Merging LegumeFederation Tripal Blast modifications

api/blast_ui.api.inc

@@ -107,12 +107,12 @@ function get_blast_database_options($type) {
  *   BLAST job (ie: 250)
  */
 function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $options, $job_id = NULL) {
-
- $output_file = file_directory_temp() .  DIRECTORY_SEPARATOR . $output_filestub . '.blast.asn';
- $output_file_xml = variable_get('file_public_path', conf_path() . '/files') . DIRECTORY_SEPARATOR . $output_filestub . '.blast.xml';
- $output_file_tsv = variable_get('file_public_path', conf_path() . '/files') . DIRECTORY_SEPARATOR . $output_filestub . '.blast.tsv';
- $output_file_html = variable_get('file_public_path', conf_path() . '/files') . DIRECTORY_SEPARATOR . $output_filestub . '.blast.html';
-
+  $output_file = file_directory_temp() .  DIRECTORY_SEPARATOR . $output_filestub . '.blast.asn';
+  $output_dir = variable_get('file_public_path', conf_path() . '/files') 
+              . DIRECTORY_SEPARATOR . 'tripal' . DIRECTORY_SEPARATOR . 'tripal_blast';
+  $output_file_xml = $output_dir . DIRECTORY_SEPARATOR . $output_filestub . '.blast.xml';
+  $output_file_tsv = $output_dir . DIRECTORY_SEPARATOR . $output_filestub . '.blast.tsv';
+  $output_file_html = $output_dir . DIRECTORY_SEPARATOR . $output_filestub . '.blast.html';
 
   print "\nExecuting $program\n\n";
   print "Query: $query\n";
@@ -123,11 +123,15 @@ function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $op
 
   // Allow administrators to use an absolute path for these commands.
   // Defaults to using $PATH.
-	$blast_path = variable_get('blast_path', '');
+	$blast_path    = variable_get('blast_path', '');
 	$blast_threads = variable_get('blast_threads', '');
 
-	$program = 	$blast_path . $program;
-	$blast_formatter_command = $blast_path .  'blast_formatter';
+	// Strip the extension off the BLAST target
+	$database = preg_replace("/(.*)\.[pn]\w\w/", '$1', $database);
+
+	// The executables:
+	$program       = $blast_path . $program;
+	$blast_formatter_command = $blast_path . 'blast_formatter';
 
   $blast_cmd = "$program -query '$query' -db '$database' -out '$output_file' -outfmt=11";
   if (!empty($options)) {
@@ -155,7 +159,9 @@ function run_BLAST_tripal_job($program, $query, $database, $output_filestub, $op
   print "\nGenerating additional download formats...\n";
 
   print "\tXML\n";
-  system("$blast_formatter_command -archive $output_file -outfmt 5 -out $output_file_xml");
+  $format_cmd = "$blast_formatter_command -archive $output_file -outfmt 5 -out $output_file_xml";
+  print "\nExecuting $format_cmd\n\n";
+  system($format_cmd);
   if(!file_exists($output_file_xml)) {
     tripal_report_error(
       'blast_ui',
@@ -274,3 +280,39 @@ function get_blastdb_linkout_regex($node, $options = array()) {
 
   return $regex;
 }
+
+
+function get_recent_jobs() {
+  $html = '';
+
+  $sid = session_id();  
+  $jobs = $_SESSION['all_jobs'][$sid];
+
+  // Remove jobs older than 48 hours
+  foreach ($jobs as $job_id => $job) {
+    if ($diff = abs(time() - strtotime($job['date'])) > 172800) {
+      unset($jobs[$job_id]);
+    }
+  }
+  $_SESSION['all_jobs'][$sid] = $jobs;
+
+  if (count($jobs) > 0) {
+    $html = "
+    <h3><strong> Recent Jobs </h3>
+    <dl>";
+
+    foreach (array_reverse($jobs) as $job) {
+      $q_def = !isset($job['query_defs'][0]) ? "Query" : $job['query_defs'][0];
+      $html .= "
+        <dd>
+          <a href='" . "../../" . $job['job_output_url'] ."'>
+            $q_def X " . $job['target'] . ' (' . $job['program'] . ') - ' . $job['date'] . "
+          </a>
+        </dd>";
+    }
+     $html .= "
+    </dl>";
+  }
+
+  return $html;
+}

