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Care Opportunities: Prevention and ASCVD Risk Calculation. Exporting. #182

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Care Opportunities: Prevention and ASCVD Risk Calculation. Exporting. #182

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1cdeda3
t q
Mar 14, 2021
0244a1e
change uspstf api request to get and use my key
Mar 14, 2021
f5c8cef
comment out drug classification in ascvd_calc
Mar 15, 2021
967a73a
remove -F -X -v files added by curl in error
Mar 16, 2021
605fea1
ascvd_calc correctly detects BP med in med list
Mar 17, 2021
dd803e1
TreatmentwithStatin feature of ascvd_calc is working as expected
Mar 18, 2021
5899cf7
fix ASCVD calc & Preventive Care in Care Opportunities, small coding …
Mar 24, 2021
d8ca1de
add newline to end of gitignore
Mar 24, 2021
27d6985
fix typo in comment
Mar 24, 2021
d460f3e
correct spelling of area-valuenow; correct indices and progress bar c…
Apr 2, 2021
7071934
upstream merge
Apr 12, 2021
341abb5
1) Crash during Export>All Charts. I forked and modified tcpdi-merger…
Apr 12, 2021
a353b48
fix duplicate key and spelling error in forms.yaml
Apr 12, 2021
f6d0657
fix fragmented answer options on HPQ form
Apr 13, 2021
6e20b0f
Add an exception to EncryptCookies.php so that download modals will g…
Apr 17, 2021
96a57de
prevent key encryption jquery.fileDownload.js so modal disappear as e…
May 16, 2021
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,5 @@ Homestead.json
/public/assets/js/web3-old.js
/public/assets/js/abi-decoder-old.js
/node_modules
.vscode
.DS_Store
1 change: 1 addition & 0 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ USER www-data

# Install all PHP dependencies
RUN composer install --no-interaction
RUN composer update shihjay2/tcpdi-merger --no-interaction

USER root

Expand Down
34 changes: 18 additions & 16 deletions app/Http/Controllers/ChartController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -756,19 +756,21 @@ public function care_opportunities(Request $request, $type)
$dropdown_array['items'] = $items;
$data['panel_dropdown'] = $this->dropdown_build($dropdown_array);
if ($type == 'prevention') {
$key = '48126e4e8ea3b83bc808850c713a5743';
$url = 'https://epssdata.ahrq.gov/';
$post = http_build_query([
$key = '48126e4e8ea3b83bc808850c713a5743'; //this is Dr. Chen's key DH
// $url = 'https://epssdata.ahrq.gov/'; //this may be an older url DH
$url = 'https://data.uspreventiveservicestaskforce.org/api/json'; //this is the one currently recommended on the uspstf web site DH
// $post = http_build_query([ //change from post to get DH
$get = http_build_query([
'key' => $key,
'age' => round($age, 0, PHP_ROUND_HALF_DOWN),
'sex' => $gender,
'pregnant' => ucfirst($row->pregnant),
'sexuallyActive' => $row->sexuallyactive,
'tobacco' => $row->tobacco
]);
$cr = curl_init($url);
curl_setopt($cr, CURLOPT_POST, 1);
curl_setopt($cr, CURLOPT_POSTFIELDS, $post);
$cr = curl_init($url . '?' . $get);
// curl_setopt($cr, CURLOPT_POST, 1); //not needed for get
// curl_setopt($cr, CURLOPT_POSTFIELDS, $post); //not needed for get
curl_setopt($cr, CURLOPT_RETURNTRANSFER, true);
curl_setopt($cr, CURLOPT_USERAGENT, $_SERVER['HTTP_USER_AGENT']);
$data1 = curl_exec($cr);
