Merge branch '7.x-1.x' of git.drupal.org:project/tripal_blast into 7.x-1.x

blast_ui.info

@@ -1,6 +1,6 @@
 name = BLAST UI
 description = Provides a user interface to allow your users to utilize NCBI's BLAST+ on your server
-version = 0.1-beta
-
+configure = admin/tripal/extension/tripal_blast/blast_ui
+project = tripal_blast
 package = Tripal Extensions
 core = 7.x

blast_ui.module

@@ -114,15 +114,27 @@ function blast_ui_menu() {
     'type' => MENU_CALLBACK,
   );
 
-  // BLAST Admin
-  $items['admin/tripal/extension/blast_ui'] = array(
-    'title' => 'BLAST User Interface',
+  // BLAST Admin  
+  $items['admin/tripal/extension/tripal_blast'] = array(
+    'title' => 'Tripal BLAST User Interface',
     'description' => 'Provides an interface allowing users to execute their own BLASTs.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('blast_ui_admin_form'),
     'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
   );
+  $items['admin/tripal/extension/tripal_blast/blast_ui'] = array(
+    'title' => 'BLAST UI',
+    'type' => MENU_DEFAULT_LOCAL_TASK,
+  );
+
+  $items['admin/tripal/extension/tripal_blast/help'] = array(
+    'title' => 'Help',
+    'page callback' => 'theme',
+    'page arguments' => array('blast_help'),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_LOCAL_TASK,
+  );
 
   return $items;
 }
@@ -154,6 +166,12 @@ function blast_ui_theme() {
     'path' => "$path/theme",
   );
 
+  // Module Help
+  $items['blast_help'] = array(
+    'template' => 'blast_help',
+    'path' => "$path/theme",
+  );
+
   // Menu Information Pages
   // These are only seen if the user has disabled the all-in-one
   // or by query type forms.
@@ -173,6 +191,15 @@ function blast_ui_theme() {
   return $items;
 }
 
+/**
+ * Implements hook_help().
+ */
+function blast_ui_help($path, $arg) {
+  if ($path == 'admin/help#blast_ui') {
+    return theme('blast_help');
+  }
+}
+
 /**
  * Facilitate presenting the result of the blast search
  *

includes/blast_ui.node.inc

@@ -168,13 +168,14 @@ function blastdb_form($node, &$form_state) {
 
   $db_options = tripal_get_db_select_options();
   $db_options[0] = '';
+  asort($db_options);
   $form['dbxref']['db_id'] = array(
     '#type' => 'select',
     '#title' => 'External Database',
     '#description' => 'The external database you would like to link-out to. '
       . 'Note that this list includes all Tripal Databases and if the database '
-      . 'you would like to link-out to is not included you can add it '
-      . '<a href="" target="_blank">Here</a>.',
+      . 'you would like to link-out to is not included you can add it through '
+      . l('Administration > Tripal > Chado Modules > Databases','admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank'))) . '.',
     '#options' => $db_options,
     '#default_value' => (isset($node->linkout->db_id->db_id)) ? $node->linkout->db_id->db_id : 0
   );

