├── screenshots ├── getting-started-1.png ├── getting-started-2.png ├── getting-started-3.png ├── getting-started-4.png ├── getting-started-5.png └── getting-started-6.png ├── autogenerated └── quarto │ ├── OSN_example_files │ └── libs │ │ ├── bootstrap │ │ ├── bootstrap-icons.woff │ │ └── bootstrap.min.js │ │ ├── quarto-html │ │ ├── tippy.css │ │ ├── quarto-syntax-highlighting.css │ │ ├── anchor.min.js │ │ ├── popper.min.js │ │ ├── tippy.umd.min.js │ │ └── quarto.js │ │ └── clipboard │ │ └── clipboard.min.js │ ├── OSN_example.ipynb │ └── OSN_example.html ├── .github ├── scripts │ ├── rstudio.Dockerfile │ ├── anvil-rstudio.Dockerfile │ ├── generate_wrapper.sh │ ├── install_missing.sh │ ├── templates │ │ ├── biocrstudio_wrapper.xml │ │ └── gxyjupyter_wrapper.xml │ └── galaxy-jupyter.Dockerfile └── workflows │ └── quarto_rendering.yaml ├── LICENSE ├── vignettes └── OSN_example.qmd └── README.md /screenshots/getting-started-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-1.png -------------------------------------------------------------------------------- /screenshots/getting-started-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-2.png -------------------------------------------------------------------------------- /screenshots/getting-started-3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-3.png -------------------------------------------------------------------------------- /screenshots/getting-started-4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-4.png -------------------------------------------------------------------------------- /screenshots/getting-started-5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-5.png -------------------------------------------------------------------------------- /screenshots/getting-started-6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/screenshots/getting-started-6.png -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/bootstrap/bootstrap-icons.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Bioconductor/BiocDeployableQuarto/main/autogenerated/quarto/OSN_example_files/libs/bootstrap/bootstrap-icons.woff -------------------------------------------------------------------------------- /.github/scripts/rstudio.Dockerfile: -------------------------------------------------------------------------------- 1 | # Run with docker build --build-arg GIT_REPO="account/repo" 2 | FROM bioconductor/bioconductor_docker:devel 3 | ARG GIT_REPO 4 | USER rstudio 5 | RUN cd /home/rstudio && git clone https://github.com/${GIT_REPO} && cd $(echo "${GIT_REPO}" | awk -F/ '{print $NF}') && ls vignettes/* | grep ".qmd" | xargs -i bash .github/scripts/install_missing.sh {} 6 | -------------------------------------------------------------------------------- /.github/scripts/anvil-rstudio.Dockerfile: -------------------------------------------------------------------------------- 1 | # Run with docker build --build-arg GIT_REPO="account/repo" 2 | FROM us.gcr.io/broad-dsp-gcr-public/anvil-rstudio-bioconductor:3.15.2 3 | ARG GIT_REPO 4 | RUN curl https://raw.githubusercontent.com/rocker-org/rocker-versioned2/master/scripts/install_quarto.sh | bash 5 | USER rstudio 6 | RUN cd /home/rstudio && git clone https://github.com/${GIT_REPO} && cd $(echo "${GIT_REPO}" | awk -F/ '{print $NF}') && ls vignettes/* | grep ".qmd" | xargs -i bash .github/scripts/install_missing.sh {} 7 | -------------------------------------------------------------------------------- /.github/scripts/generate_wrapper.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -xe 3 | 4 | mkdir -p autogenerated/wrappers/ 5 | 6 | LONGNAME=$1 7 | 8 | SHORTNAME=$2 9 | 10 | REPOSITORY=$3 11 | 12 | BRANCH=$4 13 | 14 | TYPE=$5 # biocrstudio or gxyjupyter 15 | 16 | CONTAINER="ghcr.io/$REPOSITORY:$TYPE-$BRANCH" 17 | 18 | cat << EOF >> "autogenerated/wrappers/$TYPE-$BRANCH.xml" 19 | $(sed """s@##PLACEHOLDERSHORTNAME##@${SHORTNAME}@g 20 | s@##PLACEHOLDERLONGNAME##@${LONGNAME}@g 21 | s@##PLACEHOLDERCONTAINER##@${CONTAINER}@g 22 | s@^@ @g""" .github/scripts/templates/${TYPE}_wrapper.xml) 23 | EOF 24 | -------------------------------------------------------------------------------- /.github/scripts/install_missing.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | set -x 3 | 4 | QMD=$(realpath "$1") 5 | echo $QMD 6 | mkdir -p /tmp 7 | # Extract missing R pkg or Python module from quarto error message 8 | while ( quarto render $QMD --to html 3>&1 1>&2- 2>&3- ) | grep "there is no package called" > /tmp/rmissingpkg \ 9 | || ( quarto render $QMD --to html 3>&1 1>&2- 2>&3- ) | grep "ModuleNotFoundError: No module named" > /tmp/pymissingmodule; 10 | do 11 | if [[ -s /tmp/rmissingpkg ]]; then 12 | RPKG=$(awk '{print $NF}' /tmp/rmissingpkg) 13 | # Install missing R package 14 | Rscript -e "BiocManager::install('$(echo "${RPKG:1:${#RPKG}-2}" | sed "s/'//g")')" && rm /tmp/rmissingpkg 15 | # Link reticulate with existing python3 16 | if [ $RPKG == "'reticulate'" ]; then Rscript -e "library(reticulate); use_python('$(which python3)')"; fi 17 | 18 | elif [[ -s /tmp/pymissingmodule ]]; then 19 | PYMOD=$(awk '{print $NF}' /tmp/pymissingmodule | sed "s/'//g") 20 | # Install missing python module 21 | python3 -m pip install $PYMOD && rm /tmp/pymissingmodule 22 | fi 23 | done 24 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2022 Alexandru Mahmoud 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /.github/scripts/templates/biocrstudio_wrapper.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | ##PLACEHOLDERCONTAINER## 4 | 5 | 6 | 7 | 8787 8 | 9 | 10 | 11 | true 12 | $__history_id__ 13 | $__galaxy_url__ 14 | 8080 15 | $__galaxy_url__ 16 | 17 | 18 | /init 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/quarto-html/tippy.css: -------------------------------------------------------------------------------- 1 | .tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1} -------------------------------------------------------------------------------- /vignettes/OSN_example.qmd: -------------------------------------------------------------------------------- 1 | --- 2 | title: "OSN_example: demonstrate usage of Open Storage Network resources for multiplex imaging data" 3 | author: 4 | - Vincent J. Carey, stvjc at channing.harvard.edu 5 | - Ludwig Geistlinger, ludwig_geistlinger at hms.harvard.edu 6 | - Alex Mahmoud, almahmoud at channing.harvard.edu 7 | date: "`r format(Sys.time(), '%B %d, %Y')`" 8 | format: 9 | html: 10 | code-fold: true 11 | ipynb: 12 | execute: 13 | echo: true 14 | eval: true 15 | --- 16 | 17 | # Introduction 18 | 19 | The purpose of this vignette is to briefly describe access to a 20 | tissue microarray dataset lodged in the NSF ACCESS Open Storage 21 | Network (OSN). 22 | 23 | # TMA11 24 | 25 | ## Synapse repository 26 | 27 | This [Synapse](https://www.synapse.org) repository contains 28 | data related to the MCMICRO system as described in 29 | a recent [Nature Methods paper](https://doi.org/10.1038/s41592-021-01308-y). 30 | 31 | ``` 32 | https://www.synapse.org/#!Synapse:syn22345749 33 | ``` 34 | 35 | ## OSN address and query 36 | 37 | ``` 38 | You can browse the TMA11 data at the following address: https://mghp.osn.xsede.org/bir190004-bucket01/index.html#TMA11/ 39 | ``` 40 | 41 | The data is free and publicly accessible and can be downloaded locally or accessed remotely. 42 | 43 | ### Python Example 44 | 45 | In python, the fifth core in the array can be read using 46 | ```{python} 47 | import s3fs 48 | import zarr 49 | fs = s3fs.S3FileSystem(anon=True, key="dummy", secret="dummy", 50 | client_kwargs={'endpoint_url': "https://mghp.osn.xsede.org/"}) 51 | mapper = fs.get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr') 52 | zarr.load(mapper) 53 | ``` 54 | 55 | ### R example 56 | 57 | In R, the following can be used, once zarr's python library 58 | has been installed in the appropriate python distribution. 59 | 60 | ```{r} 61 | library(reticulate) 62 | s3fs = import("s3fs") 63 | zr = import("zarr") 64 | fs = s3fs$S3FileSystem(anon='True', key="dummy", secret="dummy", 65 | client_kwargs=list(endpoint_url = 'https://mghp.osn.xsede.org/')) 66 | mapper = fs$get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr') 67 | c5 = zr$load(mapper) 68 | dim(c5) 69 | ``` 70 | 71 | On a decent network connection the load takes under 20 seconds. This can also vary based on your geographical proximity to the hosting pods. The data is hosted on the Open Storage Network in the United States. 72 | 73 | The R array c5 serializes to about 1 GB of numeric data (64 x 3007 x 3007). 74 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/quarto-html/quarto-syntax-highlighting.css: -------------------------------------------------------------------------------- 1 | /* quarto syntax highlight colors */ 2 | :root { 3 | --quarto-hl-ot-color: #003B4F; 4 | --quarto-hl-at-color: #657422; 5 | --quarto-hl-ss-color: #20794D; 6 | --quarto-hl-an-color: #5E5E5E; 7 | --quarto-hl-fu-color: #4758AB; 8 | --quarto-hl-st-color: #20794D; 9 | --quarto-hl-cf-color: #003B4F; 10 | --quarto-hl-op-color: #5E5E5E; 11 | --quarto-hl-er-color: #AD0000; 12 | --quarto-hl-bn-color: #AD0000; 13 | --quarto-hl-al-color: #AD0000; 14 | --quarto-hl-va-color: #111111; 15 | --quarto-hl-bu-color: inherit; 16 | --quarto-hl-ex-color: inherit; 17 | --quarto-hl-pp-color: #AD0000; 18 | --quarto-hl-in-color: #5E5E5E; 19 | --quarto-hl-vs-color: #20794D; 20 | --quarto-hl-wa-color: #5E5E5E; 21 | --quarto-hl-do-color: #5E5E5E; 22 | --quarto-hl-im-color: #00769E; 23 | --quarto-hl-ch-color: #20794D; 24 | --quarto-hl-dt-color: #AD0000; 25 | --quarto-hl-fl-color: #AD0000; 26 | --quarto-hl-co-color: #5E5E5E; 27 | --quarto-hl-cv-color: #5E5E5E; 28 | --quarto-hl-cn-color: #8f5902; 29 | --quarto-hl-sc-color: #5E5E5E; 30 | --quarto-hl-dv-color: #AD0000; 31 | --quarto-hl-kw-color: #003B4F; 32 | } 33 | 34 | /* other quarto variables */ 35 | :root { 36 | --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; 37 | } 38 | 39 | pre > code.sourceCode > span { 40 | color: #003B4F; 41 | } 42 | 43 | code span { 44 | color: #003B4F; 45 | } 46 | 47 | code.sourceCode > span { 48 | color: #003B4F; 49 | } 50 | 51 | div.sourceCode, 52 | div.sourceCode pre.sourceCode { 53 | color: #003B4F; 54 | } 55 | 56 | code