Merge pull request #62 from zakandrewking/populate

Populate maps

.gitignore

@@ -9,4 +9,9 @@ Escher.egg-info/
 .ipynb_checkpoints/
 build/*
 env/*
-envset/*
+envset/*
+builder.html
+builder_not_minified.html
+viewer.html
+viewer_not_minified.html
+index.html

docs/notebooks/json_models_in_cobrapy.ipynb

@@ -1,7 +1,7 @@
 {
  "metadata": {
   "name": "",
-  "signature": "sha256:78a516c98e9979feee6bcc52100d8bbb8d855994bca7d4b074c18e132e9f30a4"
+  "signature": "sha256:beee6ea53eaa629f0dd6a9a4b09cf5cec6ab287a550f5c3e9348ca15129537c7"
  },
  "nbformat": 3,
  "nbformat_minor": 0,
@@ -24,22 +24,27 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "# Load a cobra model from anywhere you like\n",
-      "model = cobra.io.read_sbml_model('e-coli-core.xml')"
+      "print cobra.__version__"
      ],
      "language": "python",
      "metadata": {},
-     "outputs": [],
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "v1.0.0b2.post29-g31d9339\n"
+       ]
+      }
+     ],
      "prompt_number": 2
     },
     {
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "# Exclude the following attributes so the final json file will be smaller\n",
-      "EXCLUDE = ['notes', 'charge', 'compartment', 'annotation',\n",
-      "           'subsystem', 'reaction', 'objective_coefficient',\n",
-      "           'notes', 'genes', 'description']"
+      "# Load a cobra model from anywhere you like\n",
+      "model = cobra.io.read_sbml_model('e-coli-core.xml')"
      ],
      "language": "python",
      "metadata": {},
@@ -51,7 +56,7 @@
      "collapsed": false,
      "input": [
       "# generate a json file to load into Escher\n",
-      "cobra.io.save_json_model(model, 'e-coli-core.json', exclude_attributes=EXCLUDE)"
+      "cobra.io.save_json_model(model, 'e-coli-core.json')"
      ],
      "language": "python",
      "metadata": {},

escher/css/builder-embed.css

@@ -19,37 +19,44 @@
     fill: black; 
     stroke: none;
     text-rendering: optimizelegibility;
+    cursor: default;
 }
 .reaction-label {
     fill: rgb(32, 32, 120);
     text-rendering: optimizelegibility;
 }
-.text-label {
+.text-label .label {
+    font-size: 50px;
+}
+.text-label-input {
     font-size: 50px;
 }
 .node-circle {
     stroke-width: 2px;
     fill: none;	
     stroke: rgb(50, 50, 50);
 }
-.selected .node-circle{
+g.selected .node-circle{
     stroke-width: 3px;
     stroke: rgb(20, 113, 199);
 }
-.selected.text-label {
+g.selected .label {
     fill: rgb(20, 113, 199);
 }
 .metabolite-circle {
     stroke: rgb(162, 69, 16);
 }
-.selected .metabolite-circle {
+g.selected .metabolite-circle {
     stroke: rgb(5, 2, 0);
 }
 .segment {
-    stroke: grey;
-    stroke-width: 3px;
+    stroke: #334E75;
+    stroke-width: 6px;
     fill: none;
 }
+.arrowhead {
+    fill: #334E75;
+}
 .membrane {
     fill: none;
     stroke: rgb(255, 187, 0);
@@ -60,13 +67,13 @@
     stroke: #fff;
     shape-rendering: crispEdges;
 }
-.bezier {
+.bezier-circle {
     fill: rgb(255,255,255);	
 }
-.bezier1 {
+.bezier-circle.b1 {
     stroke: red;
 }
-.bezier2 {
+.bezier-circle.b2 {
     stroke: blue;
 }
 .connect-line{ 
@@ -100,4 +107,7 @@
 .cursor-grabbing {
     cursor: grabbing;
     cursor: -webkit-grabbing;
+}
+.edit-text-cursor {
+    cursor: text;
 }

escher/css/builder.css

@@ -135,6 +135,10 @@
     width: 100%;
     text-align: left;
 }
+.no-data-input {
+    width: 23%;
+    margin: 0 4px 0 4px;
+}
 .style-span {
     margin: 0 4px;
 }
@@ -190,4 +194,10 @@
 .input-close-button:hover {
     color: #ff3333;
     font-weight: bold;
+}
+/* text edit input */
+#text-edit-input input {
+    width: 500px;
+    border: none;
+    font-size: 22px;
 }

escher/css/index.css

@@ -5,6 +5,11 @@ body {
 /* The html and body elements cannot have any padding or margin. */
 }
 
