Merge pull request #58 from bd2kccd/development

Merge final version 1.3.4 to master.

README.md

@@ -17,28 +17,28 @@ If you want to host the application with your own hardware, follow the instructi
 #### Dependencies
 Download and uncompress the source code for each of following dependencies:
 
-* [ccd-job-queue-0.1.6](https://github.com/bd2kccd/ccd-job-queue/releases/tag/v0.1.6)
-* [ccd-mail-0.2.2](https://github.com/bd2kccd/ccd-mail/releases/tag/v0.2.2)
-* [ccd-db-0.6.3](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.3)
+* [ccd-job-queue-0.1.7](https://github.com/bd2kccd/ccd-job-queue/releases/tag/v0.1.7)
+* [ccd-mail-0.2.3](https://github.com/bd2kccd/ccd-mail/releases/tag/v0.2.3)
+* [ccd-db-0.6.4](https://github.com/bd2kccd/ccd-db/releases/tag/v0.6.4)
 * [ccd-commons-0.3.1](https://github.com/bd2kccd/ccd-commons/releases/tag/v0.3.1)
 To install the dependencies, go to the top directory of each project and do a maven install by typing **mvn install**.
 
 #### Application
-Download and uncompress the application source code  [causal-web-1.3.1](https://github.com/bd2kccd/causal-web/releases/tag/v1.3.1).  To compile and build the application, go to the directory **causal-web-1.3.1** and type **mvn package**.
+Download and uncompress the application source code  [causal-web-1.3.4](https://github.com/bd2kccd/causal-web/releases/tag/v1.3.4).  To compile and build the application, go to the directory **causal-web-1.3.4** and type **mvn package**.
 
 #### External Dependencies
-* [causal-cmd-6.0.1-SNAPSHOT-jar-with-dependencies.jar](https://github.com/cmu-phil/tetrad/releases/tag/v6.0.1-20161122)
+* [causal-cmd-0.1.2-jar-with-dependencies.jar](https://github.com/bd2kccd/causal-cmd/releases/tag/v0.1.2)
 
 ## Configure the software
 
 ### Setup the directory structure and copy libraries
 First, you need to create a workspace for the application to work in.  Create a directory called **workspace**, for an example ***/home/tuser/workspace***.  
 Inside the workspace directory, create another folder called **lib**, for example ***/home/tuser/workspace/lib***.  
 
-Copy the **causal-cmd-6.0.1.jar** to the  **workspace/lib** folder.
+Copy the **causal-cmd-0.1.2-jar-with-dependencies.jar** to the  **workspace/lib** folder.
 
 ### Configure
-There are 4 configuration files to configure located in causal-web-1.3.1/src/main/resources folder:
+There are 4 configuration files to configure located in causal-web-1.3.4/src/main/resources folder:
 1. **application-hsqldb.properties**: HSQLDB database configurations (for testing only).
 2. **application-mysql.properties**: MySQL database configurations
 3. **application.properties**: Spring Boot configurations
@@ -74,15 +74,15 @@ spring.profiles.active=scheduler,mysql
 Make sure you set **ccd.server.workspace=/home/tuser/workspace** and **ccd.folder.lib=lib** in the **ccd.properties** file.
 
 ## Compile the Program
-Go to the **causal-web** directory and run the command **mvn clean package**. This will create a jar file called **causal-web-1.3.1.jar** in the **/target** folder.
+Go to the **causal-web** directory and run the command **mvn clean package**. This will create a jar file called **causal-web-1.3.4.jar** in the **/target** folder.
 
 ### Launch the Program
 ```java
-java -jar causal-web-1.3.1.jar
+java -jar causal-web-1.3.4.jar
 ```
 To give the program 4GB of memory to run on, type the follow, using the jvm options:
 ```java
-java -Xmx4G -jar causal-web-1.3.1.jar
+java -Xmx4G -jar causal-web-1.3.4.jar
 ```
 
 To launch app in the browser

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>edu.pitt.dbmi</groupId>
     <artifactId>causal-web</artifactId>
-    <version>1.3.2</version>
+    <version>1.3.4</version>
     <packaging>jar</packaging>
 
     <name>causal-web</name>

src/main/java/edu/pitt/dbmi/ccd/web/ctrl/algo/AlgorithmResultController.java

@@ -101,6 +101,7 @@ public String showPlot(
         String username = appUser.getUsername();
         List<String> categoryNames = Arrays.asList("Runtime Parameters", "Dataset", "Filters", "FGS Parameters", "Run Options", "Algorithm Parameters", "Data Validations");
         model.addAttribute("categories", algorithmResultService.extractDataCategories(fileName, username, categoryNames));
+        model.addAttribute("isPag", algorithmResultService.isPagResult(fileName, username));
 
         return PLOT_VIEW;
     }

src/main/java/edu/pitt/dbmi/ccd/web/service/algo/AlgorithmResultService.java

@@ -35,6 +35,7 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Scanner;
 import java.util.Set;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -172,6 +173,23 @@ public List<ResultFileInfo> listResultFileInfo(final String username) {
         return Arrays.asList(array);
     }
 
