FHIRPACK Detailed Usage#

The purpose behind this Notebook is to show you some of the posibilities FHIRPACK offers.

Don’t be intimidated, start using what you need and slowly get acquainted with more complex workflows and functionality.

Feel free to refer to our Documentation, our GitLab and GitHub trackers or our Slack channel.

Boilerplate#

[1]:

%load_ext autoreload
%autoreload 2
%pprint

from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"

Pretty printing has been turned OFF

Preamble and Imports#

⚠️ Use only if you haven’t installed FHIR PACK via pip, pipenv or similar in your environment but you have instead cloned the project and are now in the /examples directory

[2]:

import sys,os
sys.path.append(os.getcwd()+'/../src/')
# sys.path

import fhirpack                     as fp
import pandas                       as pd
import fhirpy
import numpy                        as np
import fhir.resources       as fr
import json
from tqdm import tqdm
from fhirpack.constants import CONFIG

Useful Paths for Data Storage#

[3]:

DATAPATH=CONFIG.get('DATAPATH')
RESPATH=f"{DATAPATH}/fhir/"

FHIR Server Connection#

CLI Usage#

[12]:

!fp -o "getPatients" -p "given = Max" #-v

[11]:

!dotenv -f ../.env run python -m fhirpack.cli "-o" "getPatients" -p "given = Max" #-v

                                                   data                                            Patient
0     {'resourceType': 'Patient', 'id': '08674fab965...  08674fab96596e225e0fca7694e8e5cbba3a25ee453e18...
1     {'resourceType': 'Patient', 'id': '53ad3ccbbe6...  53ad3ccbbe6166066be9e216e2b9d352229fa2846b3a9b...
2     {'resourceType': 'Patient', 'id': 'e8567d4db54...  e8567d4db5492014854452992be2b3ce9eeb67b659b66d...
3     {'resourceType': 'Patient', 'id': 'e9b972a5f7d...  e9b972a5f7d398ada6368d5c5622c688291cb7f71a2b4e...
4     {'resourceType': 'Patient', 'id': '2372ec256d3...  2372ec256d326bea633973f156f1a4e9c9076126a9af56...
...                                                 ...                                                ...
9392  {'resourceType': 'Patient', 'id': 'b25c1f9292d...  b25c1f9292da6948ac9718075f20061c9d7aa254734505...
9393  {'resourceType': 'Patient', 'id': '528f19164a6...  528f19164a67e1131b290bd0f4ba02f21be58ff00f96f0...
9394  {'resourceType': 'Patient', 'id': '29a5efae5e9...  29a5efae5e90b1cf94cedd171965fb8c9c6d8b877132c9...
9395  {'resourceType': 'Patient', 'id': 'e8380b48215...  e8380b48215983ea1e7293852b28679857403b81b37b75...
9396  {'resourceType': 'Patient', 'id': 'c2abcc5ca2b...  c2abcc5ca2bbd14d7dc35d832b30f9848211efb4218de4...

[7768 rows x 2 columns]

From Custom Environment File#

[34]:

!cat ../.env.example



SCHEMA=https
PORT=80

#DOMAIN=${SCHEMA}://hapi.fhir.org
#DOMAIN=${SCHEMA}://test.hapifhir.io
#might be unstable or unavailable https://github.com/hapifhir/hapi-fhir/issues/1171#issuecomment-1179728061

DOMAIN=${SCHEMA}://hapi.fhir.org

#DOMAIN=${SCHEMA}://example.com:${PORT}
# only use port if the server is running on a non-standard port
# and this is reflected in the FHIR pagination links
# see https://gitlab.com/fhirpack/main/-/issues/75 for more information

APIBASE=${DOMAIN}/baseR4

#AUTH_METHOD=
#AUTH_PARAMS_PRESET=
#LOGINURL=${DOMAIN}/oauth/token
#OAUTH_TOKEN_ENDPOINT=${DOMAIN}/oauth/token
#OAUTH_USERNAME=username
#OAUTH_PASSWORD=password
#OAUTH_TOKEN=token

DATAPATH=./data

#EXTRACTION_BASE_TOKEN_DICOM=${OAUTH_TOKEN}

[5]:

pack= fp.PACK(envFile='./.env.example')
pack.getPatients(['2918556'])

[5]:

	data	Patient
0	{'resourceType': 'Patient', 'id': '2918556', '...	2918556

[20]:

!cat .env.example


SCHEMA=https
PORT=80

#DOMAIN=${SCHEMA}://hapi.fhir.org
#DOMAIN=${SCHEMA}://test.hapifhir.io
#might be unstable or unavailable https://github.com/hapifhir/hapi-fhir/issues/1171#issuecomment-1179728061

DOMAIN=${SCHEMA}://hapi.fhir.org

#DOMAIN=${SCHEMA}://example.com:${PORT}
# only use port if the server is running on a non-standard port
# and this is reflected in the FHIR pagination links
# see https://gitlab.com/fhirpack/main/-/issues/75 for more information

APIBASE=${DOMAIN}/baseR4

#AUTH_METHOD=
#AUTH_PARAMS_PRESET=
#LOGINURL=${DOMAIN}/oauth/token
#OAUTH_TOKEN_ENDPOINT=${DOMAIN}/oauth/token
#OAUTH_USERNAME=username
#OAUTH_PASSWORD=password
#OAUTH_TOKEN=token

LOGSPATH=./logs
DATAPATH=./data

#EXTRACTION_BASE_TOKEN_DICOM=${OAUTH_TOKEN}

[7]:

pack= fp.PACK(envFile='./.env.example')

for i,e in pack.getPatients(['2918556']).data.items():
    print(
            json.dumps(e.serialize(), indent=4, sort_keys=True)[:200],
            '\n...'
    )
# pack.getPatients(['2918556'])

{
    "active": false,
    "address": [
        {
            "city": "[Ljava.lang.String;@6486517a",
            "country": "lJltcNpfGu",
            "district": "kIATSJDTIN",
            "line": [

...

