Readme updated

README.md

@@ -1,106 +1,71 @@
-<h1 align="center">SCORe</h1>
+# Score - File Transfer & Object Storage
 
-<p align="center">Secure Cloud Object Repository</p>
+[<img hspace="5" src="https://img.shields.io/badge/chat-on--slack-blue?style=for-the-badge">](http://slack.overture.bio)
+[<img hspace="5" src="https://img.shields.io/badge/License-gpl--v3.0-blue?style=for-the-badge">](https://github.com/overture-stack/score/blob/develop/LICENSE)
+[<img hspace="5" src="https://img.shields.io/badge/Code%20of%20Conduct-2.1-blue?style=for-the-badge">](code_of_conduct.md)
 
-<p align="center">Formerly known as ICGC Storage and currently used as the storage and transfer system for ICGC cloud based projects against S3 and Azure backends.</p>
+<div>
+<img align="right" width="100vw" src="icon-score.png" alt="score-logo" hspace="30"/>
+</div>
 
-<p align="center"><a href="http://www.overture.bio/products/score" target="_blank"><img alt="General Availability" title="General Availability" src="http://www.overture.bio/img/progress-horizontal-GA.svg" width="320" /></a></p>
+Genomics data volume and velocity have increased dramatically, rendering on-premise storage insufficient and demanding specialized software tools to manage data in the cloud. [Score](https://www.overture.bio/documentation/score/) addresses this by facilitating the transfer and storage of genomics data to and from a cloud network.
 
-[![Codacy Badge](https://api.codacy.com/project/badge/Grade/201ae314ab3842baad25bc820069e90a)](https://www.codacy.com/app/overture-stack/score?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=overture-stack/score&amp;utm_campaign=Badge_Grade)
-[![Documentation Status](https://readthedocs.org/projects/score-docs/badge/?version=latest)](https://score-docs.readthedocs.io/en/latest/?badge=latest)
-[![Slack](http://slack.overture.bio/badge.svg)](http://slack.overture.bio)
+<!--Blockqoute-->
 
-## Documentation
-
-Explore documentation with the Score [Read the Docs](https://score-docs.readthedocs.io/en/develop/introduction.html).
-
-## Build
-
-To compile, test and package the system, execute the following from the root of the repository:
-
-```shell
-mvn
-```
-
-## Run
-
-See module-specific documentation below.
+</br>
 
-## Modules
-Top level system modules:
+> 
+> <div>
+> <img align="left" src="ov-logo.png" height="90"/>
+> </div>
+> 
+> *Score is a core component within the [Overture](https://www.overture.bio/) research software ecosystem. Overture is a toolkit of modular software components made to build into scalable genomics data management systems. See our [related products](#related-products) for more information on what Overture can offer.*
+> 
+> 
+<!--Blockqoute-->
 
-- [Core](score-core/README.md)
-- [Client](score-client/README.md)
-- [File System](score-fs/README.md)
-- [Server](score-server/README.md)
-- [Test](score-test/README.md)
+## Technical Specifications
 
-## Development
-Several `make` targets are provided for locally deploying dependent services using docker. 
-By using this, the developer will be able to replicate a live environment for score-server and score-client. 
-It allows the user to develop locally, and test uploads/downloads in an isolated environment.
+- Written in JAVA 
+- Supports AWS S3, Azure, Google Cloud, Openstack with Ceph, Minio and all other S3-compliant cloud storage solutions
+- Built-in [Samtools](http://www.htslib.org/) functionality including BAM and CRAM file slicing by genomic region 
+- ACL security using [OAuth 2.0](https://oauth.net/2/) and scopes based on study codes
+- Multipart Uploads and Downloads
+- REST API with [Swagger UI](https://swagger.io/tools/swagger-ui/)
+- [MD5sum](https://www.intel.com/content/www/us/en/support/programmable/articles/000078103.html) validation
 
