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Merge pull request #16 from transmart/sascha-developments
code refactoring and bugfixing
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,6 @@ | ||
| 'use strict'; | ||
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| describe('smartRUtils', function() { | ||
| 'use strict'; | ||
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| var smartRUtils; | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,47 +1,45 @@ | ||
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| main <- function( excludedPatientIDs = integer() ) { | ||
| datapoints <- parse.input(sourceLabel="datapoints", loaded_variables=loaded_variables, type="numerical") | ||
| datapoints <- na.omit(datapoints) | ||
| colnames(datapoints)[2] <- 'value' | ||
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| subsets <- parse.input(sourceLabel="subsets", loaded_variables=loaded_variables, type="categorical") | ||
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| if (nrow(subsets) > 0) { | ||
| df <- merge(datapoints, subsets, by="patientID") | ||
| levels(df$category) <- c(levels(df$category), "no subset") | ||
| df$category[df$category == ""] <- "no subset" | ||
| } else { | ||
| df <- datapoints | ||
| df$category <- "no subset" | ||
| } | ||
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| df$jitter <- runif(nrow(df), -0.5, 0.5) | ||
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| if (! is.null(excludedPatientIDs)) { | ||
| df <- df[! df$patientID %in% excludedPatientIDs, ] | ||
| } | ||
| patientIDs <- df$patientID | ||
| main <- function(excludedPatientIDs = integer()) { | ||
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| output <- list() | ||
| output$concept <- fetch_params$ontologyTerms$datapoints_n0$fullName | ||
| output$globalMin <- min(df[,2]) | ||
| output$globalMax <- max(df[,2]) | ||
| output$categories <- unique(df$category) | ||
| output$excludedPatientIDs <- excludedPatientIDs | ||
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| for (cat in unique(df$category)) { | ||
| subset <- df[df$category == cat,] | ||
| bxp <- boxplot(subset[,2], plot=FALSE) | ||
| output[[cat]] <- list() | ||
| output[[cat]]$lowerWhisker <- bxp$stats[1] | ||
| output[[cat]]$lowerHinge <- bxp$stats[2] | ||
| output[[cat]]$median <- bxp$stats[3] | ||
| output[[cat]]$upperHinge <- bxp$stats[4] | ||
| output[[cat]]$upperWhisker <- bxp$stats[5] | ||
| outlier <- subset[,2] > output[[cat]]$upperWhisker | subset[,2] < output[[cat]]$lowerWhisker | ||
| subset$outlier <- outlier | ||
| output[[cat]]$points <- subset | ||
| df1 <- loaded_variables$datapoints_n0_s1 | ||
| df1 <- prepareData(df1, excludedPatientIDs) | ||
| output <- addBoxplotStats(output, "Subset 1", df1) | ||
| output$globalMin <- min(df1$value) | ||
| output$globalMax <- max(df1$value) | ||
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| if(!is.null(loaded_variables$datapoints_n0_s2)) { | ||
| df2 <- loaded_variables$datapoints_n0_s2 | ||
| df2 <- prepareData(df2, excludedPatientIDs) | ||
| output <- addBoxplotStats(output, "Subset 2", df2) | ||
| output$globalMin <- min(df1$value, df2$value) | ||
| output$globalMax <- max(df1$value, df2$value) | ||
| } | ||
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| toJSON(output) | ||
| } | ||
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| prepareData <- function(df, excludedPatientIDs) { | ||
| df <- na.omit(df) | ||
| df$jitter <- runif(nrow(df), -0.5, 0.5) | ||
| colnames(df) <- c("patientID", "value", "jitter") | ||
| df <- df[!df$patientID %in% excludedPatientIDs, ] | ||
| df | ||
| } | ||
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| addBoxplotStats <- function(output, subset, df) { | ||
| bxp <- boxplot(df$value, plot=FALSE) | ||
| output[[subset]] <- list() | ||
| output[[subset]]$lowerWhisker <- bxp$stats[1] | ||
| output[[subset]]$lowerHinge <- bxp$stats[2] | ||
| output[[subset]]$median <- bxp$stats[3] | ||
| output[[subset]]$upperHinge <- bxp$stats[4] | ||
| output[[subset]]$upperWhisker <- bxp$stats[5] | ||
| outlier <- df$value > output[[subset]]$upperWhisker | df$value < output[[subset]]$lowerWhisker | ||
| df$outlier <- outlier | ||
| output[[subset]]$rawData <- df | ||
| output | ||
| } |
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134 changes: 58 additions & 76 deletions
134
web-app/js/smartR/_angular/directives/preprocessButton.js
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,60 @@ | ||
| //# sourceURL=preprocessButton.js | ||
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| window.smartRApp.directive('preprocessButton', ['rServeService', | ||
| function(rServeService) { | ||
| return { | ||
| restrict: 'E', | ||
| scope: { | ||
| running: '=', | ||
| params: '=', | ||
