From b91181d88b5d6b5cad7029279de544eea4166e8e Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Fri, 18 Sep 2015 10:16:15 +0000
Subject: [PATCH] - made the naming of (reads/clusters) depending on the
bclversion used for flowcell statistics - bugfix, if bclversion is undefined
- added openbis-dsu.js
SVN: 34668
---
.../as/webapps/cellStatistics/html/index.html | 70 +++-
.../as/webapps/laneStatistics/html/index.html | 16 +-
.../illumina-qgf/1/as/webapps/openbis-dsu.js | 358 ++++++++++++++++++
3 files changed, 421 insertions(+), 23 deletions(-)
create mode 100644 deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/openbis-dsu.js
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 500eda484ab..127a1899a18 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
@@ -11,6 +11,7 @@
<script type="text/javascript" src="/openbis/resources/js/FileSaver.js"></script>
<link rel="stylesheet" href="//maxcdn.bootstrapcdn.com/bootstrap/3.2.0/css/bootstrap.min.css">
<link rel="stylesheet" type="text/css" href="style.css" />
+
</head>
<body>
<div id="container" class="container">
@@ -49,6 +50,13 @@
return Number(myFloat).toFixed(2);
}
+ if (typeof String.prototype.startsWith != 'function') {
+ // see below for better implementation!
+ String.prototype.startsWith = function (str){
+ return this.indexOf(str) === 0;
+ };
+ }
+
/* -------------------------------------------------------------------*/
@@ -66,15 +74,31 @@ function loadData () {
sampleCodes.push(webAppContext.getEntityIdentifier() + ":" + i);
}
+ var clusters = ""
+ // just take the first lane to read out the BCL version
+ dsu.retrieveSampleWithPropertiesCode(sampleCodes[0], function(laneResponse) {
+ // console.log(laneResponse)
+ bclVersion = laneResponse.result[0].properties.BCL_VERSION
+ if (bclVersion !== undefined) {
+ if (bclVersion.startsWith("bcl2fastq v2")) {
+ clusters = "Clusters";
+ }
+ else {
+ clusters = "Reads";
+ }
+ }
+ else { clusters = "Reads"};
+ });
+
var deferrer = new openbisActionDeferrer(function(){
sumArray.sort(compare);
sumArrayNOINDEX.sort(compare);
- plotLaneTable (sumArrayNOINDEX, true);
+ plotLaneTable (sumArrayNOINDEX, true, clusters);
placeholder()
- plotLaneTable (sumArray, false);
+ plotLaneTable (sumArray, false, clusters);
downloadButton ("tableStats");
$("#save_as" + "tableStats").click(function() { submit_download_form("html", "tableStats"); });
- }, sampleCodes);
+ }, sampleCodes, clusters);
sampleCodes.forEach(function(sampleCode){
dsu.retrieveDataSetsForSample(sampleCode, function(response){
@@ -109,25 +133,39 @@ function loadData () {
});
};
-function plotLaneTable (sumArray, withNOINDEX) {
+function plotLaneTable (sumArray, withNOINDEX, clusters) {
- d3.select("body").append("text")
- