Dicom Rework (openemr#3731)

* Dicom Rework * - bells and whistles * - add dicom folder upload
bradymiller · Jul 12, 2020 · 5250fc6 · 5250fc6
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diff --git a/API_README.md b/API_README.md
@@ -56,7 +56,6 @@ Finally, APIs which are integrated with the new `handleProcessingResult` method
     -   [Facility API](API_README.md#post-apifacility)
     -   [Practitioner API](API_README.md#get-apipractitioner)
     -   [Patient API](API_README.md#post-apipatient)
-    -   [Immunization API](API_README.md#get-apiimmunization)
     -   [Insurance API](API_README.md#get-apipatientpidinsurance)
     -   [Appointment API](API_README.md#get-apiappointment)
     -   [Document API](API_README.md#get-apipatientpiddocument)
@@ -501,21 +500,6 @@ Response:
     }
 }
 ```
-#### GET /api/immunization
-
-Request:
-
-```sh
-curl -X GET 'http://localhost:8300/apis/api/immunization'
-```
-
-#### GET /api/immunization/:uuid
-
-Request:
-
-```sh
-curl -X GET 'http://localhost:8300/apis/api/immunization/90cde167-7b9b-4ed1-bd55-533925cb2605'
-```
 
 #### POST /api/patient/:pid/encounter
 

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -8,9 +8,8 @@ You will need a "local" version of OpenEMR to make changes to the source code. T
 
 1. [Create your own fork of OpenEMR](https://github.com/openemr/openemr/fork) (you will need a GitHub account) and `git clone` it to your local machine.
     - It's best to also add an `upstream` origin to keep your local fork up to date. [Check out this guide](https://oneemptymind.wordpress.com/2018/07/11/keeping-a-fork-up-to-date/) for more info.
-	- If you haven't already, [install git](https://git-scm.com/downloads) for your system
 2. `cd openemr` (the directory you cloned the code into)
-    - If you haven't already, [install Docker](https://docs.docker.com/install/) and [install compose](https://docs.docker.com/compose/install/) for your system
+    - If you haven't already, [install Docker](https://docs.docker.com/install/) for your system
 3. Run `docker-compose up` from your command line
     - When the build is done, you'll see the following message:
     ```sh

diff --git a/FHIR_README.md b/FHIR_README.md
@@ -36,11 +36,11 @@ Database Result -> Service Component -> FHIR Service Component -> Parse OpenEMR
     -   [FHIR Encounter API](FHIR_README.md#get-fhirencounter)
     -   [FHIR Practitioner API](FHIR_README.md#get-fhirpractitioner)
     -   [FHIR PractitionerRole API](FHIR_README.md#get-fhirpractitionerrole)
-    -   [FHIR Immunization API](FHIR_README.md#get-fhirimmunization)
     -   [FHIR Organization API](FHIR_README.md#get-fhirorganization)
     -   [FHIR AllergyIntolerance API](FHIR_README.md#get-fhirallergyintolerance)
     -   [FHIR Observation API](FHIR_README.md#get-fhirobservation)
     -   [FHIR QuestionnaireResponse API](FHIR_README.md#get-fhirquestionnaireresponse)
+    -   [FHIR Immunization API](FHIR_README.md#get-fhirimmunization)
     -   [FHIR Condition API](FHIR_README.md#get-fhircondition)
     -   [FHIR Procedure API](FHIR_README.md#get-fhirprocedure)
     -   [FHIR MedicationStatement API](FHIR_README.md#get-fhirmedicationstatement)
@@ -321,25 +321,6 @@ curl -X GET 'http://localhost:8300/apis/fhir/PractitionerRole/90de091a-91e9-4bbe
     -   speciality
     -   practitioner
 
-#### GET [base]/Immunization
-
-Request:
-
-```sh
-curl -X GET 'http://localhost:8300/apis/fhir/Immunization'
-```
-
-#### GET [base]/Immunization/:id
-
-Request:
-
-```sh
-curl -X GET 'http://localhost:8300/apis/fhir/Immunization/90feaaa2-4097-4437-966e-c425d1958dd6'
-```
-
--   Supported Search Parameters
-    -   patient
-
 #### GET /fhir/Organization
 
 Request:
@@ -421,6 +402,22 @@ curl -X POST -H 'Content-Type: application/fhir+json' 'http://localhost:8300/api
 }'
 ```
 
+#### GET /fhir/Immunization
+
+Request:
+
+```sh
+curl -X GET 'http://localhost:8300/apis/fhir/Immunization'
+```
+
+#### GET /fhir/Immunization/:id
+
+Request:
+
+```sh
+curl -X GET 'http://localhost:8300/apis/fhir/Immunization/1'
+```
+
 #### GET /fhir/Condition
 
