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@@ -131,7 +131,7 @@ function tripal_feature_permissions() {
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* @param $node
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* The node on which the operation is to be performed, or, if it does not yet exist, the
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* type of node to be created
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- *
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+ *
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* @param $op
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* The operation to be performed
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*
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@@ -141,9 +141,9 @@ function tripal_feature_permissions() {
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* @return
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* If the permission for the specified operation is not set then return FALSE. If the
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* permission is set then return NULL as this allows other modules to disable
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- * access. The only exception is when the $op == 'create'. We will always
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+ * access. The only exception is when the $op == 'create'. We will always
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* return TRUE if the permission is set.
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- *
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+ *
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* @ingroup tripal_feature
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*/
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function chado_feature_node_access($node, $op, $account) {
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@@ -189,14 +189,14 @@ function tripal_feature_menu() {
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'access arguments' => array('access chado_feature content'),
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'type' => MENU_CALLBACK,
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);
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-
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+
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$items['find/sequences/ajax'] = array(
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'title' => 'Sequence Retrieval',
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'page callback' => 'tripal_feature_seq_extract_form_ahah_update',
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'access arguments' => array('access chado_feature content'),
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'type' => MENU_CALLBACK,
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);
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-
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+
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// the administative settings menu
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$items['admin/tripal/tripal_feature'] = array(
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'title' => 'Features',
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@@ -339,7 +339,7 @@ function tripal_feature_theme() {
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'arguments' => array(NULL),
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'path' => drupal_get_path('module', 'tripal_feature') . '/theme'
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),
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-
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+
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// themed forms
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'tripal_feature_seq_extract_form' => array(
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'arguments' => array('form'),
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@@ -354,37 +354,37 @@ function tripal_feature_theme() {
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function tripal_feature_block_info() {
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$blocks['references']['info'] = t('Tripal Feature References');
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- $blocks['references']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['references']['cache'] = DRUPAL_NO_CACHE;
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$blocks['base']['info'] = t('Tripal Feature Details');
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- $blocks['base']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['base']['cache'] = DRUPAL_NO_CACHE;
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$blocks['sequence']['info'] = t('Tripal Feature Sequence');
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- $blocks['sequence']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['sequence']['cache'] = DRUPAL_NO_CACHE;
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$blocks['featureloc_sequences']['info'] = t('Tripal Feature Annotated Sequence');
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- $blocks['featureloc_sequences']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['featureloc_sequences']['cache'] = DRUPAL_NO_CACHE;
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$blocks['synonyms']['info'] = t('Tripal Feature Synonyms');
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- $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['synonyms']['cache'] = DRUPAL_NO_CACHE;
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$blocks['properties']['info'] = t('Tripal Feature Properties');
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- $blocks['properties']['cache'] = BLOCK_NO_CACHE;;
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+ $blocks['properties']['cache'] = DRUPAL_NO_CACHE;;
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$blocks['terms']['info'] = t('Tripal Annotated Terms');
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- $blocks['terms']['cache'] = BLOCK_NO_CACHE;;
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+ $blocks['terms']['cache'] = DRUPAL_NO_CACHE;;
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$blocks['alignments']['info'] = t('Tripal Feature Alignments');
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- $blocks['alignments']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['alignments']['cache'] = DRUPAL_NO_CACHE;
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$blocks['relationships']['info'] = t('Tripal Feature Relationships');
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- $blocks['relationships']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['relationships']['cache'] = DRUPAL_NO_CACHE;
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$blocks['org_feature_counts']['info'] = t('Tripal Organism Feature Counts');
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- $blocks['org_feature_counts']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['org_feature_counts']['cache'] = DRUPAL_NO_CACHE;
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$blocks['org_feature_browser']['info'] = t('Tripal Organism Feature Browser');
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- $blocks['org_feature_browser']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['org_feature_browser']['cache'] = DRUPAL_NO_CACHE;
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return $blocks;
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}
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@@ -394,11 +394,11 @@ function tripal_feature_block_info() {
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* @ingroup tripal_feature
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*/
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function tripal_feature_block_view($delta = '') {
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-
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+
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if (user_access('access chado_feature content') and arg(0) == 'node' and is_numeric(arg(1))) {
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$nid = arg(1);
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$node = node_load($nid);
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-
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+
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$block = array();
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switch ($delta) {
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case 'references':
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@@ -511,24 +511,24 @@ function chado_feature_insert($node) {
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'type_id' => $type[0]->cvterm_id,
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);
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$feature = tripal_core_chado_select('feature', array('feature_id'), $values);
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-
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+
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// add the genbank accession and synonyms
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chado_feature_add_synonyms($node->synonyms, $feature[0]->feature_id);
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// make sure the entry for this feature doesn't already exist in the chado_feature table
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// if it doesn't exist then we want to add it.
