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@@ -42,12 +42,11 @@ function tripal_library_node_info() {
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$nodes = array();
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$nodes['chado_library'] = array(
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'name' => t('Library'),
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- 'module' => 'chado_library',
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+ 'base' => 'chado_library',
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'description' => t('A library from the chado database'),
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'has_title' => FALSE,
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'title_label' => t('Library'),
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'has_body' => FALSE,
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- 'body_label' => t('Library Description'),
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'locked' => TRUE
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);
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return $nodes;
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@@ -60,13 +59,28 @@ function tripal_library_node_info() {
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*
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* @ingroup tripal_library
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*/
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-function tripal_library_perm() {
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+function tripal_library_permisssions() {
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return array(
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- 'access chado_library content',
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- 'create chado_library content',
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- 'delete chado_library content',
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- 'edit chado_library content',
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- 'administer tripal libraries',
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+ 'access chado_library content' => array(
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+ 'title' => t('View Libraries'),
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+ 'description' => t('Allow users to view library pages.'),
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+ ),
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+ 'create chado_library content' => array(
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+ 'title' => t('Create Libraries'),
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+ 'description' => t('Allow users to create new library pages.'),
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+ ),
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+ 'delete chado_library content' => array(
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+ 'title' => t('Delete Libraries'),
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+ 'description' => t('Allow users to delete library pages.'),
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+ ),
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+ 'edit chado_library content' => array(
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+ 'title' => t('Edit Libraries'),
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+ 'description' => t('Allow users to edit library pages.'),
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+ ),
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+ 'adminster tripal library' => array(
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+ 'title' => t('Administer Libraries'),
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+ 'description' => t('Allow users to administer all librarys.'),
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+ ),
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);
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}
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/**
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@@ -92,7 +106,7 @@ function tripal_library_perm() {
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*
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* @ingroup tripal_library
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*/
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-function chado_library_access($op, $node, $account) {
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+function chado_library_node_access($op, $node, $account) {
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if ($op == 'create') {
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if (!user_access('create chado_library content', $account)) {
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return FALSE;
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@@ -169,49 +183,27 @@ function tripal_library_views_api() {
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}
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/**
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- * Implementation of hook_nodeapi().
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- * Display library information for associated features or organisms
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- * This function also provides contents for indexing
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- *
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* @ingroup tripal_library
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*/
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-function tripal_library_nodeapi(&$node, $op, $teaser, $page) {
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-
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- switch ($op) {
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- // Note that this function only adds library view to an organism/feature
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- // node.
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- case 'view':
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- // add the library to the organism/feature search indexing
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- if ($node->build_mode == NODE_BUILD_SEARCH_INDEX) {
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- $node->content['tripal_library_index_version'] = array(
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- '#value' => theme('tripal_library_search_index', $node),
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- );
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- }
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- elseif ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
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- $node->content['tripal_library_index_version'] = array(
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- '#value' => theme('tripal_library_search_result', $node),
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- );
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- }
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- else {
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- switch ($node->type) {
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- case 'chado_organism':
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- // Show library if the organism/feature is not at teaser view
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- $node->content['tripal_organism_libraries'] = array(
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- '#value' => theme('tripal_organism_libraries', $node),
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- );
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- break;
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- case 'chado_feature':
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- // Show library if the organism/feature is not at teaser view
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- $node->content['tripal_feature_libraries'] = array(
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- '#value' => theme('tripal_feature_libraries', $node),
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- );
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- break;
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- }
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+function tripal_library_node_view(&$node, $view_mode, $langcode) {
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+
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+ switch ($node->type) {
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+ case 'chado_organism':
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+ if ($view_mode == 'full') {
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+ $node->content['tripal_organism_libraries'] = array(
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+ '#value' => theme('tripal_organism_libraries', $node),
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+ );
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}
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- break;
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+ break;
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+ case 'chado_feature':
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+ if ($view_mode == 'full') {
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+ $node->content['tripal_feature_libraries'] = array(
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+ '#value' => theme('tripal_feature_libraries', $node),
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+ );
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+ }
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+ break;
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}
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}
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-
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/**
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* We need to let drupal know about our theme functions and their arguments.
