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@@ -82,9 +82,11 @@ function tripal_pub_importers_list() {
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<li>Create a new importer by clicking the 'New Importer' link above, and after saving it should appear in the list below. Click the
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link labeled 'Import Pubs' to schedule a job to import the publications</li>
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<li>The first method only performs the import once. However, you can schedule the
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- importer to run peridically by adding a cron job. </li>
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+ importer to run peridically by adding a cron job. </li>
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</ol><br>");
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+ $form = drupal_get_form('tripal_pub_importer_ncbi_api_key_form');
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+ $page .= drupal_render($form);
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$table = [
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'header' => $headers,
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@@ -131,13 +133,9 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
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drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/loaders/chado_vocabs/obo_loader'), 'error');
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}
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- /**
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- * Commenting the AGL message out until we get AGL working again.
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- * spf 6/22/2018
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- * if(!extension_loaded ('yaz')){
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- * drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Pub Module help page'), 'admin/tripal/legacy/tripal_pub/help') . ' for assistance. If you do not want to use AGL you can ignore this warning.', 'warning');
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- * }
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- */
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+ if(!extension_loaded ('yaz')){
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+ drupal_set_message(t('<b>Note:</b> In order to create an importer using the USDA National Agricultural Library (AGL) you must install the yaz libraries. See the ') . l(t('Users Guide for Instructions'), 'https://tripal.readthedocs.io/en/latest/user_guide/example_genomics/pub_import.html#import-from-the-usda-national-agricultural-library') . ' for assistance. If you do not want to use AGL you can ignore this warning.', 'warning');
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+ }
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// generate the search form
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$form = drupal_get_form('tripal_pub_importer_setup_form', $pub_import_id, $action);
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@@ -150,11 +148,13 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
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$remote_db = array_key_exists('remote_db', $_SESSION['tripal_pub_import']) ? $_SESSION['tripal_pub_import']['remote_db'] : '';
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$num_criteria = array_key_exists('num_criteria', $_SESSION['tripal_pub_import']) ? $_SESSION['tripal_pub_import']['num_criteria'] : '';
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$days = array_key_exists('days', $_SESSION['tripal_pub_import']) ? $_SESSION['tripal_pub_import']['days'] : '';
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+ $latestyear = array_key_exists('latestyear', $_SESSION['tripal_pub_import']) ? $_SESSION['tripal_pub_import']['latestyear'] : '';
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$search_array = [];
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$search_array['remote_db'] = $remote_db;
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$search_array['num_criteria'] = $num_criteria;
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$search_array['days'] = $days;
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+ $search_array['latestyear'] = $latestyear;
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for ($i = 1; $i <= $num_criteria; $i++) {
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$search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_import']['criteria'][$i]['search_terms'];
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$search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_import']['criteria'][$i]['scope'];
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@@ -184,6 +184,10 @@ function tripal_pub_importer_setup_page($action = 'new', $pub_import_id = NULL)
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if (array_key_exists('Publication Dbxref', $pub) and $pub['Publication Dbxref']) {
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$raw_link = l('raw', 'admin/tripal/loaders/pub/raw/' . $pub['Publication Dbxref'], ['attributes' => ['target' => '_blank']]);
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}
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+ // indicate those that will be excluded by AGL year filtering parameters
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+ if ((array_key_exists('passfilter', $pub)) and ($pub['passfilter'] == 0 )) {
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+ $citation = '<span style="text-decoration: line-through;">' . $citation . '</span>';
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+ }
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$rows[] = [
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number_format($i),
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$citation,
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@@ -277,12 +281,13 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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$criteria = NULL;
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$remote_db = '';
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$days = '';
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+ $latestyear = '';
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$disabled = '';
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$do_contact = '';
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$num_criteria = 1;
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$loader_name = '';
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- // if this is an edit the we are pulling an import object from the database
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+ // if this is an edit then we are pulling an import object from the database
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if ($action == "edit") {
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$sql = "SELECT * FROM {tripal_pub_import} WHERE pub_import_id = :pub_import_id";
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$importer = db_query($sql, [':pub_import_id' => $pub_import_id])->fetchObject();
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@@ -290,6 +295,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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$criteria = unserialize($importer->criteria);
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$remote_db = $criteria['remote_db'];
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$days = $criteria['days'];
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+ $latestyear = $criteria['latestyear'];
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$disabled = $criteria['disabled'];
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$do_contact = $criteria['do_contact'];
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$num_criteria = $criteria['num_criteria'];
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@@ -300,6 +306,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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if (array_key_exists('tripal_pub_import', $_SESSION)) {
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$remote_db = $_SESSION['tripal_pub_import']['remote_db'];
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$days = $_SESSION['tripal_pub_import']['days'];
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+ $latestyear = $_SESSION['tripal_pub_import']['latestyear'];
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$disabled = $_SESSION['tripal_pub_import']['disabled'];
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$do_contact = $_SESSION['tripal_pub_import']['do_contact'];
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$num_criteria = $_SESSION['tripal_pub_import']['num_criteria'];
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@@ -315,21 +322,23 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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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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- $remote_db = $form_state['values']['remote_db'];
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- $days = $form_state['values']['days'];
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- $disabled = $form_state['values']['disabled'];
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- $do_contact = $form_state['values']['do_contact'];
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- $num_criteria = $form_state['values']['num_criteria'];
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- $loader_name = $form_state['values']['loader_name'];
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+ $remote_db = $form_state['values']['remote_db'] ?? null;
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+ $days = $form_state['values']['days'] ?? null;
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+ $latestyear = $form_state['values']['latestyear'] ?? null;
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+ $disabled = $form_state['values']['disabled'] ?? null;
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+ $do_contact = $form_state['values']['do_contact'] ?? null;
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+ $num_criteria = $form_state['values']['num_criteria'] ?? null;
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+ $loader_name = $form_state['values']['loader_name'] ?? null;
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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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- $remote_db = $form_state['input']['remote_db'];
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- $days = $form_state['input']['days'];
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- $disabled = $form_state['input']['disabled'];
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- $do_contact = $form_state['input']['do_contact'];
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- $loader_name = $form_state['input']['loader_name'];
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+ $remote_db = $form_state['input']['remote_db'] ?? null;
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+ $days = $form_state['input']['days'] ?? null;
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+ $latestyear = $form_state['input']['latestyear'] ?? null;
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+ $disabled = $form_state['input']['disabled'] ?? null;
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+ $do_contact = $form_state['input']['do_contact'] ?? null;
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+ $loader_name = $form_state['input']['loader_name'] ?? null;
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// because the num_criteria is a value and not a visible or hidden form
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// element it is not part of the ['input'] array, so we need to get it from the form
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@@ -381,11 +390,7 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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if (!$remote_db) {
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$remote_db = 'PMID';
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}
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- /**
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- * Removing AGL option until we get it fixed
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- * spf 6/22/2018
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- */
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- unset($remote_dbs['AGL']);
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+
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$form['themed_element']['remote_db'] = [
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'#title' => t('Source'),
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'#type' => 'select',
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@@ -405,6 +410,14 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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'#default_value' => $days,
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'#size' => 5,
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];
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+ // AGL only, this field will be removed for the pubmed loader
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+ $form['themed_element']['latestyear'] = [
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+ '#type' => 'textfield',
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+ '#title' => t('Latest year of publication'),
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+ '#description' => t('Filter returned publications for those that have been published no later than this year.'),
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+ '#default_value' => $latestyear,
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+ '#size' => 5,
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+ ];
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$form['themed_element']['disabled'] = [
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'#type' => 'checkbox',
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'#title' => t('Disabled'),
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@@ -451,6 +464,70 @@ function tripal_pub_importer_setup_form($form, &$form_state = NULL, $pub_import_
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return $form;
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}
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+/**
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+ * The form used for setting the optional NCBI API key.
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+ *
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+ * @param $form
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+ * The form element to be populated.
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+ * @param $form_state
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+ * The state of the form element to be populated.
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+ *
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+ * @return array
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+ * The populated form element.
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+ *
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+ * @ingroup tripal_pub
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+ */
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+function tripal_pub_importer_ncbi_api_key_form($form, $form_state) {
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+ $description = t('Tripal imports publications using NCBI\'s ')
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+ . l('EUtils API', 'https://www.ncbi.nlm.nih.gov/books/NBK25500/')
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+ . t(', which limits users and programs to a maximum of 3 requests per second without an API key. '
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+ . 'However, NCBI allows users and programs to an increased maximum of 10 requests per second if '
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+ . 'they provide a valid API key. This is particularly useful in speeding up large publication imports. '
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+ . 'For more information on NCBI API keys, please ')
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+ . l('see here', 'https://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Coming_in_December_2018_API_Key', array(
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+ 'attributes' => array(
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+ 'target' => 'blank',
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+ ),
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+ )) . '.';
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+
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+ $form['ncbi_api_key'] = array(
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+ '#type' => 'textfield',
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+ '#title' => t('(Optional) NCBI API key:'),
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+ '#description' => $description,
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+ '#default_value' => variable_get('tripal_pub_importer_ncbi_api_key', NULL),
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+ '#ajax' => array(
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+ 'callback' => 'tripal_pub_importer_set_ncbi_api_key',
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+ 'wrapper' => 'ncbi_api_key',
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+ ),
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+ '#prefix' => '<div id="ncbi_api_key">',
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+ '#suffix' => '</div>',
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+ );
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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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+ * This function saves the NCBI API key to the database.
