Merge pull request #654 from chgibb/beta-staging

Non-Interactive Figures
chgibb · Sep 15, 2017 · 04378ad · 04378ad
2 parents 5674ece + 7dfe017
commit 04378ad
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diff --git a/README.md b/README.md
@@ -9,8 +9,8 @@ PHAT is under development in the Zehbe Lab ([http://zehbelab.weebly.com/](http:/
 **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 Members:** Mitchell Pynn, Shane Liu, Jeremy Braun
+**Team Members:** Mitchell Pynn, Shane Liu, Jeremy Braun, Nick Catanzaro, Zachary Moorman
 
 **How to Cite PHAT (pre-print):**
 
-Gibb CM, Jackson R, Mohammed S, Fiaidhi J, Zehbe I. Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data. bioRxiv. https://doi.org/10.1101/178327
+Gibb CM, Jackson R, Mohammed S, Fiaidhi J, Zehbe I. Pathogen-Host Analysis Tool (PHAT): an Integrative Platform to Analyze Pathogen-Host Relationships in Next-Generation Sequencing Data. bioRxiv. https://doi.org/10.1101/178327
diff --git a/src/CheckForUpdateProcess.ts b/src/CheckForUpdateProcess.ts
@@ -1,4 +1,5 @@
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
+import * as atomic from "./req/operations/atomicOperations";
 import * as getUpdate from "./req/getLatestUpdate";
 
 let flags : CompletionFlags = new CompletionFlags();
@@ -28,7 +29,7 @@ process.on
                         data : res
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((arg : any) => {
                 console.log(arg);
                 flags.done = true;
@@ -41,7 +42,7 @@ process.on
                         data : arg
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }
@@ -58,7 +59,7 @@ process.on
             data : err.message
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 process.on("unhandledRejection",function(err : Error){
     console.log(err);
@@ -72,5 +73,5 @@ process.on("unhandledRejection",function(err : Error){
             data : err.message
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/DownloadAndInstallUpdateProcess.ts b/src/DownloadAndInstallUpdateProcess.ts
@@ -3,6 +3,7 @@ import * as cp from "child_process";
 
 let GitHubReleases = require("github-releases");
 
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {getReadable} from "./req/getAppPath";
 
@@ -71,7 +72,7 @@ process.on
                         );
                         installer.unref();
                     }
-                    process.exit(0);
+                    atomic.exitFork(0);
 
                 });
             });
@@ -90,7 +91,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 process.on("unhandledRejection",function(err : string){
     console.log("ERROR "+err);
@@ -104,5 +105,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/InputBamFileProcess.ts b/src/InputBamFileProcess.ts
@@ -106,7 +106,7 @@ process.on(
                 flags.done = true
                 flags.success = true;
                 update();
-                process.exit(0);
+                atomic.exitFork(0);
             })();
         }
     }

diff --git a/src/LinkRefSeqToAlignmentProcess.ts b/src/LinkRefSeqToAlignmentProcess.ts
@@ -98,7 +98,7 @@ process.on(
                 flags.success = true;
                 update();
 
-                process.exit(0);
+                atomic.exitFork(0);
             })();
         }
     }

diff --git a/src/OpenProjectProcess.ts b/src/OpenProjectProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {ProjectManifest} from "./req/projectManifest";
 import {openProject} from "./req//openProject";
@@ -40,7 +41,7 @@ process.on
                         flags : flags,
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((err) => {
                 flags.done = true;
                 flags.failure = true;
@@ -52,7 +53,7 @@ process.on
                         data : err
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }  
@@ -69,7 +70,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 
 process.on("unhandledRejection",function(err : string){
@@ -84,5 +85,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/RenderCoverageTrackProcess.ts b/src/RenderCoverageTrackProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {AlignData} from "./req/alignData"
 import * as cf from "./req/renderer/circularFigure";
@@ -39,7 +40,7 @@ process.on
                         }
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             });
         }
     }  
@@ -55,5 +56,5 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/RenderSNPTrackProcess.ts b/src/RenderSNPTrackProcess.ts
@@ -1,3 +1,4 @@
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {AlignData} from "./req/alignData"
 import * as cf from "./req/renderer/circularFigure";
@@ -39,7 +40,7 @@ process.on
                         }
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             });
         }
     }  
@@ -56,7 +57,7 @@ process.on
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
 
 process.on("unhandledRejection",function(err : string){
@@ -71,5 +72,5 @@ process.on("unhandledRejection",function(err : string){
             data : err
         }
     );
-    process.exit(1);
+    atomic.exitFork(1);
 });
diff --git a/src/RunAlignmentProcess.ts b/src/RunAlignmentProcess.ts
@@ -121,7 +121,7 @@ process.on(
                                                 flags.done = true;
                                                 flags.success = true;
                                                 update();
-                                                process.exit(0);
+                                                atomic.exitFork(0);
 