theme/blast_help.tpl.php

@@ -0,0 +1,29 @@
+<?php
+/**
+ * This template displays the help page for the BLAST UI
+ */
+?>
+
+<h3>Module Description</h3>
+<p>This module provides a basic interface to allow your users to utilize your server's NCBI BLAST+.</p>
+
+<h3>Setup Instructions</h3>
+<ol>
+<li>Install NCBI BLAST+ on your server (Tested with 2.2.26+). There is a <a href="https://launchpad.net/ubuntu/+source/ncbi-blast+">package available for Ubuntu</a> to ease installation. Optionally you can set the path to your BLAST executable <a href="<?php print url('admin/tripal/extension/tripal_blast/blast_ui');?>">in the settings</a>.</li>
+<li>Optionally, create Tripal External Database References to allow you to link the records in your BLAST database to further information. To do this simply go to <a href="<?php print url('admin/tripal/chado/tripal_db/add'); ?>" target="_blank">Tripal > Chado Modules > Databases > Add DB</a> and make sure to fill in the Database prefix which will be concatenated with the record IDs in your BLAST database to determine the link-out to additional information. Note that a regular expression can be used when creating the BLAST database to indicate what the ID is.</li>
+<li><a href="<?php print url('node/add/blastdb');?>">Create "Blast Database" nodes</a> for each dataset you want to make available for your users to BLAST against. BLAST databases should first be created using the command-line <code>makeblastdb</code> program with the <code>-parse_seqids</code> flag.</li>
+<li>It's recommended that you also install the <a href="http://drupal.org/project/tripal_daemon">Tripal Job Daemon</a> to manage BLAST jobs and ensure they are run soon after being submitted by the user. Without this additional module, administrators will have to execute the tripal jobs either manually or through use of cron jobs.</li>
+</ol>
+
+<h3>Highlighted Functionality</h3>
+<ul>
+  <li>Supports <a href="<?php print url('blast/nucleotide/nucleotide');?>">blastn</a>, 
+    <a href="<?php print url('blast/nucleotide/protein');?>">blastx</a>, 
+    <a href="<?php print url('blast/protein/protein');?>">blastp</a> and 
+    <a href="<?php print url('blast/protein/nucleotide');?>">tblastx</a> with separate forms depending upon the database/query type.</li>
+  <li>Simple interface allowing users to paste or upload a query sequence and then select from available databases. Additionally, a FASTA file can be uploaded for use as a database to BLAST against (this functionality can be disabled).</li>
+  <li>Tabular Results listing with alignment information and multiple download formats (HTML, TSV, XML) available.</li>
+  <li>Completely integrated with <a href="<?php print url('admin/tripal/tripal_jobs');?>">Tripal Jobs</a> providing administrators with a way to track BLAST jobs and ensuring long running BLASTs will not cause page time-outs</li>
+  <li>BLAST databases are made available to the module by <a href="<?php print url('node/add/blastdb');?>">creating Drupal Pages</a> describing them. This allows administrators to <a href="<?php print url('admin/structure/types/manage/blastdb/fields');?>">use the Drupal Field API to add any information they want to these pages</a>.</li>
+  <li>BLAST database records can be linked to an external source with more information (ie: NCBI) per BLAST database.</li>
+</ul>

