Merge branch 'master' of https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy

d650807d · Robert Bossy · f133289d · d45eb69b · d650807d · d650807d
Commit d650807d authored 1 year ago by Robert Bossy
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -17,10 +17,10 @@
 # https://gitlab.com/gitlab-org/gitlab/-/blob/master/lib/gitlab/ci/templates/Getting-Started.gitlab-ci.yml

 stages:          # List of stages for jobs, and their order of execution
-  - deploy
+  - generate


-prepare_taxo:     # This job runs in the build stage, which runs first.
+pages:     # This job runs in the build stage, which runs first.
  tags:
    - front
    - migale
@@ -30,7 +30,7 @@ prepare_taxo:     # This job runs in the build stage, which runs first.
    - echo ${BACDIVE_PWD} > .bacdive-password
    - ln -s /work_projet/bibliome/singularity/alvisnlp-0.9.0.sif alvisnlp-0.9.0.sif
    - mkdir log
-  stage: deploy
+  stage: generate
  script:
    - conda activate snakemake-7.5.0
    - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 20 --snakefile ncbi-download.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=8G -V -cwd -e log/ -o log/ -q short.q,long.q  -pe thread 12" --restart-times 2
@@ -38,4 +38,17 @@ prepare_taxo:     # This job runs in the build stage, which runs first.
    - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 20 --snakefile bacdive-match.snakefile match --cluster "qsub -v PYTHONPATH='' -l mem_free=8G -V -cwd -e log/ -o log/ -q short.q,long.q  -pe thread 12" --restart-times 2
    - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 20 --snakefile rewrite-taxonomy.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=8G -V -cwd -e log/ -o log/ -q short.q,long.q  -pe thread 12" --restart-times 2
    - snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 20 --snakefile compile-trie.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=8G -V -cwd -e log/ -o log/ -q short.q,long.q  -pe thread 12" --restart-times 2
+    #- mkdir output
+    #- cp -r /work_projet/omnicrobe_data/tm_workflow/extended-microorganisms-taxonomy/output/taxid_header_microorganisms.txt output/
+    - mkdir public
+    - mkdir supertaxo
+    - cp -r output/{bacdive-match,bacdive-strains,bacdive-match/bacdive-to-taxid.txt,ncbi-taxonomy/names.dmp,taxa+id_full.trie,taxa+id_full.txt,taxa+id_microorganisms.txt,taxid_full.txt,taxid_microorganisms.txt} supertaxo/
+    #- mv output supertaxo
+    - cp -r html/* public/
+    - zip -r supertaxo.zip supertaxo/*
+    - mv supertaxo.zip public/
+    - sed -i "s;supertaxo.zip;https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy/-/jobs/${CI_JOB_ID}/artifacts/download?file_type=archive;g" public/index.html
+  artifacts:
+    paths:
+      - public
  when: manual
--- a/README.md
+++ b/README.md
@@ -97,3 +97,7 @@ This will compile taxonomy tries for future use with AlvisNLP.
 The output of this step contains 2 files:
 * `taxa+id_full.trie`
 * `taxa+id_microorganisms.trie`
+
+## Generation of the Extended taxonomy
+
+The extended taxonomy is automatically and regularly generated. It can be downloaded by following this link https://omnicrobe.pages.mia.inra.fr/extended-microorganisms-taxonomy 
--- a/html/index.html
+++ b/html/index.html
+<?xml version="1.0" encoding="UTF-8"?><!--
+Copyright 2016, 2017 Institut National de la Recherche Agronomique
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+        http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+<html>
+	<head><META http-equiv="Content-Type" content="text/html; charset=UTF-8">
+		<link href="style/common.css" rel="stylesheet">
+		<link href="style/specific.css" rel="stylesheet">
