Backend - start development

The backend code contains a set of utilities that extend the OpenEMR code and enable us to develop new features quickly.
All the utilities found in the clinikal-backed repository and divided into different ZF modules according to the scope.

  • Generic-tools - contains some services, contollers, models and helper are in used in several modules.

  • Cliikal-api - contains utilities are needed for the backend of React project.

  • Fhir-api - contains models, contlllers and services for Fhir API.

In this document we review the main utilities you can find in the Generic-tools modules, we hope it gives you a good starting point to start a new development.

Controllers and models

As we've mentioned all the backend code developed in the ZF modules. Before you begin with clinikal we recommend starting a basic knowledge about the structure and functionalities in the Laminas/MVC project.

Controllers
Base controller - GenericTools\Controller\BaseController - the BaseController contains all the common functionality that needed in all the project (e.g. quick access to database models and more), the best practice is to inherit it in every controller.

Models
We supply set of Models and Table gateways for database connection according to laminas-db principles.
Most table gateways using trait \GenericTools\Model\baseTable for creating complex queries clearly and quickly.

List of available models: (GenericTools/src/GenericTools/Model)
AclTables
Documents
Facility
FormEncounter
FormVitals
Languages
Lists
Log
Patient
Prescriptions
Users
And more...

Serivces

The following powerful services enable us quick integration with several useful tools.

Pdf
Generate PDF file, render html for pdf using Laminas Rendering Views.
usage example:

$viewTemplate = 'report-tool/pdf/report-pdf';
$viewParams = [
    'title' => $title,
    'data' => $data,
    'columns' => $columns
];
$this->container->get(PdfService::class)->fileName($fileName);
$this->container->get(PdfService::class)->setStandardHeaderFooter();
$this->container->get(PdfService::class)->body($viewTemplate,$viewParams);
$this->container->get(PdfService::class)->render();

Mail
Send Email render html for pdf using Laminas Rendering Views.

$htmlTemplate  ='patients/alert/email';
$this->container->get(MailService::class)->subject($subject);
$this->container->get(MailService::class)->priority(1);
$this->container->get(MailService::class)->body($htmlTemplate, $bodyParams);
//attach pdf (optionaly)
$this->container->get(MailService::class)->attach($stringIOPDF, 'binary', 'symptoms_' . $patient->fname . '_' . $patient->lname . '_' . date("Y_m_d").'.pdf', 'application/pdf');
$status = $this->container->get(MailService::class)->send($mailList);

S3
Upload and download file from s3, integration with API's modules. requirements:
- Environment variables with access and secret keys - connection details usage example:

$s3Service = new S3Service($this->getContainer());
$s3Service->connect();
$data = $s3Service->fetchObject($fullUrl);

SSE
Server-sent events implementation
usage example:

public function patientsTrackingCheckRefresh($facility_id)
{
    $cptcTable=$this->container->get(ClinikalPatientTrackingChangesTable::class);
    $date=$cptcTable->getLastUpdateDate($facility_id);
    $sse = new SseService($cptcTable,'getLastUpdateDate',$facility_id);
    $sse->connect();
    return array();
}

Couchdb
Upload and download file from CouchDB, full integration with OpenEMR document system. usage example:

$couchdbService = new CouchdbService($this->getContainer());
$couchdbService->connect();
$document = $couchdbService->fetchDoc($couchDocId, false);

Ecxel
Generate excel file.
usage example:

$excelService = $this->container->get(ExcelService::class);
$excelService = $this->getExcelService();
$excelService->setColumnsNames($columnsName);
$excelService->setData($data);
$excelService->setTabTitle($tabTitle);
$excelService->fileName($fileName);
$excelService->downloadFile();

Report tool

The ReportTool module contains infrastructure for generate reports, the reports tool supply UI with pagination, print report as PDF and export the report to excel file.

How to adding a new report?
Every report need -
1. new class extends the ReportTool\Controller\BaseController and implements ReportInterface
class ReportContrller extends ReportBase implements ReportInterface 2. New SQL Stored Procedure the fetch the data for the report and get the filters as arguments.
3. new routing in the /config/module.config.php
4. link to route from OpenEMR json menus.

The report will show in the OpenEMR interface and not in the React view.

For example you can take a look on the Encounetrs report in the vertical-emergency-medicine-backend repository

Import data

The import data tool helps you to import lists into the database from CSV files with minimum configuration. The mechanism enables to import to list_options table or codes table. We have set of lists already mapped in to the database, and you can add additional lists as you needed.

What do you need to mapping a new list?
1. CSV file with your records, the separator between the columns must be | (pipe).
2. Create a new list class that extends BaseList implements InterfaceList.
in this class you need to map between the csv columns to the database table.
3. register the new list in the database -

INSERT INTO `moh_import_data` (`id`,`external_name`,`clinikal_name`,`static_name`,`source`,`update_at`) VALUES 
(1,'<FILE_NAME>','<LIST_NAME>','<STATIC_NAME>','CSV','2035-03-02 09:09:32');

OpenEMR modules managing

OpenEMR provides customization and extension using Zend modules, the modules can be configured and controlled in the "managing modules" screen (modules -> managing modules).
In the managing screen possible to register and enable modules and run of SQL and ACL upgrade processes. Screenshot

In the installation process of new module the file sql/install.sql run with the changes that needed in the database, in addition the file acl/acl_setup.php run with the new ACL configurations (more details in the next section).

SQL upgrade file

Every module has a internal version file (Module/version.php).
The versions needed for SQL and ACL upgrade with safe migration between the version.
The upgrade files are written according to OpenEMR principles and running with the OpenEMR mechanism.
For example, if the version in the file is 2.5.0, you need to create file 2_5_0-to-3_0_0_upgrade.sql for the queries of the next version.

Examples of sql upgrade blocks
Create new table:

#IfNotTable encounter_reasoncode_map
CREATE TABLE encounter_reasoncode_map (
eid INT(6) UNSIGNED,
reason_code  INT(6) UNSIGNED
);
#EndIf

Update recodes with conditions:

#IfNotRow3D fhir_validation_settings fhir_element Encounter filed_name status validation blockedEncounter
UPDATE `fhir_validation_settings` SET `validation` = 'blockedEncounter' WHERE
`fhir_element` = 'Encounter' and `filed_name` = 'status'AND `validation` = 'blockedIfValue';
#EndIf

Add column to table:

#IfMissingColumn lists diagnosis_valueset
ALTER TABLE `lists` ADD `diagnosis_valueset` VARCHAR(255) NULL AFTER `diagnosis`;
#EndIf

ACL managing

Clinikal comes with extensive Access Control System that based on OpenEMR ACL.
In our modules we create new Access roles, sections and objects according to the clinic type (e.g. the imaging clinic needed X-ray technician what that not needed in the other clinics).
The settings of the ACL are written in every module in the acl folder in the acl_setup.php and acl_upgrade.php and use functions from class OpenEMR\Common\Acl\AclExtended for the configurations.

Example of useful ACL functions
Add new role (nurse for emergency center with view permission):

$emergency_nurse_view =AclExtended::addNewACL('Emergency nurse', 'emergency_nurse', 'view', 'Things that emergency nurse can read but not modify');

new ACL object for Encounter report:

AclExtended::addObjectAcl('client_app', 'Client Application', 'EncountersReport','Encounters Report');

Allow nurse to show Encounter report:

AclExtended::updateAcl($emergency_nurse_view, 'Emergency nurse', 'client_app', 'Client Application', 'EncountersReport','Encounters Report', 'view');

The ACL setting can be modified in the administration interface of OpenEMR - Administration -> ACL Screenshot