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Merge branch 'master' into 2480_partition_aware_subscription

This commit is contained in:
Steven Li 2021-11-22 13:44:46 -05:00
parent 3c39011b08 35dedb8628
commit d904f0c5dc
84 changed files with 4002 additions and 342 deletions
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2
hapi-fhir-base/src/main/java/org/hl7/fhir/instance/model/api/IAnyResource.java
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@ -31,7 +31,7 @@ public interface IAnyResource extends IBaseResource {
/**
* Search parameter constant for <b>_id</b>
*/
@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="token" )
@SearchParamDefinition(name="_id", path="", description="The ID of the resource", type="token")
String SP_RES_ID = "_id";
/**

25
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/config/BatchConstants.java
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@ -54,6 +54,31 @@ public final class BatchConstants {
* MDM Clear
*/
public static final String MDM_CLEAR_JOB_NAME = "mdmClearJob";
/**
* TermCodeSystem delete
*/
public static final String TERM_CODE_SYSTEM_DELETE_JOB_NAME = "termCodeSystemDeleteJob";
public static final String TERM_CONCEPT_RELATIONS_DELETE_STEP_NAME = "termConceptRelationsDeleteStep";
public static final String TERM_CONCEPTS_DELETE_STEP_NAME = "termConceptsDeleteStep";
public static final String TERM_CODE_SYSTEM_VERSION_DELETE_STEP_NAME = "termCodeSystemVersionDeleteStep";
public static final String TERM_CODE_SYSTEM_DELETE_STEP_NAME = "termCodeSystemDeleteStep";
public static final String JOB_PARAM_CODE_SYSTEM_ID = "termCodeSystemPid";
/**
* TermCodeSystemVersion delete
*/
public static final String TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME = "termCodeSystemVersionDeleteJob";
public static final String TERM_CONCEPT_RELATIONS_UNIQUE_VERSION_DELETE_STEP_NAME = "termConceptRelationsUniqueVersionDeleteStep";
public static final String TERM_CONCEPTS_UNIQUE_VERSION_DELETE_STEP_NAME = "termConceptsUniqueVersionDeleteStep";
public static final String TERM_CODE_SYSTEM_UNIQUE_VERSION_DELETE_STEP_NAME = "termCodeSystemUniqueVersionDeleteStep";
/**
* Both: TermCodeSystem delete and TermCodeSystemVersion delete
*/
public static final String JOB_PARAM_CODE_SYSTEM_VERSION_ID = "termCodeSystemVersionPid";
public static final String BULK_EXPORT_READ_CHUNK_PARAMETER = "readChunkSize";
public static final String BULK_EXPORT_GROUP_ID_PARAMETER = "groupId";
/**

3
hapi-fhir-batch/src/main/java/ca/uhn/fhir/jpa/batch/svc/BatchJobSubmitterImpl.java
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@ -32,6 +32,8 @@ import org.springframework.batch.core.repository.JobInstanceAlreadyCompleteExcep
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.repository.JobRestartException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import static org.slf4j.LoggerFactory.getLogger;
@ -46,6 +48,7 @@ public class BatchJobSubmitterImpl implements IBatchJobSubmitter {
private JobRepository myJobRepository;
@Override
@Transactional(propagation = Propagation.NOT_SUPPORTED)
public JobExecution runJob(Job theJob, JobParameters theJobParameters) throws JobParametersInvalidException {
try {
return myJobLauncher.run(theJob, theJobParameters);

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3131-add-operation-lookup-to-remoteterminologyservice.yaml Normal file
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@ -0,0 +1,4 @@
---
type: add
issue: 3131
title: "Provided a Remote Terminology Service implementation for the $lookup Operation."

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/3138-support-externalized-binaries.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
jira: SMILE-3152
issue: 3138
title: "Previously, the package registry would not work correctly when externalized binary storage was enabled. This has been corrected."

3
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_6_0/version.yaml Normal file
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@ -0,0 +1,3 @@
---
release-date: "2021-11-18"
codename: "Raccoon"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3108-terminology-large-code-system-deletion-performance.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 3108
title: "Code System deletion background tasks were taking over a day to complete on very large CodeSystems for PostgreSQL, SQL Server and Oracle
databases. That was improved now taking less than an hour in all three platforms"

5
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3158-creation-of-versioned-placeholders.yaml Normal file
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@ -0,0 +1,5 @@
---
type: fix
issue: 3158
title: "Resource links were previously not being consistently created in cases where references were versioned and
pointing to recently auto-created placeholder resources."

4
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/5_7_0/3170-allow-language-code-validation-to-be-case-insensitive.yml Normal file
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@ -0,0 +1,4 @@
---
type: fix
issue: 3170
title: "Fixed language code validation so that it is case insensitive (eg, en-US, en-us, EN-US, EN-us should all work)"

1
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/files.properties
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@ -73,6 +73,7 @@ page.server_jpa_mdm.mdm_expansion=MDM Search Expansion
section.server_jpa_cql.title=JPA Server: CQL
page.server_jpa_cql.cql=CQL Getting Started
page.server_jpa_cql.cql_measure=CQL Measure
section.server_jpa_partitioning.title=JPA Server: Partitioning and Multitenancy
page.server_jpa_partitioning.partitioning=Partitioning and Multitenancy

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hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/measure_evaluation_sequence.png Normal file
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43
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/ref.measure.measure-evaluation.sequence.puml Normal file
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@ -0,0 +1,43 @@
@startuml measure_evaluation_sequence
!include styling.puml
title Measure $evaluate-measure
actor User as User
participant OperationProvider as "HAPI Measure Operation Provider"
participant CQLEngine as "CQL Engine"
participant HAPI as "HAPI CQL Adapters"
participant JPA as "HAPI JPA / Terminology Providers"
User -> OperationProvider: invoke $evaluate-measure
OperationProvider -> JPA: read Measure
JPA --> OperationProvider: return Measure
OperationProvider -> JPA: read Libraries
JPA --> OperationProvider: return Libraries
OperationProvider -> OperationProvider: convert FHIR Libraries to ELM libraries
OperationProvider-> CQLEngine **: create with ELM Libraries
OperationProvider -> JPA: get Subjects
JPA --> OperationProvider: return Subjects
loop each Subject
OperationProvider -> CQLEngine: set current Subject context
loop each SDE/Population
OperationProvider -> CQLEngine: evaluate SDE/Population criteria
CQLEngine -> CQLEngine: evaluate Definition
alt terminology required
CQLEngine -> HAPI: retrieve terminology
HAPI -> JPA: request terminology
JPA --> HAPI: return terminology
HAPI --> CQLEngine: return terminology
end
CQLEngine -> HAPI: retrieve data
HAPI -> JPA: request data
JPA --> HAPI: return data
HAPI --> CQLEngine: return data
CQLEngine --> OperationProvider: return SDE/Population criteria result
end
end
OperationProvider -> CQLEngine !!: destroy
OperationProvider -> OperationProvider: build MeasureReport
OperationProvider -> OperationProvider: score MeasureReport
OperationProvider -> User: return MeasureReport
@enduml

528
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/images/ref_measure_architecture_drawio.svg Normal file
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CQL Translator
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JPA
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HAPI Data Access Layer
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@startuml styling
'These are Alphora colors, they need
' to be updated to reflect the HAPI style guide
!$white = "#fff"
!$greylt000 = "#F4F6F5"
!$greylt100 = "#DDE3E0"
!$greylt200 = "#C7D1CC"
!$greylt300 = "#B0BFB8"
!$grey = $greylt000
!$greydk000 = "#404F47"
!$greydk100 = "#2E3833"
!$greydk200 = "#1C221F"
!$greydk250 = "#121614"
!$greydk300 = "#090B0A"
!$black = $greydk300
!$blue000 = "#4B7DD2"
!$blue100 = "#3064BF"
!$blue200 = "#2956A3"
!$blue300 = "#214583"
!$blue = $blue100
!$purple000 = "#645FAB"
!$purple100 = "#524D93"
!$purple200 = "#433F78"
!$purple300 = "#34315E"
!$purple = $purple100
!$green000 = "#568A67"
!$green100 = "#477154"
!$green200 = "#375841"
!$green300 = "#273F2F"
!$green = $green100
!$yellow000 = "#FBB337"
!$yellow100 = "#FAA40F"
!$yellow200 = "#DC8D04"
!$yellow300 = "#B47304"
!$yellow = $yellow100
!$red000 = "#FF6633"
!$red100 = "#FF4000"
!$red200 = "#E03800"
!$red300 = "#B82E00"
!$red = $red100
skinparam {
defaultFontName Source Sans Pro
TitleFontStyle bold
BackgroundColor $white
Shadowing false
ArrowColor $greydk000
ArrowFontColor $black
ArrowFontSize 12
ArrowFont Open Sans
DelayFontColor $black
DelayFontSize 12
ActorBorderColor $black
ActorBackgroundColor $white
ActorFontColor $black
ActorFontSize 14
ActorFontStyle bold
ParticipantBorderColor $black
ParticipantBackgroundColor $yellow
ParticipantFontColor $black
ParticipantFontSize 14
ParticipantFontStyle bold
DatabaseBorderColor $black
DatabaseBackgroundColor $yellow
DatabaseFontColor $black
DatabaseFontSize 14
DatabaseFontStyle bold
}
skinparam Sequence {
MessageAlign center
LifeLineBorderColor $black
' loop, alt, ref
GroupBodyBackgroundColor $white
GroupBackgroundColor $blue
GroupHeaderFontColor $white
GroupHeaderFontSize 12
GroupFontSize 12
BoxBackgroundColor $greylt000
BoxBorderColor $black
BoxFontColor $black
BoxFontSize 12
ReferenceBorderColor $black
ReferenceFontColor $black
ReferenceFontSize 12
ReferenceHeaderBackgroundColor $blue
DividerBackgroundColor $blue
DividerBorderColor $black
DividerFontColor $white
DividerFontSize 12
}
skinparam Note {
BackgroundColor $green
BorderColor $black
FontColor $white
FontStyle bold
FontSize 12
Font Open Sans
}
hide footbox
@enduml

17
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_cql/cql.md
View File

@ -25,14 +25,19 @@ There are two Spring beans available that add CQL processing to HAPI. You can en
* `ca.uhn.fhir.cql.config.CqlDstu3Config`
* `ca.uhn.fhir.cql.config.CqlR4Config`
## Operations
## Clinical Reasoning Operations
HAPI provides implementations for some Measure operations for DSTU3 and R4
HAPI provides implementations for some operations in DSTU3 and R4:
### $evaluate-measure
[CQL Measure](cql_measure.html)
The [$evaluate-measure](http://hl7.org/fhir/measure-operation-evaluate-measure.html) operation allows the evaluation of a clinical quality measure. This operation is invoked on an instance of a Measure resource:
## Roadmap
`http://base/Measure/measureId/$evaluate-measure?subject=124&periodStart=2014-01&periodend=2014-03`
Further development of the CQL capabilities in HAPI is planned:
The Measure will be evaluated, including any CQL that is referenced. The CQL evaluation requires that all the supporting knowledge artifacts for a given Measure be loaded on the HAPI server, including `Libaries` and `ValueSets`.
* Additional features and performance enhancements for Measure evaluation
* Additional FHIR Clinical Reasoning Module operations:
* Library $evaluate
* PlanDefinition $apply
* Support for the CPG IG Operations
* $cql

406
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_jpa_cql/cql_measure.md Normal file
View File

@ -0,0 +1,406 @@
# CQL Measure
## Introduction
The FHIR Clinical Reasoning Module defines the [Measure resource](https://www.hl7.org/fhir/measure.html) and several [associated operations](https://www.hl7.org/fhir/measure-operations.html). The Measure Resource represents a structured, computable definition of a health-related measure such as a clinical quality measure, public health indicator, or population analytics measure. These Measures can then be used for reporting, analytics, and data-exchange purposes.
Electronic Clinical Quality Measures (eCQMs) in FHIR are represented as a FHIR Measure resource containing metadata and terminology, a population criteria section, and at least one FHIR Library resource containing a data criteria section as well as the logic used to define the population criteria. The population criteria section typically contains initial population criteria, denominator criteria, and numerator criteria sub-components, among others. This is elaborated upon in greater detail in the [CQF Measures IG](http://hl7.org/fhir/us/cqfmeasures). An example of an eCQM as defined in FHIR looks like:
```json
{
"resourceType" : "Measure",
"library" : [
"http://hl7.org/fhir/us/cqfmeasures/Library/EXMLogic"
],
"group" : [
{
"population" : [
{
"code" : {
"coding" : [
{
"code" : "initial-population"
}
]
},
"criteria" : {
"language" : "text/cql.identifier",
"expression" : "Initial Population"
}
},
{
"code" : {
"coding" : [
{
"code" : "numerator"
}
]
},
"criteria" : {
"language" : "text/cql.identifier",
"expression" : "Numerator"
}
},
{
"code" : {
"coding" : [
{
"code" : "denominator"
}
]
},
"criteria" : {
"language" : "text/cql.identifier",
"expression" : "Denominator"
}
}
]
}
]
}
```
Measures are then scored according the whether a subjects (or subjects) are members of the various populations.
For example, a Measure for Breast Cancer screening might define an Initial Population (via CQL expressions) of "all women", a Denominator of "women over 35", and a Numerator of "women over 35 who have had breast cancer screenings in the past year". If the Measure is evaluated against a population of 100 women, 50 are over 35, and of those 25 have had breast cancer screenings in the past year, the final score would be 50%<sup>1</sup> (total number in numerator / total number in the denominator).
1. There are several methods for scoring Measures, this is meant only as an example.
## Operations
HAPI implements the [$evaluate-measure](https://www.hl7.org/fhir/operation-measure-evaluate-measure.html) operation. Support for additional operations is planned.
## Evaluate Measure
The `$evaluate-measure` operation is used to execute a Measure as specified by the relevant FHIR Resources against a subject or set of subjects. This implementation currently focuses primarily on supporting the narrower evaluation requirements defined by the [CQF Measures IG](http://hl7.org/fhir/us/cqfmeasures). Some support for extensions defined by other IGs is included as well, and the implementation aims to support a wider range of functionality in the future.
### Example Measure
Several example Measures are available in the [ecqm-content-r4](https://github.com/cqframework/ecqm-content-r4) IG. Full Bundles with all the required supporting resources are available [here](https://github.com/cqframework/ecqm-content-r4/tree/master/bundles/measure). You can download a Bundle and load it on your server as a transaction:
```bash
POST http://your-server-base/fhir BreastCancerScreeningFHIR-bundle.json
```
These Bundles also include example Patient clinical data so once posted Measure evaluation can be invoked with:
```bash
GET http://your-server-base/fhir/Measure/BreastCancerScreeningFHIR/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31&subject=numerator&reportType=subject
```
### Measure Features
The FHIR Measure specification defines several different types of Measures and various parameters for controlling the Measure evaluation. This section describes the features supported by HAPI.
#### Reporting Period
The `periodStart` and `periodEnd` parameters are used to control the Reporting Period for which a report is generated. This corresponds to `Measurement Period` defined in the CQL logic, as defined by the conformance requirements in the CQF Measures IG. Both `periodStart` and `periodEnd` must be used or neither must be used.
If neither are used the default reporting period specified in the CQL logic is used, as shown here
```cql
parameter "Measurement Period" Interval<DateTime>
default Interval[@2019-01-01T00:00:00.0, @2020-01-01T00:00:00.0)
```
If neither are used and there is no default reporting period in the CQL logic an error is thrown.
A request using `periodStart` and `periodEnd` looks like:
```bash
GET fhir/Measure/<MeasureId>/$evaluate-measure?periodStart=2019-01-01&periodEnd=2019-12-31
```
`periodStart` and `periodEnd` support Dates (YYYY, YYYY-MM, or YYYY-MM-DD) and DateTimes (YYYY-MM-DDThh:mm:ss+zz:zz)
#### Report Types
Measure report types determine what data is returned from the evaluation. This is controlled with the `reportType` parameter on the $evaluate-measure Operation
| Report Type | Supported | Description |
| ------------ | :----------------: | -------------------------------------------------------------------------------------------------------------- |
| subject | :white_check_mark: | Measure report for a single subject (e.g. one patient). Includes additional detail, such as evaluatedResources |
| subject-list | :white_check_mark: | Measure report including the list of subjects in each population (e.g. all the patients in the "numerator") |
| population | :white_check_mark: | Summary measure report for a population |
NOTE: There's an open issue on the FHIR specification to align these names to the MeasureReportType value set.
A request using `reportType` looks like:
```bash
GET fhir/Measure/<MeasureId>/$evaluate-measure?reportType=subject-list
```
#### Subject Types
The subject of a measure evaluation is controlled with the `subject` (R4+) and `patient` (DSTU3) operation parameters. Currently the only subject type supported by HAPI is Patient. This means that all Measure evaluation and reporting happens with respect to a Patient or set of Patient resources.
| Subject Type | Supported | Description |
| ----------------- | :------------------: | ----------------- |
| Patient | :white_check_mark: | A Patient |
| Practitioner | :white_large_square: | A Practitioner |
| Organization | :white_large_square: | An Organization |
| Location | :white_large_square: | A Location |
| Device | :white_large_square: | A Device |
| Group<sup>1</sup> | :white_large_square: | A set of subjects |
1. See next section
A request using `subject` looks like:
```bash
GET fhir/Measure/<MeasureId>/$evaluate-measure?subject=Patient/123
```
##### Selecting a set of Patients
The set of Patients used for Measure evaluation is controlled with the `subject` (R4+) or `patient` (DSTU3), and `practitioner` parameters. The two parameters are mutually exclusive.
| Parameter | Supported | Description |
| ----------------------------------------------------- | :------------------: | ----------------------------------------------------------------------- |
| Not specified | :white_check_mark: | All Patients on the server |
| `subject=XXX` or `subject=Patient/XXX` | :white_check_mark: | A single Patient |
| `practitioner=XXX` or `practitioner=Practitioner/XXX` | :white_check_mark: | All Patients whose `generalPractitioner` is the referenced Practitioner |
| `subject=Group/XXX`<sup>1</sup> | :white_large_square: | A Group containing subjects |
| `subject=XXX` AND `practitioner=XXX` | :x: | Not a valid combination |
1. Referencing a Group of Patients as the subject is defined in the ATR IG and is on the roadmap. This will allow much more control over which Patients are included in the evaluated set.
A request using `practitioner` looks like:
```bash
GET fhir/Measure/<MeasureId>/$evaluate-measure?practitioner=Practitioner/XYZ
```
#### ReportType, Subject, Practitioner Matrix
The following table shows the combinations of the `subject` (or `patient`), `practitioner` and `reportType` parameters that are valid
| | subject reportType | subject-list reportType | population reportType |
| ---------------- | :----------------: | :-------------------------------: | :-------------------------------: |
| subject parameter | :white_check_mark: | :white_check_mark: <sup>1,2</sup> | :white_check_mark: <sup>1,2</sup> |
| practitioner parameter | :x:<sup>3</sup> | :white_check_mark: | :white_check_mark: |
1. Including the subject parameter restricts the Measure evaluation to a single Patient. Omit the `subject` (or `patient`) parameter to get report for multiple Patients. The subject-list and population report types have less detail than a subject report.
2. A Group `subject` with a subject-list or population `reportType` will be a valid combination once Group support is implemented.
3. A practitioner have may zero, one, or many patients so a practitioner report always assumes a set.
#### Scoring Methods
The Measure scoring method determines how a Measure score is calculated. It is set with the [scoring](https://www.hl7.org/fhir/measure-definitions.html#Measure.scoring) element on the Measure resource.
The HAPI implementation conforms to the requirements defined by the CQF Measures IG. A more detailed description of each scoring method is linked in the table below.
| Scoring Method | Supported | Description |
| ------------------- | :------------------: | ---------------------------------------------------------------------------------------------------------------------- |
| proportion | :white_check_mark: | [Proportion Measures](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#proportion-measures) |
| ratio | :white_check_mark: | [Ratio Measures](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#ratio-measures) |
| continuous-variable | :white_check_mark: | [Continuous Variable](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#continuous-variable-measure) |
| cohort | :white_check_mark:* | [Cohort](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#cohort-definitions) |
| composite | :white_large_square: | See below |
* The cohort Measure scoring support is partial. The HAPI implementation does not yet return the required Measure observations
An example Measure resource with `scoring` defined looks like:
```json
{
"resourceType": "Measure",
"scoring": {
"coding": [ {
"system": "http://terminology.hl7.org/CodeSystem/measure-scoring",
"code": "proportion",
"display": "Proportion"
} ]
}
}
```
##### Composite Scoring
A composite Measure is scored by combining and/or aggregating the results of other Measures. The [compositeScoring](https://www.hl7.org/fhir/measure-definitions.html#Measure.compositeScoring) element is used to control how composite Measures are scored. HAPI does not currently support any composite scoring method.
| Composite Scoring Method | Supported | Description |
| ------------------------ | :------------------: | ---------------------------------------------------------------------------------------------- |
| opportunity | :white_large_square: | Combines Numerators and Denominators for each component Measure |
| all-or-nothing | :white_large_square: | Includes individuals that are in the numerator for all component Measures |
| linear | :white_large_square: | Gives an individual score based on the number of numerators in which they appear |
| weighted | :white_large_square: | Gives an individual a cored based on a weighted factor for each numerator in which they appear |
#### Populations
The HAPI implementation uses the populations defined by the CQF Measures IG for each scoring type. A matrix of the supported populations is shown in the [Criteria Names](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#criteria-names) section of the CQF Measures IG.
#### Population Criteria
The logical criteria used for determining each Measure population is defined by the [Measure.group.population.criteria](https://hl7.org/fhir/R4/measure-definitions.html#Measure.group.population.criteria) element. The Measure specification allows population criteria to be defined using FHIR Path, CQL, or other languages as appropriate. The HAPI implementation currently only supports using CQL. The relationship between a Measure Population and CQL is illustrated in the [Population Criteria](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#population-criteria) section of the CQF Measures IG.
An example Measure resource with a population criteria referencing a CQL identifier looks like:
```json
{
"resourceType": "Measure",
"group": [ {
"population": [ {
"code": {
"coding": [ {
"system": "http://terminology.hl7.org/CodeSystem/measure-population",
"code": "initial-population",
"display": "Initial Population"
} ]
},
"criteria": {
"language": "text/cql.identifier",
"expression": "Initial Population"
}
}]
}]
}
```
##### Criteria Expression Type
| Expression Type | Supported |
| --------------- | :------------------: |
| CQL | :white_check_mark: |
| FHIR Path | :white_large_square: |
#### Supplemental Data Elements
Supplemental Data Elements are used to report additional information about the subjects that may not be included in the in the Population criteria definitions. For example, it may be of interest to report the gender of all subjects for informational purposes. Supplemental data elements are defined by the [Measure.supplementalData](http://www.hl7.org/fhir/measure-definitions.html#Measure.supplementalData) element, and are reported as Observations in the evaluatedResources of the MeasureReport.
Supplemental Data Elements can be specified as either CQL definitions or FHIR Path expressions.
| Expression Type | Supported |
| --------------- | :------------------: |
| CQL | :white_check_mark: |
| FHIR Path | :white_large_square: |
An example Measure resource with some supplemental data elements set looks like:
```json
{
"resourceType": "Measure",
"supplementalData": [ {
"code": {
"text": "sde-ethnicity"
},
"criteria": {
"language": "text/cql.identifier",
"expression": "SDE Ethnicity"
}
}]
}
```
#### Stratifiers
Stratifiers are used divide Measure populations into segments of interest. For example, it may be of interest to compare the Measure score between different age groups or genders. Each stratum within a stratification is scored the same way as the overall population. Stratifiers are defined using the [Measure.group.stratifier](http://hl7.org/fhir/R4/measure-definitions.html#Measure.group.stratifier) element.
HAPI does not implement stratifier support but it's on the roadmap.
An example Measure resource with a stratifier set looks like:
```json
{
"resourceType": "Measure",
"group": [ {
"stratifier": [ {
"code": {
"text": "Stratum 1"
},
"criteria": {
"language": "text/cql.identifier",
"expression": "Stratification 1"
}
}]
}]
}
```
##### Stratifier Expression Support
As with Populations and Supplemental Data Elements the criteria used for Stratification may be defined with CQL or FHIR Path.
| Expression Type | Supported |
| --------------- | :------------------: |
| CQL | :white_large_square: |
| FHIR Path | :white_large_square: |
##### Stratifier Component Support
The Measure specification also supports multi-dimensional stratification, for cases where more than one data element is needed.
| Stratifier Type | Supported |
| ---------------- | :------------------: |
| Single Component | :white_large_square: |
| Multi Component | :white_large_square: |
#### Evaluated Resources
A FHIR MeasureReport permits referencing the Resources used when evaluating in the [MeasureReport.evaluatedResource](https://www.hl7.org/fhir/measurereport-definitions.html#MeasureReport.evaluatedResource) element. HAPI includes these resources when generating `subject` reports for a single Patient. Evaluated resources for `population` or `subject-list` reports are not included. For large populations this could quickly become an extremely large number of resources.
The evaluated resources will not include every resource on the HAPI server for a given subject. Rather, it includes only the resources that were retrieved from the server by the CQL logic that was evaluated. This corresponds to the data-requirements for a given Measure. As an example, consider the following CQL:
```cql
valueset "Example Value Set" : 'http://fhir.org/example-value-set'
define "Example Observations":
[Observation : "Example Value Set"]
```
That CQL will only select Observation Resources that have a code in the "Example Value Set". Those Observations will be reported in the Evaluated Resources while any others will not.
#### Last Received On
The `lastReceivedOn` parameter is the date the Measure was evaluated and reported. It is used to limit the number of resources reported in the Measure report for individual reports. It is currently not supported by HAPI.
#### Extensions
A number of extensions to Measure evaluation defined by various IGs are supported. They are described briefly in the table below.
| Extension | Description |
| --------- | ----------- |
| http://hl7.org/fhir/us/cqframework/cqfmeasures/StructureDefinition/cqfm-productLine | Used to evaluate different product lines (e.g. Medicare, Private, etc.) |
| http://hl7.org/fhir/StructureDefinition/cqf-measureInfo | Used to demark a Measure Observation |
| http://hl7.org/fhir/us/davinci-deqm/StructureDefinition/extension-populationReference | Used to specify the population that triggered a particular `evaluatedResource`|
There's not currently a way to configure which extensions are enabled. All supported extensions are always enabled.
## Architecture
Below are a few diagrams that show the overall architecture of Measure evaluation and how it fits into the HAPI FHIR Server.
### Component Diagram
This is a simplified component diagram of the Measure evaluation architecture
![Measure Evaluation Architecture](/hapi-fhir/docs/images/ref_measure_architecture_drawio.svg)
### Sequence Chart
This sequence chart approximates the Measure evaluation logic implemented by HAPI.
![Measure Evaluation Sequence Chart](/hapi-fhir/docs/images/measure_evaluation_sequence.png)
## FAQs
Q: I get an error saying HAPI can't locate my library, and I've verified it's on the server.
A: HAPI follows the [Library conformance requirements](https://build.fhir.org/ig/HL7/cqf-measures/measure-conformance.html#conformance-requirement-3-1) defined by the CQF Measures IG, meaning the Library must have a `logic-library` type, the name and versions of the FHIR Library and CQL Library must match, and the url of the Library must end in the name of the Library.
FHIR Libraries generated from CQL via the IG Publisher follow these requirements automatically.
Q: Does HAPI support partitions for evaluation?
A: Yes, though the Measure and associated Resources must be in the same partition as the clinical data being used.
## Roadmap
* Complete cohort implementation
* Support for stratifiers
* Support for Group subjects
* Support for FHIRPath expressions in Stratifiers, Supplemental Data Elements, and Population Criteria
* `$data-requirements`, `$collect-data`, `$submit-data`, and `$care-gaps` operations
* Support for more extensions defined in the CQF Measures, CPG, and ATR IGs

