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@@ -0,0 +1,890 @@
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+<?php
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+
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+/**
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+ * This is the chado_pub node form callback. The arguments
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+ * are out of order from a typical form because it's a defined callback
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+ */
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+
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+function chado_pub_form($node, $form_state) {
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+ $form = array();
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+
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+ // Default values can come in the following ways:
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+ //
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+ // 1) as elements of the $node object. This occurs when editing an existing pub
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+ // 2) in the $form_state['values'] array which occurs on a failed validation or
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+ // ajax callbacks from non submit form elements
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+ // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
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+ // form elements and the form is being rebuilt
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+ //
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+ // set form field defaults
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+ $pub_id = null;
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+ $title = '';
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+ $pyear = '';
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+ $uniquename = '';
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+ $type_id = '';
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+ $is_obsolete = '';
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+
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+ // some of the fields in the pub table should show up in the properties
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+ // form elements to make the form more seemless. We will add them
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+ // to this array.
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+ $more_props = array();
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+
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+ // if we are editing an existing node then the pub is already part of the node
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+ if (property_exists($node, 'pub')) {
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+ $pub = $node->pub;
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+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
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+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
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+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
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+ $pub_id = $pub->pub_id;
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+
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+ $title = $pub->title;
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+ $pyear = $pub->pyear;
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+ $uniquename = $pub->uniquename;
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+ $type_id = $pub->type_id->cvterm_id;
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+ $is_obsolete = $pub->is_obsolete;
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+
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+ // if the obsolete value is set by the database then it is in the form of
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+ // 't' or 'f', we need to convert to 1 or 0
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+ $is_obsolete = $is_obsolete == 't' ? 1 : $is_obsolete;
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+ $is_obsolete = $is_obsolete == 'f' ? 0 : $is_obsolete;
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+
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+ // set the organism_id in the form
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+ $form['pub_id'] = array(
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+ '#type' => 'value',
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+ '#value' => $pub->pub_id,
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+ );
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+
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+ // get fields from the pub table and convert them to properties. We will add these to the $more_props
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+ // array which gets passed in to the tripal_core_properties_form() API call further down
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+ if ($pub->volumetitle) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Volume Title', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->volumetitle);
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+ }
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+ if ($pub->volume) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Volume', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->volume);
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+ }
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+ if ($pub->series_name) {
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+ switch ($pub->type_id->name) {
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+ case 'Journal Article':
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+ $cvterm = tripal_cv_get_cvterm_by_name('Journal Name', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
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+ break;
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+ case 'Conference Proceedings':
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+ $cvterm = tripal_cv_get_cvterm_by_name('Conference Name', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
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+ break;
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+ default:
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+ $cvterm = tripal_cv_get_cvterm_by_name('Series Name', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->series_name);
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+ }
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+ }
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+ if ($pub->issue) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Issue', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->issue);
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+ }
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+ if ($pub->pages) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Pages', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->pages);
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+ }
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+ if ($pub->miniref) {
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+ // not sure what to do with this one
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+ }
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+ if ($pub->publisher) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Publisher', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->publisher);
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+ }
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+ if ($pub->pubplace) {
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+ $cvterm = tripal_cv_get_cvterm_by_name('Published Location', NULL, 'tripal_pub');
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+ $more_props[] = array('cvterm' => $cvterm, 'value' => $pub->pages);
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+ }
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+ }
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+ // if we are re constructing the form from a failed validation or ajax callback
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+ // then use the $form_state['values'] values
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+ if (array_key_exists('values', $form_state)) {
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+ $title = $form_state['values']['pubtitle'];
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+ $pyear = $form_state['values']['pyear'];
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+ $uniquename = $form_state['values']['uniquename'];
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+ $type_id = $form_state['values']['type_id'];
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+ $is_obsolete = $form_state['values']['is_obsolete'];
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+ }
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+ // if we are re building the form from after submission (from ajax call) then
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+ // the values are in the $form_state['input'] array
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+ if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
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+ $title = $form_state['input']['pubtitle'];
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+ $uniquename = $form_state['input']['uniquename'];
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+ $type_id = $form_state['input']['type_id'];
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+ $is_obsolete = $form_state['input']['is_obsolete'];
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+ }
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+
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+ // a drupal title can only be 255 characters, but the Chado title can be much longer.
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+ // we use the publication title as the drupal title, but we'll need to truncate it.