theme/blast_report_alignment_row.tpl.php

@@ -25,21 +25,65 @@
       Positive= 
       <?php print $hsp['Hsp_positive']; ?>/<?php print $hsp['Hsp_align-len']; ?> (<?php print $hsp['Hsp_positive']/$hsp['Hsp_align-len']*100;?>%)
     </span>
+    <span class="coord-summary">
+      Query Matches <?php print $hsp['Hsp_query-from'] . ' to ' . $hsp['Hsp_query-to']; ?>
+      Hit Matches = <?php print $hsp['Hsp_hit-from'] . ' to ' . $hsp['Hsp_hit-to']; ?>
+    </span>
   </div>
   <div class="alignment">
     <div class="alignment-row">
-      <div class="query">
-        <span class="alignment-title">Query:</span>&nbsp;&nbsp;&nbsp;
-        <span class="alignment-residues"><?php print $hsp['Hsp_qseq']; ?></span>
-      </div>
-      <div class="matches">
-        &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-        <span class="alignment-residues"><?php print $hsp['Hsp_midline']; ?></span>
-      </div>
-      <div class="subject">
-        <span class="alignment-title">Subject:</span>&nbsp;
-        <span class="alignment-residues"><?php print $hsp['Hsp_hseq']; ?></span>
-      </div>
+      <?php 
+      // We want to display the alignment with a max 60 residues per line with line numbers indicated.
+      // First break up the strings.
+      $query = str_split($hsp['Hsp_qseq'], 60);
+      $matches = str_split($hsp['Hsp_midline'], 60);
+      $hit = str_split($hsp['Hsp_hseq'], 60);
+      // determine the max length of the coordinate string to use when padding.
+      $coord_length = strlen($hsp['Hsp_hit-from']) + 3;
+      $coord_length = (strlen($hsp['Hsp_query-to']) + 3 > $coord_length) ? strlen($hsp['Hsp_query-to']) + 3 : $coord_length;
+
+      // Now foreach chink determined above...
+      foreach (array_keys($query) as $k) {
+        // Determine the current coordinates.
+        $coord['qstart'] = $hsp['Hsp_query-from'] + ($k * 60);
+        $coord['qstart'] = ($k == 0) ? $coord['qstart'] : $coord['qstart'] + 1;
+
+        $coord['hstart'] = $hsp['Hsp_hit-from'] + ($k * 60);
+        $coord['hstart'] = ($k == 0) ? $coord['hstart'] : $coord['hstart'] + 1;
+
+        $coord['qstop'] = $hsp['Hsp_query-from'] + (($k + 1) * 60);
+        $coord['qstop'] = ($coord['qstop'] > $hsp['Hsp_query-to']) ? $hsp['Hsp_query-to'] : $coord['qstop'];
+
+	$coord['hstop'] = $hsp['Hsp_hit-from'] + (($k + 1) * 60);
+        $coord['hstop'] = ($coord['hstop'] > $hsp['Hsp_hit-to']) ? $hsp['Hsp_hit-to'] : $hsp['Hsp_hit-from'];
+
+        // Pad these coordinates to ensure columned display.
+        foreach ($coord as $ck => $val) {
+          $pad_type = (preg_match('/start/', $ck)) ? STR_PAD_LEFT : STR_PAD_RIGHT;
+          $coord[$ck] = str_pad($val, $coord_length, '#', $pad_type);
+          $coord[$ck] =	str_replace('#', '&nbsp', $coord[$ck]);
+        }
+      ?>
+        <div class="alignment-subrow">
+          <div class="query">
+            <span class="alignment-title">Query:</span>&nbsp;&nbsp;
+            <span class="alignment-start-coord"><?php print $coord['qstart']; ?></span>
+            <span class="alignment-residues"><?php print $query[$k]; ?></span>
+            <span class="alignment-stop-coord"><?php print $coord['qstop']; ?></span>
+          </div>
+          <div class="matches">
+            <?php print	str_repeat('&nbsp;', 8); ?>
+            <?php print str_repeat('&nbsp;', $coord_length); ?>
+            <span class="alignment-residues"><?php print str_replace(' ', '&nbsp', $matches[$k]); ?></span>
+          </div>
+          <div class="hit">
+            <span class="alignment-title">Hit:</span>&nbsp;&nbsp;&nbsp;&nbsp;
+            <span class="alignment-start-coord"><?php print $coord['hstart']; ?></span>
+            <span class="alignment-residues"><?php print $hit[$k]; ?></span>
+            <span class="alignment-stop-coord"><?php print $coord['hstop']; ?></span>
+          </div>
+        </div>
+      <?php } ?>
     </div>
   </div>
 

theme/css/blast_report.css

@@ -63,9 +63,9 @@
 }
 #blast_report div.alignment-row{
   padding: 10px 30px;
-  height: 60px;
-  border: 1px solid #DDDDDD;
   font-family: monospace;
-  overflow-x: scroll;
   white-space: nowrap;
+}
+#blast_report div.alignment-subrow{
+  padding-bottom: 15px;
 }

theme/node--blastdb.tpl.php

@@ -97,7 +97,6 @@
 
     <table>
       <tr><th>Human-Readable Name</th><td><?php print $node->db_name; ?></td></tr>
-      <tr><th>Database Path</th><td><?php print $node->db_path; ?></td></tr>
       <tr><th>Database Type</th><td><?php print $node->db_dbtype; ?></td></tr>
     </table>