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+ *
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+ * It is called when the user makes a change to the NCBI API key field and then
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+ * moves their cursor out of the field.
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+ *
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+ * @param $form
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+ * The new form element.
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+ * @param $form_state
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+ * The state of the new form element.
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+ *
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+ * @return array
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+ * The new api key field.
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+ *
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+ * @ingroup tripal_pub
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+ */
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+function tripal_pub_importer_set_ncbi_api_key($form, $form_state) {
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+ variable_set('tripal_pub_importer_ncbi_api_key', check_plain($form_state['values']['ncbi_api_key']));
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+ drupal_set_message('NCBI API key has been saved successfully!');
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+ return $form['ncbi_api_key'];
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+}
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+
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/**
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* A helper function for the importer setup form that adds the criteria to
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* the form that belong to the importer.
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@@ -501,10 +578,14 @@ function tripal_pub_importer_setup_add_criteria_fields(&$form, &$form_state, $nu
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// if we have criteria supplied from the database then use that as the initial defaults
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if ($criteria) {
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- $search_terms = $criteria['criteria'][$i]['search_terms'];
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- $scope = $criteria['criteria'][$i]['scope'];
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- $is_phrase = $criteria['criteria'][$i]['is_phrase'];
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- $operation = $criteria['criteria'][$i]['operation'];
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+ if (array_key_exists('criteria', $criteria)) {
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+ if (array_key_exists($i, $criteria['criteria'])) {
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+ $search_terms = $criteria['criteria'][$i]['search_terms'];
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+ $scope = $criteria['criteria'][$i]['scope'];
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+ $is_phrase = $criteria['criteria'][$i]['is_phrase'];
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+ $operation = $criteria['criteria'][$i]['operation'];
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+ }
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+ }
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}
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// if the criteria comes the session
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@@ -516,12 +597,12 @@ function tripal_pub_importer_setup_add_criteria_fields(&$form, &$form_state, $nu
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}
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// If the form_state has variables then use those. This happens when an error occurs on the form or the
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- // form is resbumitted using AJAX
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+ // form is resubmitted using AJAX
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if (array_key_exists('values', $form_state)) {
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- $search_terms = $form_state['values']["search_terms-$i"];
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- $scope = $form_state['values']["scope-$i"];
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- $is_phrase = $form_state['values']["is_phrase-$i"];
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- $operation = $form_state['values']["operation-$i"];
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+ $search_terms = $form_state['values']["search_terms-$i"] ?? null;
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+ $scope = $form_state['values']["scope-$i"] ?? null;
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+ $is_phrase = $form_state['values']["is_phrase-$i"] ?? null;
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+ $operation = $form_state['values']["operation-$i"] ?? null;
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}
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$form['themed_element']['criteria'][$i]["scope-$i"] = [
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'#type' => 'select',
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@@ -641,6 +722,7 @@ function tripal_pub_importer_setup_form_validate($form, &$form_state) {
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$num_criteria = $form_state['values']['num_criteria'];
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$remote_db = $form_state['values']["remote_db"];
