Standardize code as per PSR-12 (#65)

* Bugfix: MSH for an ACK should be created with same global vars as MSG * Add linter in CI config * Fix linting issue in CI * Update badge
senaranya · Nov 1, 2021 · d41b4c6 · d41b4c6
1 parent c6cb76e
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diff --git a/.github/workflows/main_ci.yml b/.github/workflows/main_ci.yml
@@ -1,4 +1,4 @@
-name: HL7 library
+name: tests
 
 on:
   push:
@@ -36,7 +36,7 @@ jobs:
 
       - name: Install dependencies
         run: composer install --dev --prefer-dist --no-progress
-#      - name: Run linter
-#        run: composer run-script lint
+      - name: Run linter
+        run: composer run-script lint
       - name: Run test suite
         run: composer run-script test
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,8 +1,9 @@
-Contributions are more than welcome! Please review issues if you want to pick up from existing tickets. New tickets/features/CRs are welcome!
-
-Contributors are requested to add or update phpdoc for any new or existing methods being worked on.
-
-It'll be great if you update the API documentation as well (else I'll do it for you), in case if a phpdoc is changed.
+* Contributions are more than welcome!
+* Please review [issues](https://github.com/senaranya/HL7/issues) if you want to pick up from existing tickets. New tickets/features/CRs/PRs are welcome!
+* The goal of this library is to keep it generic and minimal. The focus should only be on basic HL7-related operations like creation/parsing/sending/receiving etc. No project-specific business logic should be included.
+* This library follows PSR-12 standards for coding style. You may use [phpcs](https://github.com/squizlabs/PHP_CodeSniffer#getting-started) to verify your code.
+* Add unit tests for code changes/updates. There are a number of existing tests, follow those as reference
+* Contributors are requested to add or update phpdoc for any new or existing methods being worked on. After updating/adding, please update the API documentation as well (details below)
 
 ##### Generate/update API documentation (in Markdown format) from docblocks
 * Install [clean/phpdoc-md](https://github.com/clean/phpdoc-md): `composer require --dev clean/phpdoc-md`

diff --git a/README.md b/README.md
@@ -1,5 +1,5 @@
 <p align="center">
-<a href="https://github.com/senaranya/HL7/actions"><img src="https://github.com/senaranya/hl7/actions/workflows/main_ci.yml/badge.svg?branch=master" alt="Build Status"></a>
+<a href="https://github.com/senaranya/HL7/actions"><img src="https://github.com/senaranya/hl7/actions/workflows/main_ci.yml/badge.svg?branch=master" alt="CI Status"></a>
 <a href="https://packagist.org/packages/aranyasen/hl7"><img src="https://poser.pugx.org/aranyasen/hl7/downloads" alt="Total Downloads"></a>
 <a href="https://packagist.org/packages/aranyasen/hl7"><img src="https://poser.pugx.org/aranyasen/hl7/v/stable" alt="Latest Stable Version"></a>
 <a href="https://packagist.org/packages/aranyasen/hl7"><img src="https://poser.pugx.org/aranyasen/hl7/license" alt="License"></a>
@@ -127,10 +127,10 @@ if (strpos($returnString, 'MSH') === false) {
 $msa = $ack->getSegmentsByName('MSA')[0];
 $ackCode = $msa->getAcknowledgementCode();
 if ($ackCode[1] === 'A') {
-    echo "Recieved ACK from remote\n";
+    echo "Received ACK from remote\n";
 }
 else {
-    echo "Recieved NACK from remote\n";
+    echo "Received NACK from remote\n";
     echo "Error text: " . $msa->getTextMessage();
 }
 ```
@@ -166,7 +166,8 @@ All segment level getter/setter APIs can be used in two ways -
 `$pid->setPatientName('John Doe', 6)` -> Set patient name at 6th position in PID segment  
 `$pid->getPatientAddress(12)` -> Get patient address from 12th position  
 
-### TODOs
-* Data Validation
-* Search by regex and return segment/field/index
-* Define more segments
+### Issues
+Bug reports and feature requests can be submitted on the [Github Issue Tracker](https://github.com/senaranya/HL7/issues).