Manual Setup#

[18]:

pack  = fp.PACK("http://hapi.fhir.org/baseR4")

# Another less reliable alternative server to test things:
# pack  = fp.PACK("http://test.fhir.org/r4/")

pack.getPatients(['2918556'])

[18]:

	data	Patient
0	{'resourceType': 'Patient', 'id': '2918556', '...	2918556

[24]:

pack.getPatients(['2918556']).data

[24]:

0    {'resourceType': 'Patient', 'id': '2918556', '...
Name: data, dtype: object

[25]:

pack.getPatients(['2918556']).iloc[0]

[25]:

data       {'resourceType': 'Patient', 'id': '2918556', '...
Patient                                              2918556
Name: 0, dtype: object

[31]:

# The data column always contains the raw fhirpy.lib.SyncFHIRResource objects
# that can be used according to their API.

myResource = pack.getPatients(['2918556']).data.iloc[0]
myResource.serialize()

[31]:

{'resourceType': 'Patient', 'id': '2918556', 'meta': {'versionId': '1', 'lastUpdated': '2022-04-28T09:14:12.407+00:00', 'source': '#XvmdJVuEr4W9S9I5'}, 'text': {'status': 'generated', 'div': '<div xmlns="http://www.w3.org/1999/xhtml"><div class="hapiHeaderText">muagd nrxrykl <b>KMLNNPEUVZ </b> zttwnr </div><table class="hapiPropertyTable"><tbody><tr><td>Identifier</td><td>LiwdDQHoIt</td></tr><tr><td>Address</td><td><span>[Ljava.lang.String;@74a2d899 </span><br/><span>[Ljava.lang.String;@6486517a </span><span>QHmEoccROR </span><span>lJltcNpfGu </span></td></tr><tr><td>Date of birth</td><td><span>23 April 1863</span></td></tr></tbody></table></div>'}, 'identifier': [{'use': 'official', 'type': {'coding': [{'system': 'https://wfmvwfsriv.com', 'version': 'TEGlN', 'code': 'secondary', 'display': 'VUxeSKGrSXyWRiWttgtn', 'userSelected': True}], 'text': 'ZrsDqCrqYCCqEHOIdtKkwHTusypwlhoxVRAqMWEhBPoerfPRkmMeFUJKPcnlKfHAfVmpWWTMXEClcsEQZWDqqBKQvajndOvYYjiG'}, 'system': 'https://ceyyockogw.com', 'value': 'LiwdDQHoIt', 'period': {'start': '1892-04-01', 'end': '1988-12-08'}, 'assigner': {'reference': 'SseKXOELXg', 'type': 'https://dldmpzerig.com', 'display': 'XlkPcdGvbizOJCM'}}], 'active': False, 'name': [{'use': 'old', 'text': 'MIfctqm', 'family': 'KMLnNPeuVz', 'given': ['nrxrykl'], 'prefix': ['muagd'], 'suffix': ['zttwnr'], 'period': {'start': '1940-10-30', 'end': '1969-07-27'}}], 'telecom': [{'system': 'pager', 'value': '2913897131', 'use': 'home', 'rank': 6, 'period': {'start': '1928-10-09', 'end': '1821-01-22'}}], 'gender': 'male', 'birthDate': '1863-04-23', 'deceasedDateTime': '1873-04-04T09:14:09.404316500Z', 'address': [{'use': 'old', 'type': 'postal', 'text': 'qExcvDSAJoeSvQnbxFzG', 'line': ['[Ljava.lang.String;@74a2d899'], 'city': '[Ljava.lang.String;@6486517a', 'district': 'kIATSJDTIN', 'state': 'QHmEoccROR', 'postalCode': 'pTGzgOEOYm', 'country': 'lJltcNpfGu', 'period': {'start': '1877-04-15', 'end': '1864-11-08'}}]}

For Docker Enthusiasts#

[32]:

# alternatively, if you're using our Dockerfile to run your FHIR server
# remember to run "docker-compose up" in your local clone of FHIRPACK first
# run "docker-compose up" in your local clone of FHIRPACK first

# pack  = fp.PACK("http://127.0.0.1:42112/hapi-fhir-jpaserver/fhir")
# pack  = fp.PACK(envFile="../../docker-compose.env")

# pack.getPatients(['1']).data.iloc[0].serialize()

# pack.getPatients(['146053'])

Configuring FHIRPACK from the Default Environment File (./.env)#

[22]:

pack = fp.PACK()
# pack.client.authorization

A Motivating Example#

[23]:

# for patients whose lastname is Koepp, find the root identity,
# get their associated diagnostic reports and report their ID and status

pack.getPatients(searchParams={"family":"koepp"})\
    .getRootPatients()\
            .explode()\
                    .getDiagnosticReports()\
                            .dropna()\
                                    .gatherSimplePaths(['id','status'])\
                                            .explode(['id','status'])

SEARCH[Patient]> : 100%|██████████| 13/13 [00:00<00:00, 18.66it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 12/12 [00:00<00:00, 28.99it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 13/13 [00:00<00:00, 30.77it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 9/9 [00:00<00:00, 25.92it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 9/9 [00:00<00:00, 25.51it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 20/20 [00:00<00:00, 36.14it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 5/5 [00:00<00:00, 16.15it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 1/1 [00:00<00:00,  4.17it/s]

[23]:

	id	status
0	None	None
1	None	None
2	6570895b-5943-430b-8f7b-e5df1ffc6d83	final
2	85d08e59-3e58-4518-be8b-3ccfc15cc9fa	final
2	35f7efea-6557-467e-a693-34d73a097f64	final
...	...	...
8	None	None
9	None	None
10	None	None
11	None	None
12	1516127	final

75 rows × 2 columns

FHIRPACK and FHIR Resources#

References#

[24]:

patientReference = pack.getReferences(['Patient/647487'])

patientReference.data.iloc[0].to_resource().serialize()

patientReference.getResources()

[24]:

{'resourceType': 'Patient',
 'id': '647487',
 'meta': {'versionId': '1',
  'lastUpdated': '2020-03-20T21:38:58.974+00:00',
  'source': '#bE19PhJ3nQMhB1xy'},
 'text': {'status': 'generated',
  'div': '<div xmlns="http://www.w3.org/1999/xhtml"><div class="hapiHeaderText">Series_Status: Not complete Evaluation_Status_1.0: Valid Evaluation_Status_2.0: Valid Evaluation_Status_3.0: Valid Evaluation_Status_4.0: Valid Evaluation_Status_5.0: Valid <b># 5 PENTACEL AT ≥ 4 YRS </b></div><table class="hapiPropertyTable"><tbody><tr><td>Date of birth</td><td><span>20 January 2016</span></td></tr></tbody></table></div>'},
 'name': [{'family': '# 5 Pentacel at ≥ 4 yrs',
   'given': ['Series_Status: Not complete',
    'Evaluation_Status_1.0: Valid',
    'Evaluation_Status_2.0: Valid',
    'Evaluation_Status_3.0: Valid',
    'Evaluation_Status_4.0: Valid',
    'Evaluation_Status_5.0: Valid']}],
 'gender': 'female',
 'birthDate': '2016-01-20'}

GET[None]> : 100%|██████████| 1/1 [00:00<00:00,  4.17it/s]

[24]:

	data
0	{'resourceType': 'Patient', 'id': '647487', 'm...

