FHIR Connector

The Tuva FHIR connector is a python library designed to parse FHIR JSON objects and output structured CSVs. The connector enables you to easily upload or store structured health data in a data warehouse or database for analysis, starting from pure FHIR. This library was designed for simplicity and may not handle all advanced use cases. There are no package dependencies.

Usage

The fhir connector library contains a parseFhir method that parses two inputs: a .ndjson file containing multiple fhir objects or a .json file containing a single FHIR bundle that could have various kinds of FHIR resources. parseFhir accepts configuration files, in ini format, that define the input and output files and the structure of the output file(s).

import parseFhir

parseFhir.parse("coverage.json", ["coverageConfig.ini"])
parseFhir.parse(
    "observation.json",
    [
        "observationConfig.ini",
        "practitionerConfig.ini",
        "practitionerRoleCOnfig.ini",
    ],
)

The parseFhir method streams the input file one line at a time, meaning large input files aren't committed to memory.

Configuration

parseFhir accepts two parameters: the input file and a single or list of ini file(s) that define(s) the configurations needed to parse the file.

The ini file has two sections: [GenConfig] and [Struct]. [GenConfig] defines the type of FHIR resource the ini file is processing, and a setting, WriteMode, that instructs parseFhir to either over-write the CSV file containing those resources (if it exists) or append new data onto it. [Struct] defines the structure of the CSV (the columns in the output).

    [GenConfig]
    resourceType = Coverage
    WriteMode = append

    [Struct]
    patient_id = identifier.ArrCond:use|usual.value
    name = name.ArrNotHave:period,end.ArrJoin:given
           name.ArrNotHave:period,end.family
    data_source = Hard:SynFhir

Config section: [GenConfig] - general configuration

Available configurations:

Configuration	Definition	required
resourceType	Type of FHIR resource this configuration file is mapping	yes
Anchor	Path to array or value that will server as a starting point for the fhir parsing	no
WriteMode	Determines if parseFHIR will overwrite the output file, or append to the output file	no

Example:

    [GenConfig]
    inputPath = Observation
    Anchor = component.ArrCond:code,text|Diastolic blood pressure.valueQuantity
    WriteMode = append

resourceType

The FHIR resource, or list of FHIR resources, found in your input file.In the case where your input file is a FHIR bundle or single FHIR resource, this is the same field in the resourceType key.

For example - let's say your input file (input.json, in this case), contains three kinds of resources: Observation, Practitioner, and PractitionerRole. You would need to create three ini files: one for each resource. The names of these files can be anything - but, they must contain a resourceType key that matches all the FHIR resources present in your input file.

    ; observation.ini
    [GenConfig]
    resourceType = Observation
    ...

    ; practitioner.ini
    [GenConfig]
    resourceType = Practitioner
    ...

    ; practitioner_role.ini
    [GenConfig]
    resourceType = PractitionerRole
    ...

In the case where you don't know the FHIR resources present in your desired input file, our connector contains a method called get_fhir_resource_types. This method is used internally inside parseFhir, so to get the names of the resources, it must be called and printed, like so:

    import parseFhir
    
    # get all of the FHIR resources present in `inputFile.json`
    print(parseFhir.get_fhir_resources_types_from_bundle("inputFile.json"))

Anchor

If no anchor is supplied the output will include one row per FHIR object in the input, and all paths in the Struct section must be relative to the root of the fhir object.

If an anchor is supplied, the output will include one row for every object found at that path. If the path points to an array, the output will include 0..n rows per input fhir object (one per objects found in the array at that path), e.g. anchor = diagnosis will output one row for every diagnosis found in the FHIR object, or no rows if there is no diagnosis array or if it is empty. If the anchor points to a value, it will output one row per FHIR object assuming that the path to the object exists, e.g. a config Anchor = component.ArrCond:code,text|Systolic blood pressure.valueQuantity will output one row per fhir object, only if the object contains a component with a text of "Systolic blood pressure" and if that object contains a valueQuantity value.

If an anchor is defined, paths relative to the root object can be defined in the [Struct] section like normal, or paths that start with Anchor will be evaluated relative to the current iteration of the anchor path. The following will output as many rows as there are diagnosis objects found in that array,and will output the patient_id (found in the parent object) and the code (found in the diagnosis array)

    [GenConfig]
    anchor = diagnosis

    [Struct]
    patient_id = subject.LTrim:reference|8
    code = Anchor:condition.code.coding.0.code

WriteMode

The default behavior is write, which will overwrite the file found at <. Adding WriteMode = append` in the GenConfig section will prevent the parser from writing a Header line, and will append the data to the file rather than overwriting it. This can be used if multiple files are being written to one csv.