10
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/docs/server_plain/rest_operations_search.md
View File

@ -346,7 +346,7 @@ Sort specifications can be passed into handler methods by adding a parameter of
Example URL to invoke this method:
```url
http://fhir.example.com/Patient?_identifier=urn:foo|123&_sort=given
http://fhir.example.com/Patient?identifier=urn:foo|123&_sort=given
```
<a name="limiting-results"/>
@ -364,7 +364,7 @@ of resources fetched from the database.
Example URL to invoke this method:
```url
http://fhir.example.com/Patient?_identifier=urn:foo|123&_count=10
http://fhir.example.com/Patient?identifier=urn:foo|123&_count=10
```
# Paging
@ -388,17 +388,17 @@ for more information.
Example URL to invoke this method for the first page:
```url
http://fhir.example.com/Patient?_identifier=urn:foo|123&_count=10&_offset=0
http://fhir.example.com/Patient?identifier=urn:foo|123&_count=10&_offset=0
```
or just
```url
http://fhir.example.com/Patient?_identifier=urn:foo|123&_count=10
http://fhir.example.com/Patient?identifier=urn:foo|123&_count=10
```
Example URL to invoke this method for the second page:
```url
http://fhir.example.com/Patient?_identifier=urn:foo|123&_count=10&_offset=10
http://fhir.example.com/Patient?identifier=urn:foo|123&_count=10&_offset=10
```
Note that if the paging provider is configured to be database backed, `_offset=0` behaves differently than no `_offset`. This

19
hapi-fhir-jpa/src/main/java/ca/uhn/fhir/jpa/util/TestUtil.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.google.common.collect.ImmutableSet;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import com.google.common.reflect.ClassPath;
import com.google.common.reflect.ClassPath.ClassInfo;
import org.apache.commons.io.IOUtils;
@ -74,6 +75,17 @@ public class TestUtil {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestUtil.class);
private static Set<String> ourReservedWords;
// Exceptions set because H2 sets indexes for FKs automatically so this index had to be called as the target FK field
// it is indexing to avoid SchemaMigrationTest to complain about the extra index (which doesn't exist in H2)
private static final Set<String> duplicateNameValidationExceptionList = Sets.newHashSet(
"FK_CONCEPTPROP_CONCEPT",
"FK_CONCEPTDESIG_CONCEPT",
"FK_TERM_CONCEPTPC_CHILD",
"FK_TERM_CONCEPTPC_PARENT"
);
/**
* non instantiable
*/
@ -252,7 +264,8 @@ public class TestUtil {
}
for (Index nextConstraint : table.indexes()) {
assertNotADuplicateName(nextConstraint.name(), theNames);
Validate.isTrue(nextConstraint.name().startsWith("IDX_"), nextConstraint.name() + " must start with IDX_");
Validate.isTrue(nextConstraint.name().startsWith("IDX_") || nextConstraint.name().startsWith("FK_"),
nextConstraint.name() + " must start with IDX_ or FK_ (last one when indexing a FK column)");
}
}
@ -269,7 +282,9 @@ public class TestUtil {
Validate.notNull(fk);
Validate.isTrue(isNotBlank(fk.name()), "Foreign key on " + theAnnotatedElement + " has no name()");
Validate.isTrue(fk.name().startsWith("FK_"));
assertNotADuplicateName(fk.name(), theNames);
if ( ! duplicateNameValidationExceptionList.contains(fk.name())) {
assertNotADuplicateName(fk.name(), theNames);
}
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch/BatchJobsConfig.java
View File

@ -26,6 +26,8 @@ import ca.uhn.fhir.jpa.bulk.imprt.job.BulkImportJobConfig;
import ca.uhn.fhir.jpa.delete.job.DeleteExpungeJobConfig;
import ca.uhn.fhir.jpa.reindex.job.ReindexEverythingJobConfig;
import ca.uhn.fhir.jpa.reindex.job.ReindexJobConfig;
import ca.uhn.fhir.jpa.term.job.TermCodeSystemDeleteJobConfig;
import ca.uhn.fhir.jpa.term.job.TermCodeSystemVersionDeleteJobConfig;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
@ -38,7 +40,9 @@ import org.springframework.context.annotation.Import;
DeleteExpungeJobConfig.class,
ReindexJobConfig.class,
ReindexEverythingJobConfig.class,
MdmClearJobConfig.class
MdmClearJobConfig.class,
TermCodeSystemDeleteJobConfig.class,
TermCodeSystemVersionDeleteJobConfig.class
})
public class BatchJobsConfig {
}

42
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/BaseBinaryStorageSvcImpl.java
View File

@ -20,20 +20,31 @@ package ca.uhn.fhir.jpa.binstore;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.PayloadTooLargeException;
import ca.uhn.fhir.util.BinaryUtil;
import ca.uhn.fhir.util.HapiExtensions;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hashing;
import com.google.common.hash.HashingInputStream;
import com.google.common.io.ByteStreams;
import org.apache.commons.io.input.CountingInputStream;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IBaseHasExtensions;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import org.springframework.beans.factory.annotation.Autowired;
import javax.annotation.Nonnull;
import java.io.IOException;
import java.io.InputStream;
import java.security.SecureRandom;
import java.util.Optional;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
private final SecureRandom myRandom;
@ -41,6 +52,8 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
private final int ID_LENGTH = 100;
private int myMaximumBinarySize = Integer.MAX_VALUE;
private int myMinimumBinarySize;
@Autowired
private FhirContext myFhirContext;
BaseBinaryStorageSvcImpl() {
myRandom = new SecureRandom();
@ -104,7 +117,6 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
};
}
String provideIdForNewBlob(String theBlobIdOrNull) {
String id = theBlobIdOrNull;
if (isBlank(theBlobIdOrNull)) {
@ -112,4 +124,32 @@ abstract class BaseBinaryStorageSvcImpl implements IBinaryStorageSvc {
}
return id;
}
@Override
public byte[] fetchDataBlobFromBinary(IBaseBinary theBaseBinary) throws IOException {
IPrimitiveType<byte[]> dataElement = BinaryUtil.getOrCreateData(myFhirContext, theBaseBinary);
byte[] value = dataElement.getValue();
if (value == null) {
Optional<String> attachmentId = getAttachmentId((IBaseHasExtensions) dataElement);
if (attachmentId.isPresent()) {
value = fetchBlob(theBaseBinary.getIdElement(), attachmentId.get());
} else {
throw new InternalErrorException("Unable to load binary blob data for " + theBaseBinary.getIdElement());
}
}
return value;
}
@SuppressWarnings("unchecked")
private Optional<String> getAttachmentId(IBaseHasExtensions theBaseBinary) {
return theBaseBinary
.getExtension()
.stream()
.filter(t -> HapiExtensions.EXT_EXTERNALIZED_BINARY_ID.equals(t.getUrl()))
.filter(t -> t.getValue() instanceof IPrimitiveType)
.map(t -> (IPrimitiveType<String>) t.getValue())
.map(t -> t.getValue())
.filter(t -> isNotBlank(t))
.findFirst();
}
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/IBinaryStorageSvc.java
View File

@ -20,6 +20,8 @@ package ca.uhn.fhir.jpa.binstore;
* #L%
*/
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IIdType;
import javax.annotation.Nonnull;
@ -101,4 +103,13 @@ public interface IBinaryStorageSvc {
* @return The payload as a byte array
*/
byte[] fetchBlob(IIdType theResourceId, String theBlobId) throws IOException;
/**
* Fetch the byte[] contents of a given Binary resource's `data` element. If the data is a standard base64encoded string that is embedded, return it.
* Otherwise, attempt to load the externalized binary blob via the the externalized binary storage service.
*
* @param theResourceId The resource ID The ID of the Binary resource you want to extract data bytes from
* @return The binary data blob as a byte array
*/
byte[] fetchDataBlobFromBinary(IBaseBinary theResource) throws IOException;
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/binstore/NullBinaryStorageSvcImpl.java
View File

@ -20,8 +20,10 @@ package ca.uhn.fhir.jpa.binstore;
* #L%
*/
import org.hl7.fhir.instance.model.api.IBaseBinary;
import org.hl7.fhir.instance.model.api.IIdType;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
@ -81,4 +83,9 @@ public class NullBinaryStorageSvcImpl implements IBinaryStorageSvc {
public byte[] fetchBlob(IIdType theResourceId, String theBlobId) {
throw new UnsupportedOperationException();
}
@Override
public byte[] fetchDataBlobFromBinary(IBaseBinary theResource) throws IOException {
throw new UnsupportedOperationException();
}
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/BaseConfig.java
View File

@ -155,8 +155,13 @@ import org.hl7.fhir.common.hapi.validation.support.UnknownCodeSystemWarningValid
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.graphql.IGraphQLStorageServices;
import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.SimpleJobOperator;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableListableBeanFactory;
import org.springframework.context.ApplicationContext;
@ -229,6 +234,9 @@ public abstract class BaseConfig {
private Integer searchCoordMaxPoolSize = 100;
private Integer searchCoordQueueCapacity = 200;
@Autowired
private JobLauncher myJobLauncher;
/**
* Subclasses may override this method to provide settings such as search coordinator pool sizes.
*/
@ -279,6 +287,18 @@ public abstract class BaseConfig {
return new CascadingDeleteInterceptor(theFhirContext, theDaoRegistry, theInterceptorBroadcaster);
}
@Bean
public SimpleJobOperator jobOperator(JobExplorer jobExplorer, JobRepository jobRepository, JobRegistry jobRegistry) {
SimpleJobOperator jobOperator = new SimpleJobOperator();
jobOperator.setJobExplorer(jobExplorer);
jobOperator.setJobRepository(jobRepository);
jobOperator.setJobRegistry(jobRegistry);
jobOperator.setJobLauncher(myJobLauncher);
return jobOperator;
}
@Lazy
@Bean

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermCodeSystemVersionDao.java
View File

@ -35,8 +35,8 @@ public interface ITermCodeSystemVersionDao extends JpaRepository<TermCodeSystemV
@Query("DELETE FROM TermCodeSystemVersion csv WHERE csv.myCodeSystem = :cs")
void deleteForCodeSystem(@Param("cs") TermCodeSystem theCodeSystem);
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid")
List<TermCodeSystemVersion> findByCodeSystemPid(@Param("codesystem_pid") Long theCodeSystemPid);
@Query("SELECT myId FROM TermCodeSystemVersion WHERE myCodeSystemPid = :codesystem_pid order by myId")
List<Long> findSortedPidsByCodeSystemPid(@Param("codesystem_pid") Long theCodeSystemPid);
@Query("SELECT cs FROM TermCodeSystemVersion cs WHERE cs.myCodeSystemPid = :codesystem_pid AND cs.myCodeSystemVersionId = :codesystem_version_id")
TermCodeSystemVersion findByCodeSystemPidAndVersion(@Param("codesystem_pid") Long theCodeSystemPid, @Param("codesystem_version_id") String theCodeSystemVersionId);

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDao.java
View File

@ -4,8 +4,8 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@ -40,8 +40,9 @@ public interface ITermConceptDao extends JpaRepository<TermConcept, Long>, IHapi
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system AND c.myCode = :code")
Optional<TermConcept> findByCodeSystemAndCode(@Param("code_system") TermCodeSystemVersion theCodeSystem, @Param("code") String theCode);
@Query("SELECT t.myId FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
@Modifying
@Query("DELETE FROM TermConcept WHERE myCodeSystem.myId = :cs_pid")
int deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system")
List<TermConcept> findByCodeSystemVersion(@Param("code_system") TermCodeSystemVersion theCodeSystem);

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptDesignationDao.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@ -29,10 +28,8 @@ import org.springframework.data.repository.query.Param;
public interface ITermConceptDesignationDao extends JpaRepository<TermConceptDesignation, Long>, IHapiFhirJpaRepository {
@Query("SELECT t.myId FROM TermConceptDesignation t WHERE t.myCodeSystemVersion.myId = :csv_pid")
Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("csv_pid") Long thePid);
@Query("SELECT COUNT(t) FROM TermConceptDesignation t WHERE t.myCodeSystemVersion.myId = :csv_pid")
Integer countByCodeSystemVersion(@Param("csv_pid") Long thePid);
@Modifying
@Query("DELETE FROM TermConceptDesignation WHERE myCodeSystemVersion.myId = :csv_pid")
int deleteByCodeSystemVersion(@Param("csv_pid") Long thePid);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptParentChildLinkDao.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@ -31,13 +30,11 @@ import java.util.Collection;
public interface ITermConceptParentChildLinkDao extends JpaRepository<TermConceptParentChildLink, Long>, IHapiFhirJpaRepository {
@Query("SELECT COUNT(t) FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
@Query("SELECT t.myParentPid FROM TermConceptParentChildLink t WHERE t.myChildPid = :child_pid")
Collection<Long> findAllWithChild(@Param("child_pid") Long theConceptPid);
@Query("SELECT t.myPid FROM TermConceptParentChildLink t WHERE t.myCodeSystem.myId = :cs_pid")
Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
@Modifying
@Query("DELETE FROM TermConceptParentChildLink WHERE myCodeSystemVersionPid = :cs_pid")
int deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermConceptPropertyDao.java
View File

@ -1,9 +1,8 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.TermConceptProperty;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
@ -29,8 +28,9 @@ import org.springframework.data.repository.query.Param;
public interface ITermConceptPropertyDao extends JpaRepository<TermConceptProperty, Long>, IHapiFhirJpaRepository {
@Query("SELECT t.myId FROM TermConceptProperty t WHERE t.myCodeSystemVersion.myId = :cs_pid")
Slice<Long> findIdsByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
@Modifying
@Query("DELETE FROM TermConceptProperty WHERE myCodeSystemVersion.myId = :cs_pid")
int deleteByCodeSystemVersion(@Param("cs_pid") Long thePid);
@Query("SELECT COUNT(t) FROM TermConceptProperty t WHERE t.myCodeSystemVersion.myId = :cs_pid")
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/IdHelperService.java
View File

