Line ending changes only

tranSMART-Foundation · Feb 20, 2013 · 111efb5 · 111efb5
1 parent b490b7d
commit 111efb5
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Showing 56 changed files with 6,408 additions and 6,408 deletions.
diff --git a/LICENSE b/LICENSE
diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/BoxPlotController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/BoxPlotController.groovy
@@ -15,29 +15,29 @@
 ******************************************************************/
 
 package com.recomdata.transmart.data.association
-import com.recomdata.transmart.util.ZipUtil
-import org.apache.commons.io.FileUtils
-
-class BoxPlotController {
-
-	def RModulesOutputRenderService
-
-	def boxPlotOut =
-	{
-		//This will be the array of image links.
-		def ArrayList<String> imageLinks = new ArrayList<String>()
-
-		//This will be the array of text file locations.
-		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
-
-		//Gather the image links.
+import com.recomdata.transmart.util.ZipUtil
+import org.apache.commons.io.FileUtils
+
+class BoxPlotController {
+
+	def RModulesOutputRenderService
+
+	def boxPlotOut =
+	{
+		//This will be the array of image links.
+		def ArrayList<String> imageLinks = new ArrayList<String>()
+
+		//This will be the array of text file locations.
+		def ArrayList<String> txtFiles = new ArrayList<String>()
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
+
+		//Gather the image links.
 		RModulesOutputRenderService.initializeAttributes(jobName,"BoxPlot",imageLinks)
 
-		String tempDirectory = RModulesOutputRenderService.tempDirectory
-
+		String tempDirectory = RModulesOutputRenderService.tempDirectory
+
 		//Create a directory object so we can pass it to be traversed.
 		def tempDirectoryFile = new File(tempDirectory)
 
@@ -48,10 +48,10 @@ class BoxPlotController {
 		ANOVAData = RModulesOutputRenderService.fileParseLoop(tempDirectoryFile,/.*ANOVA_RESULTS.*\.txt/,/.*ANOVA_RESULTS(.*)\.txt/,parseANOVAStr)
 		ANOVAData += RModulesOutputRenderService.fileParseLoop(tempDirectoryFile,/.*ANOVA_PAIRWISE.*\.txt/,/.*ANOVA_PAIRWISE(.*)\.txt/,parseMatrixString)
 		legendText = RModulesOutputRenderService.fileParseLoop(tempDirectoryFile,/.*legend.*\.txt/,/.*legend(.*)\.txt/,parseLegendTable)
-
-		render(template: "/plugin/boxPlot_out", model:[legendText:legendText,imageLocations:imageLinks,ANOVAData:ANOVAData,zipLink:RModulesOutputRenderService.zipLink], contextPath:pluginContextPath)
-	}
-
+
+		render(template: "/plugin/boxPlot_out", model:[legendText:legendText,imageLocations:imageLinks,ANOVAData:ANOVAData,zipLink:RModulesOutputRenderService.zipLink], contextPath:pluginContextPath)
+	}
+
 	def parseANOVAStr = {
 
 		statsInStr ->

diff --git a/...app/controllers/com/recomdata/transmart/data/association/MarkerSelectionController.groovy b/...app/controllers/com/recomdata/transmart/data/association/MarkerSelectionController.groovy
@@ -18,22 +18,22 @@ package com.recomdata.transmart.data.association
 import java.util.ArrayList;
 
 class MarkerSelectionController {
-
-	def RModulesOutputRenderService
+
+	def RModulesOutputRenderService
 
-	def markerSelectionOut = 
+	def markerSelectionOut = 
 	{
 		//This will be the array of image links.
 		def ArrayList<String> imageLinks = new ArrayList<String>()
 
 		//This will be the array of text file locations.
 		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
 
 		//Gather the image links.
-		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
+		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
 
