General Usage#

[1]:

%load_ext autoreload
%autoreload 2
%pprint off

Pretty printing has been turned OFF

[2]:

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

[3]:

%pprint

Pretty printing has been turned ON

Preamble#

[!] use only if you have NOT 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

[4]:

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

Imports#

[5]:

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#

[6]:

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

FHIR Server Connection#

CLI Usage#

[7]:

!python -m fhirpack.cli -e .env.example "-o" "getPatients" -p "given = Chalmers" #-v

SEARCH[Patient]> : 100%|██████████████████████████| 1/1 [00:01<00:00,  1.40s/it]
                                                data Patient.id
0  {'resourceType': 'Patient', 'id': '1567099', '...    1567099

[9]:

# public FHIR test servers may be unavailable sometimes
# if you prefer to test FHIRPACK using a locally running FHIR server
# you may use our provided Docker environment by changing into the
# cloned repository and running `docker-compose up``

!fp -e .env.docker -o "getPatients" -p "given = Max" #-v

SEARCH[Patient]> : 100%|██████████████████████████| 3/3 [00:01<00:00,  2.14it/s]
                                                data Patient.id
0  {'resourceType': 'Patient', 'id': '146053', 'm...     146053
1  {'resourceType': 'Patient', 'id': '146255', 'm...     146255
2  {'resourceType': 'Patient', 'id': '146496', 'm...     146496

From Custom Environment File#

[132]:

pack = fp.PACK(envFile='.env.docker')

for i,e in pack.getPatients(['146053']).data.items():
    print(
            json.dumps(e.serialize(), indent=4, sort_keys=True)[:200],
            '\n...'
    )

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00, 55.44it/s]

{
    "address": [
        {
            "city": "Walpole",
            "country": "US",
            "extension": [
                {
                    "extension": [
                        {

...



[133]:

!cat .env.example


SCHEMA=http
PORT=80

#DOMAIN=${SCHEMA}://hapi.fhir.org
#server has moved temporarily https://github.com/hapifhir/hapi-fhir/issues/1171#issuecomment-1179728061

DOMAIN=${SCHEMA}://test.hapifhir.io

#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}

From Default .env Environment File#

[134]:

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

Manual Setup#

[8]:


# pack  = fp.PACK("http://hapi.fhir.org/baseR4")
# pack  = fp.PACK(envFile=".env.example")
pack  = fp.PACK("http://test.hapifhir.io/baseR4")
pack.getPatients(['2918556'])

# pack  = fp.PACK("http://127.0.0.1:42112/hapi-fhir-jpaserver/fhir")
# pack.getPatients(['146053'])

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.09it/s]

[8]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '2918556', '... 2918556 
[136]:

#testing with another less reliable FHIR server
# pack  = fp.PACK("http://test.fhir.org/r4/")
# pack.getPatients(['11']).data.iloc[0]

Testing with A Docker FHIR Server and Synthetic Data#

[137]:

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

# pack.getPatients(['146053'])

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00, 61.56it/s]

[137]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '146053', 'm... 146053 
[138]:

# 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

# pack  = fp.PACK("http://127.0.0.1:42112/hapi-fhir-jpaserver/fhir")
# pack.getPatients(['1']).data.iloc[0].serialize()
# pack.getPatients(['146053'])

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00, 52.43it/s]

[138]:

