Api reads

php/rri/reads.php

@@ -1,7 +1,5 @@
 <?php
-
 require_once(__DIR__ . '/../../vendor/autoload.php');
-
 use GuzzleHttp\Client;
 use GuzzleHttp\Psr7\Utils;
 use GuzzleHttp\Psr7\Request;
@@ -10,6 +8,8 @@
 
 // first remove tmp courier cached file in case some other script put it there
 $context = $argv[1] ?? null;
+$ask_claude = strtoupper($argv[1] ?? '') === 'Y';
+
 if (!empty($context) && $context == 'pdf') {
     // create temp dir for cached courier font
     $tmp_dir = '/tmp/reads' . $cms_user;
@@ -45,116 +45,200 @@ function getQualifyingLungFindings(string $note): array
 {
     $note_lower = strtolower($note);
     $no_nodule  = str_contains($note_lower, 'no pulmonary nodule');
-
     return [
         'no_pulmonary_nodule' => $no_nodule,
         'pulmonary_nodule'    => !$no_nodule && str_contains($note_lower, 'pulmonary nodule'),
         'includes_guidelines' => str_contains($note_lower, 'fleischner society 2017'),
     ];
 }
 
+function suggestIcd10Codes(Client $guzzle, string $interp, string $cpt): array
+{
+    $system = <<<PROMPT
+You are a radiology ICD-10-CM coding assistant. Given a radiology report and the CPT code
+for the procedure performed, return a JSON array of suggested diagnosis codes.
+
+For each code include:
+- code: ICD-10-CM code
+- description: full code description
+- confidence: high/medium/low
+- rationale: one sentence citing the specific finding or indication
+
+CODING HIERARCHY — follow in order:
+
+1. Begin with IMPRESSION. If the impression documents a specific, confirmed finding
+   or diagnosis, code that finding as primary using the most specific ICD-10-CM code
+   available.
+
+2. If the IMPRESSION is normal, unremarkable, or negative, look to CLINICAL INDICATION:
+   a. If the indication contains a specific codeable condition (e.g. "cerebral aneurysm,
+      nonruptured", "lung nodule"), code that condition — a normal result does not
+      eliminate the underlying diagnosis.
+   b. If the indication is a symptom or vague (e.g. "headache", "rule out PE"), code
+      the symptom.
+
+3. Never code "rule out," "suspected," "probable," "possible," or "questionable"
+   conditions as confirmed — code the sign, symptom, or abnormal finding instead
+   per ICD-10-CM outpatient guidelines.
+
+4. Never return a Z51 aftercare code solely because findings are normal or the study
+   is a follow-up. Z51 requires explicit documentation of an aftercare encounter.
+
+5. If IMPRESSION reveals incidental pathology not mentioned in the indication, include
+   it as a secondary suggestion at lower confidence.
+
+Return ONLY a valid JSON array. No preamble, no markdown, no backticks.
+PROMPT;
+
+    $clean_interp = preg_replace('/(Please note:|Electronically Signed by:).*$/si', '', $interp);
+    $user_message = "CPT: {$cpt}\n\nInterpretation:\n{$clean_interp}";
+
+    try {
+        $response = $guzzle->post('https://api.anthropic.com/v1/messages', [
+            'headers' => [
+                'x-api-key'         => getenv('ANTHROPIC_API_KEY'),
+                'anthropic-version' => '2023-06-01',
+                'Content-Type'      => 'application/json',
+            ],
+            'timeout'         => 30,
+            'connect_timeout' => 10,
+            'json' => [
+                'model'      => 'claude-sonnet-4-20250514',
+                'max_tokens' => 1024,
+                'system'     => $system,
+                'messages'   => [
+                    ['role' => 'user', 'content' => $user_message]
+                ],
+            ],
+        ]);
+        $body = json_decode((string) $response->getBody(), true);
+        $raw  = $body['content'][0]['text'] ?? '[]';
+        return json_decode($raw, true) ?? [];
+    } catch (\GuzzleHttp\Exception\ConnectException $e) {
+        echo "Claude unavailable (connection timeout) \n";
+    } catch (\GuzzleHttp\Exception\RequestException $e) {
+        echo "Claude request failed: " . $e->getMessage() . " \n";
+    } catch (\Exception $e) {
+        echo "Claude error: " . $e->getMessage() . " \n";
+    }
+    return [];
+}
+
 $filename = getenv('HOME') . "/W2" . getenv('tid') . $cms_user;
 $file = file_get_contents($filename);
 $mrn = ltrim(substr($file, 0, 8), '0');
 $visit_no = substr($file, 8, 7);
+$rri_cpt = substr($file, 34, 5);
+
 if (substr($visit_no, 0, 1) == '0') {
     $visit_no = "1" . $visit_no;
 }
+
 $charcur_key = substr($file, 15, 11);
 $billing_tape_date_of_service = substr($file, 26, 8);
+
 $base_url = getenv('BASE_OEMR_URL');
-$site_id = getenv('OEMR_RRI_SITE_ID');
+$site_id  = getenv('OEMR_RRI_SITE_ID');
 $base_uri = $base_url . '/oauth2/' . $site_id . '/token';
-$guzzle = new Client(
-    ['verify' => false],
-    ['debug' => true]
-);
+
+$guzzle = new Client(['verify' => false]);
+
 $response = $guzzle->post($base_uri, [
     'form_params' => [
         'grant_type' => 'password',
-        'client_id' => getenv('OEMR_TEST_CLIENT_ID'),
-        'scope' => "openid fhirUser online_access offline_access user/Observation.read user/Patient.read",
-        'user_role' => 'users',
-        'username' => getenv('OEMR_RRI_USERNAME'),
-        'password' => getenv('OEMR_RRI_PASSWORD')
+        'client_id'  => getenv('OEMR_TEST_CLIENT_ID'),
+        'scope'      => "openid fhirUser online_access offline_access user/Observation.read user/Patient.read",
+        'user_role'  => 'users',
+        'username'   => getenv('OEMR_RRI_USERNAME'),
+        'password'   => getenv('OEMR_RRI_PASSWORD'),
     ],
 ]);
+
 $bearer = json_decode((string) $response->getBody(), true)['access_token'];
 
