diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/cellStatistics/html/index.html b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/cellStatistics/html/index.html
index 5aa956556329a32885a49771f12b0af1db0baf62..500eda484abba64070754b281e36d301ec6667a0 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/cellStatistics/html/index.html
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/cellStatistics/html/index.html
@@ -135,6 +135,29 @@ function plotLaneTable (sumArray, withNOINDEX) {
;
// create rows
+ console.log("Sumarray")
+ console.log(sumArray)
+ //sumArray.splice(1,3)
+
+
+ // litte hack which removes three lanes of the FC view, as the NextSeq has four lanes
+ // as specified by Illumina, but logically it is only one lane
+ // So if the FC has four lanes we assume it is a NextSeq run and therefore we remove the last three
+ // lanes via the splice method
+ if (sumArray.length == 4) {
+ sumArray.splice(1,3)
+ }
+
+ /*
+ for (i=0; i< sumArray.length; i++) {
+ console.log(sumArray[i].numberOfSamples)
+ if (sumArray[i].numberOfSamples == 0) {
+ console.log("NO samples in "+ i)
+ sumArray.splice(i,1)
+ }
+ }
+ */
+
var tr = laneTableStats.selectAll("tr")
.data(sumArray).enter().append("tr")
// cells
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/images/openBIS_Logo.svg b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/images/openBIS_Logo.svg
index 811623c73d2ef53c4a15be466eee3af98cf19822..70ac6c77f2774a5a5e8f6875e3c8ae1acb8e952a 100755
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/images/openBIS_Logo.svg
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/images/openBIS_Logo.svg
@@ -1,68 +1,68 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!-- Generator: Adobe Illustrator 15.0.2, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
-<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
-<svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
- width="400.023px" height="174.566px" viewBox="0 0 400.023 174.566" enable-background="new 0 0 400.023 174.566"
- xml:space="preserve">
-<g id="Layer_1">
- <g>
- <text transform="matrix(1 0 0 1 46.4854 154.2764)"><tspan x="0" y="0" fill="#010101" font-family="'HelveticaNeue-Bold'" font-size="93.505" letter-spacing="-4">open</tspan><tspan x="204.679" y="0" fill="#231F20" font-family="'HelveticaNeue'" font-size="93.505">BIS</tspan></text>
- <rect x="204.234" y="158.748" fill="none" width="192.64" height="14.936"/>
- <text transform="matrix(1 0 0 1 204.2329 169.876)" fill="#010101" font-family="'HelveticaNeue'" font-size="15.5842">Biology Information System</text>
- <g>
- <g>
- <g>
- <g>
- <polygon fill="#068172" points="125.213,81.967 141.416,98.167 147.252,92.333 131.053,76.132 125.213,76.132 "/>
- </g>
- <g>
- <g>
- <polygon fill="#068172" points="120.206,81.967 104.005,98.167 98.168,92.333 114.368,76.132 120.206,76.132 "/>
- </g>
- <g>
- <polygon fill="#068172" points="120.206,65.286 104.005,49.084 98.168,54.92 114.368,71.12 120.206,71.12 "/>
- </g>
- </g>
- </g>
- <g>
- <polygon fill="#068172" points="125.213,65.286 141.416,49.084 147.252,54.92 131.053,71.12 125.213,71.12 "/>
- </g>
- </g>
- <g>
- <g>
- <polygon fill="#A4A4A4" points="76.131,16.201 92.331,0 98.168,5.836 81.969,22.036 76.13,22.036 "/>
- </g>
- <g>
- <g>
