<?php
// $Id: biblio_pm.module,v 1.1.2.12 2010-10-13 16:52:03 rjerome Exp $
/*
 * @file pubmed.module
 *
 */

function biblio_pm_form_biblio_node_form_alter(&$form, &$form_state) {
  if(phpversion() > 5 && !isset($form_state['storage']) && !isset($form['#node']->nid)) {
    $form['biblio_pubmed_lookup'] = array(
        '#type' => 'fieldset',
        '#title' => t('PubMed Lookup'),
        '#weight' => -20,
        '#collapsible' => TRUE,
        '#collapsed' => TRUE,
    );

    $form['biblio_pubmed_lookup']['PMID'] = array(
        '#type' => 'textfield',
        '#title' => t('PubMed ID'),
        '#required' => FALSE,
        '#default_value' => '',
        '#description' => t('Enter a PubMed ID</b>'),
        '#size' => 60,
        '#maxlength' => 255,
        '#weight' => -4
    );
    $form['biblio_pubmed_lookup']['pubmed_submit'] = array(
        '#type' => 'submit',
        '#value' => t('Populate using PubMed')
    );
    $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']);
}

function biblio_pm_form_biblio_node_form_validate($form, &$form_state) {
  $node_data = array();
  if (strlen($pmid = $form_state['values']['PMID'])) {
    module_load_include('php','biblio','pubmed/EntrezClient');
    module_load_include('php','biblio','pubmed/EntrezPubmedArticle');
    $Eclient = new BiblioEntrezClient;
    try {
      $result = $Eclient->fetch($pmid);
    } catch (Exception $e) {
       form_set_error($e->getMessage());
    }
    if(!isset($result->PubmedArticle)) {
      unset($form_state['values']['biblio_type']);
      unset($form_state['post']['biblio_type']);
      form_set_error('PMID', 'No data available for PubMed ID: '.check_plain($pmid));
      return;
    }
    $data = new BiblioEntrezPubmedArticle($result->PubmedArticle);
    $node_data = $data->getBiblio();
  }
  if(!empty($node_data)) {
    $form_state['values'] = array_merge($form_state['values'], $node_data);
    $form_state['storage']['biblio_type']  = $node_data['biblio_type'];

    return;
  }

}

function biblio_pm_biblio_import_options() {
  return array('biblio_pm' => t('PubMed ID List'));
}

function biblio_pm_biblio_import($file, $terms = array(), $batch = FALSE, $session_id = NULL, $save = TRUE, $string = FALSE) {
  $nids = array();
  $dups = array();
  return _biblio_pm_import($file, $terms, $batch, $session_id);
}

function _biblio_pm_import($file, $terms, $batch, $session_id) {
  module_load_include('php', 'biblio_pm', 'EntrezClient');
  module_load_include('php', 'biblio_pm', 'EntrezPubmedArticle');
  $pmids = file($file->filepath, FILE_IGNORE_NEW_LINES | FILE_SKIP_EMPTY_LINES);
  if (empty($pmids)) {
    drupal_set_message("Could not open PubMed ID file", 'error');
    return;
  }
  $retmax = 100;
  $resmax = count($pmids);
  $start = 0;
  $Eclient = new BiblioEntrezClient;
  $Eclient->post($pmids);
  $Eclient->setReturnMax($retmax);
  $nids = array();
  $dups = array();
  $node = new stdClass();
  $data = new BiblioEntrezPubmedArticle();
  while (($result = $Eclient->fetchRecords($start)) && $start < $resmax ) {
    foreach ($result->xpath('//PubmedArticle') as $article) {
      //$data->setArticle($article);
      $node = $data->setArticle($article)->getBiblio();
      if (isset($node)) {
        if (!empty($terms)) {
          if (!isset($node['taxonomy'])) $node['taxonomy'] = array();
          $node['taxonomy'] = array_merge($terms, $node['taxonomy']);
        }
        if (! ($dup = biblio_pm_check_md5($node['biblio_pubmed_md5']))) {
          $nid = biblio_save_node($node, $batch, $session_id);
          if (isset($nid)) {
            $nids[] = $nid;
          }
        }
        else {
          $dups[] = $dup;
        }
        $node = null;
      }
      $start++;
    }

  }

  return array($nids, $dups);
}

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'));
}

function biblio_pm_biblio_lookup_link($node) {
  return biblio_pm_link('node', $node);
}

function biblio_pm_link($type, $node = NULL, $teaser = FALSE) {
  if ($type == 'node' && $node->type == 'biblio' && !empty($node->biblio_pubmed_id)) {
    $link  = 'http://www.ncbi.nlm.nih.gov/pubmed/' . $node->biblio_pubmed_id . '?dopt=Abstract';
    return array('biblio_pubmed' => array(
        'title'      => t('PubMed'),
        'href'       => $link,
        'attributes' => array('title' => t("Click to view the PubMed listing for this node")),
    ));
  }
  return ;
}


function biblio_pm_nodeapi(&$node, $op, $a3 = NULL, $a4 = NULL) {
  if($node->type != 'biblio') return;
  $callback = '_biblio_pm_' . str_replace(' ', '_', $op);
  if (function_exists($callback)) {
    $ret = $callback($node, $a3, $a4);
  }
  return $ret;
}

function _biblio_pm_delete($node) {
  db_query('DELETE FROM {biblio_pubmed} WHERE nid = %d', $node->nid);
}

function _biblio_pm_view($node) {

}

function _biblio_pm_insert($node) {
  if (isset($node->biblio_pubmed_id) && !empty($node->biblio_pubmed_id)) {
    drupal_write_record('biblio_pubmed', $node);
  }
}

function _biblio_pm_update($node) {
  if (isset($node->biblio_pubmed_id) && !empty($node->biblio_pubmed_id)) {
    drupal_write_record('biblio_pubmed', $node, 'nid');
  }
}

function _biblio_pm_load($node) {
  static $result = array();
  if (empty($result[$node->nid])) {
    return $result[$node->nid] = db_fetch_array(db_query('SELECT  biblio_pubmed_id  FROM {biblio_pubmed} WHERE nid = %d', $node->nid));
  }
  return $result[$node->nid] ;
}

function biblio_pm_check_md5($md5) {
  static $pm_md5s = array();
  if (empty($pm_md5s)) {
    $result = db_query("SELECT * FROM {biblio_pubmed} ");
    while ($row = db_fetch_object($result)) {
      $pm_md5s[$row->biblio_pubmed_md5] = $row->nid;
    }
  }
  if (isset($pm_md5s[$md5])) {
    return $pm_md5s[$md5];
  }
  else {
    $pm_md5s[$md5] = TRUE; // gaurd against duplicates in the same import
    return;
  }
}