-There are 2 modes:
-
-### 1. Development Mode
-The purpose of this mode is to decrease the wait time between building and testing against dependent services.
-This mode will run a `mvn package` if the `*-dist.tar.gz` files are missing, and copy them into a container for them to be run. 
-This method allows for fast developement, since the `mvn package` step is handled on the **Docker host**.
-In addition, the debug ports `5005` and `5006` are exposed for both `score-client` and `score-server`, respectively, allowing developers to debug the docker containers.
-This mode can be enabled using the `DEMO_MODE=0` override. This is the default behaviour if the variable `DEMO_MODE` is not defined.
-
-#### Debugging the score-client with IntelliJ
-Since the JVM debug port is exposed by the `score-client` docker container, IntelliJ can **remotely debug** a running docker container. 
-To do this, a **docker image run profile** must be created with the configuration outputted by the `make intellij-score-client-config` command, which will output a basic upload command, however it can be modified to be any score-client command.
-Then, a **remote debug profile** must be created, with the following config:
-
-```
-Host: localhost
-Port: 5005
-Use module classpath: score-client
-```
-and in the `Before launch: Activate tool window` section, click the `+` sign, and select `Launch docker before debug`. 
-Then ensure the `Docker configuration` field is set to the name of the previously created **docker image run profile**  and that `Custom Options` is set to `-p 5005:5005`. In order for the debugger to bind to the debug port in time, 
-a delay needs to be introduced after starting the container. To do this, click the `+` sign again, and select `Launch docker before debug`, and select `Run External Tool` and a window will pop-up. Input the following:
-
-```
-Name:      Sleep for 5 seconds
-Program:   /usr/bin/sleep
-Arguments: 5
-```
-and click `OK`.
-
-Finally,  start debugging by simply running the **remote debug profile** and it will call the **docker image run profile** before launch. 
-
-#### Debugging the score-server with IntelliJ
-Since the `score-server` is a server and exposes the 5006 debug port, configuration is much easier. First, start the server with `make clean start-score-server`. Then, create a **remote debug profile** in Intellij with the following configuration:
-```
-Host: localhost
-Port: 5006
-Use module classpath: score-server
-```
-and then run it in debug mode. 
+## Documentation
 
+- :construction: Developer documentation, including instructions for running Score from source can be found in the [Wiki](https://github.com/overture-stack/score/wiki) :construction:
+- For user documentation, including installation, configuration and usage guides, see the Overture websites [Score documentation page](https://www.overture.bio/documentation/score/)
 
+## Support & Contributions
 
-### 2. Demo Mode
-The purpose of this mode is to demo the current `score-server` and `score-client` code by building it in **inside the Docker image**, 
-as opposed to the **Docker host** as is done in Development mode and then running the containers.
-This mode will not run `mvn package` on the Docker host, but instead inside the Docker container.
-This method is very slow, since maven will download dependencies every time a build is triggered, however creates a completely isolated environment for testing.
-This mode can be enabled using the `DEMO_MODE=1` make variable override. For example, to start the score-server, the following command would be run:
+- Filing an [issue](https://github.com/overture-stack/score/issues)
+- Making a [contribution](CONTRIBUTING.md)
+- Connect with us on [Slack](http://slack.overture.bio)
+- Add or Upvote a [feature request](https://github.com/overture-stack/score/issues?q=is%3Aopen+is%3Aissue+label%3Anew-feature+sort%3Areactions-%2B1-desc)
 
-```bash
-make start-score-server DEMO_MODE=1
-```
+## Related Software 
 
-For more information on the different targets, run `make help` or read the comments above each target for a description
+<div>
+  <img align="right" alt="Overture overview" src="https://www.overture.bio/static/124ca0fede460933c64fe4e50465b235/a6d66/system-diagram.png" width="45%" hspace="5">
+</div>
 
+Score commonly works in tandem with our metadata service, [Song](https://github.com/overture-stack/SONG). While Score handles object storage and file transfer, Song validates and tracks all the associated file metadata. 
 
-## Changes
+All our core microservices are included in the Overture **Data Management System** (DMS). Built from our core collection of microservices, the DMS offers turnkey installation, configuration, and deployment of Overture software. For more information on the DMS, read our [DMS documentation](https://www.overture.bio/documentation/dms/).
 
-Change log for the user-facing system modules may be found in [CHANGES.md](CHANGES.md).
+See the links below for information on our other research software tools:
 
-## License
+</br>
 
-Copyright and license information may be found in [LICENSE.md](LICENSE.md).
+|Software|Description|
+|---|---|
+|[Ego](https://www.overture.bio/products/ego/)|An authorization and user management service|
+|[Ego UI](https://www.overture.bio/products/ego-ui/)|A UI for managing Ego authentication and authorization services|
+|[Score](https://www.overture.bio/products/score/)| Transfer data to and from any cloud-based storage system|
+|[Song](https://www.overture.bio/products/song/)|Catalog and manage metadata associated to file data spread across cloud storage systems|
+|[Maestro](https://www.overture.bio/products/maestro/)|Organizing your distributed data into a centralized Elasticsearch index|
+|[Arranger](https://www.overture.bio/products/arranger/)|A search API with reusable UI components that build into configurable and functional data portals|
+|[DMS-UI](https://github.com/overture-stack/dms-ui)|A simple web browser UI that integrates Ego and Arranger|

code_of_conduct.md

@@ -0,0 +1,133 @@
+
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[INSERT CONTACT METHOD].
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations