Release 0.0.2:

- Include the log panel
CNIC-Proteomics · Sep 20, 2019 · 63a47ac · 63a47ac
1 parent 2ebe7d0
commit 63a47ac
Show file tree

Hide file tree

Showing 14 changed files with 390 additions and 176 deletions.
diff --git a/app/assets/css/main.css b/app/assets/css/main.css
@@ -101,3 +101,56 @@ section.tab-content > .form-inline {
 #processor button#stop {
     margin-left: 0.1em;
 }
+
+/* loader */
+.loading-page {
+    z-index: 10000;
+    background: transparent;
+    width: 99%;
+    height: 99%;
+    position: absolute;
+    display: none;
+}
+.loading-icon {
+    position: absolute;
+    left: 50%;
+    top: 50%;
+    z-index: 1;
+    width: 150px;
+    height: 150px;
+    margin: -75px 0 0 -75px;
+    border: 16px solid #f3f3f3;
+    border-radius: 50%;
+    border-top: 16px solid goldenrod;
+    width: 120px;
+    height: 120px;
+    -webkit-animation: spin 2s linear infinite;
+    animation: spin 2s linear infinite;
+}
+@-webkit-keyframes spin {
+    0% { -webkit-transform: rotate(0deg); }
+    100% { -webkit-transform: rotate(360deg); }
+}
+@keyframes spin {
+    0% { transform: rotate(0deg); }
+    100% { transform: rotate(360deg); }
+}
+
+/* Add animation to "page content" */
+.animate-bottom {
+    position: relative;
+    -webkit-animation-name: animatebottom;
+    -webkit-animation-duration: 1s;
+    animation-name: animatebottom;
+    animation-duration: 1s
+}
+
+@-webkit-keyframes animatebottom {
+    from { bottom:-100px; opacity:0 } 
+    to { bottom:0px; opacity:1 }
+}
+
+@keyframes animatebottom { 
+    from{ bottom:-100px; opacity:0 } 
+    to{ bottom:0; opacity:1 }
+}
diff --git a/app/processes.html b/app/processes.html
@@ -23,7 +23,7 @@
 <body>
   <header></header>
 
-  <section class="processes" id="processes"></section>
+  <section class="logger" id="logger"></section>
 
   <section class="processor" id="processor"></section>
 

diff --git a/app/renderer-process/exceptor.js b/app/renderer-process/exceptor.js
@@ -8,6 +8,23 @@ function showMessageBox(head, message, end=false) {
   }
 };
 
