added missing file, fixed mistake with two form_alter hooks in pub module

tripal_feature/includes/gff_loader.inc

@@ -1024,7 +1024,7 @@ function tripal_feature_load_gff3_parents($feature, $cvterm, $parents, $organism
     $parentcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
       array(':cvname' => 'sequence', ':name' => $parent_type, ':synonym' => $parent_type))->fetchObject();
     $relcvterm = chado_query("EXECUTE sel_cvterm_cvname_cvtname_synonym (:cvname, :name, :synonym)", 
-      array(':cvname' => 'relationship', ':name' => $rel_type, ':synonymn' => $rel_type))->fetchObject();
+      array(':cvname' => 'relationship', ':name' => $rel_type, ':synonym' => $rel_type))->fetchObject();
     $values = array(
         'organism_id' => $organism_id,
         'uniquename' => $parent,

tripal_feature/includes/tripal_feature.form.inc

@@ -0,0 +1,270 @@
+<?php 
+
+/**
+ * Implementation of hook_form
+ * 
+ * @param  $node
+ * @param  $param
+ * 
+ * @return 
+ *   Drupal form array
+ *   
+ * @ingroup tripal_feature
+ */
+function chado_feature_form($node, &$form_state) {
+
+  $form = array();
+
+  // Default values can come in the following ways:
+  //
+  // 1) as elements of the $node object.  This occurs when editing an existing feature
+  // 2) in the $form_state['values'] array which occurs on a failed validation or
+  //    ajax callbacks from non submit form elements
+  // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
+  //    form elements and the form is being rebuilt
+  //
+  // set form field defaults
+  $feature      = null;
+  $feature_id   = null;
+  $uniquename   = '';
+  $fname        = '';
+  $feature_type = '';
+  $organism_id  = '';  
+  $residues     = '';
+  $is_obsolete  = '';
+  $analyses     = '';
+  $references   = '';
+  $synonyms     = '';
+  
+  // if we are editing an existing node then the feature is already part of the node
+  if (property_exists($node, 'feature')) {
+    $feature = $node->feature;
+    $feature = tripal_core_expand_chado_vars($feature, 'field', 'feature.residues');
+    $feature_id   = $feature->feature_id;
+    $uniquename   = $feature->uniquename;
+    $fname        = $feature->name;
+    $feature_type = $feature->type_id->name;
+    $organism_id  = $feature->organism_id->organism_id;
+    $residues     = $feature->residues;
+    $is_obsolete  = $feature->is_obsolete;
+    
+    // get the synonyms from a previous post
+    $synonyms = '';
+    if(property_exists($node, 'synonyms')) {
+      $synonyms = $node->synonyms;
+    }
+    
+    // get synonyms from the database if we don't already have them
+    if (!$synonyms) {
+      $options = array('return_array' => 1);
+      $feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_synonym', $options);
+      $feature_synonyms = $feature->feature_synonym;      
+      foreach ($feature_synonyms as $index => $synonym) {
+        $synonyms .= $synonym->synonym_id->name . "\n";
+      }
+    }
+  }
+  // if we are re constructing the form from a failed validation or ajax callback
+  // then use the $form_state['values'] values
+  if (array_key_exists('values', $form_state)) {
+    $uniquename   = $form_state['values']['uniquename'];
+    $fname        = $form_state['values']['fname'];
+    $feature_type = $form_state['values']['feature_type'];
+    $organism_id  = $form_state['values']['organism_id'];
+    $residues     = $form_state['values']['residues'];
+    $is_obsolete  = $form_state['values']['is_obsolete'];
+    $synonyms     = $form_state['values']['synonyms'];
+  }
+  // if we are re building the form from after submission (from ajax call) then
+  // the values are in the $form_state['input'] array
+  if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
+    $uniquename   = $form_state['input']['uniquename'];
+    $fname        = $form_state['input']['fname'];
+    $feature_type = $form_state['input']['feature_type'];
+    $organism_id  = $form_state['input']['organism_id'];
+    $residues     = $form_state['input']['residues'];
+    $is_obsolete  = array_key_exists('is_obsolete', $form_state['input']) ? $form_state['input']['is_obsolete'] : FALSE;
+    $synonyms     = $form_state['input']['synonyms'];
+  }
+
+  // We need to pass above variables for preview to show
+  $form['feature'] = array(
+    '#type' => 'value',
+    '#value' => $feature
+  );
+
+  // keep track of the feature id if we have one.  If we do have one then
+  // this would indicate an update as opposed to an insert.
+  $form['feature_id'] = array(
+    '#type' => 'value',
+    '#value' => $feature_id,
+  );
+  $form['fname']= array(
+    '#type' => 'textfield',
+    '#title' => t('Feature Name'),
+    '#required' => TRUE,
+    '#default_value' => $fname,
+    '#description' => t('Enter the name used by humans to refer to this feature.'),
+    '#maxlength' => 255
+  );
+  $form['uniquename']= array(
+    '#type' => 'textfield',
+    '#title' => t('Unique Feature Name'),
+    '#required' => TRUE,
+    '#default_value' => $uniquename,
+    '#description' => t('Enter a unique name for this feature.  This name must be unique for the organism and feature type.'),
+    '#maxlength' => 255
+  );
+  // get the sequence ontology CV ID
+  $values = array('name' => 'sequence');
+  $cv = tripal_core_chado_select('cv', array('cv_id'), $values);
+  $cv_id = $cv[0]->cv_id;
+
+  $form['feature_type'] = array(