@ -316,12 +316,15 @@ public class IdHelperService {
TypedQuery<ForcedId> query = myEntityManager.createQuery(criteriaQuery);
List<ForcedId> results = query.getResultList();
for (ForcedId nextId : results) {
ResourcePersistentId persistentId = new ResourcePersistentId(nextId.getResourceId());
populateAssociatedResourceId(nextId.getResourceType(), nextId.getForcedId(), persistentId);
retVal.add(persistentId);
// Check if the nextId has a resource ID. It may have a null resource ID if a commit is still pending.
if (nextId.getResourceId() != null) {
ResourcePersistentId persistentId = new ResourcePersistentId(nextId.getResourceId());
populateAssociatedResourceId(nextId.getResourceType(), nextId.getForcedId(), persistentId);
retVal.add(persistentId);
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getForcedId());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, persistentId);
String key = toForcedIdToPidKey(theRequestPartitionId, nextId.getResourceType(), nextId.getForcedId());
myMemoryCacheService.putAfterCommit(MemoryCacheService.CacheEnum.FORCED_ID_TO_PID, key, persistentId);
}
}
}

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptDesignation.java
View File

@ -30,8 +30,9 @@ import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = {
}, indexes = {
@Table(name = "TRM_CONCEPT_DESIG", uniqueConstraints = { }, indexes = {
// must have same name that indexed FK or SchemaMigrationTest complains because H2 sets this index automatically
@Index(name = "FK_CONCEPTDESIG_CONCEPT", columnList = "CONCEPT_PID", unique = false)
})
public class TermConceptDesignation implements Serializable {
private static final long serialVersionUID = 1L;

3
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -27,6 +27,9 @@ import java.io.Serializable;
@Entity
@Table(name = "TRM_CONCEPT_PC_LINK", indexes = {
// must have same name that indexed FK or SchemaMigrationTest complains because H2 sets this index automatically
@Index(name = "FK_TERM_CONCEPTPC_CHILD", columnList = "CHILD_PID", unique = false),
@Index(name = "FK_TERM_CONCEPTPC_PARENT", columnList = "PARENT_PID", unique = false)
})
public class TermConceptParentChildLink implements Serializable {
private static final long serialVersionUID = 1L;

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -36,6 +36,7 @@ import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.Index;
import javax.persistence.JoinColumn;
import javax.persistence.Lob;
import javax.persistence.ManyToOne;
@ -48,7 +49,9 @@ import static org.apache.commons.lang3.StringUtils.left;
import static org.apache.commons.lang3.StringUtils.length;
@Entity
@Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = {
@Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = { }, indexes = {
// must have same name that indexed FK or SchemaMigrationTest complains because H2 sets this index automatically
@Index(name = "FK_CONCEPTPROP_CONCEPT", columnList = "CONCEPT_PID", unique = false)
})
public class TermConceptProperty implements Serializable {
public static final int MAX_PROPTYPE_ENUM_LENGTH = 6;

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -41,16 +41,26 @@ import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.util.VersionEnum;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import static java.util.stream.Collectors.toSet;
@SuppressWarnings({"SqlNoDataSourceInspection", "SpellCheckingInspection"})
public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
private final Set<FlagEnum> myFlags;
// H2, Derby, MariaDB, and MySql automatically add indexes to foreign keys
public static final DriverTypeEnum[] NON_AUTOMATIC_FK_INDEX_PLATFORMS = new DriverTypeEnum[] {
DriverTypeEnum.POSTGRES_9_4, DriverTypeEnum.ORACLE_12C, DriverTypeEnum.MSSQL_2012 };
/**
* Constructor
*/
@ -76,8 +86,44 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
init540(); // 20210218 - 20210520
init550(); // 20210520 -
init560(); // 20211027 -
init570(); // 20211102 -
}
private void init570() {
Builder version = forVersion(VersionEnum.V5_7_0);
// both indexes must have same name that indexed FK or SchemaMigrationTest complains because H2 sets this index automatically
version.onTable("TRM_CONCEPT_PROPERTY")
.addIndex("20211102.1", "FK_CONCEPTPROP_CONCEPT")
.unique(false)
.withColumns("CONCEPT_PID")
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
version.onTable("TRM_CONCEPT_DESIG")
.addIndex("20211102.2", "FK_CONCEPTDESIG_CONCEPT")
.unique(false)
.withColumns("CONCEPT_PID")
// H2, Derby, MariaDB, and MySql automatically add indexes to foreign keys
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
version.onTable("TRM_CONCEPT_PC_LINK")
.addIndex("20211102.3", "FK_TERM_CONCEPTPC_CHILD")
.unique(false)
.withColumns("CHILD_PID")
// H2, Derby, MariaDB, and MySql automatically add indexes to foreign keys
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
version.onTable("TRM_CONCEPT_PC_LINK")
.addIndex("20211102.4", "FK_TERM_CONCEPTPC_PARENT")
.unique(false)
.withColumns("PARENT_PID")
// H2, Derby, MariaDB, and MySql automatically add indexes to foreign keys
.onlyAppliesToPlatforms(NON_AUTOMATIC_FK_INDEX_PLATFORMS);
}
private void init560() {
init560_20211027();
}

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/packages/JpaPackageCache.java
View File

@ -27,6 +27,7 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.dao.data.INpmPackageDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionDao;
import ca.uhn.fhir.jpa.dao.data.INpmPackageVersionResourceDao;
@ -123,6 +124,9 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
@Autowired
private PartitionSettings myPartitionSettings;
@Autowired(required = false)//It is possible that some implementers will not create such a bean.
private IBinaryStorageSvc myBinaryStorageSvc;
@Override
@Transactional
public NpmPackage loadPackageFromCacheOnly(String theId, @Nullable String theVersion) {
@ -172,13 +176,37 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private IHapiPackageCacheManager.PackageContents loadPackageContents(NpmPackageVersionEntity thePackageVersion) {
IFhirResourceDao<? extends IBaseBinary> binaryDao = getBinaryDao();
IBaseBinary binary = binaryDao.readByPid(new ResourcePersistentId(thePackageVersion.getPackageBinary().getId()));
try {
byte[] content = fetchBlobFromBinary(binary);
PackageContents retVal = new PackageContents()
.setBytes(content)
.setPackageId(thePackageVersion.getPackageId())
.setVersion(thePackageVersion.getVersionId())
.setLastModified(thePackageVersion.getUpdatedTime());
return retVal;
} catch (IOException e) {
throw new InternalErrorException("Failed to load package. There was a problem reading binaries", e);
}
}
PackageContents retVal = new PackageContents()
.setBytes(binary.getContent())
.setPackageId(thePackageVersion.getPackageId())
.setVersion(thePackageVersion.getVersionId())
.setLastModified(thePackageVersion.getUpdatedTime());
return retVal;
/**
* Helper method which will attempt to use the IBinaryStorageSvc to resolve the binary blob if available. If
* the bean is unavailable, fallback to assuming we are using an embedded base64 in the data element.
* @param theBinary the Binary who's `data` blob you want to retrieve
* @return a byte array containing the blob.
*
* @throws IOException
*/
private byte[] fetchBlobFromBinary(IBaseBinary theBinary) throws IOException {
if (myBinaryStorageSvc != null) {
return myBinaryStorageSvc.fetchDataBlobFromBinary(theBinary);
} else {
byte[] value = BinaryUtil.getOrCreateData(myCtx, theBinary).getValue();
if (value == null) {
throw new InternalErrorException("Failed to fetch blob from Binary/" + theBinary.getIdElement());
}
return value;
}
}
@SuppressWarnings("unchecked")
@ -487,14 +515,12 @@ public class JpaPackageCache extends BasePackageCacheManager implements IHapiPac
private IBaseResource loadPackageEntity(NpmPackageVersionResourceEntity contents) {
try {
ResourcePersistentId binaryPid = new ResourcePersistentId(contents.getResourceBinary().getId());
IBaseBinary binary = getBinaryDao().readByPid(binaryPid);
byte[] resourceContentsBytes = BinaryUtil.getOrCreateData(myCtx, binary).getValue();
String resourceContents = new String(resourceContentsBytes, StandardCharsets.UTF_8);
FhirContext packageContext = getFhirContext(contents.getFhirVersion());
return EncodingEnum.detectEncoding(resourceContents).newParser(packageContext).parseResource(resourceContents);
ResourcePersistentId binaryPid = new ResourcePersistentId(contents.getResourceBinary().getId());
IBaseBinary binary = getBinaryDao().readByPid(binaryPid);
byte[] resourceContentsBytes= fetchBlobFromBinary(binary);
String resourceContents = new String(resourceContentsBytes, StandardCharsets.UTF_8);
FhirContext packageContext = getFhirContext(contents.getFhirVersion());
return EncodingEnum.detectEncoding(resourceContents).newParser(packageContext).parseResource(resourceContents);
} catch (Exception e) {
throw new RuntimeException("Failed to load package resource " + contents, e);
}

72
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcImpl.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
@ -59,8 +60,9 @@ import org.hl7.fhir.r4.model.ConceptMap;
import org.hl7.fhir.r4.model.ValueSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.Job;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionSynchronizationManager;
@ -86,6 +88,7 @@ import java.util.UUID;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
@ -108,8 +111,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@Autowired
protected IdHelperService myIdHelperService;
@Autowired
private PlatformTransactionManager myTransactionManager;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ITermVersionAdapterSvc myTerminologyVersionAdapterSvc;
@ -124,6 +125,13 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
@Autowired
private IResourceTableDao myResourceTableDao;
@Autowired
private IBatchJobSubmitter myJobSubmitter;
@Autowired @Qualifier(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME)
private Job myTermCodeSystemVersionDeleteJob;
@Override
public ResourcePersistentId getValueSetResourcePid(IIdType theIdType) {
return myIdHelperService.resolveResourcePersistentIds(RequestPartitionId.allPartitions(), theIdType.getResourceType(), theIdType.getIdPart());
@ -262,44 +270,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
return childTermConcepts;
}
@Override
@Transactional
public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
assert TransactionSynchronizationManager.isActualTransactionActive();
ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
myEntityManager.flush();
TermCodeSystem cs = myCodeSystemDao.findById(theCodeSystem.getPid()).orElseThrow(IllegalStateException::new);
cs.setCurrentVersion(null);
myCodeSystemDao.save(cs);
myCodeSystemDao.flush();
List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
List<Long> codeSystemVersionPids = codeSystemVersions
.stream()
.map(TermCodeSystemVersion::getPid)
.collect(Collectors.toList());
for (Long next : codeSystemVersionPids) {
deleteCodeSystemVersion(next);
}
myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
myCodeSystemDao.delete(theCodeSystem);
myEntityManager.flush();
}
@Override
@Transactional(propagation = Propagation.NEVER)
public void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion) {
assert !TransactionSynchronizationManager.isActualTransactionActive();
// Delete TermCodeSystemVersion
ourLog.info(" * Deleting TermCodeSystemVersion {}", theCodeSystemVersion.getCodeSystemVersionId());
deleteCodeSystemVersion(theCodeSystemVersion.getPid());
}
/**
* Returns the number of saved concepts
*/
@ -512,26 +482,6 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
return existing;
}
private void deleteCodeSystemVersion(final Long theCodeSystemVersionPid) {
assert TransactionSynchronizationManager.isActualTransactionActive();
ourLog.info(" * Marking code system version {} for deletion", theCodeSystemVersionPid);
Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
if (codeSystemOpt.isPresent()) {
TermCodeSystem codeSystem = codeSystemOpt.get();
if (codeSystem.getCurrentVersion() != null && codeSystem.getCurrentVersion().getPid().equals(theCodeSystemVersionPid)) {
ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
codeSystem.setCurrentVersion(null);
myCodeSystemDao.save(codeSystem);
}
}
TermCodeSystemVersion codeSystemVersion = myCodeSystemVersionDao.findById(theCodeSystemVersionPid).orElseThrow(() -> new IllegalStateException());
codeSystemVersion.setCodeSystemVersionId("DELETED_" + UUID.randomUUID().toString());
myCodeSystemVersionDao.save(codeSystemVersion);
myDeferredStorageSvc.deleteCodeSystemVersion(codeSystemVersion);
}
private void validateDstu3OrNewer() {
Validate.isTrue(myContext.getVersion().getVersion().isEqualOrNewerThan(FhirVersionEnum.DSTU3), "Terminology operations only supported in DSTU3+ mode");

187
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImpl.java
View File

@ -20,12 +20,11 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
@ -37,6 +36,7 @@ import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
import org.apache.commons.lang3.Validate;
@ -45,10 +45,15 @@ import org.hl7.fhir.r4.model.ValueSet;
import org.quartz.JobExecutionContext;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameter;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.launch.JobExecutionNotRunningException;
import org.springframework.batch.core.launch.JobOperator;
import org.springframework.batch.core.launch.NoSuchJobExecutionException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
@ -59,13 +64,17 @@ import javax.annotation.PostConstruct;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import java.util.Queue;
import java.util.UUID;
import java.util.concurrent.ConcurrentLinkedQueue;
import java.util.concurrent.TimeUnit;
import java.util.function.Supplier;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_VERSION_ID;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
private static final Logger ourLog = LoggerFactory.getLogger(TermDeferredStorageSvcImpl.class);
@ -75,6 +84,9 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
final private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
final private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
final private List<TermConceptParentChildLink> myConceptLinksToSaveLater = Collections.synchronizedList(new ArrayList<>());
final private List<JobExecution> myCurrentJobExecutions = Collections.synchronizedList(new ArrayList<>());
@Autowired
protected ITermConceptDao myConceptDao;
@Autowired
@ -83,10 +95,6 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
protected ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired
protected PlatformTransactionManager myTransactionMgr;
@Autowired
protected ITermConceptPropertyDao myConceptPropertyDao;
@Autowired
protected ITermConceptDesignationDao myConceptDesignationDao;
private boolean myProcessDeferred = true;
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@ -97,6 +105,19 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
@Autowired
private ITermCodeSystemStorageSvc myCodeSystemStorageSvc;
@Autowired
private IBatchJobSubmitter myJobSubmitter;
@Autowired
private JobOperator myJobOperator;
@Autowired @Qualifier(TERM_CODE_SYSTEM_DELETE_JOB_NAME)
private org.springframework.batch.core.Job myTermCodeSystemDeleteJob;
@Autowired @Qualifier(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME)
private org.springframework.batch.core.Job myTermCodeSystemVersionDeleteJob;
@Override
public void addConceptToStorageQueue(TermConcept theConcept) {
Validate.notNull(theConcept);
@ -122,28 +143,26 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
}
@Override
@Transactional
public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
theCodeSystem.setCodeSystemUri("urn:uuid:" + UUID.randomUUID().toString());
myCodeSystemDao.save(theCodeSystem);
myDeferredCodeSystemsDeletions.add(theCodeSystem);
}
@Override
@Transactional
public void deleteCodeSystemForResource(ResourceTable theCodeSystemToDelete) {
// there are use cases (at least in tests) where the code system is not present for the resource but versions are,
// so, as code system deletion also deletes versions, we try the system first but if not present we also try versions
TermCodeSystem termCodeSystemToDelete = myCodeSystemDao.findByResourcePid(theCodeSystemToDelete.getResourceId());
if (termCodeSystemToDelete != null) {
termCodeSystemToDelete.setCodeSystemUri("urn:uuid:" + UUID.randomUUID());
myCodeSystemDao.save(termCodeSystemToDelete);
myDeferredCodeSystemsDeletions.add(termCodeSystemToDelete);
return;
}
List<TermCodeSystemVersion> codeSystemVersionsToDelete = myCodeSystemVersionDao.findByCodeSystemResourcePid(theCodeSystemToDelete.getResourceId());
for (TermCodeSystemVersion codeSystemVersionToDelete : codeSystemVersionsToDelete) {
if (codeSystemVersionToDelete != null) {
myDeferredCodeSystemVersionsDeletions.add(codeSystemVersionToDelete);
}
}
TermCodeSystem codeSystemToDelete = myCodeSystemDao.findByResourcePid(theCodeSystemToDelete.getResourceId());
if (codeSystemToDelete != null) {
deleteCodeSystem(codeSystemToDelete);
}
}
@Override
public void setProcessDeferred(boolean theProcessDeferred) {
myProcessDeferred = theProcessDeferred;
@ -236,14 +255,26 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
myDeferredCodeSystemsDeletions.clear();
myConceptLinksToSaveLater.clear();
myDeferredCodeSystemVersionsDeletions.clear();
clearJobExecutions();
}
private void runInTransaction(Runnable theRunnable) {
assert !TransactionSynchronizationManager.isActualTransactionActive();
new TransactionTemplate(myTransactionMgr).executeWithoutResult(tx -> theRunnable.run());
private void clearJobExecutions() {
for (JobExecution jobExecution : myCurrentJobExecutions) {
if (! jobExecution.isRunning()) { continue; }
try {
myJobOperator.stop(jobExecution.getId());
} catch (NoSuchJobExecutionException | JobExecutionNotRunningException theE) {
ourLog.error("Couldn't stop job execution {}: {}", jobExecution.getId(), theE);
}
}
myCurrentJobExecutions.clear();
}
private <T> T runInTransaction(Supplier<T> theRunnable) {
assert !TransactionSynchronizationManager.isActualTransactionActive();
@ -315,98 +346,53 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
return !myDeferredCodeSystemVersionsDeletions.isEmpty();
}
private void processDeferredCodeSystemDeletions() {
for (TermCodeSystem next : myDeferredCodeSystemsDeletions) {
myCodeSystemStorageSvc.deleteCodeSystem(next);
deleteTermCodeSystemOffline(next.getPid());
}
myDeferredCodeSystemsDeletions.clear();
}
private void processDeferredCodeSystemVersionDeletions() {
for (TermCodeSystemVersion next : myDeferredCodeSystemVersionsDeletions) {
processDeferredCodeSystemVersionDeletions(next.getPid());
deleteTermCodeSystemVersionOffline(next.getPid());
}
myDeferredCodeSystemVersionsDeletions.clear();
}
private void processDeferredCodeSystemVersionDeletions(long theCodeSystemVersionPid) {
assert !TransactionSynchronizationManager.isActualTransactionActive();
ourLog.info(" * Deleting CodeSystemVersion[id={}]", theCodeSystemVersionPid);
PageRequest page1000 = PageRequest.of(0, 1000);
private void deleteTermCodeSystemVersionOffline(Long theCodeSystemVersionPid) {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_VERSION_ID, new JobParameter(theCodeSystemVersionPid, true) ));
// Parent/Child links
{
String descriptor = "parent/child links";
Supplier<Slice<Long>> loader = () -> myConceptParentChildLinkDao.findIdsByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptParentChildLinkDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptParentChildLinkDao);
try {
JobExecution jobExecution = myJobSubmitter.runJob(myTermCodeSystemVersionDeleteJob, jobParameters);
myCurrentJobExecutions.add(jobExecution);
} catch (JobParametersInvalidException theE) {
throw new InternalErrorException("Offline job submission for TermCodeSystemVersion: " +
theCodeSystemVersionPid + " failed: " + theE);
}
// Properties
{
String descriptor = "concept properties";
Supplier<Slice<Long>> loader = () -> myConceptPropertyDao.findIdsByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptPropertyDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptPropertyDao);
}
// Designations
{
String descriptor = "concept designations";
Supplier<Slice<Long>> loader = () -> myConceptDesignationDao.findIdsByCodeSystemVersion(page1000, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptDesignationDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptDesignationDao);
}
// Concepts
{
String descriptor = "concepts";
// For some reason, concepts are much slower to delete, so use a smaller batch size
PageRequest page100 = PageRequest.of(0, 100);
Supplier<Slice<Long>> loader = () -> myConceptDao.findIdsByCodeSystemVersion(page100, theCodeSystemVersionPid);
Supplier<Integer> counter = () -> myConceptDao.countByCodeSystemVersion(theCodeSystemVersionPid);
doDelete(descriptor, loader, counter, myConceptDao);
}
runInTransaction(() -> {
Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(theCodeSystemVersionPid);
if (codeSystemOpt.isPresent()) {
TermCodeSystem codeSystem = codeSystemOpt.get();
ourLog.info(" * Removing code system version {} as current version of code system {}", theCodeSystemVersionPid, codeSystem.getPid());
codeSystem.setCurrentVersion(null);
myCodeSystemDao.save(codeSystem);
}
ourLog.info(" * Deleting code system version");
Optional<TermCodeSystemVersion> csv = myCodeSystemVersionDao.findById(theCodeSystemVersionPid);
if (csv.isPresent()) {
myCodeSystemVersionDao.delete(csv.get());
}
});
}
private <T> void doDelete(String theDescriptor, Supplier<Slice<Long>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, Long> theDao) {
assert !TransactionSynchronizationManager.isActualTransactionActive();
int count;
ourLog.info(" * Deleting {}", theDescriptor);
int totalCount = runInTransaction(theCounter);
StopWatch sw = new StopWatch();
count = 0;
while (true) {
Slice<Long> link = runInTransaction(theLoader);
if (!link.hasContent()) {
break;
}
private void deleteTermCodeSystemOffline(Long theCodeSystemPid) {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_ID, new JobParameter(theCodeSystemPid, true) ));
runInTransaction(() -> link.forEach(theDao::deleteById));
try {
count += link.getNumberOfElements();
ourLog.info(" * {} {} deleted ({}/{}) remaining - {}/sec - ETA: {}", count, theDescriptor, count, totalCount, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
JobExecution jobExecution = myJobSubmitter.runJob(myTermCodeSystemDeleteJob, jobParameters);
myCurrentJobExecutions.add(jobExecution);
} catch (JobParametersInvalidException theE) {
throw new InternalErrorException("Offline job submission for TermCodeSystem: " +
theCodeSystemPid + " failed: " + theE);
}
}
@ -419,9 +405,14 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
retVal &= !isDeferredValueSets();
retVal &= !isDeferredConceptMaps();
retVal &= !isDeferredCodeSystemDeletions();
retVal &= !isJobsExecuting();
return retVal;
}
private boolean isJobsExecuting() {
return myCurrentJobExecutions.stream().anyMatch(JobExecution::isRunning);
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermCodeSystemStorageSvc.java
View File

