Merge pull request #91 from susom/dev

editor feature

Duster.php

@@ -31,9 +31,8 @@ public function redcap_every_page_top($project_id) {
       && strpos(PAGE, "index.php") !== false
       && isset($_GET['action']) && $_GET['action'] === 'create'
       && $this->isUserAllowed() === true) {
-        // $this->emDebug("In Every Page Top Hook project id :" . $this->getProjectId() . " Page is " . PAGE);
-        $some = "<script> let dusterUrl = '" . $this->getUrl("pages/newProjectIntro.php", false, true) . "' ; </script>";
-        echo $some;
+        echo "<script> const isSunet = '" . !str_contains($this->getUser()->getUsername(), '@') . "'; </script>";
+        echo "<script> const dusterUrl = '" . $this->getUrl("pages/newProjectIntro.php", false, true) . "' ; </script>";
         $script = <<<EOD
                 <script>
                     $(document).ready(function() {
@@ -48,6 +47,10 @@ public function redcap_every_page_top($project_id) {
                         div += "</div>";
 
                         $("#project_template_radio0").closest('td').append(div) ;
+                        if (!isSunet) {
+                           $("#project_template_duster").attr('disabled', true);
+                           $("#duster_option").append("<br><small>You must be logged into REDCap with your SUNet to use DUSTER.</small>");
+                        }
 
                         // show DUSTER radio button option if purpose is research
                         $("#purpose").change(function() {
@@ -114,19 +117,29 @@ private function getValidToken($service) {
     return $token;
   }
 
-  /**
-   * returns the URL for the REDCap API
-   * @return string
-   */
-  public function getRedcapApiUrl() {
-      $is_local_dev = $this->getSystemSetting('local-dev');
-      if($is_local_dev === true) {
-          return APP_PATH_WEBROOT_FULL . "api/";
+    /**
+     * returns a REDCap URL
+     * @param $path
+     * @return string
+     */
+  public function getRedcapUrl($path = ""):string {
+      $server_type = $this->getSystemSetting('server-type');
+      $pathname = $path === "" ? $path : $path . "/";
+      if($server_type === "development") {
+          return 'https://127.0.0.1/' . $pathname;
       } else {
-          return 'https://127.0.0.1/api/';
+          return APP_PATH_WEBROOT_FULL . $pathname;
       }
   }
 
+    /**
+     * returns the servername that should be used
+     * @return string
+     */
+    public function getRedcapServerAlias():string {
+        return $this->getSystemSetting('server-type') === "development" ? '127.0.0.1' : SERVER_NAME;
+    }
+
   /**
    * sends a STARR-API GET request
    * @param $url

classes/DusterConfigClass.php

@@ -12,7 +12,7 @@
 
 class DusterConfigClass
 {
-    private $project_id, $duster_config, $module;
+    private $project_id, $duster_config, $design_config, $module;
     private $rp_info_form = array('form_name' => 'rp_info', 'form_label' => 'Researcher-Provided Information');
     private $demographics_form = array('form_name' => 'demographics', 'form_label' => 'Demographics');
 
@@ -30,17 +30,9 @@ public function loadConfig()
         $config_url = $config_url .
             ((substr($config_url, -1) === '/') ? "" : "/") . SERVER_NAME . '/' . $this->project_id
             . '?redcap_user=' . $this->module->getUser()->getUserName();
-        $this->duster_config = $this->module->starrApiGetRequest($config_url, 'ddp');
-    }
-
-    public function loadDesignConfig () {
-      // build and send GET request to config webservice
-      $config_url = $this->module->getSystemSetting("starrapi-config-url");
-      // add a '/' at the end of the url if it's not there
-      $config_url = $config_url .
-        ((substr($config_url, -1) === '/') ? "" : "/") . 'design/' . SERVER_NAME . '/' . $this->project_id
-        . '?redcap_user=' . $this->module->getUser()->getUserName();
-      $this->design_config = $this->module->starrApiGetRequest($config_url, 'ddp');
+        $config_object = $this->module->starrApiGetRequest($config_url, 'ddp');
+        $this->duster_config = json_decode($config_object['config'], true);
+        $this->design_config = json_decode($config_object['design_config'], true);
     }
 
