[Bug] - Fix histopathology modifier values not being imported in CIM-11

migrations/Version20260611053328.php

@@ -0,0 +1,26 @@
+<?php
+
+declare(strict_types=1);
+
+namespace DoctrineMigrations;
+
+use Doctrine\DBAL\Schema\Schema;
+use Doctrine\Migrations\AbstractMigration;
+
+final class Version20260611053328 extends AbstractMigration
+{
+    public function getDescription(): string
+    {
+        return 'Add category column to cim_11_modifier_value';
+    }
+
+    public function up(Schema $schema): void
+    {
+        $this->addSql('ALTER TABLE cim_11_modifier_value ADD category VARCHAR(255) DEFAULT NULL');
+    }
+
+    public function down(Schema $schema): void
+    {
+        $this->addSql('ALTER TABLE cim_11_modifier_value DROP COLUMN category');
+    }
+}

src/Command/Cim11Import.php

@@ -10,19 +10,28 @@
 use Symfony\Component\Console\Attribute\AsCommand;
 use Symfony\Component\Console\Command\Command;
 use Symfony\Component\Console\Input\InputInterface;
+use Symfony\Component\Console\Input\InputOption;
 use Symfony\Component\Console\Output\OutputInterface;
 
 #[AsCommand('app:cim11:import')]
 class Cim11Import extends Command
 {
     private array $modifierValues = [];
 
+    /** @var array<string, array{title: string, code: string, parent_id: string}> */
+    private array $modifierTree = [];
+
+    /** @var array<string, list<string>> */
+    private array $modifierChildren = [];
+
     private array $diseases = [];
 
     private array $cim11Mapping = [];
 
     private string $importId;
 
+    private bool $forceModifiers = false;
+
     private OutputInterface $output;
 
     public function __construct(
@@ -32,12 +41,19 @@ public function __construct(
         parent::__construct();
     }
 
+    protected function configure(): void
+    {
+        $this->addOption('force-modifiers', null, InputOption::VALUE_NONE, 'Force re-import of modifiers even if already set on a disease');
+    }
+
     public function execute(InputInterface $input, OutputInterface $output): int
     {
         ini_set('memory_limit', '-1');
         $this->importId = uniqid();
         $this->output = $output;
+        $this->forceModifiers = (bool) $input->getOption('force-modifiers');
 
+        $this->buildModifierTree();
         $this->importModifiers();
         $this->importDiseases();
 
@@ -100,8 +116,11 @@ private function importDiseases(): void
                 }
 
                 if ($cim11Disease->hasModifier($case)) {
-                    $this->output->writeln("Modifier {$case->value} already set in $cim11Disease");
-                    continue;
+                    if (!$this->forceModifiers) {
+                        $this->output->writeln("Modifier {$case->value} already set in $cim11Disease");
+                        continue;
+                    }
+                    $cim11Disease->removeModifier($case);
                 }
 
                 $modifier = new Cim11Modifier();
@@ -112,13 +131,7 @@ private function importDiseases(): void
 
                 $modifier->setMultiple('NotAllowed' !== $elem['allowMultipleValues']);
 
-                foreach ($elem['ids'] as $id) {
-                    $value = $this->modifierValues[$id] ?? null;
-
-                    if (!$value) {
-                        $this->output->writeln("Value {$id} not found");
-                        continue;
-                    }
+                foreach ($this->resolveModifierValues($elem['ids']) as $value) {
                     $modifier->addValue($value);
                 }
                 $modifier->setCim11($cim11Disease);
@@ -136,6 +149,27 @@ private function importDiseases(): void
         $this->em->flush();
     }
 
+    private function buildModifierTree(): void
+    {
+        $file = "{$this->projectDir}/var/modifiers.csv";
+
+        $this->readCsv($file, ',', function (array $data) {
+            if (!$data['id']) {
+                return;
+            }
+
+            $this->modifierTree[$data['id']] = [
+                'title' => $data['title'],
+                'code' => $data['code'],
+                'parent_id' => $data['parent_id'],
+            ];
+
+            if ($data['parent_id']) {
+                $this->modifierChildren[$data['parent_id']][] = $data['id'];
+            }
+        });
+    }
+
     private function importModifiers(): void
     {
         $this->output->writeln('Importing modifiers...');
@@ -144,8 +178,6 @@ private function importModifiers(): void
 