+
+### Contributing
+See [CONTRIBUTING.md](CONTRIBUTING.md) for information.
diff --git a/composer.json b/composer.json
@@ -36,7 +36,7 @@
     },
     "scripts": {
         "test": "vendor/bin/phpunit tests/ --coverage-text",
-        "lint": "vendor/bin/phpcs src/"
+        "lint": "vendor/bin/phpcs --standard=psr12 src/"
     },
     "extra": {
         "branch-alias": {

diff --git a/src/Exceptions/HL7ConnectionException.php b/src/Exceptions/HL7ConnectionException.php
@@ -7,4 +7,4 @@
 class HL7ConnectionException extends Exception
 {
 
-}
+}
diff --git a/src/Exceptions/HL7Exception.php b/src/Exceptions/HL7Exception.php
@@ -7,4 +7,4 @@
 class HL7Exception extends Exception
 {
 
-}
+}
diff --git a/src/HL7/Connection.php b/src/HL7/Connection.php
@@ -56,8 +56,8 @@ public function __construct(string $host, int $port, int $timeout = 10)
             throw new HL7ConnectionException('Please install ext-sockets to run Connection');
         }
         $this->setSocket($host, $port, $timeout);
-        $this->MESSAGE_PREFIX = "\013";
-        $this->MESSAGE_SUFFIX = "\034\015";
+        $this->MESSAGE_PREFIX = "\013"; # Octal 13 (Hex: 0B): Vertical Tab
+        $this->MESSAGE_SUFFIX = "\034\015"; # 34 (Hex: 1C): file separator character, 15 (Hex: 0D): Carriage return
         $this->timeout = $timeout;
     }
 
@@ -147,7 +147,9 @@ public function send(Message $msg, string $responseCharEncoding = 'UTF-8', bool
                 break;
             }
             if ((time() - $startTime) > $this->timeout) {
-                throw new HL7ConnectionException("Response partially received. Timed out listening for end-of-message from server");
+                throw new HL7ConnectionException(
+                    "Response partially received. Timed out listening for end-of-message from server"
+                );
             }
         }
 
@@ -181,8 +183,7 @@ private function close(): void
     {
         try {
             socket_close($this->socket);
-        }
-        catch (Exception $e) {
+        } catch (Exception $e) {
             echo 'Failed to close socket: ' . socket_strerror(socket_last_error()) . PHP_EOL;
         }
     }

diff --git a/src/HL7/Message.php b/src/HL7/Message.php
@@ -61,21 +61,27 @@ class Message
      * If the message couldn't be created, for example due to a erroneous HL7 message string, an error is raised.
      * @param string|null $msgStr
      * @param array|null $hl7Globals Set control characters or HL7 properties. e.g., ['HL7_VERSION' => '2.5']
-     * @param bool $keepEmptySubFields Set this to true to retain empty sub fields
+     * @param bool $keepEmptySubFields Set this to true to retain empty sub-fields
      * @param bool $resetIndices Reset Indices of each segment to 1.
      * @param bool $autoIncrementIndices True: auto-increment for each instance of same segment.
-     * @param bool|null $doNotSplitRepetition If true, repeated segments will be in single array instead of sub-arrays. Since this is non-standard, it may be removed in future
+     * @param bool|null $doNotSplitRepetition If true, repeated segments will be in single array instead of sub-arrays.
+     *     Note: Since this is non-standard, it may be removed in future!
      * @throws HL7Exception
-     * @throws \ReflectionException
      */
-    public function __construct(string $msgStr = null, array $hl7Globals = null, bool $keepEmptySubFields = false, bool $resetIndices = false, bool $autoIncrementIndices = true, bool $doNotSplitRepetition = null)
-    {
+    public function __construct(
+        string $msgStr = null,
+        array $hl7Globals = null,
+        bool $keepEmptySubFields = false,
+        bool $resetIndices = false,
+        bool $autoIncrementIndices = true,
+        bool $doNotSplitRepetition = null
+    ) {
         // Array holding the segments
         $this->segments = [];
 
         // Control characters and other HL7 properties
         $this->segmentSeparator = $hl7Globals['SEGMENT_SEPARATOR'] ?? '\n';
-        $this->segmentEndingBar = $hl7Globals['SEGMENT_ENDING_BAR'] ?? true; // Bar (|) at end of each segment. Default: Present
+        $this->segmentEndingBar = $hl7Globals['SEGMENT_ENDING_BAR'] ?? true; // '|' at end of each segment
         $this->fieldSeparator = $hl7Globals['FIELD_SEPARATOR'] ?? '|';
         $this->componentSeparator = $hl7Globals['COMPONENT_SEPARATOR'] ?? '^';
         $this->subcomponentSeparator = $hl7Globals['SUBCOMPONENT_SEPARATOR'] ?? '&';
@@ -136,12 +142,10 @@ public function __construct(string $msgStr = null, array $hl7Globals = null, boo
                     if ($segmentName === 'MSH') {
                         array_unshift($fields, $this->fieldSeparator); # First field for MSH is '|'
                         $segment = new $className($fields);
-                    }
-                    else {
+                    } else {
                         $segment = new $className($fields, $autoIncrementIndices);
                     }
-                }
-                else {
+                } else {
                     $segment = new Segment($segmentName, $fields);
                 }
 
@@ -179,7 +183,7 @@ public function addSegment(Segment $segment): bool
      * @param null|int $index Index where segment is inserted
      * @throws \InvalidArgumentException
      */
-    public function insertSegment(Segment $segment, $index = null): void
+    public function insertSegment(Segment $segment, int $index = null): void
     {
         if ($index > count($this->segments)) {
             throw new InvalidArgumentException("Index out of range. Index: $index, Total segments: " .
