Merge remote-tracking branch 'upstream/master' into new-ontology-mro

pporrasebi · Oct 1, 2015 · 2a1bb02 · 2a1bb02
2 parents 94b07c9 + bfab0ec
commit 2a1bb02
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Showing 85 changed files with 11,614 additions and 340 deletions.
diff --git a/Makefile b/Makefile
@@ -4,15 +4,15 @@ ONTS := $(wildcard ontology/*md)
 # All principles .md file
 PRINCIPLES := $(wildcard principles/*md)
 
-all: _config.yml registry/ontologies.yml
+all: pull yml registry/ontologies.ttl
+yml: _config.yml registry/ontologies.yml
 
-test: validate all
+test: validate yml
 
 integration-test: test valid-purl-report.txt
 
-t:
-	echo $(ONTS)
-
+pull:
+	git pull
 
 # Create the site-wide config file by combining all metadata on ontologies + principles
 #  and combining with site-wide metadata.
@@ -33,13 +33,19 @@ registry/ontologies.yml: $(ONTS)
 principles/all.yml: $(PRINCIPLES)
 	./util/extract-metadata.py concat-principles -o $@.tmp $^  && mv $@.tmp $@
 
-# TODO: add @context
+# Use a generic yaml->json conversion, but adding a @content
 registry/ontologies.jsonld: registry/ontologies.yml
 	./util/yaml2json.py $< > $@.tmp && mv $@.tmp $@
 
-# TODO
-registry/ontologies.ttl: registry/ontologies.jsonld
-	riot registry/context.jsonld $< > $@.tmp && mv $@.tmp $@
+# Use Apache-Jena RIOT to convert jsonld to n-triples
+# NOTE: UGLY HACK. If there is a problem then Jena will write WARN message (to stdout!!!), there appears to
+#  be no way to get it to flag this even with strict and check options, so we do a check with grep, ugh.
+# see: http://stackoverflow.com/questions/20860222/why-do-i-have-these-warnings-with-jena-2-11-0
+registry/ontologies.nt: registry/ontologies.jsonld
+	riot --base=http://purl.obolibrary.org/obo/ --strict --check -q registry/context.jsonld $< > $@.tmp && mv $@.tmp $@ && egrep '(WARN|ERROR)' $@ && exit 1 || echo ok
+
+registry/ontologies.ttl: registry/ontologies.nt
+	rdfcat -out ttl $< > $@.tmp && mv $@.tmp $@
 
 
 validate: $(ONTS)
@@ -54,3 +60,14 @@ validate: $(ONTS)
 # See: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/18
 valid-purl-report.txt: registry/ontologies.yml
 	./util/processor.py -i $< check-urls > $@.tmp && mv $@.tmp $@
+
+sparql-consistency-report.txt: registry/ontologies.yml
+	./util/processor.py -i $< sparql-compare > $@.tmp && mv $@.tmp $@
+
+# output of central OBO build
+# See FAQ for more details, and also README.md
+jenkins-output.txt:
+	wget http://build.berkeleybop.org/job/simple-build-obo-all/lastBuild/consoleFull -O $@
+
+reports/%.csv: registry/ontologies.ttl sparql/%.sparql
+	arq --data $< --query sparql/$*.sparql --results csv > $@.tmp && mv $@.tmp $@
diff --git a/README.md b/README.md
@@ -153,6 +153,8 @@ TODO: add a quick guide to yaml, and the tags we use.
 
 ## Central OBO library build
 
+(see also the FAQ entry on this)
+
 The central OBO build runs here:
 
  * http://build.berkeleybop.org/job/simple-build-obo-all/

diff --git a/_config.yml b/_config.yml
diff --git a/_includes/navbar.html b/_includes/navbar.html
@@ -12,7 +12,7 @@
       <!-- TODO: copy source -->
       <!-- see also: http://stackoverflow.com/questions/18474564/bootstrap-3-navbar-with-logo -->
       <a class="navbar-brand" href="/">
-        <img style="max-width:50px; margin-top: -7px;" src="http://obofoundry.org/images/foundrylogo.gif"/>
+        <img style="max-width:50px; margin-top: -7px;" src="/images/foundrylogo.png"/>
       </a>
     </div>
 
@@ -46,17 +46,21 @@
           <ul class="dropdown-menu">
             <li><a href="/">Ontology Table</a></li>
             <li><a href="/id-policy.html">ID Policy</a></li>
+            <li role="separator" class="divider"></li>
             <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology">Ontologies Metadata Source</a></li>
-            <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/registry/ontologies.yml">Ontology YAML</a></li>
+            <li><a href="https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/registry/">Combined Metadata</a></li>
+            <li><a href="https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.yml">Ontology YAML</a></li>
+            <li><a href="https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.jsonld">Ontology JSON-LD <i>alpha</i></a></li>
+            <li><a href="https://raw.githubusercontent.com/OBOFoundry/OBOFoundry.github.io/master/registry/ontologies.ttl">Ontology RDF/Turtle <i>alpha</i></a></li>
           </ul>
         </li>
 
