tripal_pub.pub_citation.inc

Functions to manage citations

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tripal_pub/includes/tripal_pub.pub_citation.inc
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  1. <?php

  2. /**

  3.  * @file

  4.  * Functions to manage citations

  5.  */

  6. 

  7. /**

  8.  * The admin form for submitting job to create citations

  9.  *

  10.  * @param $form_state

  11.  *

  12.  * @ingroup tripal_pub

  13.  */

  14. function tripal_pub_citation_form($form, &$form_state) {

  15. 

  16.   $form['instructions'] = array(

  17.     '#markup' => '<p>Use this form to unify publication citations. Citations are created automtically when

  18.       importing publications but citations are set by the user when publications are added manually.

  19.       Or publications added to the Chado database by tools other than the Tripal Publication Importer may

  20.       not have citations set. If you are certain that all necessary information for all publications is present (e.g.

  21.       authors, volume, issue, page numbers, etc.) but citations are not consistent, then you can

  22.       choose to update all citations for all publications using the form below. Alternatively, you

  23.       can update citations only for publication that do not already have one.</p>'

  24.   );

  25. 

  26.   $form['options'] = array(

  27.     '#type' => 'radios',

  28.     '#options' => array(

  29.       'all' => 'Create citation for all publications. Replace the existing citation if it exists.',

  30.       'new' => 'Create citation for publication only if it does not already have one.'),

  31.     '#default_value' => 'all'

  32.   );

  33. 

  34.   $form['submit'] = array(

  35.     '#type' => 'submit',

  36.     '#value' => t('Submit')

  37.   );

  38. 

  39.   return $form;

  40. }

  41. 

  42. /**

  43.  * Submit form. Create Tripal job for citations

  44.  *

  45.  * @param $form_state

  46.  *

  47.  * @ingroup tripal_pub

  48.  */

  49. function tripal_pub_citation_form_submit(&$form_state) {

  50.   $options [0] = $form_state['options']['#value'];

  51.   tripal_add_job("Create citations ($options[0])", 'tripal_pub', 'tripal_pub_create_citations', $options, $user->uid);

  52. }

  53. 

  54. /**

  55.  * Launch the Tripal job to generate citations. Called by tripal jobs

  56.  *

  57.  * @param $options

  58.  *  Options pertaining to what publications to generate citations for.

  59.  *  One of the following must be present:

  60.  *   - all: Create and replace citation for all pubs

  61.  *   - new: Create citation for pubs that don't already have one

  62.  *

  63.  * @ingroup tripal_pub

  64.  */

  65. function tripal_pub_create_citations($options) {

  66.   $skip_existing = TRUE;

  67.   $sql = "

  68.     SELECT cvterm_id

  69.     FROM {cvterm}

  70.     WHERE

  71.       name = 'Citation' AND

  72.       cv_id = (SELECT cv_id FROM {cv} WHERE name = 'tripal_pub')

  73.   ";

  74.   $citation_type_id = chado_query($sql)->fetchField();

  75. 

  76.   // Create and replace citation for all pubs

  77.   if ($options == 'all') {

  78.     $sql = "SELECT pub_id FROM {pub} P WHERE pub_id <> 1";

  79.     $skip_existing = FALSE;

  80.   }

  81.   // Create citation for pubs that don't already have one

  82.   else if ($options == 'new') {

  83.     $sql = "

  84.       SELECT pub_id

  85.       FROM {pub} P

  86.       WHERE

  87.         (SELECT value

  88.          FROM {pubprop} PB

  89.          WHERE type_id = :type_id AND P.pub_id = PB.pub_id AND rank = 0) IS NULL

  90.         AND  pub_id <> 1

  91.     ";

  92.     $skip_existing = TRUE;

  93.   }

  94. 

  95.   $result = chado_query($sql, array(':type_id' => $citation_type_id));

  96.   $counter_updated = 0;

  97.   $counter_generated = 0;

  98.   while ($pub = $result->fetchObject()) {

  99.     $pub_arr = tripal_pub_get_publication_array($pub->pub_id, $skip_existing);

  100.     if ($pub_arr) {

  101.       $citation = tripal_pub_create_citation($pub_arr);

  102.       print $citation . "\n\n";

  103.       // Replace if citation exists. This condition is never TRUE if $skip_existing is TRUE

  104.       if ($pub_arr['Citation']) {

  105.         $sql = "

  106.           UPDATE {pubprop} SET value = :value

  107.           WHERE pub_id = :pub_id  AND type_id = :type_id AND rank = :rank

  108.         ";

  109.         chado_query($sql, array(':value' => $citation, ':pub_id' => $pub->pub_id,

  110.           ':type_id' => $citation_type_id, ':rank' => 0));

  111.         $counter_updated ++;

  112.       // Generate a new citation

  113.       } else {

  114.         $sql = "

  115.           INSERT INTO {pubprop} (pub_id, type_id, value, rank)

  116.           VALUES (:pub_id, :type_id, :value, :rank)

  117.         ";

  118.         chado_query($sql, array(':pub_id' => $pub->pub_id, ':type_id' => $citation_type_id,

  119.           ':value' => $citation, ':rank' => 0));

  120.         $counter_generated ++;

  121.       }

  122.     }

  123.   }

  124.   print "$counter_generated citations generated. $counter_updated citations updated.\n";

  125. }

  126. 

  127. 

  128. /**

  129.  * This function generates citations for publications.  It requires

  130.  * an array structure with keys being the terms in the Tripal

  131.  * publication ontology.  This function is intended to be used

  132.  * for any function that needs to generate a citation.

  133.  *

  134.  * @param $pub

  135.  *   An array structure containing publication details where the keys

  136.  *   are the publication ontology term names and values are the

  137.  *   corresponding details.  The pub array can contain the following

  138.  *   keys with corresponding values:

  139.  *     - Publication Type:  an array of publication types. a publication can have more than one type

  140.  *     - Authors: a  string containing all of the authors of a publication

  141.  *     - Journal Name:  a string containing the journal name

  142.  *     - Journal Abbreviation: a string containing the journal name abbreviation

  143.  *     - Series Name: a string containing the series (e.g. conference proceedings) name

  144.  *     - Series Abbreviation: a string containing the series name abbreviation

  145.  *     - Volume: the serives volume number

  146.  *     - Issue: the series issue number

  147.  *     - Pages: the page numbers for the publication

  148.  *     - Publication Date:  A date in the format "Year Month Day"

  149.  *

  150.  * @return

  151.  *   A text string containing the citation

  152.  *

  153.  * @ingroup tripal_pub

  154.  */

  155. function tripal_pub_create_citation($pub) {

  156.   $citation = '';

  157.   $pub_type = '';

  158. 

  159.   // An article may have more than one publication type. For example,

  160.   // a publication type can be 'Journal Article' but also a 'Clinical Trial'.

  161.   // Therefore, we need to select the type that makes most sense for

  162.   // construction of the citation. Here we'll iterate through them all

  163.   // and select the one that matches best.

  164.   if (is_array($pub['Publication Type'])) {

  165.     foreach ($pub['Publication Type'] as $ptype) {

  166.       if ($ptype == 'Journal Article' ) {

  167.         $pub_type = $ptype;

  168.         break;

  169.       }

  170.       else if ($ptype == 'Conference Proceedings'){

  171.         $pub_type = $ptype;

  172.         break;

  173.       }

  174.       else if ($ptype == 'Review') {

  175.         $pub_type = $ptype;

  176.         break;

  177.       }

  178.       else if ($ptype == 'Book') {

  179.         $pub_type = $ptype;

  180.         break;

  181.       }

  182.       else if ($ptype == 'Letter') {

  183.         $pub_type = $ptype;

  184.         break;

  185.       }

  186.       else if ($ptype == 'Book Chapter') {

  187.         $pub_type = $ptype;

  188.         break;

  189.       }

  190.       else if ($ptype == "Research Support, Non-U.S. Gov't") {

  191.         $pub_type = $ptype;

  192.         // we don't break because if the article is also a Journal Article

  193.         // we prefer that type

  194.       }

  195.     }

  196.     // If we don't have a recognized publication type, then just use the

  197.     // first one in the list.

  198.     if (!$pub_type) {

  199.       $pub_type = $pub['Publication Type'][0];

  200.     }

  201.   }

  202.   else {

  203.     $pub_type = $pub['Publication Type'];

  204.   }

  205. 

  206.   //----------------------

  207.   // Journal Article

  208.   //----------------------

  209.   if ($pub_type == 'Journal Article') {

  210.     if (array_key_exists('Authors', $pub)) {

  211.       $citation = $pub['Authors'] . '. ';

  212.     }

  213. 

  214.     $citation .= $pub['Title'] .  '. ';

  215. 

