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[BI-693] Upgrade micronaut to 2.5.13 #146

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Merged
ctucker3 merged 30 commits into from
Jun 3, 2022
Merged

[BI-693] Upgrade micronaut to 2.5.13 #146

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0049db7
Upgrade to micronaut 1.3.7
Jan 12, 2022
f934b1d
micronaut update 2.0.0: app working. bearer token removed. some tests…
Jan 13, 2022
323bfe3
micronaut update 2.0.0: bearer token removed
Jan 13, 2022
affb0ce
micronaut update 2.0.0: Add bearer token back in
Jan 13, 2022
3bb6709
micronaut update 2.0.0: Tests are working.
Jan 13, 2022
2afb97a
micronaut update 2.1.0: flyway is broken
Jan 18, 2022
99c1e92
fix tests after rebasing on develop
Jan 31, 2022
74bd361
micronaut upgrade: version 2.1.0 tests pass
Jan 31, 2022
413af95
micronuat upgrade: fix 2.2.0 @MicronautTest import
Feb 2, 2022
af10a3e
micronaut upgrade: fix 2.2.0 migrations reference
Feb 2, 2022
cac4167
micronuat upgrade: fix more 2.2.0 @MicronautTest imports
Feb 2, 2022
e116c59
micronaut upgrade: fix trait dao temp table to list contains
Feb 2, 2022
17f8432
micronaut upgrade: 2.2.0 fix jackson deserialization of @SuperBuilder
Feb 2, 2022
2595226
micronaut upgrade: 2.2.0 all tests pass
Feb 2, 2022
9c9ba45
micronaut upgrade: 2.3.0 tests pass
Feb 2, 2022
207b4fb
micronaut upgrade: 2.4.0 remove clashing and unnecessary httpstatusex…
Feb 3, 2022
27f1b43
micronaut upgrade: 2.4.0 all tests pass
Feb 3, 2022
9b44e6e
micronaut upgrade: 2.5.0 all tests pass
Feb 3, 2022
a293fc1
micronaut upgrade: 2.5.13 all tests pass
Feb 3, 2022
e8cc27b
library upgrades: batch 1 all tests pass
Feb 3, 2022
2d1fb05
library upgrade: batch 2 all tests pass
Feb 3, 2022
dfee51f
library upgrades: batch 3 all tests pass, added fixes
Feb 3, 2022
7777a14
library upgrades: batch 4 all tests pass
Feb 3, 2022
aa45418
library upgrades: batch 5 all tests pass
Feb 3, 2022
f3d9cfd
library upgrades: reorder package versions for clarity
Feb 3, 2022
7c32235
micronaut upgrade: remove working files
Feb 7, 2022
25b479c
micronaut upgrade: fix tests
Feb 7, 2022
ce92f21
micronaut upgrade: remove broken import
Apr 19, 2022
477ea09
micronaut upgrade: remove unused imports
May 26, 2022
6950a80
micronaut upgrade: clean up test comments
May 26, 2022
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87 changes: 51 additions & 36 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -52,8 +52,7 @@
</developers>

<properties>
<micronaut.version>1.3.3</micronaut.version>
<micronaut.security.version>1.3.2</micronaut.security.version>
<micronaut.version>2.5.13</micronaut.version>
<jdk.version>13</jdk.version>
<maven.compiler.target>${jdk.version}</maven.compiler.target>
<maven.compiler.source>${jdk.version}</maven.compiler.source>
Expand All @@ -64,17 +63,31 @@
<maven-failsafe-plugin.version>2.19.1</maven-failsafe-plugin.version>
<jvm.options>--enable-preview</jvm.options>

<jooq.version>3.12.3</jooq.version>
<postgres.version>42.2.6</postgres.version>
<logback.version>1.2.3</logback.version>
<lombok.version>1.18.16</lombok.version>
<gson.version>2.8.6</gson.version>
<spock.version>1.1.2</spock.version>
<jooq.version>3.16.3</jooq.version>
<postgres.version>42.3.2</postgres.version>
<logback.version>1.2.10</logback.version>
<lombok.version>1.18.22</lombok.version>
<gson.version>2.8.9</gson.version>
<geojson-jackson.version>1.14</geojson-jackson.version>
<apache-commons-csv.version>1.8</apache-commons-csv.version>
<apache-commons-csv.version>1.9.0</apache-commons-csv.version>
<apache-commons-lang.version>3.12.0</apache-commons-lang.version>
<testcontainers.version>1.16.3</testcontainers.version>
<!-- Version of flyway dependent on version of micronaut -->
<flyway.version>7.7.3</flyway.version>
<guava.version>31.0.1-jre</guava.version>
<okhttp.version>4.9.3</okhttp.version>
<mockito.version>4.3.1</mockito.version>
<brapi-java-client.version>2.0.2</brapi-java-client.version>
<commons-io.version>2.11.0</commons-io.version>
<tika-app.version>2.2.1</tika-app.version>
<!-- Version of apache-poi depends on version of tika. Tika uses these. -->
<apache-poi.version>4.1.2</apache-poi.version>
<apache-poi-ooxml.version>4.1.2</apache-poi-ooxml.version>
<apache-commons-lang.version>3.10</apache-commons-lang.version>
<javaxmail.version>1.6.2</javaxmail.version>
<st4.version>4.3.1</st4.version>
<tablesaw.version>0.42.0</tablesaw.version>
<alphanumeric-comparator.version>1.4.1</alphanumeric-comparator.version>
<cloning.version>1.10.3</cloning.version>
</properties>

