Add documentation site (retype) to main repository

.github/workflows/retype-action.yml

@@ -0,0 +1,22 @@
+
+name: Publish Retype powered website to GitHub Pages
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+
+jobs:
+  publish:
+    name: Publish to retype branch
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: retypeapp/action-build@latest
+
+      - uses: retypeapp/action-github-pages@latest
+        with:
+          update-branch: true

.gitignore

@@ -106,4 +106,5 @@ pom.xml.*
 db-scripts/src/main/resources/cgds-test.sql
 pom.xml.*
 Dockerfile.local
-.factorypath
+.factorypath
+.retype

CNAME

@@ -0,0 +1 @@
+software.cbioportal.org

documentation/404.md

@@ -0,0 +1,91 @@
+# File Not Found
+
+<script>
+window.redirectMap = {
+    "5.1-data-loading/data-loading/file-formats":"file-formats",
+    "2.1-deployment/architecture-overview":"architecture-overview",
+    "6.-web-api-and-clients/api-and-api-clients":"web-api-and-api-clients",
+    "2.2-authorization-and-authentication/authenticating-users-via-tokens":"deployment/authorization-and-authentication/authenticating-users-via-tokens",
+    "2.4-integration-with-other-webservices/oncokb-data-access":"deployment/integration-with-other-webservices/oncokb-data-access",
+    "4.-development/release-procedure#a-note-on-versioning":"release-procedure",
+    "2.1.2-deploy-without-docker/deploying":"deployment/deploy-without-docker/deploying",
+    "2.2-authorization-and-authentication/authenticating-users-via-tokens":"deployment/authorization-and-authentication/authenticating-users-via-tokens",
+    "1.-general/news":"news",
+    "1.-general/faq":"user-guide/faq",
+    "1.-general/about-us":"about-us",
+    "1.-general/rfc-list":"rfc-list",
+    "2.1-deployment/architecture-overview":"architecture-overview",
+    "2.1-deployment/hardware-requirements":"hardware-requirements",
+    "2.1.1-deploy-with-docker-recommended/docker":"deployment/docker",
+    "2.1.1-deploy-with-docker-recommended/import_data":"deployment/docker/import_data",
+    "2.1.1-deploy-with-docker-recommended/example_commands":"deployment/docker/example_commands",
+    "2.1.1-deploy-with-docker-recommended/using-keycloak":"deployment/docker/using-keycloak",
+    "2.1.2-deploy-without-docker/software-requirements":"deployment/deploy-without-docker/software-requirements",
+    "2.1.2-deploy-without-docker/pre-build-steps":"deployment/deploy-without-docker/pre-build-steps",
+    "2.1.2-deploy-without-docker/build-from-source":"deployment/deploy-without-docker/build-from-source",
+    "2.1.2-deploy-without-docker/import-the-seed-database":"deployment/deploy-without-docker/import-the-seed-database",
+    "2.1.2-deploy-without-docker/deploying":"deployment/deploy-without-docker/deploying",
+    "2.1.2-deploy-without-docker/load-sample-cancer-study":"deployment/deploy-without-docker/load-sample-cancer-study",
+    "2.2-authorization-and-authentication/user-authorization":"deployment/authorization-and-authentication/user-authorization",
+    "2.2-authorization-and-authentication/authenticating-users-via-saml":"deployment/authorization-and-authentication/authenticating-users-via-saml",
+    "2.2-authorization-and-authentication/authenticating-users-via-ldap":"deployment/authorization-and-authentication/authenticating-users-via-ldap",
+    "2.2-authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak":"deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak",