  216.     if (array_key_exists('Journal Name', $pub)) {

  217.       $citation .= $pub['Journal Name'] . '. ';

  218.     }

  219.     elseif (array_key_exists('Journal Abbreviation', $pub)) {

  220.       $citation .= $pub['Journal Abbreviation'] . '. ';

  221.     }

  222.     elseif (array_key_exists('Series Name', $pub)) {

  223.       $citation .= $pub['Series Name'] . '. ';

  224.     }

  225.     elseif (array_key_exists('Series Abbreviation', $pub)) {

  226.       $citation .= $pub['Series Abbreviation'] . '. ';

  227.     }

  228.     if (array_key_exists('Publication Date', $pub)) {

  229.       $citation .= $pub['Publication Date'];

  230.     }

  231.     elseif (array_key_exists('Year', $pub)) {

  232.       $citation .= $pub['Year'];

  233.     }

  234.     if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {

  235.       $citation .= '; ';

  236.     }

  237.     if (array_key_exists('Volume', $pub)) {

  238.       $citation .= $pub['Volume'];

  239.     }

  240.     if (array_key_exists('Issue', $pub)) {

  241.       $citation .= '(' . $pub['Issue'] . ')';

  242.     }

  243.     if (array_key_exists('Pages', $pub)) {

  244.       if (array_key_exists('Volume', $pub)) {

  245.         $citation .= ':';

  246.       }

  247.       $citation .= $pub['Pages'];

  248.     }

  249.     $citation .= '.';

  250.   }

  251.   //----------------------

  252.   // Review

  253.   //----------------------

  254.   elseif ($pub_type == 'Review') {

  255.     if (array_key_exists('Authors', $pub)) {

  256.       $citation = $pub['Authors'] . '. ';

  257.     }

  258. 

  259.     $citation .= $pub['Title'] .  '. ';

  260. 

  261.     if (array_key_exists('Journal Name', $pub)) {

  262.       $citation .= $pub['Journal Name'] . '. ';

  263.     }

  264.     elseif (array_key_exists('Journal Abbreviation', $pub)) {

  265.       $citation .= $pub['Journal Abbreviation'] . '. ';

  266.     }

  267.     elseif (array_key_exists('Series Name', $pub)) {

  268.       $citation .= $pub['Series Name'] . '. ';

  269.     }

  270.     elseif (array_key_exists('Series Abbreviation', $pub)) {

  271.       $citation .= $pub['Series Abbreviation'] . '. ';

  272.     }

  273.     if (array_key_exists('Publication Date', $pub)) {

  274.       $citation .= $pub['Publication Date'];

  275.     }

  276.     elseif (array_key_exists('Year', $pub)) {

  277.       $citation .= $pub['Year'];

  278.     }

  279.     if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {

  280.       $citation .= '; ';

  281.     }

  282.     if (array_key_exists('Volume', $pub)) {

  283.       $citation .= $pub['Volume'];

  284.     }

  285.     if (array_key_exists('Issue', $pub)) {

  286.       $citation .= '(' . $pub['Issue'] . ')';

  287.     }

  288.     if (array_key_exists('Pages', $pub)) {

  289.       if (array_key_exists('Volume', $pub)) {

  290.         $citation .= ':';

  291.       }

  292.       $citation .= $pub['Pages'];

  293.     }

  294.     $citation .= '.';

  295.   }

  296.   //----------------------

  297.   // Research Support, Non-U.S. Gov't

  298.   //----------------------

  299.   elseif ($pub_type == "Research Support, Non-U.S. Gov't") {

  300.     if (array_key_exists('Authors', $pub)) {

  301.       $citation = $pub['Authors'] . '. ';

  302.     }

  303. 

  304.     $citation .= $pub['Title'] .  '. ';

  305. 

  306.     if (array_key_exists('Journal Name', $pub)) {

  307.       $citation .= $pub['Journal Name'] . '. ';

  308.     }

  309.     if (array_key_exists('Publication Date', $pub)) {

  310.       $citation .= $pub['Publication Date'];

  311.     }

  312.     elseif (array_key_exists('Year', $pub)) {

  313.       $citation .= $pub['Year'];

  314.     }

  315.     $citation .= '.';

  316.   }

  317.   //----------------------

  318.   // Letter

  319.   //----------------------

  320.   elseif ($pub_type == 'Letter') {

  321.     if (array_key_exists('Authors', $pub)) {

  322.       $citation = $pub['Authors'] . '. ';

  323.     }

  324. 

