Barcode Endpoint + Introduction of Specimen Sample Numbers

jsx/biobankIndex.js

@@ -266,7 +266,6 @@ class BiobankIndex extends React.Component {
    */
   createSpecimens(list, current, print) {
     const {options, data} = this.state;
-    const labelParams = [];
     const projectIds = current.projectIds;
     const centerId = current.centerId;
     const availableId = Object.keys(options.container.stati).find(
@@ -321,10 +320,6 @@ class BiobankIndex extends React.Component {
 
       // if specimen type id is not set yet, this will throw an error
       if (specimen.typeId) {
-        labelParams.push({
-          barcode: container.barcode,
-          type: options.specimen.types[specimen.typeId].label,
-        });
       }
 
       specimen.container = container;
@@ -353,7 +348,7 @@ class BiobankIndex extends React.Component {
       return Promise.reject(errors);
     }
 
-    const printBarcodes = () => {
+    const printBarcodes = (entities) => {
       return new Promise((resolve) => {
         if (print) {
           Swal.fire({
@@ -363,21 +358,40 @@ class BiobankIndex extends React.Component {
             cancelButtonText: 'No',
             showCancelButton: true,
           })
-          .then((result) => result.value && this.printLabel(labelParams))
+          .then((result) => {
+            if (result.value) {
+              const labelParams = [];
+              Object.values(entities.specimens).forEach((specimen) => {
+                labelParams.push({
+                  barcode: specimen.barcode,
+                  type: options.specimen.types[specimen.typeId].label,
+                  pscid: specimen.candidatePSCID,
+                  sampleNumber: specimen.sampleNumber,
+                });
+              });
+              return this.printLabel(labelParams);
+            }
+          })
           .then(() => resolve());
+          .catch((error) => {
+            console.error('Printing error:', error);
+            resolve();
+          });
         } else {
           resolve();
         }
       });
     };
 
-    return printBarcodes()
-    .then(() => post(list, this.props.specimenAPI, 'POST'))
-    .then((entities) => {
-      this.setData('containers', entities.containers);
-      this.setData('specimens', entities.specimens);
-    })
-    .then(() => Promise.resolve());
+    return post(list, this.props.specimenAPI, 'POST')
+      .then((entities) => {
+        return printBarcodes(entities)
+          .then(() => {
+            this.setData('containers', entities.containers);
+            this.setData('specimens', entities.specimens);
+          });
+      })
+      .then(() => Promise.resolve());
   }
 
   /**

jsx/header.js

@@ -135,8 +135,10 @@ class Header extends Component {
     const barcodePathDisplay = this.props.getBarcodePathDisplay(parentBarcodes);
     const printBarcode = () => {
       const labelParams = [{
-        barcode: container.barcode,
+        barcode: specimen.barcode,
         type: options.specimen.types[specimen.typeId].label,
+        pscid: specimen.candidatePSCID,
+        sampleNumber: specimen.sampleNumber,
       }];
       this.props.printLabel(labelParams)
         .then(() => (Swal.fire('Print Barcode Number: ' + container.barcode)));

jsx/specimenForm.js

@@ -151,25 +151,35 @@ class SpecimenForm extends React.Component {
     return increment;
   };
 
+  async fetchBarcodes(count) {
+    try {
+      const response = await fetch(`${loris.BaseURL}/biobank/barcodes?count=${count}`);
+      const data = await response.json();
+      return data.barcodes;
+    } catch (error) {
+      console.error('Error fetching barcodes:', error);
+      return [];
+    }
+  }
+
   /**
    * Generate barcodes and store in the component state.
    */
-  generateBarcodes() {
-    const {options} = this.props;
-    let {list, current} = this.state;
-    const pscid = options.candidates[current.candidateId].pscid;
-    [list] = Object.keys(list)
-      .reduce(([result, increment], key, i) => {
-        const specimen = this.state.list[key];
-        if (!specimen.container.barcode) {
-          const barcode = padBarcode(pscid, increment);
-          specimen.container.barcode = barcode;
-          increment = this.incrementBarcode(pscid, increment);
-        }
+  async generateBarcodes() {
+    const { options } = this.props;
+    let { list, current } = this.state;
+    const count = Object.keys(list).length;
+
+    const barcodes = await this.fetchBarcodes(count);
+
+    list = Object.keys(list).reduce((result, key, index) => {
+        const specimen = list[key];
+        specimen.container.barcode = barcodes[index];
         result[key] = specimen;
-        return [result, increment];
-    }, [{}, this.incrementBarcode(pscid)]);
-    this.setState({list});
+        return result;
+    }, {});
+
+    this.setState({ list });
   };
 