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+ $form['title'] = array(
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+ '#type' => 'hidden',
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+ '#value' => substr($title, 0, 255),
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+ );
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+ $form['pubtitle'] = array(
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+ '#type' => 'textarea',
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+ '#title' => t('Publication Title'),
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+ '#default_value' => $title,
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+ '#required' => TRUE,
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+ );
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+ // get the list of publication types. In the Tripal publication
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+ // ontologies these are all grouped under the term 'Publication Type'
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+ // we want the default to be 'Journal Article'
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+ $sql = "
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+ SELECT
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+ CVTS.cvterm_id, CVTS.name
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+ FROM {cvtermpath} CVTP
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+ INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
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+ INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
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+ INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
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+ WHERE
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+ CV.name = 'tripal_pub' AND CVTO.name = 'Publication Type' AND
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+ NOT CVTS.is_obsolete = 1
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+ ORDER BY CVTS.name ASC
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+ ";
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+ $results = chado_query($sql);
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+ $pub_types = array();
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+ while ($pub_type = $results->fetchObject()) {
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+ $pub_types[$pub_type->cvterm_id] = $pub_type->name;
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+ // if we don't have a default type then set the default to be 'Journal Article'
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+ if (strcmp($pub_type->name,"Journal Article") == 0 and !$type_id) {
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+ $type_id = $pub_type->cvterm_id;
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+ }
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+ }
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+
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+ $form['type_id'] = array(
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+ '#type' => 'select',
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+ '#title' => t('Publication Type'),
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+ '#options' => $pub_types,
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+ '#required' => TRUE,
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+ '#default_value' => $type_id,
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+ );
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+ $form['pyear'] = array(
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+ '#type' => 'textfield',
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+ '#title' => t('Publication Year'),
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+ '#default_value' => $pyear,
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+ '#required' => TRUE,
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+ '#size' => 5,
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+ '#description' => t('Enter the year of publication. Also, if available, please add a <b>Publication Date</b> property to specify the full date of publication.'),
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+ );
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+ $form['uniquename'] = array(
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+ '#type' => 'textarea',
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+ '#title' => t('Citation'),
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+ '#default_value' => $uniquename,
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+ '#description' => t('All publications must have a unique citation.
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+ <b>Please enter the full citation for this publication or leave blank and one will be generated
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+ automatically if possible</b>. For PubMed style citations list
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+ the last name of the author followed by initials. Each author should be separated by a comma. Next comes
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+ the title, followed by the series title (e.g. journal name), publication date (4 digit year, 3 character Month, day), volume, issue and page numbers. You may also use HTML to provide a link in the citation.
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+ Below is an example: <pre>Medeiros PM, Ladio AH, Santos AM, Albuquerque UP. <a href="http://www.ncbi.nlm.nih.gov/pubmed/23462414" target="_blank">Does the selection of medicinal plants by Brazilian local populations
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+ suffer taxonomic influence?</a> J Ethnopharmacol. 2013 Apr 19; 146(3):842-52.</pre>'),
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+ );
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+ $form['is_obsolete'] = array(
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+ '#type' => 'checkbox',
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+ '#title' => t('Is Obsolete? (Check for Yes)'),
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+ '#default_value' => $is_obsolete,
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+ );
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+
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+ // get publication properties list
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+ $properties_select = array();
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+ $properties_select[] = 'Select a Property';
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+ $sql = "
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+ SELECT
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+ DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
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+ FROM {cvtermpath} CVTP
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+ INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
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+ INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
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+ INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
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+ WHERE CV.name = 'tripal_pub' and
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+ (CVTO.name = 'Publication Details' OR CVTS.name = 'Publication Type') AND
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+ NOT CVTS.is_obsolete = 1
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+ ORDER BY CVTS.name ASC
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+ ";
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+ $prop_types = chado_query($sql);
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+ while ($prop = $prop_types->fetchObject()) {
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+ // add all properties except the Citation. That property is set via the uniquename field
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+ if ($prop->name != 'Citation') {
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+ $properties[$prop->cvterm_id] = $prop->name;
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+ }
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+ }
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+
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+ // add in the properties fields. The 'Citation' term is special because it serves
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+ // both as a property and as the uniquename for the publiation table so we exclude it
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+ // as it shouldn't be selected as a property
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+ $exclude = array("Citation");
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+ $instructions = '';
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+ tripal_core_properties_form($form, $form_state, 'pubprop', 'pub_id', 'tripal_pub',
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+ $properties, $pub_id, $exclude, $more_props, $instructions, 'Properties');
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+
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+ return $form;
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+
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+}
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+/*
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+ *
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+ */
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+function chado_pub_validate($node, $form, &$form_state) {
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+
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+ // get the submitted values
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+ $title = trim($node->pubtitle);
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+ $pyear = trim($node->pyear);
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+ $uniquename = trim($node->uniquename);
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+ $is_obsolete = $node->is_obsolete;
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+ $type_id = $node->type_id;
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+
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+ // if this is a delete then don't validate
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+ if($node->op == 'Delete') {
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+ return;
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+ }
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+
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+ // we are syncing if we do not have a node ID but we do have a pub_id. We don't
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+ // need to validate during syncing so just skip it.
