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@@ -1,66 +1,225 @@
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<?php
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function tripal_core_extensions_form($form, &$form_state = NULL) {
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- $tab = $_GET['tab'];
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-
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- $form['extensions'] = array(
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- '#type' => 'vertical_tabs',
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- '#default_tab' => $tab,
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- );
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-
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- // Get the RSS feed XML from the tripa.info website.
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- $content = file_get_contents("http://tripal.info/rss/extensions.xml");
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+ // Get the RSS feed XML from the tripa.info website and save it to
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+ // a temp file so that we don't have to keep pulling the XML
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+ // everythime the page is loaded. If the temp file is older than 1 hours
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+ // then we'll pull it again. The number of seconds in an hour is 3600
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+ $tmp_file = sys_get_temp_dir() . '/tripal_rss_extensions.xml';
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+ if (!file_exists($tmp_file) or time() - filemtime($tmp_file) > 3600) {
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+ $content = file_get_contents("http://tripal.info/rss/extensions.xml");
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+ file_put_contents($tmp_file, $content);
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+ }
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+ else {
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+ $content = file_get_contents($tmp_file);
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+ }
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$xml = new SimpleXmlElement($content);
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$namespace = "http://tripal.info/rss/extensions/";
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- // Parse the items into an array indexed by category and compatible versions.
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- $items = array();
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+
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+ $tab = array_key_exists('tab', $_GET) ? $_GET['tab'] : '';
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+
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+ // Get any filters by categories.
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+ $filters = array();
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+ if (array_key_exists('values', $form_state)) {
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+ foreach ($form_state['values'] as $key => $value) {
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+ // Get the category to be filtered on.
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+ $matches = array();
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+ if (preg_match('/^categories-(.*?)$/', $key, $matches)) {
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+ if ($value == 'any') {
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+ continue;
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+ }
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+ $filters[$matches[1]] = $value;
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+ }
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+ }
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+ }
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+
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+ // Parse the items into an array indexed by type and compatible versions.
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+ $extensions = array();
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$types = array();
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+ $type_ids = array();
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$categories = array();
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- foreach ($xml->channel->item as $item) {
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- $type = (string) $item->category;
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+ $cvs = array();
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+ $tvs = array();
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+ foreach ($xml->channel->item as $extension) {
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+ // Get the type of extension, convert that into a machine-readable name,
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+ // and build the array of types.
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+ $type = (string) $extension->category;
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+ $type_id = preg_replace('/[^\w]/','_', strtolower($type));
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+ $type_ids[$type] = $type_id;
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+ if (!in_array($type_id, $types)) {
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+ $types[$type] = 1;
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+ }
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+
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+ // Get the categories list for this item.
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+ $cats = preg_split('/, /', (string) $extension->children($namespace)->categories);
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+
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+ // Get the guid for this extension
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+ $guid = (string) $extension->guid;
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+
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// In order to get fields in the 'tripal_extension' name space we must
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// pass in the $namespace to the children function. We first get the
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// Tripal versions, then the chado versions and organize the elements
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// accordintly.
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- $tvs = preg_split('/, /', (string) $item->children($namespace)->tripal_version);
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- foreach($tvs as $tv) {
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- $cvs = preg_split('/, /', (string) $item->children($namespace)->chado_version);
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- foreach($cvs as $cv) {
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- // Index the items by category, tripal version and chado version
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- $items[$tv][$cv][$type][] = $item;
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- if (!in_array($type, $types)) {
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- $types[] = $type;
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+ $tvs_temp = preg_split('/, /', (string) $extension->children($namespace)->tripal_version);
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+ foreach($tvs_temp as $tv) {
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+ $tvs[$tv] = 1;
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+ $cvs_temp = preg_split('/, /', (string) $extension->children($namespace)->chado_version);
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+ foreach($cvs_temp as $cv) {
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+ $cvs[$cv] = 1;
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+
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+ // Keep track of the categories this item has been assigned.
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+ foreach ($cats as $cat) {
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+ $categories[$tv][$cv][$type][$cat] = 1;
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+ $categories['any'][$cv][$type][$cat] = 1;
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+ $categories[$tv]['any'][$type][$cat] = 1;
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+ $categories['any']['any'][$type][$cat] = 1;
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+ }
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+
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+ // If there are filters then only include extensions that match the filters.
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+ if (array_key_exists($type_id, $filters) and !in_array($filters[$type_id], $cats)) {
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+ continue;
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}
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+
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+ // Index the items by type, tripal version and chado version.
