Issue #72: Updating API to include 2.1 improvements: 04fdc88

legacy/tripal_feature/includes/tripal_feature.seq_extract.inc

@@ -0,0 +1,506 @@
+<?php
+/**
+ * @file
+ * Interface for downloading feature sequences
+ */
+
+/**
+ * The page allowing users to download feature sequences
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_feature_seq_extract_download() {
+
+  if (!array_key_exists('tripal_feature_seq_extract', $_SESSION)) {
+    drupal_goto('find/sequences');
+  }
+
+  $genus      = $_SESSION['tripal_feature_seq_extract']['genus'];
+  $species    = $_SESSION['tripal_feature_seq_extract']['species'];
+  $analysis   = $_SESSION['tripal_feature_seq_extract']['analysis'];
+  $ftype      = $_SESSION['tripal_feature_seq_extract']['ftype'];
+  $fnames     = $_SESSION['tripal_feature_seq_extract']['fnames'];
+  $upstream   = $_SESSION['tripal_feature_seq_extract']['upstream'];
+  $downstream = $_SESSION['tripal_feature_seq_extract']['downstream'];
+  $format     = $_SESSION['tripal_feature_seq_extract']['format'];
+  $use_parent = $_SESSION['tripal_feature_seq_extract']['use_parent'];
+  $aggregate  = $_SESSION['tripal_feature_seq_extract']['aggregate'];
+  $agg_types  = $_SESSION['tripal_feature_seq_extract']['agg_types'];
+
+  // Split the sub features and remove any surrounding white space
+  $agg_types = preg_split("/[\n|,]/", $agg_types);
+  for ($i = 0; $i < count($agg_types); $i++) {
+    $agg_types[$i] = trim($agg_types[$i]);
+  }
+
+
+
+  header('Content-Type: text; utf-8');
+  if ($ftype == 'polypeptide') {
+    header('Content-Disposition: attachment; filename="sequences.fna"');
+  }
+  else {
+    header('Content-Disposition: attachment; filename="sequences.fnn"');
+  }
+
+  $seqs = tripal_get_bulk_feature_sequences(array(
+    'genus' => $genus,
+    'species' => $species,
+    'analysis_name' => $analysis,
+    'type' => $ftype,
+    'feature_name' => $fnames['items_array'],
+    'upstream' => $upstream,
+    'downstream' => $downstream,
+    'output_format' => $format,
+    'derive_from_parent' => $use_parent,
+    'aggregate' => $aggregate,
+    'sub_feature_types' => $agg_types,
+    'width' => 60
+  ));
+
+  if (count($seqs) == 0) {
+    print ">No sequences found that match the criteria.";
+  }
+
+  foreach ($seqs as $seq) {
+    print ">" . $seq['defline'] . "\r\n";
+    print $seq['residues'] . "\r\n";
+  }
+}
+
+
+
+/**
+ * Form to choose which features to extract sequence for
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_feature_seq_extract_form($form, &$form_state) {
+
+  $form['#true'] = TRUE;
+
+  // Intialize the defaults
+  $dgenus      = '';
+  $dspecies    = '';
+  $danalysis   = '';
+  $dftype      = '';
+  $dfnames     = '';
+  $dupstream   = '';
+  $ddownstream = '';
+  $duse_parent = '';
+  $daggregate  = '';
+  $dagg_types  = '';
+
+  if (array_key_exists('tripal_feature_seq_extract', $_SESSION)) {
+    $dgenus      = $_SESSION['tripal_feature_seq_extract']['genus'];
+    $dspecies    = $_SESSION['tripal_feature_seq_extract']['species'];
+    $danalysis   = $_SESSION['tripal_feature_seq_extract']['analysis'];
+    $dftype      = $_SESSION['tripal_feature_seq_extract']['ftype'];
+    $dfnames     = $_SESSION['tripal_feature_seq_extract']['fnames'];
+    $dupstream   = $_SESSION['tripal_feature_seq_extract']['upstream'];
+    $ddownstream = $_SESSION['tripal_feature_seq_extract']['downstream'];
+    $duse_parent = $_SESSION['tripal_feature_seq_extract']['use_parent'];
+    $daggregate  = $_SESSION['tripal_feature_seq_extract']['aggregate'];
+    $dagg_types  = $_SESSION['tripal_feature_seq_extract']['agg_types'];
+  }
+
+  // we want to allow the query string to provide values for the form
+  if (array_key_exists('fnames', $_GET) and $_GET['fnames']) {
+    $dfnames = $_GET['fnames'];
+  }
+  if (array_key_exists('genus', $_GET) and $_GET['genus']) {
+    $dgenus = $_GET['genus'];
+  }
+  if (array_key_exists('species', $_GET) and $_GET['species']) {
+    $dspecies = $_GET['species'];
+  }
+  if (array_key_exists('ftype', $_GET) and $_GET['ftype']) {
+    $dftype = $_GET['ftype'];
+  }
+  if (array_key_exists('analysis', $_GET) and $_GET['analysis']) {
+    $danalysis = $_GET['analysis'];
+  }
+  if (array_key_exists('upstream', $_GET) and $_GET['upstream']) {
+    $dupstream = $_GET['upstream'];
+  }
+  if (array_key_exists('downstream', $_GET) and $_GET['downstream']) {
+    $ddownstream = $_GET['downstream'];
+  }
+  if (array_key_exists('use_parent', $_GET) and $_GET['use_parent']) {
+    $duse_parent = $_GET['use_parent'];
+  }
+  if (array_key_exists('aggregate', $_GET) and $_GET['aggregate']) {
+    $daggregate = $_GET['aggregate'];
+  }
+  if (array_key_exists('agg_types', $_GET) and $_GET['agg_types']) {
+    $dagg_types = $_GET['agg_types'];
+  }
+
+  // get defaults from the form state
+  if (array_key_exists('values', $form_state)) {
+    $dgenus      = $form_state['values']['genus'];
+    $dspecies    = $form_state['values']['species'];
+    $danalysis   = $form_state['values']['analysis'];
+    $dftype      = $form_state['values']['ftype'];
+    $dfnames     = $form_state['values']['fnames'];
+    $dupstream   = $form_state['values']['upstream'];
+    $ddownstream = $form_state['values']['downstream'];
+    $dformat     = $form_state['values']['format'];
+    $duse_parent = $form_state['values']['use_parent'];
+    $daggregate  = $form_state['values']['aggregate'];
+    $dagg_types  = $form_state['values']['agg_types'];
+  }
+
+  // Because we're using Tripal's file_upload_combo form element we
+  // need to allow the form to upload files
+  $form['#attributes']['enctype'] = 'multipart/form-data';
+  $form['#method'] = 'POST';
+
+  $form['description'] = array(
+    '#markup' => t('Use this form to retrieve sequences in FASTA format.')
+  );
+
+  $sql = "
+    SELECT DISTINCT genus
+    FROM {organism}
+    ORDER BY genus
+  ";
+  $results = chado_query($sql);
+  $genus = array();
+  $genus[] = '';
+  while ($organism = $results->fetchObject()) {
+    $genus[$organism->genus] = $organism->genus;
+  }
+
+  $form['genus'] = array(
+    '#title'         => t('Genus'),
+    '#type'          => 'select',
+    '#options'       => $genus,
+    '#default_value' => $dgenus,
+    '#multiple'      => FALSE,
+    '#description'   => t('The organism\'s genus. If specified, features for all organism with this genus will be retrieved.'),
+    '#ajax' => array(
+      'callback'    => 'tripal_feature_seq_extract_form_ajax_callback',
+      'wrapper' => 'tripal-feature-seq-extract-form',
+      'event'   => 'change',
+      'method'  => 'replace',
+    ),
+  );
+
+  $species = array();
+  $species[] = '';
+  if ($dgenus) {
+    $sql = "
+      SELECT DISTINCT species
+      FROM {organism}
+      WHERE genus = :genus
+      ORDER BY species
+    ";
+    $results = chado_query($sql, array(':genus' => $dgenus));
+    while ($organism = $results->fetchObject()) {
+      $species[$organism->species] = $organism->species;
+    }
+  }
+  $form['species'] = array(
+    '#title'         => t('Species'),
+    '#type'          => 'select',
+    '#options'       => $species,
+    '#default_value' => $dspecies,
+    '#multiple'      => FALSE,
+    '#description'   => t('The organism\'s species name. If specified, features for all organisms with this species will be retrieved.  Please first select a genus'),
+    '#ajax' => array(
+      'callback'    => 'tripal_feature_seq_extract_form_ajax_callback',
+      'wrapper' => 'tripal-feature-seq-extract-form',
+      'event'   => 'change',
+      'method'  => 'replace',
+    ),
+  );
+
+  $analyses = array();
+  $analyses[] = '';
+  if ($dgenus) {
+    $sql = "
+      SELECT DISTINCT A.analysis_id, A.name
+      FROM {analysis_organism} AO
+        INNER JOIN {analysis} A ON A.analysis_id = AO.analysis_id
+        INNER JOIN {organism} O ON O.organism_id = AO.organism_id