+    "2.2-authorization-and-authentication/authenticating-users-via-tokens":"deployment/authorization-and-authentication/authenticating-users-via-tokens",
+    "2.3-customization/customizing-your-instance-of-cbioportal":"deployment/customization/customizing-your-instance-of-cbioportal",
+    "2.3-customization/portal.properties-reference":"deployment/customization/portal.properties-reference",
+    "2.3-customization/caching":"deployment/customization/caching",
+    "2.3-customization/layout":"deployment/customization/studyview/#how-does-the-study-view-organize-the-charts",
+    "2.3-customization/priority":"deployment/customization/studyview/#study-view-customization-with-priority-data",
+    "2.4-integration-with-other-webservices/oncokb-data-access":"deployment/integration-with-other-webservices/oncokb-data-access",
+    "3.-cbioportal-maintenance/updating-your-cbioportal-installation":"updating-your-cbioportal-installation",
+    "3.-cbioportal-maintenance/updating-gene-and-gene_alias-tables":"updating-gene-and-gene_alias-tables",
+    "4.-development/feature-development-guide":"feature-development-guide",
+    "4.-development/cbioportal-er-diagram":"cbioportal-er-diagram",
+    "4.-development/build-different-frontend":"build-different-frontend",
+    "4.-development/session-service-working":"ession-service-working",
+    "4.-development/manual-test-cases":"manual-test-cases",
+    "4.-development/release-procedure":"release-procedure",
+    "4.-development/deployment-procedure":"deployment-procedure",
+    "5.1-data-loading/data-loading":"data-loading",
+    "5.2-datasets/downloads":"downloads",
+    "6.-web-api-and-clients/api-and-api-clients":"web-api-and-clients",
+    "7.-user-guide/user-guide":"user-guide",
+    "5.1-data-loading/data-loading/using-the-dataset-validator":"using-the-dataset-validator",
+    "5.1-data-loading/data-loading/using-the-metaimport-script":"using-the-metaimport-script",
+    "5.1-data-loading/data-loading/file-formats/z-score-normalization-script":"z-score-normalization-script",
+    "5.1-data-loading/data-loading/data-loading-maintaining-studies":"data-loading-maintaining-studies",
+    "5.1-data-loading/data-loading/data-loading-for-developers":"data-loading-for-developers",
+    "5.1-data-loading/data-loading/data-loading-tips-and-best-practices":"data-loading-tips-and-best-practices",
+    "5.1-data-loading/data-loading/import-gene-sets":"import-gene-sets",
+    "5.1-data-loading/data-loading/import-gene-panels":"import-gene-panels",
+};
+
+let newLocation = null;
+Object.keys(redirectMap).forEach(function(path){
+    if ((new RegExp(path + "$").test(window.location.pathname))) {
+        let root = document.querySelector("[name=turbo-root]")?.content || "";
+        root = root.replace("/","");
+        newLocation = `${window.location.protocol}//${window.location.hostname}${window.location.port ? ":" : ""}${window.location.port}/${root}/${window.redirectMap[path]}${window.location.hash}`; 
+    } 
+
+});
+
+if (newLocation) {
+    window.location.href = newLocation;
+} else {
+    document.getElementById("file-not-found").innerHTML = ` 
+    <h1>Document not found</h1>
+    <p>We recently changed our link structure and you may have a defunct url.  Please search for your topic above.</p> 
+    `;
+    document.getElementById("file-not-found").style.display = "block";
+}
+</script>
+
+
+
+
+<h2 id=""></h2>
+
+
+
+