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$node_check_sql = "
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- SELECT * FROM {chado_feature}
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+ SELECT * FROM {chado_feature}
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WHERE feature_id = :feature_id
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";
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$node_check = db_query($node_check_sql, array(':feature_id' => $feature[0]->feature_id))->fetchObject();
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if (!$node_check) {
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// next add the item to the drupal table
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$sql = "
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- INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date)
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+ INSERT INTO {chado_feature} (nid, vid, feature_id, sync_date)
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VALUES (:nid, :vid, :feature_id, :time)
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";
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- db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid,
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+ db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid,
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':feature_id' => $feature[0]->feature_id, ':time' => REQUEST_TIME));
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}
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}
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@@ -577,7 +577,7 @@ function chado_feature_update($node) {
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);
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$options = array('return_record' => TRUE);
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$status = tripal_core_chado_update('feature', $match, $values, $options);
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-
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+
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// add the genbank synonyms
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chado_feature_add_synonyms($node->synonyms, $feature_id);
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}
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@@ -589,7 +589,7 @@ function chado_feature_update($node) {
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WATCHDOG_WARNING
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);
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}
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-
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+
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}
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/**
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@@ -662,11 +662,11 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
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$synonym = chado_query($synonym_sql, array(':name' => $syn))->fetchObject();
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if (!$synonym) {
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$synonym_isql = "
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- INSERT INTO {synonym} (name, synonym_sgml, type_id)
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- VALUES (:name, :synonym_sgml,
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- (SELECT cvterm_id
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- FROM {CVTerm} CVT
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- INNER JOIN CV ON CVT.cv_id = CV.cv_id
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+ INSERT INTO {synonym} (name, synonym_sgml, type_id)
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+ VALUES (:name, :synonym_sgml,
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+ (SELECT cvterm_id
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+ FROM {CVTerm} CVT
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+ INNER JOIN CV ON CVT.cv_id = CV.cv_id
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WHERE CV.name = 'feature_property' and CVT.name = 'synonym')
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)
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";
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@@ -680,7 +680,7 @@ function chado_feature_add_synonyms($synonyms, $feature_id) {
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// now add in our new sysnonym
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$feature_syn_isql = "
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- INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id)
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+ INSERT INTO {feature_synonym} (synonym_id,feature_id,pub_id)
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VALUES (:synonym_id, :feature_id, :pub_id)";
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$args = array(':synonym_id' => $synonym->synonym_id, ':feature_id' => $feature_id, ':pub_id'=> 1);
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if (!chado_query($feature_syn_isql, $args)) {
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@@ -703,12 +703,12 @@ function chado_feature_add_gbaccession($accession, $feature_id) {
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// remove any old accession from genbank dbEST
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$fdbxref_dsql = "
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- DELETE FROM {feature_dbxref}
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- WHERE feature_id = :feature_id and dbxref_id IN
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- (SELECT DBX.dbxref_id
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- FROM {dbxref} DBX
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- INNER JOIN DB ON DB.db_id = DBX.db_id
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- INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id
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+ DELETE FROM {feature_dbxref}
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+ WHERE feature_id = :feature_id and dbxref_id IN
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+ (SELECT DBX.dbxref_id
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+ FROM {dbxref} DBX
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+ INNER JOIN DB ON DB.db_id = DBX.db_id
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+ INNER JOIN feature_dbxref FDBX ON DBX.dbxref_id = FDBX.dbxref_id
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WHERE DB.name = 'DB:Genbank' and FDBX.feature_id = :feature_id
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)
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";
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@@ -841,8 +841,8 @@ function chado_feature_form($node, $param) {
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// get the sequence ontology CV ID
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$values = array('name' => 'sequence');
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- $cv = tripal_core_chado_select('cv', array('cv_id'), $values);
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- $cv_id = $cv[0]->cv_id;
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+ $cv = tripal_core_chado_select('cv', array('cv_id'), $values);
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+ $cv_id = $cv[0]->cv_id;
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$form['feature_type'] = array(
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'#title' => t('Feature Type'),
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@@ -917,7 +917,7 @@ function chado_feature_form($node, $param) {
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*/
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function chado_feature_validate($node) {
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$result = 0;
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-
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+
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// make sure the feature type is a real sequence ontology term