 Request:

diff --git a/_rest_routes.inc.php b/_rest_routes.inc.php
@@ -30,7 +30,6 @@
 use OpenEMR\RestControllers\AuthRestController;
 use OpenEMR\RestControllers\ONoteRestController;
 use OpenEMR\RestControllers\DocumentRestController;
-use OpenEMR\RestControllers\ImmunizationRestController;
 use OpenEMR\RestControllers\InsuranceRestController;
 use OpenEMR\RestControllers\MessageRestController;
 
@@ -346,14 +345,6 @@
         RestConfig::authorization_check("patients", "notes");
         return (new MessageRestController())->delete($pid, $mid);
     },
-    "GET /api/immunization" => function () {
-        RestConfig::authorization_check("patients", "med");
-        return (new ImmunizationRestController())->getAll($_GET);
-    },
-    "GET /api/immunization/:id" => function ($id) {
-        RestConfig::authorization_check("patients", "med");
-        return (new ImmunizationRestController())->getOne($id);
-    },
 
 );
 
@@ -474,11 +465,11 @@
     },
     "GET /fhir/Immunization" => function () {
         RestConfig::authorization_check("patients", "med");
-        return (new FhirImmunizationRestController())->getAll($_GET);
+        return (new FhirImmunizationRestController(null))->getAll($_GET);
     },
     "GET /fhir/Immunization/:id" => function ($id) {
         RestConfig::authorization_check("patients", "med");
-        return (new FhirImmunizationRestController())->getOne($id);
+        return (new FhirImmunizationRestController(null))->getOne($id);
     },
     "GET /fhir/Condition" => function () {
         RestConfig::authorization_check("patients", "med");

diff --git a/controllers/C_Document.class.php b/controllers/C_Document.class.php
@@ -122,6 +122,33 @@ function upload_action($patient_id, $category_id)
         return $this->list_action($patient_id);
     }
 
+    function zip_dicom_folder($study_name = null)
+    {
+        $zip = new ZipArchive();
+        $zip_name = $GLOBALS['temporary_files_dir'] . "/" . $study_name;
+        if ($zip->open($zip_name, (ZipArchive::CREATE | ZipArchive::OVERWRITE)) === true) {
+            foreach ($_FILES['dicom_folder']['name'] as $i => $name) {
+                $zfn = $GLOBALS['temporary_files_dir'] . "/" . $name;
+                move_uploaded_file($_FILES['dicom_folder']['tmp_name'][$i], $zfn);
+                $fparts = explode(".", $zfn);
+                $fext = strtolower(end($fparts));
+                // disregard other file ext's
+                if ($fext == 'dcm') {
+                    $zip->addFile($zfn, $name);
+                }
+            }
+            $zip->close();
+        } else {
+            return false;
+        }
+        $file_array['name'][] = $study_name;
+        $file_array['type'][] = 'zip';
+        $file_array['tmp_name'][] = $zip_name;
+        $file_array['error'][] = '';
+        $file_array['size'][] = filesize($zip_name);
+        return $file_array;
+    }
+
     //Upload multiple files on single click
     function upload_action_process()
     {
@@ -167,6 +194,19 @@ function upload_action_process()
             $patient_id = $_POST['patient_id'];
         }
 
+        if (!empty($_FILES['dicom_folder']['name'][0])) {
+            // let's zip um up then pass along new zip
+            $study_name = $_POST['destination'] ? (trim($_POST['destination']) . ".zip") : 'DicomStudy.zip';
+            $study_name =  preg_replace('/\s+/', '_', $study_name);
+            $_POST['destination'] = "";
+            $zipped = $this->zip_dicom_folder($study_name);
+            if ($zipped) {
+                $_FILES['file'] = $zipped;
+            }
+            // and off we go! just fall through and let routine
+            // do its normal file processing..
+        }
+
         $sentUploadStatus = array();
         if (count($_FILES['file']['name']) > 0) {
             $upl_inc = 0;

diff --git a/interface/patient_file/summary/immunizations.php b/interface/patient_file/summary/immunizations.php
@@ -16,7 +16,6 @@
 
 use OpenEMR\Common\Csrf\CsrfUtils;
 use OpenEMR\Common\Logging\EventAuditLogger;
-use OpenEMR\Common\Uuid\UuidRegistry;
 use OpenEMR\Core\Header;
 
 if (isset($_GET['mode'])) {
@@ -32,7 +31,6 @@
     if ($_GET['mode'] == "add") {
         $sql = "REPLACE INTO immunizations set
             id = ?,
-            uuid = ?,
             administered_date = if(?,?,NULL),
             immunization_id = ?,
             cvx_code = ?,
@@ -58,7 +56,6 @@
             ordering_provider = ?";
         $sqlBindArray = array(
             trim($_GET['id']),
-            UuidRegistry::isValidStringUUID($_GET['uuid']) ? UuidRegistry::uuidToBytes($_GET['uuid']) : null,
             trim($_GET['administered_date']), trim($_GET['administered_date']),
             trim($_GET['form_immunization_id']),
             trim($_GET['cvx_code']),
@@ -111,10 +108,6 @@
         $result = sqlQuery($sql, array($_GET['id']));
 
