Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We鈥檒l occasionally send you account related emails.

Already on GitHub? Sign in to your account

Federated Amazon S3 support for IGV desktop, migration towards Java11, Gradle and better release engineering #620

Open
wants to merge 79 commits into
base: master
from
Open
Changes from all commits
Commits
Show all changes
79 commits
Select commit Hold shift + click to select a range
73005fa
First successful oauth flow with AWS Cognito+Google social login
brainstorm Jan 13, 2019
9a3b67f
Working AWS Cognito+Google federated example. Now we should parse the鈥
brainstorm Jan 15, 2019
8e12acb
Add cognito Oauth flow logic and JWT helper functions
brainstorm Jan 16, 2019
b112c58
First AWS S3 listing through cognito authenticated user using STS
brainstorm Jan 16, 2019
953bbe0
Bump htsjdk version to make sure all S3 bugs are addressed. Now it ge鈥
brainstorm Jan 17, 2019
f5a948d
Polish gradle dependencies, we do not want to pull all of AWS jdk. Re鈥
brainstorm Jan 21, 2019
2489e26
Kill custom getAuthPage function and fix scope for AWS while keeping 鈥
brainstorm Jan 21, 2019
8ebedae
Drafting the UI event mechanism via GenericLoadDialog inspired on the鈥
brainstorm Jan 22, 2019
6b5a758
First working version of S3 file browser with JTree. Fix Oauth state 鈥
brainstorm Jan 30, 2019
9d5d8a5
Finally working for .bam files, thanks @reisingerf for all the UI hel鈥
brainstorm Jan 30, 2019
5b2122c
Merge branch 'master' into aws_support
brainstorm Jan 30, 2019
e815af1
Remove stray AWS test constant. Run gradle build from .travis.yml to 鈥
brainstorm Jan 30, 2019
2d461c2
Java8 seems to build fine, apply the same dependencies/repository dir鈥
brainstorm Jan 30, 2019
a19ae27
Drop htsjdk from Gradle, @igvteam seems to prefer .jars under /lib in鈥
brainstorm Jan 30, 2019
d57e327
Factor out a bit Amazon/Google-specific bits from Oauth via getters/s鈥
brainstorm Jan 31, 2019
170dfcf
Refactor the actionListener for the dynamic S3 JTree loader Swing dia鈥
brainstorm Jan 31, 2019
f024b0c
Narrowed outstanding XXX (TODOs) to just ResourceLocator ones. Catch 鈥
brainstorm Jan 31, 2019
e288214
Fix more Oauth2 profile defects. Add logged in message in statusbar. 鈥
brainstorm Feb 1, 2019
069ff8b
Need to rethink/refactor the whole token refresh logic. Disabling cro鈥
brainstorm Feb 1, 2019
2b2e4cf
Fix remaining oustanding XXX from the resourcelocator and manually au鈥
brainstorm Feb 6, 2019
8bb2d77
Correct defects on oauth-config.json handling of optional vs mandator鈥
brainstorm Feb 6, 2019
17f2e3c
Clarify current OAuth config parsing logic, does not support multi-pr鈥
brainstorm Feb 7, 2019
ffd905e
Ignore IDEA .iml files [ci skip]
brainstorm Feb 7, 2019
7b9d2f3
GoogleUtils compiles fine locally, temporarily invalidating travisCI 鈥
brainstorm Feb 7, 2019
73f3645
Invalidate TravisCI cache explicitly: https://docs.travis-ci.com/user鈥
brainstorm Feb 7, 2019
d5a6faf
Only build on script, gradle assemble first on install
brainstorm Feb 7, 2019
b7b504a
Line 326 on ResourceLocator is pointing to an old asset there seems t鈥
brainstorm Feb 7, 2019
d7b795a
TravisCI docs misleading about ./gradlew or gradlew
brainstorm Feb 7, 2019
d634ff7
travisci sudo should bypass the cache, according to docs: https://doc鈥
brainstorm Feb 7, 2019
49dd392
Actually validate that travisci cache is the issue. All those commits鈥
brainstorm Feb 7, 2019
d04a85b
Not a TravisCI artifact but IDEA editor perhaps?
brainstorm Feb 7, 2019
85443d1
Local build for umccr-specific releases
brainstorm Feb 7, 2019
993b7d3
No need to assemble/check, build does it all, including tests
brainstorm Feb 7, 2019
422b7a6
Setup TravisCI-triggered GitHub releases for IGV-UMCCR
brainstorm Feb 7, 2019
cf905e3
Build release artifacts and push them to releases on TravisCI pass
brainstorm Feb 7, 2019
693e8bc
Activate globbing for release objects
brainstorm Feb 7, 2019
a9e9ab3
Avoid duplicated releases
brainstorm Feb 7, 2019
82743a5
