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#374 - Extend api to save and load cohort and dataselection #459

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#374 - Extend api to save and load cohort and dataselection #459

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2428a6f
#374 - Extend API to save and load cohort and dataselection
michael-82 Feb 18, 2025
acb10cc
#374 - Extend API to save and load cohort and dataselection
michael-82 Feb 28, 2025
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8 changes: 4 additions & 4 deletions .github/scripts/post-elastic-test-queries.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ access_token="$(curl -s --request POST \
--data password=testpassword \
--data scope=openid | jq '.access_token' | tr -d '"')"

response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/terminology/entry/search?searchterm=Blutdruck")
response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v5/terminology/entry/search?searchterm=Blutdruck")
http_code="${response: -3}"
json_body=$(cat response_body)

Expand All @@ -63,7 +63,7 @@ else
exit 1
fi

response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/terminology/entry/$onto_example_id")
response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v5/terminology/entry/$onto_example_id")
http_code="${response: -3}"
json_body=$(cat response_body)

Expand All @@ -79,7 +79,7 @@ else
exit 1
fi

response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry/search?searchterm=Vectorcardiogram")
response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v5/codeable-concept/entry/search?searchterm=Vectorcardiogram")
http_code="${response: -3}"
json_body=$(cat response_body)

Expand All @@ -95,7 +95,7 @@ else
exit 1
fi

response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v4/codeable-concept/entry?ids=$cc_example_id")
response=$(curl -s -w "%{http_code}" --header "Authorization: Bearer $access_token" -o response_body "http://localhost:8091/api/v5/codeable-concept/entry?ids=$cc_example_id")
http_code="${response: -3}"
json_body=$(cat response_body)

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2 changes: 1 addition & 1 deletion .github/scripts/post-test-query.sh
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Expand Up @@ -10,7 +10,7 @@ access_token="$(curl -s --request POST \
--data scope=openid | jq '.access_token' | tr -d '"')"

response=$(curl -s -i \
--url http://localhost:8091/api/v4/query \
--url http://localhost:8091/api/v5/query/feasibility \
--header "Authorization: Bearer $access_token" \
--header 'Content-Type: application/json' \
--data '{
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -148,7 +148,7 @@ jobs:
needs: tests
runs-on: ubuntu-latest
env:
ONTOLOGY_GIT_TAG: v3.0.2-alpha.5
ONTOLOGY_GIT_TAG: v3.1.0
ELASTIC_HOST: http://localhost:9200
ELASTIC_FILEPATH: https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/download/TAGPLACEHOLDER/
ELASTIC_FILENAME: elastic.zip
Expand Down
7 changes: 7 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

## [UNRELEASED] - 2025-mm-dd

### Changed
- REST API changed to v5
### Removed
- Query Templates have been removed

## [6.1.0] - 2025-02-14

- Based on ontology **[v3.1.0](https://github.com/medizininformatik-initiative/fhir-ontology-generator/releases/tag/v3.1.0)**
Expand Down
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -12,7 +12,7 @@

<groupId>de.medizininformatik-initiative</groupId>
<artifactId>DataportalBackend</artifactId>
<version>6.2.0-SNAPSHOT</version>
<version>7.0.0-SNAPSHOT</version>

<name>Dataportal Backend</name>
<description>Backend of the Dataportal</description>
Expand Down
12 changes: 4 additions & 8 deletions src/main/java/de/numcodex/feasibility_gui_backend/config/RateLimitingConfig.java
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@@ -1,18 +1,14 @@
package de.numcodex.feasibility_gui_backend.config;

import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.PATH_API;
import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.PATH_DETAILED_OBFUSCATED_RESULT;
import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.PATH_QUERY;
import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.PATH_ID_MATCHER;
import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.PATH_SUMMARY_RESULT;

import de.numcodex.feasibility_gui_backend.query.ratelimiting.RateLimitingInterceptor;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Lazy;
import org.springframework.stereotype.Component;
import org.springframework.web.servlet.config.annotation.InterceptorRegistry;
import org.springframework.web.servlet.config.annotation.WebMvcConfigurer;

import static de.numcodex.feasibility_gui_backend.config.WebSecurityConfig.*;

