From 61e5451c056291ae4ccd5f03564a5cf76779f169 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Wed, 2 Oct 2024 10:05:31 -0400 Subject: [PATCH 1/3] remove extra qoute --- markdown/documentation/guides/download/clientdownload.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/markdown/documentation/guides/download/clientdownload.md b/markdown/documentation/guides/download/clientdownload.md index 7effc3b7..8421e3e5 100644 --- a/markdown/documentation/guides/download/clientdownload.md +++ b/markdown/documentation/guides/download/clientdownload.md @@ -103,7 +103,7 @@ docker run -d -it --name score-client \ Add the manifest to the `./guideMaterials/dataDownload` folder in your QuickStart repository. For simplicity, update its name to manifest.tsv. After moving and renaming the manifest, you can run the provided command: ```bash -docker exec score-client sh -c "score-client download --manifest /output/manifest.tsv --output-dir /output"" +docker exec score-client sh -c "score-client download --manifest /output/manifest.tsv --output-dir /output" ``` From 3f10e0c1d27de708899a852971bf7b94e70e8072 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Tue, 5 Nov 2024 20:49:05 -0500 Subject: [PATCH 2/3] Website update for new docs site --- constants/external-links.js | 84 ++++++------- constants/pages.js | 1 - constants/products.js | 3 +- src/components/NavBar/index.js | 56 +++------ src/components/NavBar/styles.scss | 8 +- src/components/ServicesPageSection/index.js | 7 +- src/components/SupportFooter/index.js | 74 +++++++++--- src/pages/about-us/index.js | 24 ++-- src/pages/getting-started/index.js | 127 +++++++++----------- src/pages/services/index.js | 2 +- 10 files changed, 196 insertions(+), 190 deletions(-) diff --git a/constants/external-links.js b/constants/external-links.js index b774efc6..4540bb37 100644 --- a/constants/external-links.js +++ b/constants/external-links.js @@ -1,21 +1,32 @@ +// Overture Docs + Demo + export const DEMO_LINK = 'https://demo.overture.bio/'; -export const DOCKER_DOWNLOAD = - 'https://www.docker.com/products/docker-desktop/'; +export const DOCUMENTATION_LINK = 'https://main--overturedev.netlify.app/'; +export const OVERTURE_GITHUB_LINK = 'https://github.com/overture-stack/'; +export const OVERTURE_DOCUMENTATION_CONTRIBUTION_LINK = + 'https://main--overturedev.netlify.app/community/contribution'; +export const OVERTURE_GITHUB_DISSCUSSION_LINK = + 'https://github.com/overture-stack/docs/discussions'; +export const OVERTURE_DOCUMENTATION_SUPPORT_LINK = + 'https://main--overturedev.netlify.app/community/support'; export const FEATURE_REQUESTS = 'https://github.com/overture-stack/website/issues/new?assignees=&labels=&projects=&template=Feature_Requests.md'; +export const USER_GUIDES = + 'https://main--overturedev.netlify.app/guides/user-guides/'; +export const ADMINISTRATION_GUIDES = + 'https://main--overturedev.netlify.app/guides/administration-guides/'; +export const DEPLOYMENT_GUIDES = + 'https://main--overturedev.netlify.app/guides/deployment-guide/'; +export const API_REFERENCE_GUIDE = + 'https://main--overturedev.netlify.app/guides/api-reference'; +export const OVERTURE_DOCUMENTATION_CORE_SOFTWARE = + 'https://main--overturedev.netlify.app/docs/core-software/'; +export const OVERTURE_DOCUMENTATION_UNDER_DEVELOPMENT = + 'https://main--overturedev.netlify.app/docs/under-development/'; + +// Case Study Links -export const ICGC_ARGO_LINK = 'https://www.icgc-argo.org/'; -export const ICGC_ARGO_PORTAL_LINK = 'https://platform.icgc-argo.org/'; -export const CGC_LINK = 'https://cancercollaboratory.org/'; -export const FAQ_LINK = - 