Fixes for production

app/config.yml

@@ -1,4 +1,4 @@
 threshold: 0.1
 ksize: 21
-#index_server: "http://index"
+index_server: "http://index"
 metadata_duckdb: "/data/metadata.duckdb"

app/functions.py

@@ -42,7 +42,10 @@ def getacc(signatures, config, http, threshold=0.1):
     r = http.request('POST',
                      f"{base_url}/search",
                      body=buf.getvalue(),
-                     headers={'Content-Type': 'application/json'})
+                     headers={'Content-Type': 'application/json'},
+                     timeout=300,
+                     retries=3,
+                     )
     if r.status != 200:
         raise SearchError(r.data.decode('utf-8'), r.status)
 

app/static/dashboard.js

@@ -201,7 +201,12 @@ function createdashboard(jsonData, paragraphElement, navElement) {
   // Data prep for plots  ////////////////////////////////////////////////
   //////////////////////////////////////////////////////////////////
   // Create the column definitions for the Tabulator table
-  const columns = Object.keys(jsonData[0]).map((key) => {
+  const commonKeys = Object.keys(jsonData[0]);
+  const values = Array.from({ length: commonKeys.length }, () => []);
+
+  const columns = commonKeys.map((key, j) => {
+    values[j] = jsonData.map((obj) => obj[key]);
+
     // check if columns are numeric or not
     const isNumericColumn = jsonData.every(
       (row) => !isNaN(parseFloat(row[key]))

app/templates/advanced.html

@@ -217,19 +217,51 @@ <h3 style="margin-left: 20px; margin-top: 40px">2) Select metadata</h3>
         const startTime = performance.now();
         var data = {};
 
+        const MAX_NB_RETRY = 5;
+        const RETRY_DELAY_MS = 200;
+
+        async function fetchRetry(input, init) {
+            let retryLeft = MAX_NB_RETRY;
+            while (retryLeft > 0){
+                try {
+                    return await fetch(input, init);
+                }
+                catch (err) {
+                    // TODO: callback to update UI with retry count?
+                    await sleep(RETRY_DELAY_MS)
+                }
+                finally {
+                    retryLeft -= 1;
+                }
+            }
+            throw new Error(`Too many retries`);
+        }
+
+        function sleep(delay){
+            return new Promise((resolve) => setTimeout(resolve, delay));
+        }
+
         //Do fetch request to proper route and create dashboard
-        fetch("/advanced", {
+        fetchRetry("/advanced", {
           method: "POST",
           headers: {
             "Content-Type": "application/json",
           },
           body: JSON.stringify(formdata),
         })
-          .then((response) => response.json())
-          .then((jsonData) =>
+          .then((response) =>  {
+            // TODO: update UI to say we have the results
+            console.log("got the data!")
+            return response.json()
+          })
+          .then((jsonData) => {
+            // TODO: update UI to say we are generating graphs
+            console.log("preparing the graphs!")
             createdashboard(jsonData, paragraphElement, navElement)
-          )
+          })
           .catch((error) => {
+            // TODO: update UI to say request failed =(
+            console.log("oops, request failed =(")
             console.error("Error sending data to Flask server:", error);
           });
       });

app/templates/examples.html

@@ -177,19 +177,51 @@ <h6>Refresh the page to try a different genome.</h6>
           formdata = Pelagi_sig;
         }
 
+        const MAX_NB_RETRY = 5;
+        const RETRY_DELAY_MS = 200;
+
+        async function fetchRetry(input, init) {
+            let retryLeft = MAX_NB_RETRY;
+            while (retryLeft > 0){
+                try {
+                    return await fetch(input, init);
+                }
+                catch (err) {
+                    // TODO: callback to update UI with retry count?
+                    await sleep(RETRY_DELAY_MS)
+                }
+                finally {
+                    retryLeft -= 1;
+                }
+            }
+            throw new Error(`Too many retries`);
+        }
+
+        function sleep(delay){
+            return new Promise((resolve) => setTimeout(resolve, delay));
+        }
+
         //Do fetch request to proper route and create dashboard
-        fetch("/", {
+        fetchRetry("/", {
           method: "POST",
           headers: {
             "Content-Type": "application/json",
           },
           body: JSON.stringify(formdata),
         })
-          .then((response) => response.json())
-          .then((jsonData) =>
+          .then((response) =>  {
+            // TODO: update UI to say we have the results
+            console.log("got the data!")
+            return response.json()
+          })
+          .then((jsonData) => {
+            // TODO: update UI to say we are generating graphs
+            console.log("preparing the graphs!")
             createdashboard(jsonData, paragraphElement, navElement)
-          )
+          })
           .catch((error) => {
+            // TODO: update UI to say request failed =(
+            console.log("oops, request failed =(")
             console.error("Error sending data to Flask server:", error);
           });
       });

app/templates/index.html

@@ -123,19 +123,51 @@ <h6>
         const startTime = performance.now();
         var data = {};
 
+        const MAX_NB_RETRY = 5;
+        const RETRY_DELAY_MS = 200;
+
+        async function fetchRetry(input, init) {
+            let retryLeft = MAX_NB_RETRY;
+            while (retryLeft > 0){
+                try {
+                    return await fetch(input, init);
+                }
+                catch (err) {
+                    // TODO: callback to update UI with retry count?
+                    await sleep(RETRY_DELAY_MS)
+                }
+                finally {
+                    retryLeft -= 1;
+                }
+            }
+            throw new Error(`Too many retries`);
+        }
+
+        function sleep(delay){
+            return new Promise((resolve) => setTimeout(resolve, delay));
+        }
+
         //Do fetch request to proper route and create dashboard
-        fetch("/", {
+        fetchRetry("/", {
           method: "POST",
           headers: {
             "Content-Type": "application/json",
           },
           body: JSON.stringify(formdata),
         })
-          .then((response) => response.json())
-          .then((jsonData) =>
+          .then((response) =>  {
+            // TODO: update UI to say we have the results
+            console.log("got the data!")
+            return response.json()
+          })
+          .then((jsonData) => {
+            // TODO: update UI to say we are generating graphs
+            console.log("preparing the graphs!")
             createdashboard(jsonData, paragraphElement, navElement)
-          )
+          })
           .catch((error) => {
+            // TODO: update UI to say request failed =(
+            console.log("oops, request failed =(")
             console.error("Error sending data to Flask server:", error);
           });
       });