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+ $item = array();
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+ foreach ($extension->children() as $child) {
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+ $item[$child->getName()] = (string) $child;
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+ }
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+ foreach ($extension->children($namespace) as $child) {
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+ $item[$namespace][$child->getName()] = (string) $child;
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+ }
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+ $extensions[$tv][$cv][$type][$guid] = $item;
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+ $extensions['any'][$cv][$type][$guid] = $item;
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+ $extensions[$tv]['any'][$type][$guid] = $item;
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+ $extensions['any']['any'][$type][$guid] = $item;
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}
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}
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}
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+ // Convert the arrays from an associative array into a normal array, and sort.
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+ $types = array_keys($types);
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+ sort($types);
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+ $cvs = array_keys($cvs);
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+ sort($cvs);
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+ $tvs = array_keys($tvs);
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+ sort($tvs);
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// Get the Chado version and convert to the expected format
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$chado_version = chado_get_version(TRUE);
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$chado_version = preg_replace('/^(\d\.\d).*$/', "v$1x", $chado_version);
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+ $my_chado_version = $chado_version;
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+ // The default value can come from the pager links (thus via $_GET) or
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+ // via ajax call (thus via $form_state).
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+ if (array_key_exists('cv', $_GET)) {
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+ $chado_version = $_GET['cv'];
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+ }
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+ if (array_key_exists('values', $form_state) and array_key_exists('cv', $form_state['values'])) {
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+ $chado_version = $form_state['values']['cv'];
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+ }
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// Get the Tripal version. This is the version set in the tripal_core.info
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$info = system_get_info('module', 'tripal_core');
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$tripal_version = $info['version'];
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$tripal_version = preg_replace('/^.*?-(\d\.\d+).*$/', "v$1", $tripal_version);
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+ $my_tripal_version = $tripal_version;
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+ if (array_key_exists('tv', $_GET)) {
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+ $tripal_version = $_GET['tv'];
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+ }
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+ if (array_key_exists('values', $form_state) and array_key_exists('tv', $form_state['values'])) {
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+ $tripal_version = $form_state['values']['tv'];
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+ }
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+ // Add the instructions.
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$form['instructions'] = array(
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'#type' => 'item',
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'#markup' => t('This page will help you find extensions that are available
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- for Tripal. Select an extension type from the vertical tabs to see
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- the each type of extension.')
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+ for Tripal. Select an extension type from the vertical tabs. The content
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+ of this page is constructed from an RSS feed provided by tripal.info.
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+ There may be no content if the tripal.info site is unavailable. The RSS
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+ feed will be cached for one hour.')
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+ );
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+ // Add the filters fieldset.
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+ $form['filters'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Filters',
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+ '#description' => t('You can filter which extensions are visible by
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+ changing the Tripal ahd Chado versions. By default only those
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+ extensions that are compatible with the currently installed Tripal
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+ and Chado verions are shown.'),
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE,
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+ );
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+ $summary_message = 'Currently showing extensions compatible with ';
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+ if ($tripal_version != 'any' and $chado_version != 'any') {
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+ $summary_message .= "<strong>Tripal $tripal_version</strong> and <strong>Chado $chado_version</strong>.";
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+ }
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+ elseif ($tripal_version == 'any' and $chado_version != 'any') {
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+ $summary_message .= "<strong>any Tripal</strong> version and <strong>Chado $chado_version</strong>.";
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+ }
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+ elseif ($tripal_version != 'any' and $chado_version == 'any') {
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+ $summary_message .= "<strong>Tripal $tripal_version</strong> and <strong>any Chado</strong> version.";
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+ }
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+ elseif ($tripal_version == 'any' and $chado_version == 'any') {
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+ $summary_message .= "<strong>any Tripal</strong> version and <strong>any Chado</strong> version.";
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+ }
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+ $form['filter_summary'] = array(
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+ '#type' => 'item',
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+ '#markup' => $summary_message,
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);
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- // Build the fieldsets for each category
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- sort($types);
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- $type_ids = array();
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+ // Add the Tripal version select box.
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+ $options = array();
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+ $options['any'] = '--Any--';
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+ foreach ($tvs as $tv) {
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+ $options[$tv] = $tv;
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+ }
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+ $form['filters']['tv'] = array(
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+ '#type' => 'select',
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+ '#title' => 'Tripal',
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+ '#options' => $options,
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+ '#default_value' => $tripal_version,
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+ '#ajax' => array(
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+ 'callback' => "tripal_core_extensions_form_ajax_callback",
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+ 'wrapper' => 'tripal_core_extensions',
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+ 'effect' => 'fade',
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+ 'method' => 'replace',
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+ ),
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+ '#prefix' => '<div style="float: left;">',
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+ '#suffix' => '</div>'
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+ );
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+
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+ // Add the Chado version select box.