'https://oicr.on.ca/information-practices-frequently-asked-questions/'; export const GDC_LINK = 'https://portal.gdc.cancer.gov/'; -export const OVERTURE_GITHUB_LINK = 'https://github.com/overture-stack/'; -export const GITHUB_ISSUES_LINK = `${OVERTURE_GITHUB_LINK}roadmap/issues`; -export const GITHUB_SUBMIT_ISSUES_LINK = - 'https://github.com/overture-stack/website/issues/new?assignees=&labels=bug&projects=&template=bug_report.md&title=BUG+-+'; -export const GITHUB_REQUEST_FEATURES_LINK = - 'https://github.com/overture-stack/website/issues/new?assignees=&labels=new-feature&projects=&template=Feature_Request.md&title=Feature+Request+'; export const HCMIS_LINK = 'https://hcmi-searchable-catalog.nci.nih.gov/'; export const HCMIS_PORTAL_LINK = 'https://hcmi-searchable-catalog.nci.nih.gov/'; export const ICGC_LINK = 'https://dcc.icgc.org/'; @@ -23,26 +34,32 @@ export const IHCC_LINK = 'https://ihccglobal.org/'; export const IHCC_PORTAL_LINK = 'https://atlas.ihccglobal.org/'; export const KIDS_FIRST_LINK = 'https://portal.kidsfirstdrc.org/login?redirect_path=/dashboard?'; +export const VIRUSSEQ_LINK = + 'https://genomecanada.ca/challenge-areas/cancogen/virusseq/'; +export const VIRUSSEQ_PORTAL_LINK = 'https://virusseq-dataportal.ca/explorer'; +export const ICGC_ARGO_LINK = 'https://www.icgc-argo.org/'; +export const ICGC_ARGO_PORTAL_LINK = 'https://platform.icgc-argo.org/'; +export const CGC_LINK = 'https://cancercollaboratory.org/'; + +// Misc Links + +export const DOCKER_DOWNLOAD = + 'https://www.docker.com/products/docker-desktop/'; export const NETLIFY_IMAGE_LINK = 'https://www.netlify.com/img/global/badges/netlify-color-bg.svg'; export const NETLIFY_LINK = 'https://www.netlify.com/'; export const OICR_LINK = 'https://oicr.on.ca'; -export const OVERTURE_YOUTUBE_LINK = - 'https://www.youtube.com/embed/NrgL8vpFm5s'; export const POLICIES_LINK = 'https://oicr.on.ca/oicr-policies-and-procedures/'; export const PRIVACY_EMAIL_LINK = 'mailto:privacy@oicr.on.ca'; -export const SLACK_LINK = - 'https://join.slack.com/t/overture-bio/shared_invite/zt-21tdumtdh-9fP1TFeLepK4~Lc377rOYw'; export const TEAM_BLOG_LINK = 'https://softeng.oicr.on.ca/'; export const TEAM_LINK = 'https://softeng.oicr.on.ca/team/'; -export const VIRUSSEQ_LINK = - 'https://genomecanada.ca/challenge-areas/cancogen/virusseq/'; -export const VIRUSSEQ_PORTAL_LINK = 'https://virusseq-dataportal.ca/explorer'; export const EMAIL_LINK = 'mailto:contact@overture.bio'; export const GI_PROGRAM_LINK = 'https://oicr.on.ca/programs/genome-informatics/'; +export const FAQ_LINK = + 'https://oicr.on.ca/information-practices-frequently-asked-questions/'; -// PRODUCTS LINKS +// Product Links // arranger export const ARRANGER_GETTING_STARTED_LINK = @@ -53,9 +70,7 @@ export const ARRANGER_UPDATES_LINK = export const ARRANGER_GITHUB_LINK = 'https://github.com/overture-stack/arranger'; -// DMS -export const DMS_RELEASE_NOTES = `${OVERTURE_GITHUB_LINK}dms/releases`; -export const CANARIE_LINK = 'https://www.canarie.ca/'; +// stage export const STAGE_GITHUB_LINK = 'https://github.com/overture-stack/stage'; // ego @@ -63,32 +78,11 @@ export const EGO_SQL_LINK = `${OVERTURE_GITHUB_LINK}ego/blob/develop/src/main/re export const EGO_UPDATES_LINK = 'https://www.overture.bio/documentation/ego/'; export const EGO_GITHUB_LINK = 'https://github.com/overture-stack/ego'; -// jukebox -export const JUKEBOX_BLOG_POST_LINK = - 'http://softeng.oicr.on.ca/kevin_hartmann/2018/03/28/Drops-of-Jupyter/'; -export const JUPYTER_LINK = 'https://jupyter.org/index.html'; -export const JUPYTER_INSTALL_LINK = 'https://jupyter.org/install.html'; - -// oncojs -export const LOLLIPLOT_EXAMPLE_LINK = - 