From b791b4380b772b14f5749b9bc77f1ea8e6227d34 Mon Sep 17 00:00:00 2001
From: Igor Pisarev <pisarevi@janelia.hhmi.org>
Date: Fri, 1 May 2020 12:01:48 -0400
Subject: [PATCH 1/3] bump n5 related artifacts

---
 pom.xml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pom.xml b/pom.xml
index a9b9128c..ab155403 100644
--- a/pom.xml
+++ b/pom.xml
@@ -661,11 +661,11 @@
 		<!-- N5 - https://github.com/saalfeldlab/n5 -->
 
 		<imglib2-label-multisets.version>0.9.0</imglib2-label-multisets.version>
-		<n5.version>2.1.4</n5.version>
-		<n5-imglib2.version>3.4.1</n5-imglib2.version>
+		<n5.version>2.2.0</n5.version>
+		<n5-imglib2.version>3.5.0</n5-imglib2.version>
 		<n5-hdf5.version>1.0.4</n5-hdf5.version>
-		<n5-aws-s3.version>3.0.0</n5-aws-s3.version>
-		<n5-google-cloud.version>2.3.1</n5-google-cloud.version>
+		<n5-aws-s3.version>3.1.1</n5-aws-s3.version>
+		<n5-google-cloud.version>3.2.1</n5-google-cloud.version>
 		<n5-viewer_fiji.version>2.2.0</n5-viewer_fiji.version>
 
 		<!--

From 940b5fe5e640b14b946fcdca2967295aa94e6663 Mon Sep 17 00:00:00 2001
From: Igor Pisarev <pisarevi@janelia.hhmi.org>
Date: Fri, 1 May 2020 12:05:54 -0400
Subject: [PATCH 2/3] remove old dependencies of n5-google-cloud that are not
 used anymore

the changes were made in https://github.com/saalfeldlab/n5-google-cloud/pull/11
---
 pom.xml | 22 ++--------------------
 1 file changed, 2 insertions(+), 20 deletions(-)

diff --git a/pom.xml b/pom.xml
index ab155403..14663e1d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -853,11 +853,8 @@
 		<cglib.version>3.3.0</cglib.version>
 
 		<!-- Google Cloud Storage - https://github.com/googleapis/google-cloud-java -->
-		<google-api-services-oauth2.version>v2-rev20190313-1.30.8</google-api-services-oauth2.version>
-		<google-cloud-resourcemanager.version>0.117.1-alpha</google-cloud-resourcemanager.version>
-		<google-cloud-storage.version>1.104.0</google-cloud-storage.version>
-		<google-http-client-jackson2.version>1.34.2</google-http-client-jackson2.version>
-		<google-oauth-client-jetty.version>1.30.5</google-oauth-client-jetty.version>
+		<google-cloud-resourcemanager.version>0.117.2-alpha</google-cloud-resourcemanager.version>
+		<google-cloud-storage.version>1.106.0</google-cloud-storage.version>
 
 		<!-- Gson - https://code.google.com/p/google-gson/ -->
 		<gson.version>2.8.6</gson.version>
@@ -3129,11 +3126,6 @@
 			</dependency>
 
 			<!-- Google Cloud Storage - https://github.com/googleapis/google-cloud-java -->
-			<dependency>
-				<groupId>com.google.apis</groupId>
-				<artifactId>google-api-services-oauth2</artifactId>
-				<version>${google-api-services-oauth2.version}</version>
-			</dependency>
 			<dependency>
 				<groupId>com.google.cloud</groupId>
 				<artifactId>google-cloud-resourcemanager</artifactId>
@@ -3144,16 +3136,6 @@
 				<artifactId>google-cloud-storage</artifactId>
 				<version>${google-cloud-storage.version}</version>
 			</dependency>
-			<dependency>
-				<groupId>com.google.http-client</groupId>
-				<artifactId>google-http-client-jackson2</artifactId>
-				<version>${google-http-client-jackson2.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>com.google.oauth-client</groupId>
-				<artifactId>google-oauth-client-jetty</artifactId>
-				<version>${google-oauth-client-jetty.version}</version>
-			</dependency>
 
 			<!-- Gson - https://code.google.com/p/google-gson/ -->
 			<dependency>

From f90c3fa0478ebedc79589f3372c625e1b1684e0a Mon Sep 17 00:00:00 2001
From: Igor Pisarev <pisarevi@janelia.hhmi.org>
Date: Fri, 1 May 2020 13:06:02 -0400
Subject: [PATCH 3/3] downgrade jackson-databind to match version used in spark
 and aws-sdk

spark uses 2.6.7.1, and aws-java-sdk-s3 uses 2.6.7.3. There are no conflicts between the two, so we can explicitly use the latter.

When running spark with the newer version of jackson-databind (2.10.2), it produces the following runtime error:

Exception in thread "main" java.lang.ExceptionInInitializerError
	at org.apache.spark.SparkContext.withScope(SparkContext.scala:693)
	at org.apache.spark.SparkContext.parallelize(SparkContext.scala:710)
	at org.apache.spark.api.java.JavaSparkContext.parallelize(JavaSparkContext.scala:134)
	at org.janelia.stitching.PipelineFusionStepExecutor.fuse(PipelineFusionStepExecutor.java:276)
	at org.janelia.stitching.PipelineFusionStepExecutor.runImpl(PipelineFusionStepExecutor.java:179)
	at org.janelia.stitching.PipelineFusionStepExecutor.run(PipelineFusionStepExecutor.java:69)
	at org.janelia.stitching.StitchingSpark.run(StitchingSpark.java:87)
	at org.janelia.stitching.StitchingSpark.main(StitchingSpark.java:34)
Caused by: com.fasterxml.jackson.databind.JsonMappingException: Incompatible Jackson version: 2.10.2
	at com.fasterxml.jackson.module.scala.JacksonModule$class.setupModule(JacksonModule.scala:64)
	at com.fasterxml.jackson.module.scala.DefaultScalaModule.setupModule(DefaultScalaModule.scala:19)
	at com.fasterxml.jackson.databind.ObjectMapper.registerModule(ObjectMapper.java:808)
	at org.apache.spark.rdd.RDDOperationScope$.<init>(RDDOperationScope.scala:82)
	at org.apache.spark.rdd.RDDOperationScope$.<clinit>(RDDOperationScope.scala)
	... 8 more
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 14663e1d..f196ff44 100644
--- a/pom.xml
+++ b/pom.xml
@@ -872,7 +872,7 @@
 		<jackrabbit-webdav.version>2.21.0</jackrabbit-webdav.version>
 
 		<!-- Jackson - https://github.com/FasterXML/jackson -->
-		<jackson-databind.version>2.10.2</jackson-databind.version>
+		<jackson-databind.version>2.6.7.3</jackson-databind.version>
 
 		<!-- Java Advanced Imaging - https://java.net/projects/jai-core -->
 		<jai.version>1.1.3</jai.version>