RubinLab · acavit · Jun 19, 2021 · Jun 22, 2021 · Jun 22, 2021 · Jun 24, 2021
diff --git a/config/index.js b/config/index.js
@@ -59,7 +59,8 @@ config.thickDb = config.thickDb || {
 };
 config.maxConcurrent = config.maxConcurrent || 5;
 config.disableStats = config.disableStats || false;
-config.statsEpad = config.statsEpad || 'https://epad-public.stanford.edu';
+config.statsEpad =
+  config.statsEpad || process.env.STATSEPAD || 'https://epadlite-public.stanford.edu';
 config.limitStudies = process.env.LIMIT_STUDIES || config.limitStudies;
 config.disableDICOMSend = process.env.DISABLE_DICOM_SEND === 'true' || config.disableDICOMSend;
 config.unassignedProjectID = config.unassignedProjectID || 'nonassigned';
@@ -82,6 +83,13 @@ if (process.env.CORS_ORIGIN) {
 }
 config.noResume = process.env.NO_RESUME === 'true' || config.noResume || false;
 config.secret = process.env.SECRET || config.secret || undefined;
+//  mail relay example. Required to register the app
+//  config.notificationEmail = { host: 'smtp.gmail.com' };
+//  config.notificationEmail = { port: 465 }; // ssl: 465 or 587
+//  config.notificationEmail.isTls = true; // use TLS
+//  config.notificationEmail.auth = {};
+//  config.notificationEmail.auth.user: 'example@gmail.com' ;
+//  config.notificationEmail.auth.pass: 'examplepass' ;
 config.precomputeReports = process.env.PRECOMPUTE_REPORTS
   ? JSON.parse(process.env.PRECOMPUTE_REPORTS)
   : config.precomputeReports || [];

diff --git a/plugins/EpadDB.js b/plugins/EpadDB.js
@@ -2772,6 +2772,7 @@ async function epaddb(fastify, options, done) {
           });
           const onlyNameValues = [];
           const foldersToBind = [];
+          let dockeroptions = {};
           for (let i = 0; i < tempPluginParams.length; i += 1) {
             if (
               tempPluginParams[i].format === 'InputFolder' ||
@@ -2794,10 +2795,66 @@ async function epaddb(fastify, options, done) {
                 onlyNameValues.push(tempPluginParams[i].default_value);
               }
             }
+
+            if (tempPluginParams[i].paramid === 'dockeroptions') {
+              let tmpArray = [];
+              switch (tempPluginParams[i].format) {
+                case 'sharedram':
+                  dockeroptions.ShmSize = tempPluginParams[i].default_value;
+                  break;
+                case 'driver':
+                  if (!dockeroptions.DeviceRequests) {
+                    dockeroptions = {
+                      ...dockeroptions,
+                      DeviceRequests: [{ Driver: tempPluginParams[i].default_value }],
+                    };
+                  } else {
+                    dockeroptions.DeviceRequests[0].Driver = tempPluginParams[i].default_value;
+                  }
+                  break;
+                case 'deviceids':
+                  // device ids need to be passed to container as array. Expect coma separated strings and convert those to an array before sending
+
+                  if (tempPluginParams[i].default_value.split(',').length >= 1) {
+                    tmpArray = tempPluginParams[i].default_value.split(',');
+                  } else {
+                    tmpArray.push(tempPluginParams[i].default_value);
+                  }
+
+                  if (!dockeroptions.DeviceRequests) {
+                    dockeroptions = {
+                      ...dockeroptions,
+                      DeviceRequests: [{ DeviceIDs: tmpArray }],
+                    };
+                  } else {
+                    dockeroptions.DeviceRequests[0].DeviceIDs = tmpArray;
+                  }
+                  break;
+                case 'capabilities':
+                  // device ids need to be passed to container as array. Expect coma separated strings and convert those to an array before sending
+
+                  if (tempPluginParams[i].default_value.split(',').length >= 1) {
+                    tmpArray = tempPluginParams[i].default_value.split(',');
+                  } else {
+                    tmpArray.push(tempPluginParams[i].default_value);
+                  }
+                  if (!dockeroptions.DeviceRequests) {
+                    dockeroptions = {
+                      ...dockeroptions,
+                      DeviceRequests: [{ Capabilities: [tmpArray] }],
+                    };
+                  } else {
+                    dockeroptions.DeviceRequests[0].Capabilities = [tmpArray];
+                  }
+                  break;
+                default:
+              }
+            }
           }
           const returnObj = {
             paramsDocker: onlyNameValues,
             dockerFoldersToBind: foldersToBind,
+            dockeroptions: { HostConfig: dockeroptions },
           };
 
           return resolve(returnObj);
@@ -3373,15 +3430,16 @@ async function epaddb(fastify, options, done) {
           fastify.nodemailer.sendMail(mailOptions, (err, info) => {
             if (err) {
               fastify.log.error(`could not send email to ${paramTo}. Error: ${err.message}`);
-              reject(new InternalError('Error Happened while senfing an email', err));
+              reject(new InternalError('Error Happened while sending an email', err));
             } else {
               fastify.log.info(`Email accepted for ${JSON.stringify(info.accepted)}`);
               resolve(info);
             }
           });
+        } else {
+          reject(new InternalError('Mail relay settings are not found', new Error('334')));
+          //  Error : 334 means –> Provide SMTP authentication credentials.
         }
-        reject(new InternalError('Mail relay settings are not found', new Error('334')));
-        //  Error : 334 means –> Provide SMTP authentication credentials.
       })
   );
 