@@ -189,11 +193,9 @@ public function insertSegment(Segment $segment, $index = null): void
         if ($index === 0) {
             $this->resetCtrl($segment);
             array_unshift($this->segments, $segment);
-        }
-        elseif ($index === count($this->segments)) {
+        } elseif ($index === count($this->segments)) {
             $this->segments[] = $segment;
-        }
-        else {
+        } else {
             $this->segments =
                 array_merge(
                     array_slice($this->segments, 0, $index),
@@ -388,7 +390,7 @@ public function toString(bool $pretty = false)
 
     /**
      * Convert Segment object to string
-     * @param $seg
+     * @param  Segment  $seg
      * @return string
      */
     public function segmentToString(Segment $seg): string
@@ -400,9 +402,9 @@ public function segmentToString(Segment $seg): string
         foreach ($fields as $field) {
             if (is_array($field)) {
                 foreach ($field as $index => $value) {
-                    is_array($field[$index])
-                        ? ($segmentString .= implode($this->subcomponentSeparator, $field[$index]))
-                        : ($segmentString .= $field[$index]);
+                    is_array($value)
+                        ? ($segmentString .= implode($this->subcomponentSeparator, $value))
+                        : ($segmentString .= $value);
 
                     if ($index < (count($field) - 1)) {
                         $segmentString .= $this->componentSeparator;
@@ -422,7 +424,6 @@ public function segmentToString(Segment $seg): string
      * Reset index attribute of each given segment, so when those are added the indices start from 1
      *
      * @return void
-     * @throws \ReflectionException
      */
     public function resetSegmentIndices(): void
     {
@@ -450,7 +451,7 @@ private function extractComponentsFromFields(string $field, bool $keepEmptySubFi
             : PREG_SPLIT_NO_EMPTY;
 
         if ((strpos($field, $this->repetitionSeparator) !== false) && (! $this->doNotSplitRepetition)) {
-            $components = preg_split("/\\".$this->repetitionSeparator.'/', $field, -1, $pregFlags);
+            $components = preg_split("/\\" . $this->repetitionSeparator . '/', $field, -1, $pregFlags);
             $fields = [];
             foreach ($components as $index => $component) {
                 $fields[$index] = $this->extractComponentsFromFields($component, $keepEmptySubFields);
@@ -461,17 +462,15 @@ private function extractComponentsFromFields(string $field, bool $keepEmptySubFi
 
         $components = preg_split("/\\" . $this->componentSeparator . '/', $field, -1, $pregFlags);
         foreach ($components as $index => $component) {
-            $subComps = preg_split("/\\" . $this->subcomponentSeparator . '/', $components[$index]);
+            $subComps = preg_split("/\\" . $this->subcomponentSeparator . '/', $component);
             // Make it a ref or just the value
             $components[$index] = count($subComps) === 1
                 ? $subComps[0]
                 : $subComps;
         }
 
-        $field = count($components) === 1
+        return count($components) === 1
             ? $components[0]
             : $components;
-
-        return $field;
     }
 }
diff --git a/src/HL7/MessageHelpersTrait.php b/src/HL7/MessageHelpersTrait.php
@@ -31,10 +31,10 @@ public function getSegmentAsString(int $index): ?string
      *
      * @param int $segmentIndex Index for segment to get
      * @param int $fieldIndex Index for field to get
-     * @return mixed String representation of field
+     * @return null|string String representation of field
      * @access public
      */
-    public function getSegmentFieldAsString(int $segmentIndex, int $fieldIndex)
+    public function getSegmentFieldAsString(int $segmentIndex, int $fieldIndex): ?string
     {
         $segment = $this->getSegmentByIndex($segmentIndex);
 
@@ -51,17 +51,16 @@ public function getSegmentFieldAsString(int $segmentIndex, int $fieldIndex)
         $fieldString = null;
 
         if (\is_array($field)) {
-            foreach ($field as $i => $iValue) {
-                \is_array($field[$i])
-                    ? ($fieldString .= implode($this->subcomponentSeparator, $field[$i]))
-                    : ($fieldString .= $field[$i]);
+            foreach ($field as $i => $value) {
+                \is_array($value)
+                    ? ($fieldString .= implode($this->subcomponentSeparator, $value))