'https://portal.gdc.cancer.gov/genes/ENSG00000183914'; -export const ONCOGRID_EXAMPLE_LINK = - 'https://dcc.icgc.org/analysis/view/oncogrid/ce6fd9fd-b76e-488d-88a5-93bdc690f79e'; -export const SURVIVALPLOT_EXAMPLE_LINK = - 'https://dcc.icgc.org/analysis/view/phenotype/15c7c81a-7717-49e3-a0f7-be09fdc400b6'; -export const PATHWAYVIEWER_EXAMPLE_LINK = - 'https://dcc.icgc.org/genesets/R-HSA-1236974/pathway-viewer'; -export const ONCOJS_GITHUB_LINK = 'https://github.com/oncojs'; - // maestro export const MAESTRO_UPDATES_LINK = 'https://www.overture.bio/documentation/maestro/'; export const MAESTRO_GITHUB_LINK = 'https://github.com/overture-stack/maestro'; -// persona -export const PERSONA_LOCAL_LINK = 'http://localhost:3232/graphql'; -export const PERSONA_ENV_SCHEMA_LINK = `${OVERTURE_GITHUB_LINK}persona/blob/master/.env.schema`; - // song export const SONG_DOCS_LINK = 'https://www.overture.bio/documentation/song/'; export const SONG_BLOG_POST_LINK = diff --git a/constants/pages.js b/constants/pages.js index 9b4dc564..fd151e58 100644 --- a/constants/pages.js +++ b/constants/pages.js @@ -3,7 +3,6 @@ import { internalUrlJoin } from '../utils'; export const ABOUT_US_PATH = '/about-us/'; export const ACKNOWLEDGEMENTS_PATH = '/acknowledgements/'; export const CASE_STUDIES_PATH = '/case-studies/'; -export const CONTACT_US_PATH = '/contact-us/'; export const COMMUNITY_PATH = '/community/'; export const GETTING_STARTED_PATH = '/getting-started/'; export const PRIVACY_PATH = '/privacy/'; diff --git a/constants/products.js b/constants/products.js index 3e6486c8..1be284b3 100644 --- a/constants/products.js +++ b/constants/products.js @@ -1,7 +1,7 @@ import urlJoin from 'proper-url-join'; import { internalUrlJoin } from '../utils'; import { PRODUCTS_PATH } from './pages'; -import { ONCOJS_GITHUB_LINK, OVERTURE_GITHUB_LINK } from './external-links'; +import { OVERTURE_GITHUB_LINK } from './external-links'; // products info that is created or accessed programmatically // for other external link constants use external-links.js @@ -43,7 +43,6 @@ const productsObj = { title: 'Maestro', }, oncojs: { - githubUrl: ONCOJS_GITHUB_LINK, iconWhite: 'productOncoWhite', title: 'OncoJS', }, diff --git a/src/components/NavBar/index.js b/src/components/NavBar/index.js index a154d25b..37addead 100644 --- a/src/components/NavBar/index.js +++ b/src/components/NavBar/index.js @@ -3,8 +3,6 @@ * subcomponents: MegaMenu and NavLink */ import React, { Component } from 'react'; -import MegaMenu from './MegaMenu'; -import MegaMenuLink from './MegaMenuLink'; import NavLink from './NavLink'; import { Button, LinkHelper as Link } from 'components'; import { @@ -15,20 +13,18 @@ import { PRODUCTS_PATH, SERVICES_PATH, } from 'constants/pages'; -import { SLACK_LINK } from 'constants/external-links'; +import { SDOCUMENTATION_LINK } from 'constants/external-links'; import logo from './assets/overture_logo.svg'; import './styles.scss'; +import { + DOCUMENTATION_LINK, + OVERTURE_GITHUB_LINK, +} from '../../../constants/external-links'; class NavBar extends Component { render() { - const { - closeMenus, - megaMenuType, - mobileMenuOpen, - path, - toggleMegaMenu, - toggleMobileMenu, - } = this.props; + const { closeMenus, megaMenuType, mobileMenuOpen, toggleMobileMenu } = + this.props; let mobileMenuClass = mobileMenuOpen ? 'is-active' : ''; let navbarMenuClass = `navbar-menu ${mobileMenuClass}`; @@ -65,24 +61,11 @@ class NavBar extends Component { url={PRODUCTS_PATH} name="Products" /> - -
(this.popoverRef = ref)}> - {mobileMegaCheck && ( - - )} -
- + {/* grey section with three cubes */} -
{/* second column - submit issues and make contribution */}
-

