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Add a hook for interactive dropdowns during data entry #3

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merged 5 commits into from
Aug 30, 2021
Merged

Add a hook for interactive dropdowns during data entry #3

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81135ba
adds hook to em for interactive dropdowns after pubmed search
Aug 25, 2021
8a066f3
Show just titles of articles in dropdown
Aug 30, 2021
7069600
fix project settings for cron
Aug 30, 2021
8b55a87
Update README.md
devincowan Aug 30, 2021
531df43
Merge branch 'master' of github.com:devincowan/pubmedSearch
Aug 30, 2021
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269 changes: 224 additions & 45 deletions PubmedSearchExternalModule.php
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Original file line number Diff line number Diff line change
Expand Up @@ -4,35 +4,42 @@
use ExternalModules\AbstractExternalModule;
use ExternalModules\ExternalModules;

use \REDCap as REDCap;
require_once("emLoggerTrait.php");

define('SLEEP_TIME', 1);
define('MAX_RETRIES', 5);

class PubmedSearchExternalModule extends AbstractExternalModule
{
public function getPids() {
$sql="SELECT DISTINCT(s.project_id) AS project_id FROM redcap_external_modules m, redcap_external_module_settings s INNER JOIN redcap_projects AS p ON p.project_id = s.project_id WHERE p.date_deleted IS NULL AND m.external_module_id = s.external_module_id AND s.value = 'true' AND m.directory_prefix = 'pubmedSearch' AND s.`key` = 'enabled'";
$q = db_query($sql);

if ($error = db_error()) {
error_log("PubmedSearchExternalModule ERROR: $error");
}

$pids = array();
while ($row = db_fetch_assoc($q)) {
$pids[] = $row['project_id'];
}
return $pids;
$sql="SELECT DISTINCT(s.project_id) AS project_id FROM redcap_external_modules m, redcap_external_module_settings s INNER JOIN redcap_projects AS p ON p.project_id = s.project_id WHERE p.date_deleted IS NULL AND m.external_module_id = s.external_module_id AND s.value = 'true' AND m.directory_prefix = 'pubmed_search' AND s.`key` = 'enabled'";
$q = db_query($sql);

if ($error = db_error()) {
error_log("PubmedSearchExternalModule ERROR: $error");
}

$pids = array();
while ($row = db_fetch_assoc($q)) {
$pids[] = $row['project_id'];
}
return $pids;
}

public function pubmed() {
// check if cron is enabled in settings
if( ! $this->settings['enable-cron']){
return;
}
$pids = $this->getPids();
error_log("PubmedSearchExternalModule::pubmed with ".json_encode($pids));
foreach ($pids as $pid) {
$this->pubmedRun($pid);
}
}

public function pubmedRun($pid) {
public function pubmedRun($pid, $specific_record=null) {
error_log("PubmedSearchExternalModule::pubmedRun with $pid");
# field names
$firstName = $this->getProjectSetting("first_name", $pid);
Expand All @@ -56,8 +63,11 @@ public function pubmedRun($pid) {
array_push($fields, $institutionField);
}
}

$json = \REDCap::getData($pid, "json", NULL, $fields);
if (is_null($specific_record)){
$json = \REDCap::getData($pid, "json", NULL, $fields);
}else{
$json = \REDCap::getData($pid, "json", [$specific_record['record_id']], $fields);
}
$data = json_decode($json, true);

# organize the data
Expand Down Expand Up @@ -102,39 +112,77 @@ public function pubmedRun($pid) {
# process the data
$upload = array();
foreach ($names as $values) {
$row = self::getPubMed( $values[$firstName],
$values[$lastName],
$institutions[$values[$recordId]],
json_decode($values[$helper]),
$values[$citations],
$citations,
$helper);

if ($row && $row[$helper] && $row[$citations]) {
array_push($upload, array( $recordId => $values[$recordId],
$helper => $row[$helper],
$citations => $row[$citations],
$citationsCount => count(explode("\n", $row[$citations])),
));
if (is_null($specific_record)){
$row = self::getPubMed( $values[$firstName],
$values[$lastName],
$institutions[$values[$recordId]],
json_decode($values[$helper]),
$values[$citations],
$citations,
$helper);
}else{
$inst = $institutions[$values[$recordId]];
if (! in_array($specific_record['institution'], $inst)){
$inst[] = $specific_record['institution'];
}
$row = self::getPubMed(
$specific_record['first'],
$specific_record['last'],
$inst,
json_decode($values[$helper]),
$values[$citations],
$citations,
$helper, true);
}