span.ot { 57 | color: #003B4F; 58 | } 59 | 60 | code span.at { 61 | color: #657422; 62 | } 63 | 64 | code span.ss { 65 | color: #20794D; 66 | } 67 | 68 | code span.an { 69 | color: #5E5E5E; 70 | } 71 | 72 | code span.fu { 73 | color: #4758AB; 74 | } 75 | 76 | code span.st { 77 | color: #20794D; 78 | } 79 | 80 | code span.cf { 81 | color: #003B4F; 82 | } 83 | 84 | code span.op { 85 | color: #5E5E5E; 86 | } 87 | 88 | code span.er { 89 | color: #AD0000; 90 | } 91 | 92 | code span.bn { 93 | color: #AD0000; 94 | } 95 | 96 | code span.al { 97 | color: #AD0000; 98 | } 99 | 100 | code span.va { 101 | color: #111111; 102 | } 103 | 104 | code span.pp { 105 | color: #AD0000; 106 | } 107 | 108 | code span.in { 109 | color: #5E5E5E; 110 | } 111 | 112 | code span.vs { 113 | color: #20794D; 114 | } 115 | 116 | code span.wa { 117 | color: #5E5E5E; 118 | font-style: italic; 119 | } 120 | 121 | code span.do { 122 | color: #5E5E5E; 123 | font-style: italic; 124 | } 125 | 126 | code span.im { 127 | color: #00769E; 128 | } 129 | 130 | code span.ch { 131 | color: #20794D; 132 | } 133 | 134 | code span.dt { 135 | color: #AD0000; 136 | } 137 | 138 | code span.fl { 139 | color: #AD0000; 140 | } 141 | 142 | code span.co { 143 | color: #5E5E5E; 144 | } 145 | 146 | code span.cv { 147 | color: #5E5E5E; 148 | font-style: italic; 149 | } 150 | 151 | code span.cn { 152 | color: #8f5902; 153 | } 154 | 155 | code span.sc { 156 | color: #5E5E5E; 157 | } 158 | 159 | code span.dv { 160 | color: #AD0000; 161 | } 162 | 163 | code span.kw { 164 | color: #003B4F; 165 | } 166 | 167 | .prevent-inlining { 168 | content: " /home/jovyan/gitrepo && REPONAME=$(echo $GIT_REPO | awk -F'/' '{print $NF}'); git clone https://github.com/${GIT_REPO} /home/jovyan/$REPONAME && cd /home/jovyan/$REPONAME && ls vignettes/* | grep ".qmd" | xargs -i bash .github/scripts/install_missing.sh {} && chown -R 1000:100 /home/jovyan && chown -R 1000:100 /usr/local/lib/R/site-library && chown -R 1000:100 /usr/lib/R/library 43 | 44 | ENV CC=/usr/bin/gcc 45 | ENV CXX=/usr/bin/g++ 46 | -------------------------------------------------------------------------------- /.github/scripts/templates/gxyjupyter_wrapper.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | ##PLACEHOLDERCONTAINER## 4 | 5 | 6 | 7 | 8888 8 | ipython/lab 9 | ipython/lab 10 | 11 | 12 | 13 | $__history_id__ 14 | $__galaxy_url__ 15 | 8080 16 | $__galaxy_url__ 17 | 18 | 19 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, 55 | visualizations and narrative text. 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9 | // @license-end -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # BiocDeployable Template for Quarto documents 2 | 3 | This is a BiocDeployable template repository, notably for rendering and deploying Quarto documents. 4 | 5 | ## Getting Started 6 | 7 | ### 0. Background info 8 | 9 | #### Source QMD files 10 | 11 | In the [`vignettes/`](./vignettes) directory, you will find the source Quarto Markdown (.qmd) files, 12 | representing the material to be rendered and deployed. 13 | 14 | By default, this repository will have an example file containing both R and Python code. 15 | You can start by renaming and editing the example file. 16 | You can add as many qmd files as you want in the `vignettes/` directory, all of which will render all 17 | output formats in the [`autogenerated/quarto` directory](./autogenerated/quarto), as well as build 18 | Docker images with installed dependencies and rendered documents. 19 | 20 | #### Dependencies 21 | 22 | Some dependencies do not have to explicitly defined, and will be scraped at runtime by [a script](.github/scripts/install_missing.sh) 23 | in the GitHub Action, including: 24 | - R packages hosted by CRAN (eg: `install.packages("packagename")`) 25 | - R packages hosted by Bioconductor (eg: `BiocManager::install("packagename")`) 26 | - Python modules hosted by PyPi (eg: `pip install packagename`) 27 | 28 | #### TODO: Additional dependencies declaration 29 | 30 | #### Outputs 31 | 32 | The GitHub actions listed in the table above will generate two kinds of outputs: 33 | - Documents rendered by Quarto from the source QMD files, which will be pushed by the action in the [`autogenerated/quarto` directory](./autogenerated/quarto) within your GitHub repository. 34 | - Docker images which will be pushed to the [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry) with the name of your GitHub repository. 35 | 36 | ### 1. Forking the repository 37 | 38 | You can get started by creating your own repository from this template. 39 | 40 | ![use-template-button](screenshots/getting-started-1.png) 41 | 42 | Choose an all lowercase shortname for the repository, and write a brief description 43 | which will serve as your document title. You can rename your repository at a later time in the GitHub settings. 44 | 45 | ![choose-names](screenshots/getting-started-2.png) 46 | 47 | When you fork the repository, an automatic GitHub Action will be dispatched and edit your 48 | README.md, pointing links to your own repository. You can freely [edit this README file](./README.md) yourself after this initial push. 49 | 50 | ### 2. Adding your Quarto Markdown documents 51 | 52 | The next step is to add your [Quarto Markdown documents](https://quarto.org/docs/authoring/markdown-basics.html). 53 | The below walkthrough will show you how to edit documents in the browser. If you are familiar 54 | with `git`, you can make your changes locally and push as usual. 55 | 56 | #### Editing example document 57 | 58 | This repository comes with [an example document](./vignettes/OSN_example.qmd) to help get you started. 59 | You can edit this document in your browser by clicking on the pencil as shown below: 60 | ![pencil-to-edit](screenshots/getting-started-3.png) 61 | 62 | Note that you can also rename the file by editing the text shown below. Remember however to keep the `.qmd` extension which is used by the scripts. 63 | 64 | ![renaming](screenshots/getting-started-4.png) 65 | 66 | After making your changes, you can add a descriptive message then commit them back to the repository. 67 | 68 | ![committing](screenshots/getting-started-5.png) 69 | 70 | After each change is made to your repository, a new GitHub action is dispatched to try 71 | rendering your document, then generating deployable Docker images for your repository. 72 | These artifacts will be updated with each change. The table below details the GitHub actions 73 | and their outputs. 74 | 75 | #### Adding Quarto documents 76 | 77 | Beyond the example document, which you can also delete, you can add as many Quarto documents 78 | as you like to each repository, for example a document per educational module. These documents 79 | need to be added in the [`vignettes/`](./vignettes) directory, and can be done so in the 80 | browser by clicking the "Add File" button shown below. 81 | 82 | ![add-file](screenshots/getting-started-6.png) 83 | 84 | #### GitHub Actions 85 | 86 | This repository notably includes the following GitHub actions: 87 | 88 | | Description | Job Source | Outputs | Trigger | 89 | |--------------------------------------------------------------------|----------------------------------------------------------------------------------|----------------------------------------------------------------------------|---------------------| 90 | | Installing dependencies and Rendering Quarto documents | [quarto_rendering.yaml](./.github/workflows/quarto_rendering.yaml#L6) | [`autogenerated/quarto` directory](./autogenerated/quarto) | Every pushed commit | 91 | | Building Bioconductor RStudio Docker image | [docker_build.yaml#buildrstudio](./.github/workflows/quarto_rendering.yaml#L44) | [`ghcr.io/almahmoud/biocdeployablequarto:biocrstudio-main`](https://ghcr.io/almahmoud/biocdeployablequarto:biocrstudio-main) docker image | Every pushed commit | 92 | | Building Jupyter Docker image for deployment in Galaxy | [docker_build.yaml#buildgxyjupyter](./.github/workflows/quarto_rendering.yaml#L74) | [`ghcr.io/almahmoud/biocdeployablequarto:gxyjupyter-main`](https://ghcr.io/almahmoud/biocdeployablequarto:gxyjupyter-main) docker image | Every pushed commit | 93 | | Building Bioconductor RStudio Docker image for deployment on AnVIL | [docker_build.yaml#buildanvilrstudio](./.github/workflows/quarto_rendering.yaml#L104) | [`ghcr.io/almahmoud/biocdeployablequarto:biocanvil-main`](https://ghcr.io/almahmoud/biocdeployablequarto:biocanvil-main) docker image | Every pushed commit | 94 | 95 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "markdown", 5 | "metadata": {}, 6 | "source": [ 7 | "# OSN_example: demonstrate usage of Open Storage Network resources for\n", 8 | "\n", 9 | "multiplex imaging data\n", 10 | "\n", 11 | "Vincent J. Carey, stvjc at channing.harvard.edu \n", 12 | "Ludwig Geistlinger, ludwig_geistlinger at hms.harvard.edu \n", 13 | "Alex Mahmoud, almahmoud at channing.harvard.edu \n", 14 | "4/22/23\n", 15 | "\n", 16 | "# Introduction\n", 17 | "\n", 18 | "The purpose of this vignette is to briefly describe access to a tissue\n", 19 | "microarray dataset lodged in the NSF ACCESS Open Storage Network (OSN).\n", 20 | "\n", 21 | "# TMA11\n", 22 | "\n", 23 | "## Synapse repository\n", 24 | "\n", 25 | "This [Synapse](https://www.synapse.org) repository contains data related\n", 26 | "to the MCMICRO system as described in a recent [Nature Methods\n", 27 | "paper](https://doi.org/10.1038/s41592-021-01308-y).\n", 28 | "\n", 29 | " https://www.synapse.org/#!Synapse:syn22345749\n", 30 | "\n", 31 | "## OSN address and query\n", 32 | "\n", 33 | " You can browse the TMA11 data at the following address: https://mghp.osn.xsede.org/bir190004-bucket01/index.html#TMA11/\n", 34 | "\n", 35 | "The data is free and publicly accessible and can be downloaded locally\n", 36 | "or accessed remotely.