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* We create theme functions to allow users of the module to customize the
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@@ -278,17 +270,19 @@ function theme_tripal_library_search_index($node) {
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if ($node->type == 'chado_organism') {
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$content = "";
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// get the libraries for the organism
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- $sql = "SELECT * FROM {library} L ".
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- "WHERE L.organism_id = %d";
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+ $sql = "SELECT * FROM {library} L WHERE L.organism_id = :organism_id";
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$libraries = array();
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- $results = chado_query($sql, $node->organism->organism_id);
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- while ($library = db_fetch_object($results)) {
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+ $results = chado_query($sql, array(':organism_id' => $node->organism->organism_id));
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+ while ($library = $results->fetchObject()) {
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// get the description
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- $sql = "SELECT * FROM {libraryprop} LP ".
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- " INNER JOIN {CVTerm} CVT ON CVT.cvterm_id = LP.type_id ".
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- "WHERE LP.library_id = $library->library_id ".
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- " AND CVT.name = 'library_description'";
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- $desc = db_fetch_object(chado_query($sql));
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+ $sql = "
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+ SELECT *
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+ FROM {libraryprop} LP
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+ INNER JOIN {cvterm} CVT ON CVT.cvterm_id = LP.type_id
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+ WHERE LP.library_id = :library_id
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+ AND CVT.name = 'library_description'
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+ ";
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+ $desc = chado_query($sql, array(':library_id' => $library->library_id))->fetchObject();
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$library->description = $desc->value;
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$libraries[] = $library;
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}
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@@ -303,12 +297,15 @@ function theme_tripal_library_search_index($node) {
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elseif ($node->type == 'chado_feature') {
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$content = "";
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$organism_id = $node->feature->organism_id;
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- $sql = "SELECT * FROM {library} L ".
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- " INNER JOIN {Library_feature} LF ON L.library_id = LF.library_id ".
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- "WHERE LF.feature_id = " . $node->feature->feature_id;
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+ $sql = "
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+ SELECT *
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+ FROM {library} L
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+ INNER JOIN {library_feature} LF ON L.library_id = LF.library_id
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+ WHERE LF.feature_id = :feature_id
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+ ";
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$libraries = array();
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- $results = chado_query($sql);
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- while ($library = db_fetch_object($results)) {
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+ $results = chado_query($sql, array(':feature_id' => $node->feature->feature_id));
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+ while ($library = $results->fetchObject()) {
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$libraries[] = $library;
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}
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if (count($libraries) > 0) {
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@@ -345,19 +342,22 @@ function theme_tripal_library_node_libraries($node) {
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// when a feature is previewed at its creation
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elseif ($node->type == 'chado_feature' && $node->feature->feature_id) {
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$organism_id = $node->feature->organism_id;
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- $sql = "SELECT * FROM {library} L ".
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- " INNER JOIN Library_feature LF ON L.library_id = LF.library_id ".