Config Section: [Struct] - Structure of the output

The Struct section defines the output. Each key in the strut section will be a new column in the output csv. The values should be a dot notated json path to the data in the fhir object. Integers can be used to hardcode specific iterations in an array. If multiple fhir values should be concatenated into one column in the csv, they can be concatenated by notating multiple lines with separate paths. To hardcode an empty column, give the Key but no value.

[Struct]
patient_id = identifier.0.value
name = name.0.ArrJoin:given
       name.0.family
gender = gender
ethnicity =
data_source = Hard:SynFhir

There are a number of Methods that can be used to format values, choose particular iterations of an array, join values of an array, or perform other logic needed to extract the desired data

Method Name	Operates on	Description	num parameters
ArrCond	Array	Array conditional: finds the first iteration of the array that meets the given condition	2
ArrNotHave	Array	Array Not Having: finds the first iteration of the array that doesn't have the specified key	1
ArrJoin	Value Array	Array Join: Joins all values of the array and returns the concatenated list	1
Hard	nothing	Hardcodes a specific value in the given column	1
Left	value	Left: takes the first x characters of a given value	2
LTrim	value	Left Trim: removes the first x characters of a given value	2
IfEx	value	If Exists: returns one value if the key exists, otherwise returns another value	3
IfEq	value	If Equals: returns one value if the given key's value equals the value specified, otherwise returns another value	4
TimeForm	value	Timestamp Format: converts timestamps in the YYYY-MM-DDThh:mm:ss+zz:zz format expected by fhir, to the YYYY-MM-DD hh:mm:ss format required to load to redshift	1

General Setup: [Struct] Keys in config are columns in output

For every desired column in the output, add a key in the [Struct] section with the name of the desired column. The value of any column that should be populated with FHIR data should be the dot notated Json path of the value.

The FhirConnector will produce a header row for each key in struct, and then add data from each fire object to the output for any columns with valid paths. A key with no path will produce an empty column

For example, this [Struct] section:

patient_id = identifier.value
ethnicity =
birth_date = birthDate

combined with this input file:

{ "identifier" : { "type" : "mrn", "value" : "123" }, "name" : "Jim Halpert", "birthDate" : "1985-01-02" }
{ "identifier" : { "type" : "mrn", "value" : "456" }, "name" : "Michael Bluth", "birthDate" : "1972-03-04" }
{ "identifier" : { "type" : "mrn", "value" : "789" }, "name" : "Leslie Knope", "birthDate" : "1980-05-06" }

will produce this csv:

"patient_id","ethnicity","birth_date"
"123","","1985-01-02"
"456","","1972-03-04"
"789","","1980-05-06"

General Setup: Dot notated json paths

The paths to the fhir data can be defined using dot notated json paths. From the root or anchor, every child objet's key must be listed, separated by a .

Specific objects in an array can be referenced by their 0 based index.

e.g. given this json object:
{ "patient: { "identifier" : { "type" : "mrn", "value" : "123" } } , "results" : [ { "sequence" : 1 , "test" : "glucose" , "result" : "100 mg/dL"} , { "sequence" : 1 , "test" : "calcuim" , "result" : "9.0 mg/dL"} ] }

#the data can be extracted like so:
[Struct]
patient_id = patient.identifier.value
first_test = results.0.test
first_test_result = results.0.result
second_test = results.1.test
second_test_result = results.1.result

General Setup: concatenating multiple fhir paths to one field

If multiple json values should be concatenated into one column, their respective paths can be put on new lines in the config file. They will be space separated.

# this will concatenate all of the given names, the famiy name, and the suffix into one "name" field
name = name.0.ArrJoin:given
       name.0.family
       name.0.suffix

Method ArrCond: Array Conditional

Method syntax	ArrCond:param1|param2
Operates On:	Array
Param 1:	path/key to evaluate
Param 2:	value to compare

ArrCond will return the first object in the array it finds that meets the given criteria, where the value at key/path param1 = param2. If the array is empty or if none of the object in the array meet the criteria, it will return None which will get translated to a blank string in the CSV.

If the key to evaluate is not at the root level of the array object, param1 can be a path, however . must be translated to , so they are not evaluated as actual steps in the full json path. If the value to compare contains . they must be translated to , so they are not interpreted as steps in the json path. It is assumed that commas are not in the values being compared.

