tripal_analysis/tripal_analysis.admin.inc

@@ -3,24 +3,131 @@
 // Copyright 2009 Clemson University
 //
 
-/*************************************************************************
+/**
  * Purpose: Provide Guidance to new Tripal Admin
  *
- * @return HTML Formatted text
+ * @return 
+ *   HTML Formatted text
+ *
+ * @ingroup tripal_analysis
  */
 function tripal_analysis_module_description_page() {
-  $text = '';
-  
-  $text .= '<h3>Description:</h3>';
-  $text .= '<p>TODO: Basic Description of this module including mention/link to the chado module</p>';
 
-  $text .= '<h3>Post Installation Instructions:</h3>';
-  $text .= '<p>TODO: Describe any post installation intructions here. You shouldalways include setting user permissions.</p>';
+  $text .= '<h3>Tripal Analysis Administrative Tools Quick Links:</h3>';
+  $text .= "<ul>
+             <li><a href=\"".url("admin/tripal/tripal_analysis/configuration") . "\">Analysis Configuration</a></li>
+           </ul>";
+ 
+
+  $text .= '<h3>Module Description:</h3>';
+  $text .= '<p>The Tripal Analysis module provides a generic analysis content type that is intended to be
+            used when a more specialized analysis module does not exist.  Because it is generic, it does not
+            provide any visualization or data loading tools for analysis data.  Specialized analysis modules,
+            such as the Tripal Analysis Blast or Tripal Analysis KEGG modules provide loading and custom
+            visualizations for the analysis results.  These modules must be installed separately.
+            </p>';
+
+  $text .= '<h3>Setup Instructions:</h3>';
+  $text .= '<p>After installation of the analysis module or any specialized analysis module.  The following tasks should be performed
+            <ol>
+              <li><p><b>Set Permissions</b>: Each analysis module supports the Drupal user permissions interface for 
+               controlling access to the content and functions. These permissions include viewing, 
+               creating, editing or administering of
+               analysis content. The default is that only the original site administrator has these 
+               permissions.  You can <a href="'.url('admin/user/roles').'">add roles</a> for classifying users, 
+               <a href="'.url('admin/user/user').'">assign users to roles</a> and
+               <a href="'.url('admin/user/permissions').'">assign permissions</a> for the analysis content to 
+               those roles.  For a simple setup, allow anonymous users access to view organism content and 
+               allow the site administrator all other permissions.</p></li>
+
+
+               <li><p><b>Create Analysis</b>:  An analysis should be <a href="'.url('node/add').'">created</a> before data is imported into
+               chado.  The generic analysis type should only be used when a more specialized analysis module
+               (e.g. Tripal Analysis Blast module) does not already exists.  All data imported into 
+               Chado should be associated with an analysis.    
+
+               <li><p><b>Sync Analyses</b>:  If Chado has preloaded analyses then you can sync those.  This process is what
+               creates the pages for viewing an analysis on the site.  Analyses can be synced using the 
+               <a href="'.url('admin/tripal/tripal_analysis/configuration').'">Analysis Configuration page</a>. 
+               However, syncing an analyses will always create a generic analysis content type.  If you would like
+               to use a specialized analysis module for visualization of data then do not sync the analysis but recreate it
+               using the appropriate specialized analysis content type.</p></li>
+ 
+            </ol>
+            </p>';
   
