GraphPatientToXmlAndCSV

GraphPatientToXmlAndCSV is an API that takes FHIR Records and converts them to XML and XSV for every valid patient. It also generates few graphs on patient data.

Installation

Clone the project into a folder.
Ensure you have python and pip downloaded (https://www.python.org/downloads/)
Ensure you have FHIRWorks API or use (https://github.com/greenfrogs/FHIRworks_2020) to install FHIRworks api
Use pip to install matplotlib 3.2.1

pip install matplotlib

Use the package manager pip to install flask 1.1.1.

pip install flask

Use the package manager pip to install Fhir-parser 0.1.5.

pip install FHIR-Parser

Use the package manager pip to install requests 2.23.0.

pip install requests

Run the app

Run the FHIRWorks API in one terminal

dotnet run

Run the app.py in another terminal simultaneously

python app.py

Usage

Three possible Get Requests; xml, graph, csv.

XML

Request

This gets all the observations of a patient with a given patient ID in a XML format. For example,for patient ID 'd9eb4cf6-2894-4627-b912-bbdca07b0401', the get request is

GET /api/xml/observations/?patientID=d9eb4cf6-2894-4627-b912-bbdca07b0401

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 05:53:05 GMT Status: 200 OK, Content-Type: text/xml, Content-Length: 64077

<?xml version="1.0" ?>
<patient>
    <observation>
        This contains observations for patient number d9eb4cf6-2894-4627-b912-bbdca07b0401
        <Observation1>
            <effective_datetime>01/09/2011</effective_datetime>
            <encounter_uuid>5591633b-1e91-4029-818a-366631ccb952</encounter_uuid>
            <issued_datetime>01/09/2011</issued_datetime>
            <patient_uuid>d9eb4cf6-2894-4627-b912-bbdca07b0401</patient_uuid>
            <status>final</status>
            <type>vital-signs</type>
            <uuid>541b3ad4-b3f1-4750-87d4-ef38b370ef0d</uuid>
            <Component11>
                <Value1>Body Mass Index</Value1>
                <Value2>29.67</Value2>
                <Value3>kg/m2</Value3>
                <Value4>29.67kg/m2</Value4>
                <Value5>39156-5</Value5>
                <Value6>http://loinc.org</Value6>
            </Component11>
        </Observation1>
        <?other observations from 1 to 75.................... ?>
        <Observation75>
            <effective_datetime>11/10/2019</effective_datetime>
            <encounter_uuid>b216caef-e88b-4837-abf8-904f7c02ef0a</encounter_uuid>
            <issued_datetime>11/10/2019</issued_datetime>
            <patient_uuid>d9eb4cf6-2894-4627-b912-bbdca07b0401</patient_uuid>
            <status>final</status>
            <type>survey</type>
            <uuid>7b4b3677-b24a-4df3-a5fc-860ccd92055b</uuid>
            <Component751>
                <Value1>Tobacco smoking status NHIS</Value1>
                <Value2>None</Value2>
                <Value3/>
                <Value4>N/A</Value4>
                <Value5>72166-2</Value5>
                <Value6>http://loinc.org</Value6>
            </Component751>
        </Observation75>
    </observation>
</patient>

Request

This gets all the properties of a patient with a given patient ID in a XML format. For example, for patient ID 'd9eb4cf6-2894-4627-b912-bbdca07b0401', the get request is

GET /api/xml/properties/?patientID=d9eb4cf6-2894-4627-b912-bbdca07b0401

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 05:57:16 GMT Status: 200 OK, Content-Type: text/xml, Content-Length: 2840

