From c643ea074447e0d86ac6e2fb965635eb6790b883 Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Wed, 9 Apr 2025 19:53:31 +0000 Subject: [PATCH 01/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index 88a710d18..370a8d713 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+924 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/8c0ed2278a591998781b39c656d22c314c2cf897 +version=v1.1.0+928 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/88640ec738554246f68fdcb78ba1790e046ac9cb From 1062f71cafcc585a8f494df2e91f22701993a7dc Mon Sep 17 00:00:00 2001 From: mlm483 <128052931+mlm483@users.noreply.github.com> Date: Tue, 15 Apr 2025 13:11:31 -0400 Subject: [PATCH 02/12] [BI-2595] - added logging --- .../org/breedinginsight/services/UserService.java | 2 ++ .../breedinginsight/utilities/email/EmailUtil.java | 13 +++++++++++-- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/src/main/java/org/breedinginsight/services/UserService.java b/src/main/java/org/breedinginsight/services/UserService.java index 7502ff8b2..b78fdf8a6 100644 --- a/src/main/java/org/breedinginsight/services/UserService.java +++ b/src/main/java/org/breedinginsight/services/UserService.java @@ -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); } diff --git a/src/main/java/org/breedinginsight/utilities/email/EmailUtil.java b/src/main/java/org/breedinginsight/utilities/email/EmailUtil.java index a839715a1..7aef12550 100644 --- a/src/main/java/org/breedinginsight/utilities/email/EmailUtil.java +++ b/src/main/java/org/breedinginsight/utilities/email/EmailUtil.java @@ -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; @@ -29,6 +30,7 @@ import java.util.Date; import java.util.Properties; +@Slf4j @Singleton public class EmailUtil { @@ -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 @@ -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()); } } - } From 7f081b6def4dd3a122ebce75667569780a8eac11 Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Tue, 15 Apr 2025 17:19:31 +0000 Subject: [PATCH 03/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index 370a8d713..d4a61b089 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+928 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/88640ec738554246f68fdcb78ba1790e046ac9cb +version=v1.1.0+934 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/c2698fe74ca8d93d4cb45d4d0faa91d3efc67840 From 1bdd132bb9240dd9b30f246c2dc213ad90c67b91 Mon Sep 17 00:00:00 2001 From: mlm483 <128052931+mlm483@users.noreply.github.com> Date: Fri, 18 Apr 2025 16:23:01 -0400 Subject: [PATCH 04/12] [BI-2595] - reverted dependency changes --- pom.xml | 222 +++++++++++++++++++++++++++++++------------------------- 1 file changed, 122 insertions(+), 100 deletions(-) diff --git a/pom.xml b/pom.xml index 4280fd0b1..fe89f2ca6 100644 --- a/pom.xml +++ b/pom.xml @@ -90,9 +90,11 @@ 4.9.3 4.3.1 2.1-SNAPSHOT - 2.9.2 - - 1.26.1 + 2.11.0 + 2.2.1 + + 4.1.2 + 4.1.2 1.6.2 4.3.1 1.0.0-SNAPSHOT @@ -377,14 +379,34 @@ ${brapi-java-client.version} - org.apache.tika - tika-app - ${tika-app.version} + org.apache.commons + commons-csv + ${apache-commons-csv.version} + + + org.apache.poi + poi + ${apache-poi.version} + + + org.apache.poi + poi-ooxml + ${apache-poi-ooxml.version} org.apache.commons - commons-compress - ${commons-compress.version} + commons-lang3 + ${apache-commons-lang.version} + + + commons-io + commons-io + ${commons-io.version} + + + org.apache.tika + tika-app + ${tika-app.version} com.sun.mail @@ -468,7 +490,7 @@ shade - + *:* @@ -477,9 +499,9 @@ META-INF/*.RSA - - - + + + ${exec.mainClass} @@ -514,98 +536,98 @@ ${maven.compiler.target} - - org.jooq - jooq-codegen-maven - ${jooq.version} - - - - generate - - - + + org.jooq + jooq-codegen-maven + ${jooq.version} + + + + generate + + + + + + + org.postgresql.Driver + jdbc:postgresql://${DB_SERVER}/${DB_NAME} + ${DB_USER} + ${DB_PASSWORD} + + + org.breedinginsight.generation.JooqDaoGenerator + + org.jooq.meta.postgres.PostgresDatabase + .* + public + true + true + false + true + true + true + true + false + + flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys + + - - - org.postgresql.Driver + + + + + + PASCAL + $0_ENTITY + + + PASCAL + $0_TABLE + +
+ + + + + + org.breedinginsight.dao.db + target/generated-sources/jooq + + + true + true + false + true + + + + + + org.breedinginsight + bi-jooq-codegen + ${jooq.version} + + + + + org.flywaydb + flyway-maven-plugin + ${flyway.version} + jdbc:postgresql://${DB_SERVER}/${DB_NAME} ${DB_USER} ${DB_PASSWORD} - - - org.breedinginsight.generation.JooqDaoGenerator - - org.jooq.meta.postgres.PostgresDatabase - .* - public - true - true - false - true - true - true - true - false - - flyway_schema_history|base_entity|base_track_edit_entity|spatial_ref_sys - - - - - - - - - PASCAL - $0_ENTITY - - - PASCAL - $0_TABLE - -