   /**
@@ -377,7 +387,6 @@ class SpecimenForm extends React.Component {
             label='Generate Barcodes'
             type='button'
             onUserInput={this.generateBarcodes}
-            disabled={current.candidateId ? false : true}
           />
           <CheckboxElement
             name='printBarcodes'

php/barcodes.class.inc

@@ -0,0 +1,121 @@
+<?php
+
+namespace LORIS\biobank;
+
+use \LORIS\Http\Endpoint;
+use Psr\Http\Message\ServerRequestInterface;
+use Psr\Http\Message\ResponseInterface;
+
+class Barcodes extends Endpoint
+{
+    protected $db;
+    protected $user;
+
+    /**                                                                         
+     * Returns true if user has access to this Endpoint.                        
+     *                                                                          
+     * @param \User $user The user whose access is being checked                
+     *                                                                          
+     * @return bool                                                             
+     */                                                                         
+    function _hasAccess(\User $user) : bool                                     
+    {                                                                           
+        return true;                                                            
+    } 
+
+    /**                                                                         
+     * Return which methods are supported by this endpoint.                     
+     *                                                                          
+     * @return array supported HTTP methods                                     
+     */                                                                         
+    protected function allowedMethods() : array                                 
+    {                                                                           
+        return ['GET', 'OPTIONS'];                                          
+    }
+
+    /**                                                                         
+     * This function can be overridden in a module's page to load the necessary 
+     * resources to check the permissions of a user.                            
+     *                                                                          
+     * @param User                   $user    The user to load the resources for
+     * @param ServerRequestInterface $request The PSR15 Request being handled   
+     *                                                                          
+     * @return void                                                             
+     */                                                                         
+    public function loadResources(                                              
+        \User $user, ServerRequestInterface $request                            
+    ) : void {                                                                  
+    }   
+
+    /**                                                                         
+     * Handles Endpoint requests                                                
+     *                                                                          
+     * @param ServerRequestInterface $request The incoming PSR7 request         
+     *                                                                          
+     * @return ResponseInterface The outgoing PSR7 response                     
+     */                                                                         
+    public function handle(
+        ServerRequestInterface $request
+    ) : ResponseInterface {
+        $this->db = \NDB_Factory::singleton()->database();
+        $this->user = $request->getAttribute('user');
+
+        try {
+            switch ($request->getMethod()) {
+                case 'GET':
+                    return $this->_handleGET($request);
+                case 'OPTIONS':
+                    return (new \LORIS\Http\Response())
+                        ->withHeader('Allow', $this->allowedMethods());
+            }
+        } catch (\Exception $e) {
+            $this->db->rollBack();
+            return new \LORIS\Http\Response\JSON\InternalServerError(
+                $e->getMessage()
+            );
+        }
+    }
+
+    // NOTE: the algorithm can stay here but should 
+    /**                                                                         
+     * Handle the logic of an incoming HTTP GET request                         
+     *                                                                          
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     * @return ResponseInterface                                                 
+     */                                                                         
+    private function _handleGET(
+        ServerRequestInterface $request
+    ) : ResponseInterface {
+        $currentYear = date('y');
+
+        $queryParams = $request->getQueryParams();
+        $count = isset($queryParams['count'])
+            ? intval($queryParams['count'])
+            : 1;
+
+        // Query to get the largest barcode for the current year
+        $query = "SELECT MAX(CAST(SUBSTRING(Barcode, 3, 6) AS UNSIGNED)) AS max_number
+                  FROM biobank_container
+                  WHERE SUBSTRING(Barcode, 1, 2) = :year";
+        $params = [':year' => $currentYear];
+        $maxNumber = $this->db->pselectOne($query, $params);
+
+        $newNumber = $maxNumber
+            ? $maxNumber + 1
+            : 1;
+
+        $barcodes = [];
+        for ($i = 0; $i < $count; $i++) {
+            $newNumberFormatted = str_pad(
+                $newNumber + $i,
+                6,
+                '0',
+                STR_PAD_LEFT
+            );
+            $newBarcode = $currentYear . $newNumberFormatted;
+            $barcodes[] = $newBarcode;
+        }
+
+        return new \LORIS\Http\Response\JSON\OK(['barcodes' => $barcodes]);
+    }
+}