\n", 37 | "\n", 38 | "### Python Example\n", 39 | "\n", 40 | "In python, the fifth core in the array can be read using" 41 | ], 42 | "id": "eb6f5ea3-efed-465a-a46a-059cbc7c5f5e" 43 | }, 44 | { 45 | "cell_type": "code", 46 | "execution_count": null, 47 | "metadata": {}, 48 | "outputs": [ 49 | { 50 | "output_type": "stream", 51 | "name": "stdout", 52 | "text": [ 53 | "array([[[ 95, 73, 127, ..., 93, 77, 166],\n", 54 | " [107, 111, 126, ..., 53, 78, 62],\n", 55 | " [110, 84, 118, ..., 118, 92, 73],\n", 56 | " ...,\n", 57 | " [ 53, 55, 90, ..., 60, 91, 89],\n", 58 | " [ 74, 56, 106, ..., 123, 95, 86],\n", 59 | " [100, 57, 94, ..., 109, 112, 78]],\n", 60 | "\n", 61 | " [[199, 181, 218, ..., 232, 155, 163],\n", 62 | " [200, 203, 190, ..., 206, 180, 212],\n", 63 | " [240, 249, 207, ..., 184, 218, 163],\n", 64 | " ...,\n", 65 | " [177, 182, 188, ..., 235, 269, 192],\n", 66 | " [253, 266, 243, ..., 187, 206, 200],\n", 67 | " [245, 224, 217, ..., 170, 133, 214]],\n", 68 | "\n", 69 | " [[ 91, 80, 80, ..., 95, 15, 100],\n", 70 | " [ 59, 41, 58, ..., 72, 80, 0],\n", 71 | " [ 39, 47, 73, ..., 37, 61, 81],\n", 72 | " ...,\n", 73 | " [ 71, 51, 2, ..., 75, 41, 52],\n", 74 | " [ 62, 62, 66, ..., 70, 78, 65],\n", 75 | " [ 40, 35, 83, ..., 38, 61, 55]],\n", 76 | "\n", 77 | " ...,\n", 78 | "\n", 79 | " [[253, 258, 296, ..., 319, 252, 240],\n", 80 | " [292, 314, 296, ..., 220, 303, 267],\n", 81 | " [294, 256, 258, ..., 283, 244, 291],\n", 82 | " ...,\n", 83 | " [251, 283, 359, ..., 333, 213, 219],\n", 84 | " [268, 296, 309, ..., 277, 236, 250],\n", 85 | " [320, 258, 301, ..., 226, 250, 283]],\n", 86 | "\n", 87 | " [[ 83, 72, 91, ..., 65, 84, 58],\n", 88 | " [ 94, 76, 89, ..., 71, 113, 85],\n", 89 | " [ 98, 94, 105, ..., 129, 159, 69],\n", 90 | " ...,\n", 91 | " [ 67, 62, 85, ..., 103, 99, 93],\n", 92 | " [ 89, 55, 93, ..., 96, 85, 77],\n", 93 | " [105, 75, 111, ..., 70, 76, 106]],\n", 94 | "\n", 95 | " [[311, 223, 257, ..., 252, 288, 258],\n", 96 | " [242, 235, 278, ..., 311, 231, 229],\n", 97 | " [243, 298, 309, ..., 232, 213, 221],\n", 98 | " ...,\n", 99 | " [424, 382, 419, ..., 280, 291, 321],\n", 100 | " [402, 393, 328, ..., 325, 366, 370],\n", 101 | " [437, 418, 387, ..., 343, 402, 336]]], dtype=uint16)" 102 | ] 103 | } 104 | ], 105 | "source": [ 106 | "import s3fs\n", 107 | "import zarr\n", 108 | "fs = s3fs.S3FileSystem(anon=True, key=\"dummy\", secret=\"dummy\", \n", 109 | " client_kwargs={'endpoint_url': \"https://mghp.osn.xsede.org/\"})\n", 110 | "mapper = fs.get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr')\n", 111 | "zarr.load(mapper)" 112 | ], 113 | "id": "b976cf9d-0eb5-4129-bb43-44122e46f863" 114 | }, 115 | { 116 | "cell_type": "markdown", 117 | "metadata": {}, 118 | "source": [ 119 | "### R example\n", 120 | "\n", 121 | "In R, the following can be used, once zarr’s python library has been\n", 122 | "installed in the appropriate python distribution." 123 | ], 124 | "id": "bee2c481-3d7b-40c5-afa9-a7a92ef94aa7" 125 | }, 126 | { 127 | "cell_type": "code", 128 | "execution_count": null, 129 | "metadata": {}, 130 | "outputs": [ 131 | { 132 | "output_type": "stream", 133 | "name": "stdout", 134 | "text": [ 135 | "[1] 64 3007 3007" 136 | ] 137 | } 138 | ], 139 | "source": [ 140 | "library(reticulate)\n", 141 | "s3fs = import(\"s3fs\")\n", 142 | "zr = import(\"zarr\")\n", 143 | "fs = s3fs$S3FileSystem(anon='True', key=\"dummy\", secret=\"dummy\",\n", 144 | " client_kwargs=list(endpoint_url = 'https://mghp.osn.xsede.org/'))\n", 145 | "mapper = fs$get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr')\n", 146 | "c5 = zr$load(mapper)\n", 147 | "dim(c5)" 148 | ], 149 | "id": "329cbb85-b862-47f9-a126-9beb349c78b4" 150 | }, 151 | { 152 | "cell_type": "markdown", 153 | "metadata": {}, 154 | "source": [ 155 | "On a decent network connection the load takes under 20 seconds. This can\n", 156 | "also vary based on your geographical proximity to the hosting pods. The\n", 157 | "data is hosted on the Open Storage Network in the United States.\n", 158 | "\n", 159 | "The R array c5 serializes to about 1 GB of numeric data (64 x 3007 x\n", 160 | "3007)." 161 | ], 162 | "id": "a72e73a7-a244-43fa-946d-ebba486dff36" 163 | } 164 | ], 165 | "nbformat": 4, 166 | "nbformat_minor": 5, 167 | "metadata": { 168 | "kernelspec": { 169 | "display_name": "Python 3", 170 | "language": "python", 171 | "name": "python3" 172 | } 173 | } 174 | } -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/clipboard/clipboard.min.js: -------------------------------------------------------------------------------- 1 | /*! 2 | * clipboard.js v2.0.10 3 | * https://clipboardjs.com/ 4 | * 5 | * Licensed MIT © Zeno Rocha 6 | */ 7 | !function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1> tmpformats 54 | } 55 | export -f getformats 56 | ls vignettes/* | grep ".qmd" > tmpfiles 57 | cat tmpfiles | xargs -i bash -c "getformats {}" 58 | # List of all files to be moved 59 | cat tmpformats | sort | uniq | xargs -i bash -c "cat tmpfiles | xargs -I## bash -c \"echo ## | sed 's/.qmd/{}/g'\"" > tmpgenerated 60 | rm -rf autogenerated 61 | mkdir -p autogenerated/quarto 62 | cat tmpgenerated | xargs -i mv {} autogenerated/quarto/ 63 | rm tmpformats tmpfiles tmpgenerated 64 | git config user.name github-actions 65 | git config user.email github-actions@github.com 66 | git add . 67 | git commit -m "Rendering quarto documents on $(echo $(date +'%m-%d-%y-%H-%M-%S'))" 68 | git push 69 | 70 | buildrstudio: 71 | name: Build RStudio image 72 | runs-on: ubuntu-latest 73 | needs: quartotests 74 | steps: 75 | - uses: actions/checkout@v3 76 | - name: Login to docker hub 77 | uses: docker/login-action@v2 78 | with: 79 | registry: ghcr.io 80 | username: ${{ github.actor }} 81 | password: ${{ secrets.GITHUB_TOKEN }} 82 | 83 | - name: Extract metadata (tags, labels) for Docker 84 | id: meta 85 | uses: docker/metadata-action@v4 86 | with: 87 | images: ghcr.io/${{ github.repository }} 88 | tags: | 89 | type=raw,value=biocrstudio-{{branch}} 90 | 91 | - name: Build and push Docker image 92 | uses: docker/build-push-action@v3 93 | with: 94 | build-args: | 95 | GIT_REPO=${{github.repository}} 96 | file: .github/scripts/rstudio.Dockerfile 97 | push: true 98 | tags: ${{ steps.meta.outputs.tags }} 99 | labels: ${{ steps.meta.outputs.labels }} 100 | 101 | - name: "Repository metadata" 102 | uses: varunsridharan/action-repository-meta@main 103 | with: 104 | REPOSITORY: ${{github.repository}} 105 | env: 106 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 107 | - name: Push run_id 108 | uses: nick-fields/retry@v2 109 | with: 110 | timeout_minutes: 10 111 | max_attempts: 20 112 | shell: bash 113 | command: | 114 | git config --global --add safe.directory "$GITHUB_WORKSPACE" 115 | 116 | LONGNAME="$REPOSITORY_DESCRIPTION" 117 | SHORTNAME="$(echo ${{github.repository}} | awk -F'/' '{print $NF}')" 118 | REPOSITORY="${{github.repository}}" 119 | BRANCH="${GITHUB_REF#refs/heads/}" 120 | 121 | bash .github/scripts/generate_wrapper.sh "$LONGNAME" "$SHORTNAME" "$REPOSITORY" "$BRANCH" "biocrstudio" 122 | 123 | mkdir -p /tmp 124 | cp -r autogenerated/wrappers /tmp/ 125 | git pull origin main || git reset --hard origin/main 126 | cp -r /tmp/wrappers autogenerated/ 127 | 128 | git config user.name github-actions 129 | git config user.email github-actions@github.com 130 | git add . 131 | git commit -m "Generated Galaxy wrappers on $(echo $(date +'%m-%d-%y-%H-%M-%S'))" 132 | git push 133 | 134 | buildgxyjupyter: 135 | name: Build Galaxy Jupyter image 136 | runs-on: ubuntu-latest 137 | needs: quartotests 138 | steps: 139 | - uses: actions/checkout@v3 140 | - name: Login to docker hub 141 | uses: docker/login-action@v2 142 | with: 143 | registry: ghcr.io 144 | username: ${{ github.actor }} 145 | password: ${{ secrets.GITHUB_TOKEN }} 146 | 147 | - name: Extract metadata (tags, labels) for Docker 148 | id: meta 149 | uses: docker/metadata-action@v4 150 | with: 151 | images: ghcr.io/${{ github.repository }} 152 | tags: | 153 | type=raw,value=gxyjupyter-{{branch}} 154 | 155 | - name: Build and push Docker image 156 | uses: docker/build-push-action@v3 157 | with: 158 | build-args: | 159 | GIT_REPO=${{github.repository}} 160 | file: .github/scripts/galaxy-jupyter.Dockerfile 161 | push: true 162 | tags: ${{ steps.meta.outputs.tags }} 163 | labels: ${{ steps.meta.outputs.labels }} 164 | - name: "Repository metadata" 165 | uses: varunsridharan/action-repository-meta@main 166 | with: 167 | REPOSITORY: ${{github.repository}} 168 | env: 169 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 170 | - name: Push run_id 171 | uses: nick-fields/retry@v2 172 | with: 173 | timeout_minutes: 10 174 | max_attempts: 20 175 | shell: bash 176 | command: | 177 | git config --global --add safe.directory "$GITHUB_WORKSPACE" 178 | 179 | LONGNAME="$REPOSITORY_DESCRIPTION" 180 | SHORTNAME="$(echo ${{github.repository}} | awk -F'/' '{print $NF}')" 181 | REPOSITORY="${{github.repository}}" 182 | BRANCH="${GITHUB_REF#refs/heads/}" 183 | 184 | bash .github/scripts/generate_wrapper.sh "$LONGNAME" "$SHORTNAME" "$REPOSITORY" "$BRANCH" "biocrstudio" 185 | 186 | mkdir -p /tmp 187 | cp -r autogenerated/wrappers /tmp/ 188 | git pull origin main || git reset --hard origin/main 189 | cp -r /tmp/wrappers autogenerated/ 190 | 191 | git config user.name github-actions 192 | git config user.email github-actions@github.com 193 | git add . 194 | git commit -m "Generated Galaxy wrappers on $(echo $(date +'%m-%d-%y-%H-%M-%S'))" 195 | git push 196 | 197 | buildanvilrstudio: 198 | name: Build AnVIL RStudio image 199 | runs-on: ubuntu-latest 200 | needs: quartotests 201 | steps: 202 | - uses: actions/checkout@v3 203 | - name: Login to docker hub 204 | uses: docker/login-action@v2 205 | with: 206 | registry: ghcr.io 207 | username: ${{ github.actor }} 208 | password: ${{ secrets.GITHUB_TOKEN }} 209 | 210 | - name: Extract metadata (tags, labels) for Docker 211 | id: meta 212 | uses: docker/metadata-action@v4 213 | with: 214 | images: ghcr.io/${{ github.repository }} 215 | tags: | 216 | type=raw,value=biocanvil-{{branch}} 217 | 218 | - name: Build and push Docker image 219 | uses: docker/build-push-action@v3 220 | with: 221 | build-args: | 222 | GIT_REPO=${{github.repository}} 223 | file: .github/scripts/anvil-rstudio.Dockerfile 224 | push: true 225 | tags: ${{ steps.meta.outputs.tags }} 226 | labels: ${{ steps.meta.outputs.labels }} 227 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | OSN_example: demonstrate usage of Open Storage Network resources for multiplex imaging data 15 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 |
110 | 111 |
112 | 113 |
114 |
115 |