   
   $text .= '<h3>Features of this Module:</h3>';
-  $text .= '<p>TODO: Discuss the Features of this module including links. Some features to consider are creating content, details pages/node content, editing/deleteing, basic listings and vies integration. See admin/tripal/tripal_stock for an example.</p>';
-  
+  $text .= '<p>Aside from providing a generic content type the Tripal Analysis module also provides the following functionality
+            <ul>
+            
+              <li><p><b>Basic Analysis Lookup View</b>: This module provides a basic <a href="'.url('analyses').'">analysis search 
+              tool</a> for finding or listing analyses in Chado. It does not require indexing for Drupal searching but relies
+              on Drupal Views.  <a href="http://drupal.org/project/views">Drupal Views</a> must be installed. </p></li>              
+
+            </ul>
+            </p>';
+
+   $text .= '<h3>Page Customizations</h3>';
+   $text .= '<p>There are several ways to customize the look-and-feel for the way Chado data is presented through Tripal. 
+             Below is a description of several methods.  These methods may be used in conjunction with one another to
+             provide fine-grained control. 
+             <ul>
+
+             <li><p><b>Integration with Drupal Panels</b>:  <a href="http://drupal.org/project/views">Drupal Panels</a> 
+              allows for customization of a page layout if you don\'t want to do PHP/Javascript/CSS programming.  
+              Tripal comes with pre-set layouts for analysis pages.  However, 
+              Panels become useful if you prefer a layout that is different from the pre-set layouts.  Chado content
+              is provided to Panels in the form of Drupal "blocks" which you can then place anywhere on a page using the 
+              Panel\'s GUI.</p></li>
+
+             <li><p><b>Drupal\'s Content Construction Kit (CCK)</b>: the 
+             <a href="http://drupal.org/project/cck">Content Construction Kit (CCK) </a> is a powerful way to add non-Chado content
+             to any page without need to edit template files or knowing PHP.  You must first download and install CCK.
+             With CCK, the site administartor can create a new field to appear on the page.  For example, currently,
+             the Chado publication module is not yet supported by Tripal.  Therefore, the site administrator can add a text 
+             field to the analysis pages.  This content is not stored in Chado, but will appear on the analysis page.  A field
+             added by CCK will also appear in the form when editing a analysis to allow users to manually enter the appropriate
+             text.  If the default pre-set layout and themeing for Tripal is used, it is better to create the CCK element,
+             indicate that it is not to be shown (using the CCK interface), then manually add the new content type 
+             where desired by editing the templates (as described below).  If using Panels, the CCK field can be added to the
+             location desired using the Panels interface.</p></li>
+
+             <li><p><b>Drupal Node Templates</b>:  The Tripal packages comes with a "theme_tripal" directory that contains the
+             themeing for Chado content.    The analysis module has a template file for analysis "nodes" (Tripal analysis pages).  This file
+             is named "node-chado_analysis.tpl.php", and provides javascript, HTML and PHP code for display of the analysis
+             pages.  Specialized analysis modules will have their own template files as well, such as "node-chado_analysis-blast.tpl.php" for the
+             Tripal Analysis Blast module.  You can edit the template file to control which types of information (or which analysis "blocks") are displayed 
+             for analysis. Be sure to 
+             copy these template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
+             future Tripal updates may overwrite your customizations. See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
+             for instructions on how to access variables and other Chado content within the template file.</p></li>
+
+             <li><p><b>Analysis "Block" Templates</b>:  In the "theme_tripal" directory are subdirectories named after each tripal module (e.g. "tripal_feature", "tripal_library", etc.).
+             Inside each directory is a set of templates that control distinct types of information for each content type.  For example,
+             there is a "base" template for displaying of data directly from the Chado feature table, and a "references" 
+             template for showing external site references for a feature (data from the feature_dbxref table). 
+              These templates are used both by Drupal blocks
+             for use in Drupal Panels (as described above) or for use in the default pre-set layout that the node template 
+             provides (also desribed above).  Analyses block templates can exist in any of these directories.  For example, the Tripal Analysis Unigene
+             module uses templates in the tripal_analysis_unigene, tripal_organism, and tripal_feature directories.  Content for a unigene is then
+             cusotmizable within each of these contexts.
+             You can customize block template as you desire.  Be sure to copy the
+             template to your primary theme directory for editing. Do not edit them in the "theme_tripal" directory as
+             future Tripal updates may overwrite your customizations.  See the <a href="http://tripal.sourceforge.net/">Tripal website </a>
+             for instructions on how to access variables and other Chado content within the template files.</p></li>
+             </li>
+
+             <li><p><b>Adding Links to the "Resources" Sidebar</b>: If you use the pre-set default Tripal layout for theming, you
+             will see a "Resources" sidebar on each page.  The links that appear on the sidebar are automatically generated
+             using Javascript for all of the analysis "Blocks" that appear on the page. If you want to add additional links 
+             (e.g. a dynamic link to GBrowse for the analysis) and you want that link to appear in the 
+             "Resources" sidebar, simply edit the Drupal Node Template (as described above) and add the link to the 
+             section at the bottom of the template file where the resources section is found.</p></li>
+
+             </ul>
+             </p>';
+
   return $text;
 }
 

tripal_analysis/tripal_analysis.module

@@ -15,6 +15,8 @@
 
 require('tripal_analysis.api.inc');
 