     public function getDusterConfig()
@@ -53,9 +45,9 @@ public function getDusterConfig()
 
     public function getDesignConfig() {
       if ($this->design_config == null) {
-        $this->loadDesignConfig();
+        $this->loadConfig();
       }
-      return $this->design_config['design_config'];
+      return $this->design_config;
     }
 
     public function setDusterConfig($config)

classes/RedcapToStarrLinkConfig.php

@@ -88,7 +88,7 @@ public function configureRedcapToStarrLink($em_config) {
     /*constructs the url to call RtoStarr Link api
     @return "1" if successful*/
     private function invokeRedcapToStarrLink($action, $query) {
-        $url = APP_PATH_WEBROOT_FULL .
+        $url = $this->module->getRedcapUrl() .
             'api/?type=module&prefix=redcap_to_starr_link&page=src%2FRedcapProjectToStarrLink&NOAUTH'
             . '&action=' . $action // should be either data or records
             . '&pid=' . $this->project_id;

config.json

@@ -31,6 +31,13 @@
 				"icon": "fas fa-receipt",
 				"url": "pages/populateData.php",
 				"show-header-and-footer": true
+			},
+			{
+				"name": "DUSTER: Edit Project",
+				"key": "dustereditproject",
+				"icon": "fas fa-pen-to-square",
+				"url": "pages/editProject.php",
+				"show-header-and-footer": true
 			}
 		],
 		"control-center": [
@@ -103,10 +110,24 @@
 			"validation" : "number"
 		},
 		{
-			"key": "local-dev",
-			"name": "<b>Local Development Environment</b><br>local development flag for REDCap API URL",
-			"required": false,
-			"type": "checkbox"
+			"key": "server-type",
+			"name": "<b>Server Type</b><br>server environment flag for REDCap URL",
+			"required": true,
+			"type": "dropdown",
+			"choices": [
+				{
+					"value": "local",
+					"name": "Local"
+				},
+				{
+					"value": "development",
+					"name": "Development"
+				},
+				{
+					"value": "production",
+					"name": "Production"
+				}
+			]
 		},
 		{
 			"key": "enable-allowlist",

pages/editProject.php

@@ -2,6 +2,7 @@
 namespace Stanford\Duster;
 /** @var $module Duster */
 
+use Project;
 use REDCap;
 
 require_once $module->getModulePath() . "classes/DusterConfigClass.php";
@@ -12,39 +13,60 @@
 $pid = $module->getProjectId();
 $project_status = $module->getProjectStatus($pid);
 $user_rights = $module->getUser()->getRights($pid);
+$irb = $module->getProjectIrb($pid);
+$duster_config_obj = new DusterConfigClass($pid, $module);
+$design_config = $duster_config_obj->getDesignConfig();
+$has_design_config = $design_config !== NULL; // PHP 8.3 provides json_validate(), which checks if a string contains valid JSON.
 $editable = $project_status === "DEV"
     && strlen($user_rights['api_token']) === 32
     && $user_rights['api_import'] === '1'
-    && $user_rights['design'] === '1';
-
-if ($editable === true) {
-    $irb = $module->getProjectIrb($pid);
-    $duster_config_obj = new DusterConfigClass($pid, $module);
-    $design_config = json_encode($duster_config_obj->getDesignConfig());
-}
-
+    && $user_rights['design'] === '1'
+    && $has_design_config === true;
 ?>
 