@Component
public class RateLimitingConfig implements WebMvcConfigurer {

Expand All @@ -23,7 +19,7 @@ public class RateLimitingConfig implements WebMvcConfigurer {
@Override
public void addInterceptors(InterceptorRegistry registry) {
registry.addInterceptor(interceptor)
.addPathPatterns(PATH_API + PATH_QUERY + PATH_ID_MATCHER + PATH_SUMMARY_RESULT)
.addPathPatterns(PATH_API + PATH_QUERY + PATH_ID_MATCHER + PATH_DETAILED_OBFUSCATED_RESULT);
.addPathPatterns(PATH_API + PATH_QUERY + PATH_FEASIBILITY + PATH_ID_MATCHER + PATH_SUMMARY_RESULT)
.addPathPatterns(PATH_API + PATH_QUERY + PATH_FEASIBILITY + PATH_ID_MATCHER + PATH_DETAILED_OBFUSCATED_RESULT);
}
}
17 changes: 8 additions & 9 deletions src/main/java/de/numcodex/feasibility_gui_backend/config/WebSecurityConfig.java
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Expand Up @@ -37,17 +37,17 @@
public static final String KEY_SPRING_ADDONS_CONFIDENTIAL = "spring-addons-confidential";
public static final String KEY_SPRING_ADDONS_PUBLIC = "spring-addons-public";
public static final String PATH_ACTUATOR_HEALTH = "/actuator/health";
public static final String PATH_API = "/api/v4";
public static final String PATH_API = "/api/v5";
public static final String PATH_QUERY = "/query";
public static final String PATH_DATA = "/data";
public static final String PATH_FEASIBILITY = "/feasibility";
public static final String PATH_ID_MATCHER = "/{id:\\d+}";
public static final String PATH_USER_ID_MATCHER = "/by-user/{id:[\\w-]+}";
public static final String PATH_SAVED = "/saved";
public static final String PATH_CONTENT = "/content";
public static final String PATH_SUMMARY_RESULT = "/summary-result";
public static final String PATH_DETAILED_OBFUSCATED_RESULT = "/detailed-obfuscated-result";
public static final String PATH_DETAILED_RESULT = "/detailed-result";
public static final String PATH_TERMINOLOGY = "/terminology";
public static final String PATH_TEMPLATE = "/template";
public static final String PATH_DSE = "/dse";
public static final String PATH_CODEABLE_CONCEPT = "/codeable-concept";
public static final String PATH_SWAGGER_UI = "/swagger-ui/**";
Expand Down Expand Up @@ -102,12 +102,11 @@

http.authorizeHttpRequests(authorize -> authorize
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_TERMINOLOGY + "/**")).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY)).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_USER_ID_MATCHER)).hasAuthority(keycloakAdminRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_ID_MATCHER + PATH_SAVED)).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_ID_MATCHER + PATH_DETAILED_RESULT)).hasAuthority(keycloakAdminRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_TEMPLATE)).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_TEMPLATE + "/*")).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_DATA)).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_DATA + PATH_USER_ID_MATCHER)).hasAuthority(keycloakAdminRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_DATA + "/*")).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_FEASIBILITY)).hasAuthority(keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_QUERY + PATH_FEASIBILITY + PATH_ID_MATCHER + PATH_DETAILED_RESULT)).hasAuthority(keycloakAdminRole)

Check warning on line 109 in src/main/java/de/numcodex/feasibility_gui_backend/config/WebSecurityConfig.java

View check run for this annotation

Codecov / codecov/patch

src/main/java/de/numcodex/feasibility_gui_backend/config/WebSecurityConfig.java#L105-L109 

Added lines #L105 - L109 were not covered by tests
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + "/**")).hasAnyAuthority(keycloakAdminRole, keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_DSE + "/**")).hasAnyAuthority(keycloakAdminRole, keycloakAllowedRole)
.requestMatchers(new MvcRequestMatcher(introspector, PATH_API + PATH_CODEABLE_CONCEPT + "/**")).hasAnyAuthority(keycloakAdminRole, keycloakAllowedRole)
Expand Down
2 changes: 1 addition & 1 deletion ...gui_backend/dse/v4/DseRestController.java → ...gui_backend/dse/v5/DseRestController.java
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@@ -1,4 +1,4 @@
package de.numcodex.feasibility_gui_backend.dse.v4;
package de.numcodex.feasibility_gui_backend.dse.v5;

import de.numcodex.feasibility_gui_backend.dse.DseService;
import de.numcodex.feasibility_gui_backend.dse.api.DseProfile;
Expand Down
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