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+ $options = array();
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+ $options['any'] = '--Any--';
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+ foreach ($cvs as $cv) {
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+ $options[$cv] = $cv;
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+ }
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+ $form['filters']['cv'] = array(
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+ '#type' => 'select',
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+ '#title' => 'Chado',
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+ '#options' => $options,
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+ '#default_value' => $chado_version,
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+ '#ajax' => array(
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+ 'callback' => "tripal_core_extensions_form_ajax_callback",
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+ 'wrapper' => 'tripal_core_extensions',
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+ 'effect' => 'fade',
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+ 'method' => 'replace',
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+ ),
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+ '#prefix' => '<div style="float: left; padding-left: 10px">',
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+ '#suffix' => '</div>'
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+ );
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+
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+ // Add the vertical tabs
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+ $form['extensions'] = array(
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+ '#type' => 'vertical_tabs',
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+ '#default_tab' => $tab,
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+ );
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+
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+ // Add the fieldsets for each type
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foreach ($types as $type) {
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- $type_id = preg_replace('/[^\w]/','_', strtolower($type));
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- $type_ids[$type] = $type_id;
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$form[$type] = array(
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- '#id' => $type_id,
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+ '#id' => $type_ids[$type],
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'#type' => 'fieldset',
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'#title' => $type . 's',
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'#collapsed' => TRUE,
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@@ -69,14 +228,82 @@ function tripal_core_extensions_form($form, &$form_state = NULL) {
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);
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}
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- // Iterate through the compatible extensions. We will add a pager for
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+ // Iterate through all of the extensions and add them to the form.
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+ tripal_core_extension_form_add_extensions($form, $form_state,
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+ $extensions[$tripal_version][$chado_version], $categories, $tripal_version,
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+ $chado_version, $my_tripal_version, $my_chado_version, $type_ids,
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+ $namespace, $filters);
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+
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+ foreach ($types as $type) {
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+ if (count(element_children($form[$type])) == 0) {
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+ $form[$type]['empty'] = array(
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+ '#type' => 'item',
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+ '#markup' => '<strong>There are no matching ' . strtolower($type) . '(s).</strong>',
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+ );
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+ }
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+ }
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+
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+ $form['#prefix'] = '<div id="tripal_core_extensions">';
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+ $form['#suffix'] = '</div>';
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+ $form['#submit'][] = 'tripal_core_extensions_form_submit';
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+ return $form;
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+}
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+
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+/**
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+ * Adds each extension to the form.
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+ *
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+ * This function exits to simplify the the tripal_core_extension_form()
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+ * function.
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+ */
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+function tripal_core_extension_form_add_extensions(&$form, $form_state, $extensions,
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+ $categories, $tripal_version, $chado_version, $my_tripal_version,
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+ $my_chado_version, $type_ids, $namespace, $filters) {
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+
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+ // Iterate through the extensions. We will add a pager for
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// each type of extension, and display only those that should appear
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// on the page.
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$type_index = 0;
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- foreach ($items[$tripal_version][$chado_version] as $type => $items) {
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+ foreach ($extensions as $type => $extensions) {
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+ $total_items = count($extensions);
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+
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+ // Indicate how many matching extensions were found
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+ $form[$type]['total_found'] = array(
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+ '#type' => 'item',
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+ '#markup' => '<strong>Found ' . $total_items . ' matching ' . strtolower($type) . '(s)</strong>',
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+ );
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+
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+ // Add the category select box;
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+ $cats = array_keys($categories[$tripal_version][$chado_version][$type]);
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+ sort($cats);
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+ $options = array();
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+ $options['any'] = '--Any--';
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+ foreach ($cats as $cat) {
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+ $options[$cat] = $cat;
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+ }
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+ // The default value can come from the pager links (thus via $_GET) or
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+ // via ajax call (thus via $form_state).
