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Merge branch 'develop' of https://github.com/EMResearch/EMB into suts-for-wm
# Conflicts: # .gitignore
2 parents 3f54e7e + 351d30d commit b3e0a86

40 files changed

Lines changed: 3155 additions & 97 deletions

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‎.gitignore‎

Lines changed: 3 additions & 1 deletion
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@@ -288,4 +288,6 @@ jdk_17_maven/em/embedded/rest/familie-ba-sak/target/
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/jdk_17_maven/em/embedded/grpc/signal-registration/target/
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/jdk_17_maven/em/external/grpc/signal-registration/target/
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/jdk_17_maven/em/external/web/spring-petclinic/target/
291-
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/jdk_8_maven/cs/rest/original/session-service/target/
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/jdk_8_maven/em/embedded/rest/session-service/target/
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/jdk_8_maven/em/external/rest/session-service/target/

‎README.md‎

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@@ -71,6 +71,8 @@ More details (e.g., #LOCs and used databases) on these APIs can be found [in thi
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### REST: Java/Kotlin
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* Session Service (not-known license), [jdk_8_maven/cs/rest/original/session-service](jdk_8_maven/cs/rest/original/session-service), from [https://github.com/cBioPortal/session-service](https://github.com/cBioPortal/session-service)
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* Bibliothek (MIT), [jdk_17_gradle/cs/rest/bibliothek](jdk_17_gradle/cs/rest/bibliothek), from [https://github.com/PaperMC/bibliothek](https://github.com/PaperMC/bibliothek)
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* Reservations API (not-known license), [jdk_11_gradle/cs/rest/reservations-api](jdk_11_gradle/cs/rest/reservations-api), from [https://github.com/cyrilgavala/reservations-api](https://github.com/cyrilgavala/reservations-api)

‎jdk_11_gradle/em/embedded/graphql/patio-api/src/main/java/em/embedded/patio/EmbeddedEvoMasterController.java‎

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@@ -2,24 +2,21 @@
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import io.micronaut.context.ApplicationContext;
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import io.micronaut.runtime.Micronaut;
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import org.evomaster.client.java.controller.AuthUtils;
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import org.evomaster.client.java.controller.EmbeddedSutController;
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import org.evomaster.client.java.controller.InstrumentedSutStarter;
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import org.evomaster.client.java.controller.api.dto.auth.AuthenticationDto;
8-
import org.evomaster.client.java.controller.api.dto.auth.JsonTokenPostLoginDto;
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import org.evomaster.client.java.controller.api.dto.SutInfoDto;
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import org.evomaster.client.java.controller.api.dto.database.schema.DatabaseType;
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import org.evomaster.client.java.sql.DbCleaner;
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import org.evomaster.client.java.sql.SqlScriptRunner;
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import org.evomaster.client.java.sql.SqlScriptRunnerCached;
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import org.evomaster.client.java.controller.internal.SutController;
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import org.evomaster.client.java.sql.DbSpecification;
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import org.evomaster.client.java.controller.problem.GraphQlProblem;
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import org.evomaster.client.java.controller.problem.ProblemInfo;
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import org.testcontainers.containers.GenericContainer;
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import patio.Application;
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21-
import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.sql.Connection;
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import java.sql.DriverManager;
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import java.sql.SQLException;
@@ -157,17 +154,12 @@ public SutInfoDto.OutputFormat getPreferredOutputFormat() {
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@Override
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public List<AuthenticationDto> getInfoForAuthentication() {
159156

160-
JsonTokenPostLoginDto token = new JsonTokenPostLoginDto();
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token.userId = "Stark";
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token.headerPrefix = "JWT ";
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token.endpoint = "/graphql";
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token.jsonPayload = "{\"query\": \"{login(email: \\\"tstark@email.com\\\",password: \\\"avengers\\\"){tokens{authenticationToken}}}\"}";
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token.extractTokenField = "/data/login/tokens/authenticationToken";
166-
167-
AuthenticationDto dto = new AuthenticationDto("Stark");
168-
dto.jsonTokenPostLogin = token;
169-
170-
return List.of(dto);
157+
return List.of(AuthUtils.getForJWT(
158+
"Stark",
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"/graphql",
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"{\"query\": \"{login(email: \\\"tstark@email.com\\\",password: \\\"avengers\\\"){tokens{authenticationToken}}}\"}",
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"/data/login/tokens/authenticationToken"
162+
));
171163
}
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‎jdk_11_gradle/em/embedded/rest/reservations-api/src/main/java/em/embedded/reservationsapi/EmbeddedEvoMasterController.java‎

