Add contributing, code conduct, joss docs (#827)

CODE_OF_CONDUCT.md

@@ -0,0 +1,73 @@
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age,
+body size, disability, ethnicity, gender identity and expression, level of
+experience, nationality, personal appearance, race, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+  advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers 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, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an
+appointed representative at an online or offline event. Representation of a
+project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team. All complaints will be reviewed and
+investigated and will result in a response that is deemed necessary and
+appropriate to the circumstances. The project team is obligated to maintain
+confidentiality with regard to the reporter of an incident. Further details of
+specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant], version 1.4,
+available at https://contributor-covenant.org/version/1/4
+
+[Contributer Covenant]: https://contributor-covenant.org

CONTRIBUTING.md

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+# Contributing
+
+First off - Thank you for your interest in contributing to the Open OnDemand project!
+
+There is no pull request too small! Everything from simple misspellings to very
+large feature requests are welcome.  If you're not quite sure where to get started
+you can search our list of [good first issues].
+
+Please note we have a [code of conduct], please follow it in all your
+interactions with the project.
+
+## Issues
+
+Issues, bug reports, questions and feature requests are always welcome.  Feel
+free to open an issue and use any [issue labels] as appropriate.
+
+We mostly use [Discourse] for general questions or help.  If you're unsure
+of where to route your question, Discourse may be the best forum for it.
+
+## Other Repositories
+
+There are other repositories to Open OnDemand that are important as well.  You may want to check
+these out too.
+
+* [repository for the Open OnDemand website](https://github.com/OSC/openondemand.org)
+* [repository for the Open OnDemand documentation](https://github.com/OSC/ood-documentation)
+* [repository for the Open OnDemand core library](https://github.com/OSC/ood_core)
+
+## Pull Request Process
+
+If you have a large feature it may be preferential to open an issue and discuss
+it first before putting a lot of work into coding something that may not be accepted. Don't
+let this discourage you though! Feel free to open tickets and engage with the development
+team on proposed changes.
+
+1. [Fork this repo].
+2. Branch off of the master branch.
+3. Create a PR to merge into the master upstream branch.  Make sure at least
+  unit tests continue to pass by executing `rake test`.
+4. We will review it and either add comments for requested changes or merge.
+  If changes are being requested, don't let this discourage you! This is a
+  natural part of getting changes right and ensuring quality in what we're building.
+
+### Tips
+
+1. Contributions accompanied by unit tests are recommended.
+2. For Ruby code we add [yarndoc] comments above all of our public interface methods as this is used to generate helpful documentation on http://www.rubydoc.info/. We do not yet have adopted a strong style guide for code in JavaScript and Python.
+3. With the PR for the change, add to the CHANGELOG a line under the "Unreleased" section specifying https://keepachangelog.com/en/1.0.0/.
+4. Follow best conventions with Ruby coding style. We haven't yet adopted a strict style guide, so unless you are using tabs or 4 spaces instead of 2 spaces you will probably not find an objection from us.
+
+
+[Discourse]: https://discourse.osc.edu
+[yardoc]: https://yardoc.org/
+[Fork this repo]: https://help.github.com/articles/fork-a-repo/
+[code of conduct]: CODE_OF_CONDUCT.md
+[issue labels]: https://github.com/OSC/ondemand/labels
+[good first issues]: https://github.com/OSC/ondemand/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22+

README.md

@@ -26,7 +26,7 @@ Installing Open OnDemand simple, use our prepacked RPM distributions or build fr
 Learn more about Open OnDemand's system architecture and request lifecycle by visiting our <a href="https://osc.github.io/ood-documentation/master/architecture.html">documentation</a>.
 
 ## Community
-Open OnDemand has an active and growing community! Don't hesistate to reach out to the developers via our [Discourse] instance if you would like more information or need help installing or configuring Open OnDemand.
+Open OnDemand has an active and growing community! Don't hesitate to reach out to the developers via our [Discourse] instance if you would like more information or need help installing or configuring Open OnDemand.
 <br/>
 <br/>
 <a href="https://discourse.osc.edu"><img src="https://upload.wikimedia.org/wikipedia/commons/c/c2/Discourse.svg" width=150></a>
@@ -46,5 +46,5 @@ This project is maintained by the <a href="https://www.osc.edu">Ohio Supercomput
 [MIT License]: http://opensource.org/licenses/MIT
 [Open OnDemand Documentation]: https://osc.github.io/ood-documentation/master/
 [installation instructions]: https://osc.github.io/ood-documentation/master/requirements.html
-[contributing guide]: https://github.com/OSC/Open-OnDemand/blob/master/CONTRIBUTING.md
+[contributing guide]: CONTRIBUTING.md
 [Discourse]: https://discourse.osc.edu

SECURITY.md

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+# Security Policy
+
+This document outlines security procedures and general policies for the `OnDemand`
+project.
+
+## Security Audits
+
+[Trusted CI](https://trustedci.org/), the NSF Cybersecurity Center of 
+Excellence, conducted an in-depth vulnerability assessment of Open OnDemand, completing 
+it in December 2018. This assessment included a careful review of the code, increasing 
+our confidence in its security. The Ohio Supercomputing Center addressed the implementation 
+issues (bugs) that were found during this review, producing a more robust revision of Open OnDemand.
+
+## Reporting a Vulnerability
+
+If you have security concerns or think you have found a vulnerability in Open OnDemand,
+please contact us directly via [email](mailto:[email protected]) on the news list found 
+[here](https://lists.osu.edu/mailman/listinfo/ood-users).  Emails sent to it are only seen by 
+the core project team.
+
+## Disclosure Policy
+
+When the team receives a security vulnerability, they will generally assign it 
+to a primary handler. This person will coordinate the fix and release process,
+involving the following steps:
+
+  * Confirm the problem and determine the affected versions.
+  * Audit code to find any potential similar problems.
+  * Prepare fixes for all releases still under maintenance. These fixes will be
+    released as fast as possible.
+
+## Comments on this Policy
+
+If you have suggestions on how this process could be improved please submit 
+a ticket, open a [Discorse](https://discourse.osc.edu/) topic or open a pull request.

codemeta.json

@@ -0,0 +1,65 @@
+{
+  "@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+  "@type": "Code",
+  "author": [
+    {
+      "@id": "https://orcid.org/0000-0002-9043-0850",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Dave Hudak",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0002-4331-8508",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Doug Johnson",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0002-5475-8779",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Alan Chalker",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0003-3208-7588",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Jeremy Nicklas",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0002-9662-412X",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Eric Franz",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0002-5494-0968",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Trey Dockendorf",
+      "affiliation": "Ohio Supercomputer Center"
+    },
+    {
+      "@id": "https://orcid.org/0000-0001-7455-6691",
+      "@type": "Person",
+      "email": "[email protected]",
+      "name": "Brian L. McMichael",
+      "affiliation": "Ohio Supercomputer Center"
+    }
+  ],
+  "identifier": "http://dx.doi.org/10.1145/2949550.2949644",
+  "codeRepository": "https://github.com/OSC/ondemand",
+  "datePublished": "2017-03-08",
+  "dateModified": "2017-11-03",
+  "dateCreated": "2015-07-01",
+  "description": "Open-source software project that enables HPC centers to install and deploy advanced web and graphical interfaces for their users.",
+  "keywords": "HPC, apps, portal, gateway, web platform",
+  "license": "MIT",
+  "title": "Open OnDemand",
+  "version": "v1.2.0"
+}