{'resourceType': 'Patient',
 'id': '1',
 'meta': {'versionId': '1',
  'lastUpdated': '2020-06-11T15:26:55.251+00:00',
  'source': '#JlcA0bg5xBW1iwXq',
  'tag': [{'system': 'https://smarthealthit.org/tags',
    'code': 'synthea-5-2019'}]},
 'text': {'status': 'generated',
  'div': '<div xmlns="http://www.w3.org/1999/xhtml">Generated by <a href="https://github.com/synthetichealth/synthea">Synthea</a>.Version identifier: v2.4.0-100-g26a4b936\n .   Person seed: 8766734163625651911  Population seed: 1559319163074</div>'},
 'extension': [{'url': 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race',
   'extension': [{'url': 'ombCategory',
     'valueCoding': {'system': 'urn:oid:2.16.840.1.113883.6.238',
      'code': '2106-3',
      'display': 'White'}},
    {'url': 'text', 'valueString': 'White'}]},
  {'url': 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity',
   'extension': [{'url': 'ombCategory',
     'valueCoding': {'system': 'urn:oid:2.16.840.1.113883.6.238',
      'code': '2186-5',
      'display': 'Not Hispanic or Latino'}},
    {'url': 'text', 'valueString': 'Not Hispanic or Latino'}]},
  {'url': 'http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName',
   'valueString': 'Aiko Jacobs'},
  {'url': 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex',
   'valueCode': 'M'},
  {'url': 'http://hl7.org/fhir/StructureDefinition/patient-birthPlace',
   'valueAddress': {'city': 'Holyoke',
    'state': 'Massachusetts',
    'country': 'US'}},
  {'url': 'http://synthetichealth.github.io/synthea/disability-adjusted-life-years',
   'valueDecimal': 0.3202898736241102},
  {'url': 'http://synthetichealth.github.io/synthea/quality-adjusted-life-years',
   'valueDecimal': 63.67971012637589}],
 'identifier': [{'system': 'https://github.com/synthetichealth/synthea',
   'value': 'e925b0f3-8006-43f6-aa31-94bd215e55e7'},
  {'type': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v2-0203',
      'code': 'MR',
      'display': 'Medical Record Number'}],
    'text': 'Medical Record Number'},
   'system': 'http://hospital.smarthealthit.org',
   'value': 'e925b0f3-8006-43f6-aa31-94bd215e55e7'},
  {'type': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v2-0203',
      'code': 'SS',
      'display': 'Social Security Number'}],
    'text': 'Social Security Number'},
   'system': 'http://hl7.org/fhir/sid/us-ssn',
   'value': '999-22-1962'},
  {'type': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v2-0203',
      'code': 'DL',
      'display': "Driver's License"}],
    'text': "Driver's License"},
   'system': 'urn:oid:2.16.840.1.113883.4.3.25',
   'value': 'S99942380'},
  {'type': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v2-0203',
      'code': 'PPN',
      'display': 'Passport Number'}],
    'text': 'Passport Number'},
   'system': 'http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber',
   'value': 'X45815551X'}],
 'name': [{'use': 'official',
   'family': 'Koepp',
   'given': ['Abdul'],
   'prefix': ['Mr.']}],
 'telecom': [{'system': 'phone', 'value': '555-978-4581', 'use': 'home'}],
 'gender': 'male',
 'birthDate': '1954-10-02',
 'address': [{'extension': [{'url': 'http://hl7.org/fhir/StructureDefinition/geolocation',
     'extension': [{'url': 'latitude', 'valueDecimal': 42.534202},
      {'url': 'longitude', 'valueDecimal': -70.969734}]}],
   'line': ['313 Lockman Row Suite 4'],
   'city': 'Peabody',
   'state': 'Massachusetts',
   'postalCode': '01940',
   'country': 'US'}],
 'maritalStatus': {'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v3-MaritalStatus',
    'code': 'M',
    'display': 'M'}],
  'text': 'M'},
 'multipleBirthBoolean': False,
 'communication': [{'language': {'coding': [{'system': 'urn:ietf:bcp:47',
      'code': 'en-US',
      'display': 'English'}],
    'text': 'English'}}]}

Introductory Example#

[24]:

# 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"})\
    .getDiagnosticReports()\
            .getPatients()\
                    .getRootPatients()\
                            .gatherSimplePaths(['id','birthDate'])

SEARCH[Patient]> : 100%|██████████| 43/43 [00:02<00:00, 20.52it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 69/69 [00:02<00:00, 32.65it/s]
SEARCH[Patient]> : 100%|██████████| 7/7 [00:00<00:00, 23.29it/s]

