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Merge pull request #2 from ebremer/develop
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Merge latest development - OpenID Connect added to SPARQL Endpoint
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@ebremer
ebremer authored Apr 6, 2023
2 parents bdb5b01 + 62a5f14 commit a7d1123
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Showing 70 changed files with 3,962 additions and 571 deletions.
72 changes: 36 additions & 36 deletions dependency-reduced-pom.xml
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Expand Up @@ -10,7 +10,7 @@
<groupId>com.ebremer</groupId>
<artifactId>Halcyon</artifactId>
<name>Halcyon</name>
<version>0.0.0</version>
<version>0.1.0</version>
<description>A whole slide image annotation, management, and visualization system</description>
<issueManagement>
<system>github</system>
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<plugins>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
<executions>
<execution>
<phase>package</phase>
Expand All @@ -368,43 +367,9 @@
<mainClass>com.ebremer.halcyon.converters.NS2OA</mainClass>
</transformer>
</transformers>
<keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
<createDependencyReducedPom>true</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>2.6.13</version>
<scope>compile</scope>
</dependency>
</dependencies>
<configuration>
<keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
<createDependencyReducedPom>true</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</plugin>
</plugins>
</build>
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<plugins>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
<executions>
<execution>
<phase>package</phase>
Expand All @@ -480,9 +446,43 @@
<mainClass>com.ebremer.halcyon.converters.Ingest</mainClass>
</transformer>
</transformers>
<keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
<createDependencyReducedPom>true</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</execution>
</executions>
<dependencies>
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-maven-plugin</artifactId>
<version>2.6.13</version>
<scope>compile</scope>
</dependency>
</dependencies>
<configuration>
<keepDependenciesWithProvidedScope>true</keepDependenciesWithProvidedScope>
<createDependencyReducedPom>true</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
</configuration>
</plugin>
</plugins>
</build>
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121 changes: 111 additions & 10 deletions pom.xml
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Expand Up @@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>com.ebremer</groupId>
<artifactId>Halcyon</artifactId>
<version>0.0.0</version>
<version>0.1.0</version>
<packaging>jar</packaging>
<name>Halcyon</name>
<description>A whole slide image annotation, management, and visualization system</description>
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<commons-pool2.ver>2.11.1</commons-pool2.ver>
<jakarta.json.version>2.0.1</jakarta.json.version>
<titanium-json-ld.ver>1.3.0</titanium-json-ld.ver>
<dcm4che.ver>5.29.1</dcm4che.ver>
<dcm4che.ver>5.29.2</dcm4che.ver>
<resteasy.version>4.7.4.Final</resteasy.version>
<infinispan.version>13.0.12.Final</infinispan.version>
<jgroups.version>4.2.21.Final</jgroups.version>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.1.0</version>
<version>3.2.1</version>
<configuration>
<rules><dependencyConvergence/></rules>
</configuration>
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<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.1.0</version>
<version>3.2.1</version>
<configuration>
<rules><dependencyConvergence/></rules>
</configuration>
</plugin>
<plugin>
<groupId>org.springframework.experimental</groupId>
<artifactId>spring-aot-maven-plugin</artifactId>
<version>0.12.1</version>
<version>0.12.2</version>
<executions>
<execution>
<id>generate</id>
Expand All @@ -305,7 +305,7 @@
<plugin>
<groupId>org.graalvm.buildtools</groupId>
<artifactId>native-maven-plugin</artifactId>
<version>0.9.13</version>
<version>0.9.20</version>
<extensions>true</extensions>
<executions>
<execution>
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<dependency>
<groupId>org.springframework.experimental</groupId>
<artifactId>spring-native</artifactId>
<version>0.12.1</version>
<version>0.12.2</version>
</dependency>
</dependencies>
</profile>
Expand All @@ -386,7 +386,7 @@
<plugin>
<groupId>org.graalvm.buildtools</groupId>
<artifactId>native-maven-plugin</artifactId>
<version>0.9.19</version>
<version>0.9.20</version>
<extensions>true</extensions>
<executions>
<execution>
Expand Down Expand Up @@ -661,13 +661,12 @@
<version>${jena.ver}</version>
<type>jar</type>
</dependency>
<!--
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-querybuilder</artifactId>
<version>${jena.ver}</version>
<type>jar</type>
</dependency>-->
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-permissions</artifactId>
Expand All @@ -685,6 +684,12 @@
<artifactId>jena-fuseki-main</artifactId>
<version>${jena.ver}</version>
</dependency>
<!--
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-fuseki-fulljar</artifactId>
<version>${jena.ver}</version>
</dependency>-->
<!-- OTHER DEPENDENCIES -->
<dependency>
<groupId>com.github.davidmoten</groupId>
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<artifactId>BeakGraph</artifactId>
<version>0.0.0</version>
</dependency>
<!-- DICOM DCM4CHEE
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-core</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-json</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-dict</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che.tool</groupId>
<artifactId>dcm4che-tool-common</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che.tool</groupId>
<artifactId>dcm4che-tool-dcm2jpg</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-imageio</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-imageio-opencv</artifactId>
<version>${dcm4che.ver}</version>
</dependency>
<dependency>
<groupId>org.dcm4che</groupId>
<artifactId>dcm4che-image</artifactId>
<version>${dcm4che.ver}</version>
</dependency> -->
<!-- Shiro -->
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-core</artifactId>
<version>1.11.0</version>
</dependency>
<dependency>
<groupId>org.apache.shiro</groupId>
<artifactId>shiro-web</artifactId>
<version>1.11.0</version>
</dependency>
<!--
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.26</version>
<type>jar</type>
</dependency>
-->
<dependency>
<groupId>com.jcabi</groupId>
<artifactId>jcabi-aspects</artifactId>
<version>0.24.1</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>org.apache.jena</groupId>
<artifactId>jena-tdb</artifactId>
<version>${jena.ver}</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-api</artifactId>
<version>0.11.5</version>
<type>jar</type>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-impl</artifactId>
<version>0.11.5</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>io.jsonwebtoken</groupId>
<artifactId>jjwt-jackson</artifactId>
<version>0.11.5</version>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
<version>1.18.26</version>
<type>jar</type>
</dependency>
</dependencies>
<pluginRepositories>
<pluginRepository>
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