Added Views Integration for tripal_analysis

tripal_analysis/tripal_analysis.module

@@ -855,3 +855,15 @@ function tripal_analysis_taxonify_features ($analysis_id = NULL, $job_id = NULL)
 		$i++;
 	}
 }
+
+/*************************************************************************
+ * Implements hook_views_api()
+ * Purpose: Essentially this hook tells drupal that there is views support for
+ *  for this module which then includes tripal_analysis.views.inc where all the
+ *  views integration code is
+ */ 
+function tripal_analysis_views_api() {
+   return array(
+      'api' => 2.0,
+   );
+}

tripal_analysis/tripal_analysis.views.inc

@@ -0,0 +1,82 @@
+<?php
+
+/**
+ *  @file
+ *  This file contains the basic functions for views integration of
+ *  chado/tripal analysis tables. Supplementary functions can be found in
+ *  ./views/
+ *
+ *  Documentation on views integration can be found at 
+ *  http://views2.logrus.com/doc/html/index.html.
+ */
+ 
+/*************************************************************************
+ * Implements hook_views_data()
+ * Purpose: Describe chado/tripal tables & fields to views
+ * @return: a data array which follows the structure outlined in the
+ *   views2 documentation for this hook. Essentially, it's an array of table
+ *   definitions keyed by chado/tripal table name. Each table definition 
+ *   includes basic details about the table, fields in that table and
+ *   relationships between that table and others (joins)
+ */
+require('views/analysis.views.inc');
+function tripal_analysis_views_data()  {
+  $data = array();
+
+  $data = array_merge($data, retrieve_analysis_views_data());
+
+  return $data;
+}
+
+/*************************************************************************
+ * Implements hook_views_handlers()
+ * Purpose: Register all custom handlers with views
+ *   where a handler describes either "the type of field", 
+ *   "how a field should be filtered", "how a field should be sorted"
+ * @return: An array of handler definitions
+ */
+function chado_analysis_views_views_handlers() {
+  return array(
+    'info' => array(
+      'path' => drupal_get_path('module', 'tripal_analysis') . '/views/handlers',
+    ),
+    'handlers' => array(
+      'views_handler_field_computed_nid' => array(
+        'parent' => 'views_handler_field_numeric',
+      ),
+      'views_handler_field_readable_date' => array(
+        'parent' => 'views_handler_field',
+      ),
+    ),
+  );
+}
+
+/**
+ * Implements hook_views_pre_render
+ * Purpose: Intercepts the view after the query has been executed
+ *   All the results are stored in $view->result
+ *   Looking up the NID here ensures the query is only executed once
+ *   for all analysis' in the table.
+ *
+ * @todo add if !<chado/drupal same db> around NID portion
+ */
+function tripal_analysis_views_pre_render	(&$view) {
+	if (preg_match('/analysis/', $view->base_table)) {
+		
+		// retrieve the analysis_id for each record in the views current page
+		$analysis_ids = array();
+		foreach ($view->result as $row_num => $row) {
+			$analysis_ids[$row_num] = $row->analysis_id;
+		}
+
+		// Using the list of analysis_ids from the view
+		// lookup the NIDs from drupal
+		// and add that to the results of the view
+		$sql = "SELECT nid, analysis_id FROM chado_analysis WHERE analysis_id IN (".implode(',',$analysis_ids).")";
+		$resource = db_query($sql);
+		while ($r = db_fetch_object($resource)) {
+			$key = array_search($r->analysis_id, $analysis_ids);
+			$view->result[$key]->nid = $r->nid;
+		}
+	}
+}

