Merge pull request #641 from chgibb/beta-staging

Loading Text for BAM Importing and Ref Indexing

scripts/opt/optIIFE.bash

@@ -7,6 +7,7 @@ if [[ "$OSTYPE" == "cygwin" ]]; then
 fi
 if [[ "$APPVEYOR" == "true" ]]; then
     exit 0
+fi
 for f in $target/*.js
 do
     if [[ "$f" != "$target/pileup.js" ]]; then

scripts/optPackage.bash

@@ -7,9 +7,10 @@ if [[ "$OSTYPE" == "cygwin" ]]; then
 fi
 
 bash scripts/opt/collapseBundle.bash
-bash scripts/opt/optIIFE.bash
+
 #bash scripts/opt/asi.bash
 bash scripts/opt/minify.bash
+bash scripts/opt/optIIFE.bash
 
 cd "$target"
 

src/AlignRenderer.ts

@@ -34,7 +34,15 @@ $
                 replyChannel : "align"
             }
         );
-
+        ipc.send(
+            "getKey",
+            <GetKeyEvent>{
+                action : "getKey",
+                channel : "application",
+                key : "operations",
+                replyChannel : "align"
+            }
+        );
         ipc.send(
             "keySub",
             <KeySubEvent>{

src/InputBamFileProcess.ts

@@ -60,20 +60,25 @@ process.on(
         {
             (async function(){
                 progressMessage = "Copying BAM";
+                update();
                 await new Promise<void>((resolve,reject) => {
                     fse.copySync(bamPath,getUnSortedBam(align));
                     resolve();
                 });
                 progressMessage = "Sorting BAM";
+                update();
                 await samToolsSort(align,logger);
 
                 progressMessage = "Getting Flag Statistics";
+                update();
                 await samToolsFlagStat(align,logger);
 
                 progressMessage = "Generating index";
+                update();
                 await samToolsIndex(align,logger);
 
                 progressMessage = "Getting mapped reads";
+                update();
                 await samToolsIdxStats(align,logger);
 
                 flags.done = true

src/InputRenderer.ts

@@ -8,6 +8,13 @@ import * as viewMgr from "./req/renderer/viewMgr";
 import * as masterView from "./req/renderer/inputRenderer/masterView";
 import * as fastqView from "./req/renderer/inputRenderer/FastqView";
 import * as fastaView from "./req/renderer/inputRenderer/FastaView";
+
+import {AtomicOperation} from "./req/operations/atomicOperations";
+import {IndexFastaForAlignment} from "./req/operations/indexFastaForAlignment";
+import {IndexFastaForVisualization} from "./req/operations/indexFastaForVisualization";
+import {InputBamFile} from "./req/operations/InputBamFile";
+import {LinkRefSeqToAlignment} from "./req/operations/LinkRefSeqToAlignment";
+
 import * as $ from "jquery";
 (<any>window).$ = $;
 require("./req/renderer/commonBehaviour");
@@ -65,6 +72,15 @@ $
                 action : "getKey"
             }
         );
+        ipc.send(
+            "getKey",
+            <GetKeyEvent>{
+                action : "getKey",
+                channel : "application",
+                key : "operations",
+                replyChannel : "input"
+            }
+        );
 
         //subscribe to changes in data
         ipc.send(
@@ -94,6 +110,16 @@ $
                 action : "keySub"
             }
         );
+        ipc.send(
+            "keySub",
+            <KeySubEvent>{
+                action : "keySub",
+                channel : "application",
+                key : "operations",
+                replyChannel : "input"
+            }
+        );
+
         viewMgr.render();
 
         //on message from main process
@@ -126,6 +152,31 @@ $
                             masterView.aligns = arg.val;
                         }
                     }
+                    let found = false;
+                    if(arg.key == "operations")
+                    {
+                        if(arg.val !== undefined)
+                        {
+                            let ops : Array<AtomicOperation> = arg.val;
+                            console.log(ops);
+                            for(let i = 0; i != ops.length; ++i)
+                            {
+                                if(ops[i].running)
+                                {
+                                    if(ops[i].name == "inputBamFile" || ops[i].name == "linkRefSeqToAlignment" ||
+                                    ops[i].name == "indexFastaForVisualization" || ops[i].name == "indexFastaForAlignment")
+                                    {
+                                        console.log("found input bam file");
+                                        masterView.progressMessage = ops[i].progressMessage;
+                                        found = true;
+                                        break;
+                                    }
+                                }
+                            }
+                        }
+                    }
+                    if(!found)
+                        masterView.progressMessage = "";
                     masterView.dataChanged();
                 }
                 viewMgr.render();

src/QCRenderer.ts

@@ -34,6 +34,15 @@ $
                 replyChannel : "QC"
             }
         );
+        ipc.send(
+            "getKey",
+            <GetKeyEvent>{
+                action : "getKey",
+                channel : "application",
+                key : "operations",
+                replyChannel : "QC"
+            }
+        );
         ipc.send(
             "getKey",
             <GetKeyEvent>{

src/req/main/main.ts

@@ -121,6 +121,11 @@ app.on
 		//on completion of any operation, wait and then broadcast the queue to listening windows
 		atomicOp.setOnComplete(
 			function(op : atomicOp.AtomicOperation){
+				//upon success of any operation except compiling templates to SVGs
+				if(op.flags.success && op.name != "compileTemplates")
+				{
+					dataMgr.saveData();
+				}
 				setTimeout(function(){
 					setImmediate(function(){
 						dataMgr.setKey("application","operations",atomicOp.operationsQueue);

src/req/operations/atomicOperations.ts

@@ -106,7 +106,7 @@ export abstract class AtomicOperation
 
 
     /**
-     * Indicates whether the current operation is currently executing
+     * Indicates whether the operation is currently executing
      * 
      * @type {boolean}
      * @memberof AtomicOperation

src/req/operations/indexFastaForAlignment.ts

@@ -77,14 +77,22 @@ export class IndexFastaForAlignment extends atomic.AtomicOperation
             return new Promise<void>(async (resolve,reject) => {
                 try
                 {
+                    self.progressMessage = "Building bowtie2 index";
+                    self.update();
                     await bowTie2Build(self);
                     self.setSuccess(self.bowtieFlags);
                     self.update();
 
+                    self.progressMessage = "Building fai index";
+                    self.update();
+
                     await samToolsFaidx(self.fasta,self);
                     self.setSuccess(self.faiFlags);
                     self.update();
 
+                    self.progressMessage = "Reading contigs";
+                    self.update();
+
                     //don't reparse contigs if we don't have to
                     //contigs are parsed during viz indexing as well
                     //if we reparse, we will clobber contig uuids and all references which point to them

src/req/operations/indexFastaForVisualization.ts

@@ -38,8 +38,12 @@ export class IndexFastaForVisualization extends atomic.AtomicOperation
             return new Promise<void>(async (resolve,reject) => {
                 try
                 {
+                    self.progressMessage = "Building 2bit archive";
+                    self.update();
                     await faToTwoBit(self);
                     self.setSuccess(self.twoBitFlags);
+
+                    self.progressMessage = "Reading contigs";
                     self.update();
 
                     //don't reparse contigs if we don't have to

src/req/renderer/inputRenderer/AlignView.ts

@@ -4,6 +4,7 @@ import {AlignData} from "./../../alignData";
 export class View extends viewMgr.View
 {
     public aligns : Array<AlignData>;
+    public progressMessage : string;
     public constructor(div : string)
     {
         super("alignView",div);
@@ -15,6 +16,7 @@ export class View extends viewMgr.View
     {
         return `
         <img class="topButton activeHover activeHoverButton" id="browseAlignFiles" src="${getReadable("img/browseButton.png")}"><br />
+        <p id="loadingText">${this.progressMessage}</p>
         <div id="alignTableDiv" style="width:100%;">
         <table style="width:100%;">
             <tr>

src/req/renderer/inputRenderer/FastaView.ts

@@ -4,6 +4,7 @@ import {Fasta} from "./../../fasta";
 export class View extends viewMgr.View
 {
     public fastaInputs : Array<Fasta>;
+    public progressMessage : string;
     public constructor(div : string)
     {
         super("fastaView",div);
@@ -14,7 +15,8 @@ export class View extends viewMgr.View
     public renderView() : string
     {
         return `
-        <img class="topButton activeHover activeHoverButton" id="browseFastaFiles" src="${getReadable("img/browseButton.png")}"><br />
+            <img class="topButton activeHover activeHoverButton" id="browseFastaFiles" src="${getReadable("img/browseButton.png")}"><br />
+            <p id="loadingText">${this.progressMessage}</p>
             <div id="fastaTableDiv" style="width:100%;">
                 <table style="width:100%;">
                     <tr>

src/req/renderer/inputRenderer/FastqView.ts

@@ -4,6 +4,7 @@ import Fastq from "./../../fastq";
 export class View extends viewMgr.View
 {
     public fastqInputs : Array<Fastq>;
+    public progressMessage : string;
     public constructor(div : string)
     {
         super("fastqView",div);
@@ -15,6 +16,7 @@ export class View extends viewMgr.View
     {
         return `
             <img class="topButton activeHover activeHoverButton" id="browseFastqFiles" src="${getReadable("img/browseButton.png")}"><br />
+            <p id="loadingText">${this.progressMessage}</p>
             <div id="fastqTableDiv" style="width:100%;">
                 <table style="width:100%;">
                     <tr>

src/req/renderer/inputRenderer/LinkRefView.ts

@@ -9,6 +9,7 @@ export class View extends viewMgr.View
     public inspectingAlign : AlignData;
     public fastaInputs : Array<Fasta>;
     public linkableRefSeqs : Array<LinkableRefSeq>;
+    public progressMessage : string;
     public constructor(div : string)
     {
         super("linkRefView",div);
@@ -24,6 +25,7 @@ export class View extends viewMgr.View
     {
         return `
             <img class="topButton activeHover activeHoverButton" id="linkRefViewGoBackAlignView" src="${getReadable("img/GoBack.png")}"><br />
+            <p id="loadingText">${this.progressMessage}</p>
             <br />
             <br />
             <p>Potentially Compatible References</p>

src/req/renderer/inputRenderer/masterView.ts

@@ -26,6 +26,7 @@ export class View extends viewMgr.View
     public fastaInputs : Array<Fasta>;
     public aligns : Array<AlignData>;
     public currentView : "fastqView" | "fastaView" | "alignView" | "linkRefView";
+    public progressMessage : string;
     public constructor(div : string)
     {
         super("masterView",div);
@@ -35,6 +36,7 @@ export class View extends viewMgr.View
         this.fastaInputs = new Array<Fasta>();
         this.aligns = new Array<AlignData>();
         this.currentView = "fastqView";
+        this.progressMessage = "";
     }
     public onMount() : void
     {
@@ -284,15 +286,34 @@ export class View extends viewMgr.View
     {
         let fastqView = <fastqView.View>viewMgr.getViewByName("fastqView",this.views);
         fastqView.fastqInputs = this.fastqInputs;
+        fastqView.progressMessage = this.progressMessage;
 
         let fastaView = <fastaView.View>viewMgr.getViewByName("fastaView",this.views);
         fastaView.fastaInputs = this.fastaInputs;
+        fastaView.progressMessage = this.progressMessage;
 
         let alignView = <alignView.View>viewMgr.getViewByName("alignView",this.views);
         alignView.aligns = this.aligns;
+        alignView.progressMessage = this.progressMessage;
 
         let linkRefView = <linkRefView.View>viewMgr.getViewByName("linkRefView",this.views);
         linkRefView.fastaInputs = this.fastaInputs;
+        linkRefView.progressMessage = this.progressMessage;
+        if(linkRefView.inspectingAlign && this.currentView == "linkRefView")
+        {
+            for(let i = 0; i != this.aligns.length; ++i)
+            {
+                if(this.aligns[i].uuid == linkRefView.inspectingAlign.uuid)
+                {
+                    if(this.aligns[i].fasta !== undefined)
+                    {
+                        this.currentView = "alignView";
+                        viewMgr.render();
+                        break;
+                    }
+                }
+            }
+        }
     }
 }
 export function addView(arr : Array<viewMgr.View>,div : string) : void

src/req/samToolsFlagStatReport.ts

@@ -19,7 +19,7 @@ export function samToolsFlagStatReportParser(report : string) : SamToolsFlagStat
         }
         if(/mapped/.test(lines[i]))
         {
-            let percentages = /(\d\d\d\.\d\d%)|(\d\d.\d\d%)/.exec(lines[i]);
+            let percentages = /(\d\d\d\.\d\d%)|(\d\d.\d\d%)|(\d.\d\d%)/.exec(lines[i]);
             if(percentages)
             {
                 let trimmed = percentages[0].substr(0,percentages[0].length - 1);

src/req/tests/L6R1HPV18AlignImported.ts

@@ -0,0 +1,13 @@
+import {AlignData} from "./../alignData";
+
+let L6R1HPV18AlignImported : AlignData;
+
+export function get() : AlignData
+{
+    return L6R1HPV18AlignImported;
+}
+
+export function set(align : AlignData) : void
+{
+    L6R1HPV18AlignImported = align;
+}