         $administered_date = new DateTime($result['administered_date']);
-        $uuid = null;
-        if (isset($result['uuid']) && !UuidRegistry::isEmptyBinaryUUID($result['uuid'])) {
-            $uuid = UuidRegistry::uuidToString($result['uuid']);
-        }
         $administered_date = $administered_date->format('Y-m-d H:i');
 
         $immuniz_amt_adminstrd = $result['amount_administered'];
@@ -353,7 +346,6 @@ function saveImmunizationObservationResults($id, $immunizationdata)
 <input type="hidden" name="mode" id="mode" value="add">
 <input type="hidden" name="id" id="id" value="<?php echo attr($id); ?>">
 <input type="hidden" name="pid" id="pid" value="<?php echo attr($pid); ?>">
-<input type="hidden" name="uuid" id="uuid" value="<?php echo attr($uuid); ?>">
 <br />
       <table border=0 cellpadding=1 cellspacing=1>
         <?php

diff --git a/library/ajax/upload.php b/library/ajax/upload.php
@@ -7,8 +7,10 @@
  * @link      https://www.open-emr.org
  * @author    Sherwin Gaddis <sherwingaddis@gmail.com>
  * @author    Brady Miller <brady.g.miller@gmail.com>
+ * @author    Jerry Padgett <sjpadgett@gmail.com>
  * @copyright Copyright (c) 2017 Sherwin Gaddis <sherwingaddis@gmail.com>
  * @copyright Copyright (c) 2018 Brady Miller <brady.g.miller@gmail.com>
+ * @copyright Copyright (c) 2020 Jerry Padgett <sjpadgett@gmail.com>
  * @license   https://github.com/openemr/openemr/blob/master/LICENSE GNU General Public License 3
  */
 
@@ -17,19 +19,60 @@
 
 use OpenEMR\Common\Csrf\CsrfUtils;
 
-if (!CsrfUtils::verifyCsrfToken($_GET["csrf_token_form"])) {
+if (!CsrfUtils::verifyCsrfToken($_REQUEST["csrf_token_form"])) {
     CsrfUtils::csrfNotVerified();
 }
 
+// check if this is for dicom image maintenance.
+$action = $_POST['action'] ?? null;
+$doc_id = (int)$_POST['doc_id'] ?? null;
+$json_data = $_POST['json_data'] ?? null;
+
+if ($action == 'save') {
+    //$data = json_decode($json_data, true);
+    //$json_data = base64_encode($data);
+    $pass_it = dicom_history_action($action, $doc_id, $json_data);
+    if ($pass_it === 'false') {
+        // query success. send back a translated message for user.
+        echo xlj("Server says thanks. Images state saved.");
+    } else {
+        echo xlj("Error! Images state save failed.");
+    }
+
+    exit();
+}
+if ($action == 'fetch') {
+    $json_data = dicom_history_action($action, $doc_id);
+    echo $json_data;
+
+    exit();
+}
+// nope! so continue on with Sherwins uploader.
 $patient_id = filter_input(INPUT_GET, 'patient_id');
 $category_id = filter_input(INPUT_GET, 'parent_id');
 
 if (!empty($_FILES)) {
-    $name     = $_FILES['file']['name'];
-    $type     = $_FILES['file']['type'];
+    $name = $_FILES['file']['name'];
+    $type = $_FILES['file']['type'];
     $tmp_name = $_FILES['file']['tmp_name'];
-    $size     = $_FILES['file']['size'];
-    $owner    = $GLOBALS['userauthorized'];
+    $size = $_FILES['file']['size'];
+    $owner = $GLOBALS['userauthorized'];
 
     addNewDocument($name, $type, $tmp_name, $error, $size, $owner, $patient_id, $category_id);
+    exit();
+}
+
+function dicom_history_action($action, $doc_id, $json_data = '')
+{
+    if ($action == 'save') {
+        $json_data = base64_encode($json_data);
+        return json_encode(sqlQuery("UPDATE documents SET document_data = ? WHERE id = ?", array($json_data, $doc_id)));
+    }
+
+    if ($action == 'fetch') {
+        $qrtn = sqlQuery("Select document_data FROM documents WHERE id = ?", array($doc_id));
+        return base64_decode($qrtn['document_data']);
+    }
+
+    return xlj("Unknown");
 }