Migrate to Quartz

.gitattributes

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+* text=auto eol=lf

.github/FUNDING.yml

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+github: [jackyzha0]

.github/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Something about Quartz isn't working the way you expect
+title: ""
+labels: bug
+assignees: ""
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots and Source**
+If applicable, add screenshots to help explain your problem.
+
+You can help speed up fixing the problem by either
+
+1. providing a simple reproduction
+2. linking to your Quartz repository where the problem can be observed
+
+**Desktop (please complete the following information):**
+
+- Quartz Version: [e.g. v4.1.2]
+- `node` Version: [e.g. v18.16]
+- `npm` version: [e.g. v10.1.0]
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea or improvement for Quartz
+title: ""
+labels: enhancement
+assignees: ""
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "npm"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/ci.yaml

@@ -0,0 +1,72 @@
+name: Build and Test
+
+on:
+  pull_request:
+    branches:
+      - v4
+  push:
+    branches:
+      - v4
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    if: ${{ github.repository == 'jackyzha0/quartz' }}
+    strategy:
+      matrix:
+        os: [windows-latest, macos-latest, ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+
+      - name: Cache dependencies
+        uses: actions/cache@v4
+        with:
+          path: ~/.npm
+          key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+          restore-keys: |
+            ${{ runner.os }}-node-
+
+      - run: npm ci
+
+      - name: Check types and style
+        run: npm run check
+
+      - name: Test
+        run: npm test
+
+      - name: Ensure Quartz builds, check bundle info
+        run: npx quartz build --bundleInfo
+
+  publish-tag:
+    if: ${{ github.repository == 'jackyzha0/quartz' && github.ref == 'refs/heads/v4' }}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - name: Setup Node
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      - name: Get package version
+        run: node -p -e '`PACKAGE_VERSION=${require("./package.json").version}`' >> $GITHUB_ENV
+      - name: Create release tag
+        uses: pkgdeps/git-tag-action@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          github_repo: ${{ github.repository }}
+          version: ${{ env.PACKAGE_VERSION }}
+          git_commit_sha: ${{ github.sha }}
+          git_tag_prefix: "v"

.gitignore

@@ -135,3 +135,14 @@ dmypy.json
 
 # emacs backup files
 **/*~
+
+.DS_Store
+node_modules
+public
+prof
+tsconfig.tsbuildinfo
+.obsidian
+.quartz-cache
+private/
+.replit
+replit.nix

.node-version

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+v20.9.0

.npmrc

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+engine-strict=true

.prettierignore

@@ -0,0 +1,3 @@
+public
+node_modules
+.quartz-cache

.prettierrc

@@ -0,0 +1,7 @@
+{
+  "printWidth": 100,
+  "quoteProps": "as-needed",
+  "trailingComma": "all",
+  "tabWidth": 2,
+  "semi": false
+}