+   '#title'       => t('Feature Type'),
+   '#type'        => 'textfield',
+   '#description' => t("Choose the feature type."),
+   '#required'    => TRUE,
+   '#default_value' => $feature_type,
+   '#autocomplete_path' => "admin/tripal/tripal_cv/cvterm/auto_name/$cv_id",
+  );
+
+  // get the list of organisms
+  $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
+  $org_rset = chado_query($sql);
+  $organisms = array();
+  $organisms[''] = '';
+  while ($organism = $org_rset->fetchObject()) {
+    $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+  }
+  $form['organism_id'] = array(
+    '#title'       => t('Organism'),
+    '#type'        => t('select'),
+    '#description' => t("Choose the organism with which this feature is associated"),
+    '#required'    => TRUE,
+    '#default_value' => $organism_id,
+    '#options'     => $organisms,
+  );
+
+  // Get synonyms
+  $syn_text = '';
+  if ($synonyms) {
+    if (is_array($synonyms)) {
+      foreach ($synonyms as $synonym) {
+        $syn_text .= "$synonym->name\n";
+      }
+    }
+    else {
+      $syn_text = $synonyms;
+    }
+  }
+  $form['synonyms']= array(
+    '#type' => 'textarea',
+    '#title' => t('Synonyms'),
+    '#required' => FALSE,
+    '#default_value' => $syn_text,
+    '#description' => t('Enter alternate names (synonmys) for this feature to help in searching and identification. You may enter as many alternate names as needed each on different lines.'),
+  );
+
+  $form['residues']= array(
+    '#type' => 'textarea',
+    '#title' => t('Residues'),
+    '#required' => FALSE,
+    '#default_value' => $residues,
+    '#description' => t('Enter the nucelotide sequences for this feature'),
+  );
+
+  $checked = '';
+  if ($is_obsolete == 't') {
+    $checked = '1';
+  }
+  $form['is_obsolete']= array(
+    '#type' => 'checkbox',
+    '#title' => t('Is Obsolete'),
+    '#required' => FALSE,
+    '#default_value' => $checked,
+    '#description' => t('Check this box if this sequence should be retired'),
+  );
+  return $form;
+}
+
+/**
+ * Implementation of hook_validate
+ * 
+ * This validation is being used for three activities:
+ *   CASE A: Update a node that exists in both drupal and chado
+ *   CASE B: Synchronizing a node from chado to drupal
+ *   CASE C: Inserting a new node that exists in niether drupal nor chado
+ *
+ * @param $node
+ *  
+ *
+ * @ingroup tripal_feature
+ */
+function chado_feature_validate($node, &$form_state) {
+  // remove surrounding white-space on submitted values
+  $node->uniquename   = trim($node->uniquename);
+  $node->fname        = trim($node->fname);
+  $node->feature_type = trim($node->feature_type); 
+  $node->residues     = trim($node->residues);
+  
+  $result = 0;
+
+  // make sure the feature type is a real sequence ontology term
+  $type = tripal_cv_get_cvterm_by_name($node->feature_type, NULL, 'sequence');
+  if (!$type) {
+    form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
+  }
+
+  // CASE A: if the nid exists then this is an update
+  if (property_exists($node, 'nid')) {
+    
+    // if this is an update, we want to make sure that a different feature for
+    // the organism doesn't already have this uniquename. We don't want to give
+    // two sequences the same uniquename
+    if (property_exists($node, 'feature_id') and $node->feature_id != 0) {
+      $sql = "
+        SELECT *
+        FROM {feature} F
+          INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
+        WHERE
+          F.uniquename     = :uname AND
+          F.organism_id    = :organism_id AND
+          CVT.name         = :cvtname AND
+          NOT f.feature_id = :feature_id
+      ";
+      $args = array(':uname' => $node->uniquename, ':organism_id' => $node->organism_id,
+        ':cvtname' => $node->feature_type, ':feature_id' => $node->feature_id);
+      $result = chado_query($sql, $args)->fetchObject();
+      if ($result) {
+        form_set_error('uniquename', t("Feature update cannot proceed. The feature name '$node->uniquename' is not unique for this organism. Please provide a unique name for this feature."));
+      }
+    }
+  }
+  else {
+    // To differentiate if we are syncing or creating a new feature altogther, see if a feature_id already exists
+    if (property_exists($node, 'feature_id') and $node->feature_id != 0) {
+      // CASE B: Synchronizing a node from chado to drupal
+      // we don't need to do anything.
+    }
+    else {
+      // CASE C: We are validating a form for inserting a new node
+      // if this is an insert then we just need to make sure this name doesn't
+      // already exist for this organism if it does then we need to throw an error
+      $sql = "
+        SELECT *
+        FROM {feature} F
+          INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
+        WHERE
+          F.uniquename  = :name AND
+          F.organism_id = :organism_id AND
+          CVT.name      = :cvtname
+      ";
+      $args = array(':name' => $node->uniquename, ':organism_id' => $node->organism_id, ':cvtname' => $node->feature_type);
+      $result = chado_query($sql, $args)->fetchObject();
+      if ($result) {
+        form_set_error('uniquename', t("Feature insert cannot proceed. The feature name '$node->uniquename' already exists for this organism. Please provide a unique name for this feature."));
+      }
+    }
+  }
+}