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@@ -7,10 +7,10 @@
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import com.mongodb.client.MongoDatabase;
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import org.bson.Document;
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import org.bson.types.ObjectId;
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import org.evomaster.client.java.controller.AuthUtils;
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import org.evomaster.client.java.controller.EmbeddedSutController;
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import org.evomaster.client.java.controller.InstrumentedSutStarter;
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import org.evomaster.client.java.controller.api.dto.auth.AuthenticationDto;
13-
import org.evomaster.client.java.controller.api.dto.auth.JsonTokenPostLoginDto;
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import org.evomaster.client.java.controller.api.dto.SutInfoDto;
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import org.evomaster.client.java.sql.DbSpecification;
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import org.evomaster.client.java.controller.problem.ProblemInfo;
@@ -200,36 +200,24 @@ public List<DbSpecification> getDbSpecifications() {
200200
@Override
201201
public List<AuthenticationDto> getInfoForAuthentication() {
202202
return Arrays.asList(
203-
new AuthenticationDto() {{
204-
name = "admin";
205-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
206-
userId = "admin";
207-
endpoint = "/api/user/login";
208-
jsonPayload = "{\"username\":\"admin\", \"password\":\""+rawPassword+"\"}";
209-
extractTokenField = "/accessToken";
210-
headerPrefix = "Bearer ";
211-
}};
212-
}},
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new AuthenticationDto() {{
214-
name = "foo";
215-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
216-
userId = "foo";
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endpoint = "/api/user/login";
218-
jsonPayload = "{\"username\":\"foo\", \"password\":\""+rawPassword+"\"}";
219-
extractTokenField = "/accessToken";
220-
headerPrefix = "Bearer ";
221-
}};
222-
}},
223-
new AuthenticationDto() {{
224-
name = "bar";
225-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
226-
userId = "bar";
227-
endpoint = "/api/user/login";
228-
jsonPayload = "{\"username\":\"bar\", \"password\":\""+rawPassword+"\"}";
229-
extractTokenField = "/accessToken";
230-
headerPrefix = "Bearer ";
231-
}};
232-
}}
203+
AuthUtils.getForJsonTokenBearer(
204+
"admin",
205+
"/api/user/login",
206+
"{\"username\":\"admin\", \"password\":\""+rawPassword+"\"}",
207+
"/accessToken"
208+
),
209+
AuthUtils.getForJsonTokenBearer(
210+
"foo",
211+
"/api/user/login",
212+
"{\"username\":\"foo\", \"password\":\""+rawPassword+"\"}",
213+
"/accessToken"
214+
),
215+
AuthUtils.getForJsonTokenBearer(
216+
"bar",
217+
"/api/user/login",
218+
"{\"username\":\"bar\", \"password\":\""+rawPassword+"\"}",
219+
"/accessToken"
220+
)
233221
);
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}
235223

‎jdk_11_gradle/em/external/graphql/patio-api/src/main/java/em/external/patio/ExternalEvoMasterController.java‎

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@@ -1,21 +1,19 @@
11
package em.external.patio;
22

3+
import org.evomaster.client.java.controller.AuthUtils;
34
import org.evomaster.client.java.controller.ExternalSutController;
45
import org.evomaster.client.java.controller.InstrumentedSutStarter;
56
import org.evomaster.client.java.controller.api.dto.auth.AuthenticationDto;
6-
import org.evomaster.client.java.controller.api.dto.auth.JsonTokenPostLoginDto;
77
import org.evomaster.client.java.controller.api.dto.SutInfoDto;
88
import org.evomaster.client.java.controller.api.dto.database.schema.DatabaseType;
99
import org.evomaster.client.java.sql.DbCleaner;
10-
import org.evomaster.client.java.sql.SqlScriptRunner;
11-
import org.evomaster.client.java.sql.SqlScriptRunnerCached;
10+
1211
import org.evomaster.client.java.sql.DbSpecification;
1312
import org.evomaster.client.java.controller.problem.GraphQlProblem;
1413
import org.evomaster.client.java.controller.problem.ProblemInfo;
1514
import org.testcontainers.containers.GenericContainer;
1615

17-
import java.io.InputStream;
18-
import java.io.InputStreamReader;
16+
1917
import java.sql.Connection;
2018
import java.sql.DriverManager;
2119
import java.sql.SQLException;
@@ -219,17 +217,12 @@ public SutInfoDto.OutputFormat getPreferredOutputFormat() {
219217
@Override
220218
public List<AuthenticationDto> getInfoForAuthentication() {
221219

222-
JsonTokenPostLoginDto token = new JsonTokenPostLoginDto();
223-
token.userId = "Stark";
224-
token.headerPrefix = "JWT ";
225-
token.endpoint = "/graphql";
226-
token.jsonPayload = "{\"query\": \"{login(email: \\\"tstark@email.com\\\",password: \\\"avengers\\\"){tokens{authenticationToken}}}\"}";
227-
token.extractTokenField = "/data/login/tokens/authenticationToken";
228-
229-
AuthenticationDto dto = new AuthenticationDto("Stark");
230-
dto.jsonTokenPostLogin = token;
231-
232-
return List.of(dto);
220+
return List.of(AuthUtils.getForJWT(
221+
"Stark",
222+
"/graphql",
223+
"{\"query\": \"{login(email: \\\"tstark@email.com\\\",password: \\\"avengers\\\"){tokens{authenticationToken}}}\"}",
224+
"/data/login/tokens/authenticationToken"
225+
));
233226
}
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235228
@Override

