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@@ -90,7 +90,7 @@ function chado_feature_form($node, &$form_state) {
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if (!$synonyms) {
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$options = array('return_array' => 1);
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$feature = tripal_core_expand_chado_vars($feature, 'table', 'feature_synonym', $options);
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- $feature_synonyms = $feature->feature_synonym;
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+ $feature_synonyms = (isset($feature->feature_synonym)) ? $feature->feature_synonym : array();
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foreach ($feature_synonyms as $index => $synonym) {
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$synonyms .= $synonym->synonym_id->name . "\n";
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}
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@@ -103,7 +103,7 @@ function chado_feature_form($node, &$form_state) {
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}
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// if we are re constructing the form from a failed validation or ajax callback
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// then use the $form_state['values'] values
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- if (array_key_exists('values', $form_state)) {
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+ if (array_key_exists('values', $form_state) and isset($form_state['values']['uniquename'])) {
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$uniquename = $form_state['values']['uniquename'];
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$fname = $form_state['values']['fname'];
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$feature_type = $form_state['values']['feature_type'];
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@@ -210,6 +210,28 @@ function chado_feature_form($node, &$form_state) {
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'#default_value' => $checked,
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'#description' => t('Check this box if this sequence should be retired'),
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);
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+
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+ // PROPERTIES FORM
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+ //---------------------------------------------
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+ $details = array(
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+ 'property_table' => 'featureprop', // the name of the prop table
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+ 'base_foreign_key' => 'feature_id', // the name of the key in your base chado table
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+ 'base_key_value' => $feature_id, // the value of feature_id for this record
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+ 'cv_name' => 'feature_property' // the cv.name of the cv governing featureprop.type_id
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+ );
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+ // Adds the form elements to your current form
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+ chado_node_properties_form($form, $form_state, $details);
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+
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+ // ADDITIONAL DBXREFS FORM
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+ //---------------------------------------------
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+ $details = array(
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+ 'linking_table' => 'feature_dbxref', // the name of the _dbxref table
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+ 'base_foreign_key' => 'feature_id', // the name of the key in your base chado table
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+ 'base_key_value' => $feature_id // the value of feature_id for this record
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+ );
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+ // Adds the form elements to your current form
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+ chado_node_additional_dbxrefs_form($form, $form_state, $details);
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+
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return $form;
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}
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@@ -409,6 +431,24 @@ function chado_feature_insert($node) {
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// add the genbank accession and synonyms
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chado_feature_add_synonyms($node->synonyms, $feature_id);
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+
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+ // * Properties Form *
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+ $details = array(
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+ 'property_table' => 'featureprop', // the name of the prop table
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+ 'base_table' => 'feature', // the name of your chado base table
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+ 'foreignkey_name' => 'feature_id', // the name of the key in your base table
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+ 'foreignkey_value' => $feature_id // the value of the feature_id key
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+ );
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+ chado_node_properties_form_update_properties($node, $details);
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+
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+ // * Additional DBxrefs Form *
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+ $details = array(
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+ 'linking_table' => 'feature_dbxref', // the name of your _dbxref table
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+ 'foreignkey_name' => 'feature_id', // the name of the key in your base table
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+ 'foreignkey_value' => $feature_id // the value of the feature_id key
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+ );
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+ chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
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+
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}
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else {
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$feature_id = $node->feature_id;
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@@ -475,6 +515,24 @@ function chado_feature_update($node) {
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// add the genbank synonyms
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chado_feature_add_synonyms($node->synonyms, $feature_id);
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+
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+ // * Properties Form *
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+ $details = array(
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+ 'property_table' => 'featureprop', // the name of the prop table
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+ 'base_table' => 'feature', // the name of your chado base table
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+ 'foreignkey_name' => 'feature_id', // the name of the key in your base table
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+ 'foreignkey_value' => $feature_id // the value of the feature_id key
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+ );
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+ chado_node_properties_form_update_properties($node, $details);
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+
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+ // * Additional DBxrefs Form *
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+ $details = array(
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+ 'linking_table' => 'feature_dbxref', // the name of your _dbxref table
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+ 'foreignkey_name' => 'feature_id', // the name of the key in your base table
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+ 'foreignkey_value' => $feature_id // the value of the feature_id key
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+ );
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+ chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
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+
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}
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else {
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drupal_set_message(t('Unable to update feature.'), 'warning');
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@@ -660,6 +718,7 @@ function tripal_feature_node_presave($node) {
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$ftype = tripal_core_chado_select('cv', array('name'), $values);
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$type = $ftype[0]->name;
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}
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+
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$values = array('organism_id' => $organism_id);
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$organism = tripal_core_chado_select('organism', array('genus', 'species'), $values);
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$node->title = "$name, $uname ($type) " . $organism[0]->genus . ' ' . $organism[0]->species;
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@@ -786,7 +845,7 @@ function tripal_feature_node_view($node, $view_mode, $langcode) {
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$node->content['tripal_feature_base'] = array(
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'#markup' => theme('tripal_feature_base', array('node' => $node)),
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'#tripal_toc_id' => 'base',
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- '#tripal_toc_title' => 'Details',
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+ '#tripal_toc_title' => 'Overview',
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'#weight' => -100,
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);
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$node->content['tripal_feature_featurepos'] = array(
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Stephen Ficklin