 <!DOCTYPE html>
 <html lang="en">
 <h3>
     DUSTER: Edit Project
 </h3>
-<?php if ($editable === true) {
+<?php
+ if ($editable === true) {
 ?>
-    <p>Hitting the button below will launch an application where you may perform the following modifications to your project:</p>
+    Hitting the button below will launch an application where you may perform the following modifications to your project:
     <ol>
       <li>Add new Researcher-Provided Information.</li>
       <li>Select additional demographics.</li>
       <li>Add new data collection windows.</li>
       <li>Add new clinical variables to pre-existing data collection windows.</li>
       <!-- <li>Select additional aggregations to pre-existing clinical variables in data collection windows.</li> -->
     </ol>
+    <strong>It is recommended you back up your project's data in case editing this project causes any issues.</strong>
+    <br>
+    Any non-DUSTER user-performed changes made to this project's current data dictionary may be lost or conflict when editing this project.
+    <ol>
+      <li>Non-DUSTER fields and forms will remain, but they may be rearranged within the data dictionary.</li>
+      <li>If you add a new DUSTER field and its field name matches a pre-existing non-DUSTER field, the non-DUSTER field will be replaced and its data will be overwritten when DUSTER fetches data.
+        <ol>Example Scenario
+            <li>You create a DUSTER project without selecting 'Race' under Demographics.</li>
+            <li>You then add a non-DUSTER field with 'race' as its REDCap field name to any of your project's instruments.</li>
+            <li>You subsequently edit your project via DUSTER and add 'Race' under the Demographics category.</li>
+            <li>Fetching data with DUSTER will save its results for 'Race' into the 'race' REDCap field, overwriting what was previously saved.</li>
+        </ol>
+      </li>
+    </ol>
+
     <button
       type="button"
       onclick="window.location = '<?php echo $module->getUrl("pages/js/duster/new-project/dist/index.html"); ?>';"
     >Launch Editor
     </button>
+
+<?php
+ } else if ($has_design_config === false) {
+    ?>
+    <strong>
+        Sorry, you cannot edit this DUSTER project. This project was created before the editing feature was released and cannot be retroactively supported.
+    </strong>
 <?php
 } else {
 ?>
@@ -88,7 +110,7 @@
         postObj['edit_mode'] = true;
         postObj['redcap_project_id'] = "<?php echo $pid; ?>";
         postObj['project_irb_number'] = "<?php echo $irb; ?>";
-        postObj['initial_design'] = <?php echo $design_config; ?>;
+        postObj['initial_design'] = <?php echo json_encode($design_config); ?>;
 
         // store URL for REDCap's 'New Project' page
         postObj['redcap_new_project_url'] = "<?php echo APP_PATH_WEBROOT_FULL . "index.php?action=create"; ?>";

pages/js/duster/new-project/dist/index.html

@@ -5,8 +5,8 @@
   <link rel="icon" href="./assets/favicon-db74ab0b.ico">
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   <title>DUSTER</title>
-  <script type="module" crossorigin src="./assets/index-66f121cc.js"></script>
-  <link rel="stylesheet" href="./assets/index-3c7798d2.css">
+  <script type="module" crossorigin src="./assets/index-39dccbbb.js"></script>
+  <link rel="stylesheet" href="./assets/index-28e3618b.css">
 </head>
 <body>
 <div id="app"></div>

pages/js/duster/new-project/src/App.vue

@@ -193,7 +193,7 @@ const rpData = ref<BasicConfig[]>([
     label:"Medical Record Number (MRN)",
     redcap_field_type:"text",
     value_type:"Identifier", // this needs to be replaced by "text" in review step
-    redcap_field_note:"8-digit number (including leading zeros, e.g., '01234567')",
+    redcap_field_note:"8-digit number (including leading zeros, e.g., '01234567') or 10-digit number (no leading zeros)",
     phi:"t",
     id: "mrn",
     duster_field_name: undefined
@@ -255,8 +255,6 @@ const initialDesign: {[key: string]:any} = ({
   collectionWindows: []
 });
 