-// We assign properties to the `module.exports` property, or reassign `module.exports` it to something totally different.
-// In  the end of the day, calls to `require` returns exactly what `module.exports` is set to.
-module.exports.showMessageBox = showMessageBox;
+function loadingWorkflow() {
+  $(`.loading-page`).show();
+  $(document.body).css({'cursor' : 'wait'});
+  $(`#main`).css({'opacity' : 0.5});
+  $(`#executor`).css({'opacity' : 0.5});
+}
+
+function stopLoadingWorkflow() {
+  $(`.loading-page`).hide();
+  $(document.body).css({'cursor' : 'default'});
+  $(`#main`).css({'opacity' : 1});
+  $(`#executor`).css({'opacity' : 1});
+}
+
+// Exporting modules
+module.exports = {
+  showMessageBox:      showMessageBox,
+  loadingWorkflow:     loadingWorkflow,
+  stopLoadingWorkflow: stopLoadingWorkflow
+};
diff --git a/app/renderer-process/executor.js b/app/renderer-process/executor.js
@@ -0,0 +1,78 @@
+/*
+  Global variables
+*/
+let importer = require('./imports');
+let exceptor = require('./exceptor');
+let sessioner = require('./sessioner');
+let path = require('path');
+let cProcess = require('child_process');
+let proc = null;
+
+
+// Exec process
+function execSyncProcess(cmd) {
+    try {
+        console.log(cmd);
+        proc = cProcess.execSync(cmd);
+    } catch (ex) {
+        console.log(`stderr: ${ex.error}`);
+        exceptor.stopLoadingWorkflow();
+        exceptor.showMessageBox('Error Message', `${ex.error}`);
+    }
+};
+
+function execProcess(cmd, log, wfname) {
+    // eexecute command line
+    console.log(cmd);
+    proc = cProcess.exec(cmd);
+
+    // save the process id in the session storage
+    sessioner.addProcessesToSession(proc.pid, log, wfname, `${__dirname}/../processes.html`);
+
+    // Handle on stderr
+    proc.stderr.on('data', (data) => {
+        console.log(`stderr: ${data}`);
+        exceptor.stopLoadingWorkflow();
+        exceptor.showMessageBox('Error Message', `${data}`);
+    });
+
+    // Handle on exit event
+    proc.on('close', (code) => {
+        console.log(`Child exited with code ${code}`);
+        exceptor.stopLoadingWorkflow();
+    });  
+};
+
+
+/*
+ * Events
+ */
+// Execute process
+if ( document.querySelector('#executor #start') !== null ) {
+    document.querySelector('#executor #start').addEventListener('click', function() {
+        // get the type of Workflow
+        let smkfile = importer.tasktable.smkfile;
+        let cfgfile = importer.tasktable.cfgfile;
+        // get the name of workflow
+        let wfname = path.basename(cfgfile, '.json');
+        // Check and retrieves parameters depending on the type of workflow
+        let params = importer.parameters.createParameters(cfgfile);
+        if ( params ) {
+            // loading...
+            exceptor.loadingWorkflow();
+            // Execute the workflow
+            setTimeout(function() {
+                let cmd_smk    = `"${process.env.ISANXOT_PYTHON3x_HOME}/tools/Scripts/snakemake.exe" --configfile "${params.cfgfile}" --snakefile "${smkfile}" --cores ${params.nthreads} --directory "${params.outdir}" --rerun-incomplete`;
+                let cmd_unlock = `${cmd_smk} --unlock `;
+                let cmd_clean  = `${cmd_smk}  --cleanup-metadata "${smkfile}"`;
+                // Sync process that Unlock the output directory
+                // First we unlock the ouput directory
+                let cmd1 = `${cmd_unlock} && ${cmd_clean}`
+                execSyncProcess(cmd1);
+                // Then, we execute the workflow
+                let cmd2 = `${cmd_smk} > "${params.logfile}" 2>&1`;
+                execProcess(cmd2, params.logfile, wfname);    
+            }, 1000); // due the execSync block everything, we have to wait until loading event is finished
+        }
+    });
+}
diff --git a/app/renderer-process/imports.js b/app/renderer-process/imports.js
@@ -27,8 +27,10 @@ function importHTMLtemplate(wfhref) {
 // Import main templates
 importHTMLtemplate(`${__dirname}/../sections/footer.html`);
 importHTMLtemplate(`${__dirname}/../sections/executor.html`);
+importHTMLtemplate(`${__dirname}/../sections/executor.html`);
 importHTMLtemplate(`${__dirname}/../sections/processor.html`);
-importHTMLtemplate(`${__dirname}/../sections/processes.html`);
+importHTMLtemplate(`${__dirname}/../sections/logger.html`);
+importHTMLtemplate(`${__dirname}/../sections/loader.html`);
 importHTMLtemplate(`${__dirname}/../sections/advance/help_adv.html`);
 importHTMLtemplate(`${__dirname}/../sections/lblfree/help_lblfree.html`);
 
@@ -52,8 +54,9 @@ if ( wfid !== undefined ) {
         var parameters = require('./lblfree/parameters');
         require('./lblfree/samples');
     }
-    // add the module to process the jobs
-    require('./processor');
+    // add the module to execute the jobs
+    // require('./processor');
+    require('./executor');
 
     // Export the In  the end of the day, calls to `require` returns exactly what `module.exports` is set to.
     module.exports.tasktable = tasktable;

diff --git a/app/renderer-process/logger.js b/app/renderer-process/logger.js
@@ -3,7 +3,14 @@ class log {
     this.pid  = pid;
     this.file = file;
     this.name = name;
-  } 
+  }
+  readLogFile() {
+    fs.readFile(this.file, 'utf8', function(err, contents) {
+      console.log(this.file);
+      console.log(contents);
+    });
+    console.log('after calling readFile');  
+  }
 }
 
 // class logger extends log {