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+ if (is_null($node->nid) and property_exists($node, 'pub_id') and $node->pub_id != 0) {
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+ return;
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+ }
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+
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+ $pub = array();
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+
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+ // make sure the year is four digits
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+ if(!preg_match('/^\d{4}$/', $pyear)){
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+ form_set_error('pyear', t('The publication year should be a 4 digit year.'));
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+ return;
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+ }
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+
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+ // get the type of publication
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+ $values = array('cvterm_id' => $type_id);
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+ $options = array('statement_name' => 'sel_pub_ty');
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+ $cvterm = tripal_core_chado_select('cvterm', array('name'), $values, $options);
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+ if (count($cvterm) == 0) {
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+ $message = t('Invalid publication type.');
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+ form_set_error('type_id', $message);
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+ return;
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+ }
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+
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+ // get the media name looking at the properties
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+ $series_name = '';
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+ foreach ($node as $element => $value) {
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+ // if this is an existing property (either previously in the database or
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+ // added via AHAH/AJAX callback)
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+ if (preg_match('/^prop_value-(\d+)-(\d+)$/', $element, $matches)) {
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+ $prop_type_id = $matches[1];
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+ $prop_type = tripal_cv_get_cvterm_by_id($prop_type_id);
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+ if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
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+ $series_name = $value;
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+ }
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+ if($prop_type->name == 'Citation') {
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+ $uniquename = $value;
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+ }
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+ $pub[$prop_type->name] = $value;
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+ }
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+ // if this is a new property (added by this submit of the form)
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+ elseif ($element == 'new_id') {
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+ $prop_type = tripal_cv_get_cvterm_by_id($value);
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+ if($prop_type->name == 'Conference Name' or $prop_type->name == 'Journal Name') {
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+ $series_name = $node->new_value;
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+ }
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+ if($prop_type->name == 'Citation') {
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+ $uniquename = $node->new_value;
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+ }
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+ $pub[$prop_type->name] = $node->new_value;
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+ }
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+ }
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+ // if the citation is missing then try to generate one
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+ if (!$uniquename) {
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+ $pub['Title'] = $title;
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+ $pub['Publication Type'][0] = $cvterm[0]->name;
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+ $pub['Year'] = $pyear;
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+ $uniquename = tripal_pub_create_citation($pub);
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+ if (!$uniquename) {
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+ form_set_error('uniquename', "Cannot automatically generate a citation for this publication type. Please add one manually.");
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+ }
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+ }
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+
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+ $skip_duplicate_check = 0;
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+
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+ // if this publication is a Patent then skip the validation below. Patents can have the title
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+ // name and year but be different
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+ if (strcmp($cvterm[0]->name,'Patent') == 0) {
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+ $skip_duplicate_check = 1;
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+ }
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+
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+ // Validating for an update
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+ if (!is_null($node->nid)) {
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+
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+ $pub_id = $node->pub_id;
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+
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+ // first get the original title, type and year before it was changed
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+ $values = array('pub_id' => $pub_id);
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+ $columns = array('title', 'pyear', 'type_id', 'series_name');
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+ $options = array('statement_name' => 'sel_pub_id');
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+ $pub = tripal_core_chado_select('pub', $columns, $values, $options);
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+