<profiles>
Expand Down Expand Up @@ -164,7 +177,7 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.configuration</groupId>
<groupId>io.micronaut.sql</groupId>
<artifactId>micronaut-jdbc-hikari</artifactId>
<scope>runtime</scope>
</dependency>
Expand All @@ -174,29 +187,26 @@
<scope>compile</scope>
</dependency>
<dependency>
<groupId>io.micronaut.configuration</groupId>
<groupId>io.micronaut.sql</groupId>
<artifactId>micronaut-jooq</artifactId>
<scope>compile</scope>
</dependency>

<dependency>
<groupId>io.micronaut</groupId>
<groupId>io.micronaut.security</groupId>
<artifactId>micronaut-security</artifactId>
<version>${micronaut.security.version}</version>
<scope>compile</scope>
</dependency>

<dependency>
<groupId>io.micronaut</groupId>
<groupId>io.micronaut.security</groupId>
<artifactId>micronaut-security-jwt</artifactId>
<version>${micronaut.security.version}</version>
<scope>compile</scope>
</dependency>

<dependency>
<groupId>io.micronaut.configuration</groupId>
<groupId>io.micronaut.security</groupId>
<artifactId>micronaut-security-oauth2</artifactId>
<version>${micronaut.security.version}</version>
<scope>compile</scope>
</dependency>

Expand Down Expand Up @@ -229,14 +239,14 @@
</dependency>

<dependency>
<groupId>io.micronaut.configuration</groupId>
<groupId>io.micronaut.flyway</groupId>
<artifactId>micronaut-flyway</artifactId>
</dependency>

<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>28.1-jre</version>
<version>${guava.version}</version>
</dependency>

<dependency>
Expand All @@ -248,12 +258,12 @@
<dependency>
<groupId>com.squareup.okhttp3</groupId>
<artifactId>okhttp</artifactId>
<version>4.2.2</version>
<version>${okhttp.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
<version>${logback.version}</version>
<scope>runtime</scope>
</dependency>
<dependency>
Expand All @@ -276,6 +286,11 @@
<artifactId>micronaut-test-spock</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-core</artifactId>
<version>${flyway.version}</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-inline</artifactId>
Expand All @@ -296,7 +311,7 @@
<dependency>
<groupId>org.testcontainers</groupId>
<artifactId>testcontainers</artifactId>
<version>1.15.2</version>
<version>${testcontainers.version}</version>
<scope>test</scope>
</dependency>
<dependency>
Expand All @@ -307,7 +322,7 @@
<dependency>
<groupId>org.brapi</groupId>
<artifactId>brapi-java-client</artifactId>
<version>2.0.2</version>
<version>${brapi-java-client.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
Expand All @@ -332,48 +347,48 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.6</version>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-app</artifactId>
<version>1.24.1</version>
<version>${tika-app.version}</version>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>javax.mail</artifactId>
<version>1.6.2</version>
<version>${javaxmail.version}</version>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>ST4</artifactId>
<version>4.3</version>
<version>${st4.version}</version>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>tech.tablesaw</groupId>
<artifactId>tablesaw-core</artifactId>
<version>0.38.2</version>
<version>${tablesaw.version}</version>
</dependency>
<dependency>
<groupId>tech.tablesaw</groupId>
<artifactId>tablesaw-excel</artifactId>
<version>0.38.2</version>
<version>${tablesaw.version}</version>
</dependency>
<dependency>
<groupId>tech.tablesaw</groupId>
<artifactId>tablesaw-json</artifactId>
<version>0.38.2</version>
<version>${tablesaw.version}</version>
</dependency>
<dependency>
<groupId>se.sawano.java</groupId>
<artifactId>alphanumeric-comparator</artifactId>
<version>1.4.1</version>
<version>${alphanumeric-comparator.version}</version>
</dependency>
<dependency>
<groupId>io.github.kostaskougios</groupId>
<artifactId>cloning</artifactId>
<version>1.10.3</version>
<version>${cloning.version}</version>
</dependency>
</dependencies>
<build>
Expand Down Expand Up @@ -523,14 +538,14 @@
<dependency>
<groupId>org.breedinginsight</groupId>
<artifactId>bi-jooq-codegen</artifactId>
<version>1.0-SNAPSHOT</version>
<version>${jooq.version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-maven-plugin</artifactId>
<version>6.0.0</version>
<version>${flyway.version}</version>
<configuration>
<url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
<user>${DB_USER}</user>
Expand Down Expand Up @@ -560,7 +575,7 @@
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<version>5.1.0</version>
<version>5.7.0</version>
</dependency>
</dependencies>
<configuration>
Expand Down
34 changes: 0 additions & 34 deletions src/main/java/org/breedinginsight/api/auth/ApiAccessRefreshTokenGenerator.java
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