blast_ui.install

@@ -69,17 +69,18 @@ function blast_ui_schema(){
         'default' => 'link'
       ),
     ),
+
     'indexes' => array(
       'name' => array('name'),
     ),
+
     'primary key' => array('nid'),
     'unique keys' => array(
        'nid' => array('nid'),
     ),
   );
 
   return $schema;
-
 }
 
 /**

blast_ui.module

@@ -9,13 +9,14 @@
 require_once 'includes/blast_ui.form_common.inc';
 require_once 'includes/blast_ui.form_advanced_options.inc';
 // NOTE: The forms themeselves are included using hook_menu to ensure they
-// are only inlcuded when needed.
+// are only included when needed.
 
 // BLAST DB Node functionality
 require_once 'includes/blast_ui.node.inc';
 
 // BLAST Link-out functionality.
 require_once 'includes/blast_ui.linkouts.inc';
+include_once('includes/blast_ui.custom.inc');
 
 // Functions specific to themeing (ie: preprocess)
 require_once 'theme/blast_ui.theme.inc';
@@ -219,7 +220,7 @@ function show_blast_output($job_id) {
   // BLAST is in the queue, running or complete in order to determine what to show the user
   //decode the job_id
   $job_id = base64_decode($job_id);
-	$job = tripal_get_job($job_id);
+  $job = tripal_get_job($job_id);
 
   // 1) Job is in the Queue
   if ($job->start_time === NULL AND $job->end_time == NULL) {
@@ -252,50 +253,15 @@ function show_blast_output($job_id) {
  *
  */
 function ajax_blast_ui_example_sequence_callback($form, $form_state) {
-
-  // First, set a default example sequence in case administrators have not yet
-  // bothered to set their own.
   $sequence_type = $form_state['values']['query_type'];
   if ($sequence_type == 'nucleotide') {
-    $default_example_sequence = '>partial lipoxygenase Glyma15g03040
-TTTCGTATGA GATTAAAATG TGTGAAATTT TGTTTGATAG GACATGGGAA
-AGGAAAAGTT GGAAAGGCTA CAAATTTAAG AGGACAAGTG TCGTTACCAA
-CCTTGGGAGC TGGCGAAGAT GCATACGATG TTCATTTTGA ATGGGACAGT
-GACTTCGGAA TTCCCGGTGC ATTTTACATT AAGAACTTCA TGCAAGTTGA
-GTTCTATCTC AAGTCTCTAA CTCTCGAAGA CATTCCAAAC CACGGAACCA