| showSummaryStats: '=', | ||
| summaryData: '=' | ||
| }, | ||
| template: | ||
| '<input type="button" value="Preprocess" class="heim-action-button">' + | ||
| '<span style="padding-left: 10px;"></span>', | ||
| link: function(scope, element) { | ||
| var template_btn = element.children()[0]; | ||
| var template_msg = element.children()[1]; | ||
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| scope.$watch('summaryData', function (newSummaryData) { | ||
| if (newSummaryData.hasOwnProperty('allSamples')) { | ||
| // when everything is retrieved | ||
| scope.disabled = false; | ||
| } | ||
| }, true); | ||
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| template_btn.onclick = function() { | ||
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| var _init = function () { | ||
| template_btn.disabled = true; | ||
| scope.summaryData = {}; // reset | ||
| scope.disabled = true; | ||
| scope.running = true; | ||
| template_msg.innerHTML = 'Preprocessing, please wait <span class="blink_me">_</span>'; | ||
| }, | ||
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| _args = {aggregate:scope.params.aggregateProbes}, | ||
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| _preprocessData = function (_args) { | ||
| return rServeService.preprocess(_args).then(function (msg){ | ||
| return msg; | ||
| }); | ||
| }, | ||
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| _finishedPreprocessed = function (msg) { | ||
| template_msg.innerHTML = 'Success: ' + msg; | ||
| scope.disabled = false; | ||
| scope.running = false; | ||
| }, | ||
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| _afterDataPreprocessed = function (msg) { | ||
| template_btn.disabled = false; | ||
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| if (!scope.showSummaryStats) { | ||
| return _finishedPreprocessed(msg); | ||
| } | ||
| template_msg.innerHTML = 'Execute summary statistics, please wait <span class="blink_me">_</span>'; | ||
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| return rServeService.executeSummaryStats('preprocess') | ||
| .then (function (data) { | ||
| scope.summaryData = data.result; | ||
| template_msg.innerHTML = 'Success: ' + data.msg; | ||
| scope.running = false; | ||
| }, function(msg) { | ||
| template_msg.innerHTML = 'Failure: ' + msg; | ||
| scope.running = false; | ||
| }) | ||
| }; | ||
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| _init(); | ||
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| _preprocessData(_args) | ||
| .then(_afterDataPreprocessed, _afterDataPreprocessed); | ||
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| }; | ||
| } | ||
| }; | ||
| }]); | ||
| 'use strict'; | ||
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| window.smartRApp.directive('preprocessButton', [ | ||
| 'rServeService', | ||
| '$rootScope', | ||
| function(rServeService, $rootScope) { | ||
| return { | ||
| restrict: 'E', | ||
| scope: { | ||
| running: '=?', | ||
| params: '=?', | ||
| showSummaryStats: '=', | ||
| summaryData: '=' | ||
| }, | ||
| templateUrl: $rootScope.smartRPath + '/js/smartR/_angular/templates/preprocessButton.html', | ||
| link: function(scope, element) { | ||
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| var template_btn = element.children()[0]; | ||
| var template_msg = element.children()[1]; | ||
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| var _onSuccess = function() { | ||
| template_msg.innerHTML = 'Task complete!'; | ||
| template_btn.disabled = false; | ||
| scope.running = false; | ||
| }; | ||
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| var _onFail = function(msg) { | ||
| template_msg.innerHTML = 'Error: ' + msg; | ||
| template_btn.disabled = false; | ||
| scope.running = false; | ||
| }; | ||
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| var _showSummaryStats = function() { | ||
| template_msg.innerHTML = 'Execute summary statistics, please wait <span class="blink_me">_</span>'; | ||
| rServeService.executeSummaryStats('preprocess').then( | ||
| function (data) { | ||
| scope.summaryData = data.result; | ||
| _onSuccess(); | ||
| }, | ||
| _onFail | ||
| ); | ||
| }; | ||
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| template_btn.onclick = function() { | ||
| scope.summaryData = {}; | ||
| scope.disabled = true; | ||
| scope.running = true; | ||
| template_msg.innerHTML = 'Preprocessing, please wait <span class="blink_me">_</span>'; | ||
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| var params = scope.params ? scope.params : {}; | ||
| rServeService.preprocess(params).then( | ||
| scope.showSummaryStats ? _showSummaryStats : _onSuccess, | ||
| _onFail | ||
| ); | ||
| }; | ||
| } | ||
| }; | ||
| }]); |
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