@@ -3449,12 +3507,13 @@ async function epaddb(fastify, options, done) {
     ) {
       tempEpadStatServer = config.statsEpad;
     }
+    //  if (config.statsEpad) {
     if (!requestSenderServerName.includes(tempEpadStatServer)) {
-      const resultRemoteRegister = await Axios.post(`${config.statsEpad}/register`, {
+      const resultRemoteRegister = await Axios.post(`${config.statsEpad}/api/register`, {
         headers: {
           'Content-Type': 'application/json',
         },
-        tempBody,
+        ...tempBody,
       });
 
       fastify.log.info(
@@ -3464,7 +3523,6 @@ async function epaddb(fastify, options, done) {
       reply.code(resultRemoteRegister.code).send(resultRemoteRegister.data);
       return;
     }
-
     const tempName = request.body.name;
     const tempEmail = request.body.email;
     const tempOrganization = request.body.organization;
@@ -3498,7 +3556,7 @@ async function epaddb(fastify, options, done) {
         hostname: tempHostname,
         email: tempEmail,
         emailvalidationcode: tempGeneratedEmailValidationCode,
-        creator: request.epadAuth.username,
+        creator: 'registercall',
         createdtime: Date.now(),
         emailvalidationsent: Date.now(),
       });
@@ -3529,7 +3587,7 @@ async function epaddb(fastify, options, done) {
           emailvalidationcode: tempGeneratedEmailValidationCode,
           updatetime: Date.now(),
           emailvalidationsent: Date.now(),
-          updated_by: request.epadAuth.username,
+          updated_by: 'registercall',
         },
         {
           where: {

diff --git a/plugins/Ontology.js b/plugins/Ontology.js
@@ -260,7 +260,7 @@ async function Ontology(fastify, options, done) {
   fastify.decorate(
     'insertOntologyItemInternal',
     async (lexiconObj) =>
-      // this function need to call remote ontology server if no valid ontology apikey
+      // this function need to call remote ontology server if valid ontology apikey
       new Promise(async (resolve, reject) => {
         let returnObj = null;
         try {
@@ -270,7 +270,7 @@ async function Ontology(fastify, options, done) {
         }
         if (returnObj.code === 200) {
           try {
-            const nextindex = (await fastify.generateCodeValueInternal()) + 1;
+            //  const nextindex = (await fastify.generateCodeValueInternal()) + 1;
             const {
               codemeaning: CODE_MEANING,
               description,
@@ -284,19 +284,30 @@ async function Ontology(fastify, options, done) {
 
             const retVal = await models.lexicon.create({
               CODE_MEANING,
-              CODE_VALUE: `99EPAD_${nextindex}`,
               description,
               SCHEMA_DESIGNATOR,
               SCHEMA_VERSION,
               referenceuid,
               referencename,
               referencetype,
-              indexno: nextindex,
               creator,
               createdtime: Date.now(),
               updatetime: Date.now(),
             });
 
+            await models.lexicon.update(
+              {
+                CODE_VALUE: `99EPAD_${retVal.ID}`,
+                indexno: retVal.indexno,
+                updatetime: Date.now(),
+              },
+              {
+                where: {
+                  ID: retVal.ID,
+                },
+              }
+            );
+
             const resultInJson = {
               id: retVal.ID,
               codevalue: retVal.CODE_VALUE,
@@ -422,7 +433,7 @@ async function Ontology(fastify, options, done) {
         referencename,
         referencetype,
       } = request.body;
-      models.lexicon.update(
+      await models.lexicon.update(
         {
           CODE_MEANING,
           CODE_VALUE,
@@ -458,7 +469,7 @@ async function Ontology(fastify, options, done) {
     try {
       await fastify.validateApiKeyInternal(request);
       const { codevalue: CODE_VALUE } = request.params;
-      models.lexicon.destroy({
+      await models.lexicon.destroy({
         where: {
           CODE_VALUE,
         },

diff --git a/plugins/Other.js b/plugins/Other.js
@@ -1406,6 +1406,7 @@ async function other(fastify) {
         users: 'user',
         worklists: 'worklist',
         ontology: 'ontology',
+        register: 'register',
       };
       if (urlParts[urlParts.length - 1] === 'download') reqInfo.methodText = 'DOWNLOAD';
       if (levels[urlParts[urlParts.length - 1]]) {
@@ -1687,7 +1688,8 @@ async function other(fastify) {
       !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/epad/statistics`) && // disabling auth for put is dangerous
       !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/download`) &&
       !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/ontology`) &&
-      !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/decrypt?`) &&
+      !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/register`) &&
+      !req.raw.url.startsWith(`${fastify.getPrefixForRoute()}/decrypt?`) &
       req.method !== 'OPTIONS'
     ) {
       // if auth has been given in config, verify authentication
@@ -1927,6 +1929,7 @@ async function other(fastify) {
               break;
             case 'POST':
               if (
+                reqInfo.level !== 'register' &&
                 !fastify.hasCreatePermission(request, reqInfo.level) &&
                 !(
                   reqInfo.level === 'worklist' &&

diff --git a/utils/Docker.js b/utils/Docker.js
@@ -130,6 +130,8 @@ class DockerService {
           StdinOnce: false,
           HostConfig: {
             Binds: dockerFoldersToBind,
+            DeviceRequests: [...params.dockeroptions.HostConfig.DeviceRequests],
+            ShmSize: parseInt(params.dockeroptions.HostConfig.ShmSize, 10) || 64000000,
           },
         })
         // eslint-disable-next-line prefer-arrow-callback