Merge log4

.gitignore

@@ -19,4 +19,4 @@ out/
 *.bam
 *.csi.gz
 *.sai
-/examples/genomes/hg38_session.json
+/test/batch/snapshots/

README.md

@@ -13,7 +13,7 @@ we recommend the pre-built releases available at [http://software.broadinstitute
 
 Builds are executed from the IGV project directory.  Files will be created in the 'build' subdirectory.
 
-IGV is tested on **Java 11**. Previous (versions =< 2.6.3) running on Java8 have been deprecated.
+IGV requires **Java 11** to build and run.   Later versions of Java should work but we build and test  on **Java 11**. Previous (versions =< 2.6.3) running on Java8 have been deprecated.
 
 NOTE: If on a Windows platform use ```./gradlew.bat'``` in the instructions below
 
@@ -45,4 +45,15 @@ Note that Gradle creates a number of other subdirectories in 'build'.  These can
 
 #### Amazon Web Services support
 
-Public data files hosted in Amazon S3 buckets can be loaded into IGV using [https endpoints](https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingBucket.html).  Authenticated access can be configured using the UMCCR contributed AWS configuration option. For more details, refer to the [UMCCR documentation on the backend](https://umccr.org/blog/igv-amazon-backend-setup/) and [frontend for a provisioning URL step by step guide](https://umccr.org/blog/igv-amazon-frontend-setup/).
+Public data files hosted in Amazon S3 buckets can be loaded into IGV using [https endpoints](https://docs.aws.amazon.com/AmazonS3/latest/dev/UsingBucket.html).  
+
+Authenticated access using s3:// urls is supported by either (1) enabling OAuth access with Cognito using the UMCCR 
+contributed AWS configuration option, or (2) setting AWS credentials and region information as described 
+[here]( https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/credentials.html) and 
+[here](https://docs.aws.amazon.com/sdk-for-java/v1/developer-guide/java-dg-region-selection.html).
+
+For more details on using Cognito for OAuth access, see the [UMCCR documentation on the backend](https://umccr.org/blog/igv-amazon-backend-setup/) 
+and [frontend for a provisioning URL step by step guide](https://umccr.org/blog/igv-amazon-frontend-setup/).
+
+
+

build.gradle

@@ -1,6 +1,6 @@
 // The MIT License (MIT)
 //
-// Copyright (c) 2007-2019 Broad Institute
+// Copyright (c) 2007-2019 Broad Institut≈e
 //
 // Permission is hereby granted, free of charge, to any person obtaining a copy
 // of this software and associated documentation files (the "Software"), to deal
@@ -74,7 +74,6 @@ configurations {
         exclude group: 'org.codehaus.mojo', module: 'animal-sniffer-annotations'
         exclude group: 'org.checkerframework', module: 'checker-qual'
         exclude group: 'com.ibm.icu', module: 'icu4j'
-        exclude group: 'log4j', module: 'log4j'
 
         exclude group: 'xmlpull', module: 'xmlpull'
         exclude group: 'xpp3', module: 'xpp3_min'
@@ -105,35 +104,27 @@ configurations {
 dependencies {
     implementation(
             fileTree(dir: 'lib', include: '*.jar'), // first search on disk (old behavior), then maven repos
-            [group: 'org.apache.ant', name: 'ant', version: '1.10.5'],
             [group: 'com.google.code.gson', name: 'gson', version: '2.8.5'],
-            [group: 'com.google.protobuf', name: 'protobuf-java', version: '3.7.0-rc1'],
             [group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'],
             [group: 'commons-io', name: 'commons-io', version: '2.6'],
             [group: 'org.apache.commons', name: 'commons-compress', version: '1.18'],
             [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.7.3'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '2.24.1'],
-            [group: 'org.apache.logging.log4j', name: 'log4j-api', version: '2.16.0'],
-            [group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.16.0'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '3.0.5'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             //[group: 'org.bidib.com.jidesoft', name: 'jide-common', version: '3.7.3'],  // no longer in Maven Central
             [group: 'com.google.guava', name: 'guava', version: '27.0.1-jre'],
-            [group: 'org.campagnelab.goby', name: 'goby-io', version: '3.3.1'],
-            [group: 'org.campagnelab.icb', name: 'icb-utils', version: '2.0.2'],
-            [group: 'org.campagnelab.ext', name: 'jsap', version: '3.0.0'],
             [group: 'org.apache.xmlgraphics', name: 'batik-dom', version: '1.11'],
             [group: 'org.apache.xmlgraphics', name: 'batik-svggen', version: '1.11'],
             [group: 'org.apache.xmlgraphics', name: 'batik-codec', version: '1.11'],
-            [group: 'org.slf4j', name: 'slf4j-api', version: '1.7.26'],
-            [group: 'org.slf4j', name: 'slf4j-simple', version: '1.7.26'],
             [group: 'org.netbeans.external', name: 'AbsoluteLayout', version: 'RELEASE110'],
 