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$type = tripal_cv_get_cvterm_by_name($node->feature_type, NULL, 'sequence');
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if (!$type) {
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@@ -932,13 +932,13 @@ function chado_feature_validate($node) {
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SELECT *
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FROM {feature} F
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INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
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- WHERE
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- F.uniquename = :uname AND
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- F.organism_id = :orgnism_id AND
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- CVT.name = :cvtname AND
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+ WHERE
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+ F.uniquename = :uname AND
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+ F.organism_id = :orgnism_id AND
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+ CVT.name = :cvtname AND
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NOT f.feature_id = :feature_id
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";
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- $args = array(':uname' => $node->uniquename, ':organism_id' => $node->organism_id,
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+ $args = array(':uname' => $node->uniquename, ':organism_id' => $node->organism_id,
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':cvtname' => $node->feature_type, ':feature_id' => $node->feature_id);
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$result = chado_query($sql, $args)->fetchObject();
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if ($result) {
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@@ -953,9 +953,9 @@ function chado_feature_validate($node) {
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SELECT *
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FROM {feature} F
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INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
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- WHERE
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- F.uniquename = :name AND
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- F.organism_id = :organism_id AND
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+ WHERE
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+ F.uniquename = :name AND
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+ F.organism_id = :organism_id AND
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CVT.name = :cvtname
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";
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$args = array(':name' => $node->uniquename, ':organism_id' => $node->organism_id, ':cvtname' => $node->feature_type);
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@@ -992,10 +992,10 @@ function chado_feature_load($node) {
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if (strcmp($feature->name, $feature->uniquename)==0) {
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$node->title = $feature->name . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
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}
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- // in previous version of Tripal, the feature title was simply the unique name.
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+ // in previous version of Tripal, the feature title was simply the unique name.
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// so, we recreate the title just to be sure all of our feature pages are consistent
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else {
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- $node->title = $feature->name . ", " . $feature->uniquename . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
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+ $node->title = $feature->name . ", " . $feature->uniquename . " (" . $feature->type_id->name . ") " . $feature->organism_id->genus . " " . $feature->organism_id->species ;
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}
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}
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// set the title to be the feature name or uniquename as configured
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@@ -1003,7 +1003,7 @@ function chado_feature_load($node) {
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$node->title = $feature->name;
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}
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if ($title_type == 'feature_unique_name') {
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- $node->title = $feature->uniquename;
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+ $node->title = $feature->uniquename;
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}
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$additions = new stdClass();
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@@ -1029,11 +1029,11 @@ function tripal_feature_load_organism($organism_id) {
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function tripal_feature_load_synonyms($feature_id) {
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$sql = "
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- SELECT S.name
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- FROM {feature_synonym} FS
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- INNER JOIN {synonym} S ON FS.synonym_id = S.Synonym_id
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+ SELECT S.name
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+ FROM {feature_synonym} FS
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+ INNER JOIN {synonym} S ON FS.synonym_id = S.Synonym_id
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WHERE FS.feature_id = :feature_id
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- ORDER BY S.name
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+ ORDER BY S.name
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";
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$results = chado_query($sql, array(':feature_id' => $feature_id));
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$synonyms = array();
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@@ -1051,16 +1051,16 @@ function tripal_feature_load_synonyms($feature_id) {
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function tripal_feature_load_properties($feature_id) {
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$sql = "
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- SELECT
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- CVT.name as cvname, CVT.definition, CVT.is_obsolete,
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- FS.type_id, FS.value, FS.rank,
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+ SELECT
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+ CVT.name as cvname, CVT.definition, CVT.is_obsolete,
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+ FS.type_id, FS.value, FS.rank,
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DBX.dbxref_id,DBX.accession,DB.name as dbname,
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DB.urlprefix, DB.description as db_description, DB.url
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FROM {featureprop} FS
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INNER JOIN {cvterm} CVT ON FS.type_id = CVT.cvterm_id
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INNER JOIN {dbxref} DBX ON CVT.dbxref_id = DBX.dbxref_id
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INNER JOIN {db} DB ON DB.db_id = DBX.db_id
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- WHERE
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+ WHERE
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FS.feature_id = :feature_id
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ORDER BY FS.rank ASC
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";
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@@ -1080,17 +1080,17 @@ function tripal_feature_load_properties($feature_id) {
