Merge pull request #11 from lagoproject/dev

Consolidate DMP 1.1 version

_includes/generate_html_for_sites.html

+<!-- 
+################################################################################
+# Original Author: A.J. Rubio-Montero (http://orcid.org/0000-0001-6497-753X),  #
+#          CIEMAT - Sci-Track Group (http://rdgroups.ciemat.es/web/sci-track), #
+#          for the EOSC-Synergy project (EU H2020 RI Grant No 857647).         #
+# License (SPDX): BSD-3-Clause (https://opensource.org/licenses/BSD-3-Clause)  #
+# Copyright (c): 2020-today, The LAGO Collaboration (http://lagoproject.net)   #
+################################################################################
+-->
+<script src="https://code.jquery.com/jquery-3.2.1.min.js"></script>
+<script>
+function itemnize_json( json, context, link ) { 
+  var html ='';
+  if ( (link == false) || (typeof(json) === 'boolean') )  return json;
+  if ( typeof(json) === 'string' ) {
+    var element = json.split(':');
+    var innid = element[0];
+    var vocab = "@vocab";
+    if (element.length == 2) {
+      if ( (element[0] !== "http") && (element[0] !== "https") ) {
+        innid = element[1];
+        vocab = element[0];
+      } else return '<a href="'+ json +'">'+ json +'</a>';
+    } else return json;
+    var contexturl = context[vocab];
+    if ( vocab == "lago" ) { 
+        contexturl = 'https://lagoproject.github.io/DMP/schema/lagoSchema/';
+        innid = json;
+    };  
+    if ( contexturl[contexturl.length-1] !== '#' )  contexturl = contexturl + '#';
+    if ( vocab == "sdo" ) contexturl = context[vocab];
+    html = '<a href="'+ contexturl + innid +'">'+ json +'</a>';
+  } else {
+    if ( !(Array.isArray(json)) ) {
+      var json_aux = [];
+      json_aux.push(json);
+      json = json_aux;
+    };
+    for (var j=0; j<json.length; j++) {
+      var inner_json = json[j];
+      if ( !(typeof(json[j]) === 'string') ) {
+      	if ("@id" in json[j]) {
+          inner_json = json[j]["@id"];
+        } else {
+          inner_json = JSON.stringify(json[j]);
+	  link = false;
+        };
+      };
+      html = html + '<br />' + itemnize_json(inner_json, context, link);
+    };
+  };
+  return html;
+};
+function gmap_static(lat, long, type) {
+    return '<div style="width: 100%"><iframe class="iframe" src="https://maps.google.com/?ll='+lat+','+long+'&amp;z=13&amp;t='+type+'amp;iwloc=B&amp;output=embed" height="200" allowfullscreen></iframe></div>';
+};
+$().ready(function(){
+    $.getJSON( "{{ include.folder }}", function( data ) { 
+        var graphelements = data["@graph"];
+        for (var i=0; i<graphelements.length; i++) {
+            var element = graphelements[i];
+            var id = element["@id"];
+            var indexhtml = '<li><a href="#'+id+'"><strong>'+id+'</strong> ['+element["name"]+'].'+'</a></li>';
+            var headerhtml = '<h5 id="'+id+'"><a href="#'+id+'" class="anchor-heading" aria-labelledby="'+id+'"><svg viewBox="0 0 16 16" aria-hidden="true"><use xlink:href="#svg-link"></use></svg></a><strong>'+id+'</strong></h5>';
+            headerhtml = headerhtml+'<p>'+'Site located in '+element["name"];
+            if (["qualifiedAttribution"]["name"] !== "") {
+                headerhtml = headerhtml+' and managed by '+element["qualifiedAttribution"]["name"];
+            };
+            headerhtml = headerhtml+'.'+'</p>';
+            if ("comment" in element) {
+                headerhtml = headerhtml+'<p>'+ element["comment"][0]["@value"]+'</p>';
+            };
+            headerhtml = headerhtml+gmap_static(element["geometry"]["geo:latitude"],element["geometry"]["geo:longitude"],"k");
+            if (element["lago:belongsLago"]) {
+                $('#iproperties').append(indexhtml);
+                $('#properties').append(headerhtml);              
+            } else {
+                $('#iclasses').append(indexhtml);
+                $('#classes').append(headerhtml);
+            };   
+            var keysUP = Object.keys(element);
+            keysUP.splice(keysUP.indexOf("@id"),1);
+            keysUP.splice(keysUP.indexOf("@type"),1);
+            keysUP.splice(keysUP.indexOf("comment"),1);
+            keysUP.splice(keysUP.indexOf("name"),1);
+            keysUP.splice(keysUP.indexOf("lago:belongsLago"),1);
+            keysUP.splice(keysUP.indexOf("qualifiedAttribution"),1);
+            table = '<ul> The default propierties defined for <strong>'+ id + '</strong> site are:' ;
+            for (var up=0; up<keysUP.length; up++) {
+                var keys = Object.keys(element[keysUP[up]]);
+                table = table + '<li>'+ itemnize_json(keysUP[up], data["@context"], true )+' :';
+                table = table + '<table class="grid" style="width: 100%"> 
+                    <thead>
+                        <tr class="header">';  
+                for (var k=0; k<keys.length; k++) {
+                    table = table + ' <th>'+ itemnize_json([keys[k]], data["@context"], true ) + '</th>';
+                };
+                table = table +' </tr>
+                    </thead>
+                    <tbody>
+                        <tr>';
+                for (var k=0; k<keys.length; k++) {
+                    table = table +' <td>'+ itemnize_json(element[keysUP[up]][keys[k]] , data["@context"], true ) +'</td>';
+                };
+                table = table +' </tr>
+                    </tbody>
+                </table>';
+                table = table + '</li>';
+            };
+            table = table + '</ul>';
+            if (element["lago:belongsLago"]) {
+                $('#properties').append(table);				  
+            } else {
+                $('#classes').append(table);
+            };
+        };		
+    });
+});
+</script>
+
+{% if include.vocabulary == "true" %}
+
+- [**Classes**](#classes)
+  <ul id="iclasses"></ul>
+		
+- [**Properties**](#properties)
+  <ul id="iproperties"></ul>
+
+### Classes
+
+<div id="classes"></div>
+
+### Properties
+
+<div id="properties"></div>
+
+{% else %}
+
+- [**Official LAGO sites**](#lago)
+  <ul id="iproperties"></ul>
+- [**non-LAGO sites**](#non-lago)
+  <ul id="iclasses"></ul>
+
+
+### Official LAGO sites
+
+<div id="properties"></div>
+
+
+### non-LAGO sites
+
+<div id="classes"></div>
+
+
+{% endif %}
+