+    public boolean isPagResult(final String fileName, final String username) {
+        boolean isPag = false;
+
+        Path file = Paths.get(workspace, username, resultFolder, algorithmResultFolder, fileName);
+        try (Scanner scanner = new Scanner(Files.newBufferedReader(file))) {
+            scanner.nextLine();  // skip the first line
+            String line = scanner.nextLine();
+            if (line != null) {
+                isPag = line.trim().contains("GFCI");
+            }
+        } catch (IOException exception) {
+            LOGGER.error(String.format("Unable to read file '%s'.", fileName), exception);
+        }
+
+        return isPag;
+    }
+
     public Map<String, Map<String, String>> extractDataCategories(final String fileName, final String username, final List<String> categoryNames) {
         Map<String, Map<String, String>> info = new LinkedHashMap<>();
         categoryNames.forEach(key -> {

src/main/resources/banner.txt

@@ -1,7 +1,7 @@
 
- ██████╗ █████╗ ██╗   ██╗███████╗ █████╗ ██╗         ██╗    ██╗███████╗██████╗      ██╗   ██████╗    ██████╗ 
-██╔════╝██╔══██╗██║   ██║██╔════╝██╔══██╗██║         ██║    ██║██╔════╝██╔══██╗    ███║   ╚════██╗   ╚════██╗
-██║     ███████║██║   ██║███████╗███████║██║         ██║ █╗ ██║█████╗  ██████╔╝    ╚██║    █████╔╝    █████╔╝
-██║     ██╔══██║██║   ██║╚════██║██╔══██║██║         ██║███╗██║██╔══╝  ██╔══██╗     ██║    ╚═══██╗   ██╔═══╝ 
-╚██████╗██║  ██║╚██████╔╝███████║██║  ██║███████╗    ╚███╔███╔╝███████╗██████╔╝     ██║██╗██████╔╝██╗███████╗
- ╚═════╝╚═╝  ╚═╝ ╚═════╝ ╚══════╝╚═╝  ╚═╝╚══════╝     ╚══╝╚══╝ ╚══════╝╚═════╝      ╚═╝╚═╝╚═════╝ ╚═╝╚══════╝
+ ██████╗ █████╗ ██╗   ██╗███████╗ █████╗ ██╗         ██╗    ██╗███████╗██████╗      ██╗   ██████╗ ██╗  ██╗
+██╔════╝██╔══██╗██║   ██║██╔════╝██╔══██╗██║         ██║    ██║██╔════╝██╔══██╗    ███║   ╚════██╗██║  ██║
+██║     ███████║██║   ██║███████╗███████║██║         ██║ █╗ ██║█████╗  ██████╔╝    ╚██║    █████╔╝███████║
+██║     ██╔══██║██║   ██║╚════██║██╔══██║██║         ██║███╗██║██╔══╝  ██╔══██╗     ██║    ╚═══██╗╚════██║
+╚██████╗██║  ██║╚██████╔╝███████║██║  ██║███████╗    ╚███╔███╔╝███████╗██████╔╝     ██║██╗██████╔╝██╗  ██║
+ ╚═════╝╚═╝  ╚═╝ ╚═════╝ ╚══════╝╚═╝  ╚═╝╚══════╝     ╚══╝╚══╝ ╚══════╝╚═════╝      ╚═╝╚═╝╚═════╝ ╚═╝  ╚═╝

src/main/resources/ccd.properties

@@ -44,7 +44,7 @@ ccd.email.admin.sendto=${spring.mail.username}
 ccd.acct.reg.activ.required=false
 
 # LABELS
-ccd.app.title=Causal Web v1.3.2
+ccd.app.title=Causal Web v1.3.4
 ccd.app.copyright=University of Pittsburgh and Carnegie Mellon University
 
 ccd.app.agreement=TERMS AND CONDITIONS

\

src/main/resources/static/js/algo/d3jsplot.js

@@ -70,13 +70,12 @@ function plotGraph(links) {
 
     // Default distance accessor is 30
     simulation.force("link")
-            .distance(60);
+            .distance(50);
 
     // Each node conects to itself, so we can highlight this node when it's selected
     for (i = 0; i < nodes.length; i++) {
         linkedByIndex[i + "," + i] = 1;
     }
-    ;
 
     // Add all the connections based on links
     // Must call this after  simulation.force("link").links(links)
@@ -208,29 +207,25 @@ function plotGraph(links) {
     function ticked() {
         // Position nodes
         node.attr("cx", function (d) {
-            // This makes sure the nodes won't go out of the container
-            // Bounding box example: http://mbostock.github.io/d3/talk/20110921/bounding.html
-            return d.x = Math.max(nodeRadius, Math.min(svgWidth - nodeRadius, d.x));
-            //return d.x;
-        })
-                .attr("cy", function (d) {
-                    return d.y = Math.max(nodeRadius, Math.min(svgHeight - nodeRadius, d.y));
-                    //return d.y;
-                });
+                return d.x;
+            })
+            .attr("cy", function (d) {
+                return d.y;
+            });
 
         // Position links
         // Use path instead of line since IE 10 doesn't render the links correctly
         link.attr("d", positionLink).each(function () {
-            this.parentNode.insertBefore(this, this);
-        });
+                this.parentNode.insertBefore(this, this);
+            });
 
         // Position node text
         text.attr("x", function (d) {
-            return d.x + nodeRadius;
-        })
-                .attr("y", function (d) {
-                    return d.y + nodeRadius / 2;
-                });
+                return d.x - (nodeRadius / 2);
+            })
+            .attr("y", function (d) {
+                return d.y - (1.5 * nodeRadius);
+            });
     }
 
     // Position the edge link