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- "WHERE LF.feature_id = " . $node->feature->feature_id;
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+ $sql = "
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+ SELECT *
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+ FROM {library} L
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+ INNER JOIN Library_feature LF ON L.library_id = LF.library_id
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+ WHERE LF.feature_id = :feature_id
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+ ";
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$libraries = array();
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- $results = chado_query($sql);
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- while ($library = db_fetch_object($results)) {
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+ $results = chado_query($sql, array(':feature_id' => $node->feature->feature_id));
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+ while ($library = $results->fetchObject()) {
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$libraries[] = $library;
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}
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if (count($libraries) > 0) {
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$lib_additions = array();
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foreach ($libraries as $library) {
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- $sql = "SELECT nid FROM {chado_library} WHERE library_id = %d";
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- $lib_nid = db_result(db_query($sql, $library->library_id));
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+ $sql = "SELECT nid FROM {chado_library} WHERE library_id = :library_id";
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+ $lib_nid = db_query($sql, array(':library_id' => $library->library_id))->fetchField();
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if ($lib_nid) {
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$lib_url = url("node/$lib_nid");
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}
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@@ -383,7 +383,7 @@ function tripal_library_cron() {
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*
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* @ingroup tripal_library
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*/
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-function tripal_library_library_access($op, $node, $account) {
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+function tripal_library_node_access($op, $node, $account) {
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if ($op == 'create') {
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if (!user_access('create chado_library content', $account)) {
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return FALSE;
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@@ -497,12 +497,12 @@ function chado_library_form($node) {
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);
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// get the list of organisms
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- $sql = "SELECT * FROM {Organism}";
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+ $sql = "SELECT * FROM {organism}";
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$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[$organism->organism_id] =
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"$organism->genus $organism->species ($organism->common_name)";
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}
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@@ -539,21 +539,19 @@ function chado_library_validate($node) {
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// check to make sure the unique name on the library is unique
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// before we try to insert into chado.
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if ($node->library_id) {
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- $sql = "SELECT * FROM ".
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- "{Library} WHERE ".
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- "uniquename = '%s' ".
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- "AND NOT library_id = %d";
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- $lib = db_fetch_object(chado_query($sql, $node->uniquename, $node->library_id));
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+ $sql = "
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+ SELECT *
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+ FROM {library}
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+ WHERE uniquename = :uname AND NOT library_id = :library_id
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+ ";
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+ $lib = chado_query($sql, array(':uname' => $node->uniquename, ':library_id' => $node->library_id))->fetchObject();
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}
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else {
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- $sql = "SELECT * FROM ".
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- "{Library} ".
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- "WHERE uniquename = '%s'";
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- $lib = db_fetch_object(chado_query($sql, $node->uniquename));
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+ $sql = "SELECT * FROM {library} WHERE uniquename = :uname";
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+ $lib = chado_query($sql, array(':uname' => $node->uniquename))->fetchObject();
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}
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if ($lib) {
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- form_set_error('uniquename', t('The unique library name already exists. '.
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- 'Please choose another'));
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+ form_set_error('uniquename', t('The unique library name already exists. Please choose another'));
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}
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}
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/**
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@@ -588,18 +586,17 @@ function chado_library_insert($node) {
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$library_id = chado_get_id_for_node('library', $node->nid) ;
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if (!$library_id) {
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// next add the item to the drupal table
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- $sql = "INSERT INTO {chado_library} (nid, vid, library_id) ".
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- "VALUES (%d, %d, %d)";
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- db_query($sql, $node->nid, $node->vid, $library['library_id']);
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+ $sql = "
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+ INSERT INTO {chado_library} (nid, vid, library_id)
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+ VALUES (:nid, :vid, :library_id)
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+ ";
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+ db_query($sql, array(':nid' => $node->nid, ':vid' => $node->vid, ':library_id' => $library['library_id']));
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}
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}
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else {
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drupal_set_message(t('Unable to add library.', 'warning'));
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- watchdog('tripal_library',
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- 'Insert feature: Unable to create library where values: %values',
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- array('%values' => print_r($values, TRUE)),
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- WATCHDOG_WARNING
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- );
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+ watchdog('tripal_library', 'Insert feature: Unable to create library where values: %values',
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+ array('%values' => print_r($values, TRUE)), WATCHDOG_WARNING);
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}
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}
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/**
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@@ -663,8 +660,8 @@ function chado_library_view($node, $teaser = FALSE, $page = FALSE) {
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// but not genus/species/common_name. We need to get those from chado
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// database so they will show up in preview
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if (!$node->genus) {
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- $sql = "SELECT * FROM {organism} WHERE organism_id = %d";
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- $data = db_fetch_object(chado_query($sql, $node->organism_id));
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+ $sql = "SELECT * FROM {organism} WHERE organism_id = :organism_id";
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+ $data = chado_query($sql, array(':organism_id' => $node->organism_id))->fetchObject();
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$node->genus = $data->genus;
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$node->species = $data->species;
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$node->common_name = $data->common_name;
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@@ -689,97 +686,87 @@ function chado_library_delete(&$node) {
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// Remove data from {chado_library}, {node} and {node_revisions} tables of
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// drupal database
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- $sql_del = "DELETE FROM {chado_library} ".