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+ // if the title, type, year or series_name have changed then check the pub
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+ // to see if it is a duplicate of another
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+ if((strcmp(strtolower($pub[0]->title), strtolower($title)) == 0) and
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+ (strcmp(strtolower($pub[0]->series_name), strtolower($series_name)) == 0) and
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+ ($pub[0]->type_id == $type_id) and
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+ ($pub[0]->pyear == $pyear)) {
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+ $skip_duplicate_check = 1;
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+ }
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+
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+ // check to see if a duplicate publication already exists
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+ if (!$skip_duplicate_check) {
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+ chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm, $pub_id);
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+ }
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+ chado_pub_validate_check_uniquename($uniquename, $pub_id);
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+ }
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+ // Validating for an insert
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+ else {
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+ chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm);
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+ chado_pub_validate_check_uniquename($uniquename);
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+ }
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+}
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+/**
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+ *
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+ * @param unknown $uniquename
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+ */
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+function chado_pub_validate_check_uniquename($uniquename, $pub_id = NULL) {
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+
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+ $results = tripal_pub_get_pub_by_uniquename($uniquename);
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+ // make sure we don't capture our pub_id in the list (remove it)
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+ foreach ($results as $index => $found_pub_id) {
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|
+ if($found_pub_id == $pub_id){
|
|
|
+ unset($results[$index]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (count($results) > 0) {
|
|
|
+ $message = t('A publication with this unique citation already exists.');
|
|
|
+ form_set_error('uniquename', $message);
|
|
|
+ }
|
|
|
+}
|
|
|
+/**
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_pub_validate_check_duplicate($title, $pyear, $series_name, $cvterm, $pub_id = NULL) {
|
|
|
+
|
|
|
+ // make sure the publication is unique using the prefereed import duplication check
|
|
|
+ $import_dups_check = variable_get('tripal_pub_import_duplicate_check', 'title_year_media');
|
|
|
+ switch ($import_dups_check) {
|
|
|
+ case 'title_year':
|
|
|
+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, NULL);
|
|
|
+ // make sure we don't capture our pub_id in the list (remove it)
|
|
|
+ foreach ($results as $index => $found_pub_id) {
|
|
|
+ if($found_pub_id == $pub_id){
|
|
|
+ unset($results[$index]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (count($results) > 0) {
|
|
|
+ $message = t('A publication with this title and publication year, already exists.');
|
|
|
+ form_set_error('pyear', $message);
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ case 'title_year_type':
|
|
|
+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, $cvterm[0]->name, $pyear, NULL);
|
|
|
+
|
|
|
+ // make sure we don't capture our pub_id in the list (remove it)
|
|
|
+ foreach ($results as $index => $found_pub_id) {
|
|
|
+ if($found_pub_id == $pub_id){
|
|
|
+ unset($results[$index]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (count($results) > 0) {
|
|
|
+ $message = t('A publication with this title, type and publication year, already exists.');
|
|
|
+ form_set_error('pyear', $message);
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ case 'title_year_media':
|
|
|
+ $results = tripal_pub_get_pubs_by_title_type_pyear_series($title, NULL, $pyear, $series_name);
|
|
|
+
|
|
|
+ // make sure we don't capture our pub_id in the list (remove it)
|
|
|
+ foreach ($results as $index => $found_pub_id) {
|
|
|
+ if($found_pub_id == $pub_id){
|
|
|
+ unset($results[$index]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (count($results) > 0) {
|
|
|
+ $message = t('A publication with this title, media name (e.g. Journal Name) and publication year, already exists.');
|
|
|
+ form_set_error('pyear', $message);
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implement hook_access().
|
|
|
+ *
|
|
|
+ * This hook allows node modules to limit access to the node types they define.
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The node on which the operation is to be performed, or, if it does not yet exist, the
|
|
|
+ * type of node to be created
|
|
|
+ *
|
|
|
+ * @param $op
|
|
|
+ * The operation to be performed
|
|
|
+ *
|
|
|
+ * @param $account
|
|
|
+ * A user object representing the user for whom the operation is to be performed
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * If the permission for the specified operation is not set then return FALSE. If the
|
|
|
+ * permission is set then return NULL as this allows other modules to disable
|
|
|
+ * access. The only exception is when the $op == 'create'. We will always
|
|
|
+ * return TRUE if the permission is set.
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_pub_node_access($node, $op, $account ) {
|
|
|
+ if ($op == 'create') {
|
|
|
+ if (!user_access('create chado_pub content', $account)) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ return TRUE;
|
|
|
+ }
|
|
|
+
|
|
|
+ if ($op == 'update') {
|
|
|
+ if (!user_access('edit chado_pub content', $account)) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if ($op == 'delete') {
|
|
|
+ if (!user_access('delete chado_pub content', $account)) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if ($op == 'view') {
|
|
|
+ if (!user_access('access chado_pub content', $account)) {
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ return NULL;
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implementation of tripal_pub_insert().
|
|
|
+ *
|
|
|
+ * This function inserts user entered information pertaining to the Publication instance into the
|
|
|
+ * 'pubauthor', 'pubprop', 'chado_pub', 'pub' talble of the database.
