diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..f4995e498 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,103 @@ +# Contributing to Overture + +We appreciate your interest in contributing to this project. We are the 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 process the large and complex datasets being generated by our cancer research programs. Embodying OICR's values of collaboration and community, we are firm believers in open-source and open-science. As such we strongly believe in the collective power of expertise and shared resources. + +## Code of Conduct + +By participating in this project, you are expected to abide by our [Code of Conduct](/community/code-of-conduct). Please take the time to read it carefully before contributing. + +## Get Involved + +**Getting Started:** Our primary platform for community support, feature requests, and general discussions is GitHub Discussions. This allows us to keep all conversations in one place and make them easily searchable for future reference. + + +**Community Support:** Our primary platform for community support, feature requests, and general discussions is [GitHub Discussions](https://github.com/overture-stack/docs/discussions). This allows us to keep all conversations in one place and make them easily searchable for future reference. + +- **Getting Help:** If you need assistance with Overture, please create a [new discussion in our support category](https://github.com/overture-stack/docs/discussions/categories/support). + - Before creating a new discussion, please search existing discussions to see if your question has already been answered. +- **Feature Requests & Proposals:** We love hearing your ideas for improving Overture! Before making a feature request, please check our [**feature roadmap**](https://github.com/orgs/overture-stack/projects/11/views/1) to see if your idea is already planned. + - If your idea isn't on the roadmap, feel free to [**submit a feature request**](https://github.com/overture-stack/docs/discussions/categories/ideas) by creating a new discussion in our Ideas category +- **Report a Potential Bug:** We use GitHub Issues primarily for tracking confirmed bugs and ticketing development tasks. If you come across a potential bug or issue, please first post it to our [**GitHub support discussion forum**](https://github.com/overture-stack/docs/discussions/categories/support). + - This allows us to confirm the issue and gather more information if needed. If we determine that further development is required, we will create and tag you into a GitHub Issue from your discussion post. + +## Our Development Process + +We use GitHub issues and pull requests for communication related to code changes. + +### Branch Organization + +We use the following standard branches: + +- `main` is for stable production code +- `develop` is the integration branch for new features +- `feature/` for feature branches +- `release/v` for release branches +- `hotfix/` for hotfix branches + +## Pull Requests + +### Submitting a Pull Request + +We welcome and encourage pull requests from the community. To submit a pull request, please follow these steps: + +1. **Fork the Repository**: Fork the Overture repository on GitHub. +2. **Clone Your Fork**: Clone your forked repository to your local machine. +3. **Create a New Branch**: Create a new branch for your changes. Use lowercase and hyphens (e.g., `feature/user-authentication`). Include ticket/issue numbers when applicable (e.g., `feature/PROJ-123-user-authentication`). +4. **Make Your Changes**: Implement your changes and commit them to your branch. Write clear, concise commit messages in present tense (e.g., "Add feature" not "Added feature"). Reference issue numbers in commits when applicable. +5. **Push Your Changes**: Push your changes to your forked repository. +6. **Submit a Pull Request**: Open a pull request against the main repository. + +### Best Practices + +1. **Keep PRs as small as possible:** Focus on one feature or bug fix per pull request. Break large changes into smaller, more manageable pieces making it easier for reviewers to understand and approve your changes. + +2. **Use descriptive titles:** Start with a verb (e.g., "Add", "Fix", "Update", "Refactor"), briefly summarize the main purpose of the PR and include the issue number if applicable (e.g., "Fix user authentication bug (#123)"). + +3. **Describe how you tested it:** Explain the testing process you followed and mention any new automated tests you've added. + +4. **Provide a clear description:** Explain the purpose of your changes and list the main modifications you've made. Mention any potential side effects or areas that might need extra attention. + +5. **Link related issues:** Reference any related issues or pull requests. Use GitHub keywords to automatically link issues (e.g., "Closes #123", "Fixes #456"). +6. **Keep the PR's branch up-to-date:** Regularly rebase your branch on the latest main branch and resolve any merge conflicts promptly. + +7. **Respond to feedback:** Be open to suggestions and willing to make changes. Address all comments from reviewers. If you disagree with a suggestion, explain your reasoning politely. + +8. **Include documentation updates:** If your changes affect user-facing features, update or create and issue detailing the relevant changes need to the documentation. Where appropriate include inline comments for complex code sections. + +10. **Be patient:** Reviewers will likely be unable to respond immediately. However, feel free to follow up politely if you haven't received feedback after a reasonable time. + +### Using Draft Pull Requests + +Draft Pull Requests are an excellent way to document work in progress and facilitate early feedback. Use them to: + +- Organize your thoughts and process +- Share early work and ideas with the team +- Get feedback on implementation approaches before finalizing code +- Track progress on long-running features + +Guidelines for Draft Pull Requests: + +1. **Creation**: + - Open a pull request and select "Create draft pull request" + - Clearly mark the title with [WIP] or [DRAFT] prefix +2. **Description**: + - Outline the current state of the work + - List planned tasks or improvements + - Highlight areas where feedback is specifically needed +3. **Updates**: + - Regularly update the description or provide comments following commits with progress notes +- Use task lists (using `- [ ]` in Markdown) to track completion of sub-tasks +4. **Collaboration**: + - Encourage early feedback and discussion + - Use the pull request comments for design discussions +5. **Finalization**: + - Complete all planned work and address feedback + - Update tests and documentation + - Click "Ready for review" to move out of draft state + +### Merging a Pull Request + +- Ensure all CI checks pass +- Obtain the required number of approvals +- Use the project's specified merge strategy (Typically squash and merge) +- Delete the source branch after merging if no longer needed diff --git a/README.md b/README.md index da3219512..4f1282951 100644 --- a/README.md +++ b/README.md @@ -1,99 +1,85 @@ -# Arranger - Data Portal API and UI component Generation +# Arranger -[](http://slack.overture.bio) -[](https://github.com/overture-stack/arranger/blob/develop/LICENSE) -[](code_of_conduct.md) - -
-arranger-logo -
- -Arranger integrates with your underlying Elasticsearch cluster to automatically generate a powerful search API based on your configured index mapping. It consists of two main modules, **Arranger Server** and **Arranger Components**. - -**Arranger Server** is a GraphQL API that communicates with an Elasticsearch index. Arranger Server uses a consistent and custom filter notation called SQON. SQON is designed to be user-friendly, allowing humans to easily understand and create custom filters while being straightforward for software systems to interpret and process. - -**Arranger Components** are interactive and configurable UI components specifically designed to display and query complex datasets from a web browser. - - +Arranger is a versatile, data-agnostic GraphQL search API that leverages Elasticsearch, designed to simplify the process of creating powerful search interfaces for complex datasets. It's accompanied by its own React component library to generate interactive and highly configurable search UIs.
-> +> >
-> +> >
> -> *Arranger is a core service within the [Overture](https://www.overture.bio/) research software ecosystem. See our [related products](#related-products) for more information on how Overture helps organize data and enable discovery.* +> *Arranger is part of [Overture](https://www.overture.bio/), a collection of open-source software microservices used to create platforms for researchers to organize and share genomics data.* > > - - -## Documentation - -- For development resources, including set up and technical details, see our [Developer Documentation.](https://github.com/overture-stack/arranger/wiki) -- For more information on installation, configuration, and usage see our [User Documentation.](https://www.overture.bio/documentation/arranger/installation/installation/) +## Repository Structure -## Quickstart Docker Install +The repository is organized with the following directory structure: -To install Arranger using Docker, follow these steps: - -1. Clone the Arranger repository -2. Navigate to the project directory -3. With Docker running, execute the quickstart `make` target: - -```shell -make start +``` +arranger/ +├── docker/ +│ ├── elasticsearch/ +│ ├── server/ +│ ├── test/ +│ └── ui/ +├── modules/ +│ ├── admin-ui/ +│ ├── components/ +│ └── server/ +└── scripts/ ``` -The deployed services will be accessible through the following ports: +- **docker/**: Contains miscellaneous configuration files used for building Docker images of Arranger Server, and to support running a local developer environment. -| Service | Port | -|--|--| -| Arranger Server | localhost:5050/graphql | -| Elasticsearch | localhost:9200 | -| Kibana | localhost:5601 | +- **docs/**: Markdown files that contain instructions on how to use Arranger and its capabilities, contribution guidelines, etc. -**Note(s):** +- **modules/**: Core Arranger modules: + - **admin-ui/**: (Inactive) Administration interface for generating and managing Arranger configuration files. + - **components/**: React components to streamline integration of search portals with an Arranger server. + - **server/**: The "Arranger" server itself, a GraphQL service that facilitates usage of Lucene-based search engines (e.g. Elasticsearch). +- **scripts/**: Utility scripts for development, deployment, and system management. -- To generate the API Arranger requires an Elasticsearch Instance and an index mapping. For information on setting Arranger up with a default index mapping, see our [official documentation page on supplying an index mapping.](https://www.overture.bio/documentation/arranger/installation/configuration/es/) +## Documentation -- Arranger is undergoing refactoring work for what will become version 3+. An _upgrade guide_ is on its way. Current users of v2 may look at the `legacy` branch, meanwhile, where we will continue fixing newly reported bugs until further notice. +Technical resources for those working with or contributing to the project are available from our official documentation site, the following content can also be read and updated within the `/docs` folder of this repository. -- You may need to add the `--legacy-peer-deps` flag when integrating our modules into your apps. Along with the rewrite, we're steadily updating the internal dependencies, so this isn't necessary. +- **[Arranger Overview](https://main--overturedev.netlify.app/docs/core-software/Arranger/overview)** +- [**Setting up the Development Enviornment**](https://main--overturedev.netlify.app/docs/core-software/Arranger/setup) +- [**Common Usage Docs**](https://main--overturedev.netlify.app/docs/core-software/Arranger/setup) -## Support & Contributions +## Development Environment -- Filing an [issue](https://github.com/overture-stack/arranger/issues) -- Making a [contribution](CONTRIBUTING.md) -- Connect with us on [Slack](https://overture-bio.slack.com/) -- Add or Upvote a [feature request](https://github.com/overture-stack/arranger/issues?q=is%3Aopen+is%3Aissue+label%3Anew-feature+sort%3Areactions-%2B1-desc) +- [Node.js](https://nodejs.org/) (v18 or higher) +- [npm](https://www.npmjs.com/) (v8.3.0 or higher) +- [Docker](https://www.docker.com/) (v4.32.0 or higher) -## Related Products +## Support & Contributions -
- Overture overview -
+- For support, feature requests, and bug reports, please see our [Support Guide](https://main--overturedev.netlify.app/community/support). -Overture is an ecosystem of research software tools, each with narrow responsibilities, designed to reduce redundant programming efforts and enable developers and data scientists to build reliable systems that organize and share big data. +- For detailed information on how to contribute to this project, please see our [Contributing Guide](https://main--overturedev.netlify.app/docs/contribution). -All our core microservices are included in the Overture **Data Management System** (DMS). 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/). +## Related Software -See the links below for additional information on our other research software tools: +The Overture Platform includes the following Overture Components:
|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| - -## Acknowledgements +|[Score](https://github.com/overture-stack/score/)| Transfer data to and from any cloud-based storage system | +|[Song](https://github.com/overture-stack/song/)| Catalogue and manage metadata associated to file data spread across cloud storage systems | +|[Maestro](https://github.com/overture-stack/maestro/)| Organizing your distributed data into a centralized Elasticsearch index | +|[Arranger](https://github.com/overture-stack/arranger/)| A search API with reusable search UI components | +|[Stage](https://github.com/overture-stack/stage)| A React-based web portal scaffolding | +|[Lyric](https://github.com/overture-stack/lyric)| A model-agnostic, tabular data submission system | +|[Lectern](https://github.com/overture-stack/lectern)| Schema Manager, designed to validate, store, and manage collections of data dictionaries. | + +If you'd like to get started using our platform [check out our quickstart guides](https://main--overturedev.netlify.app/guides/getting-started) + +## Funding Acknowledgement Overture is supported by grant #U24CA253529 from the National Cancer Institute at the US National Institutes of Health, and additional funding from Genome Canada, the Canada Foundation for Innovation, the Canadian Institutes of Health Research, Canarie, and the Ontario Institute for Cancer Research. diff --git a/code_of_conduct.md b/code_of_conduct.md new file mode 100644 index 000000000..b98ba4790 --- /dev/null +++ b/code_of_conduct.md @@ -0,0 +1,132 @@ +# 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, 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 email 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 +[this email](contact@overture.bio). +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 \ No newline at end of file diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index 366460467..000000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line. -SPHINXOPTS = -SPHINXBUILD = sphinx-build -SPHINXPROJ = Arranger -SOURCEDIR = . -BUILDDIR = _build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) \ No newline at end of file diff --git a/docs/assets/arrangerDev.svg b/docs/assets/arrangerDev.svg new file mode 100644 index 000000000..c99b51e01 --- /dev/null +++ b/docs/assets/arrangerDev.svg @@ -0,0 +1 @@ +
e
e
Search & Exploration
Search & Exploration
Arranger Configs
Define the structure and formatting of your data
Arranger Configs...


