From afaaf9ef9f574f096859aa5474cce410fad2972f Mon Sep 17 00:00:00 2001
From: "James A. Overton" <james@overton.ca>
Date: Tue, 3 Nov 2015 16:27:51 -0500
Subject: [PATCH] Sort ontology list: Foundry, Library, Obsolete

- update extract-metadata.py to sort YAML objects
- update ontology_table.html to change sort and add classes
- add custom.css to highlight Foundry and Obsolete rows
- modify default.html to use custom.css
---
 _includes/ontology_table.html             |  5 ++---
 _includes/themes/bootstrap-3/default.html |  2 +-
 css/custom.css                            |  7 +++++++
 util/extract-metadata.py                  | 21 ++++++++++++++++++---
 4 files changed, 28 insertions(+), 7 deletions(-)
 create mode 100644 css/custom.css

diff --git a/_includes/ontology_table.html b/_includes/ontology_table.html
index 49e0ce9e0..0d29dd023 100644
--- a/_includes/ontology_table.html
+++ b/_includes/ontology_table.html
@@ -1,9 +1,8 @@
 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'  %}
-    {% for ont in sorted_ontologies %}
-    <tr>
+    {% for ont in site.ontologies %}
+    <tr class="{% if ont.in_foundry_order %}foundry{% elsif ont.is_obsolete %}obsolete{% endif %}">
       <td>
          <a href="ontology/{{ ont.id }}.html" >
            {% if ont.is_obsolete %}
diff --git a/_includes/themes/bootstrap-3/default.html b/_includes/themes/bootstrap-3/default.html
index 0e27dd515..3a076c521 100644
--- a/_includes/themes/bootstrap-3/default.html
+++ b/_includes/themes/bootstrap-3/default.html
@@ -19,7 +19,7 @@
     <link href="{{ ASSET_PATH }}/bootstrap/css/bs-sticky-footer.css" rel="stylesheet">
     
     <!-- Custom styles -->
-    <link href="{{ ASSET_PATH }}/css/style.css?body=1" rel="stylesheet" type="text/css" media="all">
+    <link href="/css/custom.css" rel="stylesheet" type="text/css" media="all">
 
     <style>
 @media (min-width: 768px) {
diff --git a/css/custom.css b/css/custom.css
new file mode 100644
index 000000000..e4c7b017e
--- /dev/null
+++ b/css/custom.css
@@ -0,0 +1,7 @@
+.foundry {
+  background-color: #f0fbff;
+}
+
+.obsolete {
+  background-color: #f6f6f6;
+}
diff --git a/util/extract-metadata.py b/util/extract-metadata.py
index 6716f78ee..dda7ac231 100755
--- a/util/extract-metadata.py
+++ b/util/extract-metadata.py
@@ -87,17 +87,32 @@ def validate_structure(obj,md):
     return errs
 
 def concat_ont_yaml(args):
+    """
+    Given arguments with files and ouput,
+    read YAML files into an array, decorate the objects, and write an output YAML file.
+    Output will be Foundry ontologies first, Library ontologies second, and obsolete last.
+    Assumes that args.files is already sorted alphabetically.
+    """
     objs = []
+    foundry = []
+    library = []
+    obsolete = []
     cfg = {}
     if (args.include):
-        f = open(args.include, 'r') 
+        f = open(args.include, 'r')
         cfg = yaml.load(f.read())
     for fn in args.files:
         (obj, md) = load_md(fn)
-        objs.append(obj)
+        if 'is_obsolete' in obj:
+          obsolete.append(obj)
+        elif 'in_foundry_order' in obj:
+          foundry.append(obj)
+        else:
+          library.append(obj)
+    objs = foundry + library + obsolete
     cfg['ontologies'] = objs
     decorate_metadata(objs)
-    f = open(args.output, 'w') 
+    f = open(args.output, 'w')
     f.write(yaml.dump(cfg))
     return cfg