- <polygon fill="#ADACAF" points="76.131,32.882 92.331,49.084 98.168,43.247 81.969,27.048 76.13,27.048 "/>
- </g>
- <g>
- <g>
- <polygon fill="#ADACAF" points="71.122,32.882 54.921,49.084 49.084,43.247 65.283,27.048 71.123,27.048 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="71.122,16.201 54.921,0 49.084,5.836 65.283,22.036 71.123,22.036 "/>
- </g>
- </g>
- </g>
- </g>
- <g>
- <g>
- <polygon fill="#ADACAF" points="27.046,65.286 43.247,49.084 49.083,54.92 32.884,71.12 27.045,71.12 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="27.046,81.967 43.247,98.167 49.083,92.333 32.884,76.132 27.045,76.132 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="22.038,81.967 5.837,98.167 0,92.333 16.199,76.132 22.038,76.132 "/>
- </g>
- <g>
- <polygon fill="#ADACAF" points="22.038,65.286 5.837,49.084 0,54.92 16.199,71.12 22.038,71.12 "/>
- </g>
- </g>
- </g>
- </g>
-</g>
-<g id="Layer_2">
-</g>
-</svg>
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 15.0.2, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+ width="400.023px" height="174.566px" viewBox="0 0 400.023 174.566" enable-background="new 0 0 400.023 174.566"
+ xml:space="preserve">
+<g id="Layer_1">
+ <g>
+ <text transform="matrix(1 0 0 1 46.4854 154.2764)"><tspan x="0" y="0" fill="#010101" font-family="'HelveticaNeue-Bold'" font-size="93.505" letter-spacing="-4">open</tspan><tspan x="204.679" y="0" fill="#231F20" font-family="'HelveticaNeue'" font-size="93.505">BIS</tspan></text>
+ <rect x="204.234" y="158.748" fill="none" width="192.64" height="14.936"/>
+ <text transform="matrix(1 0 0 1 204.2329 169.876)" fill="#010101" font-family="'HelveticaNeue'" font-size="15.5842">Biology Information System</text>
+ <g>
+ <g>
+ <g>
+ <g>
+ <polygon fill="#068172" points="125.213,81.967 141.416,98.167 147.252,92.333 131.053,76.132 125.213,76.132 "/>
+ </g>
+ <g>
+ <g>
+ <polygon fill="#068172" points="120.206,81.967 104.005,98.167 98.168,92.333 114.368,76.132 120.206,76.132 "/>
+ </g>
+ <g>
+ <polygon fill="#068172" points="120.206,65.286 104.005,49.084 98.168,54.92 114.368,71.12 120.206,71.12 "/>
+ </g>
+ </g>
+ </g>
+ <g>
+ <polygon fill="#068172" points="125.213,65.286 141.416,49.084 147.252,54.92 131.053,71.12 125.213,71.12 "/>
+ </g>
+ </g>
+ <g>
+ <g>
+ <polygon fill="#A4A4A4" points="76.131,16.201 92.331,0 98.168,5.836 81.969,22.036 76.13,22.036 "/>
+ </g>
+ <g>
+ <g>
+ <polygon fill="#ADACAF" points="76.131,32.882 92.331,49.084 98.168,43.247 81.969,27.048 76.13,27.048 "/>
+ </g>
+ <g>
+ <g>
+ <polygon fill="#ADACAF" points="71.122,32.882 54.921,49.084 49.084,43.247 65.283,27.048 71.123,27.048 "/>
+ </g>
+ <g>
+ <polygon fill="#ADACAF" points="71.122,16.201 54.921,0 49.084,5.836 65.283,22.036 71.123,22.036 "/>
+ </g>
+ </g>
+ </g>
+ </g>
+ <g>
+ <g>
+ <polygon fill="#ADACAF" points="27.046,65.286 43.247,49.084 49.083,54.92 32.884,71.12 27.045,71.12 "/>
+ </g>
+ <g>
+ <polygon fill="#ADACAF" points="27.046,81.967 43.247,98.167 49.083,92.333 32.884,76.132 27.045,76.132 "/>
+ </g>
+ <g>
+ <polygon fill="#ADACAF" points="22.038,81.967 5.837,98.167 0,92.333 16.199,76.132 22.038,76.132 "/>
+ </g>
+ <g>
+ <polygon fill="#ADACAF" points="22.038,65.286 5.837,49.084 0,54.92 16.199,71.12 22.038,71.12 "/>
+ </g>
+ </g>
+ </g>
+ </g>
+</g>
+<g id="Layer_2">
+</g>
