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@@ -174,13 +174,28 @@ function cs_node_load($nid) {
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*
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* @ingroup tripal_stock
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*/
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-function tripal_stock_perm() {
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+function tripal_stock_permissions() {
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return array(
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- 'access chado_stock content',
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- 'create chado_stock content',
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- 'edit chado_stock content',
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- 'delete chado_stock content',
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- 'administer tripal stocks',
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+ 'access chado_stock content' => array(
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+ 'title' => t('View Stocks'),
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+ 'description' => t('Allow users to view stock pages.'),
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+ ),
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+ 'create chado_stock content' => array(
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+ 'title' => t('Create Stocks'),
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+ 'description' => t('Allow users to create new stock pages.'),
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+ ),
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+ 'delete chado_stock content' => array(
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+ 'title' => t('Delete Stocks'),
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+ 'description' => t('Allow users to delete stock pages.'),
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+ ),
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+ 'edit chado_stock content' => array(
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+ 'title' => t('Edit Stocks'),
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+ 'description' => t('Allow users to edit stock pages.'),
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+ ),
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+ 'adminster tripal stock' => array(
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+ 'title' => t('Administer Stocks'),
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+ 'description' => t('Allow users to administer all stocks.'),
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+ ),
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);
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}
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@@ -357,7 +372,7 @@ function tripal_stock_node_info() {
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return array(
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'chado_stock' => array(
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'name' => t('Stock'),
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- 'module' => 'chado_stock',
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+ 'base' => 'chado_stock',
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'description' => t('A Chado Stock is a collection of material that can be sampled and have experiments performed on it.'),
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'has_title' => TRUE,
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'has_body' => FALSE,
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@@ -522,7 +537,7 @@ function chado_stock_form($node, $form_state) {
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$org_rset = chado_query($sql);
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$organisms = array();
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$organisms[''] = '';
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- while ($organism = db_fetch_object($org_rset)) {
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+ while ($organism = $org_rset->fetchObject()) {
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$organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
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}
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$form['details']['organism_id'] = array(
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@@ -586,19 +601,24 @@ function chado_stock_form($node, $form_state) {
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*/
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function chado_stock_validate($node, &$form) {
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- $int_in_chado_sql = "SELECT count(*) as count FROM {%s} WHERE %s=%d";
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- $string_in_chado_sql = "SELECT count(*) as count FROM {%s} WHERE %s='%s'";
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+ $int_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
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+ $string_in_chado_sql = "SELECT count(*) as count FROM {:table} WHERE :column = :value";
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// if this is an update, we want to make sure that a different stock for
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// the organism doesn't already have this uniquename. We don't want to give
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// two sequences the same uniquename
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if ($node->stock_id) {
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- $sql = "SELECT *
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- FROM {stock} S
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- INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
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- WHERE uniquename = '%s'
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- AND organism_id = %d AND CVT.name = '%s' AND NOT stock_id = %d";
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- $result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->stock_type, $node->stock_id));
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+ $sql = "
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+ SELECT *
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+ FROM {stock} S
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+ INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
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+ WHERE
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+ uniquename = :uname AND organism_id = :organism_id AND
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+ CVT.name = :cvtname AND NOT stock_id = :stock_id
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+ ";
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+ $result = chado_query($sql, array(':uname' => $node->uniquename,
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+ ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type,
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+ ':stock_id' => $node->stock_id))->fetchObject();
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if ($result) {
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form_set_error('uniquename', t("Stock update cannot proceed. The stock name '$node->uniquename' is not unique for this organism. Please provide a unique name for this stock."));
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}
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@@ -607,12 +627,13 @@ function chado_stock_validate($node, &$form) {
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// if this is an insert then we just need to make sure this name doesn't
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// already exist for this organism if it does then we need to throw an error
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else {
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- $sql = "SELECT *
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- FROM {Stock} S
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- INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
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- WHERE uniquename = '%s'