@ -51,11 +51,6 @@ public interface ITermCodeSystemStorageSvc {
(boolean) theRequestDetails.getUserData().getOrDefault(MAKE_LOADING_VERSION_CURRENT, Boolean.TRUE);
}
void deleteCodeSystem(TermCodeSystem theCodeSystem);
void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);
void storeNewCodeSystemVersion(ResourcePersistentId theCodeSystemResourcePid, String theSystemUri, String theSystemName,
String theSystemVersionId, TermCodeSystemVersion theCodeSystemVersion, ResourceTable theCodeSystemResourceTable,
RequestDetails theRequestDetails);

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/api/ITermDeferredStorageSvc.java
View File

@ -54,8 +54,6 @@ public interface ITermDeferredStorageSvc {
void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
void deleteCodeSystem(TermCodeSystem theCodeSystem);
void deleteCodeSystemForResource(ResourceTable theCodeSystemResourceToDelete);
void deleteCodeSystemVersion(TermCodeSystemVersion theCodeSystemVersion);

62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BaseTermCodeSystemDeleteJobConfig.java Normal file
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@ -0,0 +1,62 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
/**
* Configuration artifacts common to TermCodeSystemDeleteJobConfig and TermCodeSystemVersionDeleteJobConfig
**/
@Configuration
public class BaseTermCodeSystemDeleteJobConfig {
protected static final int TERM_CONCEPT_DELETE_TIMEOUT = 60 * 2; // two minutes
@Autowired
protected JobBuilderFactory myJobBuilderFactory;
@Autowired
protected StepBuilderFactory myStepBuilderFactory;
@Bean
public BatchTermCodeSystemVersionDeleteWriter batchTermCodeSystemVersionDeleteWriter() {
return new BatchTermCodeSystemVersionDeleteWriter();
}
@Bean
public BatchConceptRelationsDeleteWriter batchConceptRelationsDeleteWriter() {
return new BatchConceptRelationsDeleteWriter();
}
@Bean
public BatchTermConceptsDeleteWriter batchTermConceptsDeleteWriter() {
return new BatchTermConceptsDeleteWriter();
}
}

66
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchConceptRelationsDeleteWriter.java Normal file
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@ -0,0 +1,66 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import java.text.DecimalFormat;
import java.util.List;
public class BatchConceptRelationsDeleteWriter implements ItemWriter<Long> {
private static final Logger ourLog = LoggerFactory.getLogger(BatchConceptRelationsDeleteWriter.class);
private static final DecimalFormat ourDecimalFormat = new DecimalFormat("#,###");
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
@Autowired
private ITermConceptPropertyDao myConceptPropertyDao;
@Autowired
private ITermConceptDesignationDao myConceptDesignationDao;
@Override
public void write(List<? extends Long> theTermCodeSystemVersionPidList) throws Exception {
// receives input in chunks of size one
long codeSystemVersionId = theTermCodeSystemVersionPidList.get(0);
ourLog.info("Deleting term code links");
int deletedLinks = myConceptParentChildLinkDao.deleteByCodeSystemVersion(codeSystemVersionId);
ourLog.info("Deleted {} term code links", ourDecimalFormat.format(deletedLinks));
ourLog.info("Deleting term code properties");
int deletedProperties = myConceptPropertyDao.deleteByCodeSystemVersion(codeSystemVersionId);
ourLog.info("Deleted {} term code properties", ourDecimalFormat.format(deletedProperties));
ourLog.info("Deleting concept designations");
int deletedDesignations = myConceptDesignationDao.deleteByCodeSystemVersion(codeSystemVersionId);
ourLog.info("Deleted {} concept designations", ourDecimalFormat.format(deletedDesignations));
}
}

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchTermCodeSystemUniqueVersionDeleteReader.java Normal file
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@ -0,0 +1,54 @@
package ca.uhn.fhir.jpa.term.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemReader;
import org.springframework.beans.factory.annotation.Value;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_VERSION_ID;
/**
* This reader works as a pass-through by passing the received parameter once to the writer,
* in order to share the writer functionality between two jobs
*/
public class BatchTermCodeSystemUniqueVersionDeleteReader implements ItemReader<Long> {
private static final Logger ourLog = LoggerFactory.getLogger(BatchTermCodeSystemUniqueVersionDeleteReader.class);
@Value("#{jobParameters['" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "']}")
private Long myTermCodeSystemVersionPid;
// indicates if the parameter was already passed once to the writer, which indicates end of task
private boolean myParameterPassed;
@Override
public Long read() throws Exception {
if ( ! myParameterPassed) {
myParameterPassed = true;
return myTermCodeSystemVersionPid;
}
return null;
}
}

75
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchTermCodeSystemVersionDeleteReader.java Normal file
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@ -0,0 +1,75 @@
package ca.uhn.fhir.jpa.term.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemReader;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import java.util.List;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
/**
*
*/
public class BatchTermCodeSystemVersionDeleteReader implements ItemReader<Long> {
private static final Logger ourLog = LoggerFactory.getLogger(BatchTermCodeSystemVersionDeleteReader.class);
@Autowired
private ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Value("#{jobParameters['" + JOB_PARAM_CODE_SYSTEM_ID + "']}")
private Long myTermCodeSystemPid;
private List<Long> myTermCodeSystemVersionPidList;
private int myCurrentIdx = 0;
@Override
public Long read() throws Exception {
if (myTermCodeSystemVersionPidList == null) {
myTermCodeSystemVersionPidList = myTermCodeSystemVersionDao.findSortedPidsByCodeSystemPid(myTermCodeSystemPid);
}
if (myTermCodeSystemVersionPidList.isEmpty()) {
// nothing to process
ourLog.info("Nothing to process");
return null;
}
if (myCurrentIdx >= myTermCodeSystemVersionPidList.size()) {
// nothing else to process
ourLog.info("No more versions to process");
return null;
}
// still processing elements
long TermCodeSystemVersionPid = myTermCodeSystemVersionPidList.get(myCurrentIdx++);
ourLog.info("Passing termCodeSystemVersionPid: {} to writer", TermCodeSystemVersionPid);
return TermCodeSystemVersionPid;
}
}

77
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchTermCodeSystemVersionDeleteWriter.java Normal file
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@ -0,0 +1,77 @@
package ca.uhn.fhir.jpa.term.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import java.text.DecimalFormat;
import java.util.List;
import java.util.Optional;
@Component
public class BatchTermCodeSystemVersionDeleteWriter implements ItemWriter<Long> {
private static final Logger ourLog = LoggerFactory.getLogger(BatchTermCodeSystemVersionDeleteWriter.class);
@Autowired
private ITermCodeSystemDao myCodeSystemDao;
@Autowired
private ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Override
public void write(List<? extends Long> theTermCodeSystemVersionPidList) throws Exception {
// receives input in chunks of size one
long codeSystemVersionId = theTermCodeSystemVersionPidList.get(0);
ourLog.debug("Executing for codeSystemVersionId: {}", codeSystemVersionId);
// if TermCodeSystemVersion being deleted is current, disconnect it form TermCodeSystem
Optional<TermCodeSystem> codeSystemOpt = myCodeSystemDao.findWithCodeSystemVersionAsCurrentVersion(codeSystemVersionId);
if (codeSystemOpt.isPresent()) {
TermCodeSystem codeSystem = codeSystemOpt.get();
ourLog.info("Removing code system version: {} as current version of code system: {}", codeSystemVersionId, codeSystem.getPid());
codeSystem.setCurrentVersion(null);
myCodeSystemDao.save(codeSystem);
}
ourLog.info("Deleting code system version: {}", codeSystemVersionId);
Optional<TermCodeSystemVersion> csv = myTermCodeSystemVersionDao.findById(codeSystemVersionId);
csv.ifPresent(theTermCodeSystemVersion -> {
myTermCodeSystemVersionDao.delete(theTermCodeSystemVersion);
ourLog.info("Code system version: {} deleted", codeSystemVersionId);
});
}
}

51
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/BatchTermConceptsDeleteWriter.java Normal file
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@ -0,0 +1,51 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.item.ItemWriter;
import org.springframework.beans.factory.annotation.Autowired;
import java.text.DecimalFormat;
import java.util.List;
public class BatchTermConceptsDeleteWriter implements ItemWriter<Long> {
private static final Logger ourLog = LoggerFactory.getLogger(BatchTermConceptsDeleteWriter.class);
private static final DecimalFormat ourDecimalFormat = new DecimalFormat("#,###");
@Autowired
private ITermConceptDao myConceptDao;
@Override
public void write(List<? extends Long> theTermCodeSystemVersionPidList) throws Exception {
// receives input in chunks of size one
long codeSystemVersionId = theTermCodeSystemVersionPidList.get(0);
ourLog.info("Deleting concepts");
int deletedConcepts = myConceptDao.deleteByCodeSystemVersion(codeSystemVersionId);
ourLog.info("Deleted {} concepts", ourDecimalFormat.format(deletedConcepts));
}
}

122
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteJobConfig.java Normal file
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@ -0,0 +1,122 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParametersValidator;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.transaction.interceptor.DefaultTransactionAttribute;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_STEP_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_STEP_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CONCEPTS_DELETE_STEP_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CONCEPT_RELATIONS_DELETE_STEP_NAME;
/**
* Configuration for batch job which deletes a TermCodeSystem and its related TermCodeSystemVersion(s),
* TermConceptProperty(es), TermConceptDesignation(s), and TermConceptParentChildLink(s)
**/
@Configuration
public class TermCodeSystemDeleteJobConfig extends BaseTermCodeSystemDeleteJobConfig {
@Bean(name = TERM_CODE_SYSTEM_DELETE_JOB_NAME)
@Lazy
public Job termCodeSystemDeleteJob() {
return myJobBuilderFactory.get(TERM_CODE_SYSTEM_DELETE_JOB_NAME)
.validator(termCodeSystemDeleteJobParameterValidator())
.start(termConceptRelationsDeleteStep())
.next(termConceptsDeleteStep())
.next(termCodeSystemVersionDeleteStep())
.next(termCodeSystemDeleteStep())
.build();
}
@Bean
public JobParametersValidator termCodeSystemDeleteJobParameterValidator() {
return new TermCodeSystemDeleteJobParameterValidator();
}
/**
* This steps deletes TermConceptParentChildLink(s), TermConceptProperty(es) and TermConceptDesignation(s)
* related to TermConcept(s) of the TermCodeSystemVersion being deleted
*/
@Bean(name = TERM_CONCEPT_RELATIONS_DELETE_STEP_NAME)
public Step termConceptRelationsDeleteStep() {
return myStepBuilderFactory.get(TERM_CONCEPT_RELATIONS_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemVersionDeleteReader())
.writer(batchConceptRelationsDeleteWriter())
.build();
}
/**
* This steps deletes TermConcept(s) of the TermCodeSystemVersion being deleted
*/
@Bean(name = TERM_CONCEPTS_DELETE_STEP_NAME)
public Step termConceptsDeleteStep() {
DefaultTransactionAttribute attribute = new DefaultTransactionAttribute();
attribute.setTimeout(TERM_CONCEPT_DELETE_TIMEOUT);
return myStepBuilderFactory.get(TERM_CONCEPTS_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemVersionDeleteReader())
.writer(batchTermConceptsDeleteWriter())
.transactionAttribute(attribute)
.build();
}
/**
* This steps deletes the TermCodeSystemVersion
*/
@Bean(name = TERM_CODE_SYSTEM_VERSION_DELETE_STEP_NAME)
public Step termCodeSystemVersionDeleteStep() {
return myStepBuilderFactory.get(TERM_CODE_SYSTEM_VERSION_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemVersionDeleteReader())
.writer(batchTermCodeSystemVersionDeleteWriter())
.build();
}
@Bean(name = TERM_CODE_SYSTEM_DELETE_STEP_NAME)
public Step termCodeSystemDeleteStep() {
return myStepBuilderFactory.get(TERM_CODE_SYSTEM_DELETE_STEP_NAME)
.tasklet(termCodeSystemDeleteTasklet())
.build();
}
@Bean
@StepScope
public BatchTermCodeSystemVersionDeleteReader batchTermCodeSystemVersionDeleteReader() {
return new BatchTermCodeSystemVersionDeleteReader();
}
@Bean
public TermCodeSystemDeleteTasklet termCodeSystemDeleteTasklet() {
return new TermCodeSystemDeleteTasklet();
}
}

53
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteJobParameterValidator.java Normal file
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@ -0,0 +1,53 @@
package ca.uhn.fhir.jpa.term.job;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
/**
* Validates that a TermCodeSystem parameter is present
*/
public class TermCodeSystemDeleteJobParameterValidator implements JobParametersValidator {
@Override
public void validate(JobParameters theJobParameters) throws JobParametersInvalidException {
if (theJobParameters == null) {
throw new JobParametersInvalidException("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_ID + "'");
}
if ( ! theJobParameters.getParameters().containsKey(JOB_PARAM_CODE_SYSTEM_ID)) {
throw new JobParametersInvalidException("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_ID + "'");
}
Long termCodeSystemPid = theJobParameters.getLong(JOB_PARAM_CODE_SYSTEM_ID);
if (termCodeSystemPid == null) {
throw new JobParametersInvalidException("'" + JOB_PARAM_CODE_SYSTEM_ID + "' parameter is null");
}
if (termCodeSystemPid <= 0) {
throw new JobParametersInvalidException("Invalid parameter '" + JOB_PARAM_CODE_SYSTEM_ID + "' value: " + termCodeSystemPid);
}
}
}

60
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteTasklet.java Normal file
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@ -0,0 +1,60 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
@Component
public class TermCodeSystemDeleteTasklet implements Tasklet {
private static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemDeleteTasklet.class);
@Autowired
private ITermCodeSystemDao myTermCodeSystemDao;
@Autowired
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Override
public RepeatStatus execute(@NotNull StepContribution contribution, ChunkContext context) throws Exception {
long codeSystemPid = (Long) context.getStepContext().getJobParameters().get(JOB_PARAM_CODE_SYSTEM_ID);
ourLog.info("Deleting code system {}", codeSystemPid);
myTermCodeSystemDao.findById(codeSystemPid).orElseThrow(IllegalStateException::new);
myTermCodeSystemDao.deleteById(codeSystemPid);
ourLog.info("Code system {} deleted", codeSystemPid);
return RepeatStatus.FINISHED;
}
}

105
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemVersionDeleteJobConfig.java Normal file
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@ -0,0 +1,105 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobParametersValidator;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.transaction.interceptor.DefaultTransactionAttribute;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_UNIQUE_VERSION_DELETE_STEP_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CONCEPTS_UNIQUE_VERSION_DELETE_STEP_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CONCEPT_RELATIONS_UNIQUE_VERSION_DELETE_STEP_NAME;
/**
* Configuration for batch job which deletes a specific TermCodeSystemVersion and its related,
* TermConceptProperty(es), TermConceptDesignation(s), and TermConceptParentChildLink(s)
**/
@Configuration
public class TermCodeSystemVersionDeleteJobConfig extends BaseTermCodeSystemDeleteJobConfig {
@Bean(name = TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME)
@Lazy
public Job termCodeSystemVersionDeleteJob() {
return myJobBuilderFactory.get(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME)
.validator(termCodeSystemVersionDeleteJobParameterValidator())
.start(termConceptRelationsUniqueVersionDeleteStep())
.next(termConceptsUniqueVersionDeleteStep())
.next(termCodeSystemUniqueVersionDeleteStep())
.build();
}
@Bean
public JobParametersValidator termCodeSystemVersionDeleteJobParameterValidator() {
return new TermCodeSystemVersionDeleteJobParameterValidator();
}
@Bean(name = TERM_CONCEPT_RELATIONS_UNIQUE_VERSION_DELETE_STEP_NAME)
public Step termConceptRelationsUniqueVersionDeleteStep() {
return myStepBuilderFactory.get(TERM_CONCEPT_RELATIONS_UNIQUE_VERSION_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemUniqueVersionDeleteReader())
.writer(batchConceptRelationsDeleteWriter())
.build();
}
@Bean(name = TERM_CONCEPTS_UNIQUE_VERSION_DELETE_STEP_NAME)
public Step termConceptsUniqueVersionDeleteStep() {
DefaultTransactionAttribute attribute = new DefaultTransactionAttribute();
attribute.setTimeout(TERM_CONCEPT_DELETE_TIMEOUT);
return myStepBuilderFactory.get(TERM_CONCEPTS_UNIQUE_VERSION_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemUniqueVersionDeleteReader())
.writer(batchTermConceptsDeleteWriter())
.transactionAttribute(attribute)
.build();
}
@Bean(name = TERM_CODE_SYSTEM_UNIQUE_VERSION_DELETE_STEP_NAME)
public Step termCodeSystemUniqueVersionDeleteStep() {
return myStepBuilderFactory.get(TERM_CODE_SYSTEM_UNIQUE_VERSION_DELETE_STEP_NAME)
.<Long, Long>chunk(1)
.reader(batchTermCodeSystemUniqueVersionDeleteReader())
.writer(batchTermCodeSystemVersionDeleteWriter())
.build();
}
@Bean
@StepScope
public BatchTermCodeSystemUniqueVersionDeleteReader batchTermCodeSystemUniqueVersionDeleteReader() {
return new BatchTermCodeSystemUniqueVersionDeleteReader();
}
}

54
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemVersionDeleteJobParameterValidator.java Normal file
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@ -0,0 +1,54 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.batch.core.JobParametersValidator;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_VERSION_ID;
/**
* Validates that a TermCodeSystem parameter is present
*/
public class TermCodeSystemVersionDeleteJobParameterValidator implements JobParametersValidator {
@Override
public void validate(JobParameters theJobParameters) throws JobParametersInvalidException {
if (theJobParameters == null) {
throw new JobParametersInvalidException("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "'");
}
if ( ! theJobParameters.getParameters().containsKey(JOB_PARAM_CODE_SYSTEM_VERSION_ID)) {
throw new JobParametersInvalidException("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "'");
}
Long termCodeSystemPid = theJobParameters.getLong(JOB_PARAM_CODE_SYSTEM_VERSION_ID);
if (termCodeSystemPid == null) {
throw new JobParametersInvalidException("'" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "' parameter is null");
}
if (termCodeSystemPid <= 0) {
throw new JobParametersInvalidException(
"Invalid parameter '" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "' value: " + termCodeSystemPid);
}
}
}

62
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/job/TermConceptDeleteTasklet.java Normal file
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@ -0,0 +1,62 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
/**
* Deletes the TermConcept(s) related to the TermCodeSystemVersion being deleted
* Executes in its own step to be in own transaction because it is a DB-heavy operation
*/
@Component
public class TermConceptDeleteTasklet implements Tasklet {
private static final Logger ourLog = LoggerFactory.getLogger(TermConceptDeleteTasklet.class);
@Autowired
private ITermCodeSystemDao myTermCodeSystemDao;
@Autowired
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Override
public RepeatStatus execute(@NotNull StepContribution contribution, ChunkContext context) throws Exception {
long codeSystemPid = (Long) context.getStepContext().getJobParameters().get(JOB_PARAM_CODE_SYSTEM_ID);
ourLog.info("Deleting code system {}", codeSystemPid);
myTermCodeSystemDao.findById(codeSystemPid).orElseThrow(IllegalStateException::new);
myTermCodeSystemDao.deleteById(codeSystemPid);
return RepeatStatus.FINISHED;
}
}

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestDstu2Config.java
View File

@ -172,6 +172,4 @@ public class TestDstu2Config extends BaseJavaConfigDstu2 {
return requestValidator;
}
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestJPAConfig.java
View File