‎jdk_11_gradle/em/external/rest/reservations-api/src/main/java/em/external/reservationsapi/ExternalEvoMasterController.java‎

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@@ -7,10 +7,10 @@
77
import com.mongodb.client.MongoDatabase;
88
import org.bson.Document;
99
import org.bson.types.ObjectId;
10+
import org.evomaster.client.java.controller.AuthUtils;
1011
import org.evomaster.client.java.controller.ExternalSutController;
1112
import org.evomaster.client.java.controller.InstrumentedSutStarter;
1213
import org.evomaster.client.java.controller.api.dto.auth.AuthenticationDto;
13-
import org.evomaster.client.java.controller.api.dto.auth.JsonTokenPostLoginDto;
1414
import org.evomaster.client.java.controller.api.dto.SutInfoDto;
1515
import org.evomaster.client.java.sql.DbSpecification;
1616
import org.evomaster.client.java.controller.problem.ProblemInfo;
@@ -256,36 +256,24 @@ public SutInfoDto.OutputFormat getPreferredOutputFormat() {
256256
public List<AuthenticationDto> getInfoForAuthentication() {
257257

258258
return Arrays.asList(
259-
new AuthenticationDto() {{
260-
name = "admin";
261-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
262-
userId = "admin";
263-
endpoint = "/api/user/login";
264-
jsonPayload = "{\"username\":\"admin\", \"password\":\""+rawPassword+"\"}";
265-
extractTokenField = "/accessToken";
266-
headerPrefix = "Bearer ";
267-
}};
268-
}},
269-
new AuthenticationDto() {{
270-
name = "foo";
271-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
272-
userId = "foo";
273-
endpoint = "/api/user/login";
274-
jsonPayload = "{\"username\":\"foo\", \"password\":\""+rawPassword+"\"}";
275-
extractTokenField = "/accessToken";
276-
headerPrefix = "Bearer ";
277-
}};
278-
}},
279-
new AuthenticationDto() {{
280-
name = "bar";
281-
jsonTokenPostLogin = new JsonTokenPostLoginDto() {{
282-
userId = "bar";
283-
endpoint = "/api/user/login";
284-
jsonPayload = "{\"username\":\"bar\", \"password\":\""+rawPassword+"\"}";
285-
extractTokenField = "/accessToken";
286-
headerPrefix = "Bearer ";
287-
}};
288-
}}
259+
AuthUtils.getForJsonTokenBearer(
260+
"admin",
261+
"/api/user/login",
262+
"{\"username\":\"admin\", \"password\":\""+rawPassword+"\"}",
263+
"/accessToken"
264+
),
265+
AuthUtils.getForJsonTokenBearer(
266+
"foo",
267+
"/api/user/login",
268+
"{\"username\":\"foo\", \"password\":\""+rawPassword+"\"}",
269+
"/accessToken"
270+
),
271+
AuthUtils.getForJsonTokenBearer(
272+
"bar",
273+
"/api/user/login",
274+
"{\"username\":\"bar\", \"password\":\""+rawPassword+"\"}",
275+
"/accessToken"
276+
)
289277
);
290278
}
291279

‎jdk_8_maven/cs/rest/original/pom.xml‎

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1919
<module>catwatch</module>
2020
<module>languagetool</module>
2121
<module>restcountries</module>
22+
<module>session-service</module>
2223
</modules>
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2425

‎jdk_8_maven/cs/rest/original/session-service/Dockerfile‎

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1+
#
2+
# Copyright (c) 2019 The Hyve B.V.
3+
# This code is licensed under the GNU Affero General Public License (AGPL),
4+
# version 3, or (at your option) any later version.
5+
#
6+
7+
FROM maven:3-eclipse-temurin-11 as build
8+
COPY $PWD /session-service
9+
WORKDIR /session-service
10+
RUN mvn package -DskipTests -Dpackaging.type=jar
11+
12+
FROM eclipse-temurin:11
13+
# copy over target/session_service-x.y.z.jar ignore *-model.jar, that jar is
14+
# used by cbioportal/cbioportal to import the models
15+
COPY --from=build /session-service/target/*[0-9].jar /app.war
16+
CMD java ${JAVA_OPTS} -jar /app.war

‎jdk_8_maven/cs/rest/original/session-service/Procfile‎

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1+
web: SERVER_PORT=${PORT} java $JAVA_OPTS -Dspring.data.mongodb.uri=${MONGODB_URI} -jar target/*[0-9].jar

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