insert_element.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Insert Element in YAML SD Using Replace\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    " - get list of profiles\n",
    " - if insert text exists, insert new element before it\n",
    " - else print error"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "- Length Example\n",
      "- Average Blood Pressure Example\n",
      "- Heart Rate Example\n",
      "- OFC Percentile Example\n",
      "- Oxygen Saturation Example\n",
      "- Head Circumference Example\n",
      "- Pediatric BMI Example\n",
      "- Weight Example\n",
      "- Pediatric Wt Example\n",
      "- Height Example\n",
      "- Observation SatO2 FiO2 Example\n",
      "- Respiratory Rate Example\n",
      "- Blood Pressure Example\n",
      "- Temperature Example\n",
      "- BMI Example\n",
      "- BP Data Absent Example\n"
     ]
    }
   ],
   "source": [
    "from  pathlib import Path\n",
    "from yaml import load, dump, SafeLoader\n",
    "from fhir.resources.observation import Observation\n",
    "# two spaces\n",
    "new_element = '''\n",
    "# ============= new for USCDI 5 =================\n",
    "  - id: Observation.performer\n",
    "    path: Observation.performer\n",
    "    type:\n",
    "      - code: Reference\n",
    "        targetProfile:\n",
    "          - \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner\"\n",
    "          - \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-organization\"\n",
    "          - \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient\"\n",
    "          - \"http://hl7.org/fhir/StructureDefinition/PractitionerRole\"\n",
    "          - \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-careteam\"\n",
    "          - \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-relatedperson\"\n",
    "        _targetProfile:\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "          - extension:\n",
    "              - url: \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\"\n",
    "                valueBoolean: false\n",
    "    mustSupport: true\n",
    "# =================================================\n",
    "'''\n",
    "\n",
    "performer = [\n",
    "        {\n",
    "            \"reference\": \"Practitioner/practitioner1\",\n",
    "            \"display\": \"Dr Ronald Bone\"\n",
    "        }\n",
    "    ]\n",
    "\n",
    "test_string = '  - id: Observation.valueQuantity\\n'\n",
    "test_string = 'vital-signs'\n",
    "test = '''\n",
    "#==============\n",
    "  FOO\n",
    "#=============\n",
    "  - id: Observation.valueQuantity\n",
    "'''\n",
    "in_path = Path(r'/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/')\n",
    "in_path = Path(r'/Users/ehaas/Documents/FHIR/US-Core/input/examples-yaml')\n",
    "\n",
    "i = 1\n",
    "# for profile in in_path.glob('StructureDefinition*'):\n",
    "for example in in_path.glob('*.yml'):\n",
    "    # print(profile.name)\n",
    "    # print(example.name)\n",
    "    # text_yaml = profile.read_text()\n",
    "    obj = load(example.read_text(), Loader=SafeLoader)\n",
    "    # if 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs' in text_yaml:\n",
    "    try:\n",
    "      if obj['category'][0]['coding'][0]['code'] == test_string:\n",
    "        # print(f'{i}. {example.name}==============VITALS====================')\n",
    "        try:\n",
    "          if obj['performer']:\n",
    "            #  print(f'{i}. {example.name}++++++++++has .performer ++++++++++') \n",
    "             print(f\"- {obj['meta']['extension'][0]['valueString']}\")\n",
    "        except KeyError as e:\n",
    "            # print(f'{i}. {example.name}------------no .performer ---------------') \n",
    "            # obs_obj = Observation.parse_obj(obj)\n",
    "            # obs_obj.performer = performer\n",
    "            # print(obs_obj.yaml())\n",
    "            pass\n",
    "            # example.write_text(obs_obj.yaml())\n",
    "      # print(f'{i}. {profile.name}==============VITALS====================')\n",
    "      # if test_string in text_yaml:\n",
    "      #   new_string =  text_yaml.replace(test_string, f'{new_element}\\n{test_string}')\n",
    "      #   print(f'{i}. {profile.name}')\n",
    "      #   profile.write_text(new_string)\n",
    "      # else:\n",
    "      #    print(f'{i}. ==============text not found for: {profile.name}')\n",
    "      # i += 1\n",
    "    except (KeyError,TypeError) as e:\n",
    "        # print(f'{i}. {example.name}==============no category====================')\n",
    "        pass\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "# pattern1\n",
    "#   - id: Observation.valueQuantity\n",
    "\n",
    "# pattern2\n",
    "#   - id: Observation.component"
   ]
  }
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