documentation/About-Us.md

@@ -0,0 +1,117 @@
+The cBioPortal for Cancer Genomics was originally developed at [Memorial Sloan Kettering Cancer Center](https://www.mskcc.org/) (MSK). The [public cBioPortal site](https://www.cbioportal.org) is hosted by the [Center for Molecular Oncology](https://www.mskcc.org/research/molecular-oncology) at MSK. The cBioPortal software is now available under an open source license via [GitHub](https://github.com/cBioPortal/). The software is now developed and maintained by a multi-institutional team, consisting of MSK, the Dana Farber Cancer Institute, Princess Margaret Cancer Centre in Toronto, Children's Hospital of Philadelphia, [The Hyve](https://thehyve.nl) in the Netherlands, and Bilkent University in Ankara, Turkey.
+
+## Memorial Sloan Kettering Cancer Center
+* Jianjiong Gao
+* Benjamin Gross
+* Onur Sumer
+* Yichao Sun
+* Hongxin Zhang
+* Adam Abeshouse
+* Ritika Kundra
+* Ino de Bruijn
+* Robert Sheridan
+* Angelica Ochoa
+* Aaron Lisman
+* Manda Wilson
+* Avery Wang
+* Ramyasree Madupuri
+* Gaofei Zhao
+* Xiang Li
+* Anusha Satravada
+* Divya Madala
+* Nikolaus Schultz
+
+## Dana-Farber Cancer Institute
+* Ethan Cerami
+* Tali Mazor
+* Luke Sikina
+* Pieter Lukasse
+* Priti Kumari
+* Augustin Luna
+* James Lindsay
+* Chris Sander
+
+## Princess Margaret Cancer Centre, Toronto
+* Prasanna Jagannathan
+* Trevor Pugh
+
+## Children's Hospital of Philadelphia
+* David Higgins
+* Allison Heath
+* John Maris
+* Adam Resnick
+
+## The Hyve
+* Oleguer Plantalech
+* Pim van Nierop
+* Sander Rodenburg
+* Diana Baiceanu
+* Paul van Dijk
+* Sjoerd van Hagen
+* Kees van Bochove
+
+## Bilkent University
+* Ugur Dogrusoz
+* M. Salih Altun
+
+## Weill Cornell Medicine
+* Alexandros Sigaras
+* Olivier Elemento
+
+## Alumni
+* B. Arman Aksoy
+* Istemi Bahceci
+* Caitlin Byrne
+* Hsiao-Wei Chen
+* Ersin Ciftci
+* Fred Criscuolo
+* Leonard Dervishi
+* Gideon Dresdner
+* Andy Dufilie
+* Catherine Del Vecchio Fitz
+* Ziya Erkoc
+* Arthur Goldberg
+* Zachary Heins
+* Michael Heuer
+* Anders Jacobsen
+* Karthik Kalletla
+* Erik Larsson
+* Dong Li
+* Tamba Monrose
+* Peter Kok
+* Irina Pulyakhina
+* Pichai Raman
+* M. Furkan Sahin
+* Kaan Sancak
+* Jing Su
+* Sander Tan
+* Jiaojiao Wang
+* Stuart Watt
+* James Xu
+* Dionne Zaal
+* Kelsey Zhu
+* Fedde Schaeffer
+* Riza Nugraha
+* Ngoc Nguyen
+
+## Funding for the cBioPortal for Cancer Genomics is or has been provided by:
+
+### Current:
+* NCI, through [ITCR grant NCI-U24CA220457](https://itcr.nci.nih.gov/funded-project/cbioportal-cancer-genomics) and [HTAN grant NCI-U24CA233243](https://humantumoratlas.org/)
+* Marie-José and Henry R. Kravis Center for Molecular Oncology at MSK
+* Dana Farber Cancer Institute
+* American Association for Cancer Research through AACR Project GENIE
+* Prostate Cancer Foundation
+* The Cholangiocarcinoma Foundation
+* Robertson Foundation
+* Parker Institute for Cancer Immunotherapy
+
+### Past:
+* Stand Up 2 Cancer
+* The Ben & Catherine Ivy Foundation
+* NCI, as a [TCGA Genome Data Analysis Center (GDAC)](https://tcga.cancer.gov/wwd/program/research_network/gdac.asp) (NCI-U24CA143840)
+* NCRR, as the [National Resource for Network Biology (NRNB)](https://nrnb.org/) Research Resource (RR 031228-02)
+* Starr Cancer Consortium
+* Breast Cancer Research Foundation
+* Adenoid Cystic Carcinoma Research Foundation
+* POETIC Consortium