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+ $default_filter = '';
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+ if (array_key_exists('categories-' . $type_ids[$type], $_GET)) {
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+ $default_filter = $_GET['categories-' . $type_ids[$type]];
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+ }
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+ if (array_key_exists('values', $form_state) and array_key_exists('categories-' . $type_ids[$type], $form_state['values'])) {
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+ $default_filter = $form_state['values']['categories-' . $type_ids[$type]];
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+ }
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+ $form[$type]['filters']['categories-' . $type_ids[$type]] = array(
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+ '#type' => 'select',
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+ '#title' => 'Filter by Category',
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+ '#options' => $options,
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+ '#default_value' => $default_filter,
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+ '#ajax' => array(
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+ 'callback' => "tripal_core_extensions_form_ajax_callback",
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+ 'wrapper' => 'tripal_core_extensions',
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+ 'effect' => 'fade',
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+ 'method' => 'replace',
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+ ),
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+ );
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+
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// Initialize pager and gets current page
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$num_per_page = 5;
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- $total_items = count($items);
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$page = pager_default_initialize($total_items, $num_per_page, $type_index);
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// Gets first record and last record to show
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@@ -84,71 +311,155 @@ function tripal_core_extensions_form($form, &$form_state = NULL) {
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$end = ($start + $num_per_page < $total_items)? $start + $num_per_page : $total_items;
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// Iterate through each of the elements and add them to the form if
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// they are within the page
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- $item_index = 0;
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- foreach ($items as $item) {
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+ $extension_index = 0;
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+ foreach ($extensions as $guid => $extension) {
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// Skip items that aren't on our current page.
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- if ($item_index < $start or $item_index >= $end) {
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- $item_index++;
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+ if ($extension_index < $start or $extension_index >= $end) {
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+ $extension_index++;
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continue;
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}
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- // The unique guid is used to keep track of each extension in the form.
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- $guid = (string) $item->guid;
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// If this is an extension module then there will be a home page for it
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$home_page = '';
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- if ((string) $item->children($namespace)->home_page) {
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- $home_page = "<strong>Project Home: </strong>" . (string) $item->children($namespace)->home_page . "</br>";
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+ if (array_key_exists('home_page', $extension[$namespace])) {
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+ $home_page = "<strong>Project Home: </strong>" . $extension[$namespace]['home_page'] . "</br>";
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+ }
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+
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+ // Determine if this extension is compatible with this site.
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+ $incompatible = '';
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|
+ $tvs_temp = preg_split('/, /', $extension[$namespace]['tripal_version']);
|
|
|
+ $cvs_temp = preg_split('/, /', $extension[$namespace]['chado_version']);
|
|
|
+ if (!in_array($my_tripal_version, $tvs_temp)) {
|
|
|
+ $incompatible .= "<li>This extensions is not compatible with this version of Tripal.</li>";
|
|
|
+ }
|
|
|
+ if (!in_array($my_chado_version, $cvs_temp)) {
|
|
|
+ $incompatible .= "<li>This extensions is not compatible with the installed Chado version.</li>";
|
|
|
+ }
|
|
|
+ $incompatible = t($incompatible);
|
|
|
+
|
|
|
+ // Determine if this extension is already installed.
|
|
|
+ $is_installed = '';
|
|
|
+ switch ($type) {
|
|
|
+ case 'Bulk Loader Template':
|
|
|
+ $blk_id = db_select('tripal_bulk_loader_template' ,'tblt')
|
|
|
+ ->fields('tblt', array('template_id'))
|
|
|
+ ->condition('name', $extension['title'])
|
|
|
+ ->execute()
|
|
|
+ ->fetchField();
|
|
|
+ if ($blk_id) {
|
|
|
+ $is_installed = '<li>A bulk loader tempalte with this name is already installed.</li>';
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ case 'Materialized View':
|
|
|
+ $mview_id = tripal_get_mview_id($extension[$namespace]['mview_name']);
|
|
|
+ if ($mview_id) {
|
|
|
+ $is_installed = '<li>A materialized view with this name is already installed.</li>';
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ case 'Extension Module':
|
|
|
+ if (module_exists($extension[$namespace]['module_name'])) {
|
|
|
+ $is_installed = '<li>A module with this name is already installed.</li>';
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ default:
|
|
|
+ break;
|
|
|
+ }
|
|
|
+ $is_installed = t($is_installed);
|
|
|
+
|
|
|
+ // Does this module appear to be available on Drupal.org?
|
|
|
+ $project = '';
|
|
|
+ if ($type == 'Extension Module') {
|
|
|
+ // Does it have a drupal project name?
|
|
|
+ if (!array_key_exists('drupal_project', $extension[$namespace])) {
|
|
|
+ // Since it doesn't have a drupal project name is it in a sandbox?