CODE_OF_CONDUCT.md

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+# Citizen Code of Conduct
+
+## 1. Purpose
+
+A primary goal of the Quartz community is to be inclusive to the largest number of contributors, with the most varied and diverse backgrounds possible. As such, we are committed to providing a friendly, safe and welcoming environment for all, regardless of gender, sexual orientation, ability, ethnicity, socioeconomic status, and religion (or lack thereof).
+
+This code of conduct outlines our expectations for all those who participate in our community, as well as the consequences for unacceptable behavior.
+
+We invite all those who participate in the Quartz community to help us create safe and positive experiences for everyone.
+
+## 2. Open [Source/Culture/Tech] Citizenship
+
+A supplemental goal of this Code of Conduct is to increase open [source/culture/tech] citizenship by encouraging participants to recognize and strengthen the relationships between our actions and their effects on our community.
+
+Communities mirror the societies in which they exist and positive action is essential to counteract the many forms of inequality and abuses of power that exist in society.
+
+If you see someone who is making an extra effort to ensure our community is welcoming, friendly, and encourages all participants to contribute to the fullest extent, we want to know.
+
+## 3. Expected Behavior
+
+The following behaviors are expected and requested of all community members:
+
+- Participate in an authentic and active way. In doing so, you contribute to the health and longevity of this community.
+- Exercise consideration and respect in your speech and actions.
+- Attempt collaboration before conflict.
+- Refrain from demeaning, discriminatory, or harassing behavior and speech.
+- Be mindful of your surroundings and of your fellow participants. Alert community leaders if you notice a dangerous situation, someone in distress, or violations of this Code of Conduct, even if they seem inconsequential.
+- Remember that community event venues may be shared with members of the public; please be respectful to all patrons of these locations.
+
+## 4. Unacceptable Behavior
+
+The following behaviors are considered harassment and are unacceptable within our community:
+
+- Violence, threats of violence or violent language directed against another person.
+- Sexist, racist, homophobic, transphobic, ableist or otherwise discriminatory jokes and language.
+- Posting or displaying sexually explicit or violent material.
+- Posting or threatening to post other people's personally identifying information ("doxing").
+- Personal insults, particularly those related to gender, sexual orientation, race, religion, or disability.
+- Inappropriate photography or recording.
+- Inappropriate physical contact. You should have someone's consent before touching them.
+- Unwelcome sexual attention. This includes, sexualized comments or jokes; inappropriate touching, groping, and unwelcomed sexual advances.
+- Deliberate intimidation, stalking or following (online or in person).
+- Advocating for, or encouraging, any of the above behavior.
+- Sustained disruption of community events, including talks and presentations.
+
+## 5. Weapons Policy
+
+No weapons will be allowed at Quartz community events, community spaces, or in other spaces covered by the scope of this Code of Conduct. Weapons include but are not limited to guns, explosives (including fireworks), and large knives such as those used for hunting or display, as well as any other item used for the purpose of causing injury or harm to others. Anyone seen in possession of one of these items will be asked to leave immediately, and will only be allowed to return without the weapon. Community members are further expected to comply with all state and local laws on this matter.
+
+## 6. Consequences of Unacceptable Behavior
+
+Unacceptable behavior from any community member, including sponsors and those with decision-making authority, will not be tolerated.
+
+Anyone asked to stop unacceptable behavior is expected to comply immediately.
+
+If a community member engages in unacceptable behavior, the community organizers may take any action they deem appropriate, up to and including a temporary ban or permanent expulsion from the community without warning (and without refund in the case of a paid event).
+
+## 7. Reporting Guidelines
+
+If you are subject to or witness unacceptable behavior, or have any other concerns, please notify a community organizer as soon as possible. j.zhao2k19@gmail.com.
+
+Additionally, community organizers are available to help community members engage with local law enforcement or to otherwise help those experiencing unacceptable behavior feel safe. In the context of in-person events, organizers will also provide escorts as desired by the person experiencing distress.
+
+## 8. Addressing Grievances
+
+If you feel you have been falsely or unfairly accused of violating this Code of Conduct, you should notify @jackyzha0 with a concise description of your grievance. Your grievance will be handled in accordance with our existing governing policies.
+
+## 9. Scope
+
+We expect all community participants (contributors, paid or otherwise; sponsors; and other guests) to abide by this Code of Conduct in all community venues--online and in-person--as well as in all one-on-one communications pertaining to community business.
+
+This code of conduct and its related procedures also applies to unacceptable behavior occurring outside the scope of community activities when such behavior has the potential to adversely affect the safety and well-being of community members.
+
+## 10. Contact info
+
+j.zhao2k19@gmail.com
+
+## 11. License and attribution
+
+The Citizen Code of Conduct is distributed by [Stumptown Syndicate](http://stumptownsyndicate.org) under a [Creative Commons Attribution-ShareAlike license](http://creativecommons.org/licenses/by-sa/3.0/).
+
+Portions of text derived from the [Django Code of Conduct](https://www.djangoproject.com/conduct/) and the [Geek Feminism Anti-Harassment Policy](http://geekfeminism.wikia.com/wiki/Conference_anti-harassment/Policy).
+
+_Revision 2.3. Posted 6 March 2017._
+
+_Revision 2.2. Posted 4 February 2016._
+
+_Revision 2.1. Posted 23 June 2014._
+
+_Revision 2.0, adopted by the [Stumptown Syndicate](http://stumptownsyndicate.org) board on 10 January 2013. Posted 17 March 2013._

Dockerfile

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+FROM node:20-slim as builder
+WORKDIR /usr/src/app
+COPY package.json .
+COPY package-lock.json* .
+RUN npm ci
+
+FROM node:20-slim
+WORKDIR /usr/src/app
+COPY --from=builder /usr/src/app/ /usr/src/app/
+COPY . .
+CMD ["npx", "quartz", "build", "--serve"]

LICENSE.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 jackyzha0
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -2,7 +2,8 @@
 
 This repository hosts templates, scripts and contents for primary technical documentation for Developers and Administrators of the [Biomedical Data Translator](https://ncats.nih.gov/translator) project [("Translator"; Fecho _et al,_ 2022)](https://ascpt.onlinelibrary.wiley.com/doi/10.1111/cts.13301) of the [National Center for Advancing Translational Sciences ("NCATS")](https://ncats.nih.gov).
 