Resources#

Reference to Resource#

[25]:

multiPatientReference = pack.getReferences(
    [
        'Patient/1849165',
        'Patient/647487'
    ])

multiPatientReference.data.apply( lambda x:x.id )

[25]:

0    1849165
1     647487
Name: data, dtype: object

Direct Resource Access#

[26]:

pack.getPatients(searchParams={"family":"Betterhalf"})

SEARCH[Patient]> : 100%|██████████| 12/12 [00:00<00:00, 16.03it/s]

[26]:

	data
0	{'resourceType': 'Patient', 'id': '2080537', '...
1	{'resourceType': 'Patient', 'id': '2080822', '...
2	{'resourceType': 'Patient', 'id': '2153287', '...
3	{'resourceType': 'Patient', 'id': '619088', 'm...
4	{'resourceType': 'Patient', 'id': '2548478', '...
5	{'resourceType': 'Patient', 'id': '2548794', '...
6	{'resourceType': 'Patient', 'id': '2737336', '...
7	{'resourceType': 'Patient', 'id': '1376090', '...
8	{'resourceType': 'Patient', 'id': '1376092', '...
9	{'resourceType': 'Patient', 'id': '1377059', '...
10	{'resourceType': 'Patient', 'id': '1377093', '...
11	{'resourceType': 'Patient', 'id': '1388633', '...

[27]:

pack.getPatients(searchParams={}).size

SEARCH[Patient]> :   0%|          | 100/185636 [00:01<56:30, 54.72it/s]

[27]:

[30]:

multiPatientResource = pack.getResources(
    ['Patient/1849165',
     'Patient/647487']
)

multiPatientResource

GET[None]> : 100%|██████████| 2/2 [00:00<00:00,  4.36it/s]

[30]:

	data
0	{'resourceType': 'Patient', 'id': '1849165', '...
1	{'resourceType': 'Patient', 'id': '647487', 'm...

Serialization and Element Access#

[31]:

patientResource = patientReference.data.iloc[0].to_resource()

patientResource['name'][0]['given']

patientResource.serialize().get('birthDate')

[31]:

['Series_Status: Not complete',
 'Evaluation_Status_1.0: Valid',
 'Evaluation_Status_2.0: Valid',
 'Evaluation_Status_3.0: Valid',
 'Evaluation_Status_4.0: Valid',
 'Evaluation_Status_5.0: Valid']

[31]:

'2016-01-20'

[32]:

multiPatientReference.getResources()

GET[None]> : 100%|██████████| 2/2 [00:00<00:00,  4.47it/s]

[32]:

	data
0	{'resourceType': 'Patient', 'id': '1849165', '...
1	{'resourceType': 'Patient', 'id': '647487', 'm...

[33]:

multiPatientResource[:1].pretty

{
    "_birthDate": {
        "extension": [
            {
                "url": "http://hl7.org/fhir/StructureDefinition/patient-birthTime",
                "valueDateTime": "1974-12-25T14:35:45-05:00"
            }
        ]
    },
    "active": true,
    "address": [
        {
            "city": "PleasantVille",
            "district": "Rainbow",
            "line": [
                "534 Erewhon St"
            ],
            "period": {
                "start": "1974-12-25"
            },
            "postalCode": "3999",
            "state": "Vic",
            "text": "534 Erewhon St PeasantVille, Rainbow, Vic  3999",
            "type": "both",
            "use": "home"
        }
    ],
    "birthDate": "1974-12-25",
    "contact": [
        {
            "address": {
                "city": "PleasantVille",
                "district": "Rainbow",
                "line": [
                    "534 Erewhon St"
                ],
                "period": {
                    "start": "1974-12-25"
                },
                "postalCode": "3999",
                "state": "Vic",
                "type": "both",
                "use": "home"
            },
            "gender": "female",
            "name": {
                "_family": {
                    "extension": [
                        {
                            "url": "http://hl7.org/fhir/StructureDefinition/humanname-own-prefix",
                            "valueString": "VV"
                        }
                    ]
                },
                "family": "du March\u00e9",
                "given": [
                    "B\u00e9n\u00e9dicte"
                ]
            },
            "period": {
                "start": "2012"
            },
            "relationship": [
                {
                    "coding": [
                        {
                            "code": "N",
                            "system": "http://terminology.hl7.org/CodeSystem/v2-0131"
                        }
                    ]
                }
            ],
            "telecom": [
                {
                    "system": "phone",
                    "value": "+33 (237) 998327"
                }
            ]
        }
    ],
    "deceasedBoolean": false,
    "gender": "male",
    "id": "1849165",
    "identifier": [
        {
            "assigner": {
                "display": "Acme Healthcare"
            },
            "period": {
                "start": "2001-05-06"
            },
            "system": "urn:oid:1.2.36.146.595.217.0.1",
            "type": {
                "coding": [
                    {
                        "code": "MR",
                        "system": "http://terminology.hl7.org/CodeSystem/v2-0203"
                    }
                ]
            },
            "use": "usual",
            "value": "12345"
        }
    ],
    "managingOrganization": {
        "reference": "Organization/1845391"
    },
    "meta": {
        "lastUpdated": "2021-02-08T21:42:25.829+00:00",
        "source": "#PBPO58xnJNERsS1A",
        "versionId": "1"
    },
    "name": [
        {
            "family": "Chalmers",
            "given": [
                "Peter",
                "James"
            ],
            "use": "official"
        },
        {
            "given": [
                "Jim"
            ],
            "use": "usual"
        },
        {
            "family": "Windsor",
            "given": [
                "Peter",
                "James"
            ],
            "period": {
                "end": "2002"
            },
            "use": "maiden"
        }
    ],
    "resourceType": "Patient",
    "telecom": [
        {
            "use": "home"
        },
        {
            "rank": 1,
            "system": "phone",
            "use": "work",
            "value": "(03) 5555 6473"
        },
        {
            "rank": 2,
            "system": "phone",
            "use": "mobile",
            "value": "(03) 3410 5613"
        },
        {
            "period": {
                "end": "2014"
            },
            "system": "phone",
            "use": "old",
            "value": "(03) 5555 8834"
        }
    ],
    "text": {
        "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t\t<table>\n\t\t\t\t<tbody>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Name</td>\n\t\t\t\t\t\t<td>Peter James \n              <b>Chalmers</b> (&quot;Jim&quot;)\n            </td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Address</td>\n\t\t\t\t\t\t<td>534 Erewhon, Pleasantville, Vic, 3999</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Contacts</td>\n\t\t\t\t\t\t<td>Home: unknown. Work: (03) 5555 6473</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Id</td>\n\t\t\t\t\t\t<td>MRN: 12345 (Acme Healthcare)</td>\n\t\t\t\t\t</tr>\n\t\t\t\t</tbody>\n\t\t\t</table>\n\t\t</div>",
        "status": "generated"
    }
}