+      WHERE O.genus = :genus
+    ";
+    $args = array();
+    $args[':genus'] = $dgenus;
+    if ($dspecies) {
+      $sql .= " AND O.species = :species ";
+      $args[':species'] = $dspecies;
+    }
+    $sql .=" ORDER BY A.name ";
+    $results = chado_query($sql, $args);
+    while ($analysis = $results->fetchObject()) {
+      $analyses[$analysis->name] = $analysis->name;
+    }
+  }
+  $form['analysis'] = array(
+    '#title'         => t('Analyses'),
+    '#type'          => 'select',
+    '#options'       => $analyses,
+    '#default_value' => $danalysis,
+    '#multiple'      => FALSE,
+    '#description'  => t('You can limit sequences by the analyses to which it was derived or was used. If specified, only features associated with the specific analysis will be retrieved.'),
+  );
+
+  $ftype = array();
+  $ftype[] = '';
+  if ($dgenus) {
+    $sql = "
+      SELECT DISTINCT OFC.cvterm_id, OFC.feature_type
+      FROM {organism_feature_count} OFC
+      WHERE OFC.genus = :genus
+    ";
+    $args = array();
+    $args['genus'] = $dgenus;
+    if ($dspecies) {
+      $sql .= " AND OFC.species = :species";
+      $args['species'] = $dspecies;
+    }
+    $sql .= " ORDER BY OFC.feature_type ";
+    $results = chado_query($sql, $args);
+
+    while ($type = $results->fetchObject()) {
+      $ftype[$type->feature_type] = $type->feature_type;
+    }
+  }
+  $form['ftype'] = array(
+    '#title'         => t('Feature Type'),
+    '#type'          => 'select',
+    '#options'       => $ftype,
+    '#multiple'      => FALSE,
+    '#default_value' => $dftype,
+    '#description'   => t('The type of feature to retrieve (e.g. mRNA). All
+        features that match this type will be retrieved.'),
+  );
+
+  $form['fnames'] = array(
+    '#title'         => t('Feature Name'),
+    '#type'          => 'file_upload_combo',
+    '#default_value' => $dfnames,
+    '#description'   => t('The names of the features to retrieve. Separate each
+         with a new line or comma. Leave blank to retrieve all features
+        matching other criteria.'),
+    '#rows'          => 8
+  );
+  $form['upstream'] = array(
+    '#title'         => t('Upstream Bases'),
+    '#type'          => 'textfield',
+    '#description'   => t('A numeric value specifying the number of upstream
+         bases to include. Only works if the feature is aligned to a larger
+         sequence.'),
+    '#default_value' => $dupstream,
+    '#size'          => 5,
+  );
+  $form['downstream'] = array(
+    '#title'         => t('Downstream Bases'),
+    '#type'          => 'textfield',
+    '#description'   => t('A numeric value specifying the number of downstream
+        bases to incldue.  Only works if the feature is aligned to a larger
+        sequence.'),
+    '#default_value' => $ddownstream,
+    '#size'          => 5,
+  );
+  $form['advanced'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Advanced',
+    '#collapsible' => TRUE,
+    '#collapsed' => TRUE
+  );
+
+  $form['advanced']['use_parent'] = array(
+    '#title'         => t('Use Parent'),
+    '#type'          => 'checkbox',
+    '#default_value' => $duse_parent,
+    '#description'   => t('Check this box to retrieve the sequence from the
+        parent in an alignment rather than the feature itself. This is useful
+        if the same feature is aligned to multiple parents and you would like
+        to retrieve the underlying sequence from each parent.'),
+  );
+  $form['advanced']['aggregate'] = array(
+    '#title'         => t('Aggregate'),
+    '#type'          => 'checkbox',
+    '#default_value' => $daggregate,
+    '#description'   => t('Check this box to aggregate sub features into a
+        single sequence.  This is useful, for example, for obtaining CDS
+        sequence from an mRNA. Rather than retrieve the mRNA sequence, the
+        sub features of the mRNA will be aggregated and that will be returned.')