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- "WHERE nid = %d ".
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- "AND vid = %d";
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- db_query($sql_del, $node->nid, $node->vid);
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- $sql_del = "DELETE FROM {node_revisions} ".
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- "WHERE nid = %d ".
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- "AND vid = %d";
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- db_query($sql_del, $node->nid, $node->vid);
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- $sql_del = "DELETE FROM {node} ".
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- "WHERE nid = %d ".
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- "AND vid = %d";
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- db_query($sql_del, $node->nid, $node->vid);
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+ $sql_del = "DELETE FROM {chado_library} WHERE nid = :nid AND vid = :vid";
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+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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+ $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
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+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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+ $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
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+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
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// Remove data from library and libraryprop tables of chado database as well
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- chado_query("DELETE FROM {libraryprop} WHERE library_id = %d", $library_id);
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- chado_query("DELETE FROM {library} WHERE library_id = %d", $library_id);
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+ chado_query("DELETE FROM {libraryprop} WHERE library_id = :library_id", array(':library_id' => $library_id));
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+ chado_query("DELETE FROM {library} WHERE library_id = :library_id", array(':library_id' => $library_id));
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}
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/**
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- * Display block with libraries
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- * @param op - parameter to define the phase being called for the block
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- * @param delta - id of the block to return (ignored when op is list)
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- * @param edit - when op is save, contains the submitted form data
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- *
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* @ingroup tripal_library
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*/
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-function tripal_library_block($op = 'list', $delta = '0', $edit = array()) {
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- switch ($op) {
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- case 'list':
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-
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- $blocks['libreferences']['info'] = t('Tripal Library Cross References');
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- $blocks['libreferences']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['libbase']['info'] = t('Tripal Library Details');
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- $blocks['libbase']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['libterms']['info'] = t('Tripal Library Terms');
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- $blocks['libterms']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['libsynonyms']['info'] = t('Tripal Library Synonyms');
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- $blocks['libsynonyms']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['libproperties']['info'] = t('Tripal Library Properties');
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- $blocks['libproperties']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['featurelibs']['info'] = t('Tripal Feature Libraries');