OSN_example: demonstrate usage of Open Storage Network resources for multiplex imaging data

116 |
117 | 118 | 119 | 120 |
121 | 122 |
123 |
Authors
124 |
125 |

Vincent J. Carey, stvjc at channing.harvard.edu

126 |

Ludwig Geistlinger, ludwig_geistlinger at hms.harvard.edu

127 |

Alex Mahmoud, almahmoud at channing.harvard.edu

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129 |
130 | 131 |
132 |
Published
133 |
134 |

April 22, 2023

135 |
136 |
137 | 138 | 139 |
140 | 141 | 142 |
143 | 144 |
145 |

Introduction

146 |

The purpose of this vignette is to briefly describe access to a tissue microarray dataset lodged in the NSF ACCESS Open Storage Network (OSN).

147 |
148 |
149 |

TMA11

150 |
151 |

Synapse repository

152 |

This Synapse repository contains data related to the MCMICRO system as described in a recent Nature Methods paper.

153 | 
https://www.synapse.org/#!Synapse:syn22345749
154 |
155 |
156 |

OSN address and query

157 | 
You can browse the TMA11 data at the following address: https://mghp.osn.xsede.org/bir190004-bucket01/index.html#TMA11/
158 |

The data is free and publicly accessible and can be downloaded locally or accessed remotely.

159 |
160 |

Python Example

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In python, the fifth core in the array can be read using

162 |
163 |
164 | Code 165 | 
import s3fs
166 | import zarr
167 | fs = s3fs.S3FileSystem(anon=True, key="dummy", secret="dummy", 
168 |     client_kwargs={'endpoint_url': "https://mghp.osn.xsede.org/"})
169 | mapper = fs.get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr')
170 | zarr.load(mapper)
171 |
172 |
173 | 
array([[[ 95,  73, 127, ...,  93,  77, 166],
174 |         [107, 111, 126, ...,  53,  78,  62],
175 |         [110,  84, 118, ..., 118,  92,  73],
176 |         ...,
177 |         [ 53,  55,  90, ...,  60,  91,  89],
178 |         [ 74,  56, 106, ..., 123,  95,  86],
179 |         [100,  57,  94, ..., 109, 112,  78]],
180 | 
181 |        [[199, 181, 218, ..., 232, 155, 163],
182 |         [200, 203, 190, ..., 206, 180, 212],
183 |         [240, 249, 207, ..., 184, 218, 163],
184 |         ...,
185 |         [177, 182, 188, ..., 235, 269, 192],
186 |         [253, 266, 243, ..., 187, 206, 200],
187 |         [245, 224, 217, ..., 170, 133, 214]],
188 | 
189 |        [[ 91,  80,  80, ...,  95,  15, 100],
190 |         [ 59,  41,  58, ...,  72,  80,   0],
191 |         [ 39,  47,  73, ...,  37,  61,  81],
192 |         ...,
193 |         [ 71,  51,   2, ...,  75,  41,  52],
194 |         [ 62,  62,  66, ...,  70,  78,  65],
195 |         [ 40,  35,  83, ...,  38,  61,  55]],
196 | 
197 |        ...,
198 | 
199 |        [[253, 258, 296, ..., 319, 252, 240],
200 |         [292, 314, 296, ..., 220, 303, 267],
201 |         [294, 256, 258, ..., 283, 244, 291],
202 |         ...,
203 |         [251, 283, 359, ..., 333, 213, 219],
204 |         [268, 296, 309, ..., 277, 236, 250],
205 |         [320, 258, 301, ..., 226, 250, 283]],
206 | 
207 |        [[ 83,  72,  91, ...,  65,  84,  58],
208 |         [ 94,  76,  89, ...,  71, 113,  85],
209 |         [ 98,  94, 105, ..., 129, 159,  69],
210 |         ...,
211 |         [ 67,  62,  85, ..., 103,  99,  93],
212 |         [ 89,  55,  93, ...,  96,  85,  77],
213 |         [105,  75, 111, ...,  70,  76, 106]],
214 | 
215 |        [[311, 223, 257, ..., 252, 288, 258],
216 |         [242, 235, 278, ..., 311, 231, 229],
217 |         [243, 298, 309, ..., 232, 213, 221],
218 |         ...,
219 |         [424, 382, 419, ..., 280, 291, 321],
220 |         [402, 393, 328, ..., 325, 366, 370],
221 |         [437, 418, 387, ..., 343, 402, 336]]], dtype=uint16)
222 |
223 |
224 |
225 |
226 |

R example

227 |

In R, the following can be used, once zarr’s python library has been installed in the appropriate python distribution.

228 |
229 |
230 | Code 231 | 
library(reticulate)
232 | s3fs = import("s3fs")
233 | zr = import("zarr")
234 | fs = s3fs$S3FileSystem(anon='True', key="dummy", secret="dummy",
235 |     client_kwargs=list(endpoint_url = 'https://mghp.osn.xsede.org/'))
236 | mapper = fs$get_mapper('bir190004-bucket01/TMA11/zarr/5.zarr')
237 | c5 = zr$load(mapper)
238 | dim(c5)
239 |
240 |
241 | 
[1]   64 3007 3007
242 |
243 |
244 |

On a decent network connection the load takes under 20 seconds. This can also vary based on your geographical proximity to the hosting pods. The data is hosted on the Open Storage Network in the United States.

245 |

The R array c5 serializes to about 1 GB of numeric data (64 x 3007 x 3007).

246 |
247 |
248 |
249 | 250 |
251 | 252 | 385 |
386 | 387 | 388 | 389 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/quarto-html/popper.min.js: -------------------------------------------------------------------------------- 1 | /** 2 | * @popperjs/core v2.11.4 - MIT License 3 | */ 4 | 5 | !function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).Popper={})}(this,(function(e){"use strict";function t(e){if(null==e)return window;if("[object Window]"!==e.toString()){var t=e.ownerDocument;return t&&t.defaultView||window}return e}function n(e){return e instanceof t(e).Element||e instanceof Element}function r(e){return e instanceof t(e).HTMLElement||e instanceof HTMLElement}function o(e){return"undefined"!=typeof ShadowRoot&&(e instanceof t(e).ShadowRoot||e instanceof ShadowRoot)}var 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-------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/quarto-html/quarto.js: -------------------------------------------------------------------------------- 1 | const sectionChanged = new CustomEvent("quarto-sectionChanged", { 2 | detail: {}, 3 | bubbles: true, 4 | cancelable: false, 5 | composed: false, 6 | }); 7 | 8 | window.document.addEventListener("DOMContentLoaded", function (_event) { 9 | const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]'); 10 | const sidebarEl = window.document.getElementById("quarto-sidebar"); 11 | const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left"); 12 | const marginSidebarEl = window.document.getElementById( 13 | "quarto-margin-sidebar" 14 | ); 15 | // function to determine whether the element has a previous sibling that is active 16 | const prevSiblingIsActiveLink = (el) => { 17 | const sibling = el.previousElementSibling; 18 | if (sibling && sibling.tagName === "A") { 19 | return sibling.classList.contains("active"); 20 | } else { 21 | return false; 22 | } 23 | }; 24 | 25 | // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior) 26 | function fireSlideEnter(e) { 27 | const event = window.document.createEvent("Event"); 28 | event.initEvent("slideenter", true, true); 29 | window.document.dispatchEvent(event); 30 | } 31 | const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]'); 32 | tabs.forEach((tab) => { 33 | tab.addEventListener("shown.bs.tab", fireSlideEnter); 34 | }); 35 | 36 | // fire slideEnter for tabby tab activations (for htmlwidget resize behavior) 37 | document.addEventListener("tabby", fireSlideEnter, false); 38 | 39 | // Track scrolling and mark TOC links as active 40 | // get table of contents and sidebar (bail if we don't have at least one) 41 | const tocLinks = tocEl 42 | ? [...tocEl.querySelectorAll("a[data-scroll-target]")] 43 | : []; 44 | const makeActive = (link) => tocLinks[link].classList.add("active"); 45 | const removeActive = (link) => tocLinks[link].classList.remove("active"); 46 | const removeAllActive = () => 47 | [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link)); 48 | 49 | // activate the anchor for a section associated with this TOC entry 50 | tocLinks.forEach((link) => { 51 | link.addEventListener("click", () => { 52 | if (link.href.indexOf("#") !== -1) { 53 | const anchor = link.href.split("#")[1]; 54 | const heading = window.document.querySelector( 55 | `[data-anchor-id=${anchor}]` 56 | ); 57 | if (heading) { 58 | // Add the class 59 | heading.classList.add("reveal-anchorjs-link"); 60 | 61 | // function to show the anchor 62 | const handleMouseout = () => { 63 | heading.classList.remove("reveal-anchorjs-link"); 64 | heading.removeEventListener("mouseout", handleMouseout); 65 | }; 66 | 67 | // add a function to clear the anchor when the user mouses out of it 68 | heading.addEventListener("mouseout", handleMouseout); 69 | } 70 | } 71 | }); 72 | }); 73 | 74 | const sections = tocLinks.map((link) => { 75 | const target = link.getAttribute("data-scroll-target"); 76 | if (target.startsWith("#")) { 77 | return window.document.getElementById(decodeURI(`${target.slice(1)}`)); 78 | } else { 79 | return window.document.querySelector(decodeURI(`${target}`)); 80 | } 81 | }); 82 | 83 | const sectionMargin = 200; 84 | let currentActive = 0; 85 | // track whether we've initialized state the first time 86 | let init = false; 87 | 88 | const updateActiveLink = () => { 89 | // The index from bottom to top (e.g. reversed list) 90 | let sectionIndex = -1; 91 | if ( 92 | window.innerHeight + window.pageYOffset >= 93 | window.document.body.offsetHeight 94 | ) { 95 | sectionIndex = 0; 96 | } else { 97 | sectionIndex = [...sections].reverse().findIndex((section) => { 98 | if (section) { 99 | return window.pageYOffset >= section.offsetTop - sectionMargin; 100 | } else { 101 | return false; 102 | } 103 | }); 104 | } 105 | if (sectionIndex > -1) { 106 | const current = sections.length - sectionIndex - 1; 107 | if (current !== currentActive) { 108 | removeAllActive(); 109 | currentActive = current; 110 | makeActive(current); 111 | if (init) { 112 | window.dispatchEvent(sectionChanged); 113 | } 114 | init = true; 115 | } 116 | } 117 | }; 118 | 119 | const inHiddenRegion = (top, bottom, hiddenRegions) => { 120 | for (const region of hiddenRegions) { 121 | if (top <= region.bottom && bottom >= region.top) { 122 | return true; 123 | } 124 | } 125 | return false; 126 | }; 127 | 128 | const categorySelector = "header.quarto-title-block .quarto-category"; 129 | const activateCategories = (href) => { 130 | // Find any categories 131 | // Surround them with a link pointing back to: 132 | // #category=Authoring 133 | try { 134 | const categoryEls = window.document.querySelectorAll(categorySelector); 135 | for (const categoryEl of categoryEls) { 136 | const categoryText = categoryEl.textContent; 137 | if (categoryText) { 138 | const link = `${href}#category=${encodeURIComponent(categoryText)}`; 139 | const linkEl = window.document.createElement("a"); 140 | linkEl.setAttribute("href", link); 141 | for (const child of categoryEl.childNodes) { 142 | linkEl.append(child); 143 | } 144 | categoryEl.appendChild(linkEl); 145 | } 146 | } 147 | } catch { 148 | // Ignore errors 149 | } 150 | }; 151 | function hasTitleCategories() { 152 | return window.document.querySelector(categorySelector) !== null; 153 | } 154 | 155 | function offsetRelativeUrl(url) { 156 | const offset = getMeta("quarto:offset"); 157 | return offset ? offset + url : url; 158 | } 159 | 160 | function offsetAbsoluteUrl(url) { 161 | const offset = getMeta("quarto:offset"); 162 | const baseUrl = new URL(offset, window.location); 163 | 164 | const projRelativeUrl = url.replace(baseUrl, ""); 165 | if (projRelativeUrl.startsWith("/")) { 166 | return projRelativeUrl; 167 | } else { 168 | return "/" + projRelativeUrl; 169 | } 170 | } 171 | 172 | // read a meta tag value 173 | function getMeta(metaName) { 174 | const metas = window.document.getElementsByTagName("meta"); 175 | for (let i = 0; i < metas.length; i++) { 176 | if (metas[i].getAttribute("name") === metaName) { 177 | return metas[i].getAttribute("content"); 178 | } 179 | } 180 | return ""; 181 | } 182 | 183 | async function findAndActivateCategories() { 184 | const currentPagePath = offsetAbsoluteUrl(window.location.href); 185 | const response = await fetch(offsetRelativeUrl("listings.json")); 186 | if (response.status == 200) { 187 | return response.json().then(function (listingPaths) { 188 | const listingHrefs = []; 189 | for (const listingPath of listingPaths) { 190 | const pathWithoutLeadingSlash = listingPath.listing.substring(1); 191 | for (const item of listingPath.items) { 192 | if ( 193 | item === currentPagePath || 194 | item === currentPagePath + "index.html" 195 | ) { 196 | // Resolve this path against the offset to be sure 197 | // we already are using the correct path to the listing 198 | // (this adjusts the listing urls to be rooted against 199 | // whatever root the page is actually running against) 200 | const relative = offsetRelativeUrl(pathWithoutLeadingSlash); 201 | const baseUrl = window.location; 202 | const resolvedPath = new URL(relative, baseUrl); 203 | listingHrefs.push(resolvedPath.pathname); 204 | break; 205 | } 206 | } 207 | } 208 | 209 | // Look up the tree for a nearby linting and use that if we find one 210 | const nearestListing = findNearestParentListing( 211 | offsetAbsoluteUrl(window.location.pathname), 212 | listingHrefs 213 | ); 214 | if (nearestListing) { 215 | activateCategories(nearestListing); 216 | } else { 217 | // See if the referrer is a listing page for this item 218 | const referredRelativePath = offsetAbsoluteUrl(document.referrer); 219 | const referrerListing = listingHrefs.find((listingHref) => { 220 | const isListingReferrer = 221 | listingHref === referredRelativePath || 222 | listingHref === referredRelativePath + "index.html"; 223 | return isListingReferrer; 224 | }); 225 | 226 | if (referrerListing) { 227 | // Try to use the referrer if possible 228 | activateCategories(referrerListing); 229 | } else if (listingHrefs.length > 0) { 230 | // Otherwise, just fall back to the first listing 231 | activateCategories(listingHrefs[0]); 232 | } 233 | } 234 | }); 235 | } 236 | } 237 | if (hasTitleCategories()) { 238 | findAndActivateCategories(); 239 | } 240 | 241 | const findNearestParentListing = (href, listingHrefs) => { 242 | if (!href || !listingHrefs) { 243 | return undefined; 244 | } 245 | // Look up the tree for a nearby linting and use that if we find one 246 | const relativeParts = href.substring(1).split("/"); 247 | while (relativeParts.length > 0) { 248 | const path = relativeParts.join("/"); 249 | for (const listingHref of listingHrefs) { 250 | if (listingHref.startsWith(path)) { 251 | return listingHref; 252 | } 253 | } 254 | relativeParts.pop(); 255 | } 256 | 257 | return undefined; 258 | }; 259 | 260 | const manageSidebarVisiblity = (el, placeholderDescriptor) => { 261 | let isVisible = true; 262 | 263 | return (hiddenRegions) => { 264 | if (el === null) { 265 | return; 266 | } 267 | 268 | // Find the last element of the TOC 269 | const lastChildEl = el.lastElementChild; 270 | 271 | if (lastChildEl) { 272 | // Find the top and bottom o the element that is being managed 273 | const elTop = el.offsetTop; 274 | const elBottom = 275 | elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight; 276 | 277 | // Converts the sidebar to a menu 278 | const convertToMenu = () => { 279 | for (const child of el.children) { 280 | child.style.opacity = 0; 281 | child.style.overflow = "hidden"; 282 | } 283 | 284 | const toggleContainer = window.document.createElement("div"); 285 | toggleContainer.style.width = "100%"; 286 | toggleContainer.classList.add("zindex-over-content"); 287 | toggleContainer.classList.add("quarto-sidebar-toggle"); 288 | toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom 289 | toggleContainer.id = placeholderDescriptor.id; 290 | toggleContainer.style.position = "fixed"; 291 | 292 | const toggleIcon = window.document.createElement("i"); 293 | toggleIcon.classList.add("quarto-sidebar-toggle-icon"); 294 | toggleIcon.classList.add("bi"); 295 | toggleIcon.classList.add("bi-caret-down-fill"); 296 | 297 | const toggleTitle = window.document.createElement("div"); 298 | const titleEl = window.document.body.querySelector( 299 | placeholderDescriptor.titleSelector 300 | ); 301 | if (titleEl) { 302 | toggleTitle.append(titleEl.innerText, toggleIcon); 303 | } 304 | toggleTitle.classList.add("zindex-over-content"); 305 | toggleTitle.classList.add("quarto-sidebar-toggle-title"); 306 | toggleContainer.append(toggleTitle); 307 | 308 | const toggleContents = window.document.createElement("div"); 309 | toggleContents.classList = el.classList; 310 | toggleContents.classList.add("zindex-over-content"); 311 | toggleContents.classList.add("quarto-sidebar-toggle-contents"); 312 | for (const child of el.children) { 313 | if (child.id === "toc-title") { 314 | continue; 315 | } 316 | 317 | const clone = child.cloneNode(true); 318 | clone.style.opacity = 1; 319 | clone.style.display = null; 320 | toggleContents.append(clone); 321 | } 322 | toggleContents.style.height = "0px"; 323 | toggleContainer.append(toggleContents); 324 | el.parentElement.prepend(toggleContainer); 325 | 326 | // Process clicks 327 | let tocShowing = false; 328 | // Allow the caller to control whether this is dismissed 329 | // when it is clicked (e.g. sidebar navigation supports 330 | // opening and closing the nav tree, so don't dismiss on click) 331 | const clickEl = placeholderDescriptor.dismissOnClick 332 | ? toggleContainer 333 | : toggleTitle; 334 | 335 | const closeToggle = () => { 336 | if (tocShowing) { 337 | toggleContainer.classList.remove("expanded"); 338 | toggleContents.style.height = "0px"; 339 | tocShowing = false; 340 | } 341 | }; 342 | 343 | const positionToggle = () => { 344 | // position the element (top left of parent, same width as parent) 345 | const elRect = el.getBoundingClientRect(); 346 | toggleContainer.style.left = `${elRect.left}px`; 347 | toggleContainer.style.top = `${elRect.top}px`; 348 | toggleContainer.style.width = `${elRect.width}px`; 349 | }; 350 | 351 | // Get rid of any expanded toggle if the user scrolls 352 | window.document.addEventListener( 353 | "scroll", 354 | throttle(() => { 355 | closeToggle(); 356 | }, 50) 357 | ); 358 | 359 | // Handle positioning of the toggle 360 | window.addEventListener( 361 | "resize", 362 | throttle(() => { 363 | positionToggle(); 364 | }, 50) 365 | ); 366 | positionToggle(); 367 | 368 | // Process the click 369 | clickEl.onclick = () => { 370 | if (!tocShowing) { 371 | toggleContainer.classList.add("expanded"); 372 | toggleContents.style.height = null; 373 | tocShowing = true; 374 | } else { 375 | closeToggle(); 376 | } 377 | }; 378 | }; 379 | 380 | // Converts a sidebar from a menu back to a sidebar 381 | const convertToSidebar = () => { 382 | for (const child of el.children) { 383 | child.style.opacity = 1; 384 | child.style.overflow = null; 385 | } 386 | 387 | const placeholderEl = window.document.getElementById( 388 | placeholderDescriptor.id 389 | ); 390 | if (placeholderEl) { 391 | placeholderEl.remove(); 392 | } 393 | 394 | el.classList.remove("rollup"); 395 | }; 396 | 397 | if (isReaderMode()) { 398 | convertToMenu(); 399 | isVisible = false; 400 | } else { 401 | if (!isVisible) { 402 | // If the element is current not visible reveal if there are 403 | // no conflicts with overlay regions 404 | if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) { 405 | convertToSidebar(); 406 | isVisible = true; 407 | } 408 | } else { 409 | // If the element is visible, hide it if it conflicts with overlay regions 410 | // and insert a placeholder toggle (or if we're in reader mode) 411 | if (inHiddenRegion(elTop, elBottom, hiddenRegions)) { 412 | convertToMenu(); 413 | isVisible = false; 414 | } 415 | } 416 | } 417 | } 418 | }; 419 | }; 420 | 421 | // Find any conflicting margin elements and add margins to the 422 | // top to prevent overlap 423 | const marginChildren = window.document.querySelectorAll( 424 | ".column-margin.column-container > * " 425 | ); 426 | 427 | nexttick(() => { 428 | let lastBottom = 0; 429 | for (const marginChild of marginChildren) { 430 | const top = marginChild.getBoundingClientRect().top + window.scrollY; 431 | if (top < lastBottom) { 432 | const margin = lastBottom - top; 433 | marginChild.style.marginTop = `${margin}px`; 434 | } 435 | const styles = window.getComputedStyle(marginChild); 436 | const marginTop = parseFloat(styles["marginTop"]); 437 | 438 | lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; 439 | } 440 | }); 441 | 442 | // Manage the visibility of the toc and the sidebar 443 | const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, { 444 | id: "quarto-toc-toggle", 445 | titleSelector: "#toc-title", 446 | dismissOnClick: true, 447 | }); 448 | const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, { 449 | id: "quarto-sidebarnav-toggle", 450 | titleSelector: ".title", 451 | dismissOnClick: false, 452 | }); 453 | let tocLeftScrollVisibility; 454 | if (leftTocEl) { 455 | tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, { 456 | id: "quarto-lefttoc-toggle", 457 | titleSelector: "#toc-title", 458 | dismissOnClick: true, 459 | }); 460 | } 461 | 462 | // Find the first element that uses formatting in special columns 463 | const conflictingEls = window.document.body.querySelectorAll( 464 | '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]' 465 | ); 466 | 467 | // Filter all the possibly conflicting elements into ones 468 | // the do conflict on the left or ride side 469 | const arrConflictingEls = Array.from(conflictingEls); 470 | const leftSideConflictEls = arrConflictingEls.filter((el) => { 471 | if (el.tagName === "ASIDE") { 472 | return false; 473 | } 474 | return Array.from(el.classList).find((className) => { 475 | return ( 476 | className !