tripal_analysis/views/analysis.views.inc

@@ -0,0 +1,254 @@
+<?php
+	/**
+ * Purpose: this function returns the portion of the data array 
+ *   which describes the analysis table, it's fields and any joins between it and other tables
+ * @see tripal_analysis_views_data() --in tripal_analysis.views.inc
+ *
+ * @todo Add support for analysisprop table
+ * @todo Add support for multiple analysis' listed per feature
+ * @todo Add join to node table within if <chado/drupal same db>; also addd if not around nid field
+ *
+ * BASE TABLE: analysis
+ * @code
+ *   create table analysis (
+ *       analysis_id serial not null,
+ *       primary key (analysis_id),
+ *       name varchar(255),
+ *       description text,
+ *       program varchar(255) not null,
+ *       programversion varchar(255) not null,
+ *       algorithm varchar(255),
+ *       sourcename varchar(255),
+ *       sourceversion varchar(255),
+ *       sourceuri text,
+ *       timeexecuted timestamp not null default current_timestamp,
+ *       constraint analysis_c1 unique (program,programversion,sourcename)
+ *   );
+ * @endcode
+ */
+function retrieve_analysis_views_data() {
+  
+  // Basic table definition
+  $data['analysis']['table']['group'] = 'Chado Analysis';
+ 	$data['analysis']['table']['base'] = array(
+ 		'field' => 'analysis_id',
+ 		'title' => t('Chado Analysis'),
+ 		'help' => t("An analysis is a particular type of a computational analysis; it may be a blast of one sequence against another, or an all by all blast, or a different kind of analysis altogether. It is a single unit of computation."),
+ 		'database' => 'chado',
+ 	);
+
+  // Define relationships between this table and others
+  $data['analysis']['table']['join'] = array(
+    'analysisfeature' => array(
+      'left_field' => 'analysis_id',
+      'field' => 'analysis_id',
+    ),
+    'feature' => array(
+      'left_table' => 'analysisfeature',
+      'left_field' => 'analysis_id',
+      'field' => 'analysis_id',
+    ),
+  );
+
+  // Describe the joins with the analysis_feature table
+  $data['analysisfeature']['table']['join'] = array(
+    'feature' => array(
+      'left_field' => 'feature_id',
+      'field' => 'feature_id',
+    ),
+  );
+	
+	// Table Field Definitions----------------------
+	// Field: analysis_id (primary key)
+	$data['analysis']['analysis_id'] = array(
+	  'title' => 'analysis ID',
+	  'help' => 'The primary key of the analysis table.',
+	  'field' => array(
+	    'handler' => 'views_handler_field_numeric',
+	    'click sortable' => TRUE,
+	  ),
+	  'filter' => array(
+	    'handler' => 'views_handler_filter_numeric',
+	  ),
+	  'sort' => array(
+	    'handler' => 'views_handler_sort',
+	  ),
+	);
+	
+  // Calculated Field: Node ID
+  //  use custom field handler to query drupal for the node ID
+  //  this is only needed if chado is in a separate database from drupal
+	$data['analysis']['nid'] = array(
+	  'title' => 'Node ID',
+	  'help' => 'The node ID for the current analysis',
+	  'field' => array(
+	    'handler' => 'views_handler_field_computed_nid',
+	  ),
+	);
+	
+	// Field: name (varchar 255)
+ 	$data['analysis']['name'] = array(
+    'title' => t('Name'),
+    'help' => t(''),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: description (text)
+ 	$data['analysis']['description'] = array(
+    'title' => t('Description'),
+    'help' => t(''),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: program (varchar 255)
+ 	$data['analysis']['program'] = array(
+    'title' => t('Program'),
+    'help' => t('Program name, e.g. blastx, blastp, sim4, genscan.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: program version (varchar 255)
+ 	$data['analysis']['programversion'] = array(
+    'title' => t('Program Version'),
+    'help' => t('Version description, e.g. TBLASTX 2.0MP-WashU [09-Nov-2000].'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: algorithm (varchar 255)
+ 	$data['analysis']['algorithm'] = array(
+    'title' => t('Algorithm'),
+    'help' => t('Algorithm name, e.g. blast.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+ 	$data['analysis']['sourcename'] = array(
+    'title' => t('Source Name'),
+    'help' => t('Source name, e.g. cDNA, SwissProt.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: source version (varchar 255)
+ 	$data['analysis']['sourceversion'] = array(
+    'title' => t('Source Version'),
+    'help' => t('The version of the source.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: source URI/URL (text)
+ 	$data['analysis']['sourceuri'] = array(
+    'title' => t('Source URL'),
+    'help' => t('This is an optional, permanent URL or URI for the source of the analysis.'),
+    'field' => array(
+      'handler' => 'views_handler_field',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort',
+    ),
+    'filter' => array(
+      'handler' => 'views_handler_filter_string',
+    ),
+    'argument' => array(
+      'handler' => 'views_handler_argument_string',
+    ),
+  );
+
+  // Field: time executed (datetime)
+ 	$data['analysis']['timeexecuted'] = array(
+    'title' => 'Time Executed',
+    'help' => 'The date & time when this analysis was executed.',
+    'field' => array(
+      'handler' => 'views_handler_field_readable_date',
+      'click sortable' => TRUE,
+    ),
+    'sort' => array(
+      'handler' => 'views_handler_sort_date',
+    ),
+  );
+
+ 	return $data;
+}

tripal_analysis/views/handlers/views_handler_field_computed_nid.inc

@@ -0,0 +1 @@
+../../../tripal_core/views_handlers/views_handler_field_computed_nid.inc