             // Amazon deps
             [group: 'software.amazon.awssdk', name: 'cognitoidentity', version: '2.16.7'],
             [group: 'software.amazon.awssdk', name: 'sts', version: '2.16.7'],
-            [group: 'software.amazon.awssdk', name: 's3', version: '2.16.7']
+            [group: 'software.amazon.awssdk', name: 's3', version: '2.16.7'],
+            [group: 'software.amazon.awssdk', name: 'sso', version: '2.16.7']
     )
 
     testImplementation(
@@ -231,12 +222,16 @@ task createDist(type: Copy, dependsOn: jar) {
     }
     with copySpec {
         from("${buildDir}/libs")
-        from("lib") { include '*.jar' }
+        from("lib") {
+            include '*.jar' 
+        }
         into "lib"
     }
     // Copies all Maven-fetched dependency jars
     with copySpec {
-        from configurations.default
+        from configurations.default {
+            exclude '**/*log4j*.jar' 
+        }
         into "lib"
     }
     with copySpec { from("genomes/sizes") {} into "lib/genomes" }

examples/oauth/oauth-config-amazon.json

@@ -0,0 +1,16 @@
+{
+   "client_id": "3f4ujenfmr77tg12idlkebpkoh",
+   "client_secret": "en1q6638m4dogrr6erhrmitim67sjilc6htjnfmf6ljk2q3j9og",
+   "auth_provider": "Amazon",
+   "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
+   "aws_region": "ap-southeast-2",
+   "scope": "email%20openid%20profile",
+   "redirect_uris": [
+      "http://localhost:60151/oauthCallback"
+   ],
+   "authorization_endpoint": "https://igv-demo.auth.ap-southeast-2.amazoncognito.com/login",
+   "token_endpoint": "https://igv-demo.auth.ap-southeast-2.amazoncognito.com/token",
+   "aws_cognito_fed_pool_id": "ap-southeast-2:15b7bf93-18ca-40d5-99e9-38b4eb69363e",
+   "aws_cognito_pool_id": "ap-southeast-2_IYMvlZzmv",
+   "aws_cognito_role_arn": "arn:aws:iam::YOUR_AWS_ACCOUNT:role/YOUR_Cognito_igvAuth_Role"
+}

examples/oauth/oauth-config-google.json

@@ -0,0 +1,11 @@
+{
+  "client_id": "661332306814-gb4r480jnb6rres3iv8a5f48dms5ququu.apps.googleusercontent.com",
+  "client_secret": "MFqdc7apizmtb8n08Ze810V6",
+  "auth_uri": "https://accounts.google.com/o/oauth2/auth",
+  "token_uri": "https://accounts.google.com/o/oauth2/token",
+  "auth_provider_x509_cert_url": "https://www.googleapis.com/oauth2/v1/certs",
+  "redirect_uris": [
+    "http://localhost:60151/oauthCallback"
+  ],
+  "hosts": ["www.googleapis.com", "storage.cloud.google.com", "storage.googleapis.com"]
+}

examples/oauth/oauth-config-microsoft.json

@@ -0,0 +1,11 @@
+{
+  "client_id": "hbq82djj-qwer-7iub-j7zq-7i8nv72n48nq",
+  "client_secret": "cVAX64fXRikCLmtAow/cktrAtaHz/tmB3WHKhnbXN2Gq",
+  "authorization_endpoint": "https://login.microsoftonline.com/77nwe2q2-e53r-uq2p-7vdh-9z7px83zmtiv/oauth2/authorize",
+  "token_endpoint": "https://login.microsoftonline.com/77nwe2q2-e53r-wk32-7vdh-9z7px83zmtiv/oauth2/token",
+  "hosts": ["prod_host.mayo.edu", "dev_host.mayo.edu", "int_host.mayo.edu"],
+  "auth_provider": "Mayo Clinic",
+  "app_id_uri": "https://orgtools.onmicrosoft.com/6q9qk3mr-pu78-eu73-vx5a-nqw2aqidutm9",
+  "scope": "openid"
+}
+