Reduce release tag verbosity [ci skip]
brainstorm Feb 7, 2019
27b9cca
Working AWS Cognito+Google federated example. Now we should parse the鈥
brainstorm Jan 15, 2019
363386f
First AWS S3 listing through cognito authenticated user using STS
brainstorm Jan 16, 2019
67faf8c
Adding event so that UI reacts with an AWS S3 dataset selection box a鈥
brainstorm Jan 21, 2019
3b50fff
Refactor the actionListener for the dynamic S3 JTree loader Swing dia鈥
brainstorm Jan 31, 2019
6495b45
Fix more Oauth2 profile defects. Add logged in message in statusbar. 鈥
brainstorm Feb 1, 2019
3104bb2
Correct defects on oauth-config.json handling of optional vs mandator鈥
brainstorm Feb 6, 2019
2173ed6
Add working multi-jdk travisCI. Please @jrobinso @davideby consider t鈥
brainstorm Feb 7, 2019
2b9a439
Apply deploy to right umccr branch
brainstorm Feb 7, 2019
adad0ac
Push new IGV UMCCR release
brainstorm Feb 7, 2019
0cc9e9f
On deployment tags and this flag are mutually exclusive: https://docs鈥
brainstorm Feb 7, 2019
3eaf62d
Clarify current OAuth config parsing logic, does not support multi-pr鈥
brainstorm Feb 7, 2019
5137d7d
Merge branch 'master' into aws_support
brainstorm Feb 9, 2019
dcfffe7
Missing GoogleUtils import in ResourceLocator.
brainstorm Feb 9, 2019
156538e
Adjust .travis.yml for both jdk8 and 11
brainstorm Feb 9, 2019
0379a5d
Remove deploy objects since there is no interest in implementing an a鈥
brainstorm Feb 9, 2019
bad0c32
Re-triggering travisci build since there seems to be just a socket ti鈥
brainstorm Feb 10, 2019
f461531
Merge branch 'master' into aws_support
brainstorm Feb 22, 2019
acddacc
Migrate to Java11, therefore incorporating AWS SDK for Java V2, which鈥
brainstorm Mar 2, 2019
77cd0df
Fix last warning, everything compiles but when trying to run the MacA鈥
brainstorm Mar 2, 2019
0214aa1
Exclude groups that conflict with java boot layer testing. Thanks @re鈥
brainstorm Mar 4, 2019
dff774f
Override old slf4j-api implementation with newer version, just 1 fail鈥
brainstorm Mar 4, 2019
30e616c
Fish out example bam/bai/csi files from https://github.com/igvteam/ig鈥
brainstorm Mar 4, 2019
6765e6e
Update travisCI targets with new IGV Java11 namings
brainstorm Mar 4, 2019
5487bc8
No longer build for Java8, changes are backwards incompatible
brainstorm Mar 4, 2019
119246f
Bump up Gradle version, remove Java 10 limits (Java 11 bytecode is no鈥
brainstorm Mar 4, 2019
cac5aba
https://github.com/igvteam/igv/commit/8808982b4238614f49c8dca31d6bd4a鈥
brainstorm Mar 4, 2019
51e7f32
Print full trace when tests fail on CI
brainstorm Mar 4, 2019
84ff254
Merge branch 'master' into aws_support
brainstorm Mar 4, 2019
917f8b0
Add jar from upstream igv to debug/bisect this regression?: https://s鈥
brainstorm Mar 4, 2019
21cf7f1
Add correct JAR.
brainstorm Mar 4, 2019
022df72
Ignoring Goby testcase for now. Test-data needs to be regenerated for鈥
brainstorm Mar 7, 2019
84146ba
AWS presigned urls working for V2 AWS JAVA SDK with session-bound exp鈥
brainstorm Mar 12, 2019
9c1bdda
Exclude jsap and htsjdk without version since the latter is under /li鈥
brainstorm Mar 12, 2019
a7ec494
HTSJDK 2.19.0 released, solving the CSI read issues/tests. Deprecate 鈥
brainstorm Mar 18, 2019
ad7e047
Attempt to cut down on dependencies required/pulled by AWS SDK, follo鈥
brainstorm Apr 1, 2019
cfa7477
org.apache.log4j deprecation in favour of org.apache.logging.log4j (n鈥
brainstorm Apr 1, 2019
1d28991
Ignore test files
brainstorm Apr 1, 2019
a9798f4
Auto stash before rebase of "refs/heads/umccr"
brainstorm Apr 1, 2019
9037510
Add back ONE_WEEK from GenomeManager, accidental discard during rebase
brainstorm Apr 1, 2019
f30bc36
Fix SVG export by using newest batik dependencies instead of legacy o鈥
brainstorm Apr 3, 2019
c9e9d7d
Add TODO/clarification, users need an 'empty' ~/.aws/credentials to h鈥
brainstorm May 7, 2019
File filter...
Filter file types
Jump to鈥
The table of contents is too big for display.
+13,568 鈭2,475
Diff settings

