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<?php
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register_activation_hook(__FILE__, 'vcell_my_activation');
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function vcell_my_activation() {
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vcell_log_me('my_activation() invoked ... running do_this_hourly() immeciately upon activation ... and then schedule it periodically');
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vcell_do_this_hourly();
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}
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function vcell_do_this_hourly(){
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vcell_log_me('hourly processing begun');
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$publications =& vcell_get_publications_object();
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vcell_log_me('inserting publications and biomodel posts as needed');
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foreach($publications as $pub){
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$pubPost =& vcell_find_publication_post($pub->pubKey);
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if (is_null($pubPost)){
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vcell_insert_publication_post($pub);
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$pubPost =& vcell_find_publication_post($pub->pubKey);
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}
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if (!empty($pub->biomodelReferences)){
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foreach ($pub->biomodelReferences as $bioref){
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$bmKey = $bioref->bmKey;
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$biomodel =& vcell_get_biomodel_object($bmKey);
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$bmPost =& vcell_find_biomodel_post($bmKey);
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if (is_null($bmPost)){
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vcell_insert_biomodel_post($biomodel);
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}else{
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$biomodelPostId = $bmPost->ID;
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vcell_update_biomodel_post($biomodel,$biomodelPostId);
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}
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}
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}
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vcell_log_me('updating publications post ' . $pubPost->ID);
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vcell_update_publication_post($pub, $pubPost->ID);
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}
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vcell_log_me('hourly processing complete');
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}
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function &vcell_find_biomodel_post($bmKey){
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$args = array(
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'meta_key' => 'bmKey',
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'meta_value' => $bmKey,
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'category_name' => 'biomodel',
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'post_type' => 'post',
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'post_status' => 'any',
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'posts_per_page' => -1
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);
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$posts = get_posts($args);
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if (is_null($posts) || empty($posts)){
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$posts = NULL;
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return $posts;
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}else if (is_array($posts)){
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return $posts[0];
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}else{
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return $posts;
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}
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}
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function vcell_insert_biomodel_post($biomodel){
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$biomodelCatID = get_cat_ID('biomodel');
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if ($biomodelCatID == 0){
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$biomodelCatID = wp_create_category('biomodel');
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}
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$post_arr = array(
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'post_title' => 'biomodel-' . $biomodel->bmKey,
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'post_content' => vcell_get_biomodel_post_content($biomodel),
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'post_status' => 'publish',
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'post_author' => get_current_user_id(),
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'meta_input' => array(
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'bmKey' => $biomodel->bmKey,
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),
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'post_category' => array( $biomodelCatID )
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);
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$post_id = wp_insert_post($post_arr);
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return $post_id;
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}
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function vcell_update_biomodel_post($biomodel, $biomodelPostId){
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$biomodelCatID = get_cat_ID('biomodel');
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if ($biomodelCatID == 0){
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$biomodelCatID = wp_create_category('biomodel');
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}
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$post_arr = array(
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'ID' => $biomodelPostId,
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'post_title' => 'biomodel-' . $biomodel->bmKey,
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'post_content' => vcell_get_biomodel_post_content($biomodel),
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'post_status' => 'publish',
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'post_author' => get_current_user_id(),
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'meta_input' => array(
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'bmKey' => $biomodel->bmKey,
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),
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'post_category' => array( $biomodelCatID )
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);
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$post_id = wp_update_post($post_arr);
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return $post_id;
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}
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function &vcell_find_publication_post($pubKey){
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$args = array(
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'meta_key' => 'pubKey',
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'meta_value' => $pubKey,
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'category_name' => 'publication',
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'post_type' => 'post',
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'post_status' => 'any',
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'posts_per_page' => -1
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);
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$posts = get_posts($args);
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if (is_null($posts) || empty($posts)){
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$posts = NULL;
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return $posts;
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}else if (is_array($posts)){
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return $posts[0];
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}else{
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return $posts;