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- AND organism_id = %d AND CVT.name = '%s'";
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- $result = db_fetch_object(chado_query($sql, $node->uniquename, $node->organism_id, $node->stock_type));
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+ $sql = "
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+ SELECT *
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+ FROM {Stock} S
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+ INNER JOIN {cvterm} CVT ON S.type_id = CVT.cvterm_id
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+ WHERE uniquename = :uname'AND organism_id = :organism_id AND CVT.name = :cvtname";
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+ $result = chado_query($sql, array(':uname' => $node->uniquename,
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+ ':organism_id' => $node->organism_id, ':cvtname' => $node->stock_type))->fetchObject();
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if ($result) {
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form_set_error('uniquename', t("Stock insert cannot proceed. The stock name '$node->uniquename' already exists for this organism. Please provide a unique name for this stock."));
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}
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@@ -624,7 +645,7 @@ function chado_stock_validate($node, &$form) {
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form_set_error('type_id', 'Please select a type of stock.');
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}
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else {
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- $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'cvterm', 'cvterm_id', $node->type_id));
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+ $num_rows = chado_query($int_in_chado_sql, array(':table' => 'cvterm', ':column' => 'cvterm_id', ':value' => $node->type_id))->fetchObject();
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if ( $num_rows->count != 1) {
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form_set_error('type_id', "The type you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
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}
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@@ -634,7 +655,7 @@ function chado_stock_validate($node, &$form) {
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form_set_error('organism_id', 'Please select a source organism for this stock');
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}
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else {
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- $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'organism', 'organism_id', $node->organism_id));
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+ $num_rows = chado_query($int_in_chado_sql, array(':table' => 'organism', ':column' => 'organism_id', ':value' => $node->organism_id))->fetchObject();
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if ( $num_rows->count != 1 ) {
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form_set_error('organism_id', "The organism you selected is not valid. Please choose another one. (CODE:$num_rows)"); }
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}
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@@ -655,7 +676,7 @@ function chado_stock_validate($node, &$form) {
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// Check database is valid db_id in chado ( $form['values']['database_reference']['database'] )
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if ( $node->database > 0) {
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- $num_rows = db_fetch_object(chado_query($int_in_chado_sql, 'db', 'db_id', $node->database));
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+ $num_rows = chado_query($int_in_chado_sql, array(':table' => 'db', ':column' => 'db_id', ':value' => $node->database))->fetchObject();
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if ($num_rows->count != 1) {
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form_set_error('database', 'The database you selected is not valid. Please choose another one.'); }
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}
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@@ -679,13 +700,8 @@ function chado_stock_insert($node) {
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// then don't create but simply link to node
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if ($node->chado_stock_exists) {
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if (!empty($node->stock_id)) {
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- db_query(
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- "INSERT INTO {chado_stock} (nid, vid, stock_id) "
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- ."VALUES (%d, %d, %d)",
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- $node->nid,
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- $node->vid,
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- $node->stock_id
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- );
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+ $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES (:nid, :vid, :stock_id)";
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+ db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':stock_id' => $node->stock_id));
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}
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return $node;
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@@ -755,8 +771,8 @@ function chado_stock_insert($node) {
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$stock = (object) $stock;
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// add the entry to the chado_stock table
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- $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES (%d, %d, %d)";
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- db_query($sql, $node->nid, $node->vid, $stock->stock_id);
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+ $sql = "INSERT INTO {chado_stock} (nid, vid, stock_id) VALUES :nid, :vid, :stock_id)";
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+ db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':stock_id' => $stock->stock_id));
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// Move on to next stage of Stock Creation based on next_stage_path field
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if ($node->simulate_multipart) {
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@@ -906,133 +922,112 @@ function chado_stock_update($node) {
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function chado_stock_delete($node) {
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// Set stock in chado: is_obsolete = TRUE
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- chado_query(
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- "DELETE FROM {stock} WHERE stock_id=%d",
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- $node->stock->stock_id
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- );
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+ chado_query("DELETE FROM {stock} WHERE stock_id = :stock_id", array(':stock_id' => $node->stock->stock_id));
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//remove drupal node and all revisions
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- db_query(
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- "DELETE FROM {chado_stock} WHERE nid=%d",
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- $node->nid
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- );
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+ db_query("DELETE FROM {chado_stock} WHERE nid = :nid", array(':nid' => $node->nid));
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}
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/**
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- * Purpose: Implement Blocks relating to stock content
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- *
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- * @param $op
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- * What kind of information to retrieve about the block or blocks.