Index Mapping
Define the structure of your index

Index Mapping...
Event Processing
Message queuing of publication events for triggering downstream data indexing 
Event Processing...
Data Management & Storage
Data Management & Storagez

Song Schema
Define input fields with rules, logic and syntax

Song Schema...

Object Storage Providers
Score is compatible with any S3 compliant object storage provider

Object Storage Providers...
Authorization & Authentication
Authorization & Authentication

Overture API Key Provider
Extends Keyloak's functionality to support API authentication

Overture API Key Provider...Text is not SVG - cannot display \ No newline at end of file diff --git a/docs/assets/arrangercomponent.webp b/docs/assets/arrangercomponent.webp new file mode 100644 index 000000000..2fec4bba6 Binary files /dev/null and b/docs/assets/arrangercomponent.webp differ diff --git a/docs/assets/sqon_query.jpg b/docs/assets/sqon_query.jpg new file mode 100644 index 000000000..d5b70de4c Binary files /dev/null and b/docs/assets/sqon_query.jpg differ diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index d70998c24..000000000 --- a/docs/conf.py +++ /dev/null @@ -1,166 +0,0 @@ -#!/usr/bin/env python3 -# -*- coding: utf-8 -*- -# -# Ego documentation build configuration file, created by -# sphinx-quickstart on Fri Mar 16 14:17:55 2018. -# -# This file is execfile()d with the current directory set to its -# containing dir. -# -# Note that not all possible configuration values are present in this -# autogenerated file. -# -# All configuration values have a default; values that are commented out -# serve to show the default. - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -# import os -# import sys -# sys.path.insert(0, os.path.abspath('.')) - - -# -- General configuration ------------------------------------------------ - -# If your documentation needs a minimal Sphinx version, state it here. -# -# needs_sphinx = '1.0' - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: -# -# source_suffix = ['.rst', '.md'] -source_suffix = '.rst' - -# The master toctree document. -master_doc = 'index' - -# General information about the project. -project = 'Arranger' -copyright = '2018, overture.bio' -author = 'overture.bio' - -# The version info for the project you're documenting, acts as replacement for -# |version| and |release|, also used in various other places throughout the -# built documents. -# -# The short X.Y version. -version = '0.1.0' -# The full version, including alpha/beta/rc tags. -release = '0.1.0' - -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = 'sphinx' - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -# Custom sidebar templates, must be a dictionary that maps document names -# to template names. -# -# This is required for the alabaster theme -# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars -html_sidebars = { - '**': [ - 'relations.html', # needs 'show_related': True theme option to display - 'searchbox.html', - ] -} - - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = 'Arrangerdoc' - - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', -} - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - (master_doc, 'Arranger.tex', 'Arranger Documentation', - 'overture.bio', 'manual'), -] - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [ - (master_doc, 'arranger', 'Arranger Documentation', - [author], 1) -] - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - (master_doc, 'Arranger', 'Arranger Documentation', - author, 'Arranger', 'One line description of project.', - 'Miscellaneous'), -] diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 8a5786ba9..000000000 --- a/docs/index.rst +++ /dev/null @@ -1,45 +0,0 @@ -.. Arranger documentation main file, created by - sphinx-quickstart on Fri Mar 16 14:17:55 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -============ -Arranger Documentation -============ - -.. toctree:: - :maxdepth: 4 - :caption: First Steps - - src/introduction.rst - src/gettingstarted.rst - -.. toctree:: - :maxdepth: 4 - :caption: User Documentation - - src/admins.rst - src/appdevelopers.rst - src/sqon.rst - -.. toctree:: - :maxdepth: 4 - :caption: Developer Documentation - - src/installation.rst - src/architecture.rst - src/technology.rst - src/contribution.rst - - -Contribute ------------- -If you'd like to contribute to this project, it's hosted on github. - -See https://github.com/overture-stack/arranger - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`search` diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 54f16ff65..000000000 --- a/docs/make.bat +++ /dev/null @@ -1,36 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=. -set BUILDDIR=_build -set SPHINXPROJ=Arranger - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% - -:end -popd diff --git a/docs/overview.md b/docs/overview.md new file mode 100644 index 000000000..682543f37 --- /dev/null +++ b/docs/overview.md @@ -0,0 +1,73 @@ +# Overview + +Arranger is a versatile, data-agnostic GraphQL search API that leverages Elasticsearch, designed to simplify the process of creating powerful search interfaces for complex datasets. It's accompanied by its own React component library to generate interactive and highly configurable search UIs. + + :::info Arranger uses Elasticsearch 7 + + Our search platform is built on and compatible with version 7.x of Elasticsearch. All queries to ES must follow that version's syntax and conventions. + + ::: + +## Key Features + +- **Configurable Search UI:** Provides a suite of customizable search interface components based on Elasticsearch index mappings, easily tailored to fit specific data structures and user needs without extensive manual coding. +- **GraphQL API:** Arranger Server generates a GraphQL API from Elasticsearch mappings, offering: + - Efficient data retrieval + - Adaptable structure + - SQON integration for human-readable and machine-processable search queries +- **Data Agnostic:** Works with any properly structured Elasticsearch index. +- **Integration-Ready:** Designed to work with any React-based front-end UIs. + +## System Architecture + +Arranger integrates with your underlying Elasticsearch cluster to automatically generate a powerful GraphQL search API based on your configured index mapping. It consists of two main modules: + +- **Arranger Server:** The back-end search API service that: + - Generates a GraphQL API from Elasticsearch mappings + - Acts as middleware between the UI and Elasticsearch + - Simplifies querying and filtering using Serializable Query Object Notation ([SQON](https://www.overture.bio/documentation/arranger/reference/sqon/)) + - Provides an intermediary layer to avoid direct interaction with complex Elasticsearch queries + +- **Arranger Components:** A library of React components for building interactive search UIs, communicating with Arranger Server to fetch and display data. + +![Arranger Architecture](./assets/arrangerDev.svg 'Arranger Architecture Diagram') + +As part of the larger Overture.bio software suite, Arranger typically integrates with other services: + +- **Elasticsearch:** The underlying search and analytics engine (created and maintained by [Elastic](https://www.elastic.co/elasticsearch)) that Arranger interfaces with to provide powerful search capabilities. +- **Stage:** The React-based web portal scaffolding that provides the overall structure and layout, within which Arranger components are rendered to create a cohesive and interactive data exploration interface. + +![Arranger Components](./assets/arrangercomponent.webp 'Arranger Components') + +The Arranger Components image above highlights three key features: + +- **Faceted Search (Red):** Allow users to filter data using multiple dimensions. +- **Data Tables (Blue):** Display search results in a customizable, interactive table format. +- **SQON Viewers (Yellow):** Visualize and manage complex search queries. + +## Repository Structure + +The Arranger repository can be accessed from our Overture-Stack GitHub page [located here](https://github.com/overture-stack/arranger). + +``` +arranger/ +├── docker/ +│ ├── elasticsearch/ +│ ├── server/ +│ ├── test/ +│ └── ui/ +├── modules/ +│ ├── admin-ui/ +│ ├── components/ +│ └── server/ +└── scripts/ +``` + +- **`docker/`**: Contains miscellaneous configuration files used for building Docker images of Arranger Server, and to support running a local developer environment. +- **`docs/`**: Markdown files that contain instructions on how to use Arranger and its capabilities, contribution guidelines, etc. +- **`modules/`**: Core Arranger modules: + - **`admin-ui/`**: (Inactive) Administration interface for generating and managing Arranger configuration files. + - **`components/`**: React components to streamline integration of search portals with an Arranger server. + - **`server/`**: the "Arranger" server itself, a GraphQL service that facilitates usage of Lucene-based search engines (e.g. Elasticsearch). +- **`scripts/`**: Utility scripts for development, deployment, and system management. + diff --git a/docs/setup.md b/docs/setup.md new file mode 100644 index 000000000..ada7844dc --- /dev/null +++ b/docs/setup.md @@ -0,0 +1,153 @@ +# Setup + +## Prerequisites + +Before you begin, ensure you have the following installed on your system: + +- Node.js (v18) +- npm (v8.3.0 or higher) +- [Docker](https://www.docker.com/products/docker-desktop/) (v4.32.0 or higher) + +## Developer Setup + +This guide will walk you through setting up a complete development environment, including Arranger and its complementary services. + +### Setting up supporting services + +We'll use the Overture Conductor service, a flexible Docker Compose setup, to spin up Maestro's complementary services. + +1. Clone the Conductor repository and navigate to its directory: + + ```bash + git clone https://github.com/overture-stack/conductor.git + cd conductor + ``` + +2. Run the appropriate start command for your operating system: + + | Operating System | Command | + |------------------|---------| + | Unix/macOS | `make arrangerDev` | + | Windows | `./make.bat arrangerDev` | + +
+ **Click here for a detailed breakdown** + + This command will set up all complementary services for Arranger development as follows: + + ![arrangerDev](./assets/arrangerDev.svg 'Arranger Dev Environment') + + | Service | Port | Description | Purpose in Arranger Development | + |---------|------|-------------|------------------------------| + | Conductor | `9204` | Orchestrates deployments and environment setups | Manages the overall development environment | + | Elasticsearch | `9200` | Distributed search and analytics engine | Provides fast and scalable search capabilities over indexed data | + | Stage | `3000` | Web Portal Scaffolding | Houses Arranger's search UI components | + + :::note Arranger uses Elasticsearch 7 + + Our search platform is built on and compatible with version 7.x of Elasticsearch. All queries to ES must follow that version's syntax and conventions. + + ::: + + - Ensure all ports are free on your system before starting the environment. + - You may need to adjust the ports in the `docker-compose.yml` file if you have conflicts with existing services. + + For more information, see our [Conductor documentation linked here](/docs/other-software/Conductor). + +
+ +### Running the Arranger-Server + +1. Clone Arranger and navigate to its directory: + + ```bash + git clone https://github.com/overture-stack/arranger.git + cd arranger + ``` + +2. Rename the `.env.arrangerDev` file to `.env`: + + ```bash + mv .env.arrangerDev .env + ``` + + :::info + + This `.env` file is preconfigured for the Arranger dev environment quickstart: + + ``` + # ============================== + # Arranger Environment Variables + # ============================== + + # Arranger Variables + ENABLE_LOGS=false + # Elasticsearch Variables + ES_HOST=http://elasticsearch:9200 + ES_USER=elastic + ES_PASS=myelasticpassword + # Stage Variables + REACT_APP_BASE_URL=http://localhost:3000 + ``` + +