 		String tempDirectory = RModulesOutputRenderService.tempDirectory
 
@@ -46,10 +46,10 @@ class MarkerSelectionController {
 		markerSelectionTable = RModulesOutputRenderService.fileParseLoop(tempDirectoryFile,/.*CMS.*\.TXT/,/.*CMS(.*)\.TXT/,parseMarkerSelectionStr)
 
 		render(template: "/plugin/markerSelection_out", model:[imageLocations:imageLinks,markerSelectionTable:markerSelectionTable,zipLink:RModulesOutputRenderService.zipLink], , contextPath:pluginContextPath)
-
-	}
+
+	}
 
-	def parseMarkerSelectionStr = {
+	def parseMarkerSelectionStr = {
 		inStr ->
 
 		//These are the buffers we store the HTML text in.
@@ -136,7 +136,7 @@ class MarkerSelectionController {
 		buf.append("</tbody>")
 		buf.append("</table><br /><br />")
 
-		return buf.toString()
-	}
+		return buf.toString()
+	}
 
 }
diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/PCAController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/PCAController.groovy
@@ -18,22 +18,22 @@ package com.recomdata.transmart.data.association
 import java.util.ArrayList;
 
 class PCAController {
-
-	def RModulesOutputRenderService
+
+	def RModulesOutputRenderService
 
-	def pcaOut = 
+	def pcaOut = 
 	{
 		//This will be the array of image links.
 		def ArrayList<String> imageLinks = new ArrayList<String>()
 
 		//This will be the array of text file locations.
 		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
 
 		//Gather the image links.
-		RModulesOutputRenderService.initializeAttributes(jobName,"PCA",imageLinks)
+		RModulesOutputRenderService.initializeAttributes(jobName,"PCA",imageLinks)
 
 		String tempDirectory = RModulesOutputRenderService.tempDirectory
 
@@ -94,8 +94,8 @@ class PCAController {
 		geneListTable += "</tr></table><br /><br />"
 
 		render(template: "/plugin/pca_out", model:[imageLocations:imageLinks,zipLink:RModulesOutputRenderService.zipLink,summaryTable:summaryTable,geneListTable:geneListTable],contextPath:pluginContextPath)
-
-	}
+
+	}
 
 
 	def parseComponentsSummaryStr = {

diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/RHClustController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/RHClustController.groovy
@@ -18,30 +18,30 @@ package com.recomdata.transmart.data.association
 import java.util.ArrayList;
 
 class RHClustController {
-
-	def RModulesOutputRenderService
+
+	def RModulesOutputRenderService
 
-	def heatmapOut = 
+	def heatmapOut = 
 	{
 		//This will be the array of image links.
 		def ArrayList<String> imageLinks = new ArrayList<String>()
 
 		//This will be the array of text file locations.
 		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
 
 		//Gather the image links.
-		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
+		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
 
 		String tempDirectory = RModulesOutputRenderService.tempDirectory
 
 		//Traverse the temporary directory for the LinearRegression files.
 		def tempDirectoryFile = new File(tempDirectory)
 
 		render(template: "/plugin/hclust_out", model:[imageLocations:imageLinks,zipLink:RModulesOutputRenderService.zipLink],contextPath:pluginContextPath)
-
-	}
+
+	}
 
 }
diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/RHeatmapController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/RHeatmapController.groovy
@@ -18,30 +18,30 @@ package com.recomdata.transmart.data.association
 import java.util.ArrayList;
 
 class RHeatmapController {
-
-	def RModulesOutputRenderService
+
+	def RModulesOutputRenderService
 
-	def heatmapOut = 
+	def heatmapOut = 
 	{
 		//This will be the array of image links.
 		def ArrayList<String> imageLinks = new ArrayList<String>()
 
 		//This will be the array of text file locations.
 		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
 
 		//Gather the image links.
-		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
+		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
 
 		String tempDirectory = RModulesOutputRenderService.tempDirectory
 
 		//Traverse the temporary directory for the LinearRegression files.
 		def tempDirectoryFile = new File(tempDirectory)
 
 		render(template: "/plugin/heatmap_out", model:[imageLocations:imageLinks,zipLink:RModulesOutputRenderService.zipLink],contextPath:pluginContextPath)
-
-	}
+
+	}
 