_includes/generate_html_for_vocab.html

@@ -20,13 +20,15 @@ function itemnize_json( json, context, link ) {
       if ( (element[0] !== "http") && (element[0] !== "https") ) {
         innid = element[1];
         vocab = element[0];
-      } else return json;
-    };
+      } else return '<a href="'+ json +'">'+ json +'</a>';
+    } else return json;
     var contexturl = context[vocab];
-    if ( vocab == "lago" ) contexturl = '';  
+    if ( vocab == "lago" ) { 
+        contexturl = 'https://lagoproject.github.io/DMP/schema/lagoSchema/';
+        innid = json;
+    };    
     if ( contexturl[contexturl.length-1] !== '#' )  contexturl = contexturl + '#';
     if ( vocab == "sdo" ) contexturl = context[vocab];
-    else innid = json;
     html = '<a href="'+ contexturl + innid +'">'+ json +'</a>';
   } else {
     if ( !(Array.isArray(json)) ) {
@@ -69,7 +71,7 @@ $().ready(function(){
 			    <tr class="header">
 				<th>@type</th>';	  
 	  for (var k=0; k<keys.length; k++) {
-	    table = table + ' <th>'+ keys[k] + '</th>';
+	    table = table + ' <th>'+  itemnize_json(keys[k] , data["@context"], true ) + '</th>';
 	  };
 	  table = table +'	</tr>
 			</thead>

defs/sitesLago.md

@@ -70,7 +70,7 @@ As a real example, the metadata´s catalog of a simulation should include the si
 
 ## Defined LAGO sites
 
-{% include generate_html_for_vocab.html folder="/DMP/defs/sitesLago.jsonld" %}
+{% include generate_html_for_sites.html folder="/DMP/defs/sitesLago.jsonld" %}
 
