Sometimes, FHIR search is not enough. Aidbox provides more ways to search:
Search resource - similar to SearchParameter, but allows defining SQL. It is composable with other SearchParameters and Search resources.
AidboxQuery - a more general way to search using SQL. DSL to build complex queries using the new endpoint. It is not composable with other SearchParameters and Search resources.
Aidbox Search resource defines a search parameter or overrides the existing one. Search resources take precedence over FHIR SearchParameters. This may be useful for the performance optimization of built-in FHIR SearchParameters or for the implementation of complicated custom searches.
Example
PUT /Search/Patient.name
content-type: text/yaml
accept: text/yaml
name: name
resource:
id: Patient
resourceType: Entity
where: "{{table}}.resource->>'name' ilike {{param}}" # sql for search
format: "%?%" # parameter format for ilike
order-by: "{{table}}.resource#>>'{name,0,family}'" # sql for ordering (using _sort)
Search resource structure
Value parsing
In case of reference or identifier search, the value must be parsed:
resourceType and id or url in case of reference search
code and system in case of identifier search
Reference search
Allows the use of different reference types in the "where" expression. Reference can be defined in several ways:
{{param.resourceType}} for ResourceType and {{param.id}} for resource id
To refer to the value of the parameter with :text modifier use {{param.text}}
When using the :text modifier, you also need to specify "text-format", refer to {{param.text}} with ?."text-format" is a format string that will be applied to{{param.text}} before inserting it into the SQL query. It is useful for wrapping text with % for like or ilike. For example text-format: '%?%'
With the AidboxQuery resource, you can turn your SQL query into a REST endpoint.
PUT /AidboxQuery/<query-name>
params:
# define filter parameter
filter:
# make it required
isRequired: true
# it's type is string (can be integer, number, object, boolean)
type: string
# format is java format string, which will be applied to value
# this useful to get for example ilike query expr ilike '% value%'
# do not forget to escape % with one more %
format: '%% %s%%'
# you can set default value
default: 'ups'
count:
type: integer
default: 10
# sql query with parameters {{path.to.ctx.elements}}
query: 'SELECT * from patient where id ilike = {{params.filter}} limit {{params.count}}'
# if count-query is present - it will be evaluated for total property in response
count-query: 'SELECT count(*) from patient where id ilike = {{params.filter}}'
# not required. enable links in response, see the section below
enable-links: false
# not required. omit sql in query response
omit-sql: false
# not required. `query` or `execute`. see below
type: query
Example
For example, let's create a simple aggregation report for encounters parameterised by date. Create an AidboxQuery resource:
PUT /AidboxQuery/daily-report
params:
date:
isRequired: true
query: |
SELECT
resource->>'class' as class,
count(*) as count
FROM encounter
WHERE {{params.date}}
BETWEEN (resource#>>'{period,start}')::date
AND (resource#>>'{period,end}')::date
GROUP BY resource->>'class'
Call it like this (data and query keys):
GET /$query/daily-report?date=2013-06-08
Or like this (Search Bundle):
GET /fhir/Patient?_query=get-by-id&rid=patient1
The main difference is that such a query can use an additional variable available in the context of {{resourceType}}.
Query types
AidboxQuery has type field, which can be either query or execute. Default type is query. This means that SELECT statement in query parameter is expected. If you want to make SQL query with execute statements e.g. TRUNCATE, use execute type.
PUT /AidboxQuery/truncate
query: 'TRUNCATE {{resourceType}}; TRUNCATE {{resourceType}}_history'
type: execute
Return links
You can use enable-links parameter to include links in the response. Here is simple example how to use paging with AidboxQuery and include links.
PUT /AidboxQuery/q1
query: |
SELECT
sr.*
FROM ServiceRequest sr
WHERE sr.Resource #>> '{subject,id}' = {{params.patient}}
LIMIT {{params._count}} OFFSET {{params._page}}
count-query: |
SELECT count(*) FROM ServiceRequest sr
WHERE sr.Resource #>> '{subject,id}' = {{params.patient}}
enable-links: true
params:
patient:
type: string
isRequired: true
default: "pt1"
_count:
type: integer
default: 100
_page:
type: integer
default: 1
AidboxQuery expects that parameters _count and _page (exactly such names) are defined, otherwise links won't be attached.
Use like this:
GET /$query/q1?patient=pt1&_count=1&_page=2
Design AidboxQuery
To design the aidbox query, you can use POST /$query/$debug endpoint without the need to create an AidboxQuery resource:
POST /$query/$debug
query:
# AidboxQuery resource content
query: 'SELECT {{params.id}} as params_id'
params:
id: {isRequired: true}
# test params
params:
id: 'ups'
---
# actual result
data:
- {params_id: ups}
# sql query
query: ['SELECT ? as params_id', ups]
# execution plan
plan: |-
Result (cost=0.00..0.01 rows=1 width=32) (actual time=0.009..0.022 rows=1 loops=1)
Planning Time: 0.025 ms
Execution Time: 0.067 ms
# templating context
ctx:
remote-addr: 0:0:0:0:0:0:0:1
client: { ... }
params: {id: ups}
headers: {...}
uri: /$query/$debug
user: {...}
scheme: http
request-method: post
Debug AidboxQuery
You can debug AidboxQuery with _explain=true parameter:
GET /$query/daily-report?date=2013-06-08&_explain=true
plan: |-
HashAggregate (cost=27.27..27.97 rows=56 width=40) (actual time=0.443..0.459 rows=1 loops=1)
Group Key: (resource ->> 'class'::text)
-> Seq Scan on encounter (cost=0.00..26.96 rows=62 width=32) (actual time=0.398..0.420 rows=2 loops=1)
Filter: (('2013-06-08'::date >= ((resource #>> '{period,start}'::text[]))::date) AND ('2013-06-08'::date <= ((resource #>> '{period,end}'::text[]))::date))
Rows Removed by Filter: 1
Planning Time: 3.222 ms
Execution Time: 0.600 ms
ctx:
params: {date: '2013-06-08', _explain: 'true'}
resourceType: null
safe-paths:
- [resourceType]
query:
- "SELECT \n resource->>'class' as class, \n count(*) as count\nFROM encounter \nWHERE ?\nBETWEEN (resource#>>'{period,start}')::date \nAND (resource#>>'{period,end}')::date\nGROUP BY resource->>'class'"
- '2013-06-08'
Dot expressions
With parameters started with ., you can provide the exact path for the element, optionally provide coercing after :: using PostgreSQL types and the operator after $.