[34]:

fp.PACK().getDiagnosticReports(
    ['Patient/647487']
)[:1].keys

GET[DiagnosticReport]> : 100%|██████████| 1/1 [00:00<00:00,  4.40it/s]

resourceType
id
meta
meta.versionId
meta.lastUpdated
meta.source
text
text.status
text.div
name
name.family
name.given
gender
birthDate

PANDAS-Style DataFrame Operations#

[35]:

multiPatientReference[:1]

multiPatientReference[-1:]

multiPatientReference.values

multiPatientReference.info()

[35]:

	data
0	{'reference': 'Patient/1849165'}

[35]:

	data
1	{'reference': 'Patient/647487'}

[35]:

array([[<SyncFHIRReference Patient/1849165>],
       [<SyncFHIRReference Patient/647487>]], dtype=object)

<class 'fhirpack.base.Frame'>
RangeIndex: 2 entries, 0 to 1
Data columns (total 1 columns):
 #   Column  Non-Null Count  Dtype
---  ------  --------------  -----
 0   data    2 non-null      object
dtypes: object(1)
memory usage: 144.0+ bytes

fhirpack.base.Frame#

[36]:

fp.base.Frame( [[patientResource]], columns=['data'])

[36]:

	data
0	{'resourceType': 'Patient', 'id': '647487', 'm...

Extraction#

Patients#

FHIR Patient Resource

[37]:

pack.getPatients(
    [
            '647487'
    ]
)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.38it/s]

[37]:

	data
0	{'resourceType': 'Patient', 'id': '647487', 'm...

[38]:

pack.getPatients(
    [
            '647487'
    ]
).data.item().serialize()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.32it/s]

[38]:

{'resourceType': 'Patient',
 'id': '647487',
 'meta': {'versionId': '1',
  'lastUpdated': '2020-03-20T21:38:58.974+00:00',
  'source': '#bE19PhJ3nQMhB1xy'},
 'text': {'status': 'generated',
  'div': '<div xmlns="http://www.w3.org/1999/xhtml"><div class="hapiHeaderText">Series_Status: Not complete Evaluation_Status_1.0: Valid Evaluation_Status_2.0: Valid Evaluation_Status_3.0: Valid Evaluation_Status_4.0: Valid Evaluation_Status_5.0: Valid <b># 5 PENTACEL AT ≥ 4 YRS </b></div><table class="hapiPropertyTable"><tbody><tr><td>Date of birth</td><td><span>20 January 2016</span></td></tr></tbody></table></div>'},
 'name': [{'family': '# 5 Pentacel at ≥ 4 yrs',
   'given': ['Series_Status: Not complete',
    'Evaluation_Status_1.0: Valid',
    'Evaluation_Status_2.0: Valid',
    'Evaluation_Status_3.0: Valid',
    'Evaluation_Status_4.0: Valid',
    'Evaluation_Status_5.0: Valid']}],
 'gender': 'female',
 'birthDate': '2016-01-20'}

[39]:

for i,e in pack.getPatients(['647487','1849165']).itertuples():
    print (f"Row {i} with Patient ID {e.id}")

GET[Patient]> : 100%|██████████| 2/2 [00:00<00:00,  4.40it/s]

Row 0 with Patient ID 647487
Row 1 with Patient ID 1849165

[40]:

getPatientsAsList=pack.getPatients(['647487','1849165']).cast('list')

getPatientsAsList

GET[Patient]> : 100%|██████████| 2/2 [00:00<00:00,  4.42it/s]

[40]:

[[<SyncFHIRResource Patient/647487>], [<SyncFHIRResource Patient/1849165>]]

[41]:

[e.pop().id for e in getPatientsAsList]

[41]:

['647487', '1849165']

Patients as Operand and other Resources#

[42]:

patients = pack.getPatients(
    ['9ac622c4-61c8-40b4-b6d9-06cfeb3d6995',
    '1849165',
    '649231',
    '650224']
)

GET[Patient]> : 100%|██████████| 4/4 [00:00<00:00,  4.38it/s]

Root Patients and Identities#

[43]:

pack.getRootPatients(
    [
        'b558da74-7756-4845-87d5-d1cca8b79a62',
    ],
).explode().gatherSimplePaths(["id"]).id.unique()

SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.30it/s]

[43]:

array(['9ac622c4-61c8-40b4-b6d9-06cfeb3d6995'], dtype=object)

[44]:

patients.getRootPatients()

[44]:

	data
0	[{'resourceType': 'Patient', 'id': '9ac622c4-6...
1	[{'resourceType': 'Patient', 'id': '1849165', ...
2	[{'resourceType': 'Patient', 'id': '649231', '...
3	[{'resourceType': 'Patient', 'id': '650224', '...