if ($row && $row[$helper] && $row[$citations]) {
array_push($upload, array( $recordId => $values[$recordId],
$helper => $row[$helper],
$citations => $row[$citations],
$citationsCount => count(explode("\n", $row[$citations])),
));
}
}
error_log("PubmedSearchExternalModule upload: ".count($upload)." rows");

// if it's a brand new redcap record, recordid will be null, so will $names
if(!is_null($specific_record) && is_null($specific_record['record_id'])){
$row = self::getPubMed(
$specific_record['first'],
$specific_record['last'],
$specific_record['institution'],
"",
"",
$citations,
$helper,
true);
if ($row && $row[$helper] && $row[$citations]) {
array_push($upload, array( $recordId => $values[$recordId],
$helper => $row[$helper],
$citations => $row[$citations],
$citationsCount => count(explode("\n", $row[$citations])),
));
}
}

if (!empty($upload)) {
$feedback = \REDCap::saveData($pid, "json", json_encode($upload));
error_log("PubmedSearchExternalModule upload: ".json_encode($feedback));
if (is_null($specific_record) && $this->settings['enable-cron']){
$feedback = \REDCap::saveData($pid, "json", json_encode($upload));
error_log("PubmedSearchExternalModule upload: ".json_encode($feedback));
}
}
return json_encode($upload);
}

public static function getPubMed($firstName, $lastName, $institutions, $prevCitations, $citationsStr, $citationField, $citationIdField) {
public static function getPubMed($firstName, $lastName, $institutions, $prevCitations, $citationsStr, $citationField, $citationIdField, $deltas=false) {
$cs = explode("\n", $citationsStr);
$citations = array();
foreach ($cs as $c) {
if ($c) {
array_push($citations, $c);
}
}

$upload = array();
$total = 0;
$totalNew = 0;
Expand Down Expand Up @@ -181,15 +229,15 @@ public static function getPubMed($firstName, $lastName, $institutions, $prevCita
$output = curl_exec($ch);
curl_close($ch);
sleep(SLEEP_TIME);

$pmData = json_decode($output, true);
if ($pmData['esearchresult'] && $pmData['esearchresult']['idlist']) {
# if the errorlist is not blank, it might search for simplified
# it might search for simplified names and produce bad results
if (!isset($pmData['esearchresult']['errorlist'])
|| !$pmData['esearchresult']['errorlist']
|| !$pmData['esearchresult']['errorlist']['phrasesnotfound']
|| empty($pmData['esearchresult']['errorlist']['phrasesnotfound'])) {
|| !$pmData['esearchresult']['errorlist']
|| !$pmData['esearchresult']['errorlist']['phrasesnotfound']
|| empty($pmData['esearchresult']['errorlist']['phrasesnotfound'])) {
foreach ($pmData['esearchresult']['idlist'] as $pmid) {
if (!in_array($pmid, $pmids)) {
$pmids[] = $pmid;
Expand All @@ -210,7 +258,7 @@ public static function getPubMed($firstName, $lastName, $institutions, $prevCita
}
$total += count($pmids);
$totalNew += count($pmidsUnique);

$citations = array();
if (!empty($pmidsUnique)) {
$pullSize = 10;
Expand All @@ -234,15 +282,15 @@ public static function getPubMed($firstName, $lastName, $institutions, $prevCita
curl_close($ch);
sleep(SLEEP_TIME);
$data = json_decode($output, true);

# indexed by PMID
$pmcids = array();
foreach ($data['records'] as $record) {
if ($record['pmid'] && $record['pmcid']) {
$pmcids[$record['pmid']] = $record['pmcid'];
}
}

