.vr != 'SQ':\n                element_value = element_value[0]\n            return convert_to_python_number(element_value, self.vr)\n\n        # The value for \"InlineBinary\" shall be encoded as a base64 encoded\n        # string, as shown in PS3.18, Table F.3.1-1, but the example in\n        # PS3.18, Annex F.4 shows the string enclosed in a list.\n        # We support both variants, as the standard is ambiguous here,\n        # and do the same for \"BulkDataURI\".\n        value = self.value\n        if isinstance(value, list):\n            value = value[0]\n\n        if self.value_key == 'InlineBinary':\n            if not isinstance(value, (str, bytes)):\n                fmt = '\"{}\" of data element \"{}\" must be a bytes-like object.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            return base64.b64decode(value)\n\n        if self.value_key == 'BulkDataURI':\n            if not isinstance(value, str):\n                fmt = '\"{}\" of data element \"{}\" must be a string.'\n                raise TypeError(fmt.format(self.value_key, self.tag))\n            if self.bulk_data_element_handler is None:\n                warnings.warn(\n                    'no bulk data URI handler provided for retrieval '\n                    'of value of data element \"{}\"'.format(self.tag)\n                )\n                return empty_value_for_VR(self.vr, raw=True)\n            return self.bulk_data_element_handler(self.tag, self.vr, value)\n        return empty_value_for_VR(self.vr)\n\n    def get_regular_element_value(self, value):\n        \"\"\"Return a the data element value created from a json \"Value\" entry.\n\n        Parameters\n        ----------\n        value : str or int or float or dict\n            The data element's value from the json entry.\n\n        Returns\n        -------\n        dataset_class or PersonName\n        or str or int or float\n            A single value of the corresponding :class:`DataElement`.\n        \"\"\"\n        if self.vr == 'SQ':\n            return self.get_sequence_item(value)\n\n        if self.vr == 'PN':\n            return self.get_pn_element_value(value)\n\n        if self.vr == 'AT':\n            try:\n                return int(value, 16)\n            except ValueError:\n                warnings.warn('Invalid value \"{}\" for AT element - '\n                              'ignoring it'.format(value))\n            return\n        return value\n\n    def get_sequence_item(self, value):\n        \"\"\"Return a sequence item for the JSON dict `value`.\n\n        Parameters\n        ----------\n        value : dict or None\n            The sequence item from the JSON entry.\n\n        Returns\n        -------\n        dataset_class\n            The decoded dataset item.\n\n        Raises\n        ------\n        KeyError\n            If the \"vr\" key is missing for a contained element\n        \"\"\"\n        ds = self.dataset_class()\n        if value:\n            for key, val in value.items():\n                if 'vr' not in val:\n                    fmt = 'Data element \"{}\" must have key \"vr\".'\n                    raise KeyError(fmt.format(self.tag))\n                vr = val['vr']\n                unique_value_keys = tuple(\n                    set(val.keys()) & set(JSON_VALUE_KEYS)\n                )\n                from pydicom import DataElement\n                from pydicom.dataelem import empty_value_for_VR\n                if not unique_value_keys:\n                    # data element with no value\n                    elem = DataElement(\n                        tag=int(key, 16),\n                        value=empty_value_for_VR(vr),\n                        VR=vr)\n                else:\n                    value_key = unique_value_keys[0]\n                    elem = DataElement.from_json(\n                        self.dataset_class, key, vr,\n                        val[value_key], value_key\n                    )\n                ds.add(elem)\n        return ds\n\n    def get_pn_element_value(self, value):\n        \"\"\"Return PersonName value from JSON value.\n\n        Values with VR PN have a special JSON encoding, see the DICOM Standard,\n        Part 18, :dcm:`Annex F.2.2<part18/sect_F.2.2.html>`.\n\n        Parameters\n        ----------\n        value : dict\n            The person name components in the JSON entry.\n\n        Returns\n        -------\n        PersonName or str\n            The decoded PersonName object or an empty string.\n        \"\"\"\n        if not isinstance(value, dict):\n            # Some DICOMweb services get this wrong, so we\n            # workaround the issue and warn the user\n            # rather than raising an error.\n            warnings.warn(\n                'value of data element \"{}\" with VR Person Name (PN) '\n                'is not formatted correctly'.format(self.tag)\n            )\n            return value\n        else:\n            if 'Phonetic' in value:\n                comps = ['', '', '']\n            elif 'Ideographic' in value:\n                comps = ['', '']\n            else:\n                comps = ['']\n            if 'Alphabetic' in value:\n                comps[0] = value['Alphabetic']\n            if 'Ideographic' in value:\n                comps[1] = value['Ideographic']\n            if 'Phonetic' in value:\n                comps[2] = value['Phonetic']\n            elem_value = '='.join(comps)\n            return elem_value\n"}, "filelevel_patches": {"pydicom/jsonrep.py": "@@ -226,7 +226,8 @@ def get_sequence_item(self, value):\n                     value_key = unique_value_keys[0]\n                     elem = DataElement.from_json(\n                         self.dataset_class, key, vr,\n-                        val[value_key], value_key\n+                        val[value_key], value_key,\n+                        self.bulk_data_element_handler\n                     )\n                 ds.add(elem)\n         return ds"}}