== "column-body" && 477 | className.startsWith("column-") && 478 | !className.endsWith("right") && 479 | !className.endsWith("container") && 480 | className !== "column-margin" 481 | ); 482 | }); 483 | }); 484 | const rightSideConflictEls = arrConflictingEls.filter((el) => { 485 | if (el.tagName === "ASIDE") { 486 | return true; 487 | } 488 | 489 | const hasMarginCaption = Array.from(el.classList).find((className) => { 490 | return className == "margin-caption"; 491 | }); 492 | if (hasMarginCaption) { 493 | return true; 494 | } 495 | 496 | return Array.from(el.classList).find((className) => { 497 | return ( 498 | className !== "column-body" && 499 | !className.endsWith("container") && 500 | className.startsWith("column-") && 501 | !className.endsWith("left") 502 | ); 503 | }); 504 | }); 505 | 506 | const kOverlapPaddingSize = 10; 507 | function toRegions(els) { 508 | return els.map((el) => { 509 | const top = 510 | el.getBoundingClientRect().top + 511 | document.documentElement.scrollTop - 512 | kOverlapPaddingSize; 513 | return { 514 | top, 515 | bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize, 516 | }; 517 | }); 518 | } 519 | 520 | const hideOverlappedSidebars = () => { 521 | marginScrollVisibility(toRegions(rightSideConflictEls)); 522 | sidebarScrollVisiblity(toRegions(leftSideConflictEls)); 523 | if (tocLeftScrollVisibility) { 524 | tocLeftScrollVisibility(toRegions(leftSideConflictEls)); 525 | } 526 | }; 527 | 528 | window.quartoToggleReader = () => { 529 | // Applies a slow class (or removes it) 530 | // to update the transition speed 531 | const slowTransition = (slow) => { 532 | const manageTransition = (id, slow) => { 533 | const el = document.getElementById(id); 534 | if (el) { 535 | if (slow) { 536 | el.classList.add("slow"); 537 | } else { 538 | el.classList.remove("slow"); 539 | } 540 | } 541 | }; 542 | 543 | manageTransition("TOC", slow); 544 | manageTransition("quarto-sidebar", slow); 545 | }; 546 | 547 | const readerMode = !isReaderMode(); 548 | setReaderModeValue(readerMode); 549 | 550 | // If we're entering reader mode, slow the transition 551 | if (readerMode) { 552 | slowTransition(readerMode); 553 | } 554 | highlightReaderToggle(readerMode); 555 | hideOverlappedSidebars(); 556 | 557 | // If we're exiting reader mode, restore the non-slow transition 558 | if (!readerMode) { 559 | slowTransition(!readerMode); 560 | } 561 | }; 562 | 563 | const highlightReaderToggle = (readerMode) => { 564 | const els = document.querySelectorAll(".quarto-reader-toggle"); 565 | if (els) { 566 | els.forEach((el) => { 567 | if (readerMode) { 568 | el.classList.add("reader"); 569 | } else { 570 | el.classList.remove("reader"); 571 | } 572 | }); 573 | } 574 | }; 575 | 576 | const setReaderModeValue = (val) => { 577 | if (window.location.protocol !== "file:") { 578 | window.localStorage.setItem("quarto-reader-mode", val); 579 | } else { 580 | localReaderMode = val; 581 | } 582 | }; 583 | 584 | const isReaderMode = () => { 585 | if (window.location.protocol !== "file:") { 586 | return window.localStorage.getItem("quarto-reader-mode") === "true"; 587 | } else { 588 | return localReaderMode; 589 | } 590 | }; 591 | let localReaderMode = null; 592 | 593 | // Walk the TOC and collapse/expand nodes 594 | // Nodes are expanded if: 595 | // - they are top level 596 | // - they have children that are 'active' links 597 | // - they are directly below an link that is 'active' 598 | const walk = (el, depth) => { 599 | // Tick depth when we enter a UL 600 | if (el.tagName === "UL") { 601 | depth = depth + 1; 602 | } 603 | 604 | // It this is active link 605 | let isActiveNode = false; 606 | if (el.tagName === "A" && el.classList.contains("active")) { 607 | isActiveNode = true; 608 | } 609 | 610 | // See if there is an active child to this element 611 | let hasActiveChild = false; 612 | for (child of el.children) { 613 | hasActiveChild = walk(child, depth) || hasActiveChild; 614 | } 615 | 616 | // Process the collapse state if this is an UL 617 | if (el.tagName === "UL") { 618 | if (depth === 1 || hasActiveChild || prevSiblingIsActiveLink(el)) { 619 | el.classList.remove("collapse"); 620 | } else { 621 | el.classList.add("collapse"); 622 | } 623 | 624 | // untick depth when we leave a UL 625 | depth = depth - 1; 626 | } 627 | return hasActiveChild || isActiveNode; 628 | }; 629 | 630 | // walk the TOC and expand / collapse any items that should be shown 631 | 632 | if (tocEl) { 633 | walk(tocEl, 0); 634 | updateActiveLink(); 635 | } 636 | 637 | // Throttle the scroll event and walk peridiocally 638 | window.document.addEventListener( 639 | "scroll", 640 | throttle(() => { 641 | if (tocEl) { 642 | updateActiveLink(); 643 | walk(tocEl, 0); 644 | } 645 | if (!isReaderMode()) { 646 | hideOverlappedSidebars(); 647 | } 648 | }, 5) 649 | ); 650 | window.addEventListener( 651 | "resize", 652 | throttle(() => { 653 | if (!isReaderMode()) { 654 | hideOverlappedSidebars(); 655 | } 656 | }, 10) 657 | ); 658 | hideOverlappedSidebars(); 659 | highlightReaderToggle(isReaderMode()); 660 | }); 661 | 662 | // grouped tabsets 663 | window.addEventListener("pageshow", (_event) => { 664 | function getTabSettings() { 665 | const data = localStorage.getItem("quarto-persistent-tabsets-data"); 666 | if (!data) { 667 | localStorage.setItem("quarto-persistent-tabsets-data", "{}"); 668 | return {}; 669 | } 670 | if (data) { 671 | return JSON.parse(data); 672 | } 673 | } 674 | 675 | function setTabSettings(data) { 676 | localStorage.setItem( 677 | "quarto-persistent-tabsets-data", 678 | JSON.stringify(data) 679 | ); 680 | } 681 | 682 | function setTabState(groupName, groupValue) { 683 | const data = getTabSettings(); 684 | data[groupName] = groupValue; 685 | setTabSettings(data); 686 | } 687 | 688 | function toggleTab(tab, active) { 689 | const tabPanelId = tab.getAttribute("aria-controls"); 690 | const tabPanel = document.getElementById(tabPanelId); 691 | if (active) { 692 | tab.classList.add("active"); 693 | tabPanel.classList.add("active"); 694 | } else { 695 | tab.classList.remove("active"); 696 | tabPanel.classList.remove("active"); 697 | } 698 | } 699 | 700 | function toggleAll(selectedGroup, selectorsToSync) { 701 | for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) { 702 | const active = selectedGroup === thisGroup; 703 | for (const tab of tabs) { 704 | toggleTab(tab, active); 705 | } 706 | } 707 | } 708 | 709 | function findSelectorsToSyncByLanguage() { 710 | const result = {}; 711 | const tabs = Array.from( 712 | document.querySelectorAll(`div[data-group] a[id^='tabset-']`) 713 | ); 714 | for (const item of tabs) { 715 | const div = item.parentElement.parentElement.parentElement; 716 | const group = div.getAttribute("data-group"); 717 | if (!result[group]) { 718 | result[group] = {}; 719 | } 720 | const selectorsToSync = result[group]; 721 | const value = item.innerHTML; 722 | if (!selectorsToSync[value]) { 723 | selectorsToSync[value] = []; 724 | } 725 | selectorsToSync[value].push(item); 726 | } 727 | return result; 728 | } 729 | 730 | function setupSelectorSync() { 731 | const selectorsToSync = findSelectorsToSyncByLanguage(); 732 | Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => { 733 | Object.entries(tabSetsByValue).forEach(([value, items]) => { 734 | items.forEach((item) => { 735 | item.addEventListener("click", (_event) => { 736 | setTabState(group, value); 737 | toggleAll(value, selectorsToSync[group]); 738 | }); 739 | }); 740 | }); 741 | }); 742 | return selectorsToSync; 743 | } 744 | 745 | const selectorsToSync = setupSelectorSync(); 746 | for (const [group, selectedName] of Object.entries(getTabSettings())) { 747 | const selectors = selectorsToSync[group]; 748 | // it's possible that stale state gives us empty selections, so we explicitly check here. 749 | if (selectors) { 750 | toggleAll(selectedName, selectors); 751 | } 752 | } 753 | }); 754 | 755 | function throttle(func, wait) { 756 | let waiting = false; 757 | return function () { 758 | if (!waiting) { 759 | func.apply(this, arguments); 760 | waiting = true; 761 | setTimeout(function () { 762 | waiting = false; 763 | }, wait); 764 | } 765 | }; 766 | } 767 | 768 | function nexttick(func) { 769 | return setTimeout(func, 0); 770 | } 771 | -------------------------------------------------------------------------------- /autogenerated/quarto/OSN_example_files/libs/bootstrap/bootstrap.min.js: -------------------------------------------------------------------------------- 1 | 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Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;ij.