-TTCACTTCGT ATGCAACTCC TGGGTTTACA ACTCAAAATC CTACCATTCT
-GATCGCATTT TCTTTGCCAA CAATGTAAGC TACTTAAATA CTGTTATACA
-TTGTCTAACA TCTTGTTAGA GTCTTGCATG ATGTGTACCG TTTATTGTTG
-TTGTTGAACT TTACCACATG GCATGGATGC AAAAGTTGTT ATACACATAA
-ATTATAATGC AGACATATCT TCCAAGCGAG ACACCGGCTC CACTTGTCAA
-GTACAGAGAA GAAGAATTGA AGAATGTAAG AGGGGATGGA ACTGGTGAGC
-GCAAGGAATG GGATAGGATC TATGATTATG ATGTCTACAA TGACTTGGGC
-GATCCAGATA AGGGTGAAAA GTATGCACGC CCCGTTCTTG GAGGTTCTGC
-CTTACCTTAC CCTCGCAGAG GAAGAACCGG AAGAGGAAAA ACTAGAAAAG
-GTTTCTCACT AGTCACTAAT TTATTACTTT TTAATGTTTG TTTTTAGGCA
-TCTTTTCTGA TGAAATGTAT ACTTTTGATG TTTTTTTGTT TTAGCATAAC
-TGAATTAGTA AAGTGTGTTG TGTTCCTTAG AAGTTAGAAA AGTACTAAGT
-ATAAGGTCTT TGAGTTGTCG TCTTTATCTT AACAGATCCC AACAGTGAGA
-AGCCCAGTGA TTTTGTTTAC CTTCCGAGAG ATGAAGCATT TGGTCACTTG
-AAGTCATCAG ATTTTCTCGT TTATGGAATC AAATCAGTGG CTCAAGACGT
-CTTGCCCGTG TTGACTGATG CGTTTGATGG CAATCTTTTG AGCCTTGAGT
-TTGATAACTT TGCTGAAGTG CGCAAACTCT ATGAAGGTGG AGTTACACTA
-CCTACAAACT TTCTTAGCAA GATCGCCCCT ATACCAGTGG TCAAGGAAAT
-TTTTCGAACT GATGGCGAAC AGTTCCTCAA GTATCCACCA CCTAAAGTGA
-TGCAGGGTAT GCTACATATT TTGAATATGT AGAATATTAT CAATATACTC
-CTGTTTTTAT TCAACATATT TAATCACATG GATGAATTTT TGAACTGTTA';
+    $default_example_sequence = variable_get('blast_ui_nucleotide_example_sequence', 'sample');
   }
   elseif ($sequence_type == 'protein') {
-    $default_example_sequence = '>gi|166477|gb|AAA96434.1| resveratrol synthase [Arachis hypogaea]
-MVSVSGIRKVQRAEGPATVLAIGTANPPNCIDQSTYADYYFRVTNSEHMTDLKKKFQRICERTQIKNRHM
-YLTEEILKENPNMCAYKAPSLDAREDMMIREVPRVGKEAATKAIKEWGQPMSKITHLIFCTTSGVALPGV
-DYELIVLLGLDPCVKRYMMYHQGCFAGGTVLRLAKDLAENNKDARVLIVCSENTAVTFRGPSETDMDSLV
-GQALFADGAAAIIIGSDPVPEVEKPIFELVSTDQKLVPGSHGAIGGLLREVGLTFYLNKSVPDIISQNIN
-DALNKAFDPLGISDYNSIFWIAHPGGRAILDQVEQKVNLKPEKMKATRDVLSNYGNMSSACVFFIMDLMR
-KRSLEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI';
+    $default_example_sequence = variable_get('blast_ui_protein_example_sequence', 'sample');
   }
   else {
-    $default_example_sequence = '';
+    $default_example_sequence = 'unknown query type';
   }
 
