Merge pull request #142 from camicroscope/develop

For 3.10.0
camicroscope · Oct 25, 2022 · 945e448 · 945e448
2 parents aece38e + f6ce363
commit 945e448
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Showing 12 changed files with 263 additions and 423 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,11 +1,11 @@
-FROM node:16-stretch-slim
-RUN apt-get update  &&  apt-get upgrade -y  &&  apt-get install -y git build-essential python3
+FROM node:14-alpine
 RUN mkdir /src
 COPY . /src
 WORKDIR /src
 RUN npm install
 ARG viewer
 ARG fork
+RUN apk add --no-cache git
 RUN git clone https://github.com/${fork:-camicroscope}/camicroscope.git --branch=${viewer:-master}
 EXPOSE 4010
 

diff --git a/caracal.js b/caracal.js
@@ -14,21 +14,15 @@ const fs = require('fs');
 const auth = require('./handlers/authHandlers.js');
 const monitor = require('./handlers/monitorHandlers.js');
 const userFunction = require('./handlers/userFunction.js');
-const iipHandler = require('./handlers/iipHandler.js');
+const iipHandlers = require('./handlers/iipHandler.js');
+const pdbIipHandlers = require('./handlers/pathdbIipHandler.js');
 const proxyHandler = require('./handlers/proxyHandler.js');
 const permissionHandler = require('./handlers/permssionHandler.js');
 const dataHandlers = require('./handlers/dataHandlers.js');
+const fileHandlers = require('./handlers/fileHandlers.js');
 const sanitizeBody = require('./handlers/sanitizeHandler.js');
 const DataTransformationHandler = require('./handlers/dataTransformationHandler.js');
 
-// TODO -- make optional
-const DISABLE_TF = true; // DUE TO PRODUCTION STABILITY ISSUES WITH TFJS
-
-if (!DISABLE_TF) {
-  const DataSet = require('./handlers/datasetHandler.js');
-  const Model = require('./handlers/modelTrainer.js');
-}
-
 
 const {connector} = require("./service/database/connector");
 
@@ -74,7 +68,7 @@ var HANDLERS = {
   "loginHandler": function() {
     return auth.loginHandler(auth.PUBKEY);
   },
-  "loginWithHeader": auth.loginWithHeader,
+  "loginWithHeader": auth.loginWithHeader(auth.PRIKEY, userFunction),
   "sanitizeBody": function() {
     return sanitizeBody;
   },
@@ -88,8 +82,15 @@ var HANDLERS = {
   "permissionHandler": permissionHandler,
   "editHandler": auth.editHandler,
   "proxyHandler": proxyHandler,
+  "writeFile": fileHandlers.writeFile,
   "iipHandler": function() {
-    return iipHandler;
+    return iipHandlers.iipHandler;
+  },
+  "preIip": function() {
+    return iipHandlers.preIip;
+  },
+  "iipCheck": function() {
+    return pdbIipHandlers.iipCheck;
   },
   "markMulti": function() {
     return dataHandlers.Mark.multi;
@@ -120,22 +121,16 @@ var HANDLERS = {
   },
 };
 
-if (!DISABLE_TF) {
-  HANDLERS["getDataset"] = DataSet.getDataset;
-  HANDLERS["trainModel"] = Model.trainModel;
-  HANDLERS["deleteDataset"] = DataSet.deleteData;
-  HANDLERS["sendTrainedModel"] = Model.sendTrainedModel;
-} else {
-  function disabledRoute() {
-    return function(req, res) {
-      res.status(500).send('{"err":"This TF route is disabled"}');
-    };
-  }
-  HANDLERS["getDataset"] = disabledRoute;
-  HANDLERS["trainModel"] = disabledRoute;
-  HANDLERS["deleteDataset"] = disabledRoute;
-  HANDLERS["sendTrainedModel"] = disabledRoute;
+// TODO! -- remove these by fully depreciating tfjs serverside
+function disabledRoute() {
+  return function(req, res) {
+    res.status(500).send('{"err":"This TF route is disabled"}');
+  };
 }
+HANDLERS["getDataset"] = disabledRoute;
+HANDLERS["trainModel"] = disabledRoute;
+HANDLERS["deleteDataset"] = disabledRoute;
+HANDLERS["sendTrainedModel"] = disabledRoute;
 
 // register configurable services
 // TODO verify all
@@ -227,10 +222,14 @@ function masterHandler() {
   }).then(()=>{
     if (RUN_INDEXER) {
       const indexer = require('./idx_mongo.js');
-      indexer.collections();
-      indexer.indexes();
-      indexer.defaults();
-      console.log("added indexes");
+      try {
+        indexer.collections();
+        indexer.indexes();
+        indexer.defaults();
+        console.log("added indexes");
+      } catch (e) {
+        console.log("error in indexer, ", e);
+      }
     }
   }).catch((e) => {
     console.error(e);

diff --git a/handlers/authHandlers.js b/handlers/authHandlers.js
@@ -264,32 +264,34 @@ function firstSetupUserSignupExists() {
 }
 
 // Use a trusted header instead of a jwt for login. Use carefully if at all.
-function loginWithHeader(header, signKey, userFunction) {
-  return function(req, res) {
-    // get the correct header, set it to use userFunction
-    let token = {"email": req.headers[header]};
-    // login using that
-    userFunction(token).then((x) => {
-      if (x === false) {
-        res.status(401).send({
-          'err': 'User Unauthorized',
-        });
-      } else {
-        data = x;
-        delete data['exp'];
-        // sign using the mounted key
-        var token = jwt.sign(data, signKey, {
-          algorithm: 'RS256',
-          expiresIn: EXPIRY,
-        });
-        res.send({
-          'token': token,
-        });
-      }
-    }).catch((e) => {
-      console.log(e);
-      res.status(401).send(e);
-    });
+function loginWithHeader(signKey, userFunction) {
+  return function(header) {
+    return function(req, res) {
+      // get the correct header, set it to use userFunction
+      let token = {"email": req.headers[header]};
+      // login using that
+      userFunction(token).then((x) => {
+        if (x === false) {
+          res.status(401).send({
+            'err': 'User Unauthorized',
+          });
+        } else {
+          data = x;
+          delete data['exp'];
+          // sign using the mounted key
+          var token = jwt.sign(data, signKey, {
+            algorithm: 'RS256',
+            expiresIn: EXPIRY,
+          });
+          res.send({
+            'token': token,
+          });
+        }
+      }).catch((e) => {
+        console.log(e);
+        res.status(401).send(e);
+      });
+    };
   };
 }
 
@@ -299,6 +301,7 @@ auth.tokenTrade = tokenTrade;
 auth.filterHandler = filterHandler;
 auth.loginHandler = loginHandler;
 auth.editHandler = editHandler;
+auth.getToken = getToken;
 auth.firstSetupUserSignupExists = firstSetupUserSignupExists;
 auth.loginWithHeader = loginWithHeader;
 auth.CLIENT = CLIENT;

diff --git a/handlers/datasetHandler.js b/handlers/datasetHandler.js
diff --git a/handlers/fileHandlers.js b/handlers/fileHandlers.js
@@ -0,0 +1,14 @@
+const fs = require('fs').promises;
+const uuid = require("uuid");
+
+// write a file containing the request body
+function writeFile(path, prefix) {
+  return function(req, res, next) {
+    let fn = prefix + "_" + uuid.v4() + ".json";
+    fs.writeFile(path + fn, req.body).then(()=>next()).catch((e) => next(e));
+  };
+};
+
+fileHandlers = {};
+fileHandlers.writeFile = writeFile;
+module.exports = fileHandlers;