First commit. Module is in D8 structure

includes/color_scheme.inc → api/color_scheme.inc

@@ -1,5 +1,4 @@
 <?php
-
 /**
  * @file
  * TripalD3 provides a number of color schemes with configuration for site admin
@@ -74,10 +73,10 @@ function tripald3_tripald3_color_schemes() {
  * Retrieve a list of available color schemes.
  */
 function tripald3_get_color_schemes() {
-
-  $schemes = module_invoke_all('tripald3_color_schemes');
+  // Listen for all available modules (enabled) implementing tripald3_color_schemes
+  // to register a custom colour scheme.
+  $schemes = \Drupal::moduleHandler()->invokeAll('tripald3_color_schemes');
   return $schemes;
-
 }
 
 /**
@@ -110,21 +109,19 @@ function tripald3_get_scheme_colors($scheme_id, $type, $scheme = array()) {
 /**
  * Register Color Schemes with Javascript
  */
-function tripald3_register_colorschemes() {
+function tripald3_register_colorschemes($default) {
 
   $jsSettings = array('tripalD3' => array());
 
   $schemes = tripald3_get_color_schemes();
   foreach ($schemes as $id => $scheme) {
-
-    $jsSettings['tripalD3']['colorSchemes'][$id]['name'] = $scheme['name'];
-    $jsSettings['tripalD3']['colorSchemes'][$id]['quantitative'] = tripald3_get_scheme_colors($id, 'quantitative', $scheme);
-    $jsSettings['tripalD3']['colorSchemes'][$id]['categorical'] = tripald3_get_scheme_colors($id, 'categorical', $scheme);
+    $jsSettings['colorSchemes'][$id]['name'] = $scheme['name'];
+    $jsSettings['colorSchemes'][$id]['quantitative'] = tripald3_get_scheme_colors($id, 'quantitative', $scheme);
+    $jsSettings['colorSchemes'][$id]['categorical'] = tripald3_get_scheme_colors($id, 'categorical', $scheme);
   }
 
   // Add in the currently selected scheme.
-  $jsSettings['tripalD3']['colorSchemes']['selected'] = variable_get('tripald3_colorScheme', 'BlOr');
-  drupal_add_js($jsSettings, 'setting');
+  $jsSettings['colorSchemes']['selected'] = $default;
 
   return $jsSettings;
 }

api/pedigree.inc

@@ -0,0 +1,120 @@
+<?php
+/**
+ * @file
+ * Tripal D3 chado databse API
+ * @see important note on Pedigree in Controller/TripalD3RelationshipJsonController.
+ */
+
+ /**
+  * Fetch relationship from congiuration variable.
+  */
+function tripald3_get_stockrelationship() {
+  // Used to allow admin to choose which relationships to follow.
+  // Sorted alphabetically.
+  $rel_options = array();
+
+  // Get relationships for the settings form.
+  $sql = "
+    SELECT sr.type_id, cvt.name as type_name
+    FROM {stock_relationship} sr
+    LEFT JOIN {cvterm} cvt ON cvt.cvterm_id=sr.type_id
+    GROUP BY sr.type_id, cvt.name
+    ORDER BY count(sr.*) desc
+  ";
+
+  $rels = chado_query($sql);
+  foreach ($rels as $r) {
+    $rel_options[ $r->type_id ] = $r->type_name;
+  }
+
+  asort($rel_options);
+  return $rel_options;
+}
+
+/**
+ * API: check if this node would consist of a single level tree with no leaves.
+ *
+ * @param $stock_id
+ *   The unique identifier of the root stock/germplasm.
+ * @return
+ *   TRUE if there are no approved relationships attached to the root node
+ *   and FALSE otherwise.
+ */
+function tripald3_is_node_leafless_tree($stock_id) {
+  $relationship_types = tripald3_get_pedigree_relationship_types();
+
+  // Check relationships where the root is the subject.
+  $subject_rels = 0;
+  if (!empty($relationship_types['subject'])) {
+    $vars = array(':stock_id' => $stock_id);
+    $rel_placeholders = array();
+    foreach ($relationship_types['subject'] as $k => $type_name) {
+      $vars[':reltype' . $k] = $type_name;
+      $rel_placeholders[] = ':reltype' . $k;
+    }
+    $sql = 'SELECT count(*) as num_relationships
+            FROM {stock_relationship} sr
+            LEFT JOIN {cvterm} cvt ON sr.type_id=cvt.cvterm_id
+            WHERE subject_id=:stock_id
+              AND cvt.name IN (' . implode(',', $rel_placeholders) . ')';
+    $subject_rels = chado_query($sql, $vars)->fetchField();
+  }
+
+  // Check relationships where the root is the object.
+  $object_rels = 0;
+  if (!empty($relationship_types['object'])) {
+    $vars = array(':stock_id' => $stock_id);
+    $rel_placeholders = array();
+    foreach ($relationship_types['object'] as $k => $type_name) {
+      $vars[':reltype' . $k] = $type_name;
+      $rel_placeholders[] = ':reltype' . $k;
+    }
+    $sql = 'SELECT count(*) as num_relationships
+            FROM {stock_relationship} sr
+            LEFT JOIN {cvterm} cvt ON sr.type_id=cvt.cvterm_id
+            WHERE object_id=:stock_id
+              AND cvt.name IN (' . implode(',', $rel_placeholders) . ')';
+    $object_rels = chado_query($sql, $vars)->fetchField();
+  }
+
+  // If there are any relationships then return FALSE else return TRUE
+  $total = $subject_rels + $object_rels;
+  if ($total) {
+    return FALSE;
+  }
+  else {
+    return TRUE;
+  }
+}
+
+/**
+ * Restrict datapoints to this subset only.
+ */
+function tripald3_get_pedigree_relationship_types() {
+  $rels_to_restrict = \Drupal::state()->get('tripald3_stock_pedigree_rels', NULL); 
+
+  if (!$rels_to_restrict) {
+    // Get relationships used in stock table.
+    $rels = array();
+    $sql = "SELECT sr.type_id, cvt.name as type_name
+            FROM {stock_relationship} sr
+            LEFT JOIN {cvterm} cvt ON cvt.cvterm_id=sr.type_id
+            GROUP BY sr.type_id, cvt.name
+            ORDER BY count(sr.*) desc";
+
+    $rel_query = chado_query($sql);
+    foreach ($rel_query as $r) {
+      $rels[$r->type_id] = $r->type_name;
+    }
+
+    $rels_to_restrict = array(
+      'object' => array(),
+      'subject' => $rels
+    );
+  }
+  else {
+    $rels_to_restrict = unserialize($rels_to_restrict);
+  }
+
+  return $rels_to_restrict;
+}