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function tripal_feature_load_references($feature_id) {
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$sql = "
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- SELECT
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+ SELECT
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F.uniquename, F.Feature_id,
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DB.description as dbdesc, DB.db_id, DB.name as db_name, DB.urlprefix,
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- DBX.accession, DBX.dbxref_id
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- FROM {feature} F
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- INNER JOIN {feature_dbxref} FDBX ON F.feature_id = FDBX.feature_id
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- INNER JOIN {dbxref} DBX ON DBX.dbxref_id = FDBX.dbxref_id
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- INNER JOIN {db} ON DB.db_id = DBX.db_id
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- WHERE
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+ DBX.accession, DBX.dbxref_id
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+ FROM {feature} F
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+ INNER JOIN {feature_dbxref} FDBX ON F.feature_id = FDBX.feature_id
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+ INNER JOIN {dbxref} DBX ON DBX.dbxref_id = FDBX.dbxref_id
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+ INNER JOIN {db} ON DB.db_id = DBX.db_id
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+ WHERE
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F.feature_id = :feature_id
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- ORDER BY DB.name
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+ ORDER BY DB.name
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";
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$results = chado_query($sql, array(':feature_id' => $feature_id));
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$references = array();
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@@ -1126,7 +1126,7 @@ function tripal_feature_load_featurelocs($feature_id, $side = 'as_parent', $aggr
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if (strcmp($side, 'as_child')==0) {
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$sql .= "WHERE FL.feature_id = :feature_id ";
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}
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-
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+
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$flresults = chado_query($sql, array(':feature_id' => $feature_id));
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// copy the results into an array
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@@ -1185,7 +1185,7 @@ function tripal_feature_load_relationships($feature_id, $side = 'as_subject') {
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FR.subject_id, FR.type_id as relationship_type_id, FR.object_id, FR.rank,
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CVT.name as rel_type,
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FO.name as object_name, FO.uniquename as object_uniquename,
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- CVTO.name as object_type, CVTO.cvterm_id as object_type_id
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+ CVTO.name as object_type, CVTO.cvterm_id as object_type_id
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FROM {feature_relationship} FR
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INNER JOIN {cvterm} CVT ON FR.type_id = CVT.cvterm_id
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INNER JOIN {feature} FS ON FS.feature_id = FR.subject_id
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@@ -1298,8 +1298,8 @@ function tripal_feature_load_featureloc_sequences($feature_id, $featurelocs) {
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// location and then annotate it with the parts found from the relationships
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// locations determiend above.
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$sql = "
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- SELECT substring(residues from :start for :size) as residues
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- FROM {feature}
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+ SELECT substring(residues from :start for :size) as residues
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+ FROM {feature}
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WHERE feature_id = :feature_id
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";
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$floc_sequences = array();
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@@ -1395,37 +1395,37 @@ function tripal_feature_get_matched_alignments($feature) {
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// match, or %_match
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//
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$sql = "
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- SELECT
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- FL1.featureloc_id as left_featureloc_id,
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- FL1.srcfeature_id as left_srcfeature_id,
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- FL1.feature_id as left_feature_id,
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- FL1.fmin as left_fmin,
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- FL1.is_fmin_partial as left_is_fmin_partial,
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- FL1.fmax as left_fmax,
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- FL1.is_fmax_partial as left_is_fmax_partial,
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- FL1.strand as left_strand,
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- FL1.phase as left_phase,
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- FL1.locgroup as left_locgroup,
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- FL1.rank as left_rank,
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- FL2.featureloc_id as right_featureloc_id,
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- FL2.srcfeature_id as right_srcfeature_id,
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- FL2.feature_id as right_feature_id,
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- FL2.fmin as right_fmin,
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- FL2.is_fmin_partial as right_is_fmin_partial,
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- FL2.fmax as right_fmax,
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- FL2.is_fmax_partial as right_is_fmax_partial,
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- FL2.strand as right_strand,
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- FL2.phase as right_phase,
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- FL2.locgroup as right_locgroup,
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- FL2.rank as right_rank
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- FROM {feature} F1
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- INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
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- INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
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- INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
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- INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
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- WHERE
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- F1.feature_id = :feature_id AND
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- (CVT2.name = 'match' or CVT2.name like '%_match')
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+ SELECT
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+ FL1.featureloc_id as left_featureloc_id,
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+ FL1.srcfeature_id as left_srcfeature_id,
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+ FL1.feature_id as left_feature_id,
