diff --git a/biblio.module b/biblio.module
index c8e617d..c1bdcc9 100644
--- a/biblio.module
+++ b/biblio.module
@@ -1340,6 +1340,14 @@ function biblio_form_alter(&$form, $form_state, $form_id) {
if ($freetagging && $kw_vocab && isset($form['taxonomy']['tags'][$kw_vocab])) {
unset($form['taxonomy']['tags'][$kw_vocab]);
}
+
+ // For existing nodes, the DOI should not be editable.
+ if (!empty($form['biblio_doi']['#default_value'])) {
+ $form['biblio_doi_disable'] = $form['biblio_doi'];
+ $form['biblio_doi_disable']['#type'] = 'item';
+ $form['biblio_doi_disable']['#value'] = $form['biblio_doi_disable']['#default_value'];
+ $form['biblio_doi']['#access'] = FALSE;
+ }
}
}
return $form;
@@ -1756,6 +1764,14 @@ function biblio_form_validate($form, &$form_state) {
($form['#post']['biblio_type'] > 0 ? t('Save') : '');
switch ($op) {
case t('Save'):
+ // Look for DOI conflicts on save.
+ if (!empty($form_state['values']['biblio_doi'])) {
+ $conflict = (int) db_result(db_query("SELECT nid FROM {biblio} INNER JOIN {node} USING (nid, vid) WHERE biblio_doi = '%s' AND nid != %d", $doi, (int) $form['#node']->nid));
+ if ($conflict) {
+ form_set_error('biblio_doi', l(t("Another node already has this DOI."), "node/$conflict"));
+ }
+ }
+
if ($form_state['storage']['biblio_type'] == $form_state['values']['biblio_type'] ||
(!empty($form['#node']->biblio_type) && $form['#node']->biblio_type == $form_state['values']['biblio_type'])) {
unset ($form_state['storage']);
diff --git a/modules/CiteProc/biblio_citeproc.admin.inc b/modules/CiteProc/biblio_citeproc.admin.inc
index c9f6e50..6d4561d 100644
--- a/modules/CiteProc/biblio_citeproc.admin.inc
+++ b/modules/CiteProc/biblio_citeproc.admin.inc
@@ -245,7 +245,7 @@ function _install_csl($name, $csl, $sha = NULL, $all = FALSE) {
}
}
if (!$all && !empty($parent)) {
- $csl_file_contents = db_result(db_query("SELECT csl FROM biblio_citeproc_styles WHERE id = '%s'", $parent));
+ $csl_file_contents = db_result(db_query("SELECT csl FROM {biblio_citeproc_styles} WHERE id = '%s'", $parent));
if (!$csl_file_contents) {
drupal_set_message(t('You do not have the parent style file: !parent_id installed. You must install !parent_id before you can use !csl_id', array('!parent_id' => basename($parent), '!csl_id' => $name)), 'error');
}
@@ -378,7 +378,7 @@ function biblio_citeproc_csl_editor($form_state, $style) {
return;
}
if (!empty($csl->parent)) {
- $csl = db_fetch_object(db_query("SELECT id,csl FROM biblio_citeproc_styles WHERE id = '%s'", array(':id' => $csl->parent)));
+ $csl = db_fetch_object(db_query("SELECT id,csl FROM {biblio_citeproc_styles} WHERE id = '%s'", array(':id' => $csl->parent)));
}
if (isset($csl->csl)) {
diff --git a/modules/CiteProc/biblio_citeproc.module b/modules/CiteProc/biblio_citeproc.module
index ce97b50..23a23a5 100644
--- a/modules/CiteProc/biblio_citeproc.module
+++ b/modules/CiteProc/biblio_citeproc.module
@@ -85,13 +85,13 @@ function theme_biblio_citeproc_style($node, $base = 'biblio', $style_name = NULL
}
}
if (!empty($csl_id)) {
- $csl = db_fetch_object(db_query("SELECT parent,csl FROM biblio_citeproc_styles WHERE filename = '%s'", $csl_id));
+ $csl = db_fetch_object(db_query("SELECT parent,csl FROM {biblio_citeproc_styles} WHERE filename = '%s'", $csl_id));
if (!isset($csl->csl)) {
drupal_set_message(t('Biblio-CiteProc could not fetch the style file: @csl_id from the database.', array('@csl_id' => $csl_id)), 'error');
return;
}
if (!empty($csl->parent)) {
- $csl_file_contents = db_result(db_query("SELECT csl FROM biblio_citeproc_styles WHERE id = '%s'", $csl->parent));
+ $csl_file_contents = db_result(db_query("SELECT csl FROM {biblio_citeproc_styles} WHERE id = '%s'", $csl->parent));
if (!$csl_file_contents) {
drupal_set_message(t('Biblio-CiteProc could not fetch the parent style file: @csl_id from the database.', array('@csl_id' => $csl->parent)), 'error');
return;
diff --git a/modules/crossref/biblio.crossref.client.php b/modules/crossref/biblio.crossref.client.php
index 5e40fb7..f60b9ea 100644
--- a/modules/crossref/biblio.crossref.client.php
+++ b/modules/crossref/biblio.crossref.client.php
@@ -78,6 +78,50 @@ class BiblioCrossRefClient
return $this->node;
}
+ function fetchByAuthorTitle($author, $title) {
+ $qdata = simplexml_load_string('');
+ $qdata->head->email_address = $this->pid;
+ $qdata->head->doi_batch_id = uniqid('NA');
+ $qdata->body->query = '';
+ $query = $qdata->body->query;
+ $query['enable-multiple-hits'] = 'exact';
+ $query['key'] = 'key';
+ $query->article_title = $title;
+ $query->article_title['match'] = 'fuzzy';
+ $query->author = $author;
+ $query->author['search-all-authors'] = 'true';
+ $this->query = url($this->url, array(
+ 'external' => TRUE,
+ 'query' => array(
+ 'pid' => $this->pid,
+ 'noredirect' => 'true',
+ 'format' => 'unixref',
+ 'qdata' => (string) $qdata->asXml()
+ )
+ ));
+ $response = drupal_http_request($this->query);
+ if ($response->code != 200) {
+ drupal_set_message(t('Could not open crossref.org for XML author/title query.'),'error');
+ return array();
+ }
+ $xml = simplexml_load_string($response->data);
+ $results = array();
+ foreach ($xml->doi_record as $record) {
+ $result = array(
+ 'full' => $record->asXml(),
+ 'doi' => $record->xpath('.//doi[1]'),
+ 'title' => $record->xpath('.//title[1]'),
+ );
+ $result['full'] = preg_replace('@<[^>]+>@s', '.', $result['full']);
+ $result['full'] = preg_replace('@\.[\s\.]+@', '. ', $result['full']);
+ $result['full'] = trim($result['full'], '. ');
+ $result['doi'] = (string) $result['doi'][0];
+ $result['title'] = (string) $result['title'][0];
+ $results[] = $result;
+ }
+ return $results;
+ }
+
function unixref_startElement($parser, $name, $attrs) {
switch ($name) {
@@ -172,6 +216,9 @@ class BiblioCrossRefClient
break;
case 'journal_issue':
$this->node['biblio_date'] = (!empty($this->node['month']) ? $this->node['month'] . '/':'') . $this->node['year'];
+ if (empty($this->node['biblio_year'])) {
+ $this->node['biblio_year'] = $this->node['year'];
+ }
break;
case 'journal_article':
case 'conference_paper':
@@ -180,7 +227,9 @@ class BiblioCrossRefClient
case 'standard_metadata':
case 'database_date':
case 'component':
+ if (!empty($this->node['year'])) {
$this->node['biblio_year'] = $this->node['year'];
+ }
// $this->node['biblio_doi'] = $this->node['doi'];
break;
case 'issn':
diff --git a/modules/crossref/biblio_crossref.module b/modules/crossref/biblio_crossref.module
index c999616..64f4bb8 100644
--- a/modules/crossref/biblio_crossref.module
+++ b/modules/crossref/biblio_crossref.module
@@ -6,7 +6,7 @@
function biblio_crossref_form_biblio_node_form_alter(&$form, &$form_state) {
global $user;
- if (phpversion() > 5 && !$form_state['submitted'] &&
+ if (phpversion() > 5 && (!$form_state['submitted'] || isset($form_state['values']['doi_search_results'])) &&
!isset($form['#node']->nid))
{
$form['biblio_doi_lookup'] = array(
@@ -29,6 +29,27 @@ function biblio_crossref_form_biblio_node_form_alter(&$form, &$form_state) {
);
}
+ if (isset($form_state['values']['doi_search_results']) && is_array($form_state['values']['doi_search_results'])) {
+ $form['biblio_doi_lookup']['#collapsed'] = FALSE;
+ if (empty($form_state['values']['doi_search_results'])) {
+ // No results.
