[NOT YET] All of Leo: code review

.coveralls.yml

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+service_name: travis-ci

.github/PULL_REQUEST_TEMPLATE.md

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+\<your comments for this PR go here\>
+
+Have you read [CONTRIBUTING.md](../CONTRIBUTING.md) lately? If not, do that first.
+
+I, the developer opening this PR, do solemnly pinky swear that:
+
+- [ ] I've documented my API changes in Swagger
+
+In all cases:
+
+- [ ] Get two thumbsworth of review and PO signoff if necessary
+- [ ] Verify all tests go green
+- [ ] Squash and merge; you can delete your branch after this
+- [ ] Test this change deployed correctly and works on dev environment after deployment

.gitignore

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+.idea/
+/project/boot/
+/project/plugins/project
+target/
+lib_managed/
+src_managed/
+test-output/
+*.iml
+.classpath_nb
+.cache
+.classpath
+.project
+/.settings/
+/bin/
+*.log
+/config/
+*.pid
+
+# Automation exclusions
+automation/chrome/
+automation/failure_screenshots/
+automation/src/test/resources/application.conf
+automation/src/test/resources/firecloud-account.pem

.travis.yml

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+jdk:
+  - oraclejdk8
+
+language: scala
+
+scala:
+  - 2.12.2
+
+sudo: required
+
+services:
+  - docker
+
+before_install:
+  - docker rm -f mysql || true          # in case the after_success step does not run
+  - docker pull mysql/mysql-server:5.6
+  # port 3306 is not available because Travis runs its own MySQL after 2006-12-01
+  - docker run -p 3307:3306 --name mysql -e MYSQL_ROOT_PASSWORD=leonardo-test -e MYSQL_USER=leonardo-test -e MYSQL_PASSWORD=leonardo-test -e MYSQL_DATABASE=leotestdb -d mysql/mysql-server:5.6
+
+script:
+  - SBT_OPTS=-Xmx3g sbt -Denv.type=test -Dmysql.host=localhost -Dmysql.port=3307 clean coverage test coverageReport
+
+after_success:
+  - SBT_OPTS=-Xmx3g sbt coveralls
+  - docker rm -f mysql

CONTRIBUTING.md

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+# Contributing
+
+## External Contributions
+External contribution guidelines coming soon. In the interim, comments and questions are welcome in the [Issues](https://github.com/DataBiosphere/leonardo/issues).
+
+## Opening a Pull Request
+
+You most likely want to do your work on a feature branch based on develop. There is no explicit naming convention; we usually use some combination of the JIRA issue number and something alluding to the work we're doing.
+
+When you open a pull request, add the JIRA issue number (e.g. `GAWB-1234`) to the PR title. This will make a reference from JIRA to the GitHub issue. Add a brief description of your changes above the PR checkbox template.
+
+This is also a good opportunity to check that the acceptance criteria for your JIRA ticket exists and is met. Check with your PO if you have any questions there. You should also fill out a summary to go in the release notes and some instructions on what QA should be looking at.
+
+The checkboxes in the PR are important reminders to you, the developer. Please be conscientious and run through them when you open a PR.
+
+## PR approval process
+
+If your PR is particularly complex it can be helpful to add some commentary, either in the description or line-by-line in the GitHub PR view. In the latter case, consider whether those comments should be in the code itself.
+
+You should get review from two people (either through GitHub's request-review feature, or by assigning the PR to them); one of them should probably be your tech lead, though ask. Do chase your reviewers (or find others) if they're slow; we don't like to let PRs linger. If you get PR feedback it's back to you to address it and then nudge your reviewers for re-review.
+
+Your PR is ready to merge when all of the following things are true:
+
+1. Two reviewers have thumbed (or otherwise approved) your PR
+2. If your change is user-facing, your PO has seen it and signed off
+3. All tests pass, including coverage
+
+## API changes
+
+All changes to the API _must_ be documented in Swagger.

Dockerfile

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+FROM openjdk:8
+
+EXPOSE 8080
+EXPOSE 5050
+
+ENV GIT_HASH $GIT_HASH
+
+RUN mkdir /leonardo
+COPY ./leonardo*.jar /leonardo
+
+# Add Leonardo as a service (it will start when the container starts)
+CMD java $JAVA_OPTS -jar $(find /leonardo -name 'leonardo*.jar')

LICENSE-ASL-2.0

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LICENSE.txt

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+Copyright (c) 2017, Broad Institute, Inc., Verily Life Sciences LLC
+All rights reserved.
+
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+
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