documentation/Architecture-Overview.md

@@ -0,0 +1,95 @@
+# Architecture Overview
+cBioPortal consists of the following components:
+
+- [backend](https://github.com/cBioPortal/cbioportal) written in Java
+- MySQL database that the backend uses
+- [validator](https://github.com/cBioPortal/cbioportal/tree/master/core/src/main/scripts/importer)
+  which checks file formats before importing data into the database
+- [frontend](https://github.com/cBioPortal/cbioportal-frontend)
+  built with React, Mobx and Bootstrap
+- [session service](https://github.com/cBioPortal/session-service) for storing
+  user saved data such as virtual studies and groups
+- Mongo database which session service uses
+- cBioPortal also uses the APIs from various [external services](#external-services) to provide more information about a variant
+
+## Backend
+
+The [backend](https://github.com/cBioPortal/cbioportal) is written in Java and
+connects to a MySQL database to serve a REST API following the OpenAPI
+specification (https://www.cbioportal.org/api/). Note that the repo where this
+lives in (https://github.com/cBioPortal/cbioportal) also contains Java classes
+to import data as well as the validator.
+
+The backend is organized as a multi-module Maven project.
+See [cBioPortal backend code organization](Backend-Code-Organization.md).
+
+## Validator
+The
+[validator](https://github.com/cBioPortal/cbioportal/tree/master/core/src/main/scripts/importer)
+checks file formats before importing data into the database. There is a wrapper
+script `metaImport.py` that validates the data and subsequently calls the
+relevant Java classes to import the data.
+
+## Session Service
+
+The [session service](https://github.com/cBioPortal/session-service) is used
+for storing user saved data such as virtual studies and groups. See the
+[tutorials](https://www.cbioportal.org/tutorials) section to read more about
+these features. Session service is a Java app that serves a REST API backed by
+a Mongo database. The session service is served as a proxy through the
+cBioPortal backend REST API. The backend is therefore the only component that
+needs to be able to connect to it. The frontend does not connect to it
+directly. 
+
+## Frontend
+The frontend is a single page app built with React, Mobx and Bootstrap. The
+data gets pulled from the backend REST API. The frontend is by default included
+with the backend so no extra setup is required. 
+
+## External Services
+cBioPortal uses the APIs from several external services to provide more
+information about a variant:
+
+- [OncoKB](#oncokb)
+- [CIVIC](#civic)
+- [Genome Nexus](#genome-nexus)
+- [G2S](#g2s)
+
+For privacy concerns see the section: [A note on privacy](#a-note-on-privacy).
+
+### OncoKB
+[OncoKB](https://www.oncokb.org) is a precision oncology knowledge base that
+contains information about the effects and treatment implications of specific
+cancer gene alterations. See the section [OncoKB Data Access](/deployment/integration-with-other-webservices/OncoKB-Data-Access.md)
+for how to configure external OncoKB service.
+
+### CIVIC
+[CIVIC](https://civicdb.org) is a community-edited forum for discussion and
+interpretation of peer-reviewed publications pertaining to the clinical
+relevance of variants (or biomarker alterations) in cancer. For information on
+how to deploy this service yourself see:
+https://github.com/griffithlab/civic-server. It is also possible to disable
+showing CIVIC in cBioPortal by setting `show.civic=false` in the
+`portal.properties` (See [portal.properties reference](/deployment/customization/portal.properties-Reference.md#civic-integration)).
+
+### Genome Nexus
+[Genome Nexus](https://www.genomenexus.org) is a comprehensive one-stop
+resource for fast, automated and high-throughput annotation and interpretation
+of genetic variants in cancer. For information on how to deploy this service
+yourself see: https://github.com/genome-nexus/genome-nexus. For more
+information on the various annotation sources and versions provided by Genome
+Nexus see: https://docs.genomenexus.org/annotation-sources.
+
+### G2S
+[G2S (Genome to Structure)](https://g2s.genomenexus.org) maps genomic variants
+to 3D structures. cBioPortal uses it on the mutations tab to show the variants
+on a 3D structure. For information on how to deploy this service yourself see:
+https://github.com/genome-nexus/g2s.
+
+### A note on privacy
+
+cBioPortal calls these services with variant information from the cBioPortal
+database. It however does not send over information that links a variant to a
+particular sample or patient. If this is a concern for your use case we recommmend
+to deploy your own versions of these services. See the sections above to
+linkouts for instructions on how to do this.