 
 ## Plain JSON-LD file

schema/lagoSchema.jsonld

@@ -26,11 +26,11 @@
    {
     "@id": "lago:Software",
     "@type": "sdo:SoftwareSourceCode",
-    "owl:equivalentClass" : "prov: SoftwareAgent",
+    "owl:equivalentClass" : "prov:SoftwareAgent",
     "dcat:subClassOf" : "Agent",
-    "_sdo:codeRepository" : { "@type" : "sdo:URL" },
-    "_sdo:runtimePlatform" : {"@type" : "lago:runtimePlatform" },
-    "seeAlso" : [ "prov: SoftwareAgent", "sdo:SoftwareSourceCode", "Agent"],
+    "sdo:codeRepository" : { "@type" : "sdo:URL" },
+    "sdo:runtimePlatform" : {"@type" : "lago:runtimePlatform" },
+    "seeAlso" : [ "prov:SoftwareAgent", "sdo:SoftwareSourceCode", "Agent"],
     "comment" : [ { "@language" : "en", "@value" : "It identifies any concrete release of software used for simulation, measure, cleaning or analysis procedures. It always refers to a COMMIT in the source code, identified with a HASH at the CVS (but, it will be needed, a compressed file, using other type of hasisng, such as MD5SUM, to guarantee its immutability). Therefore, in GitHub, the @id is the link for the COMMIT (https://api.github.com/org/repo/git/commits/COMMIT_HASH and the sdo:codeRepository will be these COMMIT but browsable for humans ( https://github.com/org/repo/tree/COMMIT_HASH). It is mandatory assign an Agent:name. However, it is optional to use sdo:runtimePlatform (redefined as lago:runtimePlatform) to point to other lago:Software on which it was executed, for example to some deployment with Docker in GitHub." },  
                   { "@language" : "es", "@value" : "Identifica una versión concreta de un software usado para simular, medir, limpiar o analizar los datos de LAGO. Se refiere siempre a un COMMIT concreto en el código fuente, identificado con un código HASH en un CVS (o bien, si no fuera posible, a un fichero comprimido, univocamente identificado con algún tipo de HASH, como MD5SUM). Por tanto, en GitHub, el @id es el link del COMMIT https://api.github.com/org/repo/git/commits/COMMIT_HASH y la propiedad sdo:codeRepository sería ese COMMIT navegable para humanos  https://github.com/org/repo/tree/COMMIT_HASH. Es obligatorio asignar un Agent:name. Pero es opcional el uso de sdo:runtimePlatform (redefinida como lago:runtimePlatform) para señalar otro lago:Software sobre el que se ejecuta, por ejemplo una integración Docker en GitHub)." } ]
     },
@@ -81,9 +81,10 @@
     "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
     "dcat:domain": { "@id" : "lago:ArtiParams" },
     "dcat:range": { "@id" : "xsd:float" },
+    "@default" : "0.0",
     "dcat:label": "rigidity", 
-    "comment" : [ { "@language" : "en", "@value" : "Rigidity cutoff; 0 = disabled; value in GV = enabled" },  
-                  { "@language" : "es", "@value" : "Corte de la rigidez; 0 = deshabilitado; valor en GV = habilitado" } ]
+    "comment" : [ { "@language" : "en", "@value" : "Rigidity cutoff; 0.0 = disabled; value in GV = enabled" },  
+                  { "@language" : "es", "@value" : "Corte de la rigidez; 0.0 = deshabilitado; valor en GV = habilitado" } ]
    },
    {
     "@id": "lago:tMin",
@@ -165,10 +166,10 @@
     "@id": "lago:highEnergyCutsSecondaries",
     "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
     "dcat:domain": { "@id" : "lago:ArtiParams" },
-    "dcat:range": { "@id" : "xsd:boolean" },
+    "dcat:range": { "@id" : "xsd:float" },
     "dcat:label": "highEnergyCutsSecondaries",
-    "@default" : false,
-    "comment" : [ { "@language" : "en", "@value" : "Enable high energy cuts for secondaries" },  
+    "@default" : "0.0",
+    "comment" : [ { "@language" : "en", "@value" : "Enable high energy cuts for secondaries; 0.0 = disabled, value in GeV = enabled" },  
                   { "@language" : "es", "@value" : "" } ]
    },  
 {"_comment" : "------ Defining installed detectors and simulated detectors, this implies estaiblishing equivalencies among measures and software parameters --------"},
@@ -198,7 +199,17 @@
      "comment" : [ { "@language" : "en", "@value" : "" },  
                    { "@language" : "es", "@value" : "" } ]
   },
-{"_comment" : "------ common properties to describe characteristics of a DetectorSite (Agent) which are included also in a lago:CorsikaInput --------"},