|
|
|
+ if (!preg_match('/www.drupal.org\/sandbox/', $extension[$namespace]['home_page'])) {
|
|
|
+ $project = t("<li>This module does not appear to be available as a " .
|
|
|
+ "full Drupal project or within a Drupal sandbox and thus cannot ".
|
|
|
+ "be downloaded here. You may have to manually download it.</li>");
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $project = ("<li>This module is still in a Sandbox on Drupal.org, and
|
|
|
+ cannot be downloaded from here. You will have to manually download
|
|
|
+ this module.</li>");
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Make sure the bulk loader module is installed, or we cannot provide
|
|
|
+ // the bulk loader import button.
|
|
|
+ $other = '';
|
|
|
+ if ($type == 'Bulk Loader Template' and !module_exists('tripal_bulk_loader')) {
|
|
|
+ $other = t('<li>The bulk loader
|
|
|
+ module is not enabled. If you would like to import a loading template
|
|
|
+ please enable it.</li>');
|
|
|
}
|
|
|
|
|
|
// If the user click's the button to import the extension then we
|
|
|
// need the item in the submit function so we can process the import.
|
|
|
- $form[$type]['item-' . $guid] = array(
|
|
|
+ $form[$type]['extension-' . $guid] = array(
|
|
|
'#type' => 'value',
|
|
|
- '#value' => $item,
|
|
|
+ '#value' => $extension,
|
|
|
);
|
|
|
|
|
|
+ $warnings = '';
|
|
|
+ if ($incompatible or $is_installed or $project or $other) {
|
|
|
+ $warnings = '<div class="messages warning"><ul>' .
|
|
|
+ $incompatible . ' ' .
|
|
|
+ $is_installed . ' ' .
|
|
|
+ $project . ' ' .
|
|
|
+ $other . '</ul></div>';
|
|
|
+ }
|
|
|
+
|
|
|
// Create the form elements that we'll later theme into tables.
|
|
|
$form[$type][$guid]['header'] = array(
|
|
|
- '#markup' => l((string) $item->title, $item->link),
|
|
|
+ '#markup' => l($extension['title'], $extension['link']),
|
|
|
);
|
|
|
$form[$type][$guid]['details'] = array(
|
|
|
'#markup' => "" .
|
|
|
- "<strong>Type:</strong> " . $type . "</br>" .
|
|
|
- "<strong>Categories: </strong>" . (string) $item->children($namespace)->categories . "</br>" .
|
|
|
- "<strong>Authors: </strong>" . (string) $item->children($namespace)->authors . "</br>" .
|
|
|
- "<strong>Chado compatible versions: </strong>" . (string) $item->children($namespace)->chado_version . "</br>" .
|
|
|
- "<strong>Chado compatible versions: </strong>" . (string) $item->children($namespace)->tripal_version . "</br>" .
|
|
|
- $home_page .
|
|
|
- "<p>" . (string) $item->description . "</p>",
|
|
|
+ "<strong>Type:</strong> " . $type . "</br>" .
|
|
|
+ "<strong>Categories: </strong>" . $extension[$namespace]['categories'] . "</br>" .
|
|
|
+ "<strong>Authors: </strong>" . $extension[$namespace]['authors'] . "</br>" .
|
|
|
+ "<strong>Chado compatible versions: </strong>" . $extension[$namespace]['chado_version'] . "</br>" .
|
|
|
+ "<strong>Tripal compatible versions: </strong>" . $extension[$namespace]['tripal_version'] . "</br>" .
|
|
|
+ $home_page .
|
|
|
+ "<strong>tripal.info Page: </strong>" . l($extension['link'], $extension['link']) . "</br>" .
|
|
|
+ $warnings .
|
|
|
+ "<p>" . $extension['description'] . "</p>",
|
|
|
);
|
|
|
// Add an import button to each of types that can support import.