+</svg>
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/openbis-dsu-downloader.html b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/openbis-dsu-downloader.html
index 6ab8f261497ce12fb98418f907e73bac633e95e2..941a6fb603d164e480cd358b91194945b962a706 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/openbis-dsu-downloader.html
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/downloader/html/openbis-dsu-downloader.html
@@ -794,11 +794,11 @@ function onPageLoad(){
}
function log(msg){
- /*
+
if(console){
console.log(msg);
}
- */
+
}
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/invoicing/html/index.html b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/invoicing/html/index.html
index a8c4e6f935fa49bec7f52b639425c39e7ac0954e..435b335ce8c33a0199424c0a388bc91bf19c13db 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/invoicing/html/index.html
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/invoicing/html/index.html
@@ -86,7 +86,6 @@ function hideButtons(data)
/**
* See ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.IQueryApiServer.createReportFromAggregationService(String, String, String, Map<String, Object>)
- */
openbis.prototype.createReportFromAggregationService = function(dataStoreCode, serviceKey, parameters, action) {
ajaxRequest({
url: this.queryServiceUrl,
@@ -96,6 +95,7 @@ openbis.prototype.createReportFromAggregationService = function(dataStoreCode, s
});
}
+*/
function spinner (target) {
var opts = {
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/laneStatistics/html/index.html b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/laneStatistics/html/index.html
index 54f4bca9ebd4441c01e80a5b36feea672347699f..35b99a8a1c202a8bcd93742017d57cc8e6b63c79 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/laneStatistics/html/index.html
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/laneStatistics/html/index.html
@@ -114,11 +114,19 @@ function loadData () {
dataSetMap[dataSet.code] = dataSet
+ // console.log("DATA Set:")
+ // console.log(index1)
+ console.log(index2)
+
parents.forEach(function(parent){
var parentIndex1 = parent.properties['BARCODE'];
var parentIndex2 = parent.properties['INDEX2'];
- if(index1 == parentIndex1 && (!index2 || !parentIndex2 || index2 == parentIndex2)){
+ // console.log("PARENT SAMPLE:")
+ // console.log(parentIndex1)
+ // console.log(parentIndex2)
+
+ if(index1 == parentIndex1 && (!index2 || !parentIndex2 || index2 == parentIndex2 || index2 == "NOINDEX")){
dataSetToParentMap[dataSet.code] = parent;
if (!(parent.code in parentToDataSets)) {
parentToDataSets[parent.code] = [dataSet]
@@ -133,6 +141,11 @@ function loadData () {
dataSetToParentMap[dataSet.code] = parent;
parentToDataSets[parent.code] = [dataSet]
}
+ if (parentIndex2 == undefined) {
+
+ }
+
+
});
});
// console.log("SampleToParentsMap: ");
@@ -155,7 +168,7 @@ function loadData () {
});
realValueMap[key] = [cumSumYieldMbases, cumSumPfReadsSum]
});
- // console.log(realValueMap)
+ console.log(realValueMap)
statisticsArray = [];
@@ -170,6 +183,9 @@ function loadData () {
dsu.retrieveSampleParents(webAppContext.getEntityPermId(), getParentProperties);
function getParentProperties (sampleProperties) {
+
+ // d3.select("body").append("text").text("Loading...")