Expand Down Expand Up @@ -2205,7 +2207,7 @@ public function chart_action(Request $request, $table, $action, $id, $index)
$this->audit('Delete');

// $this->api_data('delete', 'rx_list', 'rxl_id', $old_rxl_id);
// UMA placeholder
// UMA (User-managed access) placeholder
$arr['message'] = trans('noshform.eie') . "!";
}
$arr['response'] = 'OK';
Expand Down Expand Up @@ -3076,7 +3078,7 @@ public function demographics(Request $request)
$return .= $this->header_build($header_arr, trans('noshform.contacts'));
foreach ($contact_arr as $key2 => $value2) {
if ($value2 !== '' && $value2 !== null) {
$return .= '<div class="row"><div class="col-md-3"><b>' . $key2 . '</b></div><div class="col-md-8">' . $value2 . '</div></div>';
$return .= '<div class="row"><div class="col-md-3"><b>' . $key2 . '</b></div><">' . $value2 . '</div></div>';
}
}
$return .= '</div></div></div>';
Expand All @@ -3090,7 +3092,7 @@ public function demographics(Request $request)
$return .= $this->header_build($header_arr, trans('noshform.other'));
foreach ($other_arr as $key4 => $value4) {
if ($value4 !== '' && $value4 !== null) {
$return .= '<div class="row"><div class="col-md-3"><b>' . $key4 . '</b></div><div class="col-md-8">' . $value4 . '</div></div>';
$return .= '<div class="row"><div class="col-md-3"><b>' . $key4 . '</b></div><">' . $value4 . '</div></div>';
}
}
$return .= '</div></div></div>';
Expand Down Expand Up @@ -3579,7 +3581,7 @@ public function encounter(Request $request, $eid, $section='s')
'standardpsych',
'standardpsych1'
];
$depreciated_array = [
$deprecated_array = [
'standardmedical',
'standardmedical1'
];
Expand Down Expand Up @@ -3635,8 +3637,8 @@ public function encounter(Request $request, $eid, $section='s')
}
if ($ros) {
$ros_val = $ros->ros;
// Convert depreciated encounter type to current
if (in_array($encounter->encounter_template, $depreciated_array)) {
// Convert deprecated encounter type to current
if (in_array($encounter->encounter_template, $deprecated_array)) {
$ros_arr = $this->array_ros();
foreach ($ros_arr as $ros_k => $ros_v) {
if ($ros->{$ros_k} !== '' && $ros->{$ros_k} !== null) {
Expand Down Expand Up @@ -3765,8 +3767,8 @@ public function encounter(Request $request, $eid, $section='s')
$pe = DB::table('pe')->where('eid', '=', $eid)->first();
if ($pe) {
$pe_val = $pe->pe;
// Convert depreciated encounter type to current
if (in_array($encounter->encounter_template, $depreciated_array)) {
// Convert deprecated encounter type to current
if (in_array($encounter->encounter_template, $deprecated_array)) {
$pe_arr = $this->array_pe();
foreach ($pe_arr as $pe_k => $pe_v) {
if ($pe->{$pe_k} !== '' && $pe->{$pe_k} !== null) {
Expand Down Expand Up @@ -4945,7 +4947,7 @@ public function encounter_details(Request $request, $eid)
$provider_arr = $this->array_providers();
$encounter_type_arr = $this->array_encounter_type();
if ($eid == '0') {
// Remove depreciated encounter types for new encounters
// Remove deprecated encounter types for new encounters
unset($encounter_type_arr['standardmedical']);
unset($encounter_type_arr['standardmedical1']);
}
Expand Down Expand Up @@ -9005,7 +9007,7 @@ public function social_history(Request $request)
$return .= $this->header_build($header_arr, trans('noshform.habits'));
foreach ($habits_arr as $key2 => $value2) {
