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Merged
mlm483 merged 17 commits into from
Apr 30, 2025
Merged

merge release/1.1 into develop #461

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88640ec
Merge pull request #453 from Breeding-Insight/bug/BI-2594
nickpalladino Apr 9, 2025
c643ea0
[autocommit] bumping build number
rob-ouser-bi Apr 9, 2025
1062f71
[BI-2595] - added logging
mlm483 Apr 15, 2025
c2698fe
Merge pull request #455 from Breeding-Insight/logging/BI-2595
mlm483 Apr 15, 2025
7f081b6
[autocommit] bumping build number
rob-ouser-bi Apr 15, 2025
1bdd132
[BI-2595] - reverted dependency changes
mlm483 Apr 18, 2025
fa35140
Merge pull request #457 from Breeding-Insight/bug/BI-2595
mlm483 Apr 23, 2025
baa7cc0
[autocommit] bumping build number
rob-ouser-bi Apr 23, 2025
88d42cd
[REVERT ME] - temporary test configuration change
mlm483 Apr 24, 2025
d3fd922
[autocommit] bumping build number
rob-ouser-bi Apr 24, 2025
a05d1e1
[BI-2608] Changed column-name from 'Long' to 'Elevation' in error mes…
davedrp Apr 23, 2025
d50dc65
Merge pull request #460 from Breeding-Insight/bug/BI-2608
davedrp Apr 29, 2025
f5d06b4
[autocommit] bumping build number
rob-ouser-bi Apr 29, 2025
c6d599d
Update src/test/java/org/breedinginsight/BrAPITest.java
mlm483 Apr 30, 2025
74201d7
[autocommit] bumping build number
rob-ouser-bi Apr 30, 2025
6904ba5
Merge branch 'develop' into release/1.1
mlm483 Apr 30, 2025
b9b0cfe
[autocommit] bumping build number
rob-ouser-bi Apr 30, 2025
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222 changes: 122 additions & 100 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -90,9 +90,11 @@
<okhttp.version>4.9.3</okhttp.version>
<mockito.version>4.3.1</mockito.version>
<brapi-java-client.version>2.1-SNAPSHOT</brapi-java-client.version>
<tika-app.version>2.9.2</tika-app.version>
<!-- Hard-coded version of transitive dependency commons compress seems to be needed. -->
<commons-compress.version>1.26.1</commons-compress.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>
<javaxmail.version>1.6.2</javaxmail.version>
<st4.version>4.3.1</st4.version>
<tablesaw.version>1.0.0-SNAPSHOT</tablesaw.version>
Expand Down Expand Up @@ -377,14 +379,34 @@
<version>${brapi-java-client.version}</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-app</artifactId>
<version>${tika-app.version}</version>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>${apache-commons-csv.version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>${apache-poi.version}</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>${apache-poi-ooxml.version}</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-compress</artifactId>
<version>${commons-compress.version}</version>
<artifactId>commons-lang3</artifactId>
<version>${apache-commons-lang.version}</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>${commons-io.version}</version>
</dependency>
<dependency>
<groupId>org.apache.tika</groupId>
<artifactId>tika-app</artifactId>
<version>${tika-app.version}</version>
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
Expand Down Expand Up @@ -468,7 +490,7 @@
<goal>shade</goal>
</goals>
<configuration>
<filters>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
Expand All @@ -477,9 +499,9 @@
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<transformers>
</filters>

<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
<mainClass>${exec.mainClass}</mainClass>
</transformer>
Expand Down Expand Up @@ -514,98 +536,98 @@
<target>${maven.compiler.target}</target>
</configuration>
</plugin>
<plugin>
<groupId>org.jooq</groupId>
<artifactId>jooq-codegen-maven</artifactId>
<version>${jooq.version}</version>
<executions>
<execution>
<goals>
<goal>generate</goal>
</goals>
</execution>
</executions>
<plugin>
<groupId>org.jooq</groupId>
<artifactId>jooq-codegen-maven</artifactId>
<version>${jooq.version}</version>
<executions>
<execution>
<goals>
<goal>generate</goal>
</goals>
</execution>
</executions>

<configuration>
<jdbc>
<driver>org.postgresql.Driver</driver>
<url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
<user>${DB_USER}</user>
<password>${DB_PASSWORD}</password>
</jdbc>
<generator>
<name>org.breedinginsight.generation.JooqDaoGenerator</name>
<database>
<name>org.jooq.meta.postgres.PostgresDatabase</name>
<includes>.*</includes>
<inputSchema>public</inputSchema>
<includeTables>true</includeTables>
<includeUDTs>true</includeUDTs>
<includeRoutines>false</includeRoutines>
<includePrimaryKeys>true</includePrimaryKeys>
<includeUniqueKeys>true</includeUniqueKeys>
<includeForeignKeys>true</includeForeignKeys>
<includeCheckConstraints>true</includeCheckConstraints>
<includeIndexes>false</includeIndexes>
<excludes>
flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys
</excludes>
</database>

<configuration>
<jdbc>
<driver>org.postgresql.Driver</driver>
<strategy>
<matchers>
<tables>
<table>
<pojoClass>
<transform>PASCAL</transform>
<expression>$0_ENTITY</expression>
</pojoClass>
<tableClass>
<transform>PASCAL</transform>
<expression>$0_TABLE</expression>
</tableClass>
</table>
</tables>
</matchers>
</strategy>