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+ FL1.fmin as left_fmin,
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+ FL1.is_fmin_partial as left_is_fmin_partial,
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+ FL1.fmax as left_fmax,
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+ FL1.is_fmax_partial as left_is_fmax_partial,
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+ FL1.strand as left_strand,
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+ FL1.phase as left_phase,
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+ FL1.locgroup as left_locgroup,
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+ FL1.rank as left_rank,
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+ FL2.featureloc_id as right_featureloc_id,
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+ FL2.srcfeature_id as right_srcfeature_id,
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+ FL2.feature_id as right_feature_id,
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+ FL2.fmin as right_fmin,
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+ FL2.is_fmin_partial as right_is_fmin_partial,
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+ FL2.fmax as right_fmax,
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+ FL2.is_fmax_partial as right_is_fmax_partial,
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+ FL2.strand as right_strand,
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+ FL2.phase as right_phase,
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+ FL2.locgroup as right_locgroup,
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+ FL2.rank as right_rank
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+ FROM {feature} F1
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+ INNER JOIN {featureloc} FL1 on FL1.srcfeature_id = F1.feature_id
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+ INNER JOIN {feature} F2 on FL1.feature_id = F2.feature_id
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+ INNER JOIN {featureloc} FL2 on FL2.feature_id = F2.feature_id
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+ INNER JOIN {cvterm} CVT2 on F2.type_id = CVT2.cvterm_id
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+ WHERE
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+ F1.feature_id = :feature_id AND
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|
+ (CVT2.name = 'match' or CVT2.name like '%_match')
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|
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ORDER BY FL1.fmin
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";
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@@ -1608,24 +1608,24 @@ function tripal_feature_load_library_feature_browser($library) {
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// get the features for this library
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$sql = "
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- SELECT F.name, F.feature_id, F.uniquename, CVT.name as cvname
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- FROM {feature} F
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- INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
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- INNER JOIN {library_feature} LF ON F.feature_id = LF.feature_id
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- INNER JOIN {library} L ON LF.library_id = L.library_id
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- WHERE LF.library_id = :library_id and ($where_cvt)
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+ SELECT F.name, F.feature_id, F.uniquename, CVT.name as cvname
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+ FROM {feature} F
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+ INNER JOIN {cvterm} CVT ON F.type_id = CVT.cvterm_id
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+ INNER JOIN {library_feature} LF ON F.feature_id = LF.feature_id
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+ INNER JOIN {library} L ON LF.library_id = L.library_id
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+ WHERE LF.library_id = :library_id and ($where_cvt)
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ORDER BY feature_id ASC
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|
";
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$args[':library_id'] = $library->libary_id;
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-
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+
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// the counting SQL
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$csql = "
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- SELECT count(*)
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+ SELECT count(*)
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FROM {feature} F
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- INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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- INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id
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- INNER JOIN {library} L on LF.library_id = L.library_id
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- WHERE LF.library_id = :library_id and ($where_cvt)
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+ INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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+ INNER JOIN {library_feature} LF on F.feature_id = LF.feature_id
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+ INNER JOIN {library} L on LF.library_id = L.library_id
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|
+ WHERE LF.library_id = :library_id and ($where_cvt)
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GROUP BY L.library_id ";
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$org_features = chado_pager_query($sql, 10, 0, $csql, $args);
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@@ -1675,25 +1675,25 @@ function tripal_feature_load_analysis_feature_browser($analysis) {
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// get the features for this library
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$sql = "
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- SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname
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- FROM {feature} F
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- INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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- INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id
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- INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id
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- WHERE A.analysis_id = :analysis_id and ($where_cvt)
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|
+ SELECT F.name,F.feature_id,F.uniquename,CVT.name as cvname
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+ FROM {feature} F
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+ INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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+ INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id
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+ INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id
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+ WHERE A.analysis_id = :analysis_id and ($where_cvt)
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|
ORDER BY feature_id ASC
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|
";
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|
|
$args[':analysis_id'] = $analysis->analysis_id;
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|
// the counting SQL
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|
|
$csql = "
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|
- SELECT count(*)
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|
+ SELECT count(*)
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|
FROM {feature} F
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- INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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|
- INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id
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- INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id
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|
- WHERE A.analysis_id = %d and ($where_cvt)
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|
- GROUP BY A.analysis_id
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|
+ INNER JOIN {cvterm} CVT on F.type_id = CVT.cvterm_id
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|
+ INNER JOIN {analysisfeature} AF on F.feature_id = AF.feature_id
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|
+ INNER JOIN {analysis} A on AF.analysis_id = A.analysis_id
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|
+ WHERE A.analysis_id = %d and ($where_cvt)
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|
|
+ GROUP BY A.analysis_id
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|
";
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|
$org_features = chado_pager_query($sql, 10, 0, $csql, $args);
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|
@@ -1843,11 +1843,11 @@ function tripal_feature_color_sequence($sequence, $parts, $defline) {
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|
* @ingroup tripal_feature
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|
|
*/
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|
|
function tripal_feature_node_presave($node) {
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|
-
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+
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|
// set the title to ensure it is always unique
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|
|
switch ($node->type) {
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|
case 'chado_feature':
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-
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+
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|
$values = array('organism_id' => $node->organism_id);
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|
$organism = tripal_core_chado_select('organism', array('genus', 'species'), $values);
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$node->title = $node->fname . ', ' . $node->uniquename . ' (' . $node->feature_type . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
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|
@@ -1860,9 +1860,9 @@ function tripal_feature_node_presave($node) {
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|
* @ingroup tripal_feature
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|
*/
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|
function tripal_feature_node_insert($node) {
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|
-
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|
- // set the URL path after inserting. We do it here because we do not
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|
- // know the feature_id in the presave
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+
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|
+ // set the URL path after inserting. We do it here because we do not
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|
+ // know the feature_id in the presave
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|
|
switch ($node->type) {
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|
|
case 'chado_feature':
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|
|
if (!$node->feature_id) {
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@@ -1870,10 +1870,10 @@ function tripal_feature_node_insert($node) {
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$chado_feature = db_query($sql, array(':nid' => $node->nid))->fetchObject();
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$node->feature_id = $chado_feature->feature_id;
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}
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-
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+
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|
// remove any previous alias
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|
db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
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-
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+
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|
// set the URL for this feature page
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|
$url_alias = tripal_feature_get_feature_url($node);
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|
path_set_alias("node/$node->nid", $url_alias);
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|
@@ -1910,14 +1910,14 @@ function tripal_feature_node_view($node, $view_mode, $langcode) {
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*
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|
* @ingroup tripal_feature
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|
*/
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|
-function tripal_feature_node_update($node) {
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-
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|
+function tripal_feature_node_update($node) {
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+
|
|
|
// add items to other nodes, build index and search results
|
|
|
switch ($node->type) {
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|
|
case 'chado_feature':
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|
// remove any previous alias
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|
|
db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
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-
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|
+
|
|
|
// set the URL for this feature page
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|
|
$url_alias = tripal_feature_get_feature_url($node);
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path_set_alias("node/$node->nid", $url_alias);
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|
@@ -2315,15 +2315,15 @@ function tripal_feature_coder_ignore() {
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|
* features is shown.
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|
*/
|
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|
function tripal_feature_match_features_page($id) {
|
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|
-
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|
+
|
|
|
// if the URL alias configuration is set such that the URL
|
|
|
// always begins with 'feature' then we want to use the ID as it is and
|
|
|
// forward it on. Otherwise, try to find the matching feature.
|
|
|
- $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]');
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|
+ $url_alias = variable_get('chado_feature_url_string', '/feature/[genus]/[species]/[type]/[uniquename]');
|
|
|
if (!$url_alias) {
|
|
|
$url_alias = '/feature/[genus]/[species]/[type]/[uniquename]';
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|
|
- }
|
|
|
- $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
|
|
|
+ }
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|
|
+ $url_alias = preg_replace('/^\//', '', $url_alias); // remove any preceeding forward slash
|
|
|
if (preg_match('/^feature\//', $url_alias)) {
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|
|
drupal_goto($id);
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|
|
}
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|
@@ -2388,16 +2388,16 @@ function tripal_feature_match_features_page($id) {
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- *
|
|
|
+ *
|
|
|
* @param unknown_type $form
|
|
|
* @param unknown_type $form_state
|
|
|
* @param unknown_type $form_id
|
|
|
*/
|
|
|
function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
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|
|
- if ($form_id == "tripal_feature_seq_extract_form") {
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|
|
+ if ($form_id == "tripal_feature_seq_extract_form") {
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|
|
// 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");
|
|
|
}
|
|
|
-}
|
|
|
+}
|
Lacey Sanderson