Merge pull request #58 from camicroscope/develop

"real" 3.8.0
camicroscope · Sep 17, 2020 · 5473792 · 5473792
2 parents 860ecca + 5c7d11e
commit 5473792
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Showing 4 changed files with 367 additions and 1 deletion.
diff --git a/.travis.yml b/.travis.yml
@@ -2,7 +2,7 @@ os: linux
 dist: xenial
 language: node_js
 node_js:
-   - "12"
+   - "14"
 install:
     - npm install
     - npm install -g mocha

diff --git a/caracal.js b/caracal.js
@@ -18,12 +18,15 @@ const dataHandlers = require('./handlers/dataHandlers.js');
 const sanitizeBody = require('./handlers/sanitizeHandler.js');
 const DataSet = require('./handlers/datasetHandler.js');
 const Model = require('./handlers/modelTrainer.js');
+const DataTransformationHandler = require('./handlers/dataTransformationHandler.js');
 // TODO validation of data
 
 var WORKERS = process.env.NUM_THREADS || 4;
 
 var PORT = process.env.PORT || 4010;
 
+var MONGO_URI = process.env.MONGO_URI || 'mongodb://localhost';
+
 const app = express();
 app.use(cookieParser());
 /** app.use(helmet.contentSecurityPolicy({
@@ -213,4 +216,7 @@ var startApp = function(app) {
 
 throng(WORKERS, startApp(app));
 