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- * Possible values include list, configure, save, view.
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- * @param $delta
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- * Which block to return (not applicable if $op is 'list').
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- * @param $edit
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- * If $op is 'save', the submitted form data from the configuration form.
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- *
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- * @return
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- * One of the following depending on $op: An array of block descriptions (list), the configuration
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- * form (configure), nothing (save), an array defining subject and content for the block indexed
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- * by $delta (view)
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- *
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* @ingroup tripal_stock
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*/
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-function tripal_stock_block($op = 'list', $delta = 0, $edit=array()) {
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- switch ($op) {
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- case 'list':
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- $blocks['base']['info'] = t('Tripal Stock Details');
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- $blocks['base']['cache'] = BLOCK_NO_CACHE;
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+function tripal_stock_block_info() {
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+ $blocks['base']['info'] = t('Tripal Stock Details');
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+ $blocks['base']['cache'] = BLOCK_NO_CACHE;
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- $blocks['properties']['info'] = t('Tripal Stock Properties');
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- $blocks['properties']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['properties']['info'] = t('Tripal Stock Properties');
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+ $blocks['properties']['cache'] = BLOCK_NO_CACHE;
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- $blocks['references']['info'] = t('Tripal Stock References');
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- $blocks['references']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['references']['info'] = t('Tripal Stock References');
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+ $blocks['references']['cache'] = BLOCK_NO_CACHE;
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- $blocks['relationships_as_object']['info'] = t('Tripal Stock Relationships');
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- $blocks['relationships_as_object']['cache'] = BLOCK_NO_CACHE;
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+ $blocks['relationships_as_object']['info'] = t('Tripal Stock Relationships');
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+ $blocks['relationships_as_object']['cache'] = BLOCK_NO_CACHE;
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- $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
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- $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['collections']['info'] = t('Tripal Stock Collections');
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- $blocks['collections']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
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- $blocks['phenotypes']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
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- $blocks['genotypes']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['locations']['info'] = t('Tripal Stock Locations');
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- $blocks['locations']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
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- $blocks['orgstocks']['cache'] = BLOCK_NO_CACHE;
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-
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-
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+ $blocks['synonyms']['info'] = t('Tripal Stock Synonyms');
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+ $blocks['synonyms']['cache'] = BLOCK_NO_CACHE;
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+
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+ $blocks['collections']['info'] = t('Tripal Stock Collections');
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+ $blocks['collections']['cache'] = BLOCK_NO_CACHE;
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+
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+ $blocks['phenotypes']['info'] = t('Tripal Stock Phenotypes');
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+ $blocks['phenotypes']['cache'] = BLOCK_NO_CACHE;
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+
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+ $blocks['genotypes']['info'] = t('Tripal Stock Genotypes');
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+ $blocks['genotypes']['cache'] = BLOCK_NO_CACHE;
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+
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+ $blocks['locations']['info'] = t('Tripal Stock Locations');
