The HAPI JPA Server supports optional indexing via Hibernate Search when configured to use Lucene or Elasticsearch.
This is required to support the _content, or _text search parameters.
When enabled, searches for _text and _content are forwarded to the underlying Hibernate Search engine, which can be backed by either Elasticsearch or Lucene.
By default, search is supported in the way indicated in the FHIR Specification on _text/_content Search. This means that queries like the following can be evaluated:
GET [base]/Observation?_content=cancer OR metastases OR tumor
To understand how this works, look at the following example. During ingestion, the fields required for _content and _text searches are stored in the backing engine, after undergoing normalization and analysis. For example consider this Observation:
{
"resourceType" : "Observation",
"code" : {
"coding" : [{
"system" : "http://loinc.org",
"code" : "15074-8",
"display" : "Glucose [Moles/volume] in Blood Found during patient's visit!"
}]
}
"valueQuantity" : {
"value" : 6.3,
"unit" : "mmol/l",
"system" : "http://unitsofmeasure.org",
"code" : "mmol/L"
}
}
In the display section, once parsed and analyzed, will result in the followings tokens being generated to be able to be searched on:
["glucose", "mole", "volume", "blood", "found", "during", "patient", "visit"]
You will notice that plurality is removed, and the text has been normalized, and special characters removed. When searched for, the search terms will be normalized in the same fashion.
However, the default implementation will not allow you to search for an exact match over a long string that contains special characters or other characters which could be broken apart during tokenization. E.g. an exact match for _content=[Moles/volume] would not return this result.
In order to perform such an exact string match in Lucene/Elasticsearch, you should modify the _text or _content Search Parameter with the :contains modifier, as follows:
GET [base]/Observation?_content:contains=[Moles/volume]
Using :contains on the _text or _content modifies the search engine to perform a direct substring match anywhere within the field.
Additional indexing is implemented for simple search parameters of type token, string, and reference.
These implement the basic search, as well as several modifiers:
This experimental feature is enabled via the setAdvancedHSearchIndexing() property of JpaStorageSettings.
Extended Lucene Indexing supports all of the core search parameter types. These include:
We support date searches using the eq, ne, lt, gt, ge, and le comparisons.
See https://www.hl7.org/fhir/search.html#date.
The Extended Lucene string search indexing supports the default search, as well as :contains, :exact, and :text modifiers.
:exact matches the entire string, matching case and accents.:contains match any substring of the text, ignoring case and accents.:text provides a rich search syntax as using a modified Simple Query Syntax.See https://www.hl7.org/fhir/search.html#string.
The :text modifier for token and string uses a modified version of the Simple Query Syntax provided by Lucene and Elasticsearch.
Terms are delimited by whitespace, or query punctuation "'()|+.
Literal uses of these characters must be escaped by \.
If the query contains any SQS query punctuation, the query is treated as a normal SQS query.
But when the query only contains one or more bare terms, and does not use any query punctuation, a modified syntax is used.
In modified syntax, each search term is converted to a prefix search to match standard FHIR string searching behaviour.
When multiple terms are present, they must all match (i.e. AND).
For OR behaviour use the | operator between terms.
To match only whole words, but not match by prefix, quote bare terms with the " or ' characters.
Examples:
| Fhir Query String | Executed Query | Matches | No Match | Note |
|---|---|---|---|---|
| Smit | Smit* | John Smith | John Smi | |
| Jo Smit | Jo* Smit* | John Smith | John Frank | Multiple bare terms are AND |
| frank | john | frank | john | Frank Smith | Franklin Smith | SQS characters disable prefix wildcard |
| 'frank' | 'frank' | Frank Smith | Franklin Smith | Quoted terms are exact match |
The Extended Lucene Indexing supports the default token search by code, system, or system+code,
as well as with the :text modifier.
The :text modifier provides the same modified Simple Query Syntax used by string :text searches.
See https://www.hl7.org/fhir/search.html#token.
| Parameter | Supported | type |
|---|---|---|
| _id | no | |
| _lastUpdated | yes | date |
| _tag | yes | token |
| _profile | yes | URI |
| _security | yes | token |
| _text | yes | string(R4) special(R5) |
| _content | yes | string(R4) special(R5) |
| _list | no | |
| _has | no | |
| _type | no | |
| _source | yes | URI |
The Extended Lucene Indexing supports an extension of the $expand operation on ValueSet with a new contextDirection value of existing. In this mode, the context parameter is interpreted as a SearchParameter reference (by resource type and code), and the filter is interpreted as a query token. The expansion will contain the most frequent Coding values matching the filter.
E.g. the query
GET /ValueSet/$expand?contextDirection=existing&context=Observation.code:text&filter=press
will return a ValueSet containing the most common values indexed under Observation.code whose display text contains a word starting with "press", such as http://loinc.org|8478-0 - "Mean blood pressure".
This extension is only valid at the type level, and requires that Extended Lucene Indexing be enabled.
As an experimental feature with the extended indexing, the full resource can be stored in the search index. This allows some queries to return results without using the relational database. Note: This does not support the $meta-add or $meta-delete operations. Full reindexing is required when this option is enabled after resources have been indexed.
This experimental feature is enabled via the setStoreResourceInHSearchIndex() option of JpaStorageSettings.
ElasticSearch writes are asynchronous by default. This means that when writing to an ElasticSearch instance (independent of HAPI FHIR), the data you write will not be available to subsequent reads for a short period of time while the indexes synchronize.
ElasticSearch states that this behaviour leads to better overall performance and throughput on the system.
This can cause issues, particularly in unit tests where data is being examined shortly after it is written.
You can force synchronous writing to them in HAPI FHIR JPA by setting the Hibernate Search synchronization strategy. This setting is internally setting the ElasticSearch refresh=wait_for option. Be warned that this will have a negative impact on overall performance. THE HAPI FHIR TEAM has not tried to quantify this impact but the ElasticSearch docs seem to make a fairly big deal about it.
It is possible to sort with Lucene indexing and full text searching enabled. For example, this will work: Practitioner?_sort=family.
Also, chained sorts will work: PractitionerRole?_sort=practitioner.family.
However, chained sorting combined with full text searches will fail. For example, this query will fail with an error: PractitionerRole?_text=blah&_sort=practitioner.family