+
for (var i = 0; i < sampleProperties.result.length; i++) {
targetedArray.push ({
'targeted_yield_in_gigabases_pf' : sampleProperties.result[i].properties.TARGETED_YIELD_IN_GIGABASES_PF,
@@ -178,29 +194,33 @@ function loadData () {
'parentSampleCode' : sampleProperties.result[i].code
});
}
- console.log("targetedArray:");
- console.log(targetedArray);
- console.log(dataSetProperties)
- console.log("realValueMap:")
- console.log(realValueMap)
+ // console.log("targetedArray:");
+ // console.log(targetedArray);
+ // console.log(dataSetProperties)
+ // console.log("realValueMap:")
+ // console.log(realValueMap)
for (var i = 0; i < dataSetProperties.result.length; i++) {
for (var j = 0; j < targetedArray.length; j++) {
if (targetedArray[j]['externalSampleName'] == dataSetProperties.result[i].properties.EXTERNAL_SAMPLE_NAME){
+ console.log(targetedArray[j]['externalSampleName'])
+
+ console.log(realValueMap)
+ console.log(targetedArray[j])
statisticsArray.push({
'qgfName' : targetedArray[j]['parentSampleCode'],
'externalSampleName' : dataSetProperties.result[i].properties.EXTERNAL_SAMPLE_NAME,
'index1': dataSetProperties.result[i].properties.BARCODE,
'index2': dataSetProperties.result[i].properties.INDEX2,
- 'percFilteringPass' : parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_PASSED_FILTERING),
+ 'percFilteringPass' : parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_PASSED_FILTERING).toFixed(2),
'rawReadsSum' : dataSetProperties.result[i].properties.RAW_READS_SUM,
'pfReadsSum' : dataSetProperties.result[i].properties.PF_READS_SUM,
'rawYieldMbases' : dataSetProperties.result[i].properties.RAW_YIELD_MBASES,
'yieldMbases' : dataSetProperties.result[i].properties.YIELD_MBASES,
- 'percRawClustersPerLane': parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_RAW_CLUSTERS_PER_LANE),
- 'pfMeanQualityScore' : parseFloat(dataSetProperties.result[i].properties.PFMEANQUALITYSCORE),
- 'pfYieldq30Percentage' : parseFloat(dataSetProperties.result[i].properties.PFYIELDQ30PERCENTAGE),
+ 'percRawClustersPerLane': parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_RAW_CLUSTERS_PER_LANE).toFixed(2),
+ 'pfMeanQualityScore' : parseFloat(dataSetProperties.result[i].properties.PFMEANQUALITYSCORE).toFixed(2),
+ 'pfYieldq30Percentage' : parseFloat(dataSetProperties.result[i].properties.PFYIELDQ30PERCENTAGE).toFixed(2),
'real_yield_in_gigabases_pf' : realValueMap[targetedArray[j]['parentSampleCode']][0],
'real_read_count_in_million_pf' : realValueMap[targetedArray[j]['parentSampleCode']][1],
'targeted_yield_in_gigabases_pf' : parseFloat(targetedArray[j]['targeted_yield_in_gigabases_pf']),
@@ -214,14 +234,14 @@ function loadData () {
'externalSampleName' : "NOINDEX",
'index1': dataSetProperties.result[i].properties.BARCODE,
'index2': dataSetProperties.result[i].properties.INDEX2,
- 'percFilteringPass' : parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_PASSED_FILTERING),
+ 'percFilteringPass' : parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_PASSED_FILTERING).toFixed(2),
'rawReadsSum' : dataSetProperties.result[i].properties.RAW_READS_SUM,
'pfReadsSum' : dataSetProperties.result[i].properties.PF_READS_SUM,
'rawYieldMbases' : dataSetProperties.result[i].properties.RAW_YIELD_MBASES,
'yieldMbases' : dataSetProperties.result[i].properties.YIELD_MBASES,
- 'percRawClustersPerLane': parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_RAW_CLUSTERS_PER_LANE),
- 'pfMeanQualityScore' : parseFloat(dataSetProperties.result[i].properties.PFMEANQUALITYSCORE),
- 'pfYieldq30Percentage' : parseFloat(dataSetProperties.result[i].properties.PFYIELDQ30PERCENTAGE),
+ 'percRawClustersPerLane': parseFloat(dataSetProperties.result[i].properties.PERCENTAGE_RAW_CLUSTERS_PER_LANE).toFixed(2),
+ 'pfMeanQualityScore' : parseFloat(dataSetProperties.result[i].properties.PFMEANQUALITYSCORE).toFixed(2),