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- $blocks['featurelibs']['cache'] = BLOCK_NO_CACHE;
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-
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- $blocks['orglibs']['info'] = t('Tripal Organism Libraries');
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- $blocks['orglibs']['cache'] = BLOCK_NO_CACHE;
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-
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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_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
|
|
|
- $nid = arg(1);
|
|
|
- $node = node_load($nid);
|
|
|
-
|
|
|
- $block = array();
|
|
|
- switch ($delta) {
|
|
|
- case 'libreferences':
|
|
|
- $block['subject'] = t('Cross References');
|
|
|
- $block['content'] = theme('tripal_library_references', $node);
|
|
|
- break;
|
|
|
- case 'libbase':
|
|
|
- $block['subject'] = t('Library Details');
|
|
|
- $block['content'] = theme('tripal_library_base', $node);
|
|
|
- break;
|
|
|
- case 'libsynonyms':
|
|
|
- $block['subject'] = t('Synonyms');
|
|
|
- $block['content'] = theme('tripal_library_synonyms', $node);
|
|
|
- break;
|
|
|
- case 'libproperties':
|
|
|
- $block['subject'] = t('Properties');
|
|
|
- $block['content'] = theme('tripal_library_properties', $node);
|
|
|
- break;
|
|
|
- case 'libterms':
|
|
|
- $block['subject'] = t('Library Terms');
|
|
|
- $block['content'] = theme('tripal_library_terms', $node);
|
|
|
- break;
|
|
|
- case 'featurelibs':
|
|
|
- $block['subject'] = t('Libraries');
|
|
|
- $block['content'] = theme('tripal_feature_libraries', $node);
|
|
|
- break;
|
|
|
- case 'orglibs':
|
|
|
- $block['subject'] = t('Libraries');
|
|
|
- $block['content'] = theme('tripal_organism_libraries', $node);
|
|
|
- break;
|
|
|
- default :
|
|
|
- }
|
|
|
- return $block;
|
|
|
- }
|
|
|
+function tripal_library_block_info() {
|
|
|
+
|
|
|
+ $blocks['libreferences']['info'] = t('Tripal Library Cross References');
|
|
|
+ $blocks['libreferences']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['libbase']['info'] = t('Tripal Library Details');
|
|
|
+ $blocks['libbase']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['libterms']['info'] = t('Tripal Library Terms');
|
|
|
+ $blocks['libterms']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['libsynonyms']['info'] = t('Tripal Library Synonyms');
|
|
|
+ $blocks['libsynonyms']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['libproperties']['info'] = t('Tripal Library Properties');
|
|
|
+ $blocks['libproperties']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['featurelibs']['info'] = t('Tripal Feature Libraries');
|
|
|
+ $blocks['featurelibs']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ $blocks['orglibs']['info'] = t('Tripal Organism Libraries');
|
|
|
+ $blocks['orglibs']['cache'] = BLOCK_NO_CACHE;
|
|
|
+
|
|
|
+ return $blocks;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * @ingroup tripal_library
|
|
|
+ */
|
|
|
+function tripal_library_block_view($delta = '') {
|
|
|
+
|
|
|
+ if (user_access('access chado_library content') and arg(0) == 'node' and is_numeric(arg(1))) {
|
|
|
+ $nid = arg(1);
|
|
|
+ $node = node_load($nid);
|
|
|
+
|
|
|
+ $block = array();
|
|
|
+ switch ($delta) {
|
|
|
+ case 'libreferences':
|
|
|
+ $block['subject'] = t('Cross References');
|
|
|
+ $block['content'] = theme('tripal_library_references', $node);
|
|
|
+ break;
|
|
|
+ case 'libbase':
|
|
|
+ $block['subject'] = t('Library Details');
|
|
|
+ $block['content'] = theme('tripal_library_base', $node);
|
|
|
+ break;
|
|
|
+ case 'libsynonyms':
|
|
|
+ $block['subject'] = t('Synonyms');
|
|
|
+ $block['content'] = theme('tripal_library_synonyms', $node);
|
|
|
+ break;
|
|
|
+ case 'libproperties':
|
|
|
+ $block['subject'] = t('Properties');
|
|
|
+ $block['content'] = theme('tripal_library_properties', $node);
|
|
|
+ break;
|
|
|
+ case 'libterms':
|
|
|
+ $block['subject'] = t('Library Terms');
|
|
|
+ $block['content'] = theme('tripal_library_terms', $node);
|
|
|
+ break;
|
|
|
+ case 'featurelibs':
|
|
|
+ $block['subject'] = t('Libraries');
|
|
|
+ $block['content'] = theme('tripal_feature_libraries', $node);
|
|
|
+ break;
|
|
|
+ case 'orglibs':
|
|
|
+ $block['subject'] = t('Libraries');
|
|
|
+ $block['content'] = theme('tripal_organism_libraries', $node);
|
|
|
+ break;
|
|
|
+ default :
|
|
|
+ }
|
|
|
+ return $block;
|
|
|
}
|
|
|
}
|
spficklin