[45]:

pack.getResources(
    [
            'Patient/b558da74-7756-4845-87d5-d1cca8b79a62'
    ]
).getRootPatients()

GET[None]> : 100%|██████████| 1/1 [00:00<00:00,  4.59it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.41it/s]

[45]:

	data
0	[{'resourceType': 'Patient', 'id': '9ac622c4-6...

[46]:

rootPatients = patients.getResources().getRootPatients().explode()

rootPatients.gatherSimplePaths(['id','birthDate'])

GET[None]> : 100%|██████████| 4/4 [00:00<00:00, 48629.61it/s]

[46]:

	id	birthDate
0	9ac622c4-61c8-40b4-b6d9-06cfeb3d6995	1981-01-01
1	1849165	1974-12-25
2	649231	2018-12-21
3	650224	2007-02-08

[47]:

rootPatients.data[0].name

[47]:

[{'family': 'TestFamily', 'given': ['TestGiven']}]

[48]:

for link in rootPatients.data[0]['link']:
    lpat=link.other.to_resource()
    print(lpat.id)

b558da74-7756-4845-87d5-d1cca8b79a62

Linked Patients#

[49]:

pack.getLinkedPatients(
    [
            '9ac622c4-61c8-40b4-b6d9-06cfeb3d6995',
    ]
)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.64it/s]

[49]:

	data
0	[{'resourceType': 'Patient', 'id': 'b558da74-7...

Conditions#

FHIR Condition Resource

[50]:

conditions = pack.getConditions(
    searchParams={
            'code':'44465007',
            '_sort': '-onset-date',
    }
)[:5]

conditions

SEARCH[Condition]> : 100%|██████████| 36/36 [00:00<00:00, 90.74it/s]

[50]:

	data
0	{'resourceType': 'Condition', 'id': '1584692',...
1	{'resourceType': 'Condition', 'id': '1591180',...
2	{'resourceType': 'Condition', 'id': '1402386',...
3	{'resourceType': 'Condition', 'id': '1403562',...
4	{'resourceType': 'Condition', 'id': '1495528',...

Patients for Conditions#

[51]:

conditions.getPatients().explode().gatherSimplePaths(['id','name.given','name.family'])

SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.46it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.27it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.31it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.44it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.28it/s]

[51]:

	id	name.given	name.family
0	1583909	[[Shayne60]]	[Miller503]
1	1590885	[[Ty725]]	[Sporer811]
2	1402076	[[Phyliss]]	[Nyambura]
3	1403421	[[Stefania]]	[Bethwell]
4	1495412	[[Hallie315], [Hallie315]]	[Donnelly343, Osinski784]

[52]:

conditions\
    .getPatients()\
            .explode()\
                    .data.apply(lambda x:x.id)\
                            .to_csv(f"data.ignore")

SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.38it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.41it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.39it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.47it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.37it/s]

[53]:

!cat data.ignore

[54]:

conditions = pd.read_csv( f"data.ignore", index_col=0)
conditions.shape
conditions

[54]:

(5, 1)

[54]:

	data
0	1583909
1	1590885
2	1402076
3	1403421
4	1495412

Conditions for Patient#

[55]:

pack.getPatients(['8cbf1128-3644-47a1-9cc8-05f1aac6071d']).getConditions().explode()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.18it/s]
SEARCH[Condition]> : 100%|██████████| 5/5 [00:00<00:00, 20.75it/s]

[55]:

	data
0	{'resourceType': 'Condition', 'id': '2b7a4d69-...
0	{'resourceType': 'Condition', 'id': '0fc73e7c-...
0	{'resourceType': 'Condition', 'id': 'cb1bab6c-...
0	{'resourceType': 'Condition', 'id': 'bc301bbf-...
0	{'resourceType': 'Condition', 'id': '5db4866a-...

Observations#

FHIR Observation Resource

[ ]:

pack\
    .getPatients(['Patient/258974'])\
            .getConditions(searchParams={"code":"44465007"})\
                    .explode()\
                            .getPatients(searchParams={"family":"Keebler762"})

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.42it/s]
SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  4.40it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.37it/s]

	data
0	[{'resourceType': 'Patient', 'id': '258974', '...

[ ]:

from datetime import datetime

interesting = pack.getPatients(['Patient/2164033']).\
    getObservations(
        searchParams={
            "code":"http ://loinc.org|29463-7",
            }
    )\
        .gatherSimplePaths(['id','issued','code.coding.code'])\
            .explode(['id','issued','code.coding.code'])

interesting.issued = pd.to_datetime(interesting.issued).dropna().apply(lambda x:x.replace(tzinfo=None))
interesting[interesting.issued> datetime.fromisoformat('2021-01-01T00:00:00')]

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.95it/s]
SEARCH[Observation]> : 100%|██████████| 1/1 [00:00<00:00,  4.23it/s]

	id	issued	code.coding.code
0	2164039	2021-06-05 05:30:23.291	[29463-7]

Episodes of Care#

FHIR EpisodeOfCare Resource

[56]:

rootPatients[:2]

[56]:

	data
0	{'resourceType': 'Patient', 'id': '9ac622c4-61...
1	{'resourceType': 'Patient', 'id': '1849165', '...

[57]:

pack.getPatients(['P0522-patientBSJ1']).getEpisodesOfCare()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.41it/s]
SEARCH[EpisodeOfCare]> : 100%|██████████| 1/1 [00:00<00:00,  4.37it/s]

[57]:

	data
0	[{'resourceType': 'EpisodeOfCare', 'id': 'P052...

Family Member Histories#

FHIR FamilyMemberHistory Resource

[58]:

pack.getPatients(['Patient/2866670']).getFamilyMemberHistories()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.09it/s]
SEARCH[FamilyMemberHistory]> : 100%|██████████| 1/1 [00:00<00:00,  4.49it/s]

[58]:

	data
0	[{'resourceType': 'FamilyMemberHistory', 'id':...

Medication Administrations#

FHIR MedicationAdministration Resource

[59]:

pack.getPatients(['Patient/31678']).getMedicationAdministrations()[:5]

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.33it/s]
SEARCH[MedicationAdministration]> : 100%|██████████| 1/1 [00:00<00:00,  4.50it/s]

[59]:

	data
0	[{'resourceType': 'MedicationAdministration', ...