                                             });
                                         });

diff --git a/src/SaveCurrentProjectProcess.ts b/src/SaveCurrentProjectProcess.ts
@@ -1,11 +1,11 @@
-import {handleForkFailures} from "./req/operations/atomicOperations";
+import * as atomic from "./req/operations/atomicOperations";
 import {AtomicOperationForkEvent,CompletionFlags} from "./req/atomicOperationsIPC";
 import {ProjectManifest} from "./req/projectManifest";
 import {saveCurrentProject} from "./req//saveCurrentProject";
 
 let proj : ProjectManifest;
 let flags : CompletionFlags = new CompletionFlags();
-handleForkFailures();
+atomic.handleForkFailures();
 process.on
 (
     "message",function(ev : AtomicOperationForkEvent)
@@ -29,7 +29,7 @@ process.on
                         flags : flags,
                     }
                 );
-                process.exit(0);
+                atomic.exitFork(0);
             }).catch((err) => {
                 flags.done = true;
                 flags.failure = true;
@@ -41,7 +41,7 @@ process.on
                         data : err
                     }
                 );
-                process.exit(1);
+                atomic.exitFork(1);
             });
         }
     }  

diff --git a/src/circularGenomeBuilder.html b/src/circularGenomeBuilder.html
@@ -69,6 +69,11 @@ <h5 class="modal-title" id="modalTitle">Modal title</h5>
             					<li><a href="#" id="deleteFigure">Delete Figure</a></li>
           					</ul>
 						</li>
+						<li class="dropdown">
+							<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">Figure Options</a>
+							<ul class="dropdown-menu" id="figureOptions">
+							</ul>
+					  </li>
 						<li><a href="#" id="navBarLoadingText"></a></li>
       				</ul>
 

diff --git a/src/circularGenomeBuilderRenderer.ts b/src/circularGenomeBuilderRenderer.ts
@@ -156,25 +156,33 @@ $
                                         totalTracks++;
                                         if(ops[i].flags.done && ops[i].flags.success)
                                         {
-                                            console.log("compiled "+ops[i].uuid);
                                             if(ops[i].uuid)
                                             {
+                                                console.log("compiled "+ops[i].uuid);
                                                 tc.removeTrack(ops[i].uuid);
                                                 genomeView.firstRender = true;
                                             }
+                                            else if(ops[i].compileBase)
+                                            {
+                                                console.log("compiled base figure");
+                                                tc.resetBaseFigureSVG();
+                                                genomeView.firstRender = true;
+                                            }
                                         }
                                     }
                                 }
                             }
                             if(totalTracks > 0)
                                 document.getElementById("navBarLoadingText").innerHTML = `Recalculating ${totalTracks} tracks`;
-                            if(totalTracks == 1)
+                            if(totalTracks == 0)
                             {
-                                setTimeout(function(){
-                                    document.getElementById("navBarLoadingText").innerHTML = ``;
-                                },1000);
+                                document.getElementById("navBarLoadingText").innerHTML = ``;
                             }
                         }
+                        else if(arg.val === undefined)
+                        {
+                            document.getElementById("navBarLoadingText").innerHTML = ``;
+                        }
                     }
                 }
                 viewMgr.render();

diff --git a/src/compileTemplatesProcess.ts b/src/compileTemplatesProcess.ts
@@ -81,8 +81,9 @@ function compileAndSend()
         data : {
             figure : figure
         }
+    },function(){
+        process.exit(0);
     });
-    process.exit(0);
 }
 
 process.on(

diff --git a/src/guiTests/req/closeToolBar.ts b/src/guiTests/req/closeToolBar.ts
@@ -11,7 +11,6 @@ export async function closeToolBar() : Promise<void>
                 {
                     console.log("Failed to open tool bar!");
                     console.log(toolBar);
-                    //process.exit(1);
                 }
                 toolBar[0].close();
                 resolve();

diff --git a/src/req/operations/CheckForUpdate.ts b/src/req/operations/CheckForUpdate.ts
@@ -23,38 +23,26 @@ export class CheckForUpdate extends atomic.AtomicOperation
         this.closeLogOnSuccess = true;
         this.logRecord = atomic.openLog(this.name,"Check for Update");
         let self = this;
-        this.checkForUpdateProcess = cp.fork(getReadable("CheckForUpdate.js"));
-        this.addPID(this.checkForUpdateProcess.pid);
-        this.checkForUpdateProcess.on(
-            "message",function(ev : AtomicOperationForkEvent)
+        this.checkForUpdateProcess = atomic.makeFork("CheckForUpdate.js",<AtomicOperationForkEvent>{
+            setData : true,
+            data : <AtomicOperationIPC>{}
+        },function(ev : AtomicOperationForkEvent){
+            self.logObject(ev);
+            if(ev.finishedSettingData == true)
             {
-                self.logObject(ev);
-                if(ev.finishedSettingData == true)
-                {
-                    self.checkForUpdateProcess.send(
-                        <AtomicOperationForkEvent>{
-                            run : true
-                        }
-                    );
-                }
-                if(ev.update == true)
-                {
-                    self.extraData = ev.data;
-                    self.flags = ev.flags;
-                    self.update();
-                }
-            }
-        );
-        setTimeout(
-            function(){
                 self.checkForUpdateProcess.send(
                     <AtomicOperationForkEvent>{
-                        setData : true,
-                        data : <AtomicOperationIPC>{
-                        }
+                        run : true
                     }
                 );
-            },500
-        );
+            }
+            if(ev.update == true)
+            {
+                self.extraData = ev.data;
+                self.flags = ev.flags;
+                self.update();
+            }    
+        });
+        this.addPID(this.checkForUpdateProcess.pid);
     }
 }