|
|
|
+ *
|
|
|
+ * @parm $node
|
|
|
+ * Then node which contains the information stored within the node-ID
|
|
|
+ *
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_pub_insert($node) {
|
|
|
+
|
|
|
+ $title = trim($node->pubtitle);
|
|
|
+ $pyear = trim($node->pyear);
|
|
|
+ $uniquename = trim($node->uniquename);
|
|
|
+ $is_obsolete = $node->is_obsolete;
|
|
|
+ $type_id = $node->type_id;
|
|
|
+
|
|
|
+ // we need an array suitable for the tripal_pub_create_citation() function
|
|
|
+ // to automatically generate a citation if a uniquename doesn't already exist
|
|
|
+ $pub_arr = array();
|
|
|
+
|
|
|
+ // if there is an pub_id in the $node object then this must be a sync so
|
|
|
+ // we can skip adding the pub as it is already there, although
|
|
|
+ // we do need to proceed with the rest of the insert
|
|
|
+ if (!property_exists($node, 'pub_id')) {
|
|
|
+
|
|
|
+ $properties = array(); // stores all of the properties we need to add
|
|
|
+ $cross_refs = array(); // stores any cross references for this publication
|
|
|
+
|
|
|
+ // get the properties from the form
|
|
|
+ $properties = tripal_core_properties_form_retreive($node, 'tripal_pub');
|
|
|
+
|
|
|
+ // get the list of properties for easy lookup (without doing lots of database queries
|
|
|
+ $properties_list = array();
|
|
|
+ $sql = "
|
|
|
+ SELECT CVTS.cvterm_id, CVTS.name, CVTS.definition
|
|
|
+ FROM {cvtermpath} CVTP
|
|
|
+ INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
|
|
|
+ INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
|
|
|
+ INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
|
|
|
+ WHERE CV.name = 'tripal_pub' and CVTO.name = 'Publication Details' and
|
|
|
+ NOT CVTS.is_obsolete = 1
|
|
|
+ ORDER BY CVTS.name ASC
|
|
|
+ ";
|
|
|
+ $prop_types = chado_query($sql);
|
|
|
+ while ($prop = $prop_types->fetchObject()) {
|
|
|
+ $properties_list[$prop->cvterm_id] = $prop->name;
|
|
|
+ // The 'Citation' term is special because it serves
|
|
|
+ // both as a property and as the uniquename for the
|
|
|
+ // pub and we want it stored in both the pub table and the pubprop table
|
|
|
+ if ($prop->name == 'Citation') {
|
|
|
+ $properties[$prop->name][0] = $node->uniquename;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // iterate through all of the properties and remove those that really are
|
|
|
+ // part of the pub table fields
|
|
|
+ $volume = '';
|
|
|
+ $volumetitle = '';
|
|
|
+ $issue = '';
|
|
|
+ $pages = '';
|
|
|
+ $publisher = '';
|
|
|
+ $series_name = '';
|
|
|
+ $pubplace = '';
|
|
|
+ $miniref = '';
|
|
|
+ $cross_refs = array();
|
|
|
+ foreach ($properties as $name => $element) {
|
|
|
+ $value = trim($element[0]);
|
|
|
+
|
|
|
+ // populate our $pub_array for building a citation
|
|
|
+ $pub_arr[$name] = $value;
|
|
|
+
|
|
|
+ // remove properties that are stored in the pub table
|
|
|
+ if ($name == "Volume") {
|
|
|
+ $volume = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Volume Title") {
|
|
|
+ $volumetitle = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Issue") {
|
|
|
+ $issue = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Pages") {
|
|
|
+ $pages = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Publisher") {
|
|
|
+ $publisher = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Series Name" or $name == "Journal Name" or $name == "Conference Name") {
|
|
|
+ $series_name = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Journal Country" or $name == "Published Location") {
|
|
|
+ $pubplace = $value;
|
|
|
+ // allow this property to go into the pubprop table so we don't loose info
|
|
|
+ // so don't unset it. But it will also go into the pub.pubplace field
|
|
|
+ }
|
|
|
+ elseif ($name == "Publication Dbxref") {
|
|
|
+ // we will add the cross-references to the pub_dbxref table
|
|
|
+ // but we also want to keep the property in the pubprop table so don't unset it
|
|
|
+ $cross_refs[] = $value;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // generate a citation for this pub if one doesn't already exist
|
|
|
+ if (!$node->uniquename and array_key_exists('Citation', $properties)) {