   // If the Show Example checkbox is true then put the example in the textfield
@@ -313,5 +279,24 @@ KRSLEEGLKTTGEGLDWGVLFGFGPGLTIETVVLRSVAI';
   }
 
   return $form['query']['FASTA'];
+}
+
 
-}
+/**
+ * Enable web services API
+ *
+ * @param $owner
+ *   
+ * @param $api
+ *
+ * @return $result
+ *  
+ */
+function blast_ui_ctools_plugin_api($owner, $api) {
+  if ($owner == 'services' && $api == 'services') {
+    return array(
+      'version' => 3,
+      'file' => 'includes/blast_ui.services.inc'
+    );
+  }
+}

includes/blast_ui.admin.inc

@@ -136,7 +136,7 @@ function blast_ui_admin_form_validate($form, &$form_state) {
  *
  */
 function blast_ui_admin_form_submit($form, $form_state) {
-
+  variable_set('blast_path', $form_state['values']['blast_path']);
   variable_set('blast_ui_allow_target_upload', $form_state['values']['target_upload']);
 	variable_set('blast_threads', $form_state['values']['blast_threads']);
   variable_set('blast_ui_nucleotide_example_sequence', $form_state['values']['nucleotide_example']);

includes/blast_ui.custom.inc

@@ -0,0 +1,129 @@
+<?php
+/*
+ * customized for PeanutBase
+ *
+ */
+
+function tripal_custom_generate_linkout($url_prefix, $hit, $info, $options = array()) {
+// uncomment to see contents of hit object
+//echo "hit:<pre>";var_dump($hit);echo "</pre>";
+// uncomment to see contents of info object
+//echo "info:<pre>";var_dump($info);echo "</pre>";
+
+  $url = false;
+  $hit_name = $hit->{'Hit_def'};
+//echo "hit name: $hit_name ... ";
+
+  if ($info['Target'] == 'All genomes') {
+    // default regex
+    $regex = "/^\w+\.(\S+).*/";
+
+    if (preg_match('/^aradu/', $hit_name) == 1) {
+      $blastdb_name = 'PeanutBase_aradu_gbrowse';
+    }
+    else if (preg_match('/^araip/', $hit_name) == 1) {
+      $blastdb_name = 'PeanutBase_araip_gbrowse';
+    }
+    else if (preg_match('/^cajca/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_cajca_gbrowse';
+    }
+    else if (preg_match('/^cicar/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_cicar_gbrowse';
+    }
+    else if (preg_match('/^glyma/', $hit_name) == 1) {
+      $blastdb_name = 'SoyBase_glyma_gbrowse';
+    }
+    else if (preg_match('/^lotja/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_lotja_gbrowse';
+    }
+    else if (preg_match('/^medtr/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_medtr_gbrowse';
+    }
+    else if (preg_match('/^phavu/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_phavu_gbrowse';
+    }
+    else if (preg_match('/^vigra/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_vigra_gbrowse';
+    }
+    else {
+      // Don't know what to do with this hit
+      drupal_set_message("Don't know how to create GBrowse linkout for $hit_name", 'error');
+    }  
+
+    $hit_name = preg_replace($regex, '$1', $hit_name);
+    $hit->{'linkout_id'} = $hit_name;
+    if ($blastdb_info = tripal_custom_getBLASTdbinfo($blastdb_name)) {
+//echo "generate gbrowse link with " . $blastdb_info['urlprefix'] . " $hit<br>";
+      $url = tripal_blast_generate_linkout_gbrowse($blastdb_info['urlprefix'], $hit, $info, $options);
+    }
+  }//handle All genomes BLAST target
+
+  else {
+    // default regex:
+    $regex = "/^\w+\.(\S+)/";
+
+    if (preg_match('/^aradu/', $hit_name) == 1) {
+      $blastdb_name = 'PeanutBase_aradu_gene';
+    }
+    else if (preg_match('/^araip/', $hit_name) == 1) {
+      $blastdb_name = 'PeanutBase_araip_gene';
+    }
+    else if (preg_match('/^cajca/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_cajca_gene';
+    }
+    else if (preg_match('/^cicar/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_cicar_gene';
+    }
+    else if (preg_match('/^glyma/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_glyma_gene';
+      if (preg_match("/^\w+\.(\S+)\.p/", $hit_name)) {
+        //glyma protein
+        $regex = "/^\w+\.(\S+)\.p/";
+      }
+    }
+    else if (preg_match('/^lotja/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_lotja_gene';
+    }
+    else if (preg_match('/^medtr/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_medtr_gene';
+    }
+    else if (preg_match('/^phavu/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_phavu_gene';
+    }
+    else if (preg_match('/^vigra/', $hit_name) == 1) {
+      $blastdb_name = 'LegumeInfo_vigra_gene';
+    }
+    else {
+      // Don't know what to do with this hit
+      drupal_set_message("Don't know how to create linkout for $hit_name", 'error');
+    }  
+
+    $hit_name = preg_match($regex, $hit_name, $matches);
+//echo "<br>Using $regex, found matches:<pre>" . var_dump($matches);echo "</pre>";
+//echo "<br>Use [" . $matches[1] . "]<br>";
+    $hit->{'linkout_id'} = $matches[1];
+//echo "look for gene link for $blastdb_name with " . $hit->{'linkout_id'} . "<br>";
+    if ($blastdb_info = tripal_custom_getBLASTdbinfo($blastdb_name)) {
+//echo "generate gbrowse link with " . $blastdb_info['urlprefix'] . " $hit<br>";
+      $url = tripal_blast_generate_linkout_link($blastdb_info['urlprefix'], $hit, $info, $options);
+    }
+  }
+  return $url;
+}
+
+
+function tripal_custom_getBLASTdbinfo($blastdb_name) {
+  $sql = "
+    SELECT urlprefix 
+    FROM {db} WHERE name='$blastdb_name'";
+//echo "$sql<br>";
+  if ($res = chado_query($sql)) {
+    if ($row=$res->fetchObject()) {
+      return array(
+        'urlprefix' => $row->urlprefix, 
+      );
+    }
+  }
+
+  return false;
+}//tripal_custom_getBLASTdbinfo