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}
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}
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function vcell_update_publication_post($publication, $pubPostId){
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$publicationCatID = get_cat_ID('publication');
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if ($publicationCatID == 0){
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$publicationCatID = wp_create_category('publication');
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}
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$publicationYearCatName = 'publication-' . $publication->year;
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$publicationYearCatID = get_cat_ID($publicationYearCatName);
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if ($publicationYearCatID == 0){
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$publicationYearCatID = wp_create_category($publicationYearCatName);
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}
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$post_arr = array(
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'ID' => $pubPostId,
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'post_title' => vcell_get_publication_post_title($publication),
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'post_content' => vcell_get_publication_post_content($publication),
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'post_status' => 'publish',
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'post_author' => get_current_user_id(),
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'meta_input' => array(
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'pubKey' => $publication->pubKey,
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),
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'post_category' => array( $publicationCatID, $publicationYearCatID )
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);
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$post_id = wp_update_post($post_arr);
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return $post_id;
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}
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function vcell_insert_publication_post($publication){
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$publicationCatID = get_cat_ID('publication');
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if ($publicationCatID == 0){
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$publicationCatID = wp_create_category('publication');
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}
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$publicationYearCatName = 'publication-' . $publication->year;
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$publicationYearCatID = get_cat_ID($publicationYearCatName);
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if ($publicationYearCatID == 0){
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$publicationYearCatID = wp_create_category($publicationYearCatName);
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}
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$post_arr = array(
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'post_title' => vcell_get_publication_post_title($publication),
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'post_content' => vcell_get_publication_post_content($publication),
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'post_status' => 'publish',
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'post_date' => date("Y-m-d H:i:s", strtotime("Jan 1, " . $publication->year) ),
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'post_author' => get_current_user_id(),
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'meta_input' => array(
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'pubKey' => $publication->pubKey,
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),
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'post_category' => array( $publicationCatID, $publicationYearCatID )
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);
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$post_id = wp_insert_post($post_arr);
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return $post_id;
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}
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function &vcell_get_biomodel_object($bmKey) {
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$json = file_get_contents("https://vcellapi.cam.uchc.edu/biomodel/" . $bmKey);
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$biomodel = json_decode($json);
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return $biomodel;
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}
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function &vcell_get_biomodel_vcml_object($bmKey){
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$vcmlString = file_get_contents("https://vcellapi.cam.uchc.edu/biomodel/" . $bmKey . '/biomodel.vcml');
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vcell_log_me("bmKey is " . $bmKey . ", vcmlString is '" . $vcmlString . "'");
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$biomodel_vcml = new SimpleXMLElement($vcmlString) or die('unable to retrieve vcml');
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return $biomodel_vcml;
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}
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function &vcell_get_publication_object($pubKey) {
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$json = file_get_contents("https://vcellapi.cam.uchc.edu/publication/" . $pubKey);
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$publication = json_decode($json);
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return $publication;
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}
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function &vcell_get_publications_object() {
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vcell_log_me('calling vcellapi for publications');
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$json = file_get_contents("https://vcellapi.cam.uchc.edu/publication");
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vcell_log_me('vcellapi publications json = ' . $json );
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$publications = json_decode($json);
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return $publications;
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}
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function vcell_get_publication_post_title($publication) {
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$authorText = '';
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if (sizeof($publication->authors)>1){
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$authorText = explode(',', reset($publication->authors))[0] . ' et al., ';
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}else{
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$authorText = reset($publication->authors) . ', ';
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}
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$authorText .= $publication->year;
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return $authorText;
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}
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function vcell_get_publication_post_content($publication) {
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$authorText = '';
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$bFirst = 1;
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foreach ($publication->authors as $author){
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if ($bFirst == 1){
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$authorText = $author;
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$bFirst = 0;
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}else{
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$authorText .= ", " . $author;
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}
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}
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$modellinktext = '';
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vcell_log_me('getting publication post content for pubKey ' . $publication->pubKey);
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if (sizeof($publication->biomodelReferences)>0){