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+ $blocks['locations']['cache'] = BLOCK_NO_CACHE;
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+
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+ $blocks['orgstocks']['info'] = t('Tripal Organism Stocks');
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+ $blocks['orgstocks']['cache'] = BLOCK_NO_CACHE;
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- return $blocks;
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-
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- case 'view':
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- if (user_access('access chado_stock 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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- $block = array();
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- switch ($delta) {
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- case 'base':
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- $block['subject'] = t('Stock Details');
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- $block['content'] = theme('tripal_stock_base', $node);
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- break;
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-
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- case 'properties':
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- $block['subject'] = t('Properties');
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- $block['content'] = theme('tripal_stock_properties', $node);
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- break;
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-
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- case 'references':
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- $block['subject'] = t('References');
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- $block['content'] = theme('tripal_stock_references', $node);
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- break;
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-
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- case 'relationships':
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- $block['subject'] = t('Relationships');
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- $block['content'] = theme('tripal_stock_relationships', $node);
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- break;
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-
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- case 'synonyms':
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- $block['subject'] = t('Synonyms');
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- $block['content'] = theme('tripal_stock_synonyms', $node);
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- break;
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-
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- case 'collections':
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- $block['subject'] = t('Stock Collections');
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- $block['content'] = theme('tripal_stock_collections', $node);
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- break;
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-
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- case 'phenotypes':
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- $block['subject'] = t('Stock Phenotypes');
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- $block['content'] = theme('tripal_stock_phenotypes', $node);
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- break;
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-
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- case 'genotypes':
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- $block['subject'] = t('Stock Genotypes');
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- $block['content'] = theme('tripal_stock_genotypes', $node);
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- break;
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-
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- case 'locations':
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- $block['subject'] = t('Stock Locations');
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- $block['content'] = theme('tripal_stock_locations', $node);
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- break;
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-
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- case 'orgstocks':
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- $block['subject'] = t('Organism Stocks');
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- $block['content'] = theme('tripal_organism_stocks', $node);
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- break;
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+ return $blocks;
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+}
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+/**
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+ *
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+ * @ingroup tripal_stock
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+ */
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+function tripal_stock_block_view($delta = '') {
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- }
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- return $block;