Example
GET /Patient?.name.0.family=Johnson
=> WHERE resource#>>'{name,0,family}' = 'Jonhnson'
GET /Patient?.name.0.family$contains=Joh
=> WHERE resource#>>'{name,0,family}' ilike '%John%'
GET /Encounter?.start::timestamptz$gt=2015-01-01
=> WHERE (resource#>>'{start}')::timestamptz > '2015-01-01'
GET /Patient?.contact$isnull=true
=> WHERE resource#>>'{contact}' IS NULL
Note: expressions with typecast require user input to be correct by PostgreSQL syntax. For example, for timestamptz values you must use 2015-01-01T00:00:00Z format.
$lookup
There are scenarios when you want to quickly look up patients or practitioners with the prefix search by multiple key elements like a family name, date of birth, and identifier. Prefix search means you want to say in the query string jo do 79 and find John Doe with 1979 birthdate. Sometimes, there are millions of patients in your database, and you want to do it efficiently to show type-ahead dropdown choices in your UI.
$lookup operations are especially designed to be an efficient implementation for this case.
There is no way to implement an efficient multidimensional prefix search with ranking and sorting in a relational database. $lookup based on specific assumptions to find the right trade-off: if the search returns more than count (by default 50) results, we consider that the search failed and results can have some anomalies, for example, not complete sorting.
Here is how it works.
First of all, you have to describe priority groups of attributes with by parameter. Groups are separated by ; and inside group, you specify the list of paths separated by ,. Each path expression consists of dot separated elements and indexes and should end with primitive type (examples: name.given or identifier.value).
The result will be sorted according to an order of priority groups. For example, if you want to rate first matches of name, identifier, and birth of data, and second matches in address and telecom, you will use the following expression:name.family,name.given,identifier.value,birthDate;address.state,address.city,address.line,telecom.value.
Let's say you are searching joh 1979 ny Aidbox will initially search in first priority group by expression like this:
expr = extract_space_separated(resource, paths)
where expr ilike ' % joh' AND expr ilike '% 1979'
limit 50
If this query returns 50 records, Aidbox will respond with these records.
GET /Patient/$lookup?\
by=name.family,name.given,birthDate,identifier.value;address.city,address.line&\
sort=name.family,name.given&\
q=Joh+Do+1980&\
count=50&\
limit=200
Parameters
Note: Each path expression should point to a primitive element!
by: ;-separated list of priority groups. Each group is ,-separated list of path expressions.
sort: ,-separated list of path expressions to sort by
q: is + or space separated term (prefixes) to search
limit: is internal search limit (default 200)
count: number results to return (default 50)
mode: if mode = index Aidbox returns index DDL for a specific search
Aidbox special search parameters
_explain
Use _explain parameter to inspect the search query execution plan.
GET /fhir/Encounter?subject:Patient._ilike=john&_explain=analyze
If your query is slow and you see Seq Scans , it's time to build indexes. Do not forget to run a vacuum analyze on the tables involved in query. Read more about PostgreSQL Explain.
This parameter can be used for debugging too. If an SQL error happens, _explain will show the original query:
GET /fhir/Patient?error-demo=1&_explain=0
exception: |-
ERROR: division by zero
Where: SQL function "divide" during inlining
query:
- 'SELECT "patient".* FROM "patient" WHERE (divide(1, ?) = 2) LIMIT ? OFFSET ? '
- '0'
- 100
- 0
_timeout
With _timeout parameter, you can control the search query timeout in seconds. If the query takes more than the timeout value, it will be cancelled. The default timeout value is 60 seconds.
_createdAt
Search by the creation time of the resource meta.createdAt (cts column in the database table).
GET /fhir/Patient?_createdAt=2019-01-01
You can use operators lt,le,gt,ge like in other date search parameters.
_result
By default, the search result is returned as a FHIR Bundle. You can change this behavior by setting _result=array and your search result will be returned as JSON array with resources, without the Bundle envelope:
GET /fhir/Patient?_result=array
# 200
- id: pt1
resourceType: Patient
name:
- given: [Adam]
family: Smith
- name:
- given: [Andrew]
family: John
id: pt-1
resourceType: Patient
_search-language
_search-language is experimental SearchParameter. It can be used to search for a specified language.
GET /fhir/<resource>?_search-language=<locale>&<string-param>=<value>
Any string search parameters (e.g. name) will search in the desired language if _search-language is specified in the query. Specifying only _search-language without any other string search parameters won't affect anything (except _sort).
Aidbox searches for Translation Extension and if the resource contains it and the language is correct, then searches by the content of this translation.
Structure of a resource containing translation extension:
resourceType: <resourceType>
id: <id>
name: <name>
_name:
extension:
- url: http://hl7.org/fhir/StructureDefinition/translation
extension:
- url: lang
valueCode: <locale1>
- url: content
valueString: <translation in locale1>
- url: http://hl7.org/fhir/StructureDefinition/translation
extension:
- url: lang
valueCode: <locale2>
- url: content
valueString: <translation in locale2>