- - - - - - org.breedinginsight.dao.db - target/generated-sources/jooq - - - true - true - false - true - - - - - - org.breedinginsight - bi-jooq-codegen - ${jooq.version} - - - - - org.flywaydb - flyway-maven-plugin - ${flyway.version} - - jdbc:postgresql://${DB_SERVER}/${DB_NAME} - ${DB_USER} - ${DB_PASSWORD} - - - - org.postgresql - postgresql - ${postgres.version} - - - + + + + org.postgresql + postgresql + ${postgres.version} + + + From baa7cc0af7f96f3bc759e895aa009de4813a34de Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Wed, 23 Apr 2025 21:31:54 +0000 Subject: [PATCH 05/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index d4a61b089..dda4d99a7 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+934 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/c2698fe74ca8d93d4cb45d4d0faa91d3efc67840 +version=v1.1.0+940 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/fa351401536751d7103ddf509e4d311ca34994bf From 88d42cdda9e212e689e1ad348a07e903706d502d Mon Sep 17 00:00:00 2001 From: mlm483 <128052931+mlm483@users.noreply.github.com> Date: Thu, 24 Apr 2025 14:58:40 -0400 Subject: [PATCH 06/12] [REVERT ME] - temporary test configuration change --- src/test/java/org/breedinginsight/BrAPITest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/org/breedinginsight/BrAPITest.java b/src/test/java/org/breedinginsight/BrAPITest.java index 8c5c35bad..e6e6072d6 100644 --- a/src/test/java/org/breedinginsight/BrAPITest.java +++ b/src/test/java/org/breedinginsight/BrAPITest.java @@ -49,7 +49,7 @@ public class BrAPITest extends DatabaseTest { public BrAPITest() { super(); - brapiContainer = new GenericContainer<>("breedinginsight/brapi-java-server:develop") + brapiContainer = new GenericContainer<>("breedinginsight/brapi-java-server:rc") .withNetwork(super.getNetwork()) .withImagePullPolicy(PullPolicy.ageBased(Duration.ofMinutes(60))) .withExposedPorts(8080) From d3fd92241b5b992c94cf5982f6b16f730154d3ae Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Thu, 24 Apr 2025 19:37:30 +0000 Subject: [PATCH 07/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index dda4d99a7..99563b0b5 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+940 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/fa351401536751d7103ddf509e4d311ca34994bf +version=v1.1.0+943 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/88d42cdda9e212e689e1ad348a07e903706d502d From a05d1e1a83381577986ab7c5b904b4c7d39e4ffa Mon Sep 17 00:00:00 2001 From: David Randolph Phillips Date: Wed, 23 Apr 2025 16:00:22 -0400 Subject: [PATCH 08/12] [BI-2608] Changed column-name from 'Long' to 'Elevation' in error message --- .../create/workflow/steps/ValidatePendingImportObjectsStep.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java b/src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java index b1391c483..ee570c238 100644 --- a/src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java +++ b/src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/workflow/steps/ValidatePendingImportObjectsStep.java @@ -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); } } From f5d06b40cc7770fb121fdec88de024558ecc2a92 Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Tue, 29 Apr 2025 17:35:06 +0000 Subject: [PATCH 09/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index 99563b0b5..3e26e3f83 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+943 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/88d42cdda9e212e689e1ad348a07e903706d502d +version=v1.1.0+948 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/d50dc656df8d551465d34fed891b89709dcb365c From c6d599d8ea6cdd3f75f60f329715f82cbe08b6f5 Mon Sep 17 00:00:00 2001 From: mlm483 <128052931+mlm483@users.noreply.github.com> Date: Wed, 30 Apr 2025 16:07:32 -0400 Subject: [PATCH 10/12] Update src/test/java/org/breedinginsight/BrAPITest.java --- src/test/java/org/breedinginsight/BrAPITest.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/test/java/org/breedinginsight/BrAPITest.java b/src/test/java/org/breedinginsight/BrAPITest.java index e6e6072d6..8c5c35bad 100644 --- a/src/test/java/org/breedinginsight/BrAPITest.java +++ b/src/test/java/org/breedinginsight/BrAPITest.java @@ -49,7 +49,7 @@ public class BrAPITest extends DatabaseTest { public BrAPITest() { super(); - brapiContainer = new GenericContainer<>("breedinginsight/brapi-java-server:rc") + brapiContainer = new GenericContainer<>("breedinginsight/brapi-java-server:develop") .withNetwork(super.getNetwork()) .withImagePullPolicy(PullPolicy.ageBased(Duration.ofMinutes(60))) .withExposedPorts(8080) From 74201d78bc1d0670fc47d37a9a3b810e5e4489d1 Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Wed, 30 Apr 2025 20:07:46 +0000 Subject: [PATCH 11/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index 3e26e3f83..c67efc6c8 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+948 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/d50dc656df8d551465d34fed891b89709dcb365c +version=v1.1.0+955 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/c6d599d8ea6cdd3f75f60f329715f82cbe08b6f5 From b9b0cfe507a150476d7783e8cf7267f00dd7c416 Mon Sep 17 00:00:00 2001 From: rob-ouser-bi Date: Wed, 30 Apr 2025 20:10:35 +0000 Subject: [PATCH 12/12] [autocommit] bumping build number --- src/main/resources/version.properties | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/resources/version.properties b/src/main/resources/version.properties index c67efc6c8..8267797c6 100644 --- a/src/main/resources/version.properties +++ b/src/main/resources/version.properties @@ -15,5 +15,5 @@ # -version=v1.1.0+955 -versionInfo=https://github.com/Breeding-Insight/bi-api/commit/c6d599d8ea6cdd3f75f60f329715f82cbe08b6f5 +version=v1.1.0+957 +versionInfo=https://github.com/Breeding-Insight/bi-api/commit/6904ba563f374f7791fe93689eb324d1d55e9a5f