@ -1,6 +1,8 @@
package ca.uhn.fhir.jpa.config;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import ca.uhn.fhir.jpa.subscription.SubscriptionTestUtil;
@ -70,4 +72,10 @@ public class TestJPAConfig {
public BatchJobHelper batchJobHelper(JobExplorer theJobExplorer) {
return new BatchJobHelper(theJobExplorer);
}
@Bean
@Lazy
public IBinaryStorageSvc binaryStorage() {
return new MemoryBinaryStorageSvcImpl();
}
}

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java
View File

@ -1,21 +1,28 @@
package ca.uhn.fhir.jpa.dao.dstu3;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.Enumerations;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.nio.charset.StandardCharsets;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.fail;
public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
@Autowired private BatchJobHelper myBatchJobHelper;
@AfterAll
public static void afterClassClearContext() {
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
@ -64,6 +71,7 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
cs.addConcept().setCode("B");
myCodeSystemDao.update(cs, mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(()->{
assertEquals(2, myConceptDao.count());
});
@ -77,6 +85,7 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
cs.addConcept().setCode("C");
myCodeSystemDao.update(cs, mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(()->{
assertEquals(1, myConceptDao.count());
});
@ -86,6 +95,7 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
myCodeSystemDao.delete(id);
});
myTerminologyDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
runInTransaction(()->{
assertEquals(0L, myConceptDao.count());
});

50
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCreatePlaceholdersR4Test.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.util.HapiExtensions;
import com.google.common.collect.Sets;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.AuditEvent;
import org.hl7.fhir.r4.model.BooleanType;
@ -29,6 +30,7 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import java.util.HashSet;
import java.util.List;
import static org.hamcrest.CoreMatchers.equalTo;
@ -650,4 +652,52 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
assertNotNull(retObservation);
}
@Test
public void testMultipleVersionedReferencesToAutocreatedPlaceholder() {
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
HashSet<String> refPaths = new HashSet<>();
refPaths.add("Observation.subject");
myModelConfig.setAutoVersionReferenceAtPaths(refPaths);
Observation obs1 = new Observation();
obs1.setId("Observation/DEF1");
Reference patientRef = new Reference("Patient/RED");
obs1.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
Observation obs2 = new Observation();
obs2.setId("Observation/DEF2");
obs2.setSubject(patientRef);
builder.addTransactionUpdateEntry(obs1);
builder.addTransactionUpdateEntry(obs2);
mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
// verify links created to Patient placeholder from both Observations
IBundleProvider outcome = myPatientDao.search(SearchParameterMap.newSynchronous().addRevInclude(IBaseResource.INCLUDE_ALL));
assertEquals(3, outcome.getAllResources().size());
}
@Test
public void testMultipleReferencesToAutocreatedPlaceholder() {
myDaoConfig.setAutoCreatePlaceholderReferenceTargets(true);
Observation obs1 = new Observation();
obs1.setId("Observation/DEF1");
Reference patientRef = new Reference("Patient/RED");
obs1.setSubject(patientRef);
BundleBuilder builder = new BundleBuilder(myFhirCtx);
Observation obs2 = new Observation();
obs2.setId("Observation/DEF2");
obs2.setSubject(patientRef);
builder.addTransactionUpdateEntry(obs1);
builder.addTransactionUpdateEntry(obs2);
mySystemDao.transaction(new SystemRequestDetails(), (Bundle) builder.getBundle());
// verify links created to Patient placeholder from both Observations
IBundleProvider outcome = myPatientDao.search(SearchParameterMap.newSynchronous().addRevInclude(IBaseResource.INCLUDE_ALL));
assertEquals(3, outcome.getAllResources().size());
}
}

9
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java
View File

@ -2,15 +2,19 @@ package ca.uhn.fhir.jpa.dao.r4;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.nio.charset.StandardCharsets;
import java.util.List;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
@ -18,6 +22,8 @@ import static org.junit.jupiter.api.Assertions.assertNull;
public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
@Autowired private BatchJobHelper myBatchJobHelper;
@Test
public void testIndexContained() throws Exception {
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
@ -58,6 +64,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
// Now the background scheduler will do its thing
myTerminologyDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
runInTransaction(() -> {
assertEquals(0, myTermCodeSystemDao.count());
assertEquals(0, myTermCodeSystemVersionDao.count());
@ -116,6 +123,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
// Now the background scheduler will do its thing
myTerminologyDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
// Entities for first resource should be gone now.
runInTransaction(() -> {
@ -150,6 +158,7 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
// Now the background scheduler will do its thing
myTerminologyDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
// The remaining versions and Code System entities should be gone now.
runInTransaction(() -> {

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4Test.java
View File

@ -45,6 +45,7 @@ import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import org.apache.commons.io.IOUtils;
@ -109,6 +110,7 @@ import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
@ -128,6 +130,8 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.Future;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.apache.commons.lang3.StringUtils.defaultString;
import static org.hamcrest.MatcherAssert.assertThat;
@ -155,6 +159,9 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4Test.class);
@Autowired
private BatchJobHelper myBatchJobHelper;
@AfterEach
public final void after() {
myDaoConfig.setAllowExternalReferences(new DaoConfig().isAllowExternalReferences());
@ -356,6 +363,7 @@ public class FhirResourceDaoR4Test extends BaseJpaR4Test {
myResourceReindexingSvc.markAllResourcesForReindexing();
myResourceReindexingSvc.forceReindexingPass();
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(() -> {
assertEquals(3L, myTermConceptDao.count());

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoR5CodeSystemTest.java
View File

@ -2,22 +2,25 @@ package ca.uhn.fhir.jpa.dao.r5;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import org.apache.commons.io.IOUtils;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r5.model.CodeSystem;
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.nio.charset.StandardCharsets;
import java.util.List;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
public class FhirResourceDaoR5CodeSystemTest extends BaseJpaR5Test {
@Autowired private BatchJobHelper myBatchJobHelper;
@Test
public void testDeleteLargeCompleteCodeSystem() {
@ -42,6 +45,7 @@ public class FhirResourceDaoR5CodeSystemTest extends BaseJpaR5Test {
// Now the background scheduler will do its thing
myTermDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
runInTransaction(() -> {
assertEquals(0, myTermCodeSystemDao.count());
assertEquals(0, myTermCodeSystemVersionDao.count());
@ -100,6 +104,7 @@ public class FhirResourceDaoR5CodeSystemTest extends BaseJpaR5Test {
// Now the background scheduler will do its thing
myTermDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
// Entities for first resource should be gone now.
runInTransaction(() -> {
@ -134,6 +139,7 @@ public class FhirResourceDaoR5CodeSystemTest extends BaseJpaR5Test {
// Now the background scheduler will do its thing
myTermDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
// The remaining versions and Code System entities should be gone now.
runInTransaction(() -> {

72
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/packages/NpmR4Test.java
View File

@ -270,6 +270,78 @@ public class NpmR4Test extends BaseJpaR4Test {
});
}
@Test
public void testInstallR4PackageWithExternalizedBinaries() throws Exception {
myDaoConfig.setAllowExternalReferences(true);
myInterceptorService.registerInterceptor(myBinaryStorageInterceptor);
byte[] bytes = loadClasspathBytes("/packages/hl7.fhir.uv.shorthand-0.12.0.tgz");
myFakeNpmServlet.myResponses.put("/hl7.fhir.uv.shorthand/0.12.0", bytes);
PackageInstallationSpec spec = new PackageInstallationSpec().setName("hl7.fhir.uv.shorthand").setVersion("0.12.0").setInstallMode(PackageInstallationSpec.InstallModeEnum.STORE_AND_INSTALL);
PackageInstallOutcomeJson outcome = myPackageInstallerSvc.install(spec);
assertEquals(1, outcome.getResourcesInstalled().get("CodeSystem"));
// Be sure no further communication with the server
JettyUtil.closeServer(myServer);
// Make sure we can fetch the package by ID and Version
NpmPackage pkg = myPackageCacheManager.loadPackage("hl7.fhir.uv.shorthand", "0.12.0");
assertEquals("Describes FHIR Shorthand (FSH), a domain-specific language (DSL) for defining the content of FHIR Implementation Guides (IG). (built Wed, Apr 1, 2020 17:24+0000+00:00)", pkg.description());
// Make sure we can fetch the package by ID
pkg = myPackageCacheManager.loadPackage("hl7.fhir.uv.shorthand", null);
assertEquals("0.12.0", pkg.version());
assertEquals("Describes FHIR Shorthand (FSH), a domain-specific language (DSL) for defining the content of FHIR Implementation Guides (IG). (built Wed, Apr 1, 2020 17:24+0000+00:00)", pkg.description());
// Make sure DB rows were saved
runInTransaction(() -> {
NpmPackageEntity pkgEntity = myPackageDao.findByPackageId("hl7.fhir.uv.shorthand").orElseThrow(() -> new IllegalArgumentException());
assertEquals("hl7.fhir.uv.shorthand", pkgEntity.getPackageId());
NpmPackageVersionEntity versionEntity = myPackageVersionDao.findByPackageIdAndVersion("hl7.fhir.uv.shorthand", "0.12.0").orElseThrow(() -> new IllegalArgumentException());
assertEquals("hl7.fhir.uv.shorthand", versionEntity.getPackageId());
assertEquals("0.12.0", versionEntity.getVersionId());
assertEquals(3001, versionEntity.getPackageSizeBytes());
assertEquals(true, versionEntity.isCurrentVersion());
assertEquals("hl7.fhir.uv.shorthand", versionEntity.getPackageId());
assertEquals("4.0.1", versionEntity.getFhirVersionId());
assertEquals(FhirVersionEnum.R4, versionEntity.getFhirVersion());
NpmPackageVersionResourceEntity resource = myPackageVersionResourceDao.findCurrentVersionByCanonicalUrl(Pageable.unpaged(), FhirVersionEnum.R4, "http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand").getContent().get(0);
assertEquals("http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand", resource.getCanonicalUrl());
assertEquals("0.12.0", resource.getCanonicalVersion());
assertEquals("ImplementationGuide-hl7.fhir.uv.shorthand.json", resource.getFilename());
assertEquals("4.0.1", resource.getFhirVersionId());
assertEquals(FhirVersionEnum.R4, resource.getFhirVersion());
assertEquals(6155, resource.getResSizeBytes());
});
// Fetch resource by URL
runInTransaction(() -> {
IBaseResource asset = myPackageCacheManager.loadPackageAssetByUrl(FhirVersionEnum.R4, "http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand");
assertThat(myFhirCtx.newJsonParser().encodeResourceToString(asset), containsString("\"url\":\"http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand\",\"version\":\"0.12.0\""));
});
// Fetch resource by URL with version
runInTransaction(() -> {
IBaseResource asset = myPackageCacheManager.loadPackageAssetByUrl(FhirVersionEnum.R4, "http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand|0.12.0");
assertThat(myFhirCtx.newJsonParser().encodeResourceToString(asset), containsString("\"url\":\"http://hl7.org/fhir/uv/shorthand/ImplementationGuide/hl7.fhir.uv.shorthand\",\"version\":\"0.12.0\""));
});
// Search for the installed resource
runInTransaction(() -> {
SearchParameterMap map = SearchParameterMap.newSynchronous();
map.add(StructureDefinition.SP_URL, new UriParam("http://hl7.org/fhir/uv/shorthand/CodeSystem/shorthand-code-system"));
IBundleProvider result = myCodeSystemDao.search(map);
assertEquals(1, result.sizeOrThrowNpe());
IBaseResource resource = result.getResources(0, 1).get(0);
assertEquals("CodeSystem/shorthand-code-system/_history/1", resource.getIdElement().toString());
});
myInterceptorService.unregisterInterceptor(myBinaryStorageInterceptor);
}
@Test
public void testNumericIdsInstalledWithNpmPrefix() throws Exception {
myDaoConfig.setAllowExternalReferences(true);

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest;
import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
@ -19,16 +20,20 @@ import org.hl7.fhir.instance.model.api.IBaseOperationOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Transactional;
import java.io.IOException;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDstu3Test {
@Autowired private BatchJobHelper myBatchJobHelper;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3CodeSystemTest.class);
public static FhirContext ourCtx = FhirContext.forDstu3Cached();
@ -133,6 +138,8 @@ public class ResourceProviderDstu3CodeSystemTest extends BaseResourceProviderDst
runInTransaction(() -> assertEquals(26L, myConceptDao.count()));
myTerminologyDeferredStorageSvc.saveDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_DELETE_JOB_NAME);
runInTransaction(() -> assertEquals(24L, myConceptDao.count()));
}

8
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermCodeSystemStorageSvcTest.java
View File

@ -5,12 +5,15 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.fail;
@ -18,6 +21,10 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
@Autowired
private BatchJobHelper myBatchJobHelper;
@Test
public void testStoreNewCodeSystemVersionForExistingCodeSystemNoVersionId() {
CodeSystem firstUpload = createCodeSystemWithMoreThan100Concepts();
@ -126,6 +133,7 @@ public class TermCodeSystemStorageSvcTest extends BaseJpaR4Test {
myTerminologyDeferredStorageSvc.setProcessDeferred(true);
myTerminologyDeferredStorageSvc.saveDeferred();
myTerminologyDeferredStorageSvc.setProcessDeferred(false);
myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
assertEquals(theExpectedConceptCount, runInTransaction(() -> myTermConceptDao.count()));
}

21
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TermDeferredStorageSvcImplTest.java
View File

@ -10,10 +10,17 @@ import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.batch.core.JobExecution;
import org.springframework.test.util.ReflectionTestUtils;
import org.springframework.transaction.PlatformTransactionManager;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Optional;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.mockito.ArgumentMatchers.anyLong;
import static org.mockito.ArgumentMatchers.same;
import static org.mockito.Mockito.times;
@ -33,6 +40,9 @@ public class TermDeferredStorageSvcImplTest {
@Mock
private ITermCodeSystemVersionDao myTermCodeSystemVersionDao;
@Mock
private JobExecution myJobExecution;
@Test
public void testSaveDeferredWithExecutionSuspended() {
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
@ -41,6 +51,17 @@ public class TermDeferredStorageSvcImplTest {
}
@Test
public void testStorageNotEmptyWhileJobsExecuting() {
TermDeferredStorageSvcImpl svc = new TermDeferredStorageSvcImpl();
ReflectionTestUtils.setField(svc, "myCurrentJobExecutions", Collections.singletonList(myJobExecution));
when(myJobExecution.isRunning()).thenReturn(true, false);
assertFalse(svc.isStorageQueueEmpty());
assertTrue(svc.isStorageQueueEmpty());
}
@Test
public void testSaveDeferred_Concept() {
TermConcept concept = new TermConcept();

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincJpaTest.java
View File

@ -5,20 +5,22 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.IOException;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY_DEFAULT;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotEquals;
import static org.junit.jupiter.api.Assertions.fail;
public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
@Autowired private BatchJobHelper myBatchJobHelper;
private TermLoaderSvcImpl mySvc;
private ZipCollectionBuilder myFiles;
@BeforeEach
@ -62,6 +64,7 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME );
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
@ -87,6 +90,7 @@ public class TerminologyLoaderSvcLoincJpaTest extends BaseJpaR4Test {
TerminologyLoaderSvcLoincTest.addLoincMandatoryFilesWithPropertiesFileToZip(myFiles, "v268_loincupload.properties");
mySvc.loadLoinc(myFiles.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(false, TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME );
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());

36
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplCurrentVersionR4Test.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.config.BaseConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermValueSet;
@ -14,6 +15,7 @@ import ca.uhn.fhir.rest.api.server.IBundleProvider;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.param.UriParam;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import org.apache.commons.lang3.StringUtils;
@ -25,6 +27,7 @@ import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.mockito.Answers;
@ -33,6 +36,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.test.annotation.DirtiesContext;
import org.springframework.util.ResourceUtils;
import javax.persistence.EntityManager;
@ -50,6 +54,7 @@ import java.util.Properties;
import java.util.Set;
import java.util.stream.Collectors;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;
@ -75,6 +80,7 @@ import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_PROPERTIES_FILE;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
import static java.util.stream.Collectors.joining;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_ALL_VALUESET_ID;
@ -130,9 +136,11 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
@Autowired
private ITermReadSvc myITermReadSvc;
@Autowired
@Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT)
private IValidationSupport myJpaPersistedResourceValidationSupport;
@Autowired @Qualifier(BaseConfig.JPA_VALIDATION_SUPPORT)
private IValidationSupport myJpaPersistedResourceValidationSupport;
@Autowired private BatchJobHelper myBatchJobHelper;
private ZipCollectionBuilder myFiles;
private ServletRequestDetails myRequestDetails = new ServletRequestDetails();
@ -690,6 +698,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
String currentVer = "2.68";
uploadLoincCodeSystem(currentVer, true);
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runCommonValidations(Lists.newArrayList(nonCurrentVer, currentVer));
@ -711,6 +720,7 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
String lastCurrentVer = "2.69";
uploadLoincCodeSystem(lastCurrentVer, true);
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runCommonValidations(Lists.newArrayList(firstCurrentVer, noCurrentVer, lastCurrentVer));
@ -775,11 +785,27 @@ public class TerminologySvcImplCurrentVersionR4Test extends BaseJpaR4Test {
}
private TermCodeSystemVersion fetchCurrentCodeSystemVersion() {
runInTransaction(() -> {
List<TermCodeSystem> tcsList = myEntityManager.createQuery("from TermCodeSystem").getResultList();
List<TermCodeSystemVersion> tcsvList = myEntityManager.createQuery("from TermCodeSystemVersion").getResultList();
ourLog.error("tcslist: {}", tcsList.stream().map(tcs -> tcs.toString()).collect(joining("\n", "\n", "")));
ourLog.error("tcsvlist: {}", tcsvList.stream().map(v -> v.toString()).collect(joining("\n", "\n", "")));
if (tcsList.size() != 1) {
throw new IllegalStateException("More than one TCS: " +
tcsList.stream().map(tcs -> String.valueOf(tcs.getPid())).collect(joining()));
}
if (tcsList.get(0).getCurrentVersion() == null) {
throw new IllegalStateException("Current version is null in TCS: " + tcsList.get(0).getPid());
}
});
return runInTransaction(() -> (TermCodeSystemVersion) myEntityManager.createQuery(
"select tcsv from TermCodeSystemVersion tcsv join fetch tcsv.myCodeSystem tcs " +
"where tcs.myCurrentVersion = tcsv").getSingleResult());
"select tcsv from TermCodeSystemVersion tcsv join fetch tcsv.myCodeSystem tcs " +
"where tcs.myCurrentVersion = tcsv").getSingleResult());
}
private static void addBaseLoincMandatoryFilesToZip(
ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException {
theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplR4Test.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermValueSet;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeableConcept;
@ -18,6 +19,7 @@ import org.hl7.fhir.r4.model.codesystems.HttpVerb;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
@ -29,6 +31,7 @@ import java.util.List;
import java.util.Optional;
import java.util.Set;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static org.hamcrest.MatcherAssert.assertThat;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.jupiter.api.Assertions.assertEquals;
@ -39,6 +42,9 @@ import static org.junit.jupiter.api.Assertions.fail;
public class TerminologySvcImplR4Test extends BaseTermR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(TerminologySvcImplR4Test.class);
@Autowired private BatchJobHelper myBatchJobHelper;
ConceptValidationOptions optsNoGuess = new ConceptValidationOptions();
ConceptValidationOptions optsGuess = new ConceptValidationOptions().setInferSystem(true);
@ -424,6 +430,7 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
IIdType id_v2 = myCodeSystemDao.update(codeSystem, mySrd).getId().toUnqualified();
myTerminologyDeferredStorageSvc.saveAllDeferred();
myBatchJobHelper.awaitAllBulkJobCompletions(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME);
runInTransaction(() -> {
List<TermCodeSystemVersion> termCodeSystemVersions_updated = myTermCodeSystemVersionDao.findAll();

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/ZipCollectionBuilder.java
View File

@ -28,7 +28,7 @@ public class ZipCollectionBuilder {
/**
* Constructor
*/
ZipCollectionBuilder() {
public ZipCollectionBuilder() {
myFiles = new ArrayList<>();
}