|
|
|
+ $pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
|
|
|
+ $pub_arr['Title'] = $node->pubtitle;
|
|
|
+ $pub_arr['Publication Type'][0] = $pub_type->name;
|
|
|
+ $pub_arr['Year'] = $node->pyear;
|
|
|
+ $node->uniquename = tripal_pub_create_citation($pub_arr);
|
|
|
+ $properties['Citation'][0] = $node->uniquename;
|
|
|
+ }
|
|
|
+
|
|
|
+ // insert the pub record
|
|
|
+ $values = array(
|
|
|
+ 'title' => $node->pubtitle,
|
|
|
+ 'series_name' => substr($series_name, 0, 255),
|
|
|
+ 'type_id' => $node->type_id,
|
|
|
+ 'pyear' => $node->pyear,
|
|
|
+ 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
|
|
|
+ 'uniquename' => $node->uniquename,
|
|
|
+ 'volumetitle' => $volumetitle,
|
|
|
+ 'volume' => $volume,
|
|
|
+ 'issue' => $issue,
|
|
|
+ 'pages' => $pages,
|
|
|
+ 'miniref' => substr($miniref, 0, 255),
|
|
|
+ 'publisher' => substr($publisher, 0, 255),
|
|
|
+ 'pubplace' => substr($pubplace, 0, 255),
|
|
|
+ );
|
|
|
+ $pub = tripal_core_chado_insert('pub', $values);
|
|
|
+ if (!$pub) {
|
|
|
+ drupal_set_message("Error inserting publication", "error");
|
|
|
+ watchdog('tripal_pub', "Error inserting publication", array(), WATCHDOG_ERROR);
|
|
|
+ return;
|
|
|
+ }
|
|
|
+ $pub_id = $pub['pub_id'];
|
|
|
+
|
|
|
+ // now add in the properties
|
|
|
+ foreach ($properties as $property => $elements) {
|
|
|
+ foreach ($elements as $rank => $value) {
|
|
|
+
|
|
|
+ $status = tripal_pub_insert_property($pub['pub_id'], $property, $value, FALSE);
|
|
|
+ if (!$status) {
|
|
|
+ drupal_set_message("Error cannot add property: $property", "error");
|
|
|
+ watchdog('tripal_pub', "Error cannot add property: %prop",
|
|
|
+ array('%property' => $property), WATCHDOG_ERROR);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // add in any database cross-references
|
|
|
+ foreach ($cross_refs as $index => $ref) {
|
|
|
+ $pub_dbxref = tripal_pub_add_pub_dbxref($pub['pub_id'], trim($ref));
|
|
|
+ if (!$pub_dbxref) {
|
|
|
+ drupal_set_message("Error cannot add publication cross reference: $ref", "error");
|
|
|
+ watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
|
|
|
+ array('%ref' => $ref), WATCHDOG_ERROR);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $pub_id = $node->pub_id;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Make sure the entry for this pub doesn't already exist in the
|
|
|
+ // chado_pub table if it doesn't exist then we want to add it.
|
|
|
+ $check_org_id = chado_get_id_for_node('pub', $node->nid);
|
|
|
+ if (!$check_org_id) {
|
|
|
+ $record = new stdClass();
|
|
|
+ $record->nid = $node->nid;
|
|
|
+ $record->vid = $node->vid;
|
|
|
+ $record->pub_id = $pub_id;
|
|
|
+ drupal_write_record('chado_pub', $record);
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+/*
|
|
|
+ *
|
|
|
+* Implements hook_update
|
|
|
+*
|
|
|
+* The purpose of the function is to allow the module to take action when an edited node is being
|
|
|
+* updated. It updates any name changes to the database tables that werec reated upon registering a Publication.
|
|
|
+* As well, the database will be changed, so the user changed information will be saved to the database.
|
|
|
+*
|
|
|
+* @param $node
|
|
|
+* The node being updated
|
|
|
+*
|
|
|
+* @ingroup tripal_pub
|
|
|
+*/
|
|
|
+function chado_pub_update($node) {
|
|
|
+ $title = trim($node->pubtitle);
|
|
|
+ $pyear = trim($node->pyear);
|
|
|
+ $uniquename = trim($node->uniquename);
|
|
|
+ $is_obsolete = $node->is_obsolete;
|
|
|
+ $type_id = $node->type_id;
|
|
|
+
|
|
|
+ // we need an array suitable for the tripal_pub_create_citation() function
|
|
|
+ // to automatically generate a citation if a uniquename doesn't already exist
|
|
|
+ $pub_arr = array();
|
|
|
+
|
|
|
+ // get the publication ID for this publication
|
|
|
+ $pub_id = chado_get_id_for_node('pub', $node->nid) ;
|
|
|
+
|
|
|
+ $properties = array(); // stores all of the properties we need to add
|
|
|
+ $cross_refs = array(); // stores any cross references for this publication
|
|
|
+
|
|
|
+ // get the properties from the form
|
|
|
+ $properties = tripal_core_properties_form_retreive($node, 'tripal_pub');