-The repository uses the [`mkdocs`](https://www.mkdocs.org/) tooling to generate and manage an indexed compendium of the documentation for [Open Access licensed](LICENSE) hosting on its [Official Site (https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/)](https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/).
+This repository uses Quartz v4, you can read the [documentation here](https://quartz.jzhao.xyz/)
+
 
 ## Getting Started
 
@@ -44,12 +45,4 @@ The Translator `mkdocs` documentation is hierarchically structured as follows:
         teams/
             index.md  # project details about Translator
             ...
-        faq.md        # frequently asked questions
-        glossary.md   # basic glossary of Translator buzzwords
-        license.md
-
-with some utility resources:
 
-        img/          # shared images
-        includes/     # shared site abbreviation file, etc
-        stylesheets/  # CSS styles for the site

content/Abbreviations.md

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+* **NIH**: National Institutes of Health
+* **NCATS**: National Center for Advancing Translational Sciences
+* **Biolink Model**: Open-source data model that can be used to formalize the relationships between data structures in translational science. 
+* **KP**: Knowledge Provider
+* **KPs**: Knowledge Providers
+* **ARA**: Autonomous Relay Agent
+* **ARAs**: Autonomous Relay Agents
+* **ARS**: Autonomous Relay System
+* **ARAX**: Expander Agent
+* **SRI**: Standards and Reference Implementation
+* **TRAPI**: Translator Reasoner API
+* **COHD**: Columbia Open Health Data
+* **EPC**: Evidence, Provenance and Confidence
+* **TCDC**: Translator Clinical Data Committee
+* **ITRB**: Information Technology Resources Branch
+* **API**: Application Programming Interface
+* **KG**: Knowledge Graph
+* **HTML**: Hyper Text Markup Language
+* **LLM**: Large Language Model
+* **LLMs**: Large Language Models
+* **ML**: Machine Learning
+* **DL**: Deep Learning
+* **QA**: Question Answering
+* **API**: Application Programming Interface
+* **UI**: User Interface
+* **CLI**: Command-Line Interface
+* **PyPI**: Python Packaging Index
+* **PyPA**: Python Packaging Authority
+* **PEP**: Python Enhancement Proposal
+* **YAML**: Depending on whom you ask, YAML stands for "Yet Another Markup Language", or "YAML Ain't Markup Language"
+* **JSON**: JavaScript Object Notation
+* **URL**: Uniform Resource Locator
+* **URI**: Uniform Resource Identifier
+* **IRI**: International Resource Identifier
+* **GPU**: Graphics Processing Unit
+* **CPU**: Central Processing Unit
+* **TPU**: Tensor Processing Unit
+* **RDF**: Resource Description Framework
+* **PDF**: Portable Document Format
+* **ZSH**: The Z shell (Zsh) is a Unix shell that can be used as an interactive login shell, and as a command interpreter for shell scripting.
+* **BASH**: The Bourne-Again SHell (BASH) is a Unix shell that can be used as an interactive login shell, and as a command interpreter for shell scripting.
+* **OpenAPI**: OpenAPI, formerly known as Swagger, is a specification language for HTTP APIs that defines structure and syntax in a way that is not wedded to the programming language the API is created in.
+* **SmartAPI**: SmartAPI: a standardized catalog of OpenAPI sites, with enhanced service metadata (https://smart-api.info/)
+* **JS**: JavaScript
+* **TS**: TypeScript
+* **CSS**: Cascading Style Sheets
+* **CSV**: Comma-Separated Value
+* **TSV**: Tab-Separated Value
+* **PSV**: Pipe-Separated Value
+* **ODT**: Open Document Format

docs/glossary.md → content/Translator Glossary of Terms.md

@@ -1,5 +1,3 @@
-# Translator Glossary of Terms
-
 ## Translator UI: Web interface to the Translator system
 * Displays scored and ranked results and evidence, confidence, and provenance from the ARS
 * Currently only supports a select set of templated queries

docs/architecture/ars_usage.md → content/architecture/Autonomous Relay System.md

@@ -1,5 +1,3 @@
-# Autonomous Relay System
-
 The Autonomous Relay System (ARS) was developed by the Link Brokers team for NCATS Biomedical Data Translator
 
 The ARS is built by NCATS staff and relays translator queries from the user to the autonomous relay agents (ARAs) using an iterative process to generate results in the form of a knowledge graph that is then provided to the user.