2.0

inrae · May 27, 2024 · 9809612 · 9809612
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diff --git a/AUTHORS b/AUTHORS
@@ -1,3 +1,3 @@
 Daniel Jacob, INRAE, UMR 1332 BFP: Authorship, Design, Architecture, Coding, Testing, Debugging, Documentation, Maintenance, Support, Management
-François Ehrenmann, INRAE UMR 1202 BIOGECO: Authorship, Design, Architecture, Coding, Testing, Debugging, Documentation
-Philippe Chaumeil, INRAE UMR 1202 BIOGECO: Authorship, Design, Architecture, Coding, Testing, Debugging, Documentation
+François Ehrenmann, INRAE UMR 1202 BIOGECO: Authorship, Design, Architecture, Coding, Testing, Debugging
+Philippe Chaumeil, INRAE UMR 1202 BIOGECO: Authorship, Design, Architecture, Coding, Testing, Debugging
diff --git a/codemeta.json b/codemeta.json
@@ -5,7 +5,7 @@
     "codeRepository": "https://github.com/inrae/pgd-mmdt",
     "dateCreated": "2021-01-01",
     "datePublished": "2023-10-29",
-    "dateModified": "2023-10-29",
+    "dateModified": "2024-04-27",
     "downloadUrl": "https://github.com/inrae/pgd-mmdt/archive/refs/tags/2.0.tar.gz",
     "issueTracker": "https://github.com/inrae/pgd-mmdt/issues",
     "name": "Maggot",
@@ -39,6 +39,17 @@
         "https://inrae.github.io/pgd-mmdt/"
     ],
     "author": [
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-6687-7169",
+            "givenName": "Daniel",
+            "familyName": "Jacob",
+            "email": "[email protected]",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "INRAE UMR 1332 Biologie du Fruit et Pathogènes"
+            }
+        },
         {
             "@type": "Person",
             "@id": "https://orcid.org/0000-0003-2727-0070",
@@ -59,17 +70,6 @@
                 "@type": "Organization",
                 "name": "INRAE UMR 1202 BioGeCo"
             }
-        },
-        {
-            "@type": "Person",
-            "@id": "https://orcid.org/0000-0002-6687-7169",
-            "givenName": "Daniel",
-            "familyName": "Jacob",
-            "email": "[email protected]",
-            "affiliation": {
-                "@type": "Organization",
-                "name": "INRAE UMR 1332 Biologie du Fruit et Pathogènes"
-            }
         }
     ],
     "contributor": [

diff --git a/web/css/style.css b/web/css/style.css
@@ -470,7 +470,7 @@ p.selval {
 .ui-corner-top, .ui-corner-left {
 	border-top-left-radius: 10px;
 }
-.ui-tabs-vertical .ui-tabs-nav { padding: .2em .1em .2em .2em; float: left; }
+.ui-tabs-vertical .ui-tabs-nav { padding: .2em .1em .2em .2em; float: left; max-width: 200px; }
 .ui-tabs-vertical .ui-tabs-nav li { clear: left; width: 100%; border-bottom-width: 1px !important; border-right-width: 0 !important; margin: 0 -1px .2em 0; }
 .ui-tabs-vertical .ui-tabs-nav li a { display:block; }
 .ui-tabs-vertical .ui-tabs-nav li.ui-tabs-active { padding-bottom: 0; padding-right: .1em; border-right-width: 1px; }

diff --git a/web/docs/about.md b/web/docs/about.md
@@ -4,9 +4,14 @@
 # About
 ----
 
+[![SciCrunch](https://img.shields.io/badge/RRID-SCR_025261-green)](https://scicrunch.org/resolver/RRID:SCR_025261)
 [![bio.tools](https://img.shields.io/badge/bio.tools-maggot-orange)](https://bio.tools/maggot)
+[![identifiers](https://img.shields.io/badge/RDA:MSC-t81-brown)](https://rdamsc.bath.ac.uk/msc/t81)
+[![identifiers](https://img.shields.io/badge/CatOPDIPoR-maggot-magenta)](https://cat.opidor.fr/index.php/Maggot)
+<!--
 [![identifiers](https://img.shields.io/badge/identifiers-maggot-blue)](https://registry.identifiers.org/registry/maggot)
-
+[![identifiers](https://img.shields.io/badge/HAL-04256711-lightseagreen)](https://hal.inrae.fr/hal-04256711)
+-->
 .
 