+ }
+ else {
+ foreach ($form_state['values']['doi_search_results'] as $result) {
+ $info = l($result['doi'], 'http://dx.doi.org/' . $result['doi'], array(
+ 'external' => TRUE,
+ 'attributes' => array(
+ 'onclick' => "$('#edit-doi-data').val($(this).text()); return false"
+ )
+ ));
+ $info .= ': ' . $result['full'];
+ $form['biblio_doi_lookup'][] = array(
+ '#value' => "" . $info . '
',
+ '#weight' => -11
+ );
+ }
+ }
+ }
$form['biblio_doi_lookup']['doi_data'] = array(
'#type' => 'textfield',
'#title' => t('DOI'),
@@ -38,13 +59,45 @@ function biblio_crossref_form_biblio_node_form_alter(&$form, &$form_state) {
'#disabled' => empty($have_pid),
'#size' => 60,
'#maxlength' => 255,
- '#weight' => -4
+ '#weight' => -10
);
$form['biblio_doi_lookup']['doi_submit'] = array(
'#type' => 'submit',
'#disabled' => empty($have_pid),
- '#value' => t('Populate using DOI')
+ '#value' => t('Populate using DOI'),
+ '#weight' => -9
+ );
+
+ $form['biblio_doi_lookup']['doi_search_author'] = array(
+ '#type' => 'textfield',
+ '#title' => t('Author'),
+ '#required' => FALSE,
+ '#default_value' => $form_state['values']['doi_search_author'],
+ '#description' => t('Enter the LAST name of the FIRST author.'),
+ '#disabled' => empty($have_pid),
+ '#size' => 60,
+ '#maxlength' => 255,
+ '#weight' => -7
);
+ $form['biblio_doi_lookup']['doi_search_title'] = array(
+ '#type' => 'textfield',
+ '#title' => t('Title'),
+ '#required' => FALSE,
+ '#default_value' => $form_state['values']['doi_search_title'],
+ '#description' => t('Enter the exact title.'),
+ '#disabled' => empty($have_pid),
+ '#size' => 60,
+ '#maxlength' => 255,
+ '#weight' => -6
+ );
+ $form['biblio_doi_lookup']['doi_search_submit'] = array(
+ '#type' => 'submit',
+ '#disabled' => empty($have_pid),
+ '#value' => t('Search for DOI by Author and Title'),
+ '#weight' => -5
+ );
+ $form_state['values']['doi_search_results'] = NULL;
+
$form['#validate'] = array_merge(array('biblio_crossref_form_biblio_node_form_validate'), $form['#validate']); // put my validator first
}
$biblio_crossref_id = (isset($form_state['values']['biblio_crossref_id'])) ? $form_state['values']['biblio_crossref_id'] : '';
@@ -97,11 +150,22 @@ function biblio_crossref_form_biblio_node_form_validate($form, &$form_state) {
return;
}
}
- return;
+
+ if (!empty($form_state['values']['doi_search_author']) && !empty($form_state['values']['doi_search_title'])) {
+ $crossref_pid = variable_get('biblio_crossref_pid', '');
+ module_load_include('php', 'biblio_crossref', 'biblio.crossref.client');
+ $client = new BiblioCrossRefClient('', $crossref_pid);
+ $client->setUrl('http://doi.crossref.org/servlet/query');
+ $results = $client->fetchByAuthorTitle($form_state['values']['doi_search_author'], $form_state['values']['doi_search_title']);
+ $form_state['values']['doi_search_results'] = $results;
+ $form_state['rebuild'] = TRUE;
+ $form_state['submitted'] = FALSE;
+ $form_state['values']['biblio_type'] = NULL;
+ }
}
function biblio_crossref_check_doi($doi) {