+		<title>NCBI Taxonomy</title>
+	</head>
+	<body>
+		<p><b>This extended microorganism taxonomy contains a combinaison of the microorganisms subtrees from the NCBI Taxonomy and entries from BacDive.</b></p>
+
+		<ul id="NCBI SUPER TAXO>
+			<li class="document-list">
+				<a href="supertaxo.zip" download><img src="style/myw3schoolsimage.jpg" alt="FULL NCBI SUPERTAXO (unzip supertaxo after download...)"></a>
+			</li>
+		</ul>
+    </body>
+</html>
--- a/html/style/common.css
+++ b/html/style/common.css
+/*
+Copyright 2016, 2017 Institut National de la Recherche Agronomique
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+        http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+*/
+
+
+body {
+}
+
+#document-navigation {
+	font-size: 80%;
+	padding-bottom: 5mm;
+}
+
+#document-list {
+	margin-bottom: 2mm;
+}
+
+#document-previous {
+	clear: both;
+	float: left;
+}
+
+#document-next {
+	float: right;
+}
+
+#annotation-info {
+	float: left;
+	width: 25%;
+	margin-top: 4ex;
+	margin-left: 5mm;
+	position: fixed;
+}
+
+#annotation-navigation {
+	width: 3cm;
+	margin-left: auto;
+	margin-right: auto;
+}
+
+#annotation-prev {
+	margin-left: auto;
+	width: 1cm;
+}
+
+#annotation-next {
+	width: 1cm;
+	margin-left: 5mm;
+	margin-right: auto;
+}
+
+#annotation-features {
+	font-family: monospace;
+	margin-top: 10mm;
+	overflow: auto;
+	width: 95%;
+}
+
+.alvisnlp-feature {
+	clear: both;
+	float:left;
+	width: 100%;
+	white-space: nowrap;
+}
+
+.alvisnlp-feature-key {
+	font-weight: bold;
+	display: inline-block;
+	width: 40%;
+}
+
+.alvisnlp-feature-value {
+}
+
+#alvisnlp-document {
+	float:left;
+	width: 70%;
+	position: absolute;
+	left: 30%;
+}
+
+h1 {
+	font-family: sans-serif;
+}
+
+h2 {
+	font-family: sans-serif;
+}
+
+.alvisnlp-section {
+	border-top: 1px solid gray;
+}
+
+.alvisnlp-contents {
+	line-height: 200%;
+}
+
+.alvisnlp-fragment {
+	border-top: 1px dotted gray;
+	border-bottom: 1px dotted gray;
+}
+
+.alvisnlp-first-fragment {
+	border-left: 1px dotted gray;
+	border-top-left-radius: 3px;
+	border-bottom-left-radius: 3px;
+}
+
+.alvisnlp-last-fragment {
+	border-right: 1px dotted gray;
+	border-top-right-radius: 3px;
+	border-bottom-right-radius: 3px;
+}
+
+.highlight {
+	border-color: red;
+	border-style: solid;
+}
--- a/html/style/document.js
+++ b/html/style/document.js
+var start = function() {
+	$(window).keydown(function(event) {
+		switch (event.which) {
+		case 65: followPrev(); break;
+		case 68: followNext(); break;
+//		default: console.log(event);
+		}
+	});
+	
+	$('.alvisnlp-fragment').click(function(event) {
+		event.stopPropagation();
+		highlight(this);
+	});
+	
+	highlight($('.alvisnlp-fragment').get(0));
+	
+	$('#annotation-next').click(followNext);
+	$('#annotation-prev').click(followPrev);
+};
+
+var follow = function(attr) {
+	return function() {
+		var id = $('.alvisnlp-first-fragment.highlight').attr(attr);
+		if (id) {
+			var e = $('.alvisnlp-first-fragment[alvisnlp-id='+id+']').get(0);
+			highlight(e);
+		}
+	};
+}
+
+var followNext = follow('alvisnlp-next');
+var followPrev = follow('alvisnlp-prev');
+
+var highlight = function(elt) {
+	if (elt === undefined) {
+		return;
+	}
+	$('.highlight').removeClass('highlight');
+	var aid = elt.getAttribute('alvisnlp-id');
+	var allFragments = $('*[alvisnlp-id="'+aid+'"]');
+	allFragments.addClass('highlight');
+	
+	var featuresDiv = $('#annotation-features');
+	featuresDiv.empty();
+	var firstFragment = allFragments.first();
+	var keys = firstFragment.attr('alvisnlp-feature-keys').split(' ');
+	keys.forEach(function(key) {