paper.bib

@@ -0,0 +1,37 @@
+@inproceedings{Hudak2013,
+ author = {Hudak, David E. and Bitterman, Thomas and Carey, Patricia and Johnson, Douglas and Franz, Eric and Brady, Shaun and Diwan, Piyush},
+ title = {OSC OnDemand: A Web Platform Integrating Access to HPC Systems, Web and VNC Applications},
+ booktitle = {Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery},
+ series = {XSEDE '13},
+ year = {2013},
+ isbn = {978-1-4503-2170-9},
+ location = {San Diego, California, USA},
+ pages = {49:1--49:6},
+ articleno = {49},
+ numpages = {6},
+ url = {http://doi.acm.org/10.1145/2484762.2484780},
+ doi = {10.1145/2484762.2484780},
+ acmid = {2484780},
+ publisher = {ACM},
+ address = {New York, NY, USA},
+ keywords = {OpenID, REST, cyberinfrastructure, high performance computing, virtual organizations, web platform},
+}
+
+@inproceedings{Hudak2016,
+ author = {Hudak, David E. and Johnson, Douglas and Nicklas, Jeremy and Franz, Eric and McMichael, Brian and Gohar, Basil},
+ title = {Open OnDemand: Transforming Computational Science Through Omnidisciplinary Software Cyberinfrastructure},
+ booktitle = {Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale},
+ series = {XSEDE16},
+ year = {2016},
+ isbn = {978-1-4503-4755-6},
+ location = {Miami, USA},
+ pages = {43:1--43:7},
+ articleno = {43},
+ numpages = {7},
+ url = {http://doi.acm.org/10.1145/2949550.2949644},
+ doi = {10.1145/2949550.2949644},
+ acmid = {2949644},
+ publisher = {ACM},
+ address = {New York, NY, USA},
+ keywords = {Cyberinfrastructure, Federated Authentication, High Performance Computing, OnDemand, OpenID Connect, Virtual Organizations, Web apps, Web platform},
+}

paper.md

@@ -0,0 +1,71 @@
+---
+title: 'Open OnDemand: A web-based client portal for HPC centers'
+tags:
+  - HPC
+  - apps
+  - portal
+  - gateway
+  - web platform
+authors:
+ - name: Dave Hudak
+   orcid: https://orcid.org/0000-0002-9043-0850
+   affiliation: 1
+ - name: Doug Johnson
+   orcid: https://orcid.org/0000-0002-4331-8508
+   affiliation: 1
+ - name: Alan Chalker
+   orcid: https://orcid.org/0000-0002-5475-8779
+   affiliation: 1
+ - name: Jeremy Nicklas
+   orcid: https://orcid.org/0000-0003-3208-7588
+   affiliation: 1
+ - name: Eric Franz
+   orcid: https://orcid.org/0000-0002-9662-412X
+   affiliation: 1
+ - name: Trey Dockendorf
+   orcid: https://orcid.org/0000-0002-5494-0968
+   affiliation: 1
+ - name: Brian L. McMichael
+   orcid: https://orcid.org/0000-0001-7455-6691
+   affiliation: 1
+affiliations:
+ - name: The Ohio Supercomputer Center
+   index: 1
+date: 8 March 2018
+bibliography: paper.bib
+---
+
+# Summary
+
+The web has become the dominant access mechanism for remote compute services in
+every computing area except high-performance computing (HPC). Accessing HPC
+resources, either at the campus or national level typically requires advanced
+knowledge of Linux, familiarity with command-line interfaces and installation
+and configuration of custom client software (e.g., Secure Shell (SSH) and
+Virtual Network Computing (VNC)). These additional requirements create an
+accessibility gap for HPC. To help address this gap we have created the Open
+OnDemand Project [@Hudak2016], an open-source software project based on the
+proven Ohio Supercomputer Center (OSC) OnDemand platform [@Hudak2013], to allow
+HPC centers to provide advanced web and graphical interfaces for their users.
+
+Open OnDemand is the result of substantial development and integration efforts
+in four key areas. (1) The per-user NGINX (PUN) architecture including
+federated authentication using CILogon, Apache-based web proxy, per-user NGINX
+configuration, and Unix domain sockets for secure server-side communication
+between the proxy and each PUN. The PUN architecture is an original
+contribution of the project. (2) The file browser and file editor which, though
+originally based on an existing open source project, have been extensively
+modified. (3) The terminal, created by integrating an existing open source
+project with minimal effort. (4) Accessibility Apps (Dashboard, Job
+Constructor, Job Status, System Status, VDI and iHPC apps) built using the
+Rails-based AweSim AppKit (which was developed by this team on a previous
+project and leveraged here with minor modifications). The AweSim AppKit allows
+for the development of both workflow and interactive applications and includes
+mechanisms for user-based app creation, app sharing and app publishing. The
+AppKit technology is included as part of the Open OnDemand project.
+
+# Acknowledgements
+
+This work is supported by the National Science Foundation of the United States under the award NSF SI2-SSE-1534949.
+
+# References