Merge pull request #550 from chgibb/beta-staging

543, 531, Delete on Export
chgibb · Jul 25, 2017 · c0542e8 · c0542e8
2 parents 0589d9a + 35be08d
commit c0542e8
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diff --git a/README.md b/README.md
@@ -1,24 +1 @@
-[![Build Status](https://travis-ci.com/chgibb/PHAT.svg?token=zVjAYguBNwfubJJZepif&branch=master)](https://travis-ci.com/chgibb/PHAT)
-[![GPLv3 license](https://img.shields.io/badge/License-GPLv3-blue.svg)](http://perso.crans.org/besson/LICENSE.html)
-[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/Naereen/StrapDown.js/graphs/commit-activity)
-
-
-# PHAT - Pathogen Host Analysis Tool  
-### Latest Releases
-* [Windows Installer](https://github.com/chgibb/PHAT/releases/download/0.0.40/phat-win32-x64-setup.exe)  
-* [Ubuntu Linux Debian Package](https://github.com/chgibb/PHAT/releases/download/0.0.40/phat_0.0.40_amd64.deb)  
-* [Windows Portable](https://github.com/chgibb/PHAT/releases/download/0.0.40/phat-win32-x64-portable.zip)  
-* [Linux Portable](https://github.com/chgibb/PHAT/releases/download/0.0.40/phat-linux-x64-portable.tar.gz)
-#### Experimental Releases
-* [Red Hat Package Manager](https://github.com/chgibb/PHAT/releases/download/0.0.40/phat-0.0.40.x86_64.rpm)
-
-The Pathogen Host Analysis Tool (PHAT) is an application for processing and analyzing next-generation sequencing (NGS) data as it relates to relationships between pathogen and host organisms. PHAT provides quality control (QC) reporting on sequence files, alignment of sequence files against reference files, alignment viewing and Excel and comma separated values (CSV) output.
-
-PHAT is under development in the Zehbe Lab (http://zehbelab.weebly.com/) at the Thunder Bay Regional Health Research Institute (TBRHRI) and Lakehead University (LU) under the supervison of Dr. Ingeborg Zehbe. This work is supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant to Dr. Ingeborg Zehbe (#RGPIN-2015-03855) and a NSERC Alexander Graham Bell Canada Graduate Scholarship-Doctoral (CGS-D) to Robert Jackson (#454402-2014).
-
-**Project Supervisor/Principal Investigator:** Dr. Ingeborg Zehbe, LU/TBRHRI Research Chair & Senior Scientist  
-**Project Lead/Biologist:** Robert Jackson, PhD Biotech Candidate  
-**Project Lead/Software Developer:** Chris Gibb, HBSc Comp Sci Student  
-**Team Member:** Mitchell Pynn  
-**Team Member:** Shane Liu  
-**Team Member:** Jeremy Braun  
+See https://chgibb.github.io/PHATDocs/ for documentation and releases.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "phat",
-  "version": "0.0.51-beta.2",
+  "version": "0.0.51-beta.3",
   "description": "Pathogen Host Analysis Tool",
   "main": "main.js",
   "scripts": {

diff --git a/scripts/install/copyBootstrap.bash b/scripts/install/copyBootstrap.bash
@@ -0,0 +1,3 @@
+(set -o igncr) 2>/dev/null && set -o igncr; # For Cygwin on Windows compaibility
+
+cp node_modules/bootstrap/dist/css/bootstrap.min.css forDist/bootstrap.min.css
diff --git a/scripts/install/copyBootstrap.sh b/scripts/install/copyBootstrap.sh
diff --git a/scripts/install/copyMiniColorsStyles.sh → scripts/install/copyMiniColorsStyles.bash b/scripts/install/copyMiniColorsStyles.sh → scripts/install/copyMiniColorsStyles.bash
@@ -1,2 +1,4 @@
+(set -o igncr) 2>/dev/null && set -o igncr; # For Cygwin on Windows compaibility
+
 cp node_modules/@claviska/jquery-minicolors/jquery.minicolors.css forDist/styles
 cp node_modules/@claviska/jquery-minicolors/jquery.minicolors.png forDist/styles
diff --git a/src/req/QCData.ts b/src/req/QCData.ts
@@ -1,15 +1,22 @@
 import Fastq from "./fastq";
+import {getReadableAndWritable} from "./getAppPath";
 export class QCData
 {
-    public QCReport : string;
     public summary : Array<QCSummary>;
     public validID : string;
+    public reportRun : boolean;
     public constructor()
     {
-        this.QCReport = "";
+        this.reportRun = false;
         this.summary = new Array<QCSummary>();
     }
 }
+
+export function getQCReportHTML(fastq : Fastq) : string
+{
+    return getReadableAndWritable(`rt/QCReports/${fastq.uuid}/fastqc_report.html`);
+}
+
 export class QCSummary
 {
     public name : string;

diff --git a/src/req/main/main.ts b/src/req/main/main.ts
@@ -1,5 +1,7 @@
 /**
- * Bootstrap module for the main process. Requires helper modules and sets up event handlers.
+ * The heart of PHAT. Any module should be able to require this module and have a fully functioning PHAT main process. This module should 
+ * export nothing. It must be fully self contained.
+ * This behaviour is expected from integration tests. Tests will require this module and then hook into events and inspect behaviour.
  * @module req/main/main
  */
 import * as fs from "fs";

diff --git a/src/req/openProject.ts b/src/req/openProject.ts
@@ -20,6 +20,7 @@ export function openProject(
     return new Promise((resolve,reject) => {
         dataMgr.clearData();
         rimraf.sync(getReadableAndWritable("rt"));
+        rebuildRTDirectory();
 
         let projectTarBall : string;
 
@@ -52,7 +53,9 @@ export function openProject(
                         unPackedFiles++;
                         cb(totalFiles,unPackedFiles);
                         return false;
-                    }
+                    },
+                    readable : true,
+                    writable : true
                 });
                 extract.on("finish",() => {
                     if(externalProjectPath)

diff --git a/src/req/operations/GenerateQCReport.ts b/src/req/operations/GenerateQCReport.ts
@@ -117,14 +117,14 @@ export class GenerateQCReport extends atomic.AtomicOperation
 								self.abortOperationWithMessage(err);
 								return;
 							}
-							self.fastq.QCData.QCReport = self.destDir;
 							try
 							{
-								self.fastq.QCData.summary = getQCReportSummaries(`${self.fastq.QCData.QCReport}/fastqc_data.txt`);
+								self.fastq.QCData.summary = getQCReportSummaries(`${self.destDir}/fastqc_data.txt`);
+								self.fastq.QCData.reportRun = true;
 							}
 							catch(err)
 							{
-								self.abortOperationWithMessage(`Failed to get summaries for ${self.fastq.QCData.QCReport}/fastqc_data.txt
+								self.abortOperationWithMessage(`Failed to get summaries for ${self.destDir}/fastqc_data.txt
 									${err}`);
 								return;
 							}

diff --git a/src/req/operations/RunAlignment/bowTie2Align.ts b/src/req/operations/RunAlignment/bowTie2Align.ts
@@ -46,7 +46,7 @@ export function bowTie2Align(alignData : alignData,logger : atomic.AtomicOperati
             args.push(getReadable("bowtie2"));
         args.push("-x");
         args.push("\""+getReadableAndWritable(`rt/indexes/${alignData.fasta.uuid}`)+"\"");
-        if(alignData.fastqs[1] !== undefined)
+        if(alignData.fastqs[1])
         {
             args.push("-1");
             args.push(getPath(alignData.fastqs[0]));
@@ -68,7 +68,7 @@ export function bowTie2Align(alignData : alignData,logger : atomic.AtomicOperati
             invokeString += " ";
         }
         alignData.invokeString = invokeString;
-        if(alignData.fastqs[1] !== undefined)
+        if(alignData.fastqs[1])
             alignData.alias = `${alignData.fastqs[0].alias}, ${alignData.fastqs[1].alias}; ${alignData.fasta.alias}`;
         else
             alignData.alias = `${alignData.fastqs[0].alias}; ${alignData.fasta.alias}`;

diff --git a/src/req/operations/atomicOperations.ts b/src/req/operations/atomicOperations.ts
@@ -131,7 +131,8 @@ export class ForkLogger extends AtomicOperation
 export function handleForkFailures(logger? : ForkLogger,progressMessage? : string)
 {
     let signalFailure = function(err : string){
-        let flags : CompletionFlags;
+        console.log(err);
+        let flags : CompletionFlags = new CompletionFlags();
         flags.done = true;
         flags.failure = true;
         flags.success = false;

diff --git a/src/req/renderer/OutputRenderer/reportView.ts b/src/req/renderer/OutputRenderer/reportView.ts
@@ -16,6 +16,29 @@ import {renderAlignmentReportTable} from "./reportView/renderAlignmentReportTabl
 import {renderSNPPositionsTable} from "./reportView/renderSNPPositionsTable";
 import {renderMappedReadsPerContigTable} from "./reportView/renderMappedReadsPerContigTable";
 
+export class QCReportTableSortOptions
+{
+    public aliasAscending : boolean;
+    public aliasDescending : boolean;
+    public fullPathAscending : boolean;
+    public fullPathDescending : boolean;
+    public sizeInBytesAscending : boolean;
+    public sizeInBytesDescending : boolean;
+    public formattedSizeAscending : boolean;
+    public formattedSizeDescending : boolean;
+    public numberOfSequencesAscending : boolean;
+    public numberofSequencesDescending : boolean;
+    public perBaseSequenceQualityAscending : boolean;
+    public perBaseSequenceQualityDescending : boolean;
+    public perSequenceQualityScoreAscending : boolean;
+    public perSequenceQualityScoreDescending : boolean;
+    public perSequenceGCContentAscending : boolean;
+    public perSequenceGCContentDescending : boolean;
+    public sequenceDuplicationLevelsAscending : boolean;
+    public sequenceDuplicationLevelsDescending : boolean;
+    public overRepresentedSequencesAscending : boolean;
+}
+
 export function addView(arr : Array<viewMgr.View>,div : string)
 {
     arr.push(new View(div));

diff --git a/src/req/renderer/ProjectSelectionRenderer/exportProjectBrowseDialog.ts b/src/req/renderer/ProjectSelectionRenderer/exportProjectBrowseDialog.ts
@@ -1,9 +1,11 @@
 import * as fse from "fs-extra";
-
 import * as electron from "electron";
 const dialog = electron.remote.dialog;
 
-import {ProjectManifest,getTarBallPath} from "./../../projectManifest";
+const jsonFile = require("jsonfile");
+
+import * as viewMgr from "./../viewMgr";
+import {ProjectManifest,getTarBallPath,getProjectManifests} from "./../../projectManifest";
 
 export function exportProjectBrowseDialog(proj : ProjectManifest) : Promise<undefined>
 {
@@ -28,7 +30,34 @@ export function exportProjectBrowseDialog(proj : ProjectManifest) : Promise<unde
                             reject(err);
                         else
                         {
-                            resolve();
+                            let projects : Array<ProjectManifest>;
+                            projects = jsonFile.readFileSync(getProjectManifests());
+                            for(let i = 0; i != projects.length; ++i)
+                            {
+                                if(proj.uuid == projects[i].uuid)
+                                {
+                                    new Promise<void>((resolve,reject) => {
+                                        fse.remove(getTarBallPath(projects[i]),(err : Error) => {
+                                            if(err)
+                                            {
+                                                alert(`Failed to remove original project`);
+                                                reject();
+                                            }
+                                            else
+                                            {
+                                                projects.splice(i,1);
+                                                jsonFile.writeFileSync(getProjectManifests(),projects);
+                                                resolve();
+                                            }
+                                        });
+                                    }).then(() => {
+                                        viewMgr.changeView("splashView");
+                                        viewMgr.render();
+                                        resolve();
+                                    });
+                                    break;
+                                }
+                            }
                         }
                     }
                 );