[24]:
id birthDate
0 7ca61bcb-80a6-43fb-ad49-7334df273d39 2007-11-18
1 7ca61bcb-80a6-43fb-ad49-7334df273d39 2007-11-18
2 7ca61bcb-80a6-43fb-ad49-7334df273d39 2007-11-18
3 7ca61bcb-80a6-43fb-ad49-7334df273d39 2007-11-18
4 7ca61bcb-80a6-43fb-ad49-7334df273d39 2007-11-18
... ... ...
64 2744581 1956-08-03
65 2744581 1956-08-03
66 2744581 1956-08-03
67 2744581 1956-08-03
68 2744581 1956-08-03

69 rows × 2 columns

FHIR PACK Usage#

References#

[196]:

patientReference = pack.getReferences(['Patient/647487'])
patientReference.data.iloc[0].to_resource().serialize()

[196]:

{'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'}

[197]:

# getResources applied to References simplifies the conversion
# of FHIR/FHIRpy References to Resources

patientReference.getResources()

GET[None]> : 100%|██████████| 1/1 [00:00<00:00,  3.57it/s]

[197]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '647487', 'm... 647487

Resources#

Reference to Resource#

[199]:

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

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

[199]:

0    1849165
1     647487
Name: data, dtype: object

[200]:

multiPatientReference.getResources()

GET[None]> : 100%|██████████| 2/2 [00:00<00:00,  3.57it/s]

[200]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '1849165', '... 1849165
1 {'resourceType': 'Patient', 'id': '647487', 'm... 647487

Direct Resource#

[201]:

pack.getPatients(
    searchParams={"given":"max"}
)

SEARCH[Patient]> :  21%|██        | 100/476 [00:04<00:16, 22.77it/s]

[201]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '2583214', '... 2583214
1 {'resourceType': 'Patient', 'id': '2583215', '... 2583215
2 {'resourceType': 'Patient', 'id': '1709020', '... 1709020
3 {'resourceType': 'Patient', 'id': '1638431', '... 1638431
4 {'resourceType': 'Patient', 'id': '1631503', '... 1631503
... ... ...
95 {'resourceType': 'Patient', 'id': '2651939', '... 2651939
96 {'resourceType': 'Patient', 'id': '2651964', '... 2651964
97 {'resourceType': 'Patient', 'id': '2651987', '... 2651987
98 {'resourceType': 'Patient', 'id': '2651998', '... 2651998
99 {'resourceType': 'Patient', 'id': '2652009', '... 2652009

100 rows × 2 columns

[207]:

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

SEARCH[Patient]> : 100%|██████████| 12/12 [00:01<00:00,  9.67it/s]

[207]:

(12, 2)

[208]:

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

multiPatientResource

GET[None]> : 100%|██████████| 2/2 [00:00<00:00,  3.59it/s]

[208]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '1849165', '... 1849165
1 {'resourceType': 'Patient', 'id': '647487', 'm... 647487

Alterntives to Serialization and Element Access#

[209]:

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

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

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

[209]:

['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']

[209]:

'2016-01-20'

[210]:

multiPatientReference.summary
multiPatientReference.getResources().summary

[210]:
id resourceType
0 1849165 Patient
1 647487 Patient 
GET[None]> : 100%|██████████| 2/2 [00:00<00:00,  3.47it/s]

[210]:
id name.given name.family birthDate city state country
0 1849165 [[Peter, James], [Jim], [Peter, James]] [Chalmers, Windsor] 1974-12-25 None None None
1 647487 [[Series_Status: Not complete, Evaluation_Stat... [# 5 Pentacel at ≥ 4 yrs] 2016-01-20 None None None 
[211]:

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"
        }
    }
]

[214]:

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

GET[DiagnosticReport]> : 100%|██████████| 1/1 [00:00<00:00,  3.36it/s]

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

DataFrame Operations#

[215]:

multiPatientReference[:1]

multiPatientReference[-1:]

multiPatientReference.values

multiPatientReference.info()

[215]:
data
0 {'reference': 'Patient/1849165'} 
[215]:
data
1 {'reference': 'Patient/647487'} 
[215]:

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

pack.base.Frame#

[216]:

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

[216]:
data
0 {'resourceType': 'Patient', 'id': '647487', 'm...