Help make our docs better

+

+ Help make our docs better +

  • - + Submit an issue
  • - + Submit a feature request
  • - + Make a contribution
    • @@ -115,25 +139,41 @@ function SupportFooter({ location }) { {/* third column - slack link */}

    Still need help?

    - Ask us on Slack + + Check out our GitHub Discussion Forum +
    {/* joint column - second and third column*/}
    -

    Help make our docs better

    +

    + Help make our docs better +

    diff --git a/src/pages/about-us/index.js b/src/pages/about-us/index.js index f68cb611..48f21090 100644 --- a/src/pages/about-us/index.js +++ b/src/pages/about-us/index.js @@ -13,11 +13,13 @@ import { } from 'components'; import { OVERTURE_GITHUB_LINK, - GITHUB_ISSUES_LINK, - SLACK_LINK, GI_PROGRAM_LINK, } from 'constants/external-links'; import './styles.scss'; +import { + OVERTURE_DOCUMENTATION_CONTRIBUTION_LINK, + OVERTURE_DOCUMENTATION_SUPPORT_LINK, +} from '../../../constants/external-links'; const AboutUsPage = () => { return ( @@ -53,8 +55,8 @@ const AboutUsPage = () => { We are the{' '} - Genome Informatics Software Engineering team from Ontario Institute for Cancer - Research + Genome Informatics Software Engineering team from Ontario + Institute for Cancer Research . At OICR we develop new software, databases and other necessary components to store, organize and compute over the large and @@ -136,16 +138,16 @@ const AboutUsPage = () => { {/* yellow button div */}
diff --git a/src/pages/getting-started/index.js b/src/pages/getting-started/index.js index 455d9563..791557ee 100644 --- a/src/pages/getting-started/index.js +++ b/src/pages/getting-started/index.js @@ -26,7 +26,17 @@ import { DOWNLOAD_GUIDE, SUBMISSION_GUIDE, } from '../../../constants/pages'; -import { FEATURE_REQUESTS } from '../../../constants/external-links'; +import { + ADMINISTRATION_GUIDES, + API_REFERENCE_GUIDE, + DEPLOYMENT_GUIDES, + FEATURE_REQUESTS, + OVERTURE_DOCUMENTATION_CONTRIBUTION_LINK, + OVERTURE_DOCUMENTATION_CORE_SOFTWARE, + OVERTURE_DOCUMENTATION_UNDER_DEVELOPMENT, + OVERTURE_GITHUB_DISSCUSSION_LINK, + USER_GUIDES, +} from '../../../constants/external-links'; export default function GettingStartedPage() { const docsSearchIndex = process.env.GATSBY_ALGOLIA_INDEX_NAME; @@ -136,9 +146,6 @@ export default function GettingStartedPage() {
-
- -

Platform Guides

@@ -151,84 +158,66 @@ export default function GettingStartedPage() {
  • - Deployment: generalized - instructions for deploying our platform from start to finish + {' '} + User guides: stepwise guides covering + platform usage.
  • {' '} - Submission:stepwise instructions - on submitting data to our platform + Administration: detailed + stepwise instructions for customizing our platform.
  • - {' '} - Download: stepwise instructions on - downloading data from our platform + Deployment: generalized + instructions for deploying our platform from start to finish.
  • {' '} - Administration: detailed - stepwise instructions for customizing your platform + API Reference: explore + endpoints, request parameters and response schemas through a + Swagger UI.
-
-
-

Product Documentation

- - Detailed product documentation for administrators and developers - -
-
-
- {/* User Documentation bullets left */} -
-
    -
  • - Ego: authentication - and authorization for users and applications -
    • -
  • - Song: data - management with automated submission validations -
    • -
  • - Score: secure - multipart file transfers to and from object storage -
    • -
-
- {/* User Documentation bullets right */} -
-
    -
  • - Maestro: - indexes published Song metadata into Elastisearch -
    • -
  • - Arranger: - search API generation with customizable UI component - library -
    • -
  • - Stage: - react-based portal UI made to integrate with Overture - services -
    • -
-
-
-
+
+