|
|
|
switch ($type) {
|
|
|
case 'Bulk Loader Template':
|
|
|
- $form[$type][$guid]['import'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => "Import Loader",
|
|
|
- '#name' => "import-" . $guid,
|
|
|
- );
|
|
|
+ if (!$incompatible and !$is_installed and !$project) {
|
|
|
+ $form[$type][$guid]['import'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => "Import Loader",
|
|
|
+ '#name' => "import-" . $guid,
|
|
|
+ );
|
|
|
+ }
|
|
|
break;
|
|
|
case 'Materialized View':
|
|
|
- $form[$type][$guid]['import'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => "Import MView",
|
|
|
- '#name' => "import-" . $guid,
|
|
|
- );
|
|
|
+ if (!$incompatible and !$is_installed and !$project) {
|
|
|
+ $form[$type][$guid]['import'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => "Import MView",
|
|
|
+ '#name' => "import-" . $guid,
|
|
|
+ );
|
|
|
+ }
|
|
|
break;
|
|
|
case 'Extension Module':
|
|
|
- $form[$type][$guid]['import'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => "Download Module",
|
|
|
- '#name' => "import-" . $guid,
|
|
|
- );
|
|
|
+ if (!$incompatible and !$is_installed and !$project) {
|
|
|
+ $form[$type][$guid]['import'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => "Download Module",
|
|
|
+ '#name' => "import-" . $guid,
|
|
|
+ );
|
|
|
+ }
|
|
|
break;
|
|
|
default:
|
|
|
break;
|
|
|
}
|
|
|
$form[$type][$guid]['#theme'] = 'tripal_core_extensions_form_tables';
|
|
|
- $item_index++;
|
|
|
+ $extension_index++;
|
|
|
}
|
|
|
|
|
|
// Now create and theme the pager.
|
|
|
@@ -157,25 +468,31 @@ function tripal_core_extensions_form($form, &$form_state = NULL) {
|
|
|
'element' => $type_index,
|
|
|
'parameters' => array(
|
|
|
'tab' => $type_ids[$type],
|
|
|
+ 'cv' => $chado_version,
|
|
|
+ 'tv' => $tripal_version,
|
|
|
),
|
|
|
'quantity' => $num_per_page,
|
|
|
);
|
|
|
|
|
|
+ // now add the category filters to the params array
|
|
|
+ foreach ($filters as $filter_id => $value) {
|
|
|
+ $pager['parameters']['categories-' . $filter_id] = $value;
|
|
|
+ }
|
|
|
+
|
|
|
// because this may be an ajax callback, the theme_pager will set the URL to be
|
|
|
// "system/ajax", so we need to reset that
|
|
|
+ $pager = theme('pager', $pager);
|
|
|
global $base_path;
|
|
|
$pager = str_replace($base_path . "system/ajax", "", $pager) ;
|
|
|
|
|
|
$form[$type]['pager'] = array(
|
|
|
'#type' => 'item',
|
|
|
- '#markup' => theme('pager', $pager),
|
|
|
+ '#markup' => $pager,
|
|
|
);
|
|
|
$type_index++;
|
|
|
}
|
|
|
- return $form;
|
|
|
}
|
|
|
|
|
|
-
|
|
|
/**
|
|
|
* Process the import buttons.
|
|
|
*
|
|
|
@@ -188,16 +505,31 @@ function tripal_core_extensions_form_submit($form, &$form_state) {
|
|
|
$guid = preg_replace('/^import-(\d+)$/', "$1", $clicked_button);
|
|
|
if ($guid) {
|
|
|
$namespace = "http://tripal.info/rss/extensions/";
|
|
|
- $item = $form_state['values']['item-' . $guid];
|
|
|
- $type = $item->category;
|
|
|
+ $extension = $form_state['values']['extension-' . $guid];
|
|
|
+ $type = $extension['category'];
|
|
|
switch ($type) {
|
|
|
case 'Bulk Loader Template':
|
|
|
+ // TODO: we need an API function for adding a bulk loader
|
|
|
+ $id = db_insert('tripal_bulk_loader_template')
|
|
|
+ ->fields(array(
|
|
|
+ 'name' => $extension['title'],
|
|
|
+ 'template_array' => $extension[$namespace]['bulkldr_export'],
|
|
|
+ 'created' => time(),
|
|
|
+ 'changed' => time()
|
|
|
+ ))
|
|
|
+ ->execute();
|
|
|
+ if (!$id) {
|
|
|
+ drupal_set_message("Cannot import this bulk loader. Please view the 'Recent log messages' report for more details.", 'error');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message("Bulk loader succesfully added.");
|
|
|
+ }
|
|
|
break;
|
|
|
case 'Materialized View':
|
|
|
- $modulename = 'tripal_core';
|
|
|
- $mview_name = (string) $item->children($namespace)->mview_name;
|
|
|
- $mview_schema = (string) $item->children($namespace)->mview_schema;
|
|
|
- $mview_sql = (string) $item->children($namespace)->mview_sql;
|
|
|
+ $module_name = 'tripal_core';
|
|
|
+ $mview_name = $extension[$namespace]['mview_name'];
|
|
|
+ $mview_schema = $extension[$namespace]['mview_schema'];
|
|
|
+ $mview_sql = $extension[$namespace]['mview_sql'];
|
|
|
|
|
|
// Validate the contents of the schema array.