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(t){if(void 0===Fe)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let e=this._element;"parent"===this._config.reference?e=t:o(this._config.reference)?e=r(this._config.reference):"object"==typeof this._config.reference&&(e=this._config.reference);const i=this._getPopperConfig(),n=i.modifiers.find((t=>"applyStyles"===t.name&&!1===t.enabled));this._popper=qe(e,this._menu,i),n&&U.setDataAttribute(this._menu,"popper","static")}_isShown(t=this._element){return t.classList.contains(Je)}_getMenuElement(){return V.next(this._element,ei)[0]}_getPlacement(){const t=this._element.parentNode;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:''},pn={...un.DefaultType,content:"(string|element|function)"},mn={HIDE:"hide.bs.popover",HIDDEN:"hidden.bs.popover",SHOW:"show.bs.popover",SHOWN:"shown.bs.popover",INSERTED:"inserted.bs.popover",CLICK:"click.bs.popover",FOCUSIN:"focusin.bs.popover",FOCUSOUT:"focusout.bs.popover",MOUSEENTER:"mouseenter.bs.popover",MOUSELEAVE:"mouseleave.bs.popover"};class gn extends un{static get Default(){return fn}static get NAME(){return"popover"}static get Event(){return mn}static get DefaultType(){return pn}isWithContent(){return this.getTitle()||this._getContent()}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),".popover-header"),this._sanitizeAndSetContent(t,this._getContent(),".popover-body")}_getContent(){return this._resolvePossibleFunction(this._config.content)}_getBasicClassPrefix(){return"bs-popover"}static jQueryInterface(t){return this.each((function(){const e=gn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(gn);const _n="scrollspy",bn={offset:10,method:"auto",target:""},vn={offset:"number",method:"string",target:"(string|element)"},yn="active",wn=".nav-link, .list-group-item, .dropdown-item",En="position";class An extends B{constructor(t,e){super(t),this._scrollElement="BODY"===this._element.tagName?window:this._element,this._config=this._getConfig(e),this._offsets=[],this._targets=[],this._activeTarget=null,this._scrollHeight=0,j.on(this._scrollElement,"scroll.bs.scrollspy",(()=>this._process())),this.refresh(),this._process()}static get Default(){return bn}static get NAME(){return _n}refresh(){const t=this._scrollElement===this._scrollElement.window?"offset":En,e="auto"===this._config.method?t:this._config.method,n=e===En?this._getScrollTop():0;this._offsets=[],this._targets=[],this._scrollHeight=this._getScrollHeight(),V.find(wn,this._config.target).map((t=>{const s=i(t),o=s?V.findOne(s):null;if(o){const t=o.getBoundingClientRect();if(t.width||t.height)return[U[e](o).top+n,s]}return null})).filter((t=>t)).sort(((t,e)=>t[0]-e[0])).forEach((t=>{this._offsets.push(t[0]),this._targets.push(t[1])}))}dispose(){j.off(this._scrollElement,".bs.scrollspy"),super.dispose()}_getConfig(t){return(t={...bn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}}).target=r(t.target)||document.documentElement,a(_n,t,vn),t}_getScrollTop(){return this._scrollElement===window?this._scrollElement.pageYOffset:this._scrollElement.scrollTop}_getScrollHeight(){return this._scrollElement.scrollHeight||Math.max(document.body.scrollHeight,document.documentElement.scrollHeight)}_getOffsetHeight(){return this._scrollElement===window?window.innerHeight:this._scrollElement.getBoundingClientRect().height}_process(){const t=this._getScrollTop()+this._config.offset,e=this._getScrollHeight(),i=this._config.offset+e-this._getOffsetHeight();if(this._scrollHeight!==e&&this.refresh(),t>=i){const t=this._targets[this._targets.length-1];this._activeTarget!==t&&this._activate(t)}else{if(this._activeTarget&&t0)return this._activeTarget=null,void this._clear();for(let e=this._offsets.length;e--;)this._activeTarget!==this._targets[e]&&t>=this._offsets[e]&&(void 0===this._offsets[e+1]||t`${e}[data-bs-target="${t}"],${e}[href="${t}"]`)),i=V.findOne(e.join(","),this._config.target);i.classList.add(yn),i.classList.contains("dropdown-item")?V.findOne(".dropdown-toggle",i.closest(".dropdown")).classList.add(yn):V.parents(i,".nav, .list-group").forEach((t=>{V.prev(t,".nav-link, .list-group-item").forEach((t=>t.classList.add(yn))),V.prev(t,".nav-item").forEach((t=>{V.children(t,".nav-link").forEach((t=>t.classList.add(yn)))}))})),j.trigger(this._scrollElement,"activate.bs.scrollspy",{relatedTarget:t})}_clear(){V.find(wn,this._config.target).filter((t=>t.classList.contains(yn))).forEach((t=>t.classList.remove(yn)))}static jQueryInterface(t){return this.each((function(){const e=An.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(window,"load.bs.scrollspy.data-api",(()=>{V.find('[data-bs-spy="scroll"]').forEach((t=>new An(t)))})),g(An);const Tn="active",On="fade",Cn="show",kn=".active",Ln=":scope > li > .active";class xn extends B{static get NAME(){return"tab"}show(){if(this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE&&this._element.classList.contains(Tn))return;let t;const e=n(this._element),i=this._element.closest(".nav, .list-group");if(i){const e="UL"===i.nodeName||"OL"===i.nodeName?Ln:kn;t=V.find(e,i),t=t[t.length-1]}const s=t?j.trigger(t,"hide.bs.tab",{relatedTarget:this._element}):null;if(j.trigger(this._element,"show.bs.tab",{relatedTarget:t}).defaultPrevented||null!==s&&s.defaultPrevented)return;this._activate(this._element,i);const o=()=>{j.trigger(t,"hidden.bs.tab",{relatedTarget:this._element}),j.trigger(this._element,"shown.bs.tab",{relatedTarget:t})};e?this._activate(e,e.parentNode,o):o()}_activate(t,e,i){const n=(!e||"UL"!==e.nodeName&&"OL"!==e.nodeName?V.children(e,kn):V.find(Ln,e))[0],s=i&&n&&n.classList.contains(On),o=()=>this._transitionComplete(t,n,i);n&&s?(n.classList.remove(Cn),this._queueCallback(o,t,!0)):o()}_transitionComplete(t,e,i){if(e){e.classList.remove(Tn);const t=V.findOne(":scope > .dropdown-menu .active",e.parentNode);t&&t.classList.remove(Tn),"tab"===e.getAttribute("role")&&e.setAttribute("aria-selected",!1)}t.classList.add(Tn),"tab"===t.getAttribute("role")&&t.setAttribute("aria-selected",!0),u(t),t.classList.contains(On)&&t.classList.add(Cn);let n=t.parentNode;if(n&&"LI"===n.nodeName&&(n=n.parentNode),n&&n.classList.contains("dropdown-menu")){const e=t.closest(".dropdown");e&&V.find(".dropdown-toggle",e).forEach((t=>t.classList.add(Tn))),t.setAttribute("aria-expanded",!0)}i&&i()}static jQueryInterface(t){return this.each((function(){const e=xn.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(document,"click.bs.tab.data-api",'[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',(function(t){["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this)||xn.getOrCreateInstance(this).show()})),g(xn);const Dn="toast",Sn="hide",Nn="show",In="showing",Pn={animation:"boolean",autohide:"boolean",delay:"number"},jn={animation:!0,autohide:!0,delay:5e3};class Mn extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get DefaultType(){return Pn}static get Default(){return jn}static get NAME(){return Dn}show(){j.trigger(this._element,"show.bs.toast").defaultPrevented||(this._clearTimeout(),this._config.animation&&this._element.classList.add("fade"),this._element.classList.remove(Sn),u(this._element),this._element.classList.add(Nn),this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.remove(In),j.trigger(this._element,"shown.bs.toast"),this._maybeScheduleHide()}),this._element,this._config.animation))}hide(){this._element.classList.contains(Nn)&&(j.trigger(this._element,"hide.bs.toast").defaultPrevented||(this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.add(Sn),this._element.classList.remove(In),this._element.classList.remove(Nn),j.trigger(this._element,"hidden.bs.toast")}),this._element,this._config.animation)))}dispose(){this._clearTimeout(),this._element.classList.contains(Nn)&&this._element.classList.remove(Nn),super.dispose()}_getConfig(t){return t={...jn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}},a(Dn,t,this.constructor.DefaultType),t}_maybeScheduleHide(){this._config.autohide&&(this._hasMouseInteraction||this._hasKeyboardInteraction||(this._timeout=setTimeout((()=>{this.hide()}),this._config.delay)))}_onInteraction(t,e){switch(t.type){case"mouseover":case"mouseout":this._hasMouseInteraction=e;break;case"focusin":case"focusout":this._hasKeyboardInteraction=e}if(e)return void this._clearTimeout();const i=t.relatedTarget;this._element===i||this._element.contains(i)||this._maybeScheduleHide()}_setListeners(){j.on(this._element,"mouseover.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"mouseout.bs.toast",(t=>this._onInteraction(t,!1))),j.on(this._element,"focusin.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"focusout.bs.toast",(t=>this._onInteraction(t,!1)))}_clearTimeout(){clearTimeout(this._timeout),this._timeout=null}static jQueryInterface(t){return this.each((function(){const e=Mn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}return R(Mn),g(Mn),{Alert:W,Button:z,Carousel:st,Collapse:pt,Dropdown:hi,Modal:Hi,Offcanvas:Fi,Popover:gn,ScrollSpy:An,Tab:xn,Toast:Mn,Tooltip:un}})); 7 | //# sourceMappingURL=bootstrap.bundle.min.js.map --------------------------------------------------------------------------------