php/labelendpoint.class.inc

@@ -12,6 +12,7 @@
  * @link       http://www.github.com/aces/Loris/
  */
 namespace LORIS\biobank;
+use \LORIS\Http\Response\JSON\InternalServerError;
 use \Psr\Http\Message\ServerRequestInterface;
 use \Psr\Http\Server\RequestHandlerInterface;
 use \Psr\Http\Message\ResponseInterface;
@@ -50,8 +51,6 @@ class LabelEndpoint implements RequestHandlerInterface
     protected function allowedMethods() : array
     {
         return [
-            'GET',
-            'PUT',
             'POST',
             'OPTIONS',
         ];
@@ -98,26 +97,75 @@ class LabelEndpoint implements RequestHandlerInterface
      */
     public function handle(ServerRequestInterface $request) : ResponseInterface
     {
-        // TODO: Place a try catch here in case printing doesn't work for some
-        // reason.
-        switch ($request->getMethod()) {
-        case 'POST':
-            $params = json_decode($request->getBody()->getContents(), true);;
-            foreach ($params as $param) {
-                $barcode = $param['barcode'];
-                $type    = $param['type'];
-                $zpl     = "^XA,^FO330,80^BY1,^BCN,100,Y,Y,N,^CFA,"
-                    . "20^A0N,30,29^BCN,100,Y,Y,N^FD$barcode^FS,"
-                    . "^FO323,190,^CFA,20^A0N,30,29^FD$type^XZ";
-                $config  = \NDB_Config::singleton();
-                $path    = $config->getSetting('labelPrintingPath');
-                $path    = $path.'barcode.zpl';
-                $fp      = fopen($path, 'w');
-                fwrite($fp, $zpl);
+        try {
+            switch ($request->getMethod()) {
+            case 'POST':
+                return $this->_handlePOST($request); 
+            }
+        } catch (\Exception $e) {
+            // Log the error
+            error_log($e->getMessage());
+            return new InternalServerError('Printing failed');
+        }
+    }
+
+    /**
+     * Handle the logic of an incoming HTTP GET request
+     *
+     * @param ServerRequestInterface $request The incoming PSR7 request
+     * @return ResponseInterface
+     */
+    private function _handlePOST(
+        ServerRequestInterface $request
+    ) : ResponseInterface {
+        $params = json_decode($request->getBody()->getContents(), true);;
+        foreach ($params as $param) {
+            $barcode   = $param['barcode'];
+            $type      = $param['type'];
+            $pscid     = $param['pscid'];
+            $sampleNum = $param['sampleNumber'];
+
+            // Construct ZPL string
+            $zpl = "^XA"                                
+                 . "^FO330,80"                          
+                 . "^BY1"                               
+                 . "^BCN,100,Y,Y,N"                    
+                 . "^CFA,20"                          
+                 . "^A0N,30,29"                      
+                 . "^BCN,100,Y,Y,N^FD$barcode^FS"       
+                 . "^FO323,190"                         
+                 . "^CFA,20"                        
+                 . "^A0N,30,29^FD$type^FS"              
+                 . "^FO323,250"                    
+                 . "^CFA,20"                      
+                 . "^A0N,30,29^FD$pscid $sampleNum^FS"  
+                 . "^XZ";                               
+
+            $config  = \NDB_Config::singleton();
+            $path    = $config->getSetting('labelPrintingPath') . 'barcode.zpl';
+
+            // Ensure directory exists
+            $directory = dirname($path);
+            if (!is_dir($directory)) {
+                mkdir($directory, 0777, true);
+            }
+
+            // Write ZPL to file
+            if (false === ($fp = fopen($path, 'w'))) {
+                throw new \RuntimeException("Unable to open file: $path");
+            }
+            if (false === fwrite($fp, $zpl)) {
                 fclose($fp);
-                shell_exec('lp -d ZDesigner -o raw '.escapeshellarg($path));
+                throw new \RuntimeException("Unable to write to file: $path");
+            }
+            fclose($fp);
+
+            // Send the file to the printer
+            $output = shell_exec('lp -d ZDesigner -o raw ' . escapeshellarg($path));
+            if ($output === null) {
+                throw new \RuntimeException("Failed to send print job to printer");
             }
-            return new \LORIS\Http\Response\JSON\OK();
         }
+        return new \LORIS\Http\Response\JSON\OK();
     }
 }

php/module.class.inc

@@ -89,6 +89,7 @@ class Module extends \Module
             || $path == 'poolendpoint'
             || $path == 'containerendpoint'
             || $path == 'specimenendpoint'
+            || $path == 'barcodes'
         ) {
             // There is a subpage
             $pagename = explode("/", $path)[0];