|
|
|
// TODO: security issue!! Before using 'eval' on this string
|
|
|
@@ -207,12 +539,75 @@ function tripal_core_extensions_form_submit($form, &$form_state) {
|
|
|
$success = eval("\$schema_array = $mview_schema;");
|
|
|
$error = chado_validate_custom_table_schema($schema_array);
|
|
|
if ($error) {
|
|
|
- drupal_set_message("Cannot import Materialized View. $error");
|
|
|
+ drupal_set_message("Cannot import Materialized View: $error", "error");
|
|
|
}
|
|
|
- tripal_add_mview($mview_name, $modulename, $schema_array, $mview_sql);
|
|
|
+ tripal_add_mview($mview_name, $module_name, $schema_array, $mview_sql);
|
|
|
break;
|
|
|
case 'Extension Module':
|
|
|
+ if (array_key_exists('drupal_project', $extension[$namespace])) {
|
|
|
+ module_load_include('module', 'update', 'update');
|
|
|
+ module_load_include('inc', 'update', 'update.manager');
|
|
|
+ $project = $extension[$namespace]['drupal_project'];
|
|
|
+ $tar = tripal_core_extensions_get_latest_module_version($project);
|
|
|
+ if (!$tar) {
|
|
|
+ drupal_set_message('Cannot find a suitable release of this module
|
|
|
+ for download. You may need to manually install this module.', 'error');
|
|
|
+ }
|
|
|
+ else {
|
|
|
|
|
|
+ // Download the file from the Drupal repository
|
|
|
+ $local_cache = update_manager_file_get($tar);
|
|
|
+ if (!$local_cache) {
|
|
|
+ drupal_set_message('Cannot download the file. Check the
|
|
|
+ "Recent log messages" for relavent errors.', 'error');
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ // The following code was borrowed from the update_manager_install_form_submit()
|
|
|
+ // of drupal in the modules/update/update.manager.inc file.
|
|
|
+ $directory = _update_manager_extract_directory();
|
|
|
+ try {
|
|
|
+ $archive = update_manager_archive_extract($local_cache, $directory);
|
|
|
+ }
|
|
|
+ catch (Exception $e) {
|
|
|
+ drupal_set_message('Cannot extract the file. Please check
|
|
|
+ permissions in the modules directory', 'error');
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ $archive_errors = update_manager_archive_verify($project, $local_cache, $directory);
|
|
|
+ if (!empty($archive_errors)) {
|
|
|
+ foreach ($archive_errors as $error) {
|
|
|
+ drupal_set_message($error, 'error');
|
|
|
+ }
|
|
|
+ }
|
|
|
+ $project_location = $directory . '/' . $project;
|
|
|
+ try {
|
|
|
+ $updater = Updater::factory($project_location);
|
|
|
+ }
|
|
|
+ catch (Exception $e) {
|
|
|
+ drupal_set_message($e->getMessage(), 'error');
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ $project_real_location = drupal_realpath($project_location);
|
|
|
+ $arguments = array(
|
|
|
+ 'project' => $project,
|
|
|
+ 'updater_name' => get_class($updater),
|
|
|
+ 'local_url' => $project_real_location,
|
|
|
+ );
|
|
|
+ module_load_include('inc', 'update', 'update.authorize');
|
|
|
+ $filetransfer = new FileTransferLocal(DRUPAL_ROOT);
|
|
|
+ call_user_func_array('update_authorize_run_install', array_merge(array($filetransfer), $arguments));
|
|
|
+
|
|
|
+ drupal_set_message('It appears the module was downloaded and
|
|
|
+ extracted. You can now ' . l('enable this module'. 'admin/modules') . '.');
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message('Cannot download this module. The Drpual project
|
|
|
+ name is not set. You may have to manually download this module, and
|
|
|
+ if possible encourage the developers to set the project name if it
|
|
|
+ has been fully published on Drupal.org already.', 'error');
|
|
|
+ }
|
|
|
break;
|
|
|
default:
|
|
|
break;
|
|
|
@@ -220,7 +615,6 @@ function tripal_core_extensions_form_submit($form, &$form_state) {
|
|
|
}
|
|
|
}
|
|
|
|
|
|
-
|
|
|
/**
|
|
|
* The theme function for rendering each element's table.
|
|
|
*
|
|
|
@@ -259,4 +653,99 @@ function theme_tripal_core_extensions_form_tables($variables) {
|
|
|
);
|
|
|
|
|
|
return theme_table($table);
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * A callback function for the form
|
|
|
+ *
|
|
|
+ * @return unknown
|
|
|
+ */
|
|
|
+function tripal_core_extensions_form_ajax_callback($form, $form_state) {
|
|
|
+ // This function need not do anything as the form will take care of
|
|
|
+ // updates needed. We just need to return the form.