if ($value2 !== '' && $value2 !== null) {
$return .= '<div class="col-md-3"><b>' . $key2 . '</b></div><div class="col-md-8">' . $value2 . '</div>';
$return .= '<div class="col-md-3"><b>' . $key2 . '</b></div><">' . $value2 . '</div>';
}
}
$return .= '</div></div></div>';
Expand Down
66 changes: 41 additions & 25 deletions app/Http/Controllers/Controller.php
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Original file line number Diff line number Diff line change
Expand Up @@ -1493,8 +1493,8 @@ protected function array_encounter_type()
'medical' => trans('noshform.medical_encounter'),
'phone' => trans('noshform.phone_encounter'),
'virtual' => trans('noshform.virtual_encounter'),
'standardmedical1' => 'Standard Medical Visit V2', // Depreciated
'standardmedical' => 'Standard Medical Visit V1', // Depreciated
'standardmedical1' => 'Standard Medical Visit V2', // deprecated
'standardmedical' => 'Standard Medical Visit V1', // deprecated
'standardpsych' => trans('noshform.standardpsych'),
'standardpsych1' => trans('noshform.standardpsych1'),
'clinicalsupport' => trans('noshform.clinicalsupport'),
Expand Down Expand Up @@ -2778,16 +2778,20 @@ protected function ascvd_calc()
if ($vitals->bp_systolic > 200) {
$sbp = '200';
} elseif ($vitals->bp_systolic < 90) {
$spb = '90';
$sbp = '90';
} else {
$spb = $vitals->bp_systolic;
$sbp = $vitals->bp_systolic;
}
}
$htn = false;
$chol = false;
$rx = DB::table('rx_list')->where('pid', '=', Session::get('pid'))->whereNull('rxl_date_inactive')->whereNull('rxl_date_old')->get();
if ($rx->count()) {
$htn_url = 'https://rxnav.nlm.nih.gov/REST/rxclass/classMembers.json?classId=N0000001616&relaSource=NDFRT&rela=may_treat';
// $htn_url = 'https://rxnav.nlm.nih.gov/REST/rxclass/classMembers.json?classId=N0000001616&relaSource=NDFRT&rela=may_treat';
// according to https://rxnav.nlm.nih.gov/RxClassIntro.html NDFRT was replaced with MEDRT in 2018. In addition MESH identifiers
// like D006973 for HTN replace the NDFRT ids like N0000001616
// JSON structure is the same.
$htn_url = 'https://rxnav.nlm.nih.gov/REST/rxclass/classMembers.json?classId=D006973&relaSource=MEDRT&rela=may_treat';
$htn_ch = curl_init();
curl_setopt($htn_ch,CURLOPT_URL, $htn_url);
curl_setopt($htn_ch,CURLOPT_FAILONERROR,1);
Expand All @@ -2801,28 +2805,36 @@ protected function ascvd_calc()
foreach ($htn_group['drugMemberGroup']['drugMember'] as $htn_item) {
$htn_arr[] = strtolower($htn_item['minConcept']['name']);
}
$chol_url = 'https://rxnav.nlm.nih.gov/REST/rxclass/classMembers.json?classId=N0000001592&relaSource=NDFRT&rela=may_treat';
$chol_ch = curl_init();
curl_setopt($chol_ch,CURLOPT_URL, $chol_url);
curl_setopt($chol_ch,CURLOPT_FAILONERROR,1);
curl_setopt($chol_ch,CURLOPT_FOLLOWLOCATION,1);
curl_setopt($chol_ch,CURLOPT_RETURNTRANSFER,1);
curl_setopt($chol_ch,CURLOPT_TIMEOUT, 15);
$chol_json = curl_exec($chol_ch);
curl_close($chol_ch);
$chol_group = json_decode($chol_json, true);
$chol_arr = [];
foreach ($chol_group['drugMemberGroup']['drugMember'] as $chol_item) {
$chol_arr[] = strtolower($chol_item['minConcept']['name']);
}
// This hyperlipidemia Rx class search is replaced with a simple statin array on line 2825.
// Reason - 1) many meds which treat high cholesterol are not statins; 2) the list of statins
// is pretty short.