+ 'pfYieldq30Percentage' : parseFloat(dataSetProperties.result[i].properties.PFYIELDQ30PERCENTAGE).toFixed(2),
'real_yield_in_gigabases_pf' : 0,
'real_read_count_in_million_pf' : 0,
'targeted_yield_in_gigabases_pf' : parseFloat(0.0),
@@ -442,7 +462,7 @@ function plotPercFilteringPass (statisticsArray) {
else if (statisticsArray.length > 10) {var svgWidth = 5000;}
else {var svgWidth = 3000;}
- svgWidth = statisticsArray.length * 100
+ svgWidth = statisticsArray.length * 60
if (svgWidth < 200) {svgWidth = 400;}
@@ -562,7 +582,9 @@ function plotPercFilteringPass (statisticsArray) {
.enter()
.append("text")
.text(function(d) { return d.percFilteringPass + " %"; })
- .attr("x", function(d, i) { return i * 1/(1+valuePadding)*(svgWidth / statisticsArray.length) + ((svgWidth /statisticsArray.length ) /2) -15; })
+ //.attr("x", function(d, i) { return i * 1/(1+valuePadding)*(svgWidth / statisticsArray.length) + ((svgWidth /statisticsArray.length ) /2) -15; })
+ //.attr("x", function(d, i) { return i * 1/(1+0.007)*(svgWidth / statisticsArray.length) + ((svgWidth /statisticsArray.length ) /2) ; })
+ .attr ("x", function (d) {return x(d.externalSampleName+d.index1) +10;})
.attr("y", function(d) {
if (d.percFilteringPass < 40) { return svgHeight - d.percFilteringPass - margin.top - margin.bottom; }
return (svgHeight - d.percFilteringPass - margin.bottom) ;
@@ -576,7 +598,7 @@ function plotPercFilteringPass (statisticsArray) {
function plotReadsSum (statisticsArray, sums){
- svgWidth = statisticsArray.length * 100
+ svgWidth = statisticsArray.length *60
if (svgWidth < 200) {svgWidth = 300;}
var formatThousands = d3.format(",");
@@ -660,7 +682,7 @@ function plotReadsSum (statisticsArray, sums){
.append("text")
.text(function(d) { return formatThousands(d.rawReadsSum); })
//.attr("x", function(d, i) { return i * 1/(1+valuePadding)*(svgWidth / statisticsArray.length) + ((svgWidth /statisticsArray.length ) /2) -10; })
- .attr ("x", function (d) {return x(d.externalSampleName+d.index1) + 20;})
+ .attr ("x", function (d) {return x(d.externalSampleName+d.index1) + 10;})
// .attr("y", function(d) {
// return (svgHeight - margin.top - margin.bottom + 20) ;
// })
@@ -678,7 +700,7 @@ function plotReadsSum (statisticsArray, sums){
function plotPFReads (statisticsArray, sums){
- svgWidth = statisticsArray.length * 100
+ svgWidth = statisticsArray.length * 60
if (svgWidth < 200) {svgWidth = 300;}
var formatThousands = d3.format(",");
@@ -762,7 +784,7 @@ function plotPFReads (statisticsArray, sums){
.append("text")
.text(function(d) { return formatThousands(d.pfReadsSum); })
//.attr("x", function(d, i) { return i * 1/(1+valuePadding)*(svgWidth / statisticsArray.length) + ((svgWidth /statisticsArray.length ) /2) -10; })
- .attr ("x", function (d) {return x(d.externalSampleName+d.index1) + 20;})
+ .attr ("x", function (d) {return x(d.externalSampleName+d.index1) + 10;})
// .attr("y", function(d) {
// return (svgHeight - margin.top - margin.bottom + 20) ;
// })
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/sampleSheet/html/index.html b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/sampleSheet/html/index.html
index 535234ff9a1c36962fb6ac346c97187600fe98df..06d4e850cd42a7ca299d9b535bf5be3f4c1e2f75 100644
--- a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/sampleSheet/html/index.html
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/sampleSheet/html/index.html
@@ -13,6 +13,7 @@
<script>
dsu = new openbis_dsu('/openbis/openbis', '/datastore_server');
+console.log(openbis_dsu)
var context = new openbisWebAppContext();
dsu.server.useSession(context.getSessionId());
var vis;
@@ -132,7 +133,7 @@ function callAggregationService(miSeqRun)
sendEmail : mySendEmail,
miSeqRun : miSeqRun
};
- //console.log(parameters)
+ console.log(parameters)
dsu.server.createReportFromAggregationService("DSS1", "triggerCreateSampleSheet", parameters, displayReturnedTable);
}