+ **Click here for a detailed explanation of Arranger's environment variables** + + **Arranger Variables** + - `ENABLE_LOGS`: Determines whether logging is enabled + - **Elasticsearch Variables** + - `ES_HOST`: The URL of your Elasticsearch instance + - `ES_USER` and `ES_PASS`: The credentials for accessing Elasticsearch + + **Stage Variables** + + - `REACT_APP_BASE_URL`: The base URL for your front-end application (Stage) + - `REACT_APP_ARRANGER_ADMIN_ROOT`: The URL for the Arranger GraphQL endpoint +
+ + ::: + +3. Install the required npm packages: + + ```bash + npm ci + ``` + + :::warning + Python version 3.10.15 or lower is required. Python 3.12 is not supported yet. + ::: + + +4. Bootstrap the Arranger repository: + + ```bash + npm run bootstrap + ``` + +5. Run the Arranger server: + + ```bash + npm run server + ``` + +Once the server starts, you can access Arranger-Server at `http://localhost:5050/graphql`. + +### Running the Arranger Components + + +:::info Coming Soon +We are currently working on updating our development environment for Arranger Components. Documentation for implementing them, including their development setup and Storybook integration, will be available here in the near future. +::: + +## Troubleshooting + +If you encounter any issues during setup: + +1. Ensure all prerequisites are correctly installed and at the specified versions. +2. Check that all services in the Docker Compose setup are running correctly. +3. Verify that your `.env` file contains the correct configuration. +4. If you're having network issues, ensure that the ports specified in the configuration are not being used by other services. + +:::info Need Help? +If you encounter any issues or have questions about our API, please don't hesitate to reach out through our relevant [**community support channels**](/community/support). +::: \ No newline at end of file diff --git a/docs/src/admins.rst b/docs/src/admins.rst deleted file mode 100644 index 902c0a121..000000000 --- a/docs/src/admins.rst +++ /dev/null @@ -1,98 +0,0 @@ -======================= -Arranger for Administrators -======================= - -Tutorial -====================== - -To administer Arranger, the admin must: - -**1. Install Arranger.** - - View the `installation instructions `_. - -**2. Have an Elasticsearch mapping and data indexed to search.** - - View the `Indexing Demo Data `_ for a demo setup. - -**3. Admin registers the indices with arranger through the admin UI and apply configurations.** - -Using the Admin UI -====================== - -The arranger UI reflects the following pseudo entity relationship: - -.. image :: images/admin_system.png - -**1) Projects:** - - .. image :: images/projects.png - - This page lists the available projects and provides an interface for registering new projects - - Available functionalities: - - - Adding a new project - - Removing existing project - - Export configuration data (exported data can then be imported into new projects to migrate data). - - Clicking on a project id will navigate to that project's list of indices. - -**2) Indices:** - - .. image :: images/indices.png - - This page lists the indices registered to Arranger under the selected project. - - Clicking on an index name will navigate to the configuration page for the index. The following configurations are available: - - **a) Fields configurations** - - .. image :: images/fields.png - - This lists all fields available in the index and allows configuration of Arranger metadata for these fields, including: - - - **Display Name**: how the field should be displayed to user. - - **Aggregation Type**: lets the search portal know how to display aggregation filters for the field. - - **Active**: this field is **DEPRECATED** - - **Quicksearch enabled**: whether the field is enabled for quicksearch using the `@arranger/components`'s `QuickSearch` component. - - **Is primary key**: check if the field is the unique identifier for the index's main entity. - - **Is array**: check if the field is an array. Elasticsearch's mapping does not specify this information. - - For convenience, filtering on the fields can be done through the inputs above the header. - - **b) Facet panel configurations** - - .. image :: images/aggs.png - - This lists all available aggregations on the fields mentioned. On Arranger's default portal UI, this list is rendered as a facet panel. Each entry on Supported configutations: - - - Ordering the facets: drag the facet on its "hamberger menu icon" to place the facet at the desired position. Alternatively, the position can also be set through the select menu beside the icon. - - **Shown**: displays the facet in the portal's facet panel. - - **Active**: enables this facet for search. An `Active` facet will appear in the `AdvancedFacetView` component in `@arranger/components`. Only facets that are both `Active` and `Shown` will be shown in the portal's facet panel. - - **c) Data table configurations** - - .. image :: images/table.png - - This contains configuration for the data table in the default portal. Each entry in the list represents a column in the data table. Available configurations: - - - Column order: positioning can be done by dragging or using the select, similar to the facet panel. - - **Active**: enables this column to be viewed in the table. Does not show by default. - - **Default**: shows this column by default. Can only be checked if `Active` is checked. - - **Sortable**: enables sorting of the table on this field. - - **d) Quick search configurations** - - .. image :: images/quicksearch.png - - This contains configuration for the portal's quick-search feature, which allows users to filter indexed entities by text. Currently, Arranger only supports exact match on quicksearch, but free-text search is in our roadmap to support. This feature can be exposed to end-users throught the `QuickSearch` UI component from `@arranger/components`. - - Only entities (in other words, the root object and its "nested" fields in Elasticsearch) are available for quick search. - - Available configurations: - - - **Display Name**: the name to display this field as. - - **Active**: check to enable search for this entity. - - **Key Field**: the unique field that identifies each instance of this entity. - - **Search Field**: the properties of the entity to enable search on. \ No newline at end of file diff --git a/docs/src/appdevelopers.rst b/docs/src/appdevelopers.rst deleted file mode 100644 index e25540079..000000000 --- a/docs/src/appdevelopers.rst +++ /dev/null @@ -1,140 +0,0 @@ -===================================== -Arranger for Application Developers -===================================== - -Arranger comes in individual pieces that can be flexibly composed together to meet your application's needs. These include: - - `@arranger/server `_: the main server-side application - - `@arranger/components `_: UI components used for building end-user facing applications - - `@arranger/admin `_: the server-side admin Graphql API - - `@arranger/admin-ui `_: the UI interface as described in the `Arranger for Administrators `_ guide. - -Additionally, some packages that are used internally are also published. These include: - - `@arranger/schema `_: contains the Graphql schema generated and served by `@arranger/server`. - - `@arranger/mapping-utils `_: contains utility functions used for computing / interpreting elasticsearch mappings and Arranger metadata about the mappings. - - `@arranger/middleware `_: responsible for translating SQON and aggregation parameters from the `@arranger/server` to elasticsearch queries and aggregations. - -Server-side -================================ - -On the server side, `@arranger/server` and `@arranger/admin` are the relevant packages. - -Some prerequisit: - - - Elasticsearch version 6.6.1 running. - - - Kibana version 6.6.1 (optional) - - - NodeJs version 10 - -There are multiple ways to get up and running with Arranger on the server-side: - - 1) Running a stand-alone all-in-one instance: - - - Using Docker: - - 1) The latest arranger server image is available on `Dockerhub `_ - - 2) Alternatively, you may build an image using the `Dockerfile.server` file from the `Arranger source `_ - - - Running with Node: - - 1) Clone the Arranger repo: :code:`git clone git@github.com:overture-stack/arranger.git` - - 2) Navigate to the directory: :code:`cd arranger` - - 3) Install dependencies: :code:`npm ci && npm run bootstrap` - - 4) Navigate to the `modules/server` directory: :code:`cd modules/server` - - 5) Start the server: :code:`npm start` - - This will start an instance of :code:`@arranger/server` on port :code:`5050`. - - By default, this bundle also comes with the admin API from :code:`@arranger/admin` serverd at :code:`/admin/api`. From your browser, navigate to http://localhost:5050/admin/graphql to explore this API - - Limitation of this approach: the API from :code:`@arranger/admin` is **not** meant to be exposed to end-users, hence also **not horizontally scalable**. For the second a production-ready setup, please use the next option: - - 2) Running with custom express apps: - - - Example search app (horizontally scalable): - - .. code-block:: Javascript - - import express from 'express'; - import Arranger from '@arranger/server'; - - const PORT = 9000 - - Arranger({ - esHost: "http://localhost:9200" - }).then(router => { - const app = express(); - app.use(router); - app.listen(PORT, () => { - console.log(`⚡️⚡️⚡️ search API listening on port ${PORT} ⚡️⚡️⚡️ `) - }) - }) - - - Example admin app (single instance): - - .. code-block:: Javascript - - import express from "express"; - import adminGraphql from "@arranger/admin/dist"; - - const PORT = 8000 - - adminGraphql({ - esHost: "http://localhost:9200" - }).then(adminApp => { - const app = express(); - adminApp.applyMiddleware({ - app, - path: "/admin" - }); - app.listen(PORT, () => { - console.log(`⚡️⚡️⚡️ Admin API listening on port ${PORT} ⚡️⚡️⚡️`) - }) - }) - - Both applications should be interacting with the same Elasticsearch instance. Since they are two separate applications, they can be scaled separately, with separate authentication and authorization rules. - -Browser-side -================================ - -On the browser side, `@arranger/admin-ui` and `@arranger/components` are the relevant packages. Both packages are both written in `React `_, hence we recommend using React for your application for the most seamless integration. - -- `@arranger/admin-ui`: This package provides the admin interface that is documented in the `Arranger for administrator `_ section. - - **Integration with your React app:** - - 1) Install the package: :code:`npm i @arranger/admin-ui` - 2) Integrate into your app: - - .. code-block:: Javascript - - import ArrangerAdmin from '@arranger/admin-ui/dist'; - import { Route, Switch } from 'react-router-dom'; - - const ArrangerAdminPage = () => ( - - ) - - Configurations: - - :code:`basename`: tells :code:`ArrangerAdmin` to treat :code:`/admin` as the root path for client-side routing. - - :code:`apiRoot`: tells :code:`ArrangerAdmin` to communicate with back-end API hosted at :code:`http://localhost:8000` - - :code:`fetcher`: allows specifying custom data fetcher to use, this is usefull for integrating custom client-side loggins / authorization logics. :code:`fetcher` must implment the `Fetch API `_. - -- `@arranger/components`: This package provides UI components that are pre-configured to work with the `@arranger/server` API. To explore the components this package provide, follow the steps bellow: - - 1) Clone the Arranger repo: :code:`git clone git@github.com:overture-stack/arranger.git` - - 2) Navigate to the directory: :code:`cd arranger` - - 3) Install dependencies: :code:`npm ci && npm run bootstrap` - - 4) Navigate to the `modules/components` directory: :code:`cd modules/components` - - 5) Start the `Storybook `_ server: :code:`npm run storybook` - - A basic repo UI can be found at: `arranger/modules/components/stories/Portal.js` \ No newline at end of file diff --git a/docs/src/architecture.rst b/docs/src/architecture.rst deleted file mode 100644 index af19f40ed..000000000 --- a/docs/src/architecture.rst +++ /dev/null @@ -1,4 +0,0 @@ -Architecture -============================ - -**Coming Soon** \ No newline at end of file diff --git a/docs/src/contribution.rst b/docs/src/contribution.rst deleted file mode 100644 index 38d4ef5e1..000000000 --- a/docs/src/contribution.rst +++ /dev/null @@ -1,4 +0,0 @@ -Contributing to the Arranger Project -============================ - -**Coming Soon** \ No newline at end of file diff --git a/docs/src/file_centric_docs.rst b/docs/src/file_centric_docs.rst deleted file mode 100644 index 66fa946eb..000000000 --- a/docs/src/file_centric_docs.rst +++ /dev/null @@ -1,587 +0,0 @@ - -.. code-block:: - - PUT file_centric/file_centric/GF_PA4QSRH7 - { - "reference_genome": "hs37d5", - "size": 65776072338, - "file_name": "HKLYJCCXX-2.hgv.bam", - "controlled_access": true, - "instrument_models": [], - "participants": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "family_id": "FM_6BBCE6KK", - "outcome": { - "disease_related": "Not Reported", - "kf_id": "OC_2N6ARS4T", - "vital_status": "Not Applicable" - }, - "kf_id": "PT_5HYPY6F9", - "affected_status": false, - "race": "White", - "external_id": "7-11f", - "ethnicity": "Not Hispanic or Latino", - "biospecimens": [ - { - "ncit_id_tissue_type": "NCIT:C14165", - "genomic_files": [], - "kf_id": "BS_R0J8RCHY", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "DS-CDH-COL-GSO-RD", - "dbgap_consent_code": "phs001110.c1", - "external_sample_id": "7-11f", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "7-11f" - } - ], - "family": { - "family_id": "FM_6BBCE6KK", - "family_compositions": [ - { - "composition": "trio", - "shared_hpo_ids": [], - "available_data_types": [], - "family_members": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_5HYPY6F9", - "relationship": "father", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_49PFVJ0D", - "relationship": "mother", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": true, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_1H22MDCN", - "relationship": "child", - "race": "White", - "ethnicity": "Not Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [ - "SNOMEDCT:63191000119107" - ], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [ - "HP:0008012", - "HP:0002672", - "HP:0007009", - "HP:0001627" - ], - "hpo_phenotype_observed": [], - "external_id": [ - "07-0011-congenital birth defect-Negative", - "07-0011-gastrointestinal defect-Negative", - "07-0011-central nervous system defect-Negative", - "07-0011-congenital heart defect-Negative" - ], - "hpo_phenotype_observed_text": [], - "age_at_event_days": [], - "snomed_phenotype_observed": [], - "source_text_phenotype": [], - "ancestral_hpo_ids": [] - } - } - ] - } - ], - "father_id": "PT_5HYPY6F9", - "mother_id": "PT_49PFVJ0D" - }, - "study": { - "name": "Genomic Analysis of Congenital Diaphragmatic Hernia", - "attribution": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001110.v1.p1", - "release_status": "Pending", - "kf_id": "SD_46SK55A3", - "version": "v1.p1", - "short_name": "Congenital Diaphragmatic Hernia", - "external_id": "phs001110", - "data_access_authority": "dbGaP" - }, - "gender": "Male" - } - ], - "availability": "Immediate Download", - "file_format": "bam", - "experiment_strategies": [], - "latest_did": "f1ef940a-8cdf-4c83-8480-bd970beb5468", - "acl": [ - "phs001110", - "phs001110.c1", - "SD_46SK55A3" - ], - "kf_id": "GF_PA4QSRH7", - "platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "Not Reported", - "max_insert_size": 421, - "library_name": "IWG_IND-GMKFWC.CDH7-11f-1_2pA", - "experiment_strategy": "WGS", - "is_paired_end": true, - "kf_id": "SE_X8AB114M", - "instrument_model": "HiSeq X Ten", - "experiment_date": "2016-02-10T00:00:00+00:00", - "external_id": "IWG_IND-GMKFWC.CDH7-11f-1_2pA", - "platform": "Not Reported", - "mean_insert_size": 349.29, - "mean_read_length": 150 - } - ], - "external_id": "s3://kf-seq-data-bcm/chung/HKLYJCCXX-2.hgv.bam", - "is_harmonized": false - } - PUT file_centric/file_centric/GF_JWWBRFFR - { - "reference_genome": "hs37d5", - "size": 62991171434, - "file_name": "HKMFHCCXX-7.hgv.bam", - "controlled_access": true, - "instrument_models": [], - "participants": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "family_id": "FM_6VWR7XWE", - "outcome": { - "disease_related": "Not Reported", - "kf_id": "OC_2QGSTDRX", - "vital_status": "Not Applicable" - }, - "kf_id": "PT_TQPMJMDF", - "affected_status": false, - "race": "White", - "external_id": "766", - "ethnicity": "Hispanic or Latino", - "biospecimens": [ - { - "ncit_id_tissue_type": "NCIT:C14165", - "genomic_files": [], - "kf_id": "BS_NHWTYNNQ", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "DS-CDH-COL-GSO-RD", - "dbgap_consent_code": "phs001110.c1", - "external_sample_id": "766", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "766" - } - ], - "family": { - "family_id": "FM_6VWR7XWE", - "family_compositions": [ - { - "composition": "trio", - "shared_hpo_ids": [], - "available_data_types": [], - "family_members": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_TQPMJMDF", - "relationship": "father", - "race": "White", - "ethnicity": "Hispanic or Latino" - }, - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_W0FXX1S0", - "relationship": "mother", - "race": "White", - "ethnicity": "Hispanic or Latino" - }, - { - "is_proband": true, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_2MB8Y7S9", - "relationship": "child", - "race": "White", - "ethnicity": "Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [ - "SNOMEDCT:63191000119107" - ], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [ - "HP:0008012", - "HP:0002672", - "HP:0007009", - "HP:0001627" - ], - "hpo_phenotype_observed": [], - "external_id": [ - "01-0774-congenital birth defect-Negative", - "01-0774-gastrointestinal defect-Negative", - "01-0774-central nervous system defect-Negative", - "01-0774-congenital heart defect-Negative" - ], - "hpo_phenotype_observed_text": [], - "age_at_event_days": [], - "snomed_phenotype_observed": [], - "source_text_phenotype": [], - "ancestral_hpo_ids": [] - } - } - ] - } - ], - "father_id": "PT_TQPMJMDF", - "mother_id": "PT_W0FXX1S0" - }, - "study": { - "name": "Genomic Analysis of Congenital Diaphragmatic Hernia", - "attribution": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001110.v1.p1", - "release_status": "Pending", - "kf_id": "SD_46SK55A3", - "version": "v1.p1", - "short_name": "Congenital Diaphragmatic Hernia", - "external_id": "phs001110", - "data_access_authority": "dbGaP" - }, - "gender": "Male" - } - ], - "availability": "Immediate Download", - "file_format": "bam", - "experiment_strategies": [], - "latest_did": "68dbabf8-fc38-4fcd-a82e-5be412bbf340", - "acl": [ - "phs001110", - "phs001110.c1", - "SD_46SK55A3" - ], - "kf_id": "GF_JWWBRFFR", - "platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "Not Reported", - "max_insert_size": 421, - "library_name": "IWG_IND-GMKFWC.CDH766-1_2pA", - "experiment_strategy": "WGS", - "is_paired_end": true, - "kf_id": "SE_3QZ9BS30", - "instrument_model": "HiSeq X Ten", - "experiment_date": "2016-01-31T00:00:00+00:00", - "external_id": "IWG_IND-GMKFWC.CDH766-1_2pA", - "platform": "Not Reported", - "mean_insert_size": 349.29, - "mean_read_length": 150 - } - ], - "external_id": "s3://kf-seq-data-bcm/chung/HKMFHCCXX-7.hgv.bam", - "is_harmonized": false - } - PUT file_centric/file_centric/GF_5KSEA2F2 - { - "reference_genome": "hs37d5", - "size": 70709429717, - "file_name": "HKNFYCCXX-5.hgv.bam", - "controlled_access": true, - "instrument_models": [], - "participants": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "family_id": "FM_9PS4VHQ2", - "outcome": { - "disease_related": "Not Reported", - "kf_id": "OC_6Q2BD1X3", - "vital_status": "Not Applicable" - }, - "kf_id": "PT_ARN1D5B8", - "affected_status": false, - "race": "White", - "external_id": "4-9M", - "ethnicity": "Not Hispanic or Latino", - "biospecimens": [ - { - "ncit_id_tissue_type": "NCIT:C14165", - "genomic_files": [], - "kf_id": "BS_EVKA13PJ", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "DS-CDH-COL-GSO-RD", - "dbgap_consent_code": "phs001110.c1", - "external_sample_id": "4-9M", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "4-9M" - } - ], - "family": { - "family_id": "FM_9PS4VHQ2", - "family_compositions": [ - { - "composition": "trio", - "shared_hpo_ids": [], - "available_data_types": [], - "family_members": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_6EDB9B0H", - "relationship": "father", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_ARN1D5B8", - "relationship": "mother", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": true, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_AP68V2JN", - "relationship": "child", - "race": "White", - "ethnicity": "Not Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [ - "SNOMEDCT:63191000119107" - ], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [ - "HP:0008012", - "HP:0002672", - "HP:0007009", - "HP:0001627" - ], - "hpo_phenotype_observed": [], - "external_id": [ - "04-0009-congenital birth defect-Negative", - "04-0009-gastrointestinal defect-Negative", - "04-0009-central nervous system defect-Negative", - "04-0009-congenital heart defect-Negative" - ], - "hpo_phenotype_observed_text": [], - "age_at_event_days": [], - "snomed_phenotype_observed": [], - "source_text_phenotype": [], - "ancestral_hpo_ids": [] - } - } - ] - } - ], - "father_id": "PT_6EDB9B0H", - "mother_id": "PT_ARN1D5B8" - }, - "study": { - "name": "Genomic Analysis of Congenital Diaphragmatic Hernia", - "attribution": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001110.v1.p1", - "release_status": "Pending", - "kf_id": "SD_46SK55A3", - "version": "v1.p1", - "short_name": "Congenital Diaphragmatic Hernia", - "external_id": "phs001110", - "data_access_authority": "dbGaP" - }, - "gender": "Female" - } - ], - "availability": "Immediate Download", - "file_format": "bam", - "experiment_strategies": [], - "latest_did": "13c02b29-d3d3-4d00-a993-98d4342ebebb", - "acl": [ - "phs001110", - "phs001110.c1", - "SD_46SK55A3" - ], - "kf_id": "GF_5KSEA2F2", - "platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "Not Reported", - "max_insert_size": 421, - "library_name": "IWG_IND-GMKFWC.CDH4-9M-1_2pA", - "experiment_strategy": "WGS", - "is_paired_end": true, - "kf_id": "SE_4JJ6S2D5", - "instrument_model": "HiSeq X Ten", - "experiment_date": "2016-01-30T00:00:00+00:00", - "external_id": "IWG_IND-GMKFWC.CDH4-9M-1_2pA", - "platform": "Not Reported", - "mean_insert_size": 349.29, - "mean_read_length": 150 - } - ], - "external_id": "s3://kf-seq-data-bcm/chung/HKNFYCCXX-5.hgv.bam", - "is_harmonized": false - } - PUT file_centric/file_centric/GF_TKSAVY3Z - { - "reference_genome": "hs37d5", - "size": 65620100743, - "file_name": "HKM22CCXX-5.hgv.bam", - "controlled_access": true, - "instrument_models": [], - "participants": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "family_id": "FM_8PVYN86B", - "outcome": { - "disease_related": "Not Reported", - "kf_id": "OC_6G2EH9KA", - "vital_status": "Not Applicable" - }, - "kf_id": "PT_FCS416QR", - "affected_status": false, - "race": "White", - "external_id": "4-18F", - "ethnicity": "Not Hispanic or Latino", - "biospecimens": [ - { - "ncit_id_tissue_type": "NCIT:C14165", - "genomic_files": [], - "kf_id": "BS_PTBSGXBX", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "DS-CDH-COL-GSO-RD", - "dbgap_consent_code": "phs001110.c1", - "external_sample_id": "4-18F", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "4-18F" - } - ], - "family": { - "family_id": "FM_8PVYN86B", - "family_compositions": [ - { - "composition": "trio", - "shared_hpo_ids": [], - "available_data_types": [], - "family_members": [ - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_FCS416QR", - "relationship": "father", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": false, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_XSWSR7HY", - "relationship": "mother", - "race": "White", - "ethnicity": "Not Hispanic or Latino" - }, - { - "is_proband": true, - "available_data_types": [], - "diagnoses": [], - "kf_id": "PT_7F5P68ZN", - "relationship": "child", - "race": "White", - "ethnicity": "Not Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [ - "SNOMEDCT:63191000119107" - ], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [ - "HP:0008012", - "HP:0002672", - "HP:0007009", - "HP:0001627" - ], - "hpo_phenotype_observed": [], - "external_id": [ - "04-0018-congenital birth defect-Negative", - "04-0018-gastrointestinal defect-Negative", - "04-0018-central nervous system defect-Negative", - "04-0018-congenital heart defect-Negative" - ], - "hpo_phenotype_observed_text": [], - "age_at_event_days": [], - "snomed_phenotype_observed": [], - "source_text_phenotype": [], - "ancestral_hpo_ids": [] - } - } - ] - } - ], - "father_id": "PT_FCS416QR", - "mother_id": "PT_XSWSR7HY" - }, - "study": { - "name": "Genomic Analysis of Congenital Diaphragmatic Hernia", - "attribution": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001110.v1.p1", - "release_status": "Pending", - "kf_id": "SD_46SK55A3", - "version": "v1.p1", - "short_name": "Congenital Diaphragmatic Hernia", - "external_id": "phs001110", - "data_access_authority": "dbGaP" - }, - "gender": "Male" - } - ], - "availability": "Immediate Download", - "file_format": "bam", - "experiment_strategies": [], - "latest_did": "ce57474c-03a7-4496-8b83-9fa90ce64b63", - "acl": [ - "phs001110", - "phs001110.c1", - "SD_46SK55A3" - ], - "kf_id": "GF_TKSAVY3Z", - "platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "Not Reported", - "max_insert_size": 421, - "library_name": "IWG_IND-GMKFWC.CDH4-18F-1_2pA", - "experiment_strategy": "WGS", - "is_paired_end": true, - "kf_id": "SE_DDW7J2SV", - "instrument_model": "HiSeq X Ten", - "experiment_date": "2016-02-02T00:00:00+00:00", - "external_id": "IWG_IND-GMKFWC.CDH4-18F-1_2pA", - "platform": "Not Reported", - "mean_insert_size": 349.29, - "mean_read_length": 150 - } - ], - "external_id": "s3://kf-seq-data-bcm/chung/HKM22CCXX-5.hgv.bam", - "is_harmonized": false - } \ No newline at end of file diff --git a/docs/src/file_centric_mapping.rst b/docs/src/file_centric_mapping.rst deleted file mode 100644 index 6d8bd7f97..000000000 --- a/docs/src/file_centric_mapping.rst +++ /dev/null @@ -1,517 +0,0 @@ - -.. code-block:: - - PUT file_centric - {} - - PUT file_centric - { - "mappings":{ - "file_centric": { - "_meta": { - "kf-dataservice-version": "1.6.0" - }, - "properties": { - "acl": { - "type": "keyword" - }, - "availability": { - "type": "keyword" - }, - "controlled_access": { - "type": "boolean" - }, - "created_at": { - "type": "date", - "format": "yyyy-MM-dd HH:mm:ss.SSSSSS||yyyy-MM-dd HH:mm:ss||yyyy-MM-dd'T'HH:mm:ss.SSSSSS+HH:mm" - }, - "data_type": { - "type": "keyword" - }, - "experiment_strategies": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "file_format": { - "type": "keyword" - }, - "file_name": { - "type": "keyword" - }, - "instrument_models": { - "type": "keyword" - }, - "is_harmonized": { - "type": "boolean" - }, - "is_paired_end": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "latest_did": { - "type": "keyword" - }, - "modified_at": { - "type": "date", - "format": "yyyy-MM-dd HH:mm:ss.SSSSSS||yyyy-MM-dd HH:mm:ss||yyyy-MM-dd'T'HH:mm:ss.SSSSSS+HH:mm" - }, - "participants": { - "type": "nested", - "properties": { - "affected_status": { - "type": "boolean" - }, - "alias_group": { - "type": "keyword" - }, - "available_data_types": { - "type": "keyword" - }, - "biospecimens": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "analyte_type": { - "type": "keyword" - }, - "composition": { - "type": "keyword" - }, - "concentration_mg_per_ml": { - "type": "float" - }, - "consent_type": { - "type": "keyword" - }, - "dbgap_consent_code": { - "type": "keyword" - }, - "external_aliquot_id": { - "type": "keyword" - }, - "external_sample_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "method_of_sample_procurement": { - "type": "keyword" - }, - "ncit_id_anatomical_site": { - "type": "keyword" - }, - "ncit_id_tissue_type": { - "type": "keyword" - }, - "sequencing_center_id": { - "type": "keyword" - }, - "shipment_date": { - "type": "keyword" - }, - "shipment_origin": { - "type": "keyword" - }, - "source_text_anatomical_site": { - "type": "keyword" - }, - "source_text_tissue_type": { - "type": "keyword" - }, - "source_text_tumor_descriptor": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_anatomical_site": { - "type": "keyword" - }, - "volume_ul": { - "type": "float" - } - } - }, - "diagnoses": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "diagnosis": { - "type": "keyword" - }, - "diagnosis_category": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "icd_id_diagnosis": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "mondo_id_diagnosis": { - "type": "keyword" - }, - "ncit_id_diagnosis": { - "type": "keyword" - }, - "source_text_diagnosis": { - "type": "keyword" - }, - "source_text_tumor_location": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_tumor_location": { - "type": "keyword" - } - } - }, - "diagnosis_category": { - "type": "keyword" - }, - "ethnicity": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "family": { - "properties": { - "family_compositions": { - "type": "nested", - "properties": { - "available_data_types": { - "type": "keyword" - }, - "composition": { - "type": "keyword" - }, - "family_members": { - "type": "nested", - "properties": { - "affected_status": { - "type": "boolean" - }, - "alias_group": { - "type": "keyword" - }, - "available_data_types": { - "type": "keyword" - }, - "diagnoses": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "diagnosis": { - "type": "keyword" - }, - "diagnosis_category": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "icd_id_diagnosis": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "mondo_id_diagnosis": { - "type": "keyword" - }, - "ncit_id_diagnosis": { - "type": "keyword" - }, - "source_text_diagnosis": { - "type": "keyword" - }, - "source_text_tumor_location": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_tumor_location": { - "type": "keyword" - } - } - }, - "diagnosis_category": { - "type": "keyword" - }, - "ethnicity": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "gender": { - "type": "keyword" - }, - "is_proband": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "outcome": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "disease_related": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - } - } - }, - "phenotype": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "ancestral_hpo_ids": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "hpo_phenotype_not_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed_text": { - "type": "keyword" - }, - "shared_hpo_ids": { - "type": "keyword" - }, - "snomed_phenotype_not_observed": { - "type": "keyword" - }, - "snomed_phenotype_observed": { - "type": "keyword" - }, - "source_text_phenotype": { - "type": "keyword" - } - } - }, - "race": { - "type": "keyword" - }, - "relationship": { - "type": "keyword" - } - } - }, - "shared_hpo_ids": { - "type": "keyword" - } - } - }, - "family_id": { - "type": "text", - "fields": { - "keyword": { - "type": "keyword", - "ignore_above": 256 - } - } - }, - "father_id": { - "type": "keyword" - }, - "mother_id": { - "type": "keyword" - } - } - }, - "family_id": { - "type": "keyword" - }, - "gender": { - "type": "keyword" - }, - "is_proband": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "outcome": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "disease_related": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - } - } - }, - "phenotype": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "ancestral_hpo_ids": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "hpo_phenotype_not_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed_text": { - "type": "keyword" - }, - "snomed_phenotype_not_observed": { - "type": "keyword" - }, - "snomed_phenotype_observed": { - "type": "keyword" - }, - "source_text_phenotype": { - "type": "keyword" - } - } - }, - "race": { - "type": "keyword" - }, - "study": { - "properties": { - "attribution": { - "type": "text" - }, - "data_access_authority": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "investigator_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "name": { - "type": "keyword" - }, - "release_status": { - "type": "keyword" - }, - "short_name": { - "type": "keyword" - }, - "version": { - "type": "keyword" - } - } - } - } - }, - "platforms": { - "type": "keyword" - }, - "reference_genome": { - "type": "keyword" - }, - "sequencing_experiments": { - "type": "nested", - "properties": { - "experiment_date": { - "type": "keyword" - }, - "experiment_strategy": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "instrument_model": { - "type": "keyword" - }, - "is_paired_end": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "library_name": { - "type": "keyword" - }, - "library_strand": { - "type": "keyword" - }, - "max_insert_size": { - "type": "integer" - }, - "mean_depth": { - "type": "float" - }, - "mean_insert_size": { - "type": "float" - }, - "mean_read_length": { - "type": "float" - }, - "platform": { - "type": "keyword" - }, - "sequencing_center_id": { - "type": "keyword" - }, - "total_reads": { - "type": "integer" - } - } - }, - "size": { - "type": "long" - } - } - } - } - } \ No newline at end of file diff --git a/docs/src/gettingstarted.rst b/docs/src/gettingstarted.rst deleted file mode 100644 index 633241dd6..000000000 --- a/docs/src/gettingstarted.rst +++ /dev/null @@ -1,77 +0,0 @@ -Getting Started -============================ - -The easiest way to understand Arranger, is to simply use it! - -Below is a description of how to get Arranger quickly up and running, as well as a description of how Arranger works and some important terms. - -Quick Start ----------------------------------------------------- - -The goal of this quick start is to get a working application quickly up and running. - -Using `Docker `_: - -1. Download the latest version of Arranger. -2. From the Arranger root directory, run `docker-compose `_: - -.. code-block:: python - - $ docker-compose up -d - -Arranger should now be deployed locally. - -Alternatively, see the `Installation instructions `_. - - -How Arranger Works -------------------------------------------- -**1. Starting with some Elasticsearch (ES) indices with mappings.** - - Arranger makes no assumption about your data model. - - Model your `index mappings `_ and index them. - - For demo convenience, you can follow a `tutorial bellow <#indexing-demo-data>`_ to index some test data from our Kids First project. - .. seealso:: - - The `Overture `_ software suite also provides `Maestro `_ for indexing genomic data to ES - -**2. Create an API version for your project from Arranger Admin.** - - From your browser, navigate to http://localhost:8080 - - Click **"Add Project"** - - Input your project id in **snake_case** - - Click **"Add Index"** for each index you want to expose from ES, with the following fields: - - - **"Name"**: any name for your index, in **camelCase** - - **"ES Index"**: the index that you want to expose - - **"ES Type"**: the type that you want to expose - - - Click **"Add"** once finalized. - - Navigate into your newly registered project's configuration and ensure that **"Has Mapping"** is **"yes"** for all indices registered. - - `Configure your project `_ from the API and click **"Save"** to save as a new project. - -**3. View your data in a portal.