+body {
+    font-size: 15px;
+    color: #585858;
+}
+
 /* Wrapper for page content to push down footer */
 main {
     /* Negative indent footer by it's height */
@@ -42,22 +47,36 @@ footer a, a:hover, a:focus, a:visited {
 }
 .container .more {
     margin: 20px 0;
+    float: left;
+}
+.container .version {
+    margin: 20px 0;
+    float: right;
 }
 .column-button {
     width: 100%;
     margin-top: 35px;
 }
+#title-box {
+    display: inline-block;
+}
 #title {
     color: #291E1E;
     font-size: 160px;
-    font-family: tulpen-one, serif;
+    font-family: tulpen-one, Futura, serif;
     font-weight: 400;
-    /* font-style: italic; */
-    text-align: center;
 }
 #logo {
-    display: none;
-    width: 250px;
+    vertical-align: inherit;
+}
+@media (max-width: 768px) {
+    #title-box {
+	width: 100%;
+	text-align: center;
+    }
+    #logo {
+	display: none;
+    }
 }
 @media (min-width: 768px) { /*@screen-sm-min) { */
     .column-button {
@@ -66,16 +85,22 @@ footer a, a:hover, a:focus, a:visited {
     header {
 	margin-bottom: 50px;
     }
+    #title-box {
+	max-width: 400px;
+	overflow: hidden;
+    }
     #title {
+	position: relative;
+	top: 45px;
 	font-size: 230px;
 	text-align: left;
-	display: inline;
-	top: 100px;
-	position: relative;
     }
     #logo {
-	position: relative;
-	left: -20px;
-	display: inline;
+	width: 250px;
+	display: inline-block;
+	overflow: hidden;
+    }
+    #faq {
+	margin-top: 50px;
     }
 }

escher/generate_index.py

@@ -0,0 +1,49 @@
+import json
+from os import listdir
+from os.path import join, dirname, realpath, exists, isdir, relpath
+
+directory = realpath(join(dirname(realpath(__file__)), '..'))
+
+index_directories = ['maps/v1', 'models/v1']
+ignore_files = ['index.json', 'README']
+
+for index_dir in index_directories:
+    index = []
+    if not exists(join(directory, index_dir)):
+        print '%s does not exist' % index_dir
+        continue
+    for filename in listdir(join(directory, index_dir)):
+        if filename.endswith('.json') and filename not in ignore_files:
+            index.append(filename.replace('.json', ''))
+    with open(join(directory, index_dir, 'index.json'), 'w') as f:
+        json.dump(index, f)
+
+# organism index
+org_dir = join(directory, 'organisms')
+org_index = []
+model_index = []
+map_index = []
+# for all organisms
+for d in listdir(org_dir):
+    org_file = join(org_dir, d)
+    if isdir(org_file):
+        org_index.append(relpath(org_file, directory))
+    # for nested models
+    model_dir = join(org_file, 'models')
+    if isdir(model_dir):
+        for e in listdir(model_dir):
+            model_file = join(model_dir, e)
+            if model_file.endswith('.json') and model_file not in ignore_files:
+                model_index.append(relpath(model_file, directory).replace('.json', ''))
+            map_dir = join(model_file, 'maps')
+            if isdir(map_dir):
+                for f in listdir(map_dir):
+                    map_file = join(map_dir, f)
+                    if map_file.endswith('.json') and map_file not in ignore_files:
+                        map_index.append(relpath(map_file, directory).replace('.json', ''))
+
+with open(join(directory, 'index.json'), 'w') as f:
+    index = {'organisms': org_index,
+             'models': model_index,
+             'maps': map_index}
+    json.dump(index, f)