$retry = 0;
do {
$url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=xml&id=".implode(",", $pmidsUniqueForPull);
Expand Down Expand Up @@ -301,11 +349,19 @@ public static function getPubMed($firstName, $lastName, $institutions, $prevCita
}
}
}
$newCitationIds = array_merge($prevCitations, $pmidsUnique);
$uploadRow = array(
$citationIdField => self::json_encode_with_spaces($newCitationIds),
$citationField => implode("\n", $citations),
);
//
if (! $deltas){
$newCitationIds = array_merge($prevCitations, $pmidsUnique);
$uploadRow = array(
$citationIdField => self::json_encode_with_spaces($newCitationIds),
$citationField => implode("\n", $citations),
);
}else{
$uploadRow = array(
$citationIdField => json_encode($pmidsUnique),
$citationField => json_encode($citations),
);
}
return $uploadRow;
}

Expand All @@ -314,4 +370,127 @@ private static function json_encode_with_spaces($data) {
$str = preg_replace("/,/", ", ", $str);
return $str;
}

// THESE FUNCTIONS BORROWED FROM LOOKUP ASSISTANT
public $errors = array();
public $settings = array();

private function validateJson($contents) {
// // Verify file exists
// if (file_exists($path)) {
// $contents = file_get_contents($path);

// Verify contents are json
$obj = json_decode($contents);

if (json_last_error() == JSON_ERROR_NONE) {
// All good
return $contents;
} else {
$this->emError("Error decoding JSON", json_last_error_msg());
return false;
// $this->errors[] = "Error decoding path $path: " . json_last_error_msg();
}

// } else {
// $this->errors[] = "Unable to locate file $path";
// }
// return false;
}


// Take the project settings and convert them into a more friendly settings object to pass to javascript
public function loadSettings($instrument) {
$set = $this->getProjectSettings();
$set['module-path'] = $this->getPostURL();
$set['test-path'] = $this->getTestURL();
$set['record_id'] = $this->getRecordId();
$this->settings[] = $set;
}

function injectLookup($instrument)
{
$this->loadSettings($instrument);
if (!empty($this->errors)) {
$this->emDebug($this->errors);
return false;
}

// Skip out if there is nothing to do
if (empty($this->settings)) return false;

// DUMP CONTENTS TO JAVASCRIPT
// Append the select2 controls
$this->insertSelect2();

echo "<style type='text/css'>" . $this->dumpResource("css/lookup-assistant.css") . "</style>";

// // Insert our custom JS
echo "<script type='text/javascript'>" . $this->dumpResource("js/lookupAssistant.js") . "</script>";

// Insert our custom JS
echo "<script type='text/javascript'>lookupAssistant.settings = " . json_encode($this->settings) . "</script>";
echo "<script type='text/javascript'>lookupAssistant.jsDebug = " . json_encode($this->getProjectSetting('enable-js-debug')) . "</script>";
?>
<style>
.lookupIcon {
position: absolute;
}
.lookupIcon > span {
position: relative;
left: -20px;
cursor: pointer;
}
</style>
<?php
}


function redcap_data_entry_form_top($project_id, $record, $instrument, $event_id, $group_id)
{
if( ! $this->settings['enable-cron']){
$this->injectLookup($instrument);
}
}


function redcap_survey_page_top($project_id, $record, $instrument, $event_id, $group_id)
{
if( ! $this->settings['enable-cron']){
$this->injectLookup($instrument);
}
}


public function insertSelect2()
{
?>
<script type="text/javascript"><?php echo $this->dumpResource('js/select2.full.min.js'); ?></script>
<style><?php echo $this->dumpResource('css/select2.min.css'); ?></style>
<style><?php echo $this->dumpResource('css/select2-bootstrap.min.css'); ?></style>
<?php
}


public function dumpResource($name)
{
$file = $this->getModulePath() . $name;
if (file_exists($file)) {
$contents = file_get_contents($file);
return $contents;
} else {
$this->emError("Unable to find $file");
}
}

public function getPostURL(){
return $this->getUrl("ajax.php", false, false);
// return $this->getUrl("PubmedSearchExternalModule.php", false, false);
// return $this->getModulePath();
}
public function getTestURL(){
return $this->getUrl("test.xml", false, false);
// return $this->getUrl("PubmedSearchExternalModule.php", false, false);
// return $this->getModulePath();
}
}
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