Extraction#

Patient Extraction#

fhirpack.extraction.getPatients#

[218]:

pack.getPatients(
    [
            '647487'
    ]
)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.97it/s]

[218]:
data Patient.id
0 {'resourceType': 'Patient', 'id': '647487', 'm... 647487 
[219]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.05it/s]

[219]:

{'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'}

[220]:

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

GET[Patient]> : 100%|██████████| 2/2 [00:00<00:00,  3.80it/s]

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



[221]:

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

getPatientsAsList

GET[Patient]> : 100%|██████████| 2/2 [00:00<00:00,  3.85it/s]

[221]:

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

[222]:

getPatientsAsList

[222]:

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

[223]:

[e[1] for e in getPatientsAsList]

[e[0].id for e in getPatientsAsList]

[223]:

['647487', '1849165']

[223]:

['647487', '1849165']

Patients as Operand and Extracting other Resources#

[224]:

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

GET[Patient]> : 100%|██████████| 4/4 [00:01<00:00,  3.34it/s]

fhirpack.extraction.getRootPatient#

[225]:

patients.getRootPatients()

[225]:
data RootPatient.id Patient.id
0 {'resourceType': 'Patient', 'id': '9ac622c4-61... 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995
1 {'resourceType': 'Patient', 'id': '1849165', '... 1849165 1849165
2 {'resourceType': 'Patient', 'id': '649231', 'm... 649231 649231
3 {'resourceType': 'Patient', 'id': '650224', 'm... 650224 650224 
[16]:

pack.getRootPatients(
    [
        'b558da74-7756-4845-87d5-d1cca8b79a62',
    ],
).getLinkedPatients()

# .gatherSimplePaths(["id"]).id.unique()

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.17it/s]
SEARCH[RootPatient]> : 100%|██████████| 1/1 [00:00<00:00,  4.20it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.89it/s]

[16]:
data LinkedPatient.id RootPatient.id Patient.id
0 {'resourceType': 'Patient', 'id': 'b558da74-77... b558da74-7756-4845-87d5-d1cca8b79a62 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 b558da74-7756-4845-87d5-d1cca8b79a62 
[227]:

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

GET[None]> : 100%|██████████| 1/1 [00:00<00:00,  3.60it/s]
SEARCH[RootPatient]> : 100%|██████████| 1/1 [00:00<00:00,  4.04it/s]

[227]:
data RootPatient.id Patient.id
0 {'resourceType': 'Patient', 'id': '9ac622c4-61... 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 b558da74-7756-4845-87d5-d1cca8b79a62 
[228]:

rootPatients = patients.getRootPatients()

rootPatients.gatherSimplePaths(['id','name.given','name.family','birthDate'])

[228]:
id name.given name.family birthDate
0 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 [[TestGiven]] [TestFamily] 1981-01-01
1 1849165 [[Peter, James], [Jim], [Peter, James]] [Chalmers, Windsor] 1974-12-25
2 649231 [[Series_Status: Complete, Evaluation_Status_1... [Dose # 1 PCV 13 at age 12 mos # 2 at 1 yr 8 w... 2018-12-21
3 650224 [[Series_Status: Not complete, Evaluation_Stat... [# 1 at age ≥ 13 years old] 2007-02-08 
[229]:

rootPatients.data[0].name

[229]:

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

[230]:

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

b558da74-7756-4845-87d5-d1cca8b79a62

fhirpack.extraction.getLinkedPatients#

[9]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.08it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.65it/s]

[9]:
data LinkedPatient.id RootPatient.id Patient.id
0 {'resourceType': 'Patient', 'id': 'b558da74-77... b558da74-7756-4845-87d5-d1cca8b79a62 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995

fhirpack.extraction.getConditions#

Conditions#

[232]:

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

conditions

SEARCH[Condition]> : 100%|██████████| 36/36 [00:00<00:00, 67.90it/s]

[232]:
data Condition.id
0 {'resourceType': 'Condition', 'id': '1584692',... 1584692
1 {'resourceType': 'Condition', 'id': '1591180',... 1591180
2 {'resourceType': 'Condition', 'id': '1402386',... 1402386
3 {'resourceType': 'Condition', 'id': '1403562',... 1403562
4 {'resourceType': 'Condition', 'id': '1495528',... 1495528

Patients for Conditions#

[233]:

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

SEARCH[Patient]> : 100%|██████████| 5/5 [00:00<00:00, 17.46it/s]

[233]:
id name.given name.family
0 1402076 [[Phyliss]] [Nyambura]
1 1403421 [[Stefania]] [Bethwell]
2 1495412 [[Hallie315], [Hallie315]] [Donnelly343, Osinski784]
3 1583909 [[Shayne60]] [Miller503]
4 1590885 [[Ty725]] [Sporer811] 
[234]:

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

SEARCH[Patient]> : 100%|██████████| 5/5 [00:00<00:00, 18.43it/s]

[235]:

!cat data.ignore

,data
0,1402076
1,1403421
2,1495412
3,1583909
4,1590885

[236]:

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

[236]:

(5, 1)

[236]:
data
0 1402076
1 1403421
2 1495412
3 1583909
4 1590885

Conditions for Patient#

[237]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.79it/s]
SEARCH[Condition]> : 100%|██████████| 5/5 [00:00<00:00, 18.07it/s]

[237]:
data Condition.id Patient.id
0 {'resourceType': 'Condition', 'id': '2b7a4d69-... 2b7a4d69-00fd-4574-86da-bdf46b21b72b {'reference': 'Patient/8cbf1128-3644-47a1-9cc8...
1 {'resourceType': 'Condition', 'id': '0fc73e7c-... 0fc73e7c-18a8-47d8-bdc9-82df7f06e4a8 {'reference': 'Patient/8cbf1128-3644-47a1-9cc8...
2 {'resourceType': 'Condition', 'id': 'cb1bab6c-... cb1bab6c-581b-47f4-8036-429462224f55 {'reference': 'Patient/8cbf1128-3644-47a1-9cc8...
3 {'resourceType': 'Condition', 'id': 'bc301bbf-... bc301bbf-d354-4422-abe8-f7fe9c48d83c {'reference': 'Patient/8cbf1128-3644-47a1-9cc8...
4 {'resourceType': 'Condition', 'id': '5db4866a-... 5db4866a-c48a-4b62-923b-96daa243226b {'reference': 'Patient/8cbf1128-3644-47a1-9cc8...

fhipack.extraction.getEpisodesOfCare#

[238]:

rootPatients[:2]

[238]:
data RootPatient.id Patient.id
0 {'resourceType': 'Patient', 'id': '9ac622c4-61... 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995 9ac622c4-61c8-40b4-b6d9-06cfeb3d6995
1 {'resourceType': 'Patient', 'id': '1849165', '... 1849165 1849165 
[239]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.32it/s]
SEARCH[EpisodeOfCare]> : 100%|██████████| 1/1 [00:00<00:00,  3.17it/s]

[239]:
data EpisodeOfCare.id Patient.id
0 {'resourceType': 'EpisodeOfCare', 'id': 'P0522... P0522-eLTSS-episode-Initial None

fhipack.extraction.getFamilyMemberHistories#

[240]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.31it/s]
SEARCH[FamilyMemberHistory]> : 100%|██████████| 1/1 [00:00<00:00,  3.46it/s]

[240]:
data FamilyMemberHistory.id Patient.id

fhipack.extraction.getMedicationAdministrations#

[241]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.81it/s]
SEARCH[MedicationAdministration]> : 100%|██████████| 1/1 [00:00<00:00,  4.04it/s]