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$days = trim($form_state['values']["days"]);
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+ $latestyear = trim($form_state['values']["latestyear"]);
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$disabled = $form_state['values']["disabled"];
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$do_contact = $form_state['values']["do_contact"];
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$loader_name = trim($form_state['values']["loader_name"]);
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@@ -666,6 +748,10 @@ function tripal_pub_importer_setup_form_validate($form, &$form_state) {
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form_set_error("days", "Please enter a numeric, non decimal value, for the number of days.");
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$_SESSION['tripal_pub_import']['perform_search'] = 0;
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}
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+ if ($latestyear and !is_numeric($latestyear) or preg_match('/\./', $latestyear)) {
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+ form_set_error("latestyear", "Please enter a numeric, non decimal value, for latestyear.");
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+ $_SESSION['tripal_pub_import']['perform_search'] = 0;
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+ }
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// allow the selected remote database to validate any changes to the form if needed
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$callback = "tripal_pub_remote_validate_form_$remote_db";
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$form = call_user_func($callback, $form, $form_state);
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@@ -682,6 +768,7 @@ function tripal_pub_importer_setup_form_submit($form, &$form_state) {
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$num_criteria = $form_state['values']['num_criteria'];
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$remote_db = $form_state['values']["remote_db"];
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$days = trim($form_state['values']["days"]);
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+ $latestyear = trim($form_state['values']["latestyear"]);
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$loader_name = trim($form_state['values']["loader_name"]);
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$disabled = $form_state['values']["disabled"];
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$do_contact = $form_state['values']["do_contact"];
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@@ -689,6 +776,7 @@ function tripal_pub_importer_setup_form_submit($form, &$form_state) {
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// set the session variables
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$_SESSION['tripal_pub_import']['remote_db'] = $remote_db;
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$_SESSION['tripal_pub_import']['days'] = $days;
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+ $_SESSION['tripal_pub_import']['latestyear'] = $latestyear;
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$_SESSION['tripal_pub_import']['num_criteria'] = $num_criteria;
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$_SESSION['tripal_pub_import']['loader_name'] = $loader_name;
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$_SESSION['tripal_pub_import']['disabled'] = $disabled;
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@@ -795,6 +883,10 @@ function theme_tripal_pub_importer_setup_form_elements($variables) {
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$markup .= '</div>';
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$markup .= '<div id="pub-search-form-row1" style="clear:both">';
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$markup .= ' <div id="pub-search-form-row1-col1">' . drupal_render($form['days']) . '</div>';
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+ // latest year field is used ony for AGL importer
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+ if ($variables['form']['remote_db']['#value'] == 'AGL') {
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+ $markup .= ' <div id="pub-search-form-row1-col2">' . drupal_render($form['latestyear']) . '</div>';
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+ }
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$markup .= '</div>';
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$markup .= '<div id="pub-search-form-row2">' . drupal_render($form['disabled']) . '</div>';
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$markup .= '<div id="pub-search-form-row3">' . drupal_render($form['do_contact']) . '</div>';
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@@ -930,46 +1022,53 @@ function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE, $job =
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$memory = number_format(memory_get_usage()) . " bytes";
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print "Processing $i of $total_pubs. Memory usage: $memory.\r";
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- // add the publication to Chado
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- $action = '';
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- $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update, $job);
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- if ($pub_id) {
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- // add the publication cross reference (e.g. to PubMed)
|
|
|
- if ($pub_id and $pub['Publication Dbxref']) {
|
|
|