-// const myObj: {[index: string]:any} = {}
-
 const promptRestoreAutoSave = ref<boolean>(false);
 
 onMounted(() => {
@@ -497,9 +495,8 @@ const getDusterMetadata = (metadataUrl:string) => {
 };
 
 const loadEditMode = () => {
-  initialDesign.value = JSON.parse(projectConfig.initial_design);
-  initialDesign.collectionWindows = initialDesign.value.collectionWindows;
-  initialDesign.value = JSON.parse(projectConfig.initial_design);
+  initialDesign.value = projectConfig.initial_design;
+
   // transform and load researcher-provided data
   rpData.value = initialDesign.value.rpData;
   rpData.value.forEach((rp:any) => {
@@ -518,6 +515,7 @@ const loadEditMode = () => {
   }
 
   // load data collection windows
+  initialDesign.collectionWindows = projectConfig.initial_design.collectionWindows;
   collectionWindows.value = initialDesign.value.collectionWindows;
 };
 

pages/js/duster/new-project/src/components/ReviewPanel.vue

@@ -151,13 +151,54 @@
           :label="editMode ? 'Update Project' : 'Create Project'"
           icon="pi pi-check"
           severity="success"
-          @click="editMode ? updateProject() : createProject()"
+          @click="editMode ? showConfirmUpdateDialog = true : createProject()"
         />
       </template>
     </Toolbar>
   </Panel>
   <Dialog
-    v-model:visible="showCreateProjectDialog"
+    :visible="showConfirmUpdateDialog"
+    modal
+    :closable="false"
+    :style="{ width: '50vw'}"
+    header="Update Project"
+  >
+    <div
+    >
+      Are you sure you want to update this project?
+      <br>
+      <strong>It is recommended you back up your project's data in case editing this project causes any issues.</strong>
+      <br>
+      Bear in mind any non-DUSTER user-performed changes made to this project's current data dictionary may be lost or conflict when editing this project.
+      <ol>
+        <li>Non-DUSTER fields and forms will remain, but they may be rearranged within the data dictionary.</li>
+        <li>If you add a new DUSTER field and its field name matches a pre-existing non-DUSTER field, the non-DUSTER field will be replaced and its data will be overwritten when DUSTER fetches data.
+          <ol>Example Scenario
+            <li>You create a DUSTER project without selecting 'Race' under Demographics.</li>
+            <li>You then add a non-DUSTER field with 'race' as its REDCap field name to any of your project's instruments.</li>
+            <li>You subsequently edit your project via DUSTER and add 'Race' under the Demographics category.</li>
+            <li>Fetching data with DUSTER will save its results for 'Race' into the 'race' REDCap field, overwriting what was previously saved.</li>
+          </ol>
+        </li>
+      </ol>
+    </div>
+    <template #footer>
+      <Button
+          label="No, Cancel"
+          severity="secondary"
+          @click="showConfirmUpdateDialog = false"
+          autofocus
+      />
+      <Button
+          label="Yes, Update"
+          severity="primary"
+          @click="updateProject()"
+          autofocus
+      />
+    </template>
+  </Dialog>
+  <Dialog
+    :visible="showCreateProjectDialog"
     modal
     :closable="false"
     :style="{ width: '50vw' }"
@@ -651,6 +692,7 @@ const getScoresConfig = (scoresMeta:FieldMetadata[], index:number) => {
 }
 
 const showCreateProjectDialog = ref<boolean>(false);
+const showConfirmUpdateDialog = ref<boolean>(false);
 const createProjectMessage = ref<string>("");
 const createProjectError = ref<boolean>(false);
 const systemErrorMessage = ref<string>("");
@@ -753,6 +795,7 @@ const createProject = () => {
 }
 
 const updateProject = () => {
+  showConfirmUpdateDialog.value = false;
   createProjectMessage.value = "Updating REDCap Project. Please wait.";
   showCreateProjectDialog.value = true;
   const data = {

services/createProject.php

@@ -163,7 +163,7 @@
 );
 
 $ch = curl_init();
-$api_url = $module->getRedcapApiUrl();
+$api_url = $module->getRedcapUrl("api");
 
 $module->emDebug("Create Project POST Request to REDCap API URL $api_url");
 curl_setopt($ch, CURLOPT_URL, $api_url);