// $chol_url = 'https://rxnav.nlm.nih.gov/REST/rxclass/classMembers.json?classId=N0000001592&relaSource=NDFRT&rela=may_treat';
// Handy for drug - disease NDFRT - MEDRT code lookups: https://bioportal.bioontology.org/ontologies/NDFRT?p=classes&conceptid=N0000001580
// $chol_ch = curl_init();
// curl_setopt($chol_ch,CURLOPT_URL, $chol_url);
// curl_setopt($chol_ch,CURLOPT_FAILONERROR,1);
// curl_setopt($chol_ch,CURLOPT_FOLLOWLOCATION,1);
// curl_setopt($chol_ch,CURLOPT_RETURNTRANSFER,1);
// curl_setopt($chol_ch,CURLOPT_TIMEOUT, 15);
// $chol_json = curl_exec($chol_ch);
// curl_close($chol_ch);
// $chol_group = json_decode($chol_json, true);
// $chol_arr = [];
// foreach ($chol_group['drugMemberGroup']['drugMember'] as $chol_item) {
// $chol_arr[] = strtolower($chol_item['minConcept']['name']);
// }
$chol_arr = ['atorvastatin', 'fluvastatin', 'lovastatin', 'pitavastatin', 'pravastatin', 'rosuvastatin', 'simvastatin']; // DH
foreach ($rx as $rx_item) {
$rx_name = explode(' ', $rx_item->rxl_medication);
$rx_full_name = $rx_item->rxl_medication;
$rx_name = explode(' ', $rx_item->rxl_medication);
$rx_name_first = strtolower($rx_name[0]);
if (in_array($rx_name_first, $htn_arr)) {
$htn = true;
$htn = true; // ...where $htn means 'being treated for HTN => taking antihypertensive medicine'
}
if (in_array($rx_name_first, $chol_arr)) {
$chol = true;
foreach ($chol_arr as $ca) {
if (stripos($rx_full_name, $ca) !== false) { //don't use rx_name_first! Stripos is case insensitive.
$chol = true; // ...where $chol means 'taking a statin'
}
}
}
}
Expand Down Expand Up @@ -2860,6 +2872,7 @@ protected function ascvd_calc()
'age' => $age
];
$data_string = json_encode($data);
echo $data_string;
$ch = curl_init($url);
curl_setopt($ch, CURLOPT_CUSTOMREQUEST, "POST");
curl_setopt($ch, CURLOPT_POSTFIELDS, $data_string);
Expand All @@ -2877,6 +2890,7 @@ protected function ascvd_calc()
$result_arr['message'] .= '<li>' . $missing_item . '</li>';
}
$result_arr['message'] .= '</ul></div>';
$result_arr['message'] .= '</ul></div>';
}
return $result_arr;
}
Expand Down Expand Up @@ -8044,7 +8058,7 @@ protected function form_practiceinfo($result, $table, $id, $subtype)
}
if ($subtype == 'settings') {
$encounter_type_arr = $this->array_encounter_type();
// Remove depreciated encounter types for new encounters
// Remove deprecated encounter types for new encounters
unset($encounter_type_arr['standardmedical']);
unset($encounter_type_arr['standardmedical1']);
$settings_arr = [
Expand Down Expand Up @@ -8919,8 +8933,9 @@ protected function form_rx_list($result, $table, $id, $subtype)
'selectpicker' => true,
'default_value' => $rx['label']
];
// DH Removed because it causes entry in rx_list
// Removed because it causes error in rx_list
// of 0000-00-00. With code commented out entry is null.
// which causes problems with the Conditions list.
// $items[] = [
// 'name' => 'rxl_date_inactive',
// 'type' => 'hidden',
Expand All @@ -8939,6 +8954,7 @@ protected function form_rx_list($result, $table, $id, $subtype)
];
// DH Removed because it causes entry in rx_list
// of 0000-00-00. With code commented out entry is null.
// Was causing problems with the Medications list.
// $items[] = [
// 'name' => 'rxl_date_old',
// 'type' => 'hidden',
Expand Down
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