config/install/tripald3.settings.yml

@@ -0,0 +1,6 @@
+# Auto-resize svg canvass, default to false
+tripald3_autoResize: FALSE
+# Colour scheme, default to Blue orange.
+tripald3_colorScheme: BlOr
+# Stock pedigree terms used, default to empty.
+tripald3_stock_pedigree_rels: 

css/testpage.css

@@ -0,0 +1,33 @@
+div.test, pre.data, div.chart {
+  border: 1px solid #e0e0d8;
+}
+
+div.test {
+  display: flex;
+  flex-direction: row;
+  justify-content: space-around;
+  height: 400px;
+}
+
+div.test div.chart {
+  padding: 15px;
+}
+
+div.test pre {
+  margin: 0;
+  overflow: scroll;
+  font-size: 10px;
+  flex-grow: 1;
+}
+
+div.test svg {
+  border: 1px solid #e0e0d8;
+}
+
+div#test0 {
+  height: 100px;
+}
+
+div#test0 .data {
+  color: red;
+}

css/tripald3.css

@@ -1,4 +1,3 @@
-
 .tripald3-diagram {
   width: 500px;
 }
@@ -66,5 +65,5 @@ svg.tripald3-tree .tree-node {
 }
 
 .tripald3-default-watermark {
-  background-image: url(watermark.png);
+  background-image: url('../templates/image/watermark.png');
 }

css/watermark.css

@@ -13,5 +13,5 @@
 }
 
 .tripald3-default-watermark {
-  background-image: url(watermark.png);
+  background-image: url('../templates/image/watermark.png');
 }

docs/api/placeWatermark.rst

@@ -14,7 +14,7 @@ This function places a watermark overlay to diagrams to indicate proprietary con
     // Draw.
     tripalD3.drawFigure(data, {'chartType' : 'multidonut', 'elementId' : 'multidonut', ....});
 
-    // Watermark. Use default image in ``/css/watermark.png`` as watermark.
+    // Watermark. Use default image in ``/templates/image/watermark.png`` as watermark.
     tripalD3.placeWatermark();
 
     // OR use alternate image.
@@ -31,7 +31,7 @@ def ``placeWatermark(options)``:
 
   :options: A javascript object with the following key:
 
-    :watermark: by default this function will use the image located in ``/css/watermark.png`` as the preselected watermark. This can be
+    :watermark: by default this function will use the image located in ``/templates/image/watermark.png`` as the preselected watermark. This can be
     used when site requires a unified watermark across all visualizations (site-wide), simply by replacing the said image with
     the desired logotype (be sure to use the same filename). If the site requires a different image for one diagram in a page to another
     diagram in another page, this option can be used to alter the default watermark by supplying a path to an image (see example).

docs/dev_guide.rst

@@ -17,5 +17,5 @@ This guide contains tutorials for using the Tripal D3.js API to add diagrams to
 Additional Information
 ------------------------
 
- - Examples on how to use each chart in ``templates/tripald3_demo_page.tpl.php`` and viewed at Admin » Tripal » Extension Modules » Tripal D3 Diagrams » Demo
+ - Examples on how to use each chart in ``templates/tripald3_demo_page.html.twig`` and viewed at Admin » Tripal » Extension Modules » Tripal D3 Diagrams » Demo
  - In-code documentation for all functions and chart types in `js/tripalD3.*.js`

docs/dev_guide/color_scheme.rst

@@ -13,9 +13,9 @@ Making your own colour scheme available to this module is as simple as implement
     $color_schemes = array();
 
     // This key should be unique across colour schemes.
-    $color_schemes['PrpGr'] = array(
+    $color_schemes['BlkGr'] = array(
       // This name will show up in the colour scheme configuration
-      'name' => 'Purple-Green',
+      'name' => 'Black-Green',
       // These are the colours your colour scheme consists of.
       'colors' => array('#3d4051', '#753fb0', '#8f7abf', '#294090', '#6683c3', '#0C6758', '#7AB318', '#A0C55E', '#9fa7a3'),
       'pick order' => array(