Medication Requests#

FHIR MedicationRequest Resource

[60]:

pack.getPatients(['Patient/202205uscore-patient-example-1']).getMedicationRequests().explode()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.93it/s]
SEARCH[MedicationRequest]> : 100%|██████████| 3/3 [00:00<00:00, 12.37it/s]

[60]:

	data
0	{'resourceType': 'MedicationRequest', 'id': '2...
0	{'resourceType': 'MedicationRequest', 'id': '2...
0	{'resourceType': 'MedicationRequest', 'id': '2...

Diagnostic Reports#

FHIR DiagnosticReport Resource

[63]:

diagnosticReports=pack\
    .getPatients(["Patient/9b8c1901-62ee-48a7-8229-b771d59f1e5f"])\
            .getDiagnosticReports(
                    searchParams={}
                    )\
                    .explode()

diagnosticReports

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.15it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 12/12 [00:00<00:00, 27.91it/s]

[63]:

	data
0	{'resourceType': 'DiagnosticReport', 'id': '12...
0	{'resourceType': 'DiagnosticReport', 'id': '5a...
0	{'resourceType': 'DiagnosticReport', 'id': '2d...
0	{'resourceType': 'DiagnosticReport', 'id': '01...
0	{'resourceType': 'DiagnosticReport', 'id': '47...
0	{'resourceType': 'DiagnosticReport', 'id': 'b1...
0	{'resourceType': 'DiagnosticReport', 'id': '58...
0	{'resourceType': 'DiagnosticReport', 'id': '87...
0	{'resourceType': 'DiagnosticReport', 'id': '8c...
0	{'resourceType': 'DiagnosticReport', 'id': 'ac...
0	{'resourceType': 'DiagnosticReport', 'id': 'bc...
0	{'resourceType': 'DiagnosticReport', 'id': 'bf...

[64]:

paths=[
    "subject",
    "presentedForm.contentType",
    "presentedForm.data",
    "presentedForm.url",
    "presentedForm.title",
    "presentedForm.creation"
]



diagnosticReports=pack.getDiagnosticReports(
    searchParams={
            "_id":"19bdf90a-8ca4-4921-8aeb-2bf3423aaf09",
            # "identifier":"|",
            # "_content":"covid19",
            # "code":"|",
            # "issued__gt":"2010-01-01",
            # "issued__lt":"2011-01-01"
    }
)

diagnosticReports.gatherSimplePaths(paths)

SEARCH[DiagnosticReport]> : 100%|██████████| 1/1 [00:00<00:00,  4.10it/s]

[64]:

	subject	presentedForm.contentType	presentedForm.data	presentedForm.url	presentedForm.title	presentedForm.creation
0	{'reference': 'Patient/e92abcdc-a300-41e0-aa0f...	[text/plain]	[Q2pJd01UQXRNVEV0TVRNS0NpTWdRMmhwWldZZ1EyOXRjR...	None	None	None

Downloading URLs Found in Resources#

[65]:

paths=[
    'id',
    'subject.reference',
    'presentedForm.url'
]

diagnosticReports = pack.getPatients(
    ['Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc']
    )\
        .getDiagnosticReports()[:10]

diagnosticReports=diagnosticReports.gatherSimplePaths(paths)
diagnosticReports=diagnosticReports.explode('presentedForm.url')
diagnosticReports

# diagnosticReports['path']=diagnosticReports['id']+'_'+diagnosticReports['presentedForm.url'].str.split('/').str[-1:].str[0]
# diagnosticReports['data']=diagnosticReports.getURLBytes(operateOnCol='presentedForm.url')
# diagnosticReports.sendBytesToFile()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.37it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 11/11 [00:00<00:00, 23.44it/s]

[65]:

	id	subject.reference	presentedForm.url
0	[1ca4c411-116d-49d7-82e0-cde6bff90cfd, 126df18...	[Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc,...	None

[66]:

diagnosticReports.loc[:, diagnosticReports.columns!='data'][:5]

[66]:

	id	subject.reference	presentedForm.url
0	[1ca4c411-116d-49d7-82e0-cde6bff90cfd, 126df18...	[Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc,...	None

Retrieving Multiple Related Resources#

[67]:

absolutePaths=[
#    'Condition.code.coding.code',
   'Condition.id',
    'Condition.subject.reference',
    'Encounter.id',
    'Encounter.participant.individual.reference',
#     'Procedure.code.coding.display',
#     'Procedure.code.coding.code',
    'Procedure.id',
    'Procedure.status',
    'Procedure.performedDateTime'
]

result=pack.getPatients(
    ['Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc']
).getAbsolutePaths(absolutePaths)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.01it/s]
SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  4.30it/s]
SEARCH[Encounter]> : 100%|██████████| 11/11 [00:00<00:00, 45.72it/s]
SEARCH[Procedure]> : 100%|██████████| 2/2 [00:00<00:00,  8.60it/s]

[68]:

result['Procedure']

[68]:

	Procedure.id	Procedure.performedDateTime	Procedure.status
0	f262bafb-789a-44a1-9453-c21065abc4d1	None	completed
1	e65c5378-5d1a-4978-9590-c6c8846dd6d0	None	completed

[69]:

paths=[
    'valueQuantity.value',
    'valueQuantity.unit',
    'valueQuantity.system',
    'valueQuantity.code',
]

[70]:

pack.\
    getPatients(['e92abcdc-a300-41e0-aa0f-378daebe25dc'])\
            .getObservations()\
                    .explode()\
                            .gatherSimplePaths(paths)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.50it/s]

[70]:

	valueQuantity.value	valueQuantity.unit	valueQuantity.system	valueQuantity.code
0	None	None	None	None

[71]:

result["Condition"]

[71]:

	Condition.id	Condition.subject.reference
0	b8a1a1c4-f973-4b6b-a0ea-3d04bc4c8823	Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc

[72]:

result["Encounter"]

[72]:

	Encounter.id	Encounter.participant.individual.reference
0	b9f19065-c8e6-40b9-b368-b09a8fb9a8d6	[Practitioner/00000171-0929-2892-0000-00000001...
1	174d8c79-5517-4f80-967f-3939f943b2c8	[Practitioner/00000171-0929-2892-0000-00000001...
2	3f3a061a-5df2-4dc0-872c-e1e4b88955a1	[Practitioner/00000171-0929-2892-0000-00000001...
3	2b8cb0e7-5b1e-4769-a418-bf9e6dd86611	[Practitioner/00000171-0929-2892-0000-00000001...
4	36fb900c-9ff7-4131-812c-536ab50a0a5c	[Practitioner/00000171-0929-2892-0000-00000000...
5	9911ef15-1b9a-4fbd-b95d-05bd4f060269	[Practitioner/00000171-0929-2892-0000-00000001...
6	f3b1e501-aac6-4480-bf35-38474563069a	[Practitioner/00000171-0929-2892-0000-00000001...
7	969f9166-4f9a-4be6-9257-ed00b295a408	[Practitioner/00000171-0929-2892-0000-00000001...
8	806264f4-4f45-4105-a5bc-8e9a9c49b119	[Practitioner/00000171-0929-2892-0000-00000001...
9	40166ee5-0bc3-4819-96c9-e07dd26e938b	[Practitioner/00000171-0929-2892-0000-00000001...
10	48f082f8-b46c-4127-a1b4-8e3c1d71a132	[Practitioner/00000171-0929-2892-0000-00000001...

[73]:

result["Procedure"]

[73]:

	Procedure.id	Procedure.performedDateTime	Procedure.status
0	f262bafb-789a-44a1-9453-c21065abc4d1	None	completed
1	e65c5378-5d1a-4978-9590-c6c8846dd6d0	None	completed

[74]:

result['Encounter'].explode(
    'Encounter.participant.individual.reference'
)\
    .rename(
            columns={"Encounter.participant.individual.reference":"data"}
            )\
                    .dropna()\
                            .getResources()[:5]\
                                    .gatherSimplePaths(['name.given','name.family'])

GET[None]> : 100%|██████████| 11/11 [00:02<00:00,  4.38it/s]

[74]:

	name.given	name.family
0	[[Willy639]]	[Rutherford999]
1	[[Willy639]]	[Rutherford999]
2	[[Willy639]]	[Rutherford999]
3	[[Willy639]]	[Rutherford999]
4	[[Lilla884]]	[Mills423]

Imaging Studies#

FHIR ImagingStudy Resource

[75]:

conds=pack.getConditions(
    searchParams={
            "code":"C61",
            # "_content": "leber"
    }
    )
conds

SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  4.55it/s]

[75]:

	data
0	{'resourceType': 'Condition', 'id': '1849657',...

[76]:

pack\
    .getImagingStudies(searchParams={"endpoint:missing":False})\
            .gatherSimplePaths(['series.description','series.uid','identifier.value'])

# use .getDICOMInstances().sendDICOMToFiles() to download DICOM files

SEARCH[ImagingStudy]> : 100%|██████████| 4/4 [00:00<00:00, 14.80it/s]

[76]:

	series.description	series.uid	identifier.value
0	None	[IdType-2]	[Identifier-117]
1	None	[IdType-5]	[Identifier-118]
2	None	None	None
3	None	[1.2.276.0.7230010.3.1.3.8323329.10.1594989066...	[urn:oid:1.2.826.0.1.3680043.8.498.94636677472...

Transformation#

Gathering Fields from Resources#

JSON-Serialized Resource Keys#

[77]:

patients.gatherKeys().data.explode().value_counts()[:10]

[77]:

name.given        6
name.family       5
telecom.use       5
resourceType      4
id                4
telecom.system    4
gender            4
name              4
birthDate         4
telecom.value     4
Name: data, dtype: int64

[78]:

pack.getPatients(
    ['e92abcdc-a300-41e0-aa0f-378daebe25dc']
    )\
        .gatherKeys(['valueString'])\
            .explode()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.40it/s]

[78]:

	data
0	resourceType
0	id
0	meta
0	meta.versionId
0	meta.lastUpdated
...	...
0	communication.language.coding
0	communication.language.coding.system
0	communication.language.coding.code
0	communication.language.coding.display
0	communication.language.text

118 rows × 1 columns

JSON-Serialized Resource Values#

[79]:

pack.getPatients(
    ['e92abcdc-a300-41e0-aa0f-378daebe25dc'],
    # includeLinkedPatients=True
    )\
        .gatherValuesForKeys(['valueString'])\
            .explode()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.36it/s]

[79]:

	data
0	White
0	Not Hispanic or Latino
0	Nanci249 Gleichner915

Nested FHIR References#

[80]:

pack.gatherReferences(
    ['Patient/9ac622c4-61c8-40b4-b6d9-06cfeb3d6995']
    , recursive=True
)

[80]:

	referencer	referencee
0	{'reference': 'Patient/9ac622c4-61c8-40b4-b6d9...	[Patient/b558da74-7756-4845-87d5-d1cca8b79a62]
1	{'reference': 'Patient/b558da74-7756-4845-87d5...	[]

Nested Text and Narratives#

[81]:

fp.PACK().getPatients(
    ['Patient/1555106'],
    )\
        .getObservations()[:5]\
            .explode()\
                .gatherText()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.15it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:02, 266.45it/s]

[81]:

	data
0	[laboratory, Alkaline phosphatase [Enzymatic a...
1	[laboratory, 7.5804, Protein [Mass/volume] in ...
2	[laboratory, Glomerular filtration rate/1.73 s...
3	[laboratory, MCH [Entitic mass] by Automated c...
4	[laboratory, 20.88, Carbon dioxide, total [Mol...
...	...
95	[Diastolic Blood Pressure, 138, Blood Pressure...
96	[laboratory, Eosinophils/100 leukocytes in Blo...
97	[8.0379, laboratory, C reactive protein [Mass/...
98	[laboratory, Monocytes/100 leukocytes in Blood...
99	[laboratory, 35.401, Creatine kinase [Enzymati...