         $this->readCsv($file, ',', function (array $data) {
             if (!$data['code']) {
-                $this->output->writeln("No code found, skipping {$data['title']}");
-
                 return;
             }
 
@@ -159,6 +191,9 @@ private function importModifiers(): void
                 'code' => $data['code'],
             ]);
             if ($existing) {
+                if (!$existing->getCategory()) {
+                    $existing->setCategory($this->resolveCategory($data['parent_id']));
+                }
                 $this->modifierValues[$existing->getWhoId()] = $existing;
                 $this->output->writeln("{$data['title']} already exists");
 
@@ -171,6 +206,7 @@ private function importModifiers(): void
             $value->setCode($data['code']);
             $value->setName($data['title']);
             $value->setSynonyms(explode(';', $data['synonyms']));
+            $value->setCategory($this->resolveCategory($data['parent_id']));
             $value->setImportId($this->importId);
 
             $this->em->persist($value);
@@ -183,6 +219,55 @@ private function importModifiers(): void
         $this->output->writeln('All modifiers imported successfully...');
     }
 
+    /**
+     * Returns the title of the nearest block ancestor (direct parent block).
+     * Used to group coded modifier values under a human-readable category.
+     */
+    private function resolveCategory(?string $parentId): ?string
+    {
+        if (!$parentId || !isset($this->modifierTree[$parentId])) {
+            return null;
+        }
+
+        return $this->modifierTree[$parentId]['title'] ?: null;
+    }
+
+    /**
+     * Resolves a list of modifier IDs, expanding block entries (no code)
+     * into their coded leaf descendants recursively.
+     *
+     * @param list<string> $ids
+     * @return list<Cim11ModifierValue>
+     */
+    private function resolveModifierValues(array $ids): array
+    {
+        $values = [];
+
+        foreach ($ids as $id) {
+            if (isset($this->modifierValues[$id])) {
+                $values[] = $this->modifierValues[$id];
+                continue;
+            }
+
+            // Block entry — expand to coded descendants
+            $this->collectLeafValues($id, $values);
+        }
+
+        return $values;
+    }
+
+    /** @param list<Cim11ModifierValue> $values */
+    private function collectLeafValues(string $id, array &$values): void
+    {
+        foreach ($this->modifierChildren[$id] ?? [] as $childId) {
+            if (isset($this->modifierValues[$childId])) {
+                $values[] = $this->modifierValues[$childId];
+            } else {
+                $this->collectLeafValues($childId, $values);
+            }
+        }
+    }
+
     private function readCsv(string $fileName, string $separator, callable $callback, bool $convertToUtf8 = false): void
     {
         $row = 0;

src/Entity/Cim11.php

@@ -220,6 +220,17 @@ public function addModifier(Cim11Modifier $modifier): void
         }
     }
 
+    public function removeModifier(ModifierType $type): void
+    {
+        foreach ($this->modifiers as $modifier) {
+            if ($modifier->getType() === $type) {
+                $this->modifiers->removeElement($modifier);
+
+                return;
+            }
+        }
+    }
+
     public function getCim10Code(): ?string
     {
         return $this->cim10Code;

src/Entity/Cim11ModifierValue.php

@@ -42,6 +42,10 @@ class Cim11ModifierValue extends BaseEntity implements ImportableEntityInterface
     #[ORM\Column(type: 'string', length: 32, unique: true)]
     protected ?string $whoId = null;
 
+    #[Groups(['read'])]
+    #[ORM\Column(type: 'string', length: 255, nullable: true)]
+    protected ?string $category = null;
+
     #[ORM\Column(type: 'simple_array')]
     protected array $synonyms = [];
 
@@ -90,6 +94,16 @@ public function setWhoId(?string $whoId): void
         $this->whoId = $whoId;
     }
 
+    public function getCategory(): ?string
+    {
+        return $this->category;
+    }
+
+    public function setCategory(?string $category): void
+    {
+        $this->category = $category;
+    }
+
     public function getSynonyms(): array
     {
         return $this->synonyms;