+  );
+  $form['advanced']['agg_types'] = array(
+    '#title'         => t('Types to aggregate'),
+    '#type'          => 'textarea',
+    '#default_value' => $dagg_types,
+    '#description'   => t('Set this argument to the type of children to
+        aggregate.  This is useful in the case where a gene has exons, CDSs
+        and UTRs.  In this case, you may only want to aggregate CDSs and
+        exclude exons.  If you want to aggregate both CDSs and UTRs you
+        could specify both.  Please place each type on a new line.')
+  );
+  $form['retrieve_btn'] = array(
+    '#type' => 'submit',
+    '#name' => 'retrieve',
+    '#value' => 'Retrieve Sequences',
+  );
+
+  if (user_access('administer tripal')) {
+    $notice = tripal_set_message("Administrators, the " .
+        l('organism_feature_count', 'admin/tripal/schema/mviews') . " and " .
+        l('analysis_organism', 'admin/tripal/schema/mviews') . " materialized
+        views must be populated before using this form.  Those views should be re-populated
+        when new data is added.", TRIPAL_NOTICE, array('return_html' => TRUE));
+  }
+
+  $form['#prefix'] = '<div id="tripal-feature-seq-extract-form">';
+  $form['#suffix'] = $notice . '</div>';
+
+  return $form;
+}
+
+/**
+ * Theme the Form to choose which features to extract sequence for
+ *
+ * @ingroup tripal_feature
+ */
+function theme_tripal_feature_seq_extract_form(&$variables) {
+  $form = $variables['form'];
+
+  $headers = array();
+  $rows = array(
+    0 => array(
+      array('data' => drupal_render($form['description']), 'colspan' => 3),
+    ),
+    1 => array(
+      drupal_render($form['genus']),
+      drupal_render($form['species']) ,
+      drupal_render($form['ftype']),
+    ),
+    2 => array(
+      array('data' => drupal_render($form['analysis']), 'colspan' => 3),
+      //drupal_render($form['format']),
+    ),
+    3 => array(
+      array('data' =>  drupal_render($form['fnames']), 'colspan' => 2),
+      drupal_render($form['upstream']) .
+      drupal_render($form['downstream']) .
+      drupal_render($form['format']),
+    ),
+    4 => array(
+      array(
+        'data' =>  drupal_render($form['advanced']),
+        'colspan' => 3,
+      ),
+    ),
+    5 => array(
+      array(
+        'data' =>  drupal_render($form['retrieve_btn']) . drupal_render($form['reset_btn']),
+        'colspan' => 3,
+      ),
+    ),
+  );
+
+  $table_vars = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(
+      'id' => 'tripal-feature-seq-extract-form-table',
+      'border' => '0'
+    ),
+    'sticky' => FALSE,
+    'colgroups' => array(),
+    'empty' => '',
+  );
+
+  $form['rendered_form'] = array(
+    '#type' => 'item',
+    '#markup' => theme('table', $table_vars),
+  );
+  return drupal_render_children($form);
+}
+/**
+ * Ajax function which returns the form via ajax
+ */
+function tripal_feature_seq_extract_form_ajax_callback($form, &$form_state) {
+  return $form;
+}
+
+/**
+ * Validate the extract sequence form
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_feature_seq_extract_form_validate($form, &$form_state) {
+  $genus      = $form_state['values']['genus'];
+  $species    = $form_state['values']['species'];
+  $analysis   = $form_state['values']['analysis'];
+  $ftype      = $form_state['values']['ftype'];
+  $fnames     = $form_state['values']['fnames'];
+  $upstream   = $form_state['values']['upstream'];
+  $downstream = $form_state['values']['downstream'];
+  $use_parent = $form_state['values']['use_parent'];
+  $aggregate  = $form_state['values']['aggregate'];
+  $agg_types  = $form_state['values']['agg_types'];
+
+  if ($upstream and !preg_match('/^\d+$/', $upstream)) {
+    form_set_error('upstream', 'Please enter a positive numeric value for the upstream bases');
+  }
+   if ($downstream and !preg_match('/^\d+$/', $downstream)) {
+    form_set_error('downstream', 'Please enter a positive numeric value for the downstream bases');
+  }
+  if (!$genus and !$species and !$ftype and !$fnames) {
+    form_set_error('', 'Please provide a feature name, a feature type or a genus.');
+  }
+  if ($ftype == 'polypeptide' and $upstream) {