- $dbxref = [];
|
|
|
- if (preg_match('/^(.*?):(.*?)$/', trim($pub['Publication Dbxref']), $matches)) {
|
|
|
- $dbxref['db_name'] = $matches[1];
|
|
|
- $dbxref['accession'] = $matches[2];
|
|
|
- }
|
|
|
- else {
|
|
|
- tripal_report_error($message_type, TRIPAL_ERROR,
|
|
|
- 'Unable to extract the dbxref to be associated with the publication (pub ID=@pub_id) from @dbxref. This reference should be [database-name]:[accession]',
|
|
|
- [
|
|
|
- '@pub_id' => $pub_id,
|
|
|
- '@dbxref' => $pub['Publication Dbxref'],
|
|
|
- $message_opts,
|
|
|
- ]
|
|
|
- );
|
|
|
+ // implementation of year limits for AGL uses a 'passfilter' flag
|
|
|
+ if ((!array_key_exists('passfilter', $pub)) or ($pub['passfilter'] == 1 )) {
|
|
|
+
|
|
|
+ // add the publication to Chado
|
|
|
+ $action = '';
|
|
|
+ $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update, $job);
|
|
|
+ // $pub_id will be null if publication already existed
|
|
|
+ if ($pub_id) {
|
|
|
+ // add the publication cross reference (e.g. to PubMed)
|
|
|
+ if ($pub_id and $pub['Publication Dbxref']) {
|
|
|
+ $dbxref = [];
|
|
|
+ if (preg_match('/^(.*?):(.*?)$/', trim($pub['Publication Dbxref']), $matches)) {
|
|
|
+ $dbxref['db_name'] = $matches[1];
|
|
|
+ $dbxref['accession'] = $matches[2];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ tripal_report_error($message_type, TRIPAL_ERROR,
|
|
|
+ 'Unable to extract the dbxref to be associated with the publication (pub ID=@pub_id) from @dbxref. This reference should be [database-name]:[accession]',
|
|
|
+ [
|
|
|
+ '@pub_id' => $pub_id,
|
|
|
+ '@dbxref' => $pub['Publication Dbxref'],
|
|
|
+ $message_opts,
|
|
|
+ ]
|
|
|
+ );
|
|
|
+ }
|
|
|
+ $pub_dbxref = tripal_associate_dbxref('pub', $pub_id, $dbxref);
|
|
|
}
|
|
|
- $pub_dbxref = tripal_associate_dbxref('pub', $pub_id, $dbxref);
|
|
|
+ $pub['pub_id'] = $pub_id;
|
|
|
}
|
|
|
- $pub['pub_id'] = $pub_id;
|
|
|
- }
|
|
|
|
|
|
- switch ($action) {
|
|
|
- case 'error':
|
|
|
- $report['error'][] = $pub['Citation'];
|
|
|
- break;
|
|
|
- case 'inserted':
|
|
|
- $report['inserted'][] = $pub['Citation'];
|
|
|
- break;
|
|
|
- case 'updated':
|
|
|
- $report['updated'][] = $pub['Citation'];
|
|
|
- break;
|
|
|
- case 'skipped':
|
|
|
- $report['skipped'][] = $pub['Citation'];
|
|
|
- break;
|
|
|
+ switch ($action) {
|
|
|
+ case 'error':
|
|
|
+ $report['error'][] = $pub['Citation'];
|
|
|
+ break;
|
|
|
+ case 'inserted':
|
|
|
+ $report['inserted'][] = $pub['Citation'];
|
|
|
+ break;
|
|
|
+ case 'updated':
|
|
|
+ $report['updated'][] = $pub['Citation'];
|
|
|
+ break;
|
|
|
+ case 'skipped':
|
|
|
+ $report['skipped'][] = $pub['Citation'];
|
|
|
+ break;
|
|
|
+ }
|
|
|
}
|
|
|
+ // else pub failed AGL year filter
|
|
|
+ else { $report['skipped'][] = $pub['Citation']; }
|
|
|
$i++;
|
|
|
}
|
|
|
return $report;
|
|
|
@@ -1017,7 +1116,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
$pub_id = 0;
|
|
|
|
|
|
// These are options for the tripal_report_error function. We do not
|
|
|
- // want to log messages to the watchdog except for errors and to the job and
|
|
|
+ // want to log messages to the watchdog except for errors and to the job and
|
|
|
// to the terminal
|
|
|
$message_type = 'pub_import';
|
|
|
$message_opts = [
|
|
|
@@ -1035,7 +1134,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
- // Before proceeding check to see if the publication already exists. If there
|
|
|
+ // Before proceeding check to see if the publication already exists. If there
|
|
|
// is only one match and the $update_if_exists is NOT set then return FALSE.
|
|
|
$pub_ids = chado_publication_exists($pub_details);
|
|
|
|
|
|
@@ -1053,7 +1152,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
- // If we have more than one matching pub then return an error as we don't
|
|
|
+ // If we have more than one matching pub then return an error as we don't
|
|
|
// know which to update even if update_if_exists is set to TRUE.
|
|
|
if (count($pub_ids) > 1) {
|
|
|
tripal_report_error($message_type, TRIPAL_NOTICE,
|
|
|
@@ -1104,7 +1203,7 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
return FALSE;
|
|
|
}
|
|
|
|
|
|
- // The series name field in the pub table is only 255 characters, so we
|
|
|
+ // The series name field in the pub table is only 255 characters, so we
|
|
|
// should trim just in case.
|
|
|
$series_name = '';
|
|
|
if (array_key_exists('Series_Name', $pub_details)) {
|
|
|
@@ -1158,8 +1257,8 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
}
|
|
|
}
|
|
|
|
|
|
- // Before we add any new properties we need to remove those that are there
|
|
|
- // if this is an update. The only thing we don't want to remove are the
|
|
|
+ // Before we add any new properties we need to remove those that are there
|
|
|
+ // if this is an update. The only thing we don't want to remove are the
|
|
|
// 'Publication Dbxref'.
|
|
|
if ($update_if_exists) {
|
|
|
$sql = "
|
|
|
@@ -1178,12 +1277,17 @@ function tripal_pub_add_publication($pub_details, &$action, $do_contact = FALSE,
|
|
|
// Iterate through the properties and add them.
|
|
|
foreach ($pub_details as $key => $value) {
|
|
|
|
|
|
- // The pub_details may have the raw search data (e.g. in XML from PubMed.
|
|
|
+ // The pub_details may have the raw search data (e.g. in XML from PubMed.
|
|
|
// We'll irgnore this for now.
|
|
|
if ($key == 'raw') {
|
|
|
continue;
|
|
|
}
|
|
|
|
|
|
+ // Filtering flag for AGL, not a property to add here
|
|
|
+ if ($key == 'passfilter') {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+
|
|
|
// Since we're not updating the 'Publication Dbxref' on an update
|
|
|
// skip this property.
|
|
|
if ($update_if_exists and $key == 'Publication Dbxref') {
|
Douglas Senalik