|
|
|
+
|
|
|
+ // get the list of properties for easy lookup (without doing lots of database queries
|
|
|
+ $properties_list = array();
|
|
|
+ $sql = "
|
|
|
+ SELECT DISTINCT CVTS.cvterm_id, CVTS.name, CVTS.definition
|
|
|
+ FROM {cvtermpath} CVTP
|
|
|
+ INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id
|
|
|
+ INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id
|
|
|
+ INNER JOIN {cv} ON CVTO.cv_id = CV.cv_id
|
|
|
+ WHERE CV.name = 'tripal_pub' and
|
|
|
+ (CVTO.name = 'Publication Details' or CVTS.name = 'Publication Type') and
|
|
|
+ NOT CVTS.is_obsolete = 1
|
|
|
+ ORDER BY CVTS.name ASC
|
|
|
+ ";
|
|
|
+ $prop_types = chado_query($sql);
|
|
|
+ while ($prop = $prop_types->fetchObject()) {
|
|
|
+ $properties_list[$prop->cvterm_id] = $prop->name;
|
|
|
+ // The 'Citation' term is special because it serves
|
|
|
+ // both as a property and as the uniquename for the
|
|
|
+ // pub and we want it stored in both the pub table and the pubprop table
|
|
|
+ if ($prop->name == 'Citation') {
|
|
|
+ $properties[$prop->name][0] = $node->uniquename;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // iterate through all of the properties and remove those that really are
|
|
|
+ // part of the pub table fields
|
|
|
+ $volume = '';
|
|
|
+ $volumetitle = '';
|
|
|
+ $issue = '';
|
|
|
+ $pages = '';
|
|
|
+ $publisher = '';
|
|
|
+ $series_name = '';
|
|
|
+ $pubplace = '';
|
|
|
+ $miniref = '';
|
|
|
+ $cross_refs = array();
|
|
|
+ foreach ($properties as $name => $element) {
|
|
|
+ foreach ($element as $index => $value) {
|
|
|
+ // populate our $pub_array for building a citation
|
|
|
+ $pub_arr[$name] = $value;
|
|
|
+
|
|
|
+ // remove properties that are stored in the pub table
|
|
|
+ if ($name == "Volume") {
|
|
|
+ $volume = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Volume Title") {
|
|
|
+ $volumetitle = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Issue") {
|
|
|
+ $issue = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Pages") {
|
|
|
+ $pages = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Publisher") {
|
|
|
+ $publisher = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Journal Name" or $name == "Conference Name") {
|
|
|
+ $series_name = $value;
|
|
|
+ unset($properties[$name]);
|
|
|
+ }
|
|
|
+ elseif ($name == "Journal Country" or $name == "Published Location") {
|
|
|
+ $pubplace = $value;
|
|
|
+ // allow this property to go into the pubprop table so we don't loose info
|
|
|
+ // so don't unset it. But it will also go into the pub.pubplace field
|
|
|
+ }
|
|
|
+ elseif ($name == "Publication Dbxref") {
|
|
|
+ // we will add the cross-references to the pub_dbxref table
|
|
|
+ // but we also want to keep the property in the pubprop table so don't unset it
|
|
|
+ $cross_refs[] = $value;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // generate a citation for this pub if one doesn't already exist
|
|
|
+ if (!$node->uniquename) {
|
|
|
+ $pub_type = tripal_cv_get_cvterm_by_id($node->type_id);
|
|
|
+ $pub_arr['Title'] = $node->pubtitle;
|
|
|
+ $pub_arr['Publication Type'][0] = $pub_type->name;
|
|
|
+ $pub_arr['Year'] = $node->pyear;
|
|
|
+ $node->uniquename = tripal_pub_create_citation($pub_arr);
|
|
|
+ $properties['Citation'][0] = $node->uniquename;
|
|
|
+ }
|
|
|
+
|
|
|
+ // update the pub record
|
|
|
+ $match = array(
|
|
|
+ 'pub_id' => $pub_id,
|
|
|
+ );
|
|
|
+ $values = array(
|
|
|
+ 'title' => $node->pubtitle,
|
|
|
+ 'type_id' => $node->type_id,
|
|
|
+ 'pyear' => $node->pyear,
|
|
|
+ 'is_obsolete' => $node->is_obsolete ? 'true' : 'false',
|
|
|
+ 'uniquename' => $node->uniquename,
|
|
|
+ 'series_name' => substr($series_name, 0, 255),
|
|
|
+ 'volumetitle' => $volumetitle,
|
|
|
+ 'volume' => $volume,
|
|
|
+ 'issue' => $issue,
|
|
|
+ 'pages' => $pages,
|
|
|
+ 'miniref' => substr($miniref, 0, 255),
|
|
|
+ 'publisher' => substr($publisher, 0, 255),
|
|
|
+ 'pubplace' => substr($pubplace, 0, 255),
|
|
|
+ );
|
|
|
+ $status = tripal_core_chado_update('pub', $match, $values);
|
|
|
+ if (!$status) {
|
|
|
+ drupal_set_message("Error updating publication", "error");