+    form_set_error('upstream', 'When the sequence type is protein the upstream value must be unset.');
+  }
+  if ($ftype == 'polypeptide' and $downstream) {
+    form_set_error('downstream', 'When the sequence type is protein the downstream value must be unset.');
+  }
+  if ($ftype == 'polypeptide' and $use_parent) {
+    form_set_error('use_parent', 'When the sequence type is protein the "Use Parent" option must not be set.');
+  }
+}
+
+/**
+ * Submit the extract sequence form
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_feature_seq_extract_form_submit($form, &$form_state) {
+  $genus      = $form_state['values']['genus'];
+  $species    = $form_state['values']['species'];
+  $analysis   = $form_state['values']['analysis'];
+  $ftype      = $form_state['values']['ftype'];
+  $fnames     = $form_state['values']['fnames'];
+  $upstream   = $form_state['values']['upstream'];
+  $downstream = $form_state['values']['downstream'];
+  $use_parent = $form_state['values']['use_parent'];
+  $aggregate  = $form_state['values']['aggregate'];
+  $agg_types  = $form_state['values']['agg_types'];
+
+  // we must use the parent sequence if the user has selected
+  // the upstream, downstream or to aggregate
+  if ($upstream or $downstream or $aggregate) {
+    $use_parent = 1;
+  }
+
+  if ($form_state['clicked_button']['#name'] == 'retrieve') {
+    $_SESSION['tripal_feature_seq_extract']['genus']      = $genus;
+    $_SESSION['tripal_feature_seq_extract']['species']    = $species;
+    $_SESSION['tripal_feature_seq_extract']['analysis']   = $analysis;
+    $_SESSION['tripal_feature_seq_extract']['ftype']      = $ftype;
+    $_SESSION['tripal_feature_seq_extract']['fnames']     = $fnames;
+    $_SESSION['tripal_feature_seq_extract']['upstream']   = $upstream;
+    $_SESSION['tripal_feature_seq_extract']['downstream'] = $downstream;
+    $_SESSION['tripal_feature_seq_extract']['format']     = 'fasta_txt';
+    $_SESSION['tripal_feature_seq_extract']['use_parent'] = $use_parent;
+    $_SESSION['tripal_feature_seq_extract']['aggregate']  = $aggregate;
+    $_SESSION['tripal_feature_seq_extract']['agg_types']  = $agg_types;
+    $_SESSION['tripal_feature_seq_extract']['download']   = 1;
+
+    drupal_goto('find/sequences/download');
+  }
+}

legacy/tripal_feature/tripal_feature.module

@@ -112,15 +112,19 @@ function tripal_feature_menu() {
   $items['find/sequences'] = array(
     'title' => 'Sequence Retrieval',
     'description' => 'Download a file of sequences',
-    'page callback' => 'tripal_feature_seq_extract_page',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_feature_seq_extract_form'),
     'access arguments' => array('access chado_feature content'),
+    'file' =>  'includes/tripal_feature.seq_extract.inc',
+    'file path' => drupal_get_path('module', 'tripal_feature'),
     'type' => MENU_CALLBACK,
   );
 
-  $items['find/sequences/ajax'] = array(
-    'title' => 'Sequence Retrieval',
-    'page callback' => 'tripal_feature_seq_extract_form_ahah_update',
+  $items['find/sequences/download'] = array(
+    'page callback' => 'tripal_feature_seq_extract_download',
     'access arguments' => array('access chado_feature content'),
+    'file' =>  'includes/tripal_feature.seq_extract.inc',
+    'file path' => drupal_get_path('module', 'tripal_feature'),
     'type' => MENU_CALLBACK,
   );
 
@@ -322,7 +326,7 @@ function tripal_feature_theme($existing, $type, $theme, $path) {
 
   // Themed Forms
   $items['tripal_feature_seq_extract_form'] = array(
-     'arguments' => array('form'),
+     'render element' => 'form',
   );
 
   // D3 Charts.
@@ -529,12 +533,6 @@ function tripal_feature_match_features_page($id) {
  * @ingroup tripal_feature
  */
 function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
-  if ($form_id == "tripal_feature_seq_extract_form") {
-    // updating the form through the ahah callback sets the action of
-    // the form to the ahah callback URL. We need to set it back
-    // to the normal form URL
-    $form['#action'] = url("find/sequences");
-  }
   // turn off preview button for insert/updates
   if ($form_id == "chado_feature_node_form") {
     $form['actions']['preview']['#access'] = FALSE;