diff --git a/src/req/renderer/QCRenderer/reportView.ts b/src/req/renderer/QCRenderer/reportView.ts
@@ -2,20 +2,22 @@
 import * as fs from "fs";
 
 import * as viewMgr from "./../viewMgr";
+import Fastq from "./../../fastq";
+import {getQCReportHTML} from "./../../QCData";
 
 export class ReportView extends viewMgr.View
 {
-    public report : string;
+    public fastqToReport : Fastq;
     public constructor(div : string)
     {
         super('report',div);
-        this.report = "";
+        this.fastqToReport = undefined;
     }
     onMount(){}
     onUnMount(){}
     renderView()
     {
-        if(document.getElementById('reportIsOpen') || !this.report)
+        if(document.getElementById('reportIsOpen') || !this.fastqToReport)
             return undefined;
         return `
             <div class="activeHover" id='gobackbutton' style='padding: 0px 0px 5px 20px'>
@@ -24,7 +26,7 @@ export class ReportView extends viewMgr.View
             </div>
             <div id='reportIsOpen'></div>
             ${(()=>{
-                return fs.readFileSync(`${this.report}/fastqc_report.html`).toString();
+                return fs.readFileSync(getQCReportHTML(this.fastqToReport)).toString();
             })()}
         `;
     }
@@ -35,7 +37,7 @@ export class ReportView extends viewMgr.View
             return;
         if(event.target.id == "goBack")
         {
-            this.report = "";
+            this.fastqToReport = undefined;
             viewMgr.changeView('summary');
             return;
         }

diff --git a/src/req/renderer/QCRenderer/summaryView.ts b/src/req/renderer/QCRenderer/summaryView.ts
@@ -41,7 +41,7 @@ export class SummaryView extends viewMgr.View
 						if(this.fastqInputs[i].checked)
 						{
 							res += `<tr>`;
-							if(this.fastqInputs[i].QCData.QCReport == "")
+							if(!this.fastqInputs[i].QCData.reportRun)
 							{
 								res += `<td  class="activeHover" style='text-align:center;'><b id='${this.fastqInputs[i].uuid}'>click to analyze</b></td>`;
 							}
@@ -91,7 +91,7 @@ export class SummaryView extends viewMgr.View
 		{
 			if(this.fastqInputs[i].uuid == event.target.id)
 			{
-				if(this.fastqInputs[i].QCData.QCReport == "")
+				if(!this.fastqInputs[i].QCData.reportRun)
 				{
 					ipc.send(
 						"runOperation",<AtomicOperationIPC>{
@@ -104,31 +104,11 @@ export class SummaryView extends viewMgr.View
 				}
 				else
 				{
-                	(<ReportView>viewMgr.getViewByName("report")).report = this.fastqInputs[i].QCData.QCReport;
+                	(<ReportView>viewMgr.getViewByName("report")).fastqToReport = this.fastqInputs[i];
 					viewMgr.changeView('report');
 				}
 			}
 		}
-		/*
-		if(!event || !event.target || !event.target.id)
-        	return;
-
-		for(let i = 0; i != this.model.QCData.length; ++i)
-		{
-			if(this.model.QCData[i].validID == event.target.id)
-			{
-				if(this.model.QCData[i].QCReport == "")
-				{
-					this.model.generateQCReport(this.model.QCData[i].name);
-					return;
-				}
-				else
-				{
-                	(<ReportView>viewMgr.getViewByName("report")).report = this.model.QCData[i].QCReport;
-					viewMgr.changeView('report');
-				}
-			}
-		}*/
 	}
 	dataChanged(){}
 }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		(set -o igncr) 2>/dev/null && set -o igncr; # For Cygwin on Windows compaibility

		cp node_modules/bootstrap/dist/css/bootstrap.min.css forDist/bootstrap.min.css