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+ if (user_access('access chado_stock 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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+ $block = array();
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+ switch ($delta) {
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+ case 'base':
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+ $block['subject'] = t('Stock Details');
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+ $block['content'] = theme('tripal_stock_base', $node);
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+ break;
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+
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+ case 'properties':
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+ $block['subject'] = t('Properties');
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+ $block['content'] = theme('tripal_stock_properties', $node);
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+ break;
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+
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+ case 'references':
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+ $block['subject'] = t('References');
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+ $block['content'] = theme('tripal_stock_references', $node);
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+ break;
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+
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+ case 'relationships':
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+ $block['subject'] = t('Relationships');
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+ $block['content'] = theme('tripal_stock_relationships', $node);
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+ break;
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+
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+ case 'synonyms':
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+ $block['subject'] = t('Synonyms');
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+ $block['content'] = theme('tripal_stock_synonyms', $node);
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+ break;
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+
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|
|
+ case 'collections':
|
|
|
+ $block['subject'] = t('Stock Collections');
|
|
|
+ $block['content'] = theme('tripal_stock_collections', $node);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'phenotypes':
|
|
|
+ $block['subject'] = t('Stock Phenotypes');
|
|
|
+ $block['content'] = theme('tripal_stock_phenotypes', $node);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'genotypes':
|
|
|
+ $block['subject'] = t('Stock Genotypes');
|
|
|
+ $block['content'] = theme('tripal_stock_genotypes', $node);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'locations':
|
|
|
+ $block['subject'] = t('Stock Locations');
|
|
|
+ $block['content'] = theme('tripal_stock_locations', $node);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'orgstocks':
|
|
|
+ $block['subject'] = t('Organism Stocks');
|
|
|
+ $block['content'] = theme('tripal_organism_stocks', $node);
|
|
|
+ break;
|
|
|
+
|
|
|
}
|
|
|
+ return $block;
|
|
|
}
|
|
|
}
|
|
|
|
|
|
@@ -1059,9 +1054,9 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
|
|
|
INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
|
|
|
INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
|
|
|
LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
|
|
|
- WHERE SR.subject_id = %d
|
|
|
+ WHERE SR.subject_id = :stock_id
|
|
|
";
|
|
|
- $as_subject = chado_query($sql, $stock->stock_id);
|
|
|
+ $as_subject = chado_query($sql, array(':stock_id' => $stock->stock_id));
|
|
|
$sql = "
|
|
|
SELECT
|
|
|
S.name, S.uniquename, S.stock_id, CS.nid,
|
|
|
@@ -1072,9 +1067,9 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
|
|
|
INNER JOIN {cvterm} CVT on SR.type_id = CVT.cvterm_id
|
|
|
INNER JOIN {cvterm} CVTs on S.type_id = CVTs.cvterm_id
|
|
|
LEFT JOIN public.chado_stock CS on S.stock_id = CS.stock_id
|
|
|
- WHERE SR.object_id = %d
|
|
|
+ WHERE SR.object_id = :stock_id
|
|
|
";
|
|
|
- $as_object = chado_query($sql, $stock->stock_id);
|
|
|
+ $as_object = chado_query($sql, array(':stock_id' => $stock->stock_id));
|
|
|
|
|
|
// combine both object and subject relationshisp into a single array
|
|
|
$relationships = array();
|
|
|
@@ -1082,7 +1077,7 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
|
|
|
$relationships['subject'] = array();
|
|
|
|
|
|
// iterate through the object relationships
|
|
|
- while ($relationship = db_fetch_object($as_object)) {
|
|
|
+ while ($relationship = $as_object->fetchObject()) {
|
|
|
|
|
|
// get the relationship and child types
|
|
|
$rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
|
|
|
@@ -1098,7 +1093,7 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
|
|
|
}
|
|
|
|
|
|
// now add in the subject relationships
|
|
|
- while ($relationship = db_fetch_object($as_subject)) {
|
|
|
+ while ($relationship = $as_subject->fetchObject()) {
|
|
|
|
|
|
// get the relationship and child types
|
|
|
$rel_type = t(preg_replace('/_/', " ", $relationship->rel_type));
|
|
|
@@ -1118,88 +1113,74 @@ function tripal_stock_preprocess_tripal_stock_relationships(&$variables) {
|
|
|
|
|
|
}
|
|
|
/**
|
|
|
- * Implementation of hook_nodeapi().
|
|
|
- * Display stock information for associated organisms
|
|
|
- * This function also provides contents for indexing
|
|
|
- *
|
|
|
* @ingroup tripal_stock
|
|
|
*/
|
|
|