tripal_pub/tripal_pub.module

@@ -831,29 +831,6 @@ function chado_pub_delete(&$node) {
   chado_query("DELETE FROM {pub} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
 }
 
-/*
- *
- */
-
-function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
-  if ($form_id == "tripal_pub_importer_setup_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
-    if ($form_state['values']['action'] == 'edit') {
-      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
-    }
-    if ($form_state['values']['action'] == 'new') {
-      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
-    }
-  }
-  if ($form_id == "tripal_pub_search_form") {
-    $form['#action'] = url("find/publications");
-  }
-  if ($form_id == "chado_pub_node_form") {
-  }
-}
-
 /**
  *
  *
@@ -1012,4 +989,20 @@ function tripal_pub_form_alter(&$form, &$form_state, $form_id) {
   if ($form_id == "chado_pub_node_form") {
     $form['actions']['preview']['#access'] = FALSE;
   }
+  if ($form_id == "tripal_pub_importer_setup_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
+    if ($form_state['values']['action'] == 'edit') {
+      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/edit/" . $form_state['values']['pub_import_id']);
+    }
+    if ($form_state['values']['action'] == 'new') {
+      $form['#action'] = url("admin/tripal/chado/tripal_pub/import/new");
+    }
+  }
+  if ($form_id == "tripal_pub_search_form") {
+    $form['#action'] = url("find/publications");
+  }
+  if ($form_id == "chado_pub_node_form") {
+  }
 }