- return db_result(db_query("SELECT nid FROM {biblio_crossref} WHERE biblio_crossref_id = '%s'", $doi));
+ return db_result(db_query("SELECT nid FROM {biblio} INNER JOIN {node} USING (nid, vid) WHERE biblio_doi = '%s'", $doi));
}
function biblio_crossref_biblio_lookup_link_settings() {
diff --git a/modules/pubmed/EntrezClient.php b/modules/pubmed/EntrezClient.php
index 85ac80c..2d501a3 100644
--- a/modules/pubmed/EntrezClient.php
+++ b/modules/pubmed/EntrezClient.php
@@ -340,7 +340,7 @@ class BiblioEntrezClient
$xml = drupal_http_request($this->query);
- $result = @simplexml_load_string($$xml->data);
+ $result = @simplexml_load_string($xml->data);
if (!$result) {
throw new Exception('Query ' . $this->query . ' failed.');
diff --git a/modules/pubmed/biblio_pm.module b/modules/pubmed/biblio_pm.module
index ff40f0f..0150a07 100644
--- a/modules/pubmed/biblio_pm.module
+++ b/modules/pubmed/biblio_pm.module
@@ -88,8 +88,8 @@ function biblio_pm_form_biblio_node_form_alter(&$form, &$form_state) {
);
$form['#validate'] = array_merge(array('biblio_pm_form_biblio_node_form_validate'), $form['#validate']); // put my validator first
}
- $form['biblio_pubmed_id'] = array('#type' => 'value', '#value' => $form_state['values']['biblio_pubmed_id']);
- $form['biblio_pubmed_md5'] = array('#type' => 'value', '#value' => $form_state['values']['biblio_pubmed_md5']);
+ $form['biblio_pubmed_id'] = array('#type' => 'value', '#value' => $form['#node']->biblio_pubmed_id);
+ $form['biblio_pubmed_md5'] = array('#type' => 'value', '#value' => $form['#node']->biblio_pubmed_md5);
}
function biblio_pm_form_biblio_node_form_validate($form, &$form_state) {
@@ -230,7 +230,10 @@ function biblio_pm_check_pmid($pmid) {
return db_result(db_query("SELECT nid FROM {biblio_pubmed} WHERE biblio_pubmed_id = %d", $pmid));
}
function biblio_pm_biblio_lookup_link_settings() {
- return array('pubmed' => t('PubMed'));
+ return array(
+ 'pubmed' => t('PubMed'),
+ 'pmc' => t('PubMed Central'),
+ );
}
function biblio_pm_biblio_lookup_link($node) {
@@ -239,28 +242,45 @@ function biblio_pm_biblio_lookup_link($node) {
function biblio_pm_link($type, $node = NULL, $teaser = FALSE) {
$show_link = variable_get('biblio_lookup_links', array('pubmed' => TRUE));
- if (!isset($show_link['pubmed']) ||
- !$show_link['pubmed'] ||
- !isset($node) ||
- $node->type != 'biblio' ||
- !isset($node->biblio_pubmed_id)) {
- return array();
- }
+ $links = array();
- if (isset($node) && $type == 'node' && $node->type == 'biblio' && !empty($node->biblio_pubmed_id)) {
+ if (isset($node) && $type == 'node' && $node->type == 'biblio') {
+ if (!empty($show_link['pubmed']) && !empty($node->biblio_pubmed_id)) {
$link = 'http://www.ncbi.nlm.nih.gov/pubmed/'. $node->biblio_pubmed_id .'?dopt=Abstract';
- $attrs = array('title' => t("Click to view the PubMed listing for this node"));
+ $attrs = array(
+ 'title' => t("Click to view the PubMed listing")
+ );
if (variable_get('biblio_links_target_new_window', null)){