-$client = new Client(
-    ['verify' => false],
-    ['debug' => true]
-);
+$client = new Client(['verify' => false]);
+
 $headers = [
-  'Authorization' => 'Bearer ' . $bearer,
-  'Accept' => 'application/json',
+    'Authorization' => 'Bearer ' . $bearer,
+    'Accept'        => 'application/json',
 ];
+
 $request = new Request('GET', $base_url . '/apis/' . $site_id . '/fhir/Patient?identifier=' . $mrn, $headers);
-$res = $client->sendAsync($request)->wait();
-$ptObj = json_decode($res->getBody(), true);
+$res     = $client->sendAsync($request)->wait();
+$ptObj   = json_decode($res->getBody(), true);
+
 $pt_uuid = $ptObj['entry'][0]['resource']['id'] ?? null;
 if (empty($pt_uuid)) {
     echo "no patient uuid in the emr for some reason \n";
     exit;
 }
 
 $pt_name_array = $ptObj['entry'][0]['resource']['name'][0] ?? null;
-$pt_name_text = ($pt_name_array['family'] ?? '') . ", " . ($pt_name_array['given'][0] ?? '') .
-    " " . ($pt_name_array['given'][1] ?? '');
-$pt_birthdate = $ptObj['entry'][0]['resource']['birthDate'] ?? null;
-$pt_dob = new DateTimeImmutable($pt_birthdate);
-$pt_dob_line = "DOB: " . $pt_dob->format('m-d-Y');
+$pt_name_text  = ($pt_name_array['family'] ?? '') . ", " . ($pt_name_array['given'][0] ?? '') .
+                 " " . ($pt_name_array['given'][1] ?? '');
+$pt_birthdate  = $ptObj['entry'][0]['resource']['birthDate'] ?? null;
+$pt_dob        = new DateTimeImmutable($pt_birthdate);
+$pt_dob_line   = "DOB: " . $pt_dob->format('m-d-Y');
 