# returns the value of "code" of the first object of the "coding" array that has a system of "http://loinc.org"
# i.e. gets the loinc code, irrespective of the presence of additional coding
loinc = code.coding.ArrCond:system|http://loinc,org.code

# returns the "text" of the reference range that has a "type.text" of "Normal Range"
# i.e. gets the normal range of the reference range object, if it exists
reference_range = referenceRange.ArrCond:type,text|Normal Range.text

Method ArrNotHave: Array Not Having

Method syntax	ArrNotHave:param1
Operates On:	Array
Param 1:	path/key to evaluate

ArrNotHave will return the first object in the array that does not have the key/value specified, or returns none if the array is empty or if all objects contain the given path

If the key to evaluate is not at the root level of the array object, param1 can be a path, however . must be translated to , so they are not evaluated as actual steps in the full json path.

# returns value of "family" of the first object in the address array that doesn't have a "period.end" value
# i.e. returns the active last name, even if historical names are included
name.ArrNotHave:period,end.family

Method ArrJoin: Array Join

Method syntax	ArrJoin:param1
Operates On:	Array of Values
Param 1:	key of array to concanate

ArrJoin will only work on an array of values, not on an array of objects. ArrJoin will concatenate all of the values in the array together (space separated) and return them to a single column.

# returns concatenation of all values found in the "name.given" array
# i.e. concatenates firstname, middlename, and any other names included
address = name.ArrNotHave:period,end.ArrJoin:given

Method Hard: Hard code a value

Method syntax	Hard:param1
Operates On:	Nothing
Param 1:	Value to Hardcode

Hard: does not reference the input object, but rather hardcodes the same value in the output csv for every row.

# Hard codes "icd-10-pcs"
procedure_code_type = Hard:icd-10-pcs

Method Left: returns the first n characters

Method syntax	Left:param1|param2
Operates On:	Value
Param 1:	Key to take substring of
Param 2:	Number of characters to take

takes param2 characters of the value of param1 key

# gets the first 10 characters of the "order.authoredOn" field
# i.e. gets the date from a field containing a datetime
request_date = order.Left:authoredOn|10

Method Left: returns the first n characters

Method syntax	Left:param1|param2
Operates On:	Value
Param 1:	Key to take substring of
Param 2:	Number of characters to take

takes param2 characters of the value of param1 key

# gets the first 10 characters of the "order.authoredOn" field
# i.e. gets the date from a field containing a datetime
request_date = order.Left:authoredOn|10

Method LTrim: trims the first n characters

Method syntax	LTrim:param1|param2
Operates On:	Value
Param 1:	Key to take substring of
Param 2:	Number of characters at the start to drop

removes the first param2 characters of the value of param1 key and returns the result

# removes the first 10 characters from encounter.reference
# i.e. given the value "encounter\12345| , removes the "encounter\" and returns "12345"
request_date = encounter.LTrim:reference|10

Method IfEx: If value exists

Method syntax	IfEx:param1|param2|param3
Operates On:	Value
Param 1:	Key/path to evaluate
Param 2:	Value to return if key/path exists
Param 3:	Value to return if key/path does not exist

Evaluates if the key/path in param1 exists, returns param2 if it does, otherwise returns param3

if param1 is a path, convert . in dot notated path to , so they are not evaluated as steps in the full json path

# returns a 1 or 0, depending on if a "deceasedDateTime" key exists
death_flag = IfEx:deceasedDateTime|1|0

Method IfEq: If value exists

Method syntax	IfEx:param1|param2|param3|param4
Operates On:	Value
Param 1:	Key/path to evaluate
Param 2:	Value to to compare to value of evaluated path at param1
Param 3:	Value to return if equal
Param 4:	Value to return if not equal

Evaluates if the key/path in param1 equals the value in param2, returns param3 if it does, otherwise returns param4

if param1 is a path, or if param2 contains periods, convert . in parameters to , so they are not evaluated as steps in the full json path.

# returns "icd-10-cm" if the coding system is "http://www.cms.gov/Medicare/Coding/ICD10", otherwise returns "internal"
code_type = code.coding.0.IfEq:system|http://www,cms,gov/Medicare/Coding/ICD10|icd-10-cm|internal

Method TimeForm: Format Time

Method syntax	IfEx:param1|param2|param3|param4
Operates On:	Value (in FHIR dateTime format)
Param 1:	Key/path to evaluate

Converts dateTimes in the YYYY-MM-DDThh:mm:ss+zz:zz format used by fhir to the YYYY-MM-DD hh:mm:ss format required to load to a datetime/timestampe (no timezone) in redshift and other dbms.

# Converts an effectiveDatetime to redshift input format
# i.e. converts "2019-01-02T01:05:10.000Z" to "2019-01-02 01:05:10"
result_date = TimeForm:effectiveDateTime