|
|
|
+ watchdog('tripal_pub', "Error updating publication", array(), WATCHDOG_ERROR);
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ // now add in the properties by first removing any the publication
|
|
|
+ // already has and adding the ones we have
|
|
|
+ tripal_core_chado_delete('pubprop', array('pub_id' => $pub_id));
|
|
|
+ foreach ($properties as $property => $elements) {
|
|
|
+ foreach ($elements as $rank => $value) {
|
|
|
+ $status = tripal_pub_insert_property($pub_id, $property, $value, FALSE);
|
|
|
+ if (!$status) {
|
|
|
+ drupal_set_message("Error cannot add property: '$property'", "error");
|
|
|
+ watchdog('tripal_pub', "Error cannot add property: '%prop'",
|
|
|
+ array('%prop' => $property), WATCHDOG_ERROR);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // add in any database cross-references after first removing
|
|
|
+ tripal_core_chado_delete('pub_dbxref', array('pub_id' => $pub_id));
|
|
|
+ foreach ($cross_refs as $index => $ref) {
|
|
|
+ $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, trim($ref));
|
|
|
+ if (!$pub_dbxref) {
|
|
|
+ drupal_set_message("Error cannot add publication cross reference: $ref", "error");
|
|
|
+ watchdog('tripal_pub', "Error cannot add publication cross reference: %ref",
|
|
|
+ array('%ref' => $ref), WATCHDOG_ERROR);
|
|
|
+ }
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implementation of tripal_pub_load().
|
|
|
+ *
|
|
|
+ *
|
|
|
+ * @param $node
|
|
|
+ * The node that is to be accessed from the database
|
|
|
+ *
|
|
|
+ * @return $node
|
|
|
+ * The node with the information to be loaded into the database
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_pub_load($nodes) {
|
|
|
+
|
|
|
+ foreach ($nodes as $nid => $node) {
|
|
|
+ // find the pub and add in the details
|
|
|
+ $pub_id = chado_get_id_for_node('pub', $nid);
|
|
|
+
|
|
|
+ // get the pub
|
|
|
+ $values = array('pub_id' => $pub_id);
|
|
|
+ $pub = tripal_core_generate_chado_var('pub', $values);
|
|
|
+
|
|
|
+ // expand the 'text' fields as those aren't included by default
|
|
|
+ // and they really shouldn't be so large to cause problems
|
|
|
+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.title');
|
|
|
+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.volumetitle');
|
|
|
+ $pub = tripal_core_expand_chado_vars($pub, 'field', 'pub.uniquename');
|
|
|
+
|
|
|
+ // set the URL path
|
|
|
+ $nodes[$nid]->path = "pub/$pub_id";
|
|
|
+ $nodes[$nid]->pub = $pub;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Implementation of tripal_pub_delete().
|
|
|
+ *
|
|
|
+ * This function takes a node and if the delete button has been chosen by the user, the publication
|
|
|
+ * and it's details will be removed.Following,given the node-ID, the instance will be deleted from
|
|
|
+ * the 'chado_pub' table.
|
|
|
+ *
|
|
|
+ * @parm $node
|
|
|
+ * Then node which contains the information stored within the node-ID
|
|
|
+ *
|
|
|
+ */
|
|
|
+function chado_pub_delete(&$node) {
|
|
|
+
|
|
|
+ $pub_id = chado_get_id_for_node('pub', $node->nid);
|
|
|
+
|
|
|
+ // if we don't have a pub id for this node then this isn't a node of
|
|
|
+ // type chado_pub or the entry in the chado_pub table was lost.
|
|
|
+ if (!$pub_id) {
|
|
|
+ return;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Remove data from {chado_pub}, {node} and {node_revision} tables of
|
|
|
+ // drupal database
|
|
|
+ $sql_del = "DELETE FROM {chado_pub} WHERE nid = :nid AND vid = :vid";
|
|
|
+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
|
|
|
+ $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid";
|
|
|
+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
|
|
|
+ $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid";
|
|
|
+ db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
|
|
|
+
|
|
|
+ // Remove data from pub and pubprop tables of chado database as well
|
|
|
+ chado_query("DELETE FROM {pubprop} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
|
|
|
+ chado_query("DELETE FROM {pub} WHERE pub_id = :pub_id", array(':pub_id' => $pub_id));
|
|
|
+}
|
Stephen Ficklin