 ## Links

diff --git a/web/docs/doc.md b/web/docs/doc.md
@@ -1,6 +1,5 @@
 # Metadata documentation
 ----
-
 .
 
 ## DEFINITION

diff --git a/web/inc/dataverse/dataverse.inc b/web/inc/dataverse/dataverse.inc
@@ -42,7 +42,7 @@ $query = new MongoDB\Driver\Query(array(), $options);
 $obj = $client->executeQuery('pgd-db.metadata', $query)->toArray();
 $ret = count($obj);
 
-$options_dataset='<option value="">---</option>';
+$options_dataset='<option value="">--- Select a dataset ---</option>';
 if ($ret>0) {
 	foreach($obj as $arr) {
 		$value = (array)$arr;
@@ -144,8 +144,8 @@ if ($ret>0) {
 				</div>
 			</div>
 			<div style="padding-bottom: 10px;"><b>Dataverse Server URL</b>:&nbsp;<select name="server" id="server" class="form-control form-control-sm"><? echo $options_server ?></select></div>
-			<div style="padding-bottom: 10px;"><b>API-Token</b>:&nbsp;<input class="form-control form-control-sm solo" type="text" name="token" id="token" value="<? echo $API_TOKEN ?>" /></div>
-			<div style="padding-bottom: 10px;"><b>Dataverse</b>:&nbsp;<input class="form-control form-control-sm solo typeahead" type="text" name="parent" id="parent" value="<? echo $PARENT ?>" /></div>
+			<div style="padding-bottom: 10px;"><b>API-Token</b>:&nbsp;<input class="form-control form-control-sm solo" type="text" name="token" id="token" value="<? echo $API_TOKEN ?>" placeholder="Copy-paste here the API Token from your corresponding Dataverse account" /></div>
+			<div style="padding-bottom: 10px;"><b>Dataverse</b>:&nbsp;<input class="form-control form-control-sm solo typeahead" type="text" name="parent" id="parent" value="<? echo $PARENT ?>" placeholder="Entrer the first 3 letters of targeted dataverse name"/></div>
 			<input type="submit" class="btn btn-primary" style="width: 100px;" id="btnpush" name="btnpush" value="Publish"/>
 			<input type="hidden" name="jsontype" id="jsontype" value="1">
 			<br>

diff --git a/web/inc/doc/home.inc b/web/inc/doc/home.inc
@@ -4,8 +4,8 @@
 	$links[2]="https://entrepot.recherche.data.gouv.fr/";
 	$links[3]="https://www.ouvrirlascience.fr/fair-principles/";
 	$links[4]="https://www.u-picardie.fr/open-science/wp-content/uploads/2021/07/Fiche-Synthetique-Metadonnees.pdf";
-	$links[5]="https://inrae.github.io/pgd-mmdt/pdf/MAGGOT_Metadata_Jan2024.pdf?download=false";
-	$links[6]="https://inrae.github.io/pgd-mmdt/pdf/MAGGOT_Poster_Oct2023.pdf?download=false";
+	$links[5]="./doc/meta";
+	$links[6]="https://inrae.github.io/pgd-mmdt/tutorial/";
 ?>
 
