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Configuration documenation
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 - html programmatically generated from JSON schema
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@DrYak
DrYak committed Oct 13, 2021
1 parent 2c52476 commit 369a3e7
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161 changes: 161 additions & 0 deletions config/config.html
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180 changes: 180 additions & 0 deletions config/doc_assets/schema_doc.css
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body {
font: 16px/1.5em "Overpass", "Open Sans", Helvetica, sans-serif;
color: #333;
font-weight: 300;
padding: 40px;
}

.btn.btn-link {
font-size: 18px;
}

.jsfh-animated-property {
animation: eclair;
animation-iteration-count: 1;
animation-fill-mode: forwards;
animation-duration: .75s;

}

@keyframes eclair {
0%,100% {
transform: scale(1);
}
50% {
transform: scale(1.03);
}
}

.btn.btn-primary {
margin: 10px;
}

.btn.example-show.collapsed:before {
content: "show"
}

.btn.example-show:before {
content: "hide"
}

.description.collapse:not(.show) {
max-height: 100px !important;
overflow: hidden;

display: -webkit-box;
-webkit-line-clamp: 2;
-webkit-box-orient: vertical;
}

.description.collapsing {
min-height: 100px !important;
}

.collapse-description-link.collapsed:after {
content: '+ Read More';
}

.collapse-description-link:not(.collapsed):after {
content: '- Read Less';
}

.badge {
font-size: 100%;
margin-bottom: 0.5rem;
margin-top: 0.5rem;
}

.badge.value-type {
font-size: 120%;
margin-right: 5px;
margin-bottom: 10px;
}


.badge.default-value {
font-size: 120%;
margin-left: 5px;
margin-bottom: 10px;
}

.badge.restriction {
display: inline-block;
}

.badge.required-property,.badge.deprecated-property,.badge.pattern-property,.badge.no-additional {
font-size: 100%;
margin-left: 10px;
}

.accordion div.card:only-child {
border-bottom: 1px solid rgba(0, 0, 0, 0.125);
}

.examples {
padding: 1rem !important;
}

.examples pre {
margin-bottom: 0;
}

.highlight.jumbotron {
padding: 1rem !important;
}

.generated-by-footer {
margin-top: 1em;
text-align: right;
}

/* From https://github.com/richleland/pygments-css/blob/master/friendly.css, see https://github.com/trentm/python-markdown2/wiki/fenced-code-blocks */
.highlight { background: #e9ecef; } /* Changed from #f0f0f0 in the original style to be the same as bootstrap's jumbotron */
.highlight .hll { background-color: #ffffcc }
.highlight .c { color: #60a0b0; font-style: italic } /* Comment */
.highlight .err { border: 1px solid #FF0000 } /* Error */
.highlight .k { color: #007020; font-weight: bold } /* Keyword */
.highlight .o { color: #666666 } /* Operator */
.highlight .ch { color: #60a0b0; font-style: italic } /* Comment.Hashbang */
.highlight .cm { color: #60a0b0; font-style: italic } /* Comment.Multiline */
.highlight .cp { color: #007020 } /* Comment.Preproc */
.highlight .cpf { color: #60a0b0; font-style: italic } /* Comment.PreprocFile */
.highlight .c1 { color: #60a0b0; font-style: italic } /* Comment.Single */
.highlight .cs { color: #60a0b0; background-color: #fff0f0 } /* Comment.Special */
.highlight .gd { color: #A00000 } /* Generic.Deleted */
.highlight .ge { font-style: italic } /* Generic.Emph */
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #888888 } /* Generic.Output */
.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
.highlight .kp { color: #007020 } /* Keyword.Pseudo */
.highlight .kr { color: #007020; font-weight: bold } /* Keyword.Reserved */
.highlight .kt { color: #902000 } /* Keyword.Type */
.highlight .m { color: #40a070 } /* Literal.Number */
.highlight .s { color: #4070a0 } /* Literal.String */
.highlight .na { color: #4070a0 } /* Name.Attribute */
.highlight .nb { color: #007020 } /* Name.Builtin */
.highlight .nc { color: #0e84b5; font-weight: bold } /* Name.Class */
.highlight .no { color: #60add5 } /* Name.Constant */
.highlight .nd { color: #555555; font-weight: bold } /* Name.Decorator */
.highlight .ni { color: #d55537; font-weight: bold } /* Name.Entity */
.highlight .ne { color: #007020 } /* Name.Exception */
.highlight .nf { color: #06287e } /* Name.Function */
.highlight .nl { color: #002070; font-weight: bold } /* Name.Label */
.highlight .nn { color: #0e84b5; font-weight: bold } /* Name.Namespace */
.highlight .nt { color: #062873; font-weight: bold } /* Name.Tag */
.highlight .nv { color: #bb60d5 } /* Name.Variable */
.highlight .ow { color: #007020; font-weight: bold } /* Operator.Word */
.highlight .w { color: #bbbbbb } /* Text.Whitespace */
.highlight .mb { color: #40a070 } /* Literal.Number.Bin */
.highlight .mf { color: #40a070 } /* Literal.Number.Float */
.highlight .mh { color: #40a070 } /* Literal.Number.Hex */
.highlight .mi { color: #40a070 } /* Literal.Number.Integer */
.highlight .mo { color: #40a070 } /* Literal.Number.Oct */
.highlight .sa { color: #4070a0 } /* Literal.String.Affix */
.highlight .sb { color: #4070a0 } /* Literal.String.Backtick */
.highlight .sc { color: #4070a0 } /* Literal.String.Char */
.highlight .dl { color: #4070a0 } /* Literal.String.Delimiter */
.highlight .sd { color: #4070a0; font-style: italic } /* Literal.String.Doc */
.highlight .s2 { color: #4070a0 } /* Literal.String.Double */
.highlight .se { color: #4070a0; font-weight: bold } /* Literal.String.Escape */
.highlight .sh { color: #4070a0 } /* Literal.String.Heredoc */
.highlight .si { color: #70a0d0; font-style: italic } /* Literal.String.Interpol */
.highlight .sx { color: #c65d09 } /* Literal.String.Other */
.highlight .sr { color: #235388 } /* Literal.String.Regex */
.highlight .s1 { color: #4070a0 } /* Literal.String.Single */
.highlight .ss { color: #517918 } /* Literal.String.Symbol */
.highlight .bp { color: #007020 } /* Name.Builtin.Pseudo */
.highlight .fm { color: #06287e } /* Name.Function.Magic */
.highlight .vc { color: #bb60d5 } /* Name.Variable.Class */
.highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
.highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
.highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
.highlight .il { color: #40a070 } /* Literal.Number.Integer.Long */
1 change: 1 addition & 0 deletions config/doc_assets/schema_doc.min.js
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3 changes: 3 additions & 0 deletions config/hiv.yaml
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Expand Up @@ -11,3 +11,6 @@ input:

frameshift_deletions_checks:
genes_gff: "{VPIPE_BASEDIR}/../resources/hiv/gffs/GCF_000864765.1_ViralProj15476_genomic.gff"

bwa_QA:
ref_panel: "{VPIPE_BASEDIR}/../resources/hiv/5-Virus-Mix.fasta"
26 changes: 26 additions & 0 deletions utils/conda_docschema.yaml
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name: schemadocs
channels:
- defaults
- conda-forge
dependencies:
- pip
# others
- anyconfig
# json-schema-for-humans dependencies:
- click >=8.0.1
- dataclasses >=0.6
- dataclasses-json # >=0.5.6 # missing!
- htmlmin >=0.1.12
- jinja2 >=3
- markdown2 # >= 2.4.0 # missing!
- pygments >=2.10.0
- pytz >=2021.1
- pyyaml >=5.4.1
- requests >=2.26.0
- pip:
- json-schema-for-humans

##alternatives:
#npm install json-schema-to-markdown @adobe/jsonschema2md


39 changes: 39 additions & 0 deletions utils/create_config_doc
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#!/bin/bash

scriptdir="$(dirname $(which $0))"

vpipe_basdir="${scriptdir}/.."

usage() { echo -e "Usage: $0 [-b <basedir>] [ -s ]" 1>&2; (( $1 == 0 )) && echo $'\n\tThis utility generates the configuration documentation from the JSON schema.\n'; exit $1; }

while getopts "b:sh" o; do
case "${o}" in
b) vpipe_basdir=${OPTARG}
if [[ ! -d ${vpipe_basdir} ]]; then
echo "Cannot find ${vpipe_basdir}" 1>&2
usage 1
fi
;;
s) validate=1 ;;
h) usage 0 ;;
*) usage 1 ;;
esac
done

: ${validate:=0}

config_dir="${vpipe_basdir}/config"
schema_dir="${vpipe_basdir}/workflow/schemas"

generate-schema-doc --config-file "${schema_dir}/jsfh-conf.yaml" "${schema_dir}/config_schema.json" "${config_dir}/config.html"

# href=schema_doc.css>
# src=schema_doc.min.js>
#sed -Ei 's@((href|src)=)[\"]?(schema_doc\.(css|min\.js))[\"]?@\1"https://cbg-ethz.github.io/V-pipe/assets/\3"@g' "${config_dir}/config.html"
sed -Ei 's@((href|src)=)[\"]?(schema_doc\.(css|min\.js))[\"]?@\1\"doc_assets/\3\"@g' "${config_dir}/config.html"

if (( validate )); then
curl http://json-schema.org/draft-07/schema > /tmp/schema.json
anyconfig_cli --validate --schema "/tmp/schema.json" --itype json "${schema_dir}/config_schema.json"
fi

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