Always

Just for now

@@ -1,13 +1,21 @@
# Created by .gitignore support plugin (hsz.mobi)
.idea/workspace.xml
*.iml
test/data/out/
/build
/build_java11
/bin
igv.log
*.log
/.gradle
.project
.classpath
/.idea/
/.settings
/proguard_log
/proguard_log
.vscode
out/
.DS_Store
*.bedgraph
*.bam
*.csi.gz
*.sai
@@ -26,5 +26,4 @@
version=@VERSION@
build=@BUILD@
timestamp=@TIMESTAMP@
master-resource-url=@DEFAULT_MASTER_RESOURCE_URL@
development=@DEVELOPMENT@
@@ -1,15 +1,18 @@
sudo: false
language: java
# https://stackoverflow.com/questions/52930532/groovy-jdk-11-disable-the-warning-message
env:
- GROOVY_TURN_OFF_JAVA_WARNINGS=true
before_cache:
- rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
- rm -fr $HOME/.gradle/caches/*/plugin-resolution/
- rm -rf $HOME/.gradle/caches/*/plugin-resolution/
cache:
directories:
- $HOME/.gradle/caches/
- $HOME/.gradle/wrapper/
jdk: openjdk11
- "$HOME/.gradle/caches/"
- "$HOME/.gradle/wrapper/"
jdk:
- openjdk11
install:
- ./gradlew -b build_java11.gradle assemble
- "./gradlew assemble"
script:
- ./gradlew -b build_java11.gradle check
- jdk_switcher use openjdk8
- ./gradlew compileJava
- "./gradlew build --stacktrace"
12 IGV.iml
@@ -1,17 +1,13 @@
<?xml version="1.0" encoding="UTF-8"?>
<module type="JAVA_MODULE" version="4">
<module external.linked.project.id="igv" external.linked.project.path="$MODULE_DIR$" external.root.project.path="$MODULE_DIR$" external.system.id="GRADLE" external.system.module.group="" external.system.module.version="UMCCR" type="JAVA_MODULE" version="4">
<component name="NewModuleRootManager" inherit-compiler-output="true">
<exclude-output />
<content url="file://$MODULE_DIR$">
<sourceFolder url="file://$MODULE_DIR$/out/test" isTestSource="true" />
<sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
<sourceFolder url="file://$MODULE_DIR$/test/src" isTestSource="true" />
<excludeFolder url="file://$MODULE_DIR$/.gradle" />
<excludeFolder url="file://$MODULE_DIR$/build" />
<excludeFolder url="file://$MODULE_DIR$/out" />
</content>
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
<orderEntry type="library" name="ojdbc6" level="project" />
<orderEntry type="library" name="lib" level="project" />
<orderEntry type="library" name="lib1" level="project" />
<orderEntry type="library" name="java" level="project" />
</component>
</module>
@@ -1,5 +1,5 @@
# igv
[![Build Status](https://travis-ci.org/igvteam/igv.svg?branch=master)](https://travis-ci.org/igvteam/igv)
[![Build Status](https://travis-ci.org/umccr/igv.svg?branch=umccr)](https://travis-ci.org/umccr/igv)

Integrative Genomics Viewer - dekstop genome visualization tool for Mac, Windows, and Linux.

Oops, something went wrong.
ProTip! Use n and p to navigate between commits in a pull request.
You can鈥檛 perform that action at this time.