Developer Documentation

+ + Detailed product documentation for administrators and developers +
+ +
+ +
+
- If you can't find what you are looking for, please submit{' '} + If you can't find what you are looking for, please let us know{' '} - a GitHub request + + using our ideas discussion forum. +
@@ -257,16 +246,16 @@ export default function GettingStartedPage() {
diff --git a/src/pages/services/index.js b/src/pages/services/index.js index 706647db..52774509 100644 --- a/src/pages/services/index.js +++ b/src/pages/services/index.js @@ -36,7 +36,7 @@ const ServicesPage = () => { list1="Technical audits" list2="Step-by-step guidance" list3="Troubleshooting" - buttonText="Contact us on Slack" + buttonText="Community Supports" contactMessage="or email us at contact@overture.bio" /> {/* grey section */} From a0cd38203b0c776e5e7ba7e7ca41810f09efeac0 Mon Sep 17 00:00:00 2001 From: Mitchell Shiell <59712867+MitchellShiell@users.noreply.github.com> Date: Sun, 8 Dec 2024 16:20:10 -0500 Subject: [PATCH 3/3] updated and checked all links to doc site --- constants/external-links.js | 19 +++++++++---------- src/components/AnchorHeading/index.js | 8 +++++++- src/components/NavBar/index.js | 3 +-- src/components/ProductsPageSection/index.js | 2 +- src/pages/getting-started/index.js | 16 ++-------------- 5 files changed, 20 insertions(+), 28 deletions(-) diff --git a/constants/external-links.js b/constants/external-links.js index 4540bb37..0b429a63 100644 --- a/constants/external-links.js +++ b/constants/external-links.js @@ -1,28 +1,27 @@ // Overture Docs + Demo export const DEMO_LINK = 'https://demo.overture.bio/'; -export const DOCUMENTATION_LINK = 'https://main--overturedev.netlify.app/'; +export const DOCUMENTATION_LINK = 'https://docs.overture.bio/'; export const OVERTURE_GITHUB_LINK = 'https://github.com/overture-stack/'; export const OVERTURE_DOCUMENTATION_CONTRIBUTION_LINK = - 'https://main--overturedev.netlify.app/community/contribution'; + 'https://docs.overture.bio/community/contribution'; export const OVERTURE_GITHUB_DISSCUSSION_LINK = 'https://github.com/overture-stack/docs/discussions'; export const OVERTURE_DOCUMENTATION_SUPPORT_LINK = - 'https://main--overturedev.netlify.app/community/support'; + 'https://docs.overture.bio/community/support'; export const FEATURE_REQUESTS = 'https://github.com/overture-stack/website/issues/new?assignees=&labels=&projects=&template=Feature_Requests.md'; -export const USER_GUIDES = - 'https://main--overturedev.netlify.app/guides/user-guides/'; +export const USER_GUIDES = 'https://docs.overture.bio/guides/user-guides/'; export const ADMINISTRATION_GUIDES = - 'https://main--overturedev.netlify.app/guides/administration-guides/'; + 'https://docs.overture.bio/guides/administration-guides/'; export const DEPLOYMENT_GUIDES = - 'https://main--overturedev.netlify.app/guides/deployment-guide/'; + 'https://docs.overture.bio/guides/deployment-guide/'; export const API_REFERENCE_GUIDE = - 'https://main--overturedev.netlify.app/guides/api-reference'; + 'https://docs.overture.bio/guides/api-reference'; export const OVERTURE_DOCUMENTATION_CORE_SOFTWARE = - 'https://main--overturedev.netlify.app/docs/core-software/'; + 'https://docs.overture.bio/docs/core-software/'; export const OVERTURE_DOCUMENTATION_UNDER_DEVELOPMENT = - 'https://main--overturedev.netlify.app/docs/under-development/'; + 'https://docs.overture.bio/docs/under-development/'; // Case Study Links diff --git a/src/components/AnchorHeading/index.js b/src/components/AnchorHeading/index.js index 0641d98f..4406fccb 100644 --- a/src/components/AnchorHeading/index.js +++ b/src/components/AnchorHeading/index.js @@ -2,7 +2,13 @@ import React from 'react'; import { GoLink as LinkIcon } from 'react-icons/go'; import { LinkHelper as Link } from 'components'; -export default function AnchorHeading({ children, id, location, size: H, ...props }) { +export default function AnchorHeading({ + children, + id, + location, + size: H, + ...props +}) { return ( {/* need ID for the table of contents sidebar in docs section*/} diff --git a/src/components/NavBar/index.js b/src/components/NavBar/index.js index 37addead..e5fa8542 100644 --- a/src/components/NavBar/index.js +++ b/src/components/NavBar/index.js @@ -13,7 +13,6 @@ import { PRODUCTS_PATH, SERVICES_PATH, } from 'constants/pages'; -import { SDOCUMENTATION_LINK } from 'constants/external-links'; import logo from './assets/overture_logo.svg'; import './styles.scss'; import { @@ -64,7 +63,7 @@ class NavBar extends Component {
-

Getting Started

+

Run our QuickStart

{/* The img holding div below displays in mobile/tablet view.*/}