** - - From a UI: - - - Go to http://localhost:8081/?selectedKind=Portal. - - Select your project and index from the dropdown. - - Note: a production-ready white-label portal using UI components provided by Arranger is in our roadmap for Arranger. - - - From the GraphQL API: - - - Each Arranger project created through the Admin system in step 2 creates a new Graphql endpoint. - - Start a GraphQL IDE (such as `GraphiQL `_ or `GraphQL Playground `_ - - Point your IDE to :code:`http://localhost:5050//graphql` to explore the API schema (where :code:`` is the project id you have input in step 2). - - For documentation regarding this API, check out the `Arranger for Application Developers `_ guide - -Architecture -------------------------------------------- -.. image :: images/architecture.png - -Indexing Demo Data -------------------------------------------- -- From your browser, visit the locally running `Kibana `_ at http://localhost:5601 and go to `Dev Tools `_ -- Creating a :code:`file_centric` index: - - - Run `these commands `_ to create a :code:`file_centric` index and add a mapping then `these commands `_ to index some demo documents into the index - - Run `these commands `_ to create a :code:`participant_centric` index and add a mapping then `these commands `_ to index some demo documents into the index - -- You can run :code:`GET file_centric/_mapping` and :code:`GET participant_centric/_mapping` to confirm that the mapping has been created successfully diff --git a/docs/src/images/admin_system.png b/docs/src/images/admin_system.png deleted file mode 100644 index 2a990275a..000000000 Binary files a/docs/src/images/admin_system.png and /dev/null differ diff --git a/docs/src/images/aggs.png b/docs/src/images/aggs.png deleted file mode 100644 index ba5a257b6..000000000 Binary files a/docs/src/images/aggs.png and /dev/null differ diff --git a/docs/src/images/architecture.png b/docs/src/images/architecture.png deleted file mode 100644 index 03487b65f..000000000 Binary files a/docs/src/images/architecture.png and /dev/null differ diff --git a/docs/src/images/fields.png b/docs/src/images/fields.png deleted file mode 100644 index 2c1d6f07d..000000000 Binary files a/docs/src/images/fields.png and /dev/null differ diff --git a/docs/src/images/indices.png b/docs/src/images/indices.png deleted file mode 100644 index 796243da1..000000000 Binary files a/docs/src/images/indices.png and /dev/null differ diff --git a/docs/src/images/projects.png b/docs/src/images/projects.png deleted file mode 100644 index 086ad5194..000000000 Binary files a/docs/src/images/projects.png and /dev/null differ diff --git a/docs/src/images/quicksearch.png b/docs/src/images/quicksearch.png deleted file mode 100644 index d52bad6fd..000000000 Binary files a/docs/src/images/quicksearch.png and /dev/null differ diff --git a/docs/src/images/table.png b/docs/src/images/table.png deleted file mode 100644 index e04fa0770..000000000 Binary files a/docs/src/images/table.png and /dev/null differ diff --git a/docs/src/installation.rst b/docs/src/installation.rst deleted file mode 100644 index dc4126432..000000000 --- a/docs/src/installation.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _installation: - -Installation -============================ - -Coming Soon ------------------------ diff --git a/docs/src/introduction.rst b/docs/src/introduction.rst deleted file mode 100644 index c30a8afc3..000000000 --- a/docs/src/introduction.rst +++ /dev/null @@ -1,43 +0,0 @@ -============== -Introduction -============== - - -What is Arranger? -================= -`Arranger `_ is a collection of reusable components for creating centric search portals with `Elasticsearch `_. Arranger consists of the following components: - - *Arranger Search API* provides a layer that sits above your Elasticsearch cluster to expose a data-model aware `GraphQL `_ API, generated from your own Elasticsearch index mapping. - - *Arranger Components* provides a rich set of UI components that are configured to speak to the search API. - - *Arranger Admin* provides the API and UI for configuring the search API and content management for the search portal. - -Arranger is one of many products provided by `Overture `_ and is completely open-source and free for everyone to use. - -.. seealso:: - - For additional information on other products in the Overture stack, please visit https://overture.bio - -.. _introduction_features: - -Features -========== -- GraphQL API for query flexibility. -- `SQON `_ query filter notation balances between human-interpretability and machine-readability to simply search. -- Admin UI for API configuration and content management. -- Configuration import and export for easy migration. - -License -========== -Copyright (c) 2018. Ontario Institute for Cancer Research - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU Affero General Public License as -published by the Free Software Foundation, either version 3 of the -License, or (at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU Affero General Public License for more details. - -You should have received a copy of the GNU Affero General Public License -along with this program. If not, see https://www.gnu.org/licenses. diff --git a/docs/src/participant_centric_docs.rst b/docs/src/participant_centric_docs.rst deleted file mode 100644 index 410d80b9a..000000000 --- a/docs/src/participant_centric_docs.rst +++ /dev/null @@ -1,6103 +0,0 @@ - -.. code-block:: - - PUT participant_centric/participant_centric/PT_CTNN6H7K - { - "is_proband": true, - "available_data_types": [ - "Aligned Reads", - "Histology Images", - "Pathology Reports", - "Radiology Reports", - "Radiology Images", - "Operation Reports" - ], - "diagnoses": [ - { - "diagnosis": "vision disorder", - "ncit_id_diagnosis": "NCIT:C35126", - "diagnosis_category": "Other", - "source_text_diagnosis": "Visual deficit (acuity or fields)", - "kf_id": "DG_63GCS4DD", - "mondo_id_diagnosis": "MONDO:0021084", - "external_id": "Z6Y81IKQUKLT7IKL:Z0QR7QN4A.Visual deficit (acuity or fields)", - "age_at_event_days": 4326, - "uberon_id_tumor_location": "Not Reported" - }, - { - "diagnosis": "disease or disorder", - "ncit_id_diagnosis": "NCIT:2991", - 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"external_aliquot_id": "717153" - }, - { - "ncit_id_tissue_type": "NCIT:C133262", - "genomic_files": [], - "concentration_mg_per_ml": 0.018561, - "kf_id": "BS_W4ZEEWZA", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "GRU", - "age_at_event_days": 182, - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-904-N-345308.WGS", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "612655" - }, - { - "genomic_files": [], - "kf_id": "BS_279V56CC", - "analyte_type": "Virtual", - "consent_type": "GRU", - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-904-V.Virtual", - "composition": "Not Reported" - }, - { - "genomic_files": [], - "kf_id": "BS_2SSZV3EK", - "analyte_type": "Virtual", - "consent_type": "GRU", - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-2758-V.Virtual", - "composition": "Not Reported" - } - ], - "family": { - "family_compositions": [ - { - "composition": "proband-only", - 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"O4ON2VMN9RFVFZMX:PR9EUIMQJ.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:Z1K4KRVW4.Behavior/Mood disorder", - "O4ON2VMN9RFVFZMX:7316-137.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:7316-137.Other medical conditions NOS", - "O4ON2VMN9RFVFZMX:SJ94E6H7L.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:Z1K4KRVW4.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:X4U0BM8PL.Behavior/Mood disorder", - "O4ON2VMN9RFVFZMX:0H10WONKQ.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:7316-137.Hydrocephalus", - "O4ON2VMN9RFVFZMX:9YZBSRMVF.Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "O4ON2VMN9RFVFZMX:0H10WONKQ.Behavior/Mood disorder", - "O4ON2VMN9RFVFZMX:Z67SR8OOD.Behavior/Mood disorder" - ], - "hpo_phenotype_observed_text": [ - "Abnormality of nervous system physiology (HP:0012638)", - "Hydrocephalus (HP:0000238)" - ], - "age_at_event_days": [ - 2947, - 193, - 1446, - 2781, - 2051, - 3171, - 3347, - 2340 - ], - "snomed_phenotype_observed": [ - "SNOMEDCT:264552009", - "SNOMEDCT:46206005", - "SNOMEDCT:64572001", - "SNOMEDCT:230745008" - ], - "source_text_phenotype": [ - "Focal neurological deficit (cranial nerve palsies, motor deficits, sensory deficits)", - "Behavior/Mood disorder", - "Other medical conditions NOS", - "Hydrocephalus" - ], - "ancestral_hpo_ids": [ - "HP:0011345", - "HP:0001350", - "HP:0012452", - "HP:0002516", - "HP:0004408", - "HP:0010635", - "HP:0002505", - "HP:0002349", - "HP:0011146", - "HP:0012048", - "HP:0011196", - "HP:0100703", - "HP:0025013", - "HP:0000762", - "HP:0011964", - "HP:0010553", - "HP:0100024", - "HP:0008765", - "HP:0011160", - "HP:0012194", - "HP:0011197", - "HP:0007230", - "HP:0001344", - "HP:0011215", - "HP:0002333", - "HP:0030197", - 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"platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "First Stranded", - "library_name": "61658687-a39e-42eb-8c5e-2af0848da400", - "experiment_strategy": "RNA-Seq", - "is_paired_end": true, - "kf_id": "SE_WX96BY8C", - "instrument_model": "HiSeq", - "external_id": "61658687-a39e-42eb-8c5e-2af0848da400", - "platform": "Illumina" - } - ], - "external_id": "61658687-a39e-42eb-8c5e-2af0848da400.local.transcript.bam", - "is_harmonized": false - }, - { - "reference_genome": "hg19_with_GenBank_Viral_Genomes", - "size": 134819925774, - "file_name": "a36bb079-81b2-4145-a77b-267f6b888fb3.bam", - "controlled_access": true, - "instrument_models": [], - "availability": "Immediate Download", - "file_format": "bam", - "latest_did": "66a66557-b5c3-48b2-857a-179e75400a77", - "acl": [ - "SD_BHJXBDQK", - "SD_BHJXBDQK.c1" - ], - "kf_id": "GF_WC0YEF3J", - "platforms": [], - "data_type": "Aligned Reads", - "sequencing_experiments": [ - { - "library_strand": "Unstranded", - "library_name": "a36bb079-81b2-4145-a77b-267f6b888fb3", - "experiment_strategy": "WGS", - "is_paired_end": false, - "kf_id": "SE_0C4PXMTX", - "instrument_model": "HiSeq X", - "external_id": "a36bb079-81b2-4145-a77b-267f6b888fb3", - "platform": "Illumina" - } - ], - "external_id": "a36bb079-81b2-4145-a77b-267f6b888fb3.bam", - "is_harmonized": false - } - ], - "kf_id": "PT_ZZ8SBJJ5", - "race": "White", - "external_id": "C141204", - "ethnicity": "Not Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [], - "hpo_phenotype_observed": [ - "HP:0001250" - ], - "external_id": [ - "2PRERDH6UU8933H4:EFW0LX583.Other medical conditions NOS", - "2PRERDH6UU8933H4:EFW0LX583.Seizure disorder", - "2PRERDH6UU8933H4:XR3YWBLTB.Seizure disorder" - ], - "hpo_phenotype_observed_text": [ - "Seizures (HP:0001250)" - ], - "age_at_event_days": [ - 431, - 881 - ], - "snomed_phenotype_observed": [ - "SNOMEDCT:64572001", - "SNOMEDCT:128613002" - ], - "source_text_phenotype": [ - "Other medical conditions NOS", - "Seizure disorder" - ], - "ancestral_hpo_ids": [ - "HP:0002349", - "HP:0011146", - "HP:0011160", - "HP:0025121", - "HP:0011171", - "HP:0002199", - "HP:0011154", - "HP:0012008", - "HP:0011163", - "HP:0006813", - "HP:0010818", - "HP:0011174", - "HP:0011145", - "HP:0011161", - "HP:0012469", - "HP:0002373", - "HP:0010821", - "HP:0011175", - "HP:0002069", - "HP:0002123", - "HP:0011097", - "HP:0011147", - "HP:0011165", - "HP:0011164", - "HP:0012005", - "HP:0011150", - "HP:0040168", - "HP:0012847", - "HP:0007332", - "HP:0010819", - "HP:0007193", - "HP:0001327", - "HP:0011159", - "HP:0012003", - "HP:0002384", - "HP:0011173", - "HP:0011155", - "HP:0025190", - "HP:0011166", - "HP:0011158", - "HP:0011169", - "HP:0011151", - "HP:0011148", - "HP:0011162", - "HP:0010820", - "HP:0002133", - "HP:0011172", - "HP:0031165", - "HP:0011170", - "HP:0012002", - "HP:0002197", - "HP:0011156", - "HP:0001250", - "HP:0012007", - "HP:0007207", - "HP:0031475", - "HP:0011152", - "HP:0002266", - "HP:0011149", - "HP:0025191", - "HP:0011167", - "HP:0007334", - "HP:0002173", - "HP:0011153", - "HP:0002121", - "HP:0011168", - "HP:0011157", - "HP:0007270", - "HP:0007359", - "HP:0012004" - ] - }, - "biospecimens": [ - { - "ncit_id_tissue_type": "NCIT:C133262", - "genomic_files": [], - "concentration_mg_per_ml": 0.0167, - "kf_id": "BS_D3VQDD5A", - "analyte_type": "DNA", - "source_text_tissue_type": "Normal", - "consent_type": "GRU", - "age_at_event_days": 881, - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-725-N-340022.WGS", - "composition": "Peripheral Whole Blood", - "external_aliquot_id": "564245" - }, - { - "ncit_id_tissue_type": "NCIT:C8509", - "genomic_files": [], - "source_text_tumor_descriptor": "Progressive", - "concentration_mg_per_ml": 0.05, - "kf_id": "BS_CW9QV8AG", - "analyte_type": "RNA", - "ncit_id_anatomical_site": "NCIT:C12438", - "source_text_tissue_type": "Tumor", - "source_text_anatomical_site": "Central Nervous System", - "consent_type": "GRU", - "uberon_id_anatomical_site": "UBERON:0001017", - "age_at_event_days": 425, - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-725-T-340027.RNA-Seq", - "composition": "Solid Tissue", - "external_aliquot_id": "739965" - }, - { - "ncit_id_tissue_type": "NCIT:C8509", - "genomic_files": [], - "source_text_tumor_descriptor": "Progressive", - "concentration_mg_per_ml": 0.05, - "kf_id": "BS_CPZZR2R7", - "analyte_type": "DNA", - "ncit_id_anatomical_site": "NCIT:C12438", - "source_text_tissue_type": "Tumor", - "source_text_anatomical_site": "Central Nervous System", - "consent_type": "GRU", - "uberon_id_anatomical_site": "UBERON:0001017", - "age_at_event_days": 425, - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-725-T-340027.WGS", - "composition": "Solid Tissue", - "external_aliquot_id": "739820" - }, - { - "genomic_files": [], - "kf_id": "BS_W7X60DQ3", - "analyte_type": "Virtual", - "consent_type": "GRU", - "dbgap_consent_code": "SD_BHJXBDQK.c1", - "external_sample_id": "7316-725-V.Virtual", - "composition": "Not Reported" - } - ], - "family": { - "family_compositions": [ - { - "composition": "proband-only", - "shared_hpo_ids": [ - "HP:0001250" - ], - "available_data_types": [ - "Histology Images", - "Pathology Reports", - "Operation Reports", - "Aligned Reads" - ], - "family_members": [ - { - "is_proband": true, - "available_data_types": [ - "Histology Images", - "Pathology Reports", - "Operation Reports", - "Aligned Reads" - ], - "diagnoses": [], - "kf_id": "PT_ZZ8SBJJ5", - "race": "White", - "ethnicity": "Not Hispanic or Latino", - "phenotype": { - "snomed_phenotype_not_observed": [], - "shared_hpo_ids": [], - "hpo_phenotype_not_observed": [], - "hpo_phenotype_observed": [ - "HP:0001250" - ], - "external_id": [ - "2PRERDH6UU8933H4:EFW0LX583.Other medical conditions NOS", - "2PRERDH6UU8933H4:EFW0LX583.Seizure disorder", - "2PRERDH6UU8933H4:XR3YWBLTB.Seizure disorder" - ], - "hpo_phenotype_observed_text": [ - "Seizures (HP:0001250)" - ], - "age_at_event_days": [ - 431, - 881 - ], - "snomed_phenotype_observed": [ - "SNOMEDCT:64572001", - "SNOMEDCT:128613002" - ], - "source_text_phenotype": [ - "Other medical conditions NOS", - "Seizure disorder" - ], - "ancestral_hpo_ids": [ - "HP:0002349", - "HP:0011146", - "HP:0011160", - "HP:0025121", - "HP:0011171", - "HP:0002199", - "HP:0011154", - "HP:0012008", - "HP:0011163", - "HP:0006813", - "HP:0010818", - "HP:0011174", - "HP:0011145", - "HP:0011161", - "HP:0012469", - "HP:0002373", - "HP:0010821", - "HP:0011175", - "HP:0002069", - "HP:0002123", - "HP:0011097", - "HP:0011147", - "HP:0011165", - "HP:0011164", - "HP:0012005", - "HP:0011150", - "HP:0040168", - "HP:0012847", - "HP:0007332", - "HP:0010819", - "HP:0007193", - "HP:0001327", - "HP:0011159", - "HP:0012003", - "HP:0002384", - "HP:0011173", - "HP:0011155", - "HP:0025190", - "HP:0011166", - "HP:0011158", - "HP:0011169", - "HP:0011151", - "HP:0011148", - "HP:0011162", - "HP:0010820", - "HP:0002133", - "HP:0011172", - "HP:0031165", - "HP:0011170", - "HP:0012002", - "HP:0002197", - "HP:0011156", - "HP:0001250", - "HP:0012007", - "HP:0007207", - "HP:0031475", - "HP:0011152", - "HP:0002266", - "HP:0011149", - "HP:0025191", - "HP:0011167", - "HP:0007334", - "HP:0002173", - "HP:0011153", - "HP:0002121", - "HP:0011168", - "HP:0011157", - "HP:0007270", - "HP:0007359", - "HP:0012004" - ] - } - } - ] - } - ] - }, - "study": { - "name": "Pediatric Brain Tumor Atlas - Children's Brain Tumor Tissue Consortium", - "release_status": "Pending", - "kf_id": "SD_BHJXBDQK", - "short_name": "Pediatric Brain Tumors: CBTTC", - "external_id": "SD_BHJXBDQK", - "data_access_authority": "CBTTC DAC" - }, - "gender": "Male" - } \ No newline at end of file diff --git a/docs/src/participant_centric_mapping.rst b/docs/src/participant_centric_mapping.rst deleted file mode 100644 index f60d41b3f..000000000 --- a/docs/src/participant_centric_mapping.rst +++ /dev/null @@ -1,520 +0,0 @@ - -.. code-block:: - - PUT participant_centric - {} - - PUT participant_centric - { - "mappings": { - "participant_centric": { - "_meta": { - "kf-dataservice-version": "1.6.0" - }, - "properties": { - "affected_status": { - "type": "boolean" - }, - "alias_group": { - "type": "keyword" - }, - "available_data_types": { - "type": "keyword" - }, - "biospecimens": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "analyte_type": { - "type": "keyword" - }, - "composition": { - "type": "keyword" - }, - "concentration_mg_per_ml": { - "type": "float" - }, - "consent_type": { - "type": "keyword" - }, - "dbgap_consent_code": { - "type": "keyword" - }, - "external_aliquot_id": { - "type": "keyword" - }, - "external_sample_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "method_of_sample_procurement": { - "type": "keyword" - }, - "ncit_id_anatomical_site": { - "type": "keyword" - }, - "ncit_id_tissue_type": { - "type": "keyword" - }, - "sequencing_center_id": { - "type": "keyword" - }, - "shipment_date": { - "type": "keyword" - }, - "shipment_origin": { - "type": "keyword" - }, - "source_text_anatomical_site": { - "type": "keyword" - }, - "source_text_tissue_type": { - "type": "keyword" - }, - "source_text_tumor_descriptor": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_anatomical_site": { - "type": "keyword" - }, - "volume_ul": { - "type": "float" - } - } - }, - "diagnoses": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "diagnosis": { - "type": "keyword" - }, - "diagnosis_category": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "icd_id_diagnosis": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "mondo_id_diagnosis": { - "type": "keyword" - }, - "ncit_id_diagnosis": { - "type": "keyword" - }, - "source_text_diagnosis": { - "type": "keyword" - }, - "source_text_tumor_location": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_tumor_location": { - "type": "keyword" - } - } - }, - "diagnosis_category": { - "type": "keyword" - }, - "ethnicity": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "family": { - "properties": { - "family_compositions": { - "type": "nested", - "properties": { - "available_data_types": { - "type": "keyword" - }, - "composition": { - "type": "keyword" - }, - "family_members": { - "type": "nested", - "properties": { - "affected_status": { - "type": "boolean" - }, - "alias_group": { - "type": "keyword" - }, - "available_data_types": { - "type": "keyword" - }, - "diagnoses": { - "type": "nested", - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "diagnosis": { - "type": "keyword" - }, - "diagnosis_category": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "icd_id_diagnosis": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "mondo_id_diagnosis": { - "type": "keyword" - }, - "ncit_id_diagnosis": { - "type": "keyword" - }, - "source_text_diagnosis": { - "type": "keyword" - }, - "source_text_tumor_location": { - "type": "keyword" - }, - "spatial_descriptor": { - "type": "keyword" - }, - "uberon_id_tumor_location": { - "type": "keyword" - } - } - }, - "diagnosis_category": { - "type": "keyword" - }, - "ethnicity": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "gender": { - "type": "keyword" - }, - "is_proband": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "outcome": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "disease_related": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - } - } - }, - "phenotype": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "ancestral_hpo_ids": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "hpo_phenotype_not_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed_text": { - "type": "keyword" - }, - "shared_hpo_ids": { - "type": "keyword" - }, - "snomed_phenotype_not_observed": { - "type": "keyword" - }, - "snomed_phenotype_observed": { - "type": "keyword" - }, - "source_text_phenotype": { - "type": "keyword" - } - } - }, - "race": { - "type": "keyword" - }, - "relationship": { - "type": "keyword" - } - } - }, - "shared_hpo_ids": { - "type": "keyword" - } - } - }, - "family_id": { - "type": "text", - "fields": { - "keyword": { - "type": "keyword", - "ignore_above": 256 - } - } - }, - "father_id": { - "type": "keyword" - }, - "mother_id": { - "type": "keyword" - } - } - }, - "family_id": { - "type": "keyword" - }, - "files": { - "type": "nested", - "properties": { - "acl": { - "type": "keyword" - }, - "availability": { - "type": "keyword" - }, - "controlled_access": { - "type": "boolean" - }, - "created_at": { - "type": "date", - "format": "yyyy-MM-dd HH:mm:ss.SSSSSS||yyyy-MM-dd HH:mm:ss||yyyy-MM-dd'T'HH:mm:ss.SSSSSS+HH:mm" - }, - "data_type": { - "type": "keyword" - }, - "experiment_strategies": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "file_format": { - "type": "keyword" - }, - "file_name": { - "type": "keyword" - }, - "instrument_models": { - "type": "keyword" - }, - "is_harmonized": { - "type": "boolean" - }, - "is_paired_end": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "latest_did": { - "type": "keyword" - }, - "modified_at": { - "type": "date", - "format": "yyyy-MM-dd HH:mm:ss.SSSSSS||yyyy-MM-dd HH:mm:ss||yyyy-MM-dd'T'HH:mm:ss.SSSSSS+HH:mm" - }, - "platforms": { - "type": "keyword" - }, - "reference_genome": { - "type": "keyword" - }, - "sequencing_experiments": { - "type": "nested", - "properties": { - "experiment_date": { - "type": "keyword" - }, - "experiment_strategy": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "instrument_model": { - "type": "keyword" - }, - "is_paired_end": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "library_name": { - "type": "keyword" - }, - "library_strand": { - "type": "keyword" - }, - "max_insert_size": { - "type": "integer" - }, - "mean_depth": { - "type": "float" - }, - "mean_insert_size": { - "type": "float" - }, - "mean_read_length": { - "type": "float" - }, - "platform": { - "type": "keyword" - }, - "sequencing_center_id": { - "type": "keyword" - }, - "total_reads": { - "type": "integer" - } - } - }, - "size": { - "type": "long" - } - } - }, - "gender": { - "type": "keyword" - }, - "is_proband": { - "type": "boolean" - }, - "kf_id": { - "type": "keyword" - }, - "outcome": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "disease_related": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "participant_id": { - "type": "keyword" - }, - "vital_status": { - "type": "keyword" - } - } - }, - "phenotype": { - "properties": { - "age_at_event_days": { - "type": "integer" - }, - "ancestral_hpo_ids": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "hpo_phenotype_not_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed": { - "type": "keyword" - }, - "hpo_phenotype_observed_text": { - "type": "keyword" - }, - "snomed_phenotype_not_observed": { - "type": "keyword" - }, - "snomed_phenotype_observed": { - "type": "keyword" - }, - "source_text_phenotype": { - "type": "keyword" - } - } - }, - "race": { - "type": "keyword" - }, - "study": { - "properties": { - "attribution": { - "type": "text" - }, - "data_access_authority": { - "type": "keyword" - }, - "external_id": { - "type": "keyword" - }, - "investigator_id": { - "type": "keyword" - }, - "kf_id": { - "type": "keyword" - }, - "name": { - "type": "keyword" - }, - "release_status": { - "type": "keyword" - }, - "short_name": { - "type": "keyword" - }, - "version": { - "type": "keyword" - } - } - } - } - } - } - } \ No newline at end of file diff --git a/docs/src/sqon.rst b/docs/src/sqon.rst deleted file mode 100644 index cb247fbed..000000000 --- a/docs/src/sqon.rst +++ /dev/null @@ -1,72 +0,0 @@ -============= -SQON Filters -============= - -Arranger uses a custom JSON object format for filtering that is called SQON (Serializable Query Object Notation, pronounced like "Scone"). SQON provides a flexible system for combining many different filters. - - -A SQON object consists of nested objects of two types: **Operations** and **Values**. - -**Operation objects** apply boolean logic to a list of operation objects. They are of the form: - **Combination Operation (aka, Boolean Operation)** - which groups one or more filters - :: - - { - "op":"", //Operation to apply to content ["and", "or", "not"] - "content":[] //List of Operation objects that the boolean operation will apply to - } - - OR - - **Field Operation** - that applies to a filter to Value Object - - :: - - { - "op":"", //Operation to apply to content ["in", "<=", ">="] - "content":{} //Value object specifying the field and list of values that the field must be "in" or "not-in" - } - - -**Value objects** - specify a list the field name and values for it that the wrapping . This filter can specify to include or exclude fields with any of the listed values. It will have the following format: - - :: - - { - "fieldName":"", //name of the field this operation applies to - "value":[] //List of values for the field if using the "in" operation, or a scalar value for ">=" and "<=" operations - } - -**The top level of a SQON must always be a Combination Operation, even if only a single filter is being applied.** - -Sample -******* -:: - - { - op: "and", - content: [ - { - op: "or", - content: [ - { - op: "in", - content: { - fieldName: "id", - value: ["id123"] - } - } - ] - }, - { - op: "in", - content: { - fieldName: "id", - value: ["id123"] - } - } - ] - } \ No newline at end of file diff --git a/docs/src/technology.rst b/docs/src/technology.rst deleted file mode 100644 index 1173f92d3..000000000 --- a/docs/src/technology.rst +++ /dev/null @@ -1,5 +0,0 @@ -Technology Stack -============================ - -Coming Soon ---------------- diff --git a/docs/usage/01-index-mappings.md b/docs/usage/01-index-mappings.md new file mode 100644 index 000000000..cc301462d --- /dev/null +++ b/docs/usage/01-index-mappings.md @@ -0,0 +1,27 @@ +# Index Mappings + +:::tip Resources +For a comprehensive guide on index mappings, including detailed explanations, examples, and configuration instructions, please refer to our [**guide on index mappings**](/guides/administration-guides/index-mappings). + +This guide will provide: + +- A detailed breakdown of index mapping components +- File-centric vs. Analysis-centric indexing +- Info on how to update index templates +- Best practices for mapping configurations +::: + + +Index mappings are crucial for Arranger's functionality. They define how documents and their fields are stored and indexed in Elasticsearch, which directly impacts how Arranger can query and display your data. + +### Why Index Mappings Matter for Arranger + +1. **Data Model**: Mappings define the structure of your Elasticsearch documents, allowing Arranger to understand and interact with your data correctly. + +2. **GraphQL queries**: Arranger uses the index mapping to generate its GraphQL schema, which is the basis for all queries and mutations. + +:::info Arranger uses Elasticsearch 7 + +Our search platform is built on and compatible with version 7.x of Elasticsearch. All queries to ES must follow that version's syntax and conventions. + +::: diff --git a/docs/usage/02-arranger-components.md b/docs/usage/02-arranger-components.md new file mode 100644 index 000000000..a3589af3b --- /dev/null +++ b/docs/usage/02-arranger-components.md @@ -0,0 +1,140 @@ +# Arranger Configs + +Arranger offers its own front-end library of reusable components to facilitate querying Elasticsearch indices, leveraging the versatile GraphQL syntax. + +:::tip Portal Customization Guide +For more comprehensive information on customizing Arranger, including mock data and step by step instructions, we recommend [**using our local quickstart**](/guides/getting-started#overture-platform-quick-start) and following along with our [**platform guide on customizing the data portal**](/guides/administration-guides/customizing-the-data-portal) +::: + +## Configuration Files Overview + +Four main configuration files control Arranger, and its components' behaviours: + +1. **base.json**: Defines the core settings for the Elasticsearch index (Important for the Arranger Server). +2. **extended.json**: Specifies all fields and their display names. +3. **table.json**: Configures the columns displayed in the data table. +4. **facets.json**: Defines the aggregations (facets) for data exploration and filtering. + +:::info Configuration File Location +Templates of these files can be [found in the Arranger repository located here](https://github.com/overture-stack/arranger/tree/develop/modules/server/configTemplates). Active configuration files must be stored in a `configs` folder located within the `app/modules/server/` directory (unless specified otherwise using the `CONFIG_PATH` environment variable). +::: +## Base Configuration (base.json) + +The `base.json` file contains two essential fields: + +```json +{ + "documentType": "file", + "index": "my-elasticsearch-index" +} +``` + +- `documentType`: Specifies the mapping type (e.g., "file" or "analysis"). +- `index`: Names the Elasticsearch index to be used. + +## Extended Configuration (extended.json) + +The `extended.json` file defines all fields and their display names for the front-end: + +```json +{ + "extended": [ + { + "displayName": "Object ID", + "fieldName": "object_id" + }, + { + "displayName": "Analysis ID", + "fieldName": "analysis.analysis_id" + }, + { + "displayName": "Treatment Duration (Days)", + "fieldName": "analysis.donor.primaryDiagnosis.treatment.treatmentDuration" + } + ] +} +``` + +- `displayName`: How the field is shown in the UI. +- `fieldName`: The field's path in the Elasticsearch document. Use dot notation for nested fields. + +## Table Configuration (table.json) + +The `table.json` file configures the data table columns: + +```json +{ + "table": { + "columns": [ + { + "canChangeShow": true, + "fieldName": "object_id", + "show": true, + "sortable": true + }, + { + "canChangeShow": true, + "fieldName": "analysis.analysis_id", + "show": true, + "sortable": true + }, + { + "canChangeShow": true, + "fieldName": "analysis.collaborator.name", + "jsonPath": "$.analysis.collaborator.hits.edges[*].node.name", + "query": "analysis { collaborator { hits { edges { node { name } } } } }", + "show": true, + "sortable": true + } + ] + } +} +``` + +- `canChangeShow`: Whether users can toggle column visibility. +- `fieldName`: The field's path in the Elasticsearch document. +- `show`: Whether the column is visible by default. +- `sortable`: Whether the column can be sorted. +- `jsonPath`: JSON path for extracting nested data. +- `query`: GraphQL query for retrieving nested data. + +## Facet Configuration (facets.json) + +The `facets.json` file defines aggregations for filtering: + +```json +{ + "facets": { + "aggregations": [ + { + "active": true, + "fieldName": "file_type", + "show": true + }, + { + "active": true, + "fieldName": "analysis__collaborator__name", + "show": true + } + ] + } +} +``` + +- `active`: Whether the aggregation is enabled. +- `fieldName`: The field to aggregate on. Use double underscores for nested fields. +- `show`: Whether to display this aggregation in the UI. + +:::info +In `facets.json`, use double underscores (`__`) instead of dots for nested fields. For example, use `analysis__collaborator__name` instead of `analysis.collaborator.name`. +::: + +## Best Practices + +1. Ensure `fieldName` values accurately reflect your Elasticsearch document structure. +2. Use meaningful `displayName` values for better user experience. +3. Consider which columns should be sortable and visible by default in `table.json`. +4. Choose relevant fields for faceting in `facets.json` to aid in data exploration. +5. Test your configurations thoroughly to ensure they work as expected with your data. + +By properly configuring these files, you can customize Arranger to effectively display and interact with your Elasticsearch data. diff --git a/docs/usage/03-sqon-filter-notation.md b/docs/usage/03-sqon-filter-notation.md new file mode 100644 index 000000000..4391b4af5 --- /dev/null +++ b/docs/usage/03-sqon-filter-notation.md @@ -0,0 +1,107 @@ +# SQON Filter Notation + + + +Arranger uses a custom filter syntax known as Serializable Query Object Notation (SQON, pronounced like "Scone"), to provide a flexible system for combining filters in a JSON object format. + +- A SQON object consists of two types of nested objects, **Value Objects** and **Operation Objects**. + +## Value Objects + + Value objects specify the field being queried and the values used for the query. This filter can specify to include or exclude fields with any of the listed values. It will have the following format: + + ```SQON + { + "fieldName":"", //name of the field this operation applies to + "value":[] //List of values for the field if using the "in" operation, or a scalar value for ">=" and "<=" operations + } + ``` + +## Operation Logic + +Operation objects apply boolean logic (AND, OR, NOT) to a list of operation objects. These can be either **combination operations** or **field operations** + +### Combination Operations + +Combination operations are used to group one or more filters together. For example: + +```SQON +{ + "op":"", // Operation to apply to content, this can be ["and", "or", "not"] + "content":[] // List of Operation objects that the boolean operation will apply to +} +``` + +**TipL** The top level of a SQON must always be a Combination Operation, even if only a single filter is being applied. + +### Field Operations + +Field operations are used filter value objects. They have the following structure: + +```SQON +{ + "op":"", //Operation to apply to content ["in", "<=", ">="] + "content":{} //Value object specifying the field and list of values that the field must be "in" or "not-in" +} +``` + +## Example SQON + +All filters applied in the facetted search panel get displayed in the SQON viewer: + +![Entity](../assets/sqon_query.jpg 'Sqon Viewer') + +The selection of filters above is recorded in SQON as follows: + +```SQON + { + "content": [ + { + "content": { + "fieldName": "analysis.experiment.sequencing_instrument", + "value": [ + "Illumina NextSeq 550" + ] + }, + "op": "in" + }, + { + "content": { + "fieldName": "analysis.first_published_at", + "value": 1640926800000 + }, + "op": ">=" + }, + { + "content": { + "fieldName": "analysis.first_published_at", + "value": 1672549199999 + }, + "op": "<=" + }, + { + "content": { + "fieldName": "analysis.host.host_age_bin", + "value": [ + "20 - 29" + ] + }, + "op": "in" + }, + { + "content": { + "fieldName": "analysis.sample_collection.geo_loc_province", + "value": [ + "Ontario" + ] + }, + "op": "in" + } + ], + "op": "and" + } + ``` + +:::info +Note that all date values are represented as [Unix timestamps](https://www.unixtimestamp.com/). +::: diff --git a/docs/usage/usage.mdx b/docs/usage/usage.mdx new file mode 100644 index 000000000..cb39ca670 --- /dev/null +++ b/docs/usage/usage.mdx @@ -0,0 +1,7 @@ +# Usage + +The following usage docs provide instructions for common tasks and workflows in Arranger: + +

+ +