+
+
 /*************************************************************************
 *
  *
@@ -620,6 +622,13 @@ function tripal_analysis_sync_analyses ($analysis_id = NULL, $job_id = NULL){
 /**
 *
 */
+function chado_analysis_validate($node,&$form){
+   // use the analysis parent to validate the node
+   tripal_analysis_validate($node, $form); 
+}
+/**
+*
+*/
 function tripal_analysis_validate($node, &$form){
 ##dprint_r($node);
 
@@ -654,51 +663,18 @@ function tripal_analysis_validate($node, &$form){
             //---------------------------------------------------
             // The primary key for the chado analysis table is 
             // program, programversion, sourcename
-            // Check to see if this analysis really is new -ie, it doesn't have the same
-            // primary key as any other analysis 
-	        $sql = "SELECT analysis_id ".
-                "FROM {analysis} ".
-                "WHERE program='%s'".
-                "AND programversion='%s'".
-                "AND sourcename='%s'";
-	        $previous_db = tripal_db_set_active('chado');
-	        $analysis_id = db_result(db_query($sql, $node->program, $node->programversion, $node->sourcename));
-            tripal_db_set_active($previous_db);
-        
-            if($analysis_id){
-                //---------------------------------------------------
-                // this primary key already exists in chado analysis table!
-                //---------------------------------------------------
-        
-                // check to see if it has also been synced with drupal
-	            $sql = "SELECT nid FROM {chado_analysis} ".
-                                "WHERE analysis_id = %d";
-	            $node_id = db_result(db_query($sql, $analysis_id));
-	            if($node_id){
-                    //---------------------------------------------------
-                    // the analysis has already been synced with drupal, redirect the user
-                    // to modify that node or start over
-                    //---------------------------------------------------
-                    $error = 'This analysis already exists in the chado database (analysis id ';
-                    $error .= $analysis_id.') and has been synchronized ';
-                        $error .= 'with drupal. See node '.$node_id.' if you wish to update that analysis.  ';
-                    $error .= ' For a new analysis, please select a unique primary key ';
-                    $error .= '(primary key consists of sourcename, program and programversion).';
-                    form_set_error('sourcename', t($error));
-                }
-        
-                else{
-                    //---------------------------------------------------
-                    // the analysis does not exist in drupal - tell the user 
-                    // to sync from chado or create a new unique primary key
-                    //---------------------------------------------------
-                    $error = 'This analysis already exists in the chado database (analysis id ';
-                    $error .= $analysis_id.') but has not been synchronized ';
-                    $error .= 'with drupal. See the tripal admin pages to synchronize. ';
-                    $error .= ' For a new analysis, please select a unique primary key ';
-                    $error .= '(primary key consists of sourcename, program and programversion).';
-                    form_set_error('sourcename', t($error));
-                }
+
+
+            $values = array(
+               'program' => $node->program,
+               'programversion' => $node->programversion,
+               'sourcename' => $node->sourcename,
+            );
+            $analysis = tripal_core_chado_select('analysis', array('analysis_id'),$values);
+            if(sizeof($analysis) > 0){
+               form_set_error('program','Cannot add the analysis with this program,  
+                  program version and source name. An analysis with these values already exists.');
+               return;
             }
         }
     }

tripal_analysis_interpro/tripal_analysis_interpro.module

@@ -130,6 +130,13 @@ function chado_analysis_interpro_form ($node){
 	);
 	return $form;
 }
+/**
+*
+*/
+function chado_analysis_interpro_validate($node, &$form){
+   // use the analysis parent to validate the node
+   tripal_analysis_validate($node, $form); 
+}
 /**
  * 
  * 

tripal_analysis_kegg/tripal_analysis_kegg.module

@@ -247,6 +247,13 @@ function chado_analysis_kegg_form ($node){
 	);
    return $form;
 }
+/**
+*
+*/
+function chado_analysis_kegg_validate($node, &$form){
+   // use the analysis parent to validate the node
+   tripal_analysis_validate($node, $form); 
+}
 /*******************************************************************************
  *
  */

tripal_analysis_unigene/tripal_analysis_unigene.module

@@ -241,6 +241,13 @@ function chado_analysis_unigene_form ($node){
 /**
 *
 */
+function chado_analysis_unigene_validate($node, &$form){
+   // use the analysis parent to validate the node
+   tripal_analysis_validate($node, $form); 
+}
+/**
+*
+*/
 function chado_analysis_unigene_insert($node){
    // insert the analysis
    chado_analysis_insert($node);