-function tripal_stock_nodeapi(&$node, $op, $teaser, $page) {
|
|
|
-
|
|
|
- switch ($op) {
|
|
|
-
|
|
|
- // set the title to ensure it is always unique
|
|
|
- case 'presave':
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_stock':
|
|
|
-
|
|
|
- $values = array('organism_id' => $node->organism_id);
|
|
|
- $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
|
|
|
- $values = array('cvterm_id' => $node->type_id);
|
|
|
- $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
|
|
|
- $node->title = $node->sname . ', ' . $node->uniquename . ' (' . $cvterm[0]->name . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
|
|
|
- break;
|
|
|
- }
|
|
|
+function tripal_stock_node_presave($node) {
|
|
|
+
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+ $values = array('organism_id' => $node->organism_id);
|
|
|
+ $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
|
|
|
+ $values = array('cvterm_id' => $node->type_id);
|
|
|
+ $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
|
|
|
+ $node->title = $node->sname . ', ' . $node->uniquename . ' (' . $cvterm[0]->name . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
|
|
|
break;
|
|
|
-
|
|
|
- // set the URL path after inserting. We do it here because we do not
|
|
|
- // know the stock_id in the presave
|
|
|
- case 'insert':
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_stock':
|
|
|
- if (!$node->stock_id) {
|
|
|
- $sql = "SELECT * FROM {chado_stock} WHERE nid = %d";
|
|
|
- $chado_stock = db_fetch_object(db_query($sql, $node->nid));
|
|
|
- $node->stock_id = $chado_stock->stock_id;
|
|
|
- }
|
|
|
-
|
|
|
- // remove any previous alias
|
|
|
- db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid");
|
|
|
-
|
|
|
- // set the URL for this stock page
|
|
|
- $url_alias = tripal_stock_get_stock_url($node);
|
|
|
- path_set_alias("node/$node->nid", $url_alias);
|
|
|
- break;
|
|
|
+ }
|
|
|
+}
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_insert($node) {
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+ if (!$node->stock_id) {
|
|
|
+ $sql = "SELECT * FROM {chado_stock} WHERE nid = :nid";
|
|
|
+ $chado_stock = db_query($sql, array(':nid' => $node->nid))->fetchObject();
|
|
|
+ $node->stock_id = $chado_stock->stock_id;
|
|
|
}
|
|
|
- break;
|
|
|
|
|
|
- // set the URL path after inserting. We do it here because we do not
|
|
|
- // know the stock_id in the presave
|
|
|
- case 'update':
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_stock':
|
|
|
-
|
|
|
- // remove any previous alias
|
|
|
- db_query("DELETE FROM {url_alias} WHERE src = '%s'", "node/$node->nid");
|
|
|
-
|
|
|
- // set the URL for this stock page
|
|
|
- $url_alias = tripal_stock_get_stock_url($node);
|
|
|
- path_set_alias("node/$node->nid", $url_alias);
|
|
|
- break;
|
|
|
- }
|
|
|
- break;
|
|
|
+ // remove any previous alias
|
|
|
+ db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
|
|
|
|
|
|
- // add items to other nodes, build index and search results
|
|
|
- case 'view':
|
|
|
- // add the stock to the organism/feature search indexing
|
|
|
- if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
|
|
|
-
|
|
|
- }
|
|
|
- elseif ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
|
|
|
+ // set the URL for this stock page
|
|
|
+ $url_alias = tripal_stock_get_stock_url($node);
|
|
|
+ path_set_alias("node/$node->nid", $url_alias);
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_update($node) {
|
|
|
|
|
|
- }
|
|
|
- else {
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_organism':
|
|
|
- // Show stock if the organism/feature is not at teaser view
|
|
|
- $node->content['tripal_organism_stocks'] = array(
|
|
|
- '#value' => theme('tripal_organism_stocks', $node),
|
|
|
- );
|
|
|
- break;
|
|
|
- }
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_stock':
|
|
|
+
|
|
|
+ // remove any previous alias
|
|
|
+ db_query("DELETE FROM {url_alias} WHERE src = :src", array(':src' => "node/$node->nid"));
|
|
|
+
|
|
|
+ // set the URL for this stock page
|
|
|
+ $url_alias = tripal_stock_get_stock_url($node);
|
|
|
+ path_set_alias("node/$node->nid", $url_alias);
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+/**
|
|
|
+ * @ingroup tripal_stock
|
|
|
+ */
|
|
|
+function tripal_stock_node_view($node, $view_mode, $langcode) {
|
|
|
+
|
|
|
+ switch ($node->type) {
|
|
|
+ case 'chado_organism':
|
|
|
+ if ($view_mode == 'full') {
|
|
|
+ // Show stock if the organism/feature is not at teaser view
|
|
|
+ $node->content['tripal_organism_stocks'] = array(
|
|
|
+ '#value' => theme('tripal_organism_stocks', $node),
|
|
|
+ );
|
|
|
}
|
|
|
break;
|
|
|
}
|
|
|
+
|
|
|
}
|
|
|
|
|
|
/*
|
|
|
@@ -1234,9 +1215,9 @@ function tripal_stock_match_stocks_page($id) {
|
|
|
INNER JOIN {cvterm} CVT on CVT.cvterm_id = S.type_id
|
|
|
INNER JOIN public.chado_stock CS on CS.stock_id = S.stock_id
|
|
|
WHERE
|
|
|
- S.uniquename = '%s' or S.name = '%s'
|
|
|
+ S.uniquename = :uname or S.name = :name
|
|
|
";
|
|
|
- $results = chado_query($sql, $id, $id);
|
|
|
+ $results = chado_query($sql, array(':uname' => $id, ':name' => $id));
|
|
|
|
|
|
$num_matches = 0;
|
|
|
|
|
|
@@ -1244,7 +1225,7 @@ function tripal_stock_match_stocks_page($id) {
|
|
|
$header = array('Uniquename', 'Name', 'Type', 'Species');
|
|
|
$rows = array();
|
|
|
$curr_match;
|
|
|
- while ($match = db_fetch_object($results)) {
|
|
|
+ while ($match = $results->fetchObject()) {
|
|
|
$curr_match = $match;
|
|
|
$rows[] = array(
|
|
|
$match->uniquename,
|
spficklin