123
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/job/DynamicJobFlowSandbox.java Normal file
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@ -0,0 +1,123 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import com.google.common.collect.Lists;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.Step;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.job.builder.FlowBuilder;
import org.springframework.batch.core.job.builder.SimpleJobBuilder;
import org.springframework.batch.core.job.flow.Flow;
import org.springframework.batch.core.job.flow.support.SimpleFlow;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import java.util.List;
import java.util.stream.Collectors;
/**
* Not intended to ever run. Used as a sandbox for "interesting" jobs
*/
public class DynamicJobFlowSandbox {
protected static final Logger ourLog = LoggerFactory.getLogger(TermCodeSystemDeleteJobTest.class);
@Autowired
private JobBuilderFactory myJobBuilderFactory;
@Autowired
private StepBuilderFactory myStepBuilderFactory;
private List<Long> versionPidList = Lists.newArrayList(3L, 5L);
@Bean
public Job testJob() {
SimpleJobBuilder jobBuilder = myJobBuilderFactory.get("job")
.start(stepPreFlow());
// add a flow for each Pid
List<Flow> flowForEachPidList = versionPidList.stream().map(this::getFlowForPid).collect(Collectors.toList());
flowForEachPidList.forEach( flowForPid -> jobBuilder.on("COMPLETED").to(flowForPid) );
return jobBuilder.next(stepPostFlow()).build();
}
private Flow getFlowForPid(Long theLong) {
return new FlowBuilder<SimpleFlow>("flow-for-Pid-" + theLong)
.start(flowStep1(theLong))
.next(fllowStep2(theLong))
.build();
}
public Step flowStep1(long theLong) {
String name = "flow-step-1-for-Pid-" + theLong;
return myStepBuilderFactory.get(name)
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\n" + name + " executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step fllowStep2(long theLong) {
String name = "flow-step-2-for-Pid-" + theLong;
return myStepBuilderFactory.get(name)
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\n" + name + " executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step stepPreFlow() {
return myStepBuilderFactory.get("step-pre-flow")
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\nstep-pre-flow executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
public Step stepPostFlow() {
return myStepBuilderFactory.get("step-post-flow")
.tasklet((contribution, chunkContext) -> {
ourLog.info("\n\nstep-post-flow executed\n\n");
return RepeatStatus.FINISHED;
})
.build();
}
}

266
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemDeleteJobTest.java Normal file
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@ -0,0 +1,266 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameter;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Collections;
import java.util.Properties;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_ID;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_MAKE_CURRENT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_TERMS_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_HIERARCHY_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PARENT_GROUP_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_RSNA_PLAYBOOK_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_PROPERTIES_FILE;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class TermCodeSystemDeleteJobTest extends BaseJpaR4Test {
private final ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private Properties uploadProperties;
@Autowired private TermLoaderSvcImpl myTermLoaderSvc;
@Autowired private IBatchJobSubmitter myJobSubmitter;
@Autowired private BatchJobHelper myBatchJobHelper;
@Autowired @Qualifier(TERM_CODE_SYSTEM_DELETE_JOB_NAME)
private Job myTermCodeSystemDeleteJob;
private void initMultipleVersionLoad() throws Exception {
File file = ResourceUtils.getFile("classpath:loinc-ver/" + LOINC_UPLOAD_PROPERTIES_FILE.getCode());
uploadProperties = new Properties();
uploadProperties.load(new FileInputStream(file));
IFhirResourceDao<ValueSet> valueSetIFhirResourceDao = myDaoRegistry.getResourceDao(ValueSet.class);
}
@Test
public void runDeleteJobMultipleVersions() throws Exception {
initMultipleVersionLoad();
// loading a loinc CS with version loads two versions (second one with null version)
String firstCurrentVer = "2.67";
uploadLoincCodeSystem(firstCurrentVer, true);
long[] termCodeSystemPidVect = new long[1]; //bypass final restriction
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
assertNotNull(termCodeSystem);
termCodeSystemPidVect[0] = termCodeSystem.getPid();
assertEquals(2, myTermCodeSystemVersionDao.count());
assertEquals(162, myTermConceptDao.count());
});
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_ID, new JobParameter(termCodeSystemPidVect[0], true) ));
JobExecution jobExecution = myJobSubmitter.runJob(myTermCodeSystemDeleteJob, jobParameters);
myBatchJobHelper.awaitJobCompletion(jobExecution);
assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
runInTransaction(() -> {
assertEquals(0, myTermCodeSystemDao.count());
assertNull(myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org"));
assertEquals(0, myTermCodeSystemVersionDao.count());
assertEquals(0, myTermConceptDao.count());
});
}
@Test
public void runWithNoParameterFailsValidation() {
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemDeleteJob, new JobParameters())
);
assertEquals("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_ID + "'", thrown.getMessage());
}
@Test
public void runWithNullParameterFailsValidation() {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_ID, new JobParameter((Long) null, true) ));
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemDeleteJob, jobParameters)
);
assertEquals("'" + JOB_PARAM_CODE_SYSTEM_ID + "' parameter is null", thrown.getMessage());
}
@Test
public void runWithParameterZeroFailsValidation() {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_ID, new JobParameter(0L, true) ));
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemDeleteJob, jobParameters)
);
assertEquals("Invalid parameter '" + JOB_PARAM_CODE_SYSTEM_ID + "' value: 0", thrown.getMessage());
}
private IIdType uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
ZipCollectionBuilder files = new ZipCollectionBuilder();
myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent);
uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent));
assertTrue(
theVersion == null || theVersion.equals("2.67") || theVersion.equals("2.68") || theVersion.equals("2.69"),
"Version supported are: 2.67, 2.68, 2.69 and null" );
if (StringUtils.isBlank(theVersion)) {
uploadProperties.remove(LOINC_CODESYSTEM_VERSION.getCode());
} else {
uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion);
}
addLoincMandatoryFilesToZip(files, theVersion);
UploadStatistics stats = myTermLoaderSvc.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
return stats.getTarget();
}
public void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles, String theVersion) throws IOException {
String theClassPathPrefix = getClassPathPrefix(theVersion);
addBaseLoincMandatoryFilesToZip(theFiles, true, theClassPathPrefix);
theFiles.addPropertiesZip(uploadProperties, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
}
private static void addBaseLoincMandatoryFilesToZip(
ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException {
theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
if (theIncludeTop2000) {
theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
}
}
private String getClassPathPrefix(String theVersion) {
String theClassPathPrefix = "/loinc-ver/v-no-version/";
if (StringUtils.isBlank(theVersion)) return theClassPathPrefix;
switch(theVersion) {
case "2.67":
return "/loinc-ver/v267/";
case "2.68":
return "/loinc-ver/v268/";
case "2.69":
return "/loinc-ver/v269/";
}
fail("Setup failed. Unexpected version: " + theVersion);
return null;
}
}

272
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/job/TermCodeSystemVersionDeleteJobTest.java Normal file
View File

@ -0,0 +1,272 @@
package ca.uhn.fhir.jpa.term.job;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2021 Smile CDR, Inc.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.batch.api.IBatchJobSubmitter;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.term.TermLoaderSvcImpl;
import ca.uhn.fhir.jpa.term.UploadStatistics;
import ca.uhn.fhir.jpa.term.ZipCollectionBuilder;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.test.utilities.BatchJobHelper;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
import org.springframework.batch.core.Job;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameter;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersInvalidException;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.util.ResourceUtils;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.Collections;
import java.util.Properties;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.JOB_PARAM_CODE_SYSTEM_VERSION_ID;
import static ca.uhn.fhir.jpa.batch.config.BatchConstants.TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_ANSWERLIST_LINK_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_MAKE_CURRENT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_CODESYSTEM_VERSION;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_DUPLICATE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_GROUP_TERMS_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_HIERARCHY_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PARENT_GROUP_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_PRIMARY_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_RSNA_PLAYBOOK_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_UPLOAD_PROPERTIES_FILE;
import static ca.uhn.fhir.jpa.term.loinc.LoincUploadPropertiesEnum.LOINC_XML_FILE;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
public class TermCodeSystemVersionDeleteJobTest extends BaseJpaR4Test {
private final ServletRequestDetails myRequestDetails = new ServletRequestDetails();
private Properties uploadProperties;
@Autowired private TermLoaderSvcImpl myTermLoaderSvc;
@Autowired private IBatchJobSubmitter myJobSubmitter;
@Autowired private BatchJobHelper myBatchJobHelper;
@Autowired @Qualifier(TERM_CODE_SYSTEM_VERSION_DELETE_JOB_NAME)
private Job myTermCodeSystemVersionDeleteJob;
private void initMultipleVersionLoad() throws Exception {
File file = ResourceUtils.getFile("classpath:loinc-ver/" + LOINC_UPLOAD_PROPERTIES_FILE.getCode());
uploadProperties = new Properties();
uploadProperties.load(new FileInputStream(file));
IFhirResourceDao<ValueSet> valueSetIFhirResourceDao = myDaoRegistry.getResourceDao(ValueSet.class);
}
@Test
public void runDeleteJobDeleteOneVersion() throws Exception {
initMultipleVersionLoad();
String firstCurrentVer = "2.67";
uploadLoincCodeSystem(firstCurrentVer, true);
long[] termCodeSystemVersionPidVect = new long[1]; //bypass final restriction
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
TermCodeSystem termCodeSystem = myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org");
assertNotNull(termCodeSystem);
TermCodeSystemVersion termCodeSystemVersion = myTermCodeSystemVersionDao.findByCodeSystemPidVersionIsNull(termCodeSystem.getPid());
assertNotNull(termCodeSystemVersion);
termCodeSystemVersionPidVect[0] = termCodeSystemVersion.getPid();
assertEquals(2, myTermCodeSystemVersionDao.count());
assertEquals(81 * 2, myTermConceptDao.count());
});
JobParameters jobParameters = new JobParameters(Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_VERSION_ID, new JobParameter(termCodeSystemVersionPidVect[0], true) ));
JobExecution jobExecution = myJobSubmitter.runJob(myTermCodeSystemVersionDeleteJob, jobParameters);
myBatchJobHelper.awaitJobCompletion(jobExecution);
assertEquals("COMPLETED", jobExecution.getExitStatus().getExitCode());
runInTransaction(() -> {
assertEquals(1, myTermCodeSystemDao.count());
assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://loinc.org"));
assertEquals(1, myTermCodeSystemVersionDao.count());
assertEquals(81, myTermConceptDao.count());
});
}
@Test
public void runWithNoParameterFailsValidation() {
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemVersionDeleteJob, new JobParameters())
);
assertEquals("This job needs Parameter: '" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "'", thrown.getMessage());
}
@Test
public void runWithNullParameterFailsValidation() {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_VERSION_ID, new JobParameter((Long) null, true) ));
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemVersionDeleteJob, jobParameters)
);
assertEquals("'" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "' parameter is null", thrown.getMessage());
}
@Test
public void runWithParameterZeroFailsValidation() {
JobParameters jobParameters = new JobParameters(
Collections.singletonMap(
JOB_PARAM_CODE_SYSTEM_VERSION_ID, new JobParameter(0L, true) ));
JobParametersInvalidException thrown = Assertions.assertThrows(
JobParametersInvalidException.class,
() -> myJobSubmitter.runJob(myTermCodeSystemVersionDeleteJob, jobParameters)
);
assertEquals("Invalid parameter '" + JOB_PARAM_CODE_SYSTEM_VERSION_ID + "' value: 0", thrown.getMessage());
}
private IIdType uploadLoincCodeSystem(String theVersion, boolean theMakeItCurrent) throws Exception {
ZipCollectionBuilder files = new ZipCollectionBuilder();
myRequestDetails.getUserData().put(LOINC_CODESYSTEM_MAKE_CURRENT, theMakeItCurrent);
uploadProperties.put(LOINC_CODESYSTEM_MAKE_CURRENT.getCode(), Boolean.toString(theMakeItCurrent));
assertTrue(
theVersion == null || theVersion.equals("2.67") || theVersion.equals("2.68") || theVersion.equals("2.69"),
"Version supported are: 2.67, 2.68, 2.69 and null" );
if (StringUtils.isBlank(theVersion)) {
uploadProperties.remove(LOINC_CODESYSTEM_VERSION.getCode());
} else {
uploadProperties.put(LOINC_CODESYSTEM_VERSION.getCode(), theVersion);
}
addLoincMandatoryFilesToZip(files, theVersion);
UploadStatistics stats = myTermLoaderSvc.loadLoinc(files.getFiles(), mySrd);
myTerminologyDeferredStorageSvc.saveAllDeferred();
return stats.getTarget();
}
public void addLoincMandatoryFilesToZip(ZipCollectionBuilder theFiles, String theVersion) throws IOException {
String theClassPathPrefix = getClassPathPrefix(theVersion);
addBaseLoincMandatoryFilesToZip(theFiles, true, theClassPathPrefix);
theFiles.addPropertiesZip(uploadProperties, LOINC_UPLOAD_PROPERTIES_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_PRIMARY_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_LINK_FILE_SUPPLEMENTARY_DEFAULT.getCode());
}
private static void addBaseLoincMandatoryFilesToZip(
ZipCollectionBuilder theFiles, Boolean theIncludeTop2000, String theClassPathPrefix) throws IOException {
theFiles.addFileZip(theClassPathPrefix, LOINC_XML_FILE.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_GROUP_TERMS_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PARENT_GROUP_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_HIERARCHY_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_ANSWERLIST_LINK_DUPLICATE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_PART_RELATED_CODE_MAPPING_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_DOCUMENT_ONTOLOGY_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_RSNA_PLAYBOOK_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_UNIVERSAL_LAB_ORDER_VALUESET_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_IEEE_MEDICAL_DEVICE_CODE_MAPPING_TABLE_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_IMAGING_DOCUMENT_CODES_FILE_DEFAULT.getCode());
if (theIncludeTop2000) {
theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_SI_FILE_DEFAULT.getCode());
theFiles.addFileZip(theClassPathPrefix, LOINC_TOP2000_COMMON_LAB_RESULTS_US_FILE_DEFAULT.getCode());
}
}
private String getClassPathPrefix(String theVersion) {
String theClassPathPrefix = "/loinc-ver/v-no-version/";
if (StringUtils.isBlank(theVersion)) return theClassPathPrefix;
switch(theVersion) {
case "2.67":
return "/loinc-ver/v267/";
case "2.68":
return "/loinc-ver/v268/";
case "2.69":
return "/loinc-ver/v269/";
}
fail("Setup failed. Unexpected version: " + theVersion);
return null;
}
}

12
hapi-fhir-jpaserver-mdm/src/main/java/ca/uhn/fhir/jpa/mdm/config/MdmConsumerConfig.java
View File

@ -257,8 +257,16 @@ public class MdmConsumerConfig {
}
@Bean
MdmControllerHelper mdmProviderHelper(FhirContext theFhirContext, IResourceLoader theResourceLoader, IMdmSettings theMdmSettings, MessageHelper messageHelper) {
return new MdmControllerHelper(theFhirContext, theResourceLoader, theMdmSettings, messageHelper);
MdmControllerHelper mdmProviderHelper(FhirContext theFhirContext,
IResourceLoader theResourceLoader,
IMdmSettings theMdmSettings,
IMdmMatchFinderSvc theMdmMatchFinderSvc,
MessageHelper messageHelper) {
return new MdmControllerHelper(theFhirContext,
theResourceLoader,
theMdmMatchFinderSvc,
theMdmSettings,
messageHelper);
}
@Bean

7
hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/provider/BaseProviderR4Test.java
View File

@ -5,6 +5,7 @@ import ca.uhn.fhir.mdm.api.IMdmClearJobSubmitter;
import ca.uhn.fhir.mdm.api.IMdmControllerSvc;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSubmitSvc;
import ca.uhn.fhir.mdm.provider.MdmControllerHelper;
import ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus;
import ca.uhn.fhir.mdm.rules.config.MdmSettings;
import ca.uhn.fhir.mdm.util.MessageHelper;
@ -29,8 +30,6 @@ import java.util.List;
public abstract class BaseProviderR4Test extends BaseMdmR4Test {
MdmProviderDstu3Plus myMdmProvider;
@Autowired
private IMdmMatchFinderSvc myMdmMatchFinderSvc;
@Autowired
private IMdmControllerSvc myMdmControllerSvc;
@Autowired
private IMdmClearJobSubmitter myMdmClearJobSubmitter;
@ -39,6 +38,8 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
@Autowired
private MdmSettings myMdmSettings;
@Autowired
private MdmControllerHelper myMdmHelper;
@Autowired
BatchJobHelper myBatchJobHelper;
@Autowired
MessageHelper myMessageHelper;
@ -55,7 +56,7 @@ public abstract class BaseProviderR4Test extends BaseMdmR4Test {
@BeforeEach
public void before() {
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmSubmitSvc, myMdmSettings);
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmHelper, myMdmSubmitSvc, myMdmSettings);
defaultScript = myMdmSettings.getScriptText();
}

1
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/BinaryStorageEntity.java
View File

@ -30,6 +30,7 @@ public class BinaryStorageEntity {
@Id
@Column(name = "BLOB_ID", length = 200, nullable = false)
//N.B GGG: Note that the `blob id` is the same as the `externalized binary id`.
private String myBlobId;
@Column(name = "RESOURCE_ID", length = 100, nullable = false)
private String myResourceId;

9
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaConfig.java
View File

@ -21,10 +21,13 @@ package ca.uhn.fhir.jpa.config;
*/
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.binstore.IBinaryStorageSvc;
import ca.uhn.fhir.jpa.binstore.MemoryBinaryStorageSvcImpl;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ModelConfig;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
import org.springframework.context.annotation.Primary;
import org.springframework.orm.jpa.JpaTransactionManager;
@ -43,6 +46,12 @@ public class TestJpaConfig {
return daoConfig().getModelConfig();
}
@Bean
@Lazy
public IBinaryStorageSvc binaryStorage() {
return new MemoryBinaryStorageSvcImpl();
}
@Bean
@Primary
public JpaTransactionManager hapiTransactionManager(EntityManagerFactory entityManagerFactory) {

4
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/config/TestJpaDstu3Config.java
View File

@ -135,10 +135,6 @@ public class TestJpaDstu3Config extends BaseJavaConfigDstu3 {
return requestValidator;
}
@Bean
public IBinaryStorageSvc binaryStorage() {
return new MemoryBinaryStorageSvcImpl();
}
@Bean
public DefaultProfileValidationSupport validationSupportChainDstu3() {

78
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmControllerHelper.java
View File

@ -21,20 +21,36 @@ package ca.uhn.fhir.mdm.provider;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.mdm.api.IMdmMatchFinderSvc;
import ca.uhn.fhir.mdm.api.IMdmSettings;
import ca.uhn.fhir.mdm.api.MatchedTarget;
import ca.uhn.fhir.mdm.api.MdmConstants;
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
import ca.uhn.fhir.mdm.util.MessageHelper;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.rest.server.provider.ProviderConstants;
import ca.uhn.fhir.util.BundleBuilder;
import ca.uhn.fhir.validation.IResourceLoader;
import org.hl7.fhir.instance.model.api.IAnyResource;
import org.hl7.fhir.instance.model.api.IBase;
import org.hl7.fhir.instance.model.api.IBaseBackboneElement;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseDatatype;
import org.hl7.fhir.instance.model.api.IBaseExtension;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import javax.annotation.Nonnull;
import java.math.BigDecimal;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.UUID;
@Service
public class MdmControllerHelper {
@ -42,12 +58,18 @@ public class MdmControllerHelper {
private final IResourceLoader myResourceLoader;
private final IMdmSettings myMdmSettings;
private final MessageHelper myMessageHelper;
private final IMdmMatchFinderSvc myMdmMatchFinderSvc;
@Autowired
public MdmControllerHelper(FhirContext theFhirContext, IResourceLoader theResourceLoader, IMdmSettings theMdmSettings, MessageHelper theMessageHelper) {
public MdmControllerHelper(FhirContext theFhirContext,
IResourceLoader theResourceLoader,
IMdmMatchFinderSvc theMdmMatchFinderSvc,
IMdmSettings theMdmSettings,
MessageHelper theMessageHelper) {
myFhirContext = theFhirContext;
myResourceLoader = theResourceLoader;
myMdmSettings = theMdmSettings;
myMdmMatchFinderSvc = theMdmMatchFinderSvc;
myMessageHelper = theMessageHelper;
}
@ -104,4 +126,58 @@ public class MdmControllerHelper {
throw new InvalidRequestException(myMessageHelper.getMessageForUnmanagedResource());
}
}
/**
* Helper method which will return a bundle of all Matches and Possible Matches.
*/
public IBaseBundle getMatchesAndPossibleMatchesForResource(IAnyResource theResource, String theResourceType) {
List<MatchedTarget> matches = myMdmMatchFinderSvc.getMatchedTargets(theResourceType, theResource);
matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.setBundleField("type", "searchset");
builder.setBundleField("id", UUID.randomUUID().toString());
builder.setMetaField("lastUpdated", builder.newPrimitive("instant", new Date()));
IBaseBundle retVal = builder.getBundle();
for (MatchedTarget next : matches) {
boolean shouldKeepThisEntry = next.isMatch() || next.isPossibleMatch();
if (!shouldKeepThisEntry) {
continue;
}
IBase entry = builder.addEntry();
builder.addToEntry(entry, "resource", next.getTarget());
IBaseBackboneElement search = builder.addSearch(entry);
toBundleEntrySearchComponent(builder, search, next);
}
return retVal;
}
public IBaseBackboneElement toBundleEntrySearchComponent(BundleBuilder theBuilder, IBaseBackboneElement theSearch, MatchedTarget theMatchedTarget) {
theBuilder.setSearchField(theSearch, "mode", "match");
double score = theMatchedTarget.getMatchResult().getNormalizedScore();
theBuilder.setSearchField(theSearch, "score",
theBuilder.newPrimitive("decimal", BigDecimal.valueOf(score)));
String matchGrade = getMatchGrade(theMatchedTarget);
IBaseDatatype codeType = (IBaseDatatype) myFhirContext.getElementDefinition("code").newInstance(matchGrade);
IBaseExtension searchExtension = theSearch.addExtension();
searchExtension.setUrl(MdmConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE);
searchExtension.setValue(codeType);
return theSearch;
}
@Nonnull
protected String getMatchGrade(MatchedTarget theTheMatchedTarget) {
String retVal = "probable";
if (theTheMatchedTarget.isMatch()) {
retVal = "certain";
} else if (theTheMatchedTarget.isPossibleMatch()) {
retVal = "possible";
}
return retVal;
}
}