+                    : ($fieldString .= $value);
 
                 if ($i < (\count($field) - 1)) {
                     $fieldString .= $this->componentSeparator;
                 }
             }
-        }
-        else {
+        } else {
             $fieldString .= $field;
         }
 
@@ -163,7 +162,7 @@ public function getFirstSegmentInstance(string $segment)
      */
     public function removeSegment(Segment $segment, bool $reIndex = false): void
     {
-        if(($key = array_search($segment, $this->segments, true)) !== false) {
+        if (($key = array_search($segment, $this->segments, true)) !== false) {
             unset($this->segments[$key]);
         }
 

diff --git a/src/HL7/Messages/ACK.php b/src/HL7/Messages/ACK.php
@@ -22,7 +22,7 @@ class ACK extends Message
      *
      * @param Message|null $req
      * @param MSH|null $reqMsh
-     * @param array $hl7Globals Set control characters or HL7 properties. e.g., ['HL7_VERSION' => '2.5']
+     * @param array|null $hl7Globals Set control characters or HL7 properties. e.g., ['HL7_VERSION' => '2.5']
      * @throws \Exception
      * @throws \InvalidArgumentException
      */
@@ -34,14 +34,12 @@ public function __construct(Message $req = null, MSH $reqMsh = null, array $hl7G
             $msh = $req->getSegmentByIndex(0);
 
             if ($msh) {
-                $msh = new MSH($msh->getFields(1));
+                $msh = new MSH($msh->getFields(1), $hl7Globals);
+            } else {
+                $msh = new MSH(null, $hl7Globals);
             }
-            else {
-                $msh = new MSH();
-            }
-        }
-        else {
-            $msh = new MSH();
+        } else {
+            $msh = new MSH(null, $hl7Globals);
         }
 
         $msa = new MSA();
@@ -51,8 +49,7 @@ public function __construct(Message $req = null, MSH $reqMsh = null, array $hl7G
         if ($req && ($msh->getField(15) || $msh->getField(16))) {
             $this->ACK_TYPE = 'E';
             $msa->setAcknowledgementCode('CA');
-        }
-        else {
+        } else {
             $this->ACK_TYPE = 'N';
             $msa->setAcknowledgementCode('AA');
         }
@@ -79,8 +76,8 @@ public function __construct(Message $req = null, MSH $reqMsh = null, array $hl7G
      * This denotes: accept, general error and reject respectively. The ACK module will determine the right answer mode
      * (normal or enhanced) based upon the request, if not provided. The message provided in $msg will be set in MSA 3.
      *
-     * @param string $code Code to use in acknowledgement
-     * @param string $msg Acknowledgement message
+     * @param  string  $code  Code to use in acknowledgement
+     * @param  string|null  $msg  Acknowledgement message
      * @return boolean
      * @access public
      */

diff --git a/src/HL7/Request.php b/src/HL7/Request.php
@@ -1,10 +1,8 @@
 <?php
 
-
 namespace Aranyasen\HL7;
 
-
 class Request
 {
 
-}
+}
diff --git a/src/HL7/Response.php b/src/HL7/Response.php
@@ -1,10 +1,8 @@
 <?php
 
-
 namespace Aranyasen\HL7;
 
-
 class Response
 {
 
-}
+}
diff --git a/src/HL7/Segment.php b/src/HL7/Segment.php
@@ -13,11 +13,11 @@ class Segment
     /**
      * Create a segment.
      *
-     * A segment may be created with just a name or a name and an array of field
-     * values. The segment name should be a standard HL7 segment (e.g. MSH / PID etc.) that is three characters long, and
-     * upper case. If an array is given, all fields will be filled from that array. Note that for composed fields and
-     * sub-components, the array may hold sub-arrays and sub-sub-arrays. Repeated fields can not be supported the same
-     * way, since we can't distinguish between composed fields and repeated fields.
+     * A segment may be created with just a name or a name and an array of field values. The segment name should be a
+     * standard HL7 segment (e.g. MSH / PID etc.) that is three characters long, and upper case. If an array is given,
+     * all fields will be filled from that array. Note that for composed fields and sub-components, the array may hold
+     * sub-arrays and sub-sub-arrays. Repeated fields can not be supported the same way, since we can't distinguish
+     * between composed fields and repeated fields.
      *
      * Example:
      * ```php

diff --git a/src/HL7/Segments/EQU.php b/src/HL7/Segments/EQU.php
@@ -79,5 +79,4 @@ public function getAlertLevel(int $position = 4)
     {
         return $this->getField($position);
     }
-
 }