- $attrs = array_merge($attrs, array('target'=>'_blank'));
+ $attrs = array_merge($attrs, array(
+ 'target' => '_blank'
+ ));
}
- return array('biblio_pubmed' => array(
+ $links['biblio_pubmed'] = array(
'title' => t('PubMed'),
'href' => $link,
- 'attributes' => $attrs,
+ 'attributes' => $attrs
+ );
+ }
+ if (!empty($show_link['pmc']) && !empty($node->biblio_pmcid)) {
+ $link = 'http://www.ncbi.nlm.nih.gov/pmc/articles/PMC' . $node->biblio_pmcid . '/';
+ $attrs = array(
+ 'title' => t("Click to view the PubMed Central full text")
+ );
+ if (variable_get('biblio_links_target_new_window', null)) {
+ $attrs = array_merge($attrs, array(
+ 'target' => '_blank'
));
}
- return ;
+
+ $links['biblio_pmc'] = array(
+ 'title' => t('PMC Full Text'),
+ 'href' => $link,
+ 'attributes' => $attrs
+ );
+ }
+ }
+ return $links;
}
@@ -297,9 +317,57 @@ function _biblio_pm_update($node) {
}
}
-function _biblio_pm_load($node) {
- if ($node->type == 'biblio') {
- return db_fetch_array(db_query('SELECT biblio_pubmed_id FROM {biblio_pubmed} WHERE nid = %d', $node->nid));
+function _biblio_pm_load(&$node) {
+ if (!isset($node->nid)) return;
+ $fields = (array) db_fetch_array(db_query('SELECT biblio_pubmed_id, biblio_pubmed_md5, biblio_pmcid FROM {biblio_pubmed} WHERE nid = %d', $node->nid));
+ foreach ($fields as $k => $v) {
+ $node->$k = $v;
+ }
+}
+
+function _biblio_pm_presave(&$node, $a, $b) {
+ // If there is no pubmed id, try to locate it by DOI.
+ if (!isset($node->biblio_pubmed_id) || empty($node->biblio_pubmed_id)) {
+ module_load_include('php', 'biblio_pm', 'EntrezClient');
+ module_load_include('php', 'biblio_pm', 'EntrezPubmedArticle');
+ $Eclient = new BiblioEntrezClient;
+ try {
+ $Eclient->setDatabase('pubmed');
+ $Eclient->setTerm($node->biblio_doi . '[AID]');
+ $result = $Eclient->search();
+ if ($Eclient->count() == 1) {
+ $node->biblio_pubmed_id = (string) $result->IdList->Id;
+ drupal_set_message(t("Located PubMed ID: !id", array('!id' => $node->biblio_pubmed_id)));
+ if (isset($node->nid)) {
+ _biblio_pm_insert($node);
+ }
+ }
+ } catch (Exception $e) {
+ drupal_set_message($e->getMessage(), 'warning');
+ }
+ }
+
+ // If there is no pmc id, try to locate it by DOI.
+ if (!isset($node->biblio_pmcid) || empty($node->biblio_pmcid)) {
+ if (isset($node->biblio_doi) && !empty($node->biblio_doi)) {
+ module_load_include('php', 'biblio_pm', 'EntrezClient');
+ module_load_include('php', 'biblio_pm', 'EntrezPubmedArticle');
+ $Eclient = new BiblioEntrezClient;
+ try {
+ $Eclient->setDatabase('pmc');
+ $Eclient->setTerm($node->biblio_doi . '[DOI]');
+ $result = $Eclient->search();
+ if ($Eclient->count() == 1) {
+ $node->biblio_pmcid = (string) $result->IdList->Id;
+ drupal_set_message(t("Located PMC ID: !id", array('!id' => $node->biblio_pmcid)));
+ if (isset($node->nid) && (!isset($node->biblio_pubmed_id) || empty($node->biblio_pubmed_id))) {
+ _biblio_pm_insert($node);
+ }
+ }
+ } catch (Exception $e) {
+ drupal_set_message($e->getMessage(), 'warning');
+ }
+ }
}
}