69
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderDstu3Plus.java
View File

@ -72,9 +72,9 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
private static final Logger ourLog = getLogger(MdmProviderDstu3Plus.class);
private final IMdmControllerSvc myMdmControllerSvc;
private final IMdmMatchFinderSvc myMdmMatchFinderSvc;
private final IMdmSubmitSvc myMdmSubmitSvc;
private final IMdmSettings myMdmSettings;
private final MdmControllerHelper myMdmControllerHelper;
public static final int DEFAULT_PAGE_SIZE = 20;
public static final int MAX_PAGE_SIZE = 100;
@ -85,10 +85,14 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
* Note that this is not a spring bean. Any necessary injections should
* happen in the constructor
*/
public MdmProviderDstu3Plus(FhirContext theFhirContext, IMdmControllerSvc theMdmControllerSvc, IMdmMatchFinderSvc theMdmMatchFinderSvc, IMdmSubmitSvc theMdmSubmitSvc, IMdmSettings theIMdmSettings) {
public MdmProviderDstu3Plus(FhirContext theFhirContext,
IMdmControllerSvc theMdmControllerSvc,
MdmControllerHelper theMdmHelper,
IMdmSubmitSvc theMdmSubmitSvc,
IMdmSettings theIMdmSettings) {
super(theFhirContext);
myMdmControllerSvc = theMdmControllerSvc;
myMdmMatchFinderSvc = theMdmMatchFinderSvc;
myMdmControllerHelper = theMdmHelper;
myMdmSubmitSvc = theMdmSubmitSvc;
myMdmSettings = theIMdmSettings;
}
@ -98,7 +102,7 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
if (thePatient == null) {
throw new InvalidRequestException("resource may not be null");
}
return getMatchesAndPossibleMatchesForResource(thePatient, "Patient");
return myMdmControllerHelper.getMatchesAndPossibleMatchesForResource(thePatient, "Patient");
}
@Operation(name = ProviderConstants.MDM_MATCH)
@ -108,51 +112,7 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
if (theResource == null) {
throw new InvalidRequestException("resource may not be null");
}
return getMatchesAndPossibleMatchesForResource(theResource, theResourceType.getValueAsString());
}
/**
* Helper method which will return a bundle of all Matches and Possible Matches.
*/
private IBaseBundle getMatchesAndPossibleMatchesForResource(IAnyResource theResource, String theResourceType) {
List<MatchedTarget> matches = myMdmMatchFinderSvc.getMatchedTargets(theResourceType, theResource);
matches.sort(Comparator.comparing((MatchedTarget m) -> m.getMatchResult().getNormalizedScore()).reversed());
BundleBuilder builder = new BundleBuilder(myFhirContext);
builder.setBundleField("type", "searchset");
builder.setBundleField("id", UUID.randomUUID().toString());
builder.setMetaField("lastUpdated", builder.newPrimitive("instant", new Date()));
IBaseBundle retVal = builder.getBundle();
for (MatchedTarget next : matches) {
boolean shouldKeepThisEntry = next.isMatch() || next.isPossibleMatch();
if (!shouldKeepThisEntry) {
continue;
}
IBase entry = builder.addEntry();
builder.addToEntry(entry, "resource", next.getTarget());
IBaseBackboneElement search = builder.addSearch(entry);
toBundleEntrySearchComponent(builder, search, next);
}
return retVal;
}
public IBaseBackboneElement toBundleEntrySearchComponent(BundleBuilder theBuilder, IBaseBackboneElement theSearch, MatchedTarget theMatchedTarget) {
theBuilder.setSearchField(theSearch, "mode", "match");
double score = theMatchedTarget.getMatchResult().getNormalizedScore();
theBuilder.setSearchField(theSearch, "score",
theBuilder.newPrimitive("decimal", BigDecimal.valueOf(score)));
String matchGrade = getMatchGrade(theMatchedTarget);
IBaseDatatype codeType = (IBaseDatatype) myFhirContext.getElementDefinition("code").newInstance(matchGrade);
IBaseExtension searchExtension = theSearch.addExtension();
searchExtension.setUrl(MdmConstants.FIHR_STRUCTURE_DEF_MATCH_GRADE_URL_NAMESPACE);
searchExtension.setValue(codeType);
return theSearch;
return myMdmControllerHelper.getMatchesAndPossibleMatchesForResource(theResource, theResourceType.getValueAsString());
}
@Operation(name = ProviderConstants.MDM_MERGE_GOLDEN_RESOURCES)
@ -353,17 +313,6 @@ public class MdmProviderDstu3Plus extends BaseMdmProvider {
return retval;
}
@Nonnull
protected String getMatchGrade(MatchedTarget theTheMatchedTarget) {
String retVal = "probable";
if (theTheMatchedTarget.isMatch()) {
retVal = "certain";
} else if (theTheMatchedTarget.isPossibleMatch()) {
retVal = "possible";
}
return retVal;
}
private String getResourceType(String theParamName, IPrimitiveType<String> theResourceId) {
if (theResourceId != null) {
return getResourceType(theParamName, theResourceId.getValueAsString());

8
hapi-fhir-server-mdm/src/main/java/ca/uhn/fhir/mdm/provider/MdmProviderLoader.java
View File

@ -39,7 +39,7 @@ public class MdmProviderLoader {
@Autowired
private ResourceProviderFactory myResourceProviderFactory;
@Autowired
private IMdmMatchFinderSvc myMdmMatchFinderSvc;
private MdmControllerHelper myMdmControllerHelper;
@Autowired
private IMdmControllerSvc myMdmControllerSvc;
@Autowired
@ -54,7 +54,11 @@ public class MdmProviderLoader {
case DSTU3:
case R4:
myResourceProviderFactory.addSupplier(() -> {
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext, myMdmControllerSvc, myMdmMatchFinderSvc, myMdmSubmitSvc, myMdmSettings);
myMdmProvider = new MdmProviderDstu3Plus(myFhirContext,
myMdmControllerSvc,
myMdmControllerHelper,
myMdmSubmitSvc,
myMdmSettings);
return myMdmProvider;
});
break;

14
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/BaseValidatingInterceptor.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.rest.server.interceptor;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.interceptor.api.Interceptor;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
@ -310,11 +311,14 @@ public abstract class BaseValidatingInterceptor<T> extends ValidationResultEnric
return null;
}
switch (theRequestDetails.getRestOperationType()) {
case GRAPHQL_REQUEST:
return null;
default:
break;
RestOperationTypeEnum opType = theRequestDetails.getRestOperationType();
if (opType != null) {
switch (opType) {
case GRAPHQL_REQUEST:
return null;
default:
break;
}
}
FhirValidator validator;

27
hapi-fhir-test-utilities/src/main/java/ca/uhn/fhir/test/utilities/BatchJobHelper.java
View File

@ -48,17 +48,30 @@ public class BatchJobHelper {
myJobExplorer = theJobExplorer;
}
public List<JobExecution> awaitAllBulkJobCompletions(String... theJobNames) {
return awaitAllBulkJobCompletions(true, theJobNames);
}
/**
* Await and report for job completions
* @param theFailIfNotJobsFound indicate if must fail in case no matching jobs are found
* @param theJobNames The job names to match
* @return the matched JobExecution(s)
*/
public List<JobExecution> awaitAllBulkJobCompletions(boolean theFailIfNotJobsFound, String... theJobNames) {
assert theJobNames.length > 0;
List<JobInstance> matchingJobInstances = new ArrayList<>();
for (String nextName : theJobNames) {
matchingJobInstances.addAll(myJobExplorer.findJobInstancesByJobName(nextName, 0, 100));
}
if (matchingJobInstances.isEmpty()) {
List<String> wantNames = Arrays.asList(theJobNames);
List<String> haveNames = myJobExplorer.getJobNames();
fail("There are no jobs running - Want names " + wantNames + " and have names " + haveNames);
if (theFailIfNotJobsFound) {
if (matchingJobInstances.isEmpty()) {
List<String> wantNames = Arrays.asList(theJobNames);
List<String> haveNames = myJobExplorer.getJobNames();
fail("There are no jobs running - Want names " + wantNames + " and have names " + haveNames);
}
}
List<JobExecution> matchingExecutions = matchingJobInstances.stream().flatMap(jobInstance -> myJobExplorer.getJobExecutions(jobInstance).stream()).collect(Collectors.toList());
awaitJobCompletions(matchingExecutions);
@ -82,7 +95,11 @@ public class BatchJobHelper {
await().atMost(120, TimeUnit.SECONDS).until(() -> {
JobExecution jobExecution = myJobExplorer.getJobExecution(theJobExecution.getId());
ourLog.info("JobExecution {} currently has status: {}- Failures if any: {}", theJobExecution.getId(), jobExecution.getStatus(), jobExecution.getFailureExceptions());
return jobExecution.getStatus() == BatchStatus.COMPLETED || jobExecution.getStatus() == BatchStatus.FAILED;
// JM: Adding ABANDONED status because given the description, it s similar to FAILURE, and we need to avoid tests failing because
// of wait timeouts caused by unmatched statuses. Also adding STOPPED because tests were found where this wait timed out
// with jobs keeping that status during the whole wait
return jobExecution.getStatus() == BatchStatus.COMPLETED || jobExecution.getStatus() == BatchStatus.FAILED
|| jobExecution.getStatus() == BatchStatus.ABANDONED || jobExecution.getStatus() == BatchStatus.STOPPED;
});
}

14
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyService.java
View File

@ -212,7 +212,6 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
Map<String, String> map;
switch (theSystem) {
case LANGUAGES_CODESYSTEM_URL:
@ -254,9 +253,7 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
}
private LookupCodeResult lookupLanguageCode(String theCode) {
Map<String, String> languagesMap = myLanguagesLanugageMap;
Map<String, String> regionsMap = myLanguagesRegionMap;
if (languagesMap == null || regionsMap == null) {
if (myLanguagesLanugageMap == null || myLanguagesRegionMap == null) {
initializeBcp47LanguageMap();
}
@ -266,8 +263,10 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
String region;
if (hasRegionAndCodeSegments) {
language = myLanguagesLanugageMap.get(theCode.substring(0, langRegionSeparatorIndex));
region = myLanguagesRegionMap.get(theCode.substring(langRegionSeparatorIndex + 1));
// we look for languages in lowercase only
// this will allow case insensitivity for language portion of code
language = myLanguagesLanugageMap.get(theCode.substring(0, langRegionSeparatorIndex).toLowerCase());
region = myLanguagesRegionMap.get(theCode.substring(langRegionSeparatorIndex + 1).toUpperCase());
if (language == null || region == null) {
//In case the user provides both a language and a region, they must both be valid for the lookup to succeed.
@ -278,7 +277,8 @@ public class CommonCodeSystemsTerminologyService implements IValidationSupport {
}
} else {
//In case user has only provided a language, we build the lookup from only that.
language = myLanguagesLanugageMap.get(theCode);
//NB: we only use the lowercase version of the language
language = myLanguagesLanugageMap.get(theCode.toLowerCase());
if (language == null) {
ourLog.warn("Couldn't find a valid bcp47 language from code: {}", theCode);
return buildNotFoundLookupCodeResult(theCode);

169
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupport.java
View File

@ -1,6 +1,7 @@
package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.FhirVersionEnum;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.context.support.IValidationSupport;
@ -9,8 +10,8 @@ import ca.uhn.fhir.rest.client.api.IGenericClient;
import ca.uhn.fhir.util.BundleUtil;
import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.checkerframework.framework.qual.InvisibleQualifier;
import org.hl7.fhir.instance.model.api.IBaseBundle;
import org.hl7.fhir.instance.model.api.IBaseParameters;
import org.hl7.fhir.instance.model.api.IBaseResource;
@ -82,7 +83,7 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
*/
private String extractCodeSystemForCode(ValueSet theValueSet, String theCode) {
if (theValueSet.getCompose() == null || theValueSet.getCompose().getInclude() == null
|| theValueSet.getCompose().getInclude().isEmpty()) {
|| theValueSet.getCompose().getInclude().isEmpty()) {
return null;
}
@ -111,11 +112,9 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
} catch (IOException theE) {
ourLog.error("IOException trying to serialize ValueSet to json: " + theE);
}
return null;
}
private String getVersionedCodeSystem(ValueSet.ConceptSetComponent theComponent) {
String codeSystem = theComponent.getSystem();
if ( ! codeSystem.contains("|") && theComponent.hasVersion()) {
@ -124,7 +123,6 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return codeSystem;
}
@Override
public IBaseResource fetchCodeSystem(String theSystem) {
IGenericClient client = provideClient();
@ -143,6 +141,167 @@ public class RemoteTerminologyServiceValidationSupport extends BaseValidationSup
return null;
}
@Override
public LookupCodeResult lookupCode(ValidationSupportContext theValidationSupportContext, String theSystem, String theCode, String theDisplayLanguage) {
Validate.notBlank(theCode, "theCode must be provided");
IGenericClient client = provideClient();
FhirContext fhirContext = client.getFhirContext();
FhirVersionEnum fhirVersion = fhirContext.getVersion().getVersion();
switch (fhirVersion) {
case DSTU3:
case R4:
IBaseParameters params = ParametersUtil.newInstance(fhirContext);
ParametersUtil.addParameterToParametersString(fhirContext, params, "code", theCode);
if (!StringUtils.isEmpty(theSystem)) {
ParametersUtil.addParameterToParametersString(fhirContext, params, "system", theSystem);
}
if (!StringUtils.isEmpty(theDisplayLanguage)) {
ParametersUtil.addParameterToParametersString(fhirContext, params, "language", theDisplayLanguage);
}
Class<?> codeSystemClass = myCtx.getResourceDefinition("CodeSystem").getImplementingClass();
IBaseParameters outcome = client
.operation()
.onType((Class<? extends IBaseResource>) codeSystemClass)
.named("$lookup")
.withParameters(params)
.useHttpGet()
.execute();
if (outcome != null && !outcome.isEmpty()) {
switch (fhirVersion) {
case DSTU3:
return generateLookupCodeResultDSTU3(theCode, theSystem, (org.hl7.fhir.dstu3.model.Parameters)outcome);
case R4:
return generateLookupCodeResultR4(theCode, theSystem, (org.hl7.fhir.r4.model.Parameters)outcome);
}
}
break;
default:
throw new UnsupportedOperationException("Unsupported FHIR version '" + fhirVersion.getFhirVersionString() +
"'. Only DSTU3 and R4 are supported.");
}
return null;
}
private LookupCodeResult generateLookupCodeResultDSTU3(String theCode, String theSystem, org.hl7.fhir.dstu3.model.Parameters outcomeDSTU3) {
// NOTE: I wanted to put all of this logic into the IValidationSupport Class, but it would've required adding
// several new dependencies on version-specific libraries and that is explicitly forbidden (see comment in POM).
LookupCodeResult result = new LookupCodeResult();
result.setSearchedForCode(theCode);
result.setSearchedForSystem(theSystem);
result.setFound(true);
for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent parameterComponent : outcomeDSTU3.getParameter()) {
switch (parameterComponent.getName()) {
case "property":
org.hl7.fhir.dstu3.model.Property part = parameterComponent.getChildByName("part");
// The assumption here is that we may only have 2 elements in this part, and if so, these 2 will be saved
if (part != null && part.hasValues() && part.getValues().size() >= 2) {
String key = ((org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent) part.getValues().get(0)).getValue().toString();
String value = ((org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent) part.getValues().get(1)).getValue().toString();
if (!StringUtils.isEmpty(key) && !StringUtils.isEmpty(value)) {
result.getProperties().add(new StringConceptProperty(key, value));
}
}
break;
case "designation":
ConceptDesignation conceptDesignation = new ConceptDesignation();
for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent designationComponent : parameterComponent.getPart()) {
switch(designationComponent.getName()) {
case "language":
conceptDesignation.setLanguage(designationComponent.getValue().toString());
break;
case "use":
org.hl7.fhir.dstu3.model.Coding coding = (org.hl7.fhir.dstu3.model.Coding)designationComponent.getValue();
if (coding != null) {
conceptDesignation.setUseSystem(coding.getSystem());
conceptDesignation.setUseCode(coding.getCode());
conceptDesignation.setUseDisplay(coding.getDisplay());
}
break;
case "value":
conceptDesignation.setValue(((designationComponent.getValue() == null)?null:designationComponent.getValue().toString()));
break;
}
}
result.getDesignations().add(conceptDesignation);
break;
case "name":
result.setCodeSystemDisplayName(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "version":
result.setCodeSystemVersion(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "display":
result.setCodeDisplay(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "abstract":
result.setCodeIsAbstract(((parameterComponent.getValue() == null)?false:Boolean.parseBoolean(parameterComponent.getValue().toString())));
break;
}
}
return result;
}
private LookupCodeResult generateLookupCodeResultR4(String theCode, String theSystem, org.hl7.fhir.r4.model.Parameters outcomeR4) {
// NOTE: I wanted to put all of this logic into the IValidationSupport Class, but it would've required adding
// several new dependencies on version-specific libraries and that is explicitly forbidden (see comment in POM).
LookupCodeResult result = new LookupCodeResult();
result.setSearchedForCode(theCode);
result.setSearchedForSystem(theSystem);
result.setFound(true);
for (org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent parameterComponent : outcomeR4.getParameter()) {
switch (parameterComponent.getName()) {
case "property":
org.hl7.fhir.r4.model.Property part = parameterComponent.getChildByName("part");
// The assumption here is that we may only have 2 elements in this part, and if so, these 2 will be saved
if (part != null && part.hasValues() && part.getValues().size() >= 2) {
String key = ((org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent) part.getValues().get(0)).getValue().toString();
String value = ((org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent) part.getValues().get(1)).getValue().toString();
if (!StringUtils.isEmpty(key) && !StringUtils.isEmpty(value)) {
result.getProperties().add(new StringConceptProperty(key, value));
}
}
break;
case "designation":
ConceptDesignation conceptDesignation = new ConceptDesignation();
for (org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent designationComponent : parameterComponent.getPart()) {
switch(designationComponent.getName()) {
case "language":
conceptDesignation.setLanguage(designationComponent.getValue().toString());
break;
case "use":
org.hl7.fhir.r4.model.Coding coding = (org.hl7.fhir.r4.model.Coding)designationComponent.getValue();
if (coding != null) {
conceptDesignation.setUseSystem(coding.getSystem());
conceptDesignation.setUseCode(coding.getCode());
conceptDesignation.setUseDisplay(coding.getDisplay());
}
break;
case "value":
conceptDesignation.setValue(((designationComponent.getValue() == null)?null:designationComponent.getValue().toString()));
break;
}
}
result.getDesignations().add(conceptDesignation);
break;
case "name":
result.setCodeSystemDisplayName(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "version":
result.setCodeSystemVersion(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "display":
result.setCodeDisplay(((parameterComponent.getValue() == null)?null:parameterComponent.getValue().toString()));
break;
case "abstract":
result.setCodeIsAbstract(((parameterComponent.getValue() == null)?false:Boolean.parseBoolean(parameterComponent.getValue().toString())));
break;
}
}
return result;
}
@Override
public IBaseResource fetchValueSet(String theValueSetUrl) {
IGenericClient client = provideClient();

21
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/CommonCodeSystemsTerminologyServiceTest.java
View File

@ -12,6 +12,7 @@ import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
@ -54,6 +55,26 @@ public class CommonCodeSystemsTerminologyServiceTest {
assertNull(outcome);
}
@Test
public void lookupCode_languageOnlyLookup_isCaseInsensitive() {
IValidationSupport.LookupCodeResult outcomeUpper = mySvc.lookupCode(newSupport(), "urn:ietf:bcp:47", "SGN", "Sign Languages");
IValidationSupport.LookupCodeResult outcomeLower = mySvc.lookupCode(newSupport(), "urn:ietf:bcp:47", "sgn", "Sign Languages");
assertNotNull(outcomeUpper);
assertNotNull(outcomeLower);
assertTrue(outcomeLower.isFound());
assertTrue(outcomeUpper.isFound());
}
@Test
public void lookupCode_languageAndRegionLookup_isCaseInsensitive() {
IValidationSupport.LookupCodeResult outcomeUpper = mySvc.lookupCode(newSupport(), "urn:ietf:bcp:47", "EN-US", "English");
IValidationSupport.LookupCodeResult outcomeLower = mySvc.lookupCode(newSupport(), "urn:ietf:bcp:47", "en-us", "English");
assertNotNull(outcomeUpper);
assertNotNull(outcomeLower);
assertTrue(outcomeLower.isFound());
assertTrue(outcomeUpper.isFound());
}
@Test
public void testUcum_ValidateCode_Good() {
ValueSet vs = new ValueSet();