[241]:
data MedicationAdministration.id Patient.id
0 {'resourceType': 'MedicationAdministration', '... 31675 {'reference': 'Patient/31678'}

fhipack.extraction.getMedicationRequests#

[242]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.93it/s]
SEARCH[MedicationRequest]> : 100%|██████████| 3/3 [00:00<00:00, 10.68it/s]

[242]:
data MedicationRequest.id Patient.id

fhipack.extraction.getObservations#

[243]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.17it/s]
SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  3.09it/s]
SEARCH[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.89it/s]

[243]:
data Patient.id Condition.id
0 {'resourceType': 'Patient', 'id': '258974', 'm... 258974 259094 
[244]:


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,  3.55it/s]
SEARCH[Observation]> : 100%|██████████| 1/1 [00:00<00:00,  4.00it/s]

[244]:
id issued code.coding.code
0 2164039 2021-06-05 05:30:23.291 [29463-7]

fhirpack.extraction.getDiagnosticReports#

[245]:

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

diagnosticReports

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.67it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 12/12 [00:00<00:00, 25.38it/s]

[245]:
data DiagnosticReport.id Patient.id
0 {'resourceType': 'DiagnosticReport', 'id': '12... 122da94f-d24b-47ef-8409-58eb023cfb78 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
1 {'resourceType': 'DiagnosticReport', 'id': '5a... 5a1a396b-783c-495c-ace9-cedce2f0c335 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
2 {'resourceType': 'DiagnosticReport', 'id': '2d... 2d363733-58cb-4aba-b73f-487181359418 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
3 {'resourceType': 'DiagnosticReport', 'id': '01... 013d71cd-e38e-497c-9382-b21fb5eb5f53 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
4 {'resourceType': 'DiagnosticReport', 'id': '47... 471713d6-69eb-4fcf-900d-2eccf9d10f69 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
5 {'resourceType': 'DiagnosticReport', 'id': 'b1... b17c7848-f6c5-49a7-bd0a-f018ecc422de {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
6 {'resourceType': 'DiagnosticReport', 'id': '58... 58c69ea7-b4be-40a5-a59e-459b8fed660a {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
7 {'resourceType': 'DiagnosticReport', 'id': '87... 873433a5-68ed-42da-a6a0-d0ef3f7fd9ef {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
8 {'resourceType': 'DiagnosticReport', 'id': '8c... 8c5adc06-2c8c-431f-9492-d7c9ef99635d {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
9 {'resourceType': 'DiagnosticReport', 'id': 'ac... ac83cf63-9ea8-43ce-89a8-21a6b3d3319d {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
10 {'resourceType': 'DiagnosticReport', 'id': 'bc... bcd144a0-7a88-4a7c-bcb1-acf8601d6f54 {'reference': 'Patient/9b8c1901-62ee-48a7-8229...
11 {'resourceType': 'DiagnosticReport', 'id': 'bf... bf0754d5-26cd-46b3-a675-32e718d17a28 {'reference': 'Patient/9b8c1901-62ee-48a7-8229... 
[246]:

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,  3.72it/s]

[246]:
subject presentedForm.contentType presentedForm.data presentedForm.url presentedForm.title presentedForm.creation
0 {'reference': 'Patient/e92abcdc-a300-41e0-aa0f... [text/plain] [Q2pJd01UQXRNVEV0TVRNS0NpTWdRMmhwWldZZ1EyOXRjR... None None None

fhirpack.extraction.getURLBytes#

[247]:

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,  2.61it/s]
SEARCH[DiagnosticReport]> : 100%|██████████| 11/11 [00:00<00:00, 21.03it/s]

[247]:
id subject.reference presentedForm.url
0 1ca4c411-116d-49d7-82e0-cde6bff90cfd Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
1 126df183-9908-4df3-80a3-128a10fd6b3a Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
2 19bdf90a-8ca4-4921-8aeb-2bf3423aaf09 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
3 71701d6e-3bba-44c0-af75-271558aedb22 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
4 540317ac-5490-4186-8930-8bfbdaad1055 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
5 97f7f1b1-661f-4076-9352-e698cdf9ef6f Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
6 9995355f-1361-45de-aebb-a7446f8f13f7 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
7 34c775ba-b76d-4ef0-a69f-ab88e90ad151 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
8 1ff86952-9480-45b5-953d-e6056f74659f Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
9 5bd0f37e-7c1f-40ac-b654-97fa66875f70 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None 
[248]:

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

[248]:
id subject.reference presentedForm.url
0 1ca4c411-116d-49d7-82e0-cde6bff90cfd Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
1 126df183-9908-4df3-80a3-128a10fd6b3a Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
2 19bdf90a-8ca4-4921-8aeb-2bf3423aaf09 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
3 71701d6e-3bba-44c0-af75-271558aedb22 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None
4 540317ac-5490-4186-8930-8bfbdaad1055 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc None

fhirpack.extraction.base.getAbsolutePaths#

[249]:

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'
]

pack.client

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

[249]:

<SyncFHIRClient http://test.hapifhir.io/baseR4>

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.43it/s]
SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  3.64it/s]
SEARCH[Encounter]> : 100%|██████████| 11/11 [00:00<00:00, 41.63it/s]
SEARCH[Procedure]> : 100%|██████████| 2/2 [00:00<00:00,  7.70it/s]

[250]:

result['Procedure']

[250]:
Procedure.id Procedure.performedDateTime Procedure.status
0 f262bafb-789a-44a1-9453-c21065abc4d1 None completed
1 e65c5378-5d1a-4978-9590-c6c8846dd6d0 None completed 
[251]:

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

[252]:

pack.\
    getPatients(['2164033'])\
            .getObservations()\
                    .gatherSimplePaths(paths)

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.58it/s]
SEARCH[Observation]> : 100%|██████████| 1/1 [00:00<00:00,  4.05it/s]

[252]:
valueQuantity.value valueQuantity.unit valueQuantity.system valueQuantity.code
0 82.5 kg http://unitsofmeasure.org kg 
[253]:

result["Condition"]

[253]:
Condition.id Condition.subject.reference
0 b8a1a1c4-f973-4b6b-a0ea-3d04bc4c8823 Patient/e92abcdc-a300-41e0-aa0f-378daebe25dc 
[254]:

result["Encounter"]

[254]:
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... 
[255]:

result["Procedure"]

[255]:
Procedure.id Procedure.performedDateTime Procedure.status
0 f262bafb-789a-44a1-9453-c21065abc4d1 None completed
1 e65c5378-5d1a-4978-9590-c6c8846dd6d0 None completed 
[256]:

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 [00:03<00:00,  3.47it/s]

[256]:
name.given name.family
0 [[Willy639]] [Rutherford999]
1 [[Willy639]] [Rutherford999]
2 [[Willy639]] [Rutherford999]
3 [[Willy639]] [Rutherford999]
4 [[Lilla884]] [Mills423]

fhirpack.extraction.getImagingStudies#

[257]:

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

SEARCH[Condition]> : 100%|██████████| 1/1 [00:00<00:00,  2.73it/s]

[257]:
data Condition.id
0 {'resourceType': 'Condition', 'id': '1849657',... 1849657 
[258]:

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, 12.94it/s]

[258]:
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#

fhirpack.transformation.base.gatherKeys#

[259]:

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

[259]:

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

[260]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  2.82it/s]

[260]:
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

fhirpack.transformation.base.valuesForKeys#

[11]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.80it/s]

[11]:
data
0 [White, Not Hispanic or Latino, Nanci249 Gleic...

fhirpack.transformation.base.gatherReferences#

[262]:

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

[262]:
referencer referencee
0 {'reference': 'Patient/9ac622c4-61c8-40b4-b6d9... [Patient/b558da74-7756-4845-87d5-d1cca8b79a62]
1 {'reference': 'Patient/b558da74-7756-4845-87d5... []

fhirpack.transformation.base.gatherText#

[263]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.92it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:02, 239.22it/s]