         <li class="dropdown">
           <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Participate <span class="caret"></span></a>
           <ul class="dropdown-menu">
-            <li><a href="allnews.html">OBO Foundry News</a></li>
+            <li><a href="/allnews.html">OBO Foundry News</a></li>
             <li>Twitter Feed (coming soon)</li>
-            <li>Mailing lists (TODO)</li>
+            <li><a href="https://lists.sourceforge.net/lists/listinfo/obo-discuss">OBO-Discuss Mail List</a></li>
           </ul>
         </li>
 
@@ -65,12 +69,15 @@
           <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">FAQ <span class="caret"></span></a>
           <ul class="dropdown-menu">
             <!-- in theory we could auto-generate this part of the navbar -->
-            <li><a href="/faq/who-is-the-foundry.html">Who is the OBO Foundry?</a></li>
+            <!-- <li><a href="/faq/who-is-the-foundry.html">Who is the OBO Foundry?</a></li> -->
             <li role="separator" class="divider"></li>
             <li><a href="/faq/how-do-i-register-my-ontology.html">How do I register my ontology?</a></li>
             <li><a href="/faq/how-do-i-edit-metadata.html">How do I edit the metadata for my ontology?</a></li>
-            <li><a href="/faq/adding-custom-browsers">How do I add a custom browser for my ontology?</a></li>
+            <li><a href="/faq/how-do-i-add-browser.html">How do I add a custom browser for my ontology?</a></li>
+            <li><a href="/faq/what-is-the-build-field.html">What is the <code>build</code> object in the ontology metadata?</a></li>
             <li role="separator" class="divider"></li>
+            <li><i>Website</i></li>
+            <li><a href="/faq/how-do-i-modify-website.html">How do I modify the OBO website?</a></li>
           </ul>
         </li>
 
@@ -83,7 +90,7 @@
             <li><a href="/legacy/relatedprojects.html">Related</a></li>
             <li><a href="/legacy/crit.html">Criteria</a></li>
             <li><a href="/publications.html">Publications</a></li>
-            <li><a href="http://wiki.obofoundry.org">Old Wiki</a></li>
+            <li><a href="http://wiki.obofoundry.org/wiki/index.php/Main_Page">Old Wiki</a></li>
             <li><a href="https://code.google.com/p/obo-foundry-operations-committee/wiki/">Old Operation Wiki</a></li>
           </ul>
         </li>

diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html
@@ -1,3 +1,4 @@
+Download table as: [ <a href="/registry/ontologies.yml">YAML</a> | <a href="/registry/ontologies.jsonld">JSON-LD</a> | <a href="/registry/ontologies.ttl">RDF/Turtle</a>  ]
 <table class="table">
   <tbody>
     {% assign sorted_ontologies = site.ontologies | sort: 'in_foundry_order', 'last'  %}
@@ -22,6 +23,9 @@
         {% else %}
         {{ ont.title }}
         {% endif %}
+        {% if ont.license %}
+        <a href="{{ont.license.url}}"><img width="100px" src="{{ont.license.logo}}" alt="{{ont.license.label}}"/></a>
+        {% endif %}
       </td>
       <td>
         {% if ont.is_obsolete %}

diff --git a/_includes/themes/bootstrap-3/default.html b/_includes/themes/bootstrap-3/default.html
@@ -21,7 +21,33 @@
     <!-- Custom styles -->
     <link href="{{ ASSET_PATH }}/css/style.css?body=1" rel="stylesheet" type="text/css" media="all">
 
-
+    <style>
+@media (min-width: 768px) {
+  .dl-horizontal dt {
+    width: 90px;
+    }
+  .dl-horizontal dd {
+    margin-left: 111px;
+    padding-left: 15px !important;
+    }
+}
+@media (min-width: 992px) {
+  .dl-horizontal dt {
+    width: 126px;
+    }
+  .dl-horizontal dd {
+    margin-left: 146px;
+    }
+}
+@media (min-width: 1200px) {
+  .dl-horizontal dt {
+    width: 160px;
+    }
+  .dl-horizontal dd {
+    margin-left: 180px;
+    }
+}
+   </style>
 
     <!-- HTML5 Shim and Respond.js IE8 support of HTML5 elements and media queries -->
     <!-- WARNING: Respond.js doesn't work if you view the page via file:// -->