+{"_comment" : "------ common properties to describe characteristics of a DetectorSite (Agent), some of which are included also in a lago:CorsikaInput --------"},
+   {
+    "@id": "lago:belongsLago",
+    "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
+    "dcat:domain": { "@id" : "lago:DetectorSite" },
+    "dcat:range": { "@id" : "xsd:boolean" },
+    "@default" : false,
+    "dcat:label": "belongsLago",
+    "comment" : [ { "@language" : "en", "@value" : "" },
+                  { "@language" : "es", "@value" : "" } ]
+   },
    {
      "@id": "lago:obsLev",
      "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
@@ -228,6 +239,15 @@
     "comment" : [ { "@language" : "en", "@value" : " Components of the Earth's mag. field (MAGNET), Horizontal (bx) and Vertical (bx)" },  
                   { "@language" : "es", "@value" : "" } ]
    },
+    { 
+     "@id": "lago:bDate",
+     "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
+     "dcat:domain": { "@id" : "lago:MagnetComponents" },
+     "dcat:range": { "@id" : "xsd:date" },
+     "dcat:label": "bDate", 
+     "comment" : [ { "@language" : "en", "@value" : "The date for which the magnetic field values are calculated, in the form yyyy-mm-dd. (xsd:date)" },  
+                   { "@language" : "es", "@value" : "" } ]
+    },
     {
       "@id": "lago:bx",
       "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
@@ -246,6 +266,15 @@
       "comment" : [ { "@language" : "en", "@value" : "Vertical comp. of the Earth's mag. field (MAGNET) [downwards,muT], see values at https://www.ngdc.noaa.gov/geomag/calculators/magcalc.shtml#igrfwmm" },  
                     { "@language" : "es", "@value" : "Componente vertical del campo magnético de la Tierra (MAGNET) [downwards,muT], ver valores en https://www.ngdc.noaa.gov/geomag/calculators/magcalc.shtml#igrfwmm" } ]
     },
+    { 
+      "@id": "lago:bi",
+      "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
+      "dcat:domain": { "@id" : "lago:MagnetComponents" },
+      "dcat:range": { "@id": "xsd:decimal"},
+      "dcat:label": "bx",
+      "comment" : [ { "@language" : "en", "@value" : "" },  
+                    { "@language" : "es", "@value" : "" } ]
+    },
     {
       "@id": "lago:atmcrd",
       "@type" : [ "rdf:Property", "owl:ObjectProperty" ],
@@ -289,6 +318,40 @@
       "lago:corsikaParam" : "ARRANG",
       "comment" : [ { "@language" : "en", "@value" : "" },  
                     { "@language" : "es", "@value" : "" } ]
+    },
+   {
+    "@id" : "geometry",
+    "@type" : "geometry",
+    "dcat:domain" : [ { "@id" : "Location" },
+                      { "@id" : "lago:DetectorSite" } ],
+    "dcat:range" : { "@id": "geo:Point" },    
+    "dcat:label" : "point",
+    "seeAlso" : [ "https://www.w3.org/ns/locn#locn:geometry", 
+                  "https://www.w3.org/TR/vocab-dcat-2/#Property:location_geometry" ],
+    "comment" : [ { "@language" : "en", "@value" : ""},  
+                  { "@language" : "es", "@value" : "" } ]
+   },
+   {"_comment" : "Reiterative including geo:Point and its propierties. It is as is in W3C WGS84 vocab: http://www.w3.org/2003/01/geo/wgs84_pos#). Added for guiding/clarifying."},
+   {
+    "@id": "geo:latitude",
+    "@type":"http://www.w3.org/2001/XMLSchema#float",
+    "dcat:domain": { "@id": "geo:Point" },
+    "dcat:label" : "lat",
+    "owl:equivalentProperty" : { "@id": "sdo:GeoCoordinates#latitude" }
+   },
+   {
+    "@id": "geo:longitude",
+     "@type":"http://www.w3.org/2001/XMLSchema#float",
+     "dcat:label" : "long",
+     "dcat:domain": { "@id": "geo:Point" },
+     "owl:equivalentProperty" : { "@id": "sdo:GeoCoordinates#longitude" }
+    },
+   {
+    "@id": "geo:altitude",
+     "@type":"http://www.w3.org/2001/XMLSchema#float",
+     "dcat:label" : "alt",
+     "dcat:domain": { "@id": "geo:Point" },
+     "owl:equivalentProperty" : { "@id": "sdo:GeoCoordinates#altitude" }
     }
   ],
 "@context" : {
@@ -303,6 +366,7 @@
     "dcat" : "http://www.w3.org/ns/dcat#",
     "prov" : "http://www.w3.org/ns/prov#",
     "foaf" : "http://xmlns.com/foaf/0.1/",
-    "sdo" : "http://schema.org/"
+    "sdo" : "http://schema.org/",
+    "geo": "http://www.w3.org/2003/01/geo/wgs84_pos#"
   }
 }