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$modellinktext .= ' VCell BioModels referenced in publication:<br/>';
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foreach ($publication->biomodelReferences as $biomodelref){
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$bmKey = $biomodelref->bmKey;
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$bmName = $biomodelref->name;
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$ownerKey = $biomodelref->ownerKey;
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$ownerName = $biomodelref->ownerName;
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$bmPost =& vcell_find_biomodel_post($bmKey);
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if (is_null($bmPost)){
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$bmurl = '/biomodel-' . $bmKey;
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vcell_log_me(' using fake link for publication ' . $publication->pubKey . ' biomodel ' . $bmKey);
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}else{
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$bmurl = get_permalink($bmPost->ID);
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vcell_log_me(' using real link for publication ' . $publication->pubKey . ' biomodel ' . $bmKey);
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}
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$modellinktext .= ' user: ' . $ownerName . ', model name: <a href="' . $bmurl . '">' . $bmName . '</a><br/>';
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}
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}
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if (sizeof($publication->mathmodelReferences)>0){
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$modellinktext .= ' VCell MathModels referenced in publication:<br/>';
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foreach ($publication->mathmodelReferences as $mathmodelref){
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$mmKey = $mathmodelref->mmKey;
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$mmName = $mathmodelref->name;
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$ownerKey = $mathmodelref->ownerKey;
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$ownerName = $mathmodelref->ownerName;
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$mmurl = '/mathmodel-' . $mmKey;
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$modellinktext .= ' user: ' . $ownerName . ', model name: <a href="' . $mmurl . '">' . $mmName . '</a><br/>';
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}
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}
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$text = '<strong><big>' . $publication->title . '</big></strong><br/>';
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$text .= $authorText . '<br/>';
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$text .= $publication->citation . '<br/>';
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$publinktext = '';
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if (!empty($publication->pubmedid)){
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$pubmedurl = 'http://www.ncbi.nlm.nih.gov/pubmed/' . $publication->pubmedid;
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$pubmedlabel = 'PUBMED:' . $publication->pubmedid;
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$publinktext .= '<a href="' . $pubmedurl . '">' . $pubmedlabel . '</a> ';
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}
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if (!empty($publication->doi)){
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$doiurl = 'https://dx.doi.org/' . $publication->doi;
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$doilabel = 'doi:' . $publication->doi;
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$publinktext .= '<a href="' . $doiurl . '">' . $doilabel . '</a>';
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}
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$text .= $publinktext . '<br/>';
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$text .= $modellinktext;
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return $text;
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}
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function vcell_date_from_timestamp($vcell_timestamp) {
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$myDate = $vcell_timestamp/1000;
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$datetext = gmdate("D, d M Y", $myDate) . ' ' . gmdate("G:i:s \G\M\T", $myDate);
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return $datetext;
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}
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function vcell_get_biomodel_post_content($biomodel){
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$bmKey = $biomodel->bmKey;
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vcell_log_me('getting biomodel post content for bmKey ' . $bmKey . ' with name "' . $biomodel->name . '"');
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$compartmenttext = '[vcell-biomodel-compartments bmkey="' . $bmKey . '"]';
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$nametext = 'Name: <strong>"' . $biomodel->name . '"</strong>';
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$datetext = 'Saved: <strong>' . vcell_date_from_timestamp($biomodel->savedDate) . '</strong>';
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$ownertext = 'Owned by: <strong>"' . $biomodel->ownerName . '"</strong>';
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$bmBaseUrl = 'https://vcellapi.cam.uchc.edu/biomodel/' . $bmKey;
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$bmIdentifier = 'vcell identifier: <strong>biomodel-' . $bmKey . '</strong>';
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$filename = 'VCBioModel_' . $bmKey . '.vcml';
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$downloadtext = '<a href="' . $bmBaseUrl . '/biomodel.vcml" type="application/vcml+xml" download="' . $filename . '">download model (.vcml)</a>';
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$diagramtext = '<img src="https://vcellapi.cam.uchc.edu/biomodel/' . $bmKey . '/diagram"/>';
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return $nametext . '<br/>' . $datetext . '<br/>' . $bmIdentifier . '<br>' . $ownertext . '<br/><br/>' . $downloadtext . '<br/><br/>' . $diagramtext . '<br/><br/>' . $compartmenttext;
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}
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function vcell_get_biomodel_compartment_content($biomodelvcml){
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$compArray = [];
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$reactionArray = [];
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$speciesArray = [];
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$modelChildren = $biomodelvcml->BioModel->Model->children();
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foreach($modelChildren as $modelChild){
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if ($modelChild->getName() == "Feature" OR $modelChild->getName() == "Membrane"){
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$structureElement = $modelChild;
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$compartmentType = '';
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if ($structureElement->getName() == "Feature"){
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$compartmentType = "Volume";
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}else if ($structureElement->getName() == "Membrane"){
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$compartmentType = "Membrane";
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}
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array_push($compArray, array(
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'type' => $compartmentType,
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'name' => $structureElement['Name']
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));
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}else if ($modelChild->getName() == "LocalizedCompound"){
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$speciesElement = $modelChild;
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array_push($speciesArray, array(
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'structure' => $speciesElement['Structure'],
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'name' => $speciesElement['Name']
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));