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Determines the most recent downloadable package for a module.
|
|
|
+ *
|
|
|
+ * This function will connect to Drupal.org's RSS feed for a project and
|
|
|
+ * determine the most recent version of the module and return the URL
|
|
|
+ * for it's package.
|
|
|
+ *
|
|
|
+ * @param $project
|
|
|
+ */
|
|
|
+function tripal_core_extensions_get_latest_module_version($project_name) {
|
|
|
+ // First use the Drupal RESTful API to get the project
|
|
|
+ $url = "https://www.drupal.org/api-d7/node.json?type=project_module&field_project_machine_name=$project_name";
|
|
|
+ $result = json_decode(file_get_contents($url), TRUE);
|
|
|
+ $project = $result['list'][0];
|
|
|
+ $nid = $project['nid'];
|
|
|
+
|
|
|
+ // Second get the releases for this node and find releases for this Drupal
|
|
|
+ $url = "https://www.drupal.org/api-d7/node.json?type=project_release&field_release_project=$nid";
|
|
|
+ $result = json_decode(file_get_contents($url), TRUE);
|
|
|
+ $releases = $result['list'];
|
|
|
+ $drupal_version = VERSION;
|
|
|
+ $drupal_major = preg_replace('/^(\d+)\.\d+$/', "$1", $drupal_version);
|
|
|
+ $best_release = NULL;
|
|
|
+ foreach ($releases as $release) {
|
|
|
+ // This release must match the Drupal major version or it won't
|
|
|
+ // be compatiable. If it doesn't we'll skip it.
|
|
|
+ $release_version = $release['field_release_version'];
|
|
|
+ $release_drupal = preg_replace('/^(\d+)\.x-.*$/', "$1", $release_version);
|
|
|
+ if ($release_drupal != $drupal_major) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Set the current release to be the best one. On successive iterations
|
|
|
+ // we'll check to see if that is still true.
|
|
|
+ if ($best_release == NULL) {
|
|
|
+ $best_release = $release;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if ($release['field_release_version_major'] > $best_release['field_release_version_major']) {
|
|
|
+ $best_release = $release;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ if ($release['field_release_version_patch'] > $best_release['field_release_version_patch']) {
|
|
|
+ $best_release = $release;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ // If the best version has no extra part then let's keep it as this is the
|
|
|
+ // most stable release.
|
|
|
+ if (!$best_release['field_release_version_extra']) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Convert the 'extra' part to a numeric value that will let us compare
|
|
|
+ // the ranks of the release versions.
|
|
|
+ $extra_rank = array(
|
|
|
+ 'unstable' => 1,
|
|
|
+ 'alpha' => 2,
|
|
|
+ 'beta' => 3,
|
|
|
+ 'rc' => 4,
|
|
|
+ );
|
|
|
+ $matches = array();
|
|
|
+ $this_extra = 0;
|
|
|
+ if (preg_match('/^(.*?)(\d+)$/', $release['field_release_version_extra'], $matches)) {
|
|
|
+ $this_extra = $extra_rank[$matches[1]] . "." . $matches[2];
|
|
|
+ }
|
|
|
+ $best_extra = 0;
|
|
|
+ if (preg_match('/^(.*?)(\d+)$/', $best_release['field_release_version_extra'], $matches)) {
|
|
|
+ $best_extra = $extra_rank[$matches[1]] . "." . $matches[2];
|
|
|
+ }
|
|
|
+ if ($this_extra > $best_extra) {
|
|
|
+ $best_release = $release;
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // If we have a best result then build the download string.
|
|
|
+ // TODO: we may need to make another web services call to get the actual
|
|
|
+ // download path, but for now we'll hard code the construction of it.
|
|
|
+ if ($best_release) {
|
|
|
+ return 'http://ftp.drupal.org/files/projects/' . $project_name . '-' . $best_release['field_release_version'] . '.tar.gz';
|
|
|
+ }
|
|
|
+ return '';
|
|
|
}
|
Stephen Ficklin