172
hapi-fhir-validation/src/test/java/org/hl7/fhir/common/hapi/validation/support/RemoteTerminologyServiceValidationSupportTest.java
View File

@ -3,12 +3,14 @@ package org.hl7.fhir.common.hapi.validation.support;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.ConceptValidationOptions;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.parser.IJsonLikeParser;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.RequiredParam;
import ca.uhn.fhir.rest.annotation.Search;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.api.IClientInterceptor;
import ca.uhn.fhir.rest.client.api.IHttpRequest;
import ca.uhn.fhir.rest.client.api.IHttpResponse;
@ -22,12 +24,14 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.BooleanType;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeType;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.StringType;
import org.hl7.fhir.r4.model.UriType;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
@ -44,14 +48,18 @@ import static org.hamcrest.Matchers.lessThan;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class RemoteTerminologyServiceValidationSupportTest {
private static final String DISPLAY = "DISPLAY";
private static final String LANGUAGE = "en";
private static final String CODE_SYSTEM = "CODE_SYS";
private static final String CODE_SYSTEM_VERSION = "2.1";
private static final String CODE_SYSTEM_VERSION_AS_TEXT = "v2.1.12";
private static final String CODE = "CODE";
private static final String VALUE_SET_URL = "http://value.set/url";
private static final String ERROR_MESSAGE = "This is an error message";
private static FhirContext ourCtx = FhirContext.forR4();
@RegisterExtension
@ -88,7 +96,50 @@ public class RemoteTerminologyServiceValidationSupportTest {
}
@Test
public void testValidateCode_SystemCodeDisplayUrl_Success() {
public void testLookupOperation_CodeSystem_Success() {
createNextCodeSystemLookupReturnParameters(true, CODE_SYSTEM_VERSION, CODE_SYSTEM_VERSION_AS_TEXT,
DISPLAY, null);
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(null, CODE_SYSTEM, CODE);
assertNotNull(outcome, "Call to lookupCode() should return a non-NULL result!");
assertEquals(DISPLAY, outcome.getCodeDisplay());
assertEquals(CODE_SYSTEM_VERSION, outcome.getCodeSystemVersion());
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
assertEquals(CODE_SYSTEM_VERSION_AS_TEXT, myCodeSystemProvider.myNextReturnParams.getParameter("name").toString());
assertTrue(Boolean.parseBoolean(myCodeSystemProvider.myNextReturnParams.getParameter("result").primitiveValue()));
}
@Test
public void testLookupOperationWithAllParams_CodeSystem_Success() {
createNextCodeSystemLookupReturnParameters(true, CODE_SYSTEM_VERSION, CODE_SYSTEM_VERSION_AS_TEXT,
DISPLAY, null);
addAdditionalReturnParameters();
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(null, CODE_SYSTEM, CODE);
assertNotNull(outcome, "Call to lookupCode() should return a non-NULL result!");
assertEquals(DISPLAY, outcome.getCodeDisplay());
assertEquals(CODE_SYSTEM_VERSION, outcome.getCodeSystemVersion());
assertEquals(CODE_SYSTEM_VERSION_AS_TEXT, myCodeSystemProvider.myNextReturnParams.getParameter("name").toString());
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
assertTrue(Boolean.parseBoolean(myCodeSystemProvider.myNextReturnParams.getParameter("result").primitiveValue()));
validateExtraCodeSystemParams();
}
@Test
public void testLookupCode_BlankCode_ThrowsException() {
Assertions.assertThrows(IllegalArgumentException.class, () -> {
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(null, CODE_SYSTEM,
"", null);
});
}
@Test
public void testValidateCode_ValueSet_Success() {
createNextValueSetReturnParameters(true, DISPLAY, null);
IValidationSupport.CodeValidationResult outcome = mySvc.validateCode(null, null, CODE_SYSTEM, CODE, DISPLAY, VALUE_SET_URL);
@ -104,6 +155,62 @@ public class RemoteTerminologyServiceValidationSupportTest {
assertEquals(null, myValueSetProvider.myLastValueSet);
}
@Test
public void testValidateCodeWithAllParams_CodeSystem_Success() {
createNextCodeSystemReturnParameters(true, DISPLAY, null);
addAdditionalReturnParameters();
IValidationSupport.CodeValidationResult outcome = mySvc.validateCode(null, null, CODE_SYSTEM, CODE, DISPLAY, null);
assertEquals(CODE, outcome.getCode());
assertEquals(DISPLAY, outcome.getDisplay());
assertEquals(null, outcome.getSeverity());
assertEquals(null, outcome.getMessage());
validateExtraCodeSystemParams();
}
private void validateExtraCodeSystemParams() {
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
for (Parameters.ParametersParameterComponent param : myCodeSystemProvider.myNextReturnParams.getParameter()) {
String paramName = param.getName();
if (paramName.equals("result")) {
assertEquals(true, ((BooleanType)param.getValue()).booleanValue());
} else if (paramName.equals("display")) {
assertEquals(DISPLAY, param.getValue().toString());
} else if (paramName.equals("property")) {
for (Parameters.ParametersParameterComponent propertyComponent : param.getPart()) {
switch(propertyComponent.getName()) {
case "name":
assertEquals("birthDate", propertyComponent.getValue().toString());
break;
case "value":
assertEquals("1930-01-01", propertyComponent.getValue().toString());
break;
}
}
} else if (paramName.equals("designation")) {
for (Parameters.ParametersParameterComponent designationComponent : param.getPart()) {
switch(designationComponent.getName()) {
case "language":
assertEquals(LANGUAGE, designationComponent.getValue().toString());
break;
case "use":
Coding coding = (Coding)designationComponent.getValue();
assertNotNull(coding, "Coding value returned via designation use should NOT be NULL!");
assertEquals("code", coding.getCode());
assertEquals("system", coding.getSystem());
assertEquals("display", coding.getDisplay());
break;
case "value":
assertEquals("some value", designationComponent.getValue().toString());
break;
}
}
}
}
}
@Test
public void testValidateCode_SystemCodeDisplayUrl_Error() {
createNextValueSetReturnParameters(false, null, ERROR_MESSAGE);
@ -132,7 +239,6 @@ public class RemoteTerminologyServiceValidationSupportTest {
assertEquals(null, outcome.getMessage());
assertEquals(CODE, myCodeSystemProvider.myLastCode.getCode());
assertEquals(DISPLAY, myCodeSystemProvider.myLastDisplay.getValue());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
}
@ -375,6 +481,18 @@ public class RemoteTerminologyServiceValidationSupportTest {
}
}
private void createNextCodeSystemLookupReturnParameters(boolean theResult, String theVersion, String theVersionAsText,
String theDisplay, String theMessage) {
myCodeSystemProvider.myNextReturnParams = new Parameters();
myCodeSystemProvider.myNextReturnParams.addParameter("result", theResult);
myCodeSystemProvider.myNextReturnParams.addParameter("version", theVersion);
myCodeSystemProvider.myNextReturnParams.addParameter("name", theVersionAsText);
myCodeSystemProvider.myNextReturnParams.addParameter("display", theDisplay);
if (theMessage != null) {
myCodeSystemProvider.myNextReturnParams.addParameter("message", theMessage);
}
}
private void createNextValueSetReturnParameters(boolean theResult, String theDisplay, String theMessage) {
myValueSetProvider.myNextReturnParams = new Parameters();
myValueSetProvider.myNextReturnParams.addParameter("result", theResult);
@ -384,6 +502,23 @@ public class RemoteTerminologyServiceValidationSupportTest {
}
}
private void addAdditionalReturnParameters() {
// property
Parameters.ParametersParameterComponent param = myCodeSystemProvider.myNextReturnParams.addParameter().setName("property");
param.addPart().setName("name").setValue(new StringType("birthDate"));
param.addPart().setName("value").setValue(new StringType("1930-01-01"));
// designation
param = myCodeSystemProvider.myNextReturnParams.addParameter().setName("designation");
param.addPart().setName("language").setValue(new CodeType("en"));
Parameters.ParametersParameterComponent codingParam = param.addPart().setName("use");
Coding coding = new Coding();
coding.setCode("code");
coding.setSystem("system");
coding.setDisplay("display");
codingParam.setValue(coding);
param.addPart().setName("value").setValue(new StringType("some value"));
}
private static class MyCodeSystemProvider implements IResourceProvider {
private UriParam myLastUrlParam;
@ -391,8 +526,10 @@ public class RemoteTerminologyServiceValidationSupportTest {
private int myInvocationCount;
private UriType myLastUrl;
private CodeType myLastCode;
private StringType myLastDisplay;
private Coding myLastCoding;
private StringType myLastVersion;
private Parameters myNextReturnParams;
private IValidationSupport.LookupCodeResult myNextLookupCodeResult;
@Operation(name = "validate-code", idempotent = true, returnParameters = {
@OperationParam(name = "result", type = BooleanType.class, min = 1),
@ -409,11 +546,34 @@ public class RemoteTerminologyServiceValidationSupportTest {
myInvocationCount++;
myLastUrl = theCodeSystemUrl;
myLastCode = theCode;
myLastDisplay = theDisplay;
return myNextReturnParams;
}
@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters= {
@OperationParam(name="name", type=StringType.class, min=1),
@OperationParam(name="version", type=StringType.class, min=0),
@OperationParam(name="display", type=StringType.class, min=1),
@OperationParam(name="abstract", type=BooleanType.class, min=1),
})
public Parameters lookup(
HttpServletRequest theServletRequest,
@OperationParam(name="code", min=0, max=1) CodeType theCode,
@OperationParam(name="system", min=0, max=1) UriType theSystem,
@OperationParam(name="coding", min=0, max=1) Coding theCoding,
@OperationParam(name="version", min=0, max=1) StringType theVersion,
@OperationParam(name="displayLanguage", min=0, max=1) CodeType theDisplayLanguage,
@OperationParam(name="property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
RequestDetails theRequestDetails
) {
myInvocationCount++;
myLastCode = theCode;
myLastUrl = theSystem;
myLastCoding = theCoding;
myLastVersion = theVersion;
return myNextReturnParams;
}
@Search
public List<CodeSystem> find(@RequiredParam(name = "url") UriParam theUrlParam) {
myLastUrlParam = theUrlParam;
@ -429,8 +589,6 @@ public class RemoteTerminologyServiceValidationSupportTest {
private static class MyValueSetProvider implements IResourceProvider {
private Parameters myNextReturnParams;
private List<ValueSet> myNextReturnValueSets;
private UriType myLastUrl;

214
hapi-fhir-validation/src/test/java/org/hl7/fhir/dstu3/hapi/validation/RemoteTerminologyServiceValidationSupportDstu3Test.java Normal file
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@ -0,0 +1,214 @@
package org.hl7.fhir.dstu3.hapi.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import org.apache.commons.lang3.StringUtils;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.DateType;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
import javax.servlet.http.HttpServletRequest;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
public class RemoteTerminologyServiceValidationSupportDstu3Test {
private static final String DISPLAY = "DISPLAY";
private static final String LANGUAGE = "en";
private static final String CODE_SYSTEM = "CODE_SYS";
private static final String CODE_SYSTEM_VERSION = "2.1";
private static final String CODE_SYSTEM_VERSION_AS_TEXT = "v2.1.12";
private static final String CODE = "CODE";
private static FhirContext ourCtx = FhirContext.forDstu3();
@RegisterExtension
public RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx);
private RemoteTerminologyServiceValidationSupport mySvc;
private MyCodeSystemProvider myCodeSystemProvider;
@BeforeEach
public void before() {
myCodeSystemProvider = new MyCodeSystemProvider();
myRestfulServerExtension.getRestfulServer().registerProvider(myCodeSystemProvider);
String baseUrl = "http://localhost:" + myRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx);
mySvc.setBaseUrl(baseUrl);
mySvc.addClientInterceptor(new LoggingInterceptor(true));
}
@Test
public void testLookupOperation_CodeSystem_Success() {
createNextCodeSystemLookupReturnParameters(true, CODE_SYSTEM_VERSION, CODE_SYSTEM_VERSION_AS_TEXT, DISPLAY);
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(null, CODE_SYSTEM, CODE);
assertNotNull(outcome, "Call to lookupCode() should return a non-NULL result!");
assertEquals(DISPLAY, outcome.getCodeDisplay());
assertEquals(CODE_SYSTEM_VERSION, outcome.getCodeSystemVersion());
assertEquals(CODE, myCodeSystemProvider.myLastCode.asStringValue());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
for (Parameters.ParametersParameterComponent param : myCodeSystemProvider.myNextReturnParams.getParameter()) {
String paramName = param.getName();
if (paramName.equals("result")) {
assertEquals(true, ((BooleanType)param.getValue()).booleanValue());
} else if (paramName.equals("version")) {
assertEquals(CODE_SYSTEM_VERSION, param.getValue().toString());
} else if (paramName.equals("display")) {
assertEquals(DISPLAY, param.getValue().toString());
} else if (paramName.equals("name")) {
assertEquals(CODE_SYSTEM_VERSION_AS_TEXT, param.getValue().toString());
}
}
}
@Test
public void testLookupOperationWithAllParams_CodeSystem_Success() {
createNextCodeSystemLookupReturnParameters(true, CODE_SYSTEM_VERSION, CODE_SYSTEM_VERSION_AS_TEXT, DISPLAY, LANGUAGE);
addAdditionalCodeSystemLookupReturnParameters();
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(null, CODE_SYSTEM, CODE, LANGUAGE);
assertNotNull(outcome, "Call to lookupCode() should return a non-NULL result!");
assertEquals(DISPLAY, outcome.getCodeDisplay());
assertEquals(CODE_SYSTEM_VERSION, outcome.getCodeSystemVersion());
assertEquals(CODE, myCodeSystemProvider.myLastCode.asStringValue());
assertEquals(CODE_SYSTEM, myCodeSystemProvider.myLastUrl.getValueAsString());
for (Parameters.ParametersParameterComponent param : myCodeSystemProvider.myNextReturnParams.getParameter()) {
String paramName = param.getName();
if (paramName.equals("result")) {
assertEquals(true, ((BooleanType)param.getValue()).booleanValue());
} else if (paramName.equals("version")) {
assertEquals(CODE_SYSTEM_VERSION, param.getValue().toString());
} else if (paramName.equals("display")) {
assertEquals(DISPLAY, param.getValue().toString());
} else if (paramName.equals("name")) {
assertEquals(CODE_SYSTEM_VERSION_AS_TEXT, param.getValue().toString());
} else if (paramName.equals("language")) {
assertEquals(LANGUAGE, param.getValue().toString());
} else if (paramName.equals("property")) {
for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent propertyComponent : param.getPart()) {
switch(propertyComponent.getName()) {
case "name":
assertEquals("birthDate", propertyComponent.getValue().toString());
break;
case "value":
assertEquals("1930-01-01", ((DateType)propertyComponent.getValue()).asStringValue());
break;
}
}
} else if (paramName.equals("designation")) {
for (org.hl7.fhir.dstu3.model.Parameters.ParametersParameterComponent designationComponent : param.getPart()) {
switch(designationComponent.getName()) {
case "language":
assertEquals(LANGUAGE, designationComponent.getValue().toString());
break;
case "use":
Coding coding = (Coding)designationComponent.getValue();
assertNotNull(coding, "Coding value returned via designation use should NOT be NULL!");
assertEquals("code", coding.getCode());
assertEquals("system", coding.getSystem());
assertEquals("display", coding.getDisplay());
break;
case "value":
assertEquals("some value", designationComponent.getValue().toString());
break;
}
}
}
}
}
private void createNextCodeSystemLookupReturnParameters(boolean theResult, String theVersion, String theVersionAsText,
String theDisplay) {
createNextCodeSystemLookupReturnParameters(theResult, theVersion, theVersionAsText, theDisplay, null);
}
private void createNextCodeSystemLookupReturnParameters(boolean theResult, String theVersion, String theVersionAsText,
String theDisplay, String theLanguage) {
myCodeSystemProvider.myNextReturnParams = new Parameters();
myCodeSystemProvider.myNextReturnParams.addParameter().setName("result").setValue(new BooleanType(theResult));
myCodeSystemProvider.myNextReturnParams.addParameter().setName("version").setValue(new StringType(theVersion));
myCodeSystemProvider.myNextReturnParams.addParameter().setName("name").setValue(new StringType(theVersionAsText));
myCodeSystemProvider.myNextReturnParams.addParameter().setName("display").setValue(new StringType(theDisplay));
if (!StringUtils.isBlank(theLanguage)) {
myCodeSystemProvider.myNextReturnParams.addParameter().setName("language").setValue(new StringType(theLanguage));
}
}
private void addAdditionalCodeSystemLookupReturnParameters() {
// property
Parameters.ParametersParameterComponent param = myCodeSystemProvider.myNextReturnParams.addParameter().setName("property");
param.addPart().setName("name").setValue(new StringType("birthDate"));
param.addPart().setName("value").setValue(new DateType("1930-01-01"));
// designation
param = myCodeSystemProvider.myNextReturnParams.addParameter().setName("designation");
param.addPart().setName("language").setValue(new CodeType("en"));
Parameters.ParametersParameterComponent codingParam = param.addPart().setName("use");
Coding coding = new Coding();
coding.setCode("code");
coding.setSystem("system");
coding.setDisplay("display");
codingParam.setValue(coding);
param.addPart().setName("value").setValue(new StringType("some value"));
}
private static class MyCodeSystemProvider implements IResourceProvider {
private int myInvocationCount;
private UriType myLastUrl;
private CodeType myLastCode;
private Coding myLastCoding;
private StringType myLastVersion;
private CodeType myLastDisplayLanguage;
private Parameters myNextReturnParams;
@Operation(name = JpaConstants.OPERATION_LOOKUP, idempotent = true, returnParameters= {
@OperationParam(name="name", type=StringType.class, min=1),
@OperationParam(name="version", type=StringType.class, min=0),
@OperationParam(name="display", type=StringType.class, min=1),
@OperationParam(name="abstract", type=BooleanType.class, min=1),
})
public Parameters lookup(
HttpServletRequest theServletRequest,
@OperationParam(name="code", min=0, max=1) CodeType theCode,
@OperationParam(name="system", min=0, max=1) UriType theSystem,
@OperationParam(name="coding", min=0, max=1) Coding theCoding,
@OperationParam(name="version", min=0, max=1) StringType theVersion,
@OperationParam(name="displayLanguage", min=0, max=1) CodeType theDisplayLanguage,
@OperationParam(name="property", min = 0, max = OperationParam.MAX_UNLIMITED) List<CodeType> theProperties,
RequestDetails theRequestDetails
) {
myInvocationCount++;
myLastCode = theCode;
myLastUrl = theSystem;
myLastCoding = theCoding;
myLastVersion = theVersion;
myLastDisplayLanguage = theDisplayLanguage;
return myNextReturnParams;
}
@Override
public Class<? extends IBaseResource> getResourceType() {
return CodeSystem.class;
}
}
}

35
hapi-fhir-validation/src/test/java/org/hl7/fhir/r5/validation/RemoteTerminologyServiceValidationSupportR5Test.java Normal file
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@ -0,0 +1,35 @@
package org.hl7.fhir.r5.validation;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.IValidationSupport;
import ca.uhn.fhir.context.support.ValidationSupportContext;
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
import org.hl7.fhir.common.hapi.validation.support.RemoteTerminologyServiceValidationSupport;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.RegisterExtension;
public class RemoteTerminologyServiceValidationSupportR5Test {
private static final String ANY_NONBLANK_VALUE = "anything";
private static FhirContext ourCtx = FhirContext.forR5();
@RegisterExtension
public RestfulServerExtension myRestfulServerExtension = new RestfulServerExtension(ourCtx);
private RemoteTerminologyServiceValidationSupport mySvc;
@BeforeEach
public void before() {
String baseUrl = "http://localhost:" + myRestfulServerExtension.getPort();
mySvc = new RemoteTerminologyServiceValidationSupport(ourCtx);
mySvc.setBaseUrl(baseUrl);
}
@Test
public void testLookupCode_R5_ThrowsException() {
Assertions.assertThrows(UnsupportedOperationException.class, () -> {
IValidationSupport.LookupCodeResult outcome = mySvc.lookupCode(
new ValidationSupportContext(FhirContext.forR5().getValidationSupport()), ANY_NONBLANK_VALUE, ANY_NONBLANK_VALUE);
});
}
}