+const handler = new DataTransformationHandler(MONGO_URI, './json/configuration.json');
+handler.startHandler();
+
 module.exports = app; // for tests
diff --git a/handlers/dataTransformationHandler.js b/handlers/dataTransformationHandler.js
@@ -0,0 +1,164 @@
+const client = require("mongodb").MongoClient;
+const fs = require("fs");
+
+class DataTransformationHandler {
+  constructor(url, path) {
+    this.url = url;
+    this.filePath = path;
+    this.handler = null;
+    this.counter = 0;
+    this.max = 300;
+    this.id = 1;
+    this.idLength = 6;
+    this.isProcessing = false;
+  }
+
+  startHandler() {
+    console.log("||-- Start --||");
+    this.counter = 0;
+    this.max = 300;
+    this.id = 1;
+    this.handler = setInterval(this.connect.bind(this), 10000);
+  }
+
+  loadDefaultData() {
+    let rawdata;
+    let config;
+    try {
+      rawdata = fs.readFileSync(this.filePath);
+      config = JSON.parse(rawdata);
+    } catch (err) {
+      if (err.code == "ENOENT") {
+        console.log(`'${this.filePath}' File Fot Found!`);
+      } else {
+        throw err;
+      }
+    }
+    return config;
+  }
+
+  connect() {
+    if (this.isProcessing) {
+      return;
+    }
+    if (this.counter++ == this.max) {
+      this.cleanHandler();
+      return;
+    }
+    this.isProcessing = true;
+    const query = {config_name: "preset_label"};
+    client
+        .connect(this.url, {useNewUrlParser: true})
+        .then((dbc) => {
+          const collection = dbc.db("camic").collection("configuration");
+          collection.find(query).toArray((err, rs) => {
+            if (err) {
+              this.isProcessing = false;
+              console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+              console.log(err);
+              dbc.close();
+              this.cleanHandler();
+              return;
+            }
+            // add default data
+            if (rs.length < 1) {
+              // read default data from json
+              const defaultData = this.loadDefaultData();
+              // insert default data
+              collection.insertOne(defaultData, (err, result) => {
+                if (err) {
+                  this.isProcessing = false;
+                  console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+                  console.log(err);
+                  dbc.close();
+                  this.cleanHandler();
+                  return;
+                }
+                dbc.close();
+                // clear handler
+                this.cleanHandler();
+              });
+              return;
+            }
+
+            if (rs.length > 0 && rs[0].version != "1.0.0") {
+              const config = rs[0];
+              const list = [];
+              if (config.configuration && Array.isArray(config.configuration)) {
+                config.configuration.forEach((node) => {
+                  this.extractNode(node, list);
+                });
+              }
+              config.configuration = list;
+              config.version = '1.0.0';
+              if (!(list && list.length)) return;
+              collection.deleteOne(query, (err, result) => {
+                if (err) {
+                  this.isProcessing = false;
+                  console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+                  console.log(err);
+                  dbc.close();
+                  this.cleanHandler();
+                  return;
+                }
+                collection.insertOne(config, (err, result) => {
+                  if (err) {
+                    this.isProcessing = false;
+                    console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+                    console.log(err);
+                    dbc.close();
+                    this.cleanHandler();
+                    return;
+                  }
+                  this.isProcessing = false;
+                  console.log(`||-- The Document At The 'configuration' Collection Has Been Upgraded To Version 1.0.0 --||`);
+                  dbc.close();
+                  this.cleanHandler();
+                });
+              });
+            }
+          });
+        }).catch((err) => {
+          console.log(`||-- The 'Preset Labels' Document Upgrade Is Failed --||`);
+          console.log(err.message);
+          this.isProcessing = false;
+          if (this.max == this.counter) {
+            this.cleanHandler();
+          }
+        });
+  }
+  extractNode(node, list) {
+    if (node.children && Array.isArray(node.children)) {
+      node.children.forEach((n) => {
+        this.extractNode(n, list);
+      });
+    }
+    if (
+      node.data &&
+      (typeof node.data === "object" || typeof node.data === "function") &&
+      node.data !== null
+    ) {
+      const id = zeroFill(this.id++, this.idLength);
+      list.push({id, ...node.data});
+    }
+  }
+
+  cleanHandler() {
+    console.log("||-- Done --||");
+    this.counter = 0;
+    this.max = 300;
+    this.id = 1;
+    this.isProcessing = false;
+    clearInterval(this.handler);
+  }
+}
+
+function zeroFill(number, width) {
+  width -= number.toString().length;
+  if (width > 0) {
+    return new Array(width + (/\./.test(number) ? 2 : 1)).join("0") + number;
+  }
+  return number + "";
+}
+
+module.exports = DataTransformationHandler;
diff --git a/json/configuration.json b/json/configuration.json
@@ -0,0 +1,196 @@
+{
+	"configuration" : [
+		{
+			"id" : "001",
+			"color" : "#ff6296",
+			"mode" : "grid",
+			"type" : "Lymph-Positive",
+			"size" : 100
+		},
+		{
+			"id" : "002",
+			"color" : "#ff6296",
+			"mode" : "point",
+			"type" : "Lymph-Positive"
+		},
+		{
+			"id" : "003",			
+			"color" : "#62ffcb",
+			"mode" : "grid",
+			"type" : "Lymph-Negative",
+			"size" : 100
+		},
+		{
+			"id" : "004",
+			"color" : "#62ffcb",
+			"mode" : "point",
+			"type" : "Lymph-Negative"
+		},
+		{
+			"id" : "005",
+			"color" : "#ffcb62",
+			"mode" : "grid",
+			"type" : "Neutrophil-Positive",
+			"size" : 50
+		},
+		{
+			"color" : "#6296ff",
+			"mode" : "grid",
+			"type" : "Neutrophil-Negative",
+			"size" : 50,
+			"id" : "006"
+		},
+		{
+			"color" : "#ff00d9",
+			"mode" : "grid",
+			"type" : "Necrosis-Positive",
+			"size" : 100,
+			"id" : "007"
+		},
+		{
+			"color" : "#ff00d9",
+			"mode" : "grid",
+			"type" : "Necrosis-Positive",
+			"size" : 500,
+			"id" : "008"
+		},
+		{
+			"color" : "#00ff26",
+			"mode" : "grid",
+			"type" : "Necrosis-Negative",
+			"size" : 100,
+			"id" : "009"
+		},
+		{
+			"color" : "#00ff26",
+			"mode" : "grid",
+			"type" : "Necrosis-Negative",
+			"size" : 500,
+			"id" : "010"
+
+		},
+		{
+			"color" : "#790cff",
+			"mode" : "grid",
+			"type" : "Tumor-Positive",
+			"size" : 100,
+			"id" : "011"
+		},
+		{
+			"color" : "#790cff",
+			"mode" : "grid",
+			"type" : "Tumor-Positive",
+			"size" : 300,
+			"id" : "012"
+		},
+		{
+			"color" : "#790cff",
+			"mode" : "grid",
+			"type" : "Tumor-Positive",
+			"size" : 1000,
+			"id" : "013"
+		},
+		{
+			"color" : "#790cff",
+			"mode" : "grid",
+			"type" : "Tumor-Positive",
+			"size" : 2000,
+			"id" : "014"
+		},
+		{
+			"color" : "#92ff0c",
+			"mode" : "grid",
+			"type" : "Tumor-Negative",
+			"size" : 100,
+			"id" : "015"	
+		},
+		{
+			"color" : "#92ff0c",
+			"mode" : "grid",
+			"type" : "Tumor-Negative",
+			"size" : 300,
+			"id" : "016"
+		},
+		{
+			"color" : "#92ff0c",
+			"mode" : "grid",
+			"type" : "Tumor-Negative",
+			"size" : 1000,
+			"id" : "017"	
+		},
+		{
+			"color" : "#92ff0c",
+			"mode" : "grid",
+			"type" : "Tumor-Negative",
+			"size" : 2000,
+			"id" : "018"			
+		}, {
+			"color" : "#8dd3c7",
+			"mode" : "free",
+			"type" : "Prostate-Benign",
+			"id" : "019"
+		}, {
+			"color" : "#ffffb3",
+			"mode" : "free",
+			"type" : "Prostate-Gleason3",
+			"id" : "020"
+		}, {
+			"color" : "#bebada",
+			"mode" : "free",
+			"type" : "Prostate-Gleason4",
+			"id" : "021"	
+		}, {
+			"color" : "#fb8072",
+			"mode" : "free",
+			"type" : "Prostate-Gleason5",
+			"id" : "022"
+		}, {
+			"color" : "#80b1d3",
+			"mode" : "free",
+			"type" : "Prostate-CancerNOS",
+			"id" : "023"
+		}, {
+			"color" : "#fdb462",
+			"mode" : "free",
+			"type" : "NSCLC-Benign",
+			"id" : "024"
+		}, {
+			"color" : "#b3de69",
+			"mode" : "free",
+			"type" : "NSCLC-SquamousCA",
+			"id" : "025"
+		}, {
+			"color" : "#fccde5",
+			"mode" : "free",
+			"type" : "NSCLC-AdenoCA(all)",
+			"id" : "026"
+		}, {
+			"color" : "#d9d9d9",
+			"mode" : "free",
+			"type" : "NSCLC-Acinar",
+			"id" : "027"
+		}, {
+			"color" : "#bc80bd",
+			"mode" : "free",
+			"type" : "NSCLC-Lapidic",
+			"id" : "028"
+		}, {
+			"color" : "#ccebc5",
+			"mode" : "free",
+			"type" : "NSCLC-Solid",
+			"id" : "029"
+		}, {
+			"color" : "#ffed6f",
+			"mode" : "free",
+			"type" : "NSCLC-Papillary",
+			"id" : "030"
+		}, {
+			"color" : "#6a3d9a",
+			"mode" : "free",
+			"type" : "NSCLC-Micropapillary",
+			"id" : "031"
+		}
+	],
+	"config_name" : "preset_label",
+	"version" : "1.0.0"
+}