 <!DOCTYPE html>
@@ -67,7 +67,7 @@ The <b>Maggot</b> tool allows users to describe the <a href="<? echo $links[4];
 	<li>to answer certain questions of the <b>Data Management Plan</b> (<a href="<? echo $links[0]; ?>" target="_blank">DMP</a>) concerning the <b>organization, documentation, storage and sharing of data</b> in the data storage space,</li>
 	<li>to meet certain data and metadata requirements, referred to by the <a href="<? echo $links[1]; ?>" target="_blank">National Plan for Open Science</a> , in particular its second axis: “<b>Structure, Share and Open Research Data</b>” (<a href="<? echo $links[2]; ?>" target="_blank">Recherche Data Gouv</a>) in accordance with the <a href="<? echo $links[3]; ?>" target="_blank">FAIR principles</a>.</li>
 </ul>
-Maggot was designed to foster (local) <b>good data management</b>, with "(open) <b>data sharing</b>" in mind. See <a href="<? echo $links[6]; ?>" target="_blank">Poster</a> for a short overview.
+See <a href="<? echo $links[6]; ?>" target="_blank">Quick tutorail</a>.
 </font>
 </div></div>
 
@@ -121,7 +121,7 @@ Maggot was designed to foster (local) <b>good data management</b>, with "(open)
 <div id="overlay_r3" class="overlay_cl"><b>Describe</b> a dataset using metadata of different types by facilitating their entry and avoiding their re-entry thanks to personalized dictionaries, then generate the metadata file</div>
 <div id="overlay_r4" class="overlay_cl"><b>Search</b> datasets based on some metadata - assuming the metadata were previously deposited in the storage space</div>
 <div id="overlay_r5" class="overlay_cl"><b>Publish</b> the metadata of datasets along with their data files into the <i>Recherche Data Gouv</i> repository</div>
-<div id="overlay_r6" class="overlay_cl"><b>Metadata</b> schema in Maggot</div>
+<div id="overlay_r6" class="overlay_cl"><b>Metadata</b> documentation</div>
 <div id="overlay_r7" class="overlay_cl"><b>File Browser</b> allows you to browse data directories using cloud-like software</div>
 <?php
 	if ($export_zenodo==0 && $FAIRLINK==1)

diff --git a/web/inc/zenodo/zenodo.inc b/web/inc/zenodo/zenodo.inc
@@ -43,7 +43,7 @@ $query = new MongoDB\Driver\Query(array(), $options);
 $obj = $client->executeQuery('pgd-db.metadata', $query)->toArray();
 $ret = count($obj);
 
-$options_dataset='<option value="">---</option>';
+$options_dataset='<option value="">--- Select a dataset ---</option>';
 if ($ret>0) {
 	foreach($obj as $arr) {
 		$value = (array)$arr;
@@ -145,8 +145,8 @@ if ($ret>0) {
 				</div>
 			</div>
 			<div style="padding-bottom: 10px;"><b>Zenodo Server URL</b>:&nbsp;<select name="server" id="server" class="form-control form-control-sm"><? echo $options_server ?></select></div>
-			<div style="padding-bottom: 10px;"><b>API-Token</b>:&nbsp;<input class="form-control form-control-sm solo" type="text" name="token" id="token" value="<? echo $ZENODO_API_TOKEN ?>" /></div>
-			<div style="padding-bottom: 10px;"><b>Communities</b>:&nbsp;<input class="form-control form-control-sm solo typeahead" type="text" name="parent" id="parent" value="<? echo $COMMUNITIES ?>" /></div>
+			<div style="padding-bottom: 10px;"><b>API-Token</b>:&nbsp;<input class="form-control form-control-sm solo" type="text" name="token" id="token" value="<? echo $ZENODO_API_TOKEN ?>" placeholder="Copy-paste here the API Token from your corresponding Zenodo account"/></div>
+			<div style="padding-bottom: 10px;"><b>Communities</b>:&nbsp;<input class="form-control form-control-sm solo typeahead" type="text" name="parent" id="parent" value="<? echo $COMMUNITIES ?>" placeholder="Entrer the first 4 letters of targeted Community name"/></div>
 			<input type="submit" class="btn btn-primary" style="width: 100px;" id="btnpush" name="btnpush" value="Publish"/>
 			<input type="hidden" name="jsontype" id="jsontype" value="1">
 			<br>