+		var value = firstFragment.attr('alvisnlp-feature-value-' + key);
+		featuresDiv.append('<div class="alvisnlp-feature"><span class="alvisnlp-feature-key">'+key+'</span><span class="alvisnlp-feature-value">'+value+'</span></div>');
+	});
+
+	window.scrollTo(0, $(elt).position().top);
+};
--- a/html/style/jquery-1.11.1.min.js
+++ b/html/style/jquery-1.11.1.min.js
--- a/html/style/specific.css
+++ b/html/style/specific.css
+.-default {
+	background-color: #FFFFFF;
+}
+
+.Habitat {
+	background-color: #991111;
+}
+
+.Microorganism {
+	background-color: #753799;
+}
+
+.Phenotype {
+	background-color: #D4EAAE;
+}
+
+.pH {
+	background-color: #FCCA73;
+}
+
+.primer-sequence {
+	background-color: #FB9874;
+}
+
+.region-16s {
+	background-color: #B4B9CF;
+}
+
+.temperature {
+	background-color: #F99FC4;
+}
+
+.strate-0 {
+	padding-top: 1px;
+	padding-bottom: 1px;
+}
+
+.strate-0.alvisnlp-first-fragment {
+	padding-left: 1px;
+}
+
+.strate-0.alvisnlp-last-fragment {
+	padding-right: 1px;
+}
+
+.strate-1 {
+	padding-top: 3px;
+	padding-bottom: 3px;
+}
+
+.strate-1.alvisnlp-first-fragment {
+	padding-left: 2px;
+}
+
+.strate-1.alvisnlp-last-fragment {
+	padding-right: 2px;
+}
+
+.strate-2 {
+	padding-top: 5px;
+	padding-bottom: 5px;
+}
+
+.strate-2.alvisnlp-first-fragment {
+	padding-left: 3px;
+}
+
+.strate-2.alvisnlp-last-fragment {
+	padding-right: 3px;
+}
+
+.strate-3 {
+	padding-top: 7px;
+	padding-bottom: 7px;
+}
+
+.strate-3.alvisnlp-first-fragment {
+	padding-left: 4px;
+}
+
+.strate-3.alvisnlp-last-fragment {
+	padding-right: 4px;
+}
+
+.strate-4 {
+	padding-top: 9px;
+	padding-bottom: 9px;
+}
+
+.strate-4.alvisnlp-first-fragment {
+	padding-left: 5px;
+}
+
+.strate-4.alvisnlp-last-fragment {
+	padding-right: 5px;
+}
+
+.strate-5 {
+	padding-top: 11px;
+	padding-bottom: 11px;
+}
+
+.strate-5.alvisnlp-first-fragment {
+	padding-left: 6px;
+}
+
+.strate-5.alvisnlp-last-fragment {
+	padding-right: 6px;
+}
+
+.strate-6 {
+	padding-top: 13px;
+	padding-bottom: 13px;
+}
+
+.strate-6.alvisnlp-first-fragment {
+	padding-left: 7px;
+}
+
+.strate-6.alvisnlp-last-fragment {
+	padding-right: 7px;
+}
+
+.strate-7 {
+	padding-top: 15px;
+	padding-bottom: 15px;
+}
+
+.strate-7.alvisnlp-first-fragment {
+	padding-left: 8px;
+}
+
+.strate-7.alvisnlp-last-fragment {
+	padding-right: 8px;
+}
+
+.strate-8 {
+	padding-top: 17px;
+	padding-bottom: 17px;
+}
+
+.strate-8.alvisnlp-first-fragment {
+	padding-left: 9px;
+}
+
+.strate-8.alvisnlp-last-fragment {
+	padding-right: 9px;
+}
+
+.strate-9 {
+	padding-top: 19px;
+	padding-bottom: 19px;
+}
+
+.strate-9.alvisnlp-first-fragment {
+	padding-left: 10px;
+}
+
+.strate-9.alvisnlp-last-fragment {
+	padding-right: 10px;
+}
+
+
--- a/resources/public/.gitkeep
+++ b/resources/public/.gitkeep
--- a/resources/public/index.html
+++ b/resources/public/index.html
+<!DOCTYPE html>
+<html>
+   <body>
+      <style>
+         p {
+         color: green;
+         }
+      </style>
+      <p>How to trigger a file download when
+         clicking an HTML button or JavaScript?
+      <p>
+         <!-- GFG is the name of the
+            file to be downloaded-->
+         <!-- In order to run the code,
+            the location of the file
+            "geeksforgeeks.png" needs to
+            be changed to your local directory,
+            both the HTML and downloadable file
+            needs to be present in the same directory -->
+         <a href="https://forgemia.inra.fr/omnicrobe/extended-microorganisms-taxonomy/-/jobs/360816/artifacts/download?file_type=archive" download="SUPERTAXO">
+         <button type="button">Download</button>
+         </a>
+   </body>
+</html>