[263]:
data
0 [Alkaline phosphatase [Enzymatic activity/volu...
1 [laboratory, Protein [Mass/volume] in Serum or...
2 [laboratory, Glomerular filtration rate/1.73 s...
3 [MCH [Entitic mass] by Automated count, labora...
4 [laboratory, Carbon dioxide, total [Moles/volu...

fhirpack.transformation.base.gatherDates#

[264]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  4.02it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:02, 264.53it/s]

[264]:
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] 
[265]:

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

GET[Patient]> : 100%|██████████| 1/1 [00:00<00:00,  3.95it/s]
SEARCH[Observation]> :  15%|█▍        | 100/677 [00:00<00:02, 263.47it/s]

[265]:
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...

Load#

[266]:

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

[266]:

array([ True])

Utils#

Server Profiling#

[118]:

pack.countServerResources()

[118]:
resourceType count
0 Account 510
1 ActivityDefinition 284
2 AdverseEvent 116
3 AllergyIntolerance 9356
4 Appointment 29636
... ... ...
141 TestReport 11
142 TestScript 33
143 ValueSet 3126
144 VerificationResult 9
145 VisionPrescription 15

146 rows × 2 columns

Validation#

[267]:

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

[267]:
data
0 {'resourceType': 'Patient', 'id': '1555106', '...

FHIR PACK Internals#

FHIRPy#

URL Parsing#

[87]:

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

[87]:

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

Raw fetch_resource()#

[88]:

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

[88]:

{'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()#

[89]:

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

pack.client.execute(
    'DiagnosticReport/_search',
    method="post",
    data={"_id": "9fa9ab4c-9e1c-46c9-9bec-ec01b3215716"},
    params={"_count": 1},
)

[89]:

1

[89]:

{'resourceType': 'Bundle',
 'id': 'af8b2454-29bd-4fe3-b350-733131e9383a',
 'meta': {'lastUpdated': '2022-07-13T08:04:01.285+00:00'},
 'type': 'searchset',
 'link': [{'relation': 'self',
   'url': 'https://hapi.fhir.org/baseR4/DiagnosticReport/_search'},
  {'relation': 'next',
   'url': 'https://hapi.fhir.org/baseR4?_getpages=af8b2454-29bd-4fe3-b350-733131e9383a&_getpagesoffset=1&_count=1&_pretty=true&_bundletype=searchset'}],
 'entry': [{'fullUrl': 'https://hapi.fhir.org/baseR4/DiagnosticReport/6630582',
   'resource': {'resourceType': 'DiagnosticReport',
    'id': '6630582',
    'meta': {'versionId': '1',
     'lastUpdated': '2022-07-05T06:03:55.922+00:00',
     'source': '#VSn1gQals3CWesRQ'},
    'text': {'status': 'generated',
     'div': '<div xmlns="http://www.w3.org/1999/xhtml"><div class="hapiHeaderText"> Untitled Diagnostic Report </div><table class="hapiPropertyTable"><tbody><tr><td>Status</td><td>REGISTERED</td></tr><tr><td>Issued</td><td> 15 May 2013 18:32:52 </td></tr><tr><td>Conclusion</td><td>Core lab</td></tr></tbody></table></div>'},
    'identifier': [{'use': 'official',
      'system': 'http://www.bmc.nl/zorgportal/identifiers/reports',
      'value': 'dtyj'}],
    'basedOn': [{'reference': '/fhir/NutritionOrder/srth'}],
    'status': 'registered',
    'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/v2-0074',
        'code': '未輸入'}]}],
    'code': {'coding': [{'system': 'http://loinc.org', 'code': '未輸入'}]},
    'subject': {'reference': '/fhir/Patient/f001'},
    'issued': '2013-05-15T19:32:52+01:00',
    'performer': [{'reference': '/fhir/Organization/f001'}],
    'result': [{'reference': '/fhir/Observation/f001'}],
    'conclusion': 'Core lab'},
   'search': {'mode': 'match'}}]}

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()