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}else if ($modelChild->getName() == "SimpleReaction" OR $modelChild->getName() == "FluxStep"){
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$reactionElement = $modelChild;
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$reactants = [];
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$products = [];
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foreach($reactionElement->children() as $reactionChild){
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if ($reactionChild->getName() == "Reactant"){
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$reactantElement = $reactionChild;
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array_push($reactants, array(
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'species' => $reactantElement['LocalizedCompoundRef'],
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'stoichiometry' => $reactantElement['Stoichiometry']
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));
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}
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if ($reactionChild->getName() == "Product"){
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$productElement = $reactionChild;
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array_push($products, array(
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'species' => $productElement['LocalizedCompoundRef'],
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'stoichiometry' => $productElement['Stoichiometry']
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));
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}
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}
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array_push($reactionArray, array(
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'structure' => $reactionElement['Structure'],
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'name' => $reactionElement['Name'],
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'reactants' => $reactants,
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'products' => $products
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));
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}
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}
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$compartmenttext = '<strong>Compartments, Species, Reactions</strong><br/><ul>';
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foreach($compArray as $compartment){
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$compartmenttext .= '<li>';
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$compartmenttext .= ' Compartment <strong>"' . $compartment['name'] . '"</strong>. ' . ' (type: ' . $compartment['type'] . ')';
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$speciestext = '';
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foreach($speciesArray as $species){
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if (strcmp($species['structure'],$compartment['name'])==0) {
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$speciestext .= '<li>Species <strong>"' . $species['name'] . '"</strong></li>';
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}
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}
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$reactiontext = '';
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$null_set_symbol = '∅';
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$arrow_symbol = '→';
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foreach($reactionArray as $reaction){
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if (strcmp($reaction['structure'],$compartment['name'])==0) {
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$reactiontext .= '<li>';
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$reactiontext .= 'Reaction <strong>"' . $reaction['name'] . '"</strong> ';
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$reactiontext .= '(';
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$reactants = [];
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if (count($reaction['reactants'])>0){
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foreach ($reaction['reactants'] as $reactant){
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if ($reactant['stoichiometry'] == "1"){
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$reactiontext .= $reactant['species'];
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}else{
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$reactiontext .= $reactant['stoichiometry'] . ' ' . $reactant['species'];
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}
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if ($reactant != end($reaction['reactants'])){
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$reactiontext .= ' + ';
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}
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}
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}else{
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$reactiontext .= $null_set_symbol;
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}
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$reactiontext .= ' ' . $arrow_symbol . ' ';
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if (count($reaction['products'])>0){
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foreach ($reaction['products'] as $product){
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if ($product['stoichiometry'] == 1){
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$reactiontext .= $product['species'];
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}else{
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$reactiontext .= $product['stoichiometry'] . ' ' . $product['species'];
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}
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if ($product != end($reaction['products'])){
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$reactiontext .= ' + ';
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}
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}
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}else{
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|
$reactiontext .= $null_set_symbol;
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}
|
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|
$reactiontext .= ')</li>';
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}
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}
|
|
|
if (strlen($reactiontext)>0 OR strlen($speciestext)>0){
|
|
|
$compartmenttext .= '<ul>' . $speciestext . $reactiontext . '</ul>';
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|
}
|
|
|
$compartmenttext .= '</li>';
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}
|
|
|
$compartmenttext .= '</ul>';
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return $compartmenttext;
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|
}
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|
function vcell_log_me($message) {
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|
|
if (WP_DEBUG === true) {
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if (is_array($message) || is_object($message)) {
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|
error_log(print_r($message, true));
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} else {
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error_log($message);
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}
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}
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}
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function vcell_get_model_detail($atts) {
|
|
|
vcell_log_me('calling shortcode vcell-biomodel-compartments with bmKey = ' . $atts['bmkey'] );
|
|
|
vcell_log_me($atts);
|
|
|
$bmKey = $atts['bmkey'];
|
|
|
vcell_log_me('in shortcode vcell-biomodel-compartments using bmKey = ' . $bmKey );
|
|
|
try {
|
|
|
$biomodelvcml =& vcell_get_biomodel_vcml_object($bmKey);
|
|
|
$text = vcell_get_biomodel_compartment_content($biomodelvcml);
|
|
|
} catch (Exception $e) {
|
|
|
echo 'Caught exception: ', $e->getMessage(), "\n";
|
|
|
$text = "model details unavailable for this model";
|
|
|
}
|
|
|
vcell_log_me('returning ' . $text);
|
|
|
return $text;
|
|
|
}
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|
|
add_shortcode('vcell-biomodel-compartments','vcell_get_model_detail');
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?>
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