  325.     $citation .= $pub['Title'] .  '. ';

  326.     if (array_key_exists('Journal Name', $pub)) {

  327.       $citation .= $pub['Journal Name'] . '. ';

  328.     }

  329.     elseif (array_key_exists('Journal Abbreviation', $pub)) {

  330.       $citation .= $pub['Journal Abbreviation'] . '. ';

  331.     }

  332.     elseif (array_key_exists('Series Name', $pub)) {

  333.       $citation .= $pub['Series Name'] . '. ';

  334.     }

  335.     elseif (array_key_exists('Series Abbreviation', $pub)) {

  336.       $citation .= $pub['Series Abbreviation'] . '. ';

  337.     }

  338.     if (array_key_exists('Publication Date', $pub)) {

  339.       $citation .= $pub['Publication Date'];

  340.     }

  341.     elseif (array_key_exists('Year', $pub)) {

  342.       $citation .= $pub['Year'];

  343.     }

  344.     if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {

  345.       $citation .= '; ';

  346.     }

  347.     if (array_key_exists('Volume', $pub)) {

  348.       $citation .= $pub['Volume'];

  349.     }

  350.     if (array_key_exists('Issue', $pub)) {

  351.       $citation .= '(' . $pub['Issue'] . ')';

  352.     }

  353.     if (array_key_exists('Pages', $pub)) {

  354.       if (array_key_exists('Volume', $pub)) {

  355.         $citation .= ':';

  356.       }

  357.       $citation .= $pub['Pages'];

  358.     }

  359.     $citation .= '.';

  360.   }

  361.   //-----------------------

  362.   // Conference Proceedings

  363.   //-----------------------

  364.   elseif ($pub_type == 'Conference Proceedings') {

  365.     if (array_key_exists('Authors', $pub)) {

  366.       $citation = $pub['Authors'] . '. ';

  367.     }

  368. 

  369.     $citation .= $pub['Title'] .  '. ';

  370.     if (array_key_exists('Conference Name', $pub)) {

  371.       $citation .= $pub['Conference Name'] . '. ';

  372.     }

  373.     elseif (array_key_exists('Series Name', $pub)) {

  374.       $citation .= $pub['Series Name'] . '. ';

  375.     }

  376.     elseif (array_key_exists('Series Abbreviation', $pub)) {

  377.       $citation .= $pub['Series Abbreviation'] . '. ';

  378.     }

  379.     if (array_key_exists('Publication Date', $pub)) {

  380.       $citation .= $pub['Publication Date'];

  381.     }

  382.     elseif (array_key_exists('Year', $pub)) {

  383.       $citation .= $pub['Year'];

  384.     }

  385.     if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {

  386.       $citation .= '; ';

  387.     }

  388.     if (array_key_exists('Volume', $pub)) {

  389.       $citation .= $pub['Volume'];

  390.     }

  391.     if (array_key_exists('Issue', $pub)) {

  392.       $citation .= '(' . $pub['Issue'] . ')';

  393.     }

  394.     if (array_key_exists('Pages', $pub)) {

  395.       if (array_key_exists('Volume', $pub)) {

  396.         $citation .= ':';

  397.       }

  398.       $citation .= $pub['Pages'];

  399.     }

  400.     $citation .= '.';

  401.   }

  402.   //-----------------------

  403.   // Default

  404.   //-----------------------

  405.   else {

  406.     if (array_key_exists('Authors', $pub)) {

  407.       $citation = $pub['Authors'] . '. ';

  408.     }

  409.     $citation .= $pub['Title'] .  '. ';

  410.     if (array_key_exists('Series Name', $pub)) {

  411.       $citation .= $pub['Series Name'] . '. ';

  412.     }

  413.     elseif (array_key_exists('Series Abbreviation', $pub)) {

  414.       $citation .= $pub['Series Abbreviation'] . '. ';

  415.     }

  416.     if (array_key_exists('Publication Date', $pub)) {

  417.       $citation .= $pub['Publication Date'];

  418.     }

  419.     elseif (array_key_exists('Year', $pub)) {

  420.       $citation .= $pub['Year'];

  421.     }

  422.     if (array_key_exists('Volume', $pub) or array_key_exists('Issue', $pub) or array_key_exists('Pages',$pub)) {

  423.       $citation .= '; ';

  424.     }

  425.     if (array_key_exists('Volume', $pub)) {

  426.       $citation .= $pub['Volume'];

  427.     }

  428.     if (array_key_exists('Issue', $pub)) {

  429.       $citation .= '(' . $pub['Issue'] . ')';

  430.     }

  431.     if (array_key_exists('Pages', $pub)) {

  432.       if (array_key_exists('Volume', $pub)) {

  433.         $citation .= ':';

  434.       }

  435.       $citation .= $pub['Pages'];

  436.     }

  437.     $citation .= '.';

  438.   }

  439. 

  440.   return $citation;

  441. }