| <?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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|
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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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| $reactiontext .= ')</li>';
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| }
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| }
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| if (strlen($reactiontext)>0 OR strlen($speciestext)>0){
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| $compartmenttext .= '<ul>' . $speciestext . $reactiontext . '</ul>';
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| }
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| $compartmenttext .= '</li>';
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| }
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| $compartmenttext .= '</ul>';
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| return $compartmenttext;
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| }
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|
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| function vcell_log_me($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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|
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| function vcell_get_model_detail($atts) {
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| vcell_log_me('calling shortcode vcell-biomodel-compartments with bmKey = ' . $atts['bmkey'] );
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| vcell_log_me($atts);
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| $bmKey = $atts['bmkey'];
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| vcell_log_me('in shortcode vcell-biomodel-compartments using bmKey = ' . $bmKey );
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| try {
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| $biomodelvcml =& vcell_get_biomodel_vcml_object($bmKey);
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| $text = vcell_get_biomodel_compartment_content($biomodelvcml);
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| } catch (Exception $e) {
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| echo 'Caught exception: ', $e->getMessage(), "\n";
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| $text = "model details unavailable for this model";
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| }
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| vcell_log_me('returning ' . $text);
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| return $text;
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| }
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|
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| add_shortcode('vcell-biomodel-compartments','vcell_get_model_detail');
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| ?>
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