100 rows × 1 columns

Dates#

[82]:

fp.PACK().getPatients(
    ['Patient/1555106'],
    )\
        .getObservations()[:5]\
            .explode()\
                .gatherValuesForKeys(['issued'])

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.43it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:01, 304.49it/s]

[82]:

	data
0	[2020-03-18T21:53:14.197-04:00]
1	[2020-03-19T21:53:14.197-04:00]
2	[2020-03-19T21:53:14.197-04:00]
3	[2020-03-14T21:53:14.197-04:00]
4	[2020-03-19T21:53:14.197-04:00]
...	...
95	[2020-03-10T21:53:14.197-04:00]
96	[2020-03-15T21:53:14.197-04:00]
97	[2020-03-09T21:53:14.197-04:00]
98	[2020-03-15T21:53:14.197-04:00]
99	[2020-03-09T21:53:14.197-04:00]

100 rows × 1 columns

[83]:

fp.PACK().getPatients(
    ['Patient/1555106'],
    )\
        .getObservations()[:5]\
            .explode()\
                .gatherDates()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.46it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:01, 312.13it/s]

[83]:

	dates
0	[2020-03-18T21:53:14-04:00, 2020-03-18T21:53:1...
1	[2020-03-19T21:53:14-04:00, 2020-03-19T21:53:1...
2	[2020-03-19T21:53:14-04:00, 2020-03-19T21:53:1...
3	[2020-03-14T21:53:14-04:00, 2020-03-14T21:53:1...
4	[2020-03-19T21:53:14-04:00, 2020-03-19T21:53:1...
...	...
95	[2020-03-10T21:53:14-04:00, 2020-03-10T21:53:1...
96	[2020-03-15T21:53:14-04:00, 2020-03-15T21:53:1...
97	[2020-03-09T21:53:14-04:00, 2020-03-09T21:53:1...
98	[2020-03-15T21:53:14-04:00, 2020-03-15T21:53:1...
99	[2020-03-09T21:53:14-04:00, 2020-03-09T21:53:1...

100 rows × 1 columns

Load#

Exporting Frames#

[84]:

pack.validate(
    ['Patient/1555106']
    )\
        .sendResourcesToFiles(['./data.ignore'])

[84]:

array([ True])

Utils#

Server Profiling#

[ ]:

pack.countServerResources()

	resourceType	count
0	Account	501
1	ActivityDefinition	284
2	AdverseEvent	116
3	AllergyIntolerance	9031
4	Appointment	29133
...	...	...
141	TestReport	11
142	TestScript	33
143	ValueSet	3041
144	VerificationResult	9
145	VisionPrescription	15

146 rows × 2 columns

Validation#

[8]:

pack.validate(
    ['Patient/1555106']
)

[8]:

	data
0	{'resourceType': 'Patient', 'id': '1555106', '...

FHIRPACK Internals#

FHIRPy#

URL Parsing#

[ ]:

import fhirpy.base.utils as fpu
url=fpu.parse_pagination_url('/app/FHIR/r4/Condition?code=C61&_count=1&_sort=-onset-date&identifier=%7C&_Pagination=eyJvZmZzZXQiOjIwfQ%3D%3D')
url

('/app/FHIR/r4/Condition',
 {'code': ['C61'],
  '_count': ['1'],
  '_sort': ['-onset-date'],
  'identifier': ['|'],
  '_Pagination': ['eyJvZmZzZXQiOjIwfQ==']})

Raw fetch_resource()#

[ ]:

pack.client._fetch_resource(
    "Condition/1499041"
)

{'resourceType': 'Condition',
 'id': '1499041',
 'meta': {'versionId': '1',
  'lastUpdated': '2020-10-05T16:29:07.960+00:00',
  'source': '#0sjLd8ZeFHHrRHaX'},
 'clinicalStatus': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/condition-clinical',
    'code': 'active'}]},
 'verificationStatus': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/condition-ver-status',
    'code': 'confirmed'}]},
 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/condition-category',
     'code': 'encounter-diagnosis',
     'display': 'Encounter Diagnosis'}]}],
 'code': {'coding': [{'system': 'http://snomed.info/sct',
    'code': '22298006',
    'display': 'Myocardial Infarction'}],
  'text': 'Myocardial Infarction'},
 'subject': {'reference': 'Patient/1465609'},
 'onsetDateTime': '2020-04-01T09:52:49-04:00',
 'recordedDate': '2020-04-01T09:52:49-04:00',
 'asserter': {'reference': 'Practitioner/1498740'}}

Raw client.execute()#

[ ]:

pack.client.execute('/baseR4/Condition',
method='get',
params={
    'code':'C61',
    '_sort':'-onset-date',
    '_count': 1,
    '_total':'accurate'
}
).total

Customization#

fhirpack.custom.extraction.base#

[ ]:

# the fhirpack.custom package is guaranteed to never be used by us
# use it to customize fhirpack

# pack.unimplementedPluginBaseExtractorMethod()
# pack.unimplementedPluginBaseTransformerMethod()
# pack.unimplementedPluginBaseLoaderMethod()

# pack.unimplementedPluginSampleExtractorMethod()
# pack.unimplementedPluginSampleTransformerMethod()
# pack.unimplementedPluginSampleLoaderMethod()

FHIRPACK Detailed Usage

Contents

FHIRPACK Detailed Usage#

Boilerplate#

Preamble and Imports#

Useful Paths for Data Storage#

FHIR Server Connection#

CLI Usage#

From Custom Environment File#

Manual Setup#

For Docker Enthusiasts#

Configuring FHIRPACK from the Default Environment File (./.env)#

A Motivating Example#

FHIRPACK and FHIR Resources#

References#

Resources#

Reference to Resource#

Direct Resource Access#

Serialization and Element Access#

PANDAS-Style DataFrame Operations#

fhirpack.base.Frame#

Extraction#

Patients#

Patients as Operand and other Resources#

Root Patients and Identities#

Linked Patients#

Conditions#

Patients for Conditions#

Conditions for Patient#

Observations#

Episodes of Care#

Family Member Histories#

Medication Administrations#

Medication Requests#

Diagnostic Reports#

Downloading URLs Found in Resources#

Retrieving Multiple Related Resources#

Imaging Studies#

Transformation#

Gathering Fields from Resources#

JSON-Serialized Resource Keys#

JSON-Serialized Resource Values#

Nested FHIR References#

Nested Text and Narratives#

Dates#

Load#

Exporting Frames#

Utils#

Server Profiling#

Validation#

FHIRPACK Internals#

FHIRPy#

URL Parsing#

Raw fetch_resource()#

Raw client.execute()#

Customization#

fhirpack.custom.extraction.base#