<target>
<packageName>org.breedinginsight.dao.db</packageName>
<directory>target/generated-sources/jooq</directory>
</target>
<generate>
<pojos>true</pojos>
<daos>true</daos>
<fluentSetters>false</fluentSetters>
<javaTimeTypes>true</javaTimeTypes>
</generate>
</generator>
</configuration>
<dependencies>
<dependency>
<groupId>org.breedinginsight</groupId>
<artifactId>bi-jooq-codegen</artifactId>
<version>${jooq.version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-maven-plugin</artifactId>
<version>${flyway.version}</version>
<configuration>
<url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
<user>${DB_USER}</user>
<password>${DB_PASSWORD}</password>
</jdbc>
<generator>
<name>org.breedinginsight.generation.JooqDaoGenerator</name>
<database>
<name>org.jooq.meta.postgres.PostgresDatabase</name>
<includes>.*</includes>
<inputSchema>public</inputSchema>
<includeTables>true</includeTables>
<includeUDTs>true</includeUDTs>
<includeRoutines>false</includeRoutines>
<includePrimaryKeys>true</includePrimaryKeys>
<includeUniqueKeys>true</includeUniqueKeys>
<includeForeignKeys>true</includeForeignKeys>
<includeCheckConstraints>true</includeCheckConstraints>
<includeIndexes>false</includeIndexes>
<excludes>
flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys
</excludes>
</database>

<strategy>
<matchers>
<tables>
<table>
<pojoClass>
<transform>PASCAL</transform>
<expression>$0_ENTITY</expression>
</pojoClass>
<tableClass>
<transform>PASCAL</transform>
<expression>$0_TABLE</expression>
</tableClass>
</table>
</tables>
</matchers>
</strategy>

<target>
<packageName>org.breedinginsight.dao.db</packageName>
<directory>target/generated-sources/jooq</directory>
</target>
<generate>
<pojos>true</pojos>
<daos>true</daos>
<fluentSetters>false</fluentSetters>
<javaTimeTypes>true</javaTimeTypes>
</generate>
</generator>
</configuration>
<dependencies>
<dependency>
<groupId>org.breedinginsight</groupId>
<artifactId>bi-jooq-codegen</artifactId>
<version>${jooq.version}</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.flywaydb</groupId>
<artifactId>flyway-maven-plugin</artifactId>
<version>${flyway.version}</version>
<configuration>
<url>jdbc:postgresql://${DB_SERVER}/${DB_NAME}</url>
<user>${DB_USER}</user>
<password>${DB_PASSWORD}</password>
</configuration>
<dependencies>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgres.version}</version>
</dependency>
</dependencies>
</plugin>
</configuration>
<dependencies>
<dependency>
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
<version>${postgres.version}</version>
</dependency>
</dependencies>
</plugin>
</plugins>
<pluginManagement>
<plugins>
Expand Down
2 changes: 1 addition & 1 deletion ...ervices/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java
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Original file line number Diff line number Diff line change
Expand Up @@ -363,7 +363,7 @@ private void validateGeoCoordinates(ValidationErrors validationErrors, int rowNu
}

if (elevationBadValue) {
ExperimentUtilities.addRowError(ExperimentObservation.Columns.LONG, "Invalid Elevation value (numerals expected)", validationErrors, rowNum);
ExperimentUtilities.addRowError(ExperimentObservation.Columns.ELEVATION, "Invalid Elevation value (numerals expected)", validationErrors, rowNum);
}

}
Expand Down
2 changes: 2 additions & 0 deletions src/main/java/org/breedinginsight/services/UserService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -390,6 +390,8 @@ private void sendAccountSignUpEmail(BiUserEntity user, SignedJWT jwtToken) {
String filledBody = emailTemplate.render();
String subject = "Activate DeltaBreed Account";

log.debug(filledBody);

// Send email
emailUtil.sendEmail(user.getEmail(), subject, filledBody);
}
Expand Down
13 changes: 11 additions & 2 deletions src/main/java/org/breedinginsight/utilities/email/EmailUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@

import io.micronaut.context.annotation.Property;
import io.micronaut.http.server.exceptions.HttpServerException;
import lombok.extern.slf4j.Slf4j;
import org.apache.commons.lang3.StringUtils;

import javax.inject.Singleton;
Expand All @@ -29,6 +30,7 @@
import java.util.Date;
import java.util.Properties;

@Slf4j
@Singleton
public class EmailUtil {

Expand Down Expand Up @@ -66,6 +68,8 @@ protected PasswordAuthentication getPasswordAuthentication() {
public void sendEmail(String toEmail, String subject, String body){
try
{
log.debug("Sending email to: " + toEmail + " from: " + fromEmail + " with subject: " + subject);

Session session = getSmtpHost();
MimeMessage msg = new MimeMessage(session);
//set message headers
Expand All @@ -83,11 +87,16 @@ public void sendEmail(String toEmail, String subject, String body){

msg.setRecipients(Message.RecipientType.TO, InternetAddress.parse(toEmail, false));
Transport.send(msg);

log.debug("Email sent to: " + toEmail + " from: " + fromEmail + " with subject: " + subject);
}
catch (UnsupportedEncodingException | MessagingException e) {
catch (UnsupportedEncodingException e) {
log.debug("UnsupportedEncodingException " + e.getMessage());
throw new HttpServerException(e.getMessage());
} catch (MessagingException e) {
log.debug("MessagingException " + e.getMessage());
throw new HttpServerException(e.getMessage());
}
}


}
4 changes: 2 additions & 2 deletions src/main/resources/version.properties
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,6 @@
# limitations under the License.
#

version=v1.1.0+946
versionInfo=https://github.com/Breeding-Insight/bi-api/commit/f4ff8b366966fd4ccdc98f744709b32cb3176d26

version=v1.1.0+957
versionInfo=https://github.com/Breeding-Insight/bi-api/commit/6904ba563f374f7791fe93689eb324d1d55e9a5f