 $request = new Request(
     'GET',
     $base_url . '/apis/' . $site_id . '/fhir/Observation?patient=' . $pt_uuid . '&external_id=' . $visit_no,
     $headers
 );
-
-$res = $client->sendAsync($request)->wait();
-
+$res     = $client->sendAsync($request)->wait();
 $jsonObj = json_decode($res->getBody(), true);
 
 if (!empty($jsonObj['entry'])) {
-    $note = '';
+    $note  = '';
     $count = count($jsonObj['entry']);
-    $cntr = 0;
+    $cntr  = 0;
+
+    // in pdf context ask once whether to strip PROCEDURE headers
+    // in console context always strip — coders don't need it
+    if (!empty($context) && $context == 'pdf') {
+        $strip_procedure = str_contains(
+            strtoupper(readline("Strip PROCEDURE headers from reports? (y or Y) ")), 'Y'
+        );
+    } else {
+        $strip_procedure = false;
+    }
+
+    $pdf_page_count = 0;
+
     foreach ($jsonObj['entry'] as $entry) {
         $cntr++;
         $coding_display = $entry['resource']['code']['coding'][0]['display'];
-        $interp = $entry['resource']['note'][0]['text'];
-        $lung_findings = getQualifyingLungFindings($interp);
-        /* if ($cpt = isQualifyingCtCpt($coding_display)) {
-            $nodule     = $lung_findings['pulmonary_nodule'];
-            $guidelines = $lung_findings['includes_guidelines'];
-
-            if ($nodule && $guidelines) {
-                echo "\n*** Pulmonary nodule and Fleischner guidelines mentioned for {$cpt} ***\n";
-                readline("Press ENTER to continue...");
-            } elseif ($nodule && !$guidelines) {
-                echo "\n*** ALERT: Pulmonary nodule but NO Fleischner guidelines mentioned: {$cpt} ***\n";
-                readline("Press ENTER to continue...");
-            } elseif (!$nodule && $guidelines) {
-                echo "\n*** NOTE: Fleischner guidelines mentioned but no pulmonary nodule: {$cpt} ***\n";
-                readline("Press ENTER to continue...");
-            }
-        } */
+        $interp         = $entry['resource']['note'][0]['text'];
+
+        // optionally strip PROCEDURE: header line
+        if ($strip_procedure) {
+            $interp = preg_replace('/^PROCEDURE:.*\n?(?![A-Z]{2,}:).*\n?/mi', '', $interp);
+            $interp = ltrim($interp);
+        }
+
         $coding_display_length = strlen($coding_display);
-        $pt_name_text_length = strlen($pt_name_text);
+        $pt_name_text_length   = strlen($pt_name_text);
+
         if ($coding_display_length > 15 || $pt_name_text_length > 15) {
-            $banner_length = ($coding_display_length > $pt_name_text_length) ?
-                $coding_display_length : $pt_name_text_length;
+            $banner_length = ($coding_display_length > $pt_name_text_length)
+                ? $coding_display_length
+                : $pt_name_text_length;
         } else {
             $banner_length = 15;
         }
-        $note = str_pad('', $banner_length, '#') . "\n";
+
+        $note  = str_pad('', $banner_length, '#') . "\n";
         $note .= $pt_name_text . "\n";
         $note .= $pt_dob_line . "\n";
-        $note .= $coding_display . "\n";
-        $date_of_order = $entry['resource']['effectiveDateTime'] ?? '';
-        $date_of_order_utc = new DateTimeImmutable($date_of_order);
+        if (!$strip_procedure) {
+            $note .= $coding_display . "\n";
+        }
+
+        $date_of_order             = $entry['resource']['effectiveDateTime'] ?? '';
+        $date_of_order_utc         = new DateTimeImmutable($date_of_order);
         $date_of_order_utc_display = $date_of_order_utc->format('m-d-Y');
         $date_of_order_utc_compare = $date_of_order_utc->format('Ymd');
+
         if ($date_of_order_utc_compare != $billing_tape_date_of_service) {
             continue;
         }
@@ -165,45 +249,58 @@ function getQualifyingLungFindings(string $note): array
         $note .= $interp . "\n";
 