 }
diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/RKMeansController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/RKMeansController.groovy
@@ -18,30 +18,30 @@ package com.recomdata.transmart.data.association
 import java.util.ArrayList;
 
 class RKMeansController {
-
-	def RModulesOutputRenderService
+
+	def RModulesOutputRenderService
 
-	def heatmapOut = 
+	def heatmapOut = 
 	{
 		//This will be the array of image links.
 		def ArrayList<String> imageLinks = new ArrayList<String>()
 
 		//This will be the array of text file locations.
 		def ArrayList<String> txtFiles = new ArrayList<String>()
-
-		//Grab the job ID from the query string.
-		String jobName = params.jobName
+
+		//Grab the job ID from the query string.
+		String jobName = params.jobName
 
 		//Gather the image links.
-		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
+		RModulesOutputRenderService.initializeAttributes(jobName,"Heatmap",imageLinks)
 
 		String tempDirectory = RModulesOutputRenderService.tempDirectory
 
 		//Traverse the temporary directory for the LinearRegression files.
 		def tempDirectoryFile = new File(tempDirectory)
 
 		render(template: "/plugin/kclust_out", model:[imageLocations:imageLinks,zipLink:RModulesOutputRenderService.zipLink],contextPath:pluginContextPath)
-
-	}
+
+	}
 
 }
diff --git a/grails-app/controllers/com/recomdata/transmart/data/association/RModulesController.groovy b/grails-app/controllers/com/recomdata/transmart/data/association/RModulesController.groovy
@@ -14,44 +14,44 @@
 * limitations under the License.
 ******************************************************************/
 
-package com.recomdata.transmart.data.association
-
-class RModulesController {
-
-	def springSecurityService
-	def asyncJobService
-	def RModulesService
-
-	/**
-	 * Method called that will cancel a running job
-	 */
-	def canceljob = {
-		def jobName = request.getParameter("jobName")
-		def jsonResult = asyncJobService.canceljob(jobName)
-
-		response.setContentType("text/json")
-		response.outputStream << jsonResult.toString()
-	}
-
-	/**
-	 * Method that will create the new asynchronous job name
-	 * Current methodology is username-jobtype-ID from sequence generator
-	 */
-	def createnewjob = {
-		def result = asyncJobService.createnewjob(params.jobName, params.jobType)
-
-		response.setContentType("text/json")
-		response.outputStream << result.toString()
-	}
-
-
-	/**
-	 * Method that will schedule a Job 
-	 */
-	def scheduleJob = 	{
-		def jsonResult = RModulesService.scheduleJob(springSecurityService.getPrincipal().username,params)
-
-		response.setContentType("text/json")
-		response.outputStream << jsonResult.toString()
-	}
+package com.recomdata.transmart.data.association
+
+class RModulesController {
+
+	def springSecurityService
+	def asyncJobService
+	def RModulesService
+
+	/**
+	 * Method called that will cancel a running job
+	 */
+	def canceljob = {
+		def jobName = request.getParameter("jobName")
+		def jsonResult = asyncJobService.canceljob(jobName)
+
+		response.setContentType("text/json")
+		response.outputStream << jsonResult.toString()
+	}
+
+	/**
+	 * Method that will create the new asynchronous job name
+	 * Current methodology is username-jobtype-ID from sequence generator
+	 */
+	def createnewjob = {
+		def result = asyncJobService.createnewjob(params.jobName, params.jobType)
+
+		response.setContentType("text/json")
+		response.outputStream << result.toString()
+	}
+
+
+	/**
+	 * Method that will schedule a Job 
+	 */
+	def scheduleJob = 	{
+		def jsonResult = RModulesService.scheduleJob(springSecurityService.getPrincipal().username,params)
+
+		response.setContentType("text/json")
+		response.outputStream << jsonResult.toString()
+	}
 }