<?xml version="1.0" ?>
<patient>
    <properties>
        <addresses>
            <city name="0">Blackstone</city>
            <country name="0">US</country>
            <full_address name="0">358 Oberbrunner Approach Apt 4Blackstone, Massachusetts, US</full_address>
            <latitude name="0">42.05283200979602</latitude>
            <lines name="0">['358 Oberbrunner Approach Apt 4']</lines>
            <longitude name="0">-71.52523247435127</longitude>
            <postal_code name="0"/>
            <state name="0">Massachusetts</state>
        </addresses>
        <birth_date>10/21/1973</birth_date>
        <communications>
            <codes>['en-US']</codes>
            <communication>[('en-US', 'English')]</communication>
            <languages>['English']</languages>
        </communications>
        <extensions>
            <extensions name="Identifier: 1">us-core-race: White</extensions>
            <extensions name="Identifier: 2">us-core-ethnicity: Not Hispanic or Latino</extensions>
            <extensions name="Identifier: 3">patient-mothersMaidenName: Jeremy766 Gleichner915</extensions>
            <extensions name="Identifier: 4">us-core-birthsex: M</extensions>
            <extensions name="Identifier: 5">patient-birthPlace: Sharon, Massachusetts, US</extensions>
            <extensions name="Identifier: 6">disability-adjusted-life-years: 0.016479540110564225</extensions>
            <extensions name="Identifier: 7">quality-adjusted-life-years: 45.983520459889434</extensions>
        </extensions>
        <gender>male</gender>
        <identifiers>
            <identifiers name="Identifier: 1"> d9eb4cf6-2894-4627-b912-bbdca07b0401</identifiers>
            <identifiers name="Identifier: 2">Medical Record Number d9eb4cf6-2894-4627-b912-bbdca07b0401</identifiers>
            <identifiers name="Identifier: 3">Social Security Number 999-67-4686</identifiers>
            <identifiers name="Identifier: 4">Driver's License S99910651</identifiers>
            <identifiers name="Identifier: 5">Passport Number X34975298X</identifiers>
        </identifiers>
        <marital_status>
            <marital_status>M</marital_status>
        </marital_status>
        <multiple_birth/>
        <name>
            <family>Weissnat378</family>
            <full_name>Mr. Abram53 Weissnat378</full_name>
            <given>Abram53</given>
            <given_list>['Abram53']</given_list>
            <prefix>Mr.</prefix>
            <prefix_list>['Mr.']</prefix_list>
        </name>
        <telecoms>
            <number name="0">555-560-7469</number>
            <system name="0">phone</system>
            <use name="0">home</use>
        </telecoms>
        <uuid>d9eb4cf6-2894-4627-b912-bbdca07b0401</uuid>
    </properties>
</patient>

Graphs

Request

This creates a graph based on patient age groups of all patients, according to patient properties data.

GET /api/graph/age_groups?

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 17:23:26 GMT, Status: 200 OK, Content-Type: image/png, Content-Length: 13053

Body:

Request

This creates a graph based on marital status of all patients, according to patient properties data.

GET /api/graph/marital_status?

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 05:39:46 GMT, Status: 200 OK, Content-Type: image/png, Content-Length: 10676

Body:

Request

This creates a graph based on languages spoken by all patients, according to patient properties data.

GET /api/graph/languages_spoken?

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 05:44:20 GMT Status: 200 OK, Content-Type: image/png, Content-Length: 17696

Body:

CSV

Request

This gets all the properties of a patient with a given patient ID in a CSV format. For example, for patient ID 'd9eb4cf6-2894-4627-b912-bbdca07b0401', the get request is

GET /api/csv/properties/?patientID=d9eb4cf6-2894-4627-b912-bbdca07b0401

Response

Header: HTTP/1.1 200 OK, Date: Mon, 23 Mar 2020 06:18:00 GMT Status: 200 OK, Content-Type: text/xml, Content-Length: 1210 Content-Disposition:attachment; filename=result.csv

city,country,full_address,latitude,lines,longitude,postal_code,state,birth_date,codes,communication,languages,extensions0,extensions1,extensions2,extensions3,extensions4,extensions5,extensions6,gender,identifiers0,identifiers1,identifiers2,identifiers3,identifiers4,marital_status,multiple_birth,family,full_name,given,given_list,prefix,prefix_list,number,system,use,uuid,Blackstone,US,"358 Oberbrunner Approach Apt 4 Blackstone, Massachusetts
, US",42.05283200979602,['358 Oberbrunner Approach Apt 4'],-71.52523247435127,,Massachusetts,10/21/1973,['en-US'],"[('en-US', 'English')]",['English'],us-core-race: White,us-core-ethnicity: Not Hispanic or Latino,patient-mothersMaidenName: Jeremy766 Gleichner915,us-core-birthsex: M,"patient-birthPlace: Sharon, Massachusetts, US",disability-adjusted-life-years: 0.016479540110564225,quality-adjusted-life-years: 45.983520459889434,male, d9eb4cf6-2894-4627-b912-bbdca07b0401,Medical Record Number d9eb4cf6-2894-4627-b912-bbdca07b0401,Social Security Number 999-67-4686,Driver's License S99910651,Passport Number X34975298X,M,False,Weissnat378,Mr. Abram53 Weissnat378,Abram53,['Abram53'],Mr.,['Mr.'],555-560-7469,phone,home,d9eb4cf6-2894-4627-b912-bbdca07b0401

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

neharanadee/GOSH-FHIRworks2020-GraphPatientToXmlAndCSV

GraphPatientToXmlAndCSV

Installation

Run the app

Usage

XML

Request

Response

Request

Response

Graphs

Request

Response

Request

Response

Request

Response

CSV

Request

Response

Contributing

License