         if (!empty($context) && $context == 'pdf') {
-            $pdf->ezText($note, 10);
-            if ($cntr != $count) {
-                $pdf->ezNewPage();
+            // per-report prompt for PDF inclusion
+            $add_to_pdf = str_contains(
+                strtoupper(readline("Add {$coding_display} to PDF? (y or Y) ")), 'Y'
+            );
+            if ($add_to_pdf) {
+                if ($pdf_page_count > 0) {
+                    $pdf->ezNewPage();
+                }
+                $pdf->ezText($note, 10);
+                $pdf_page_count++;
             }
         } else {
             echo $note . "\n";
+            if ($ask_claude) {
+                if (str_contains($coding_display, $rri_cpt)) {
+                    $line = strtoupper(readline("Send to Claude for ICD-10 suggestions? (y or Y) "));
+                    if (str_contains($line, 'Y')) {
+                        $icd10_suggestions = suggestIcd10Codes($guzzle, $interp, $rri_cpt);
+                        foreach ($icd10_suggestions as $s) {
+                            echo sprintf("[%s] %s (%s) — \"%s\"\n",
+                                $s['confidence'],
+                                $s['code'],
+                                $s['description'],
+                                $s['rationale']
+                            );
+                        }
+                    }
+                }
+            }
         }
     }
 } else {
     echo "read not available for some reason, try mpages please \n";
 }
 
 if (!empty($context) && $context == 'pdf') {
-    $pdf_data = $pdf->ezOutput();
-    file_put_contents($charcur_key . ".pdf", $pdf_data);
-    file_put_contents('wcomp1', $charcur_key);
-
-    // just save file to rri dir if need a pdf of all reports for uhc for instance
-    /* $line = strtoupper(readline("Upload " . $charcur_key . ".pdf to change wcomp? (y or Y) "));
-    if (strpos($line, "Y") !== false) {
-        echo "uploading to change\n";
-        $cmd = "chc-wcomp";
-        exec($cmd, $output);
-        var_dump($output);
-    } else { */
-        //echo "saved pdf under rri but not uploading \n";
+    if ($pdf_page_count > 0) {
+        $pdf_data = $pdf->ezOutput();
+        file_put_contents($charcur_key . ".pdf", $pdf_data);
+        file_put_contents('wcomp1', $charcur_key);
         echo "saved pdf under rri \n";
-        //$line = strtoupper(readline("Download " . $charcur_key . ".pdf to your comp? (y or Y) "));
-        //if (strpos($line, "Y") !== false) {
-            $filename = exec('pwd') . "/" . $charcur_key . ".pdf";
-            $tty = exec('tty');
-            echo "downloading $filename \n";
-            echo " for $cms_user \n";
-    if ($cms_user == 'lynda') {
-        $cmd = "sz $filename > $tty < $tty";
-        exec($cmd, $output);
+        $filename = exec('pwd') . "/" . $charcur_key . ".pdf";
+        $tty      = exec('tty');
+        echo "downloading $filename \n";
+        echo " for $cms_user \n";
+        if ($cms_user == 'lynda') {
+            $cmd = "sz $filename > $tty < $tty";
+            exec($cmd, $output);
+        } else {
+            echo "                not implemented for " . $cms_user . "\n";
+        }
     } else {
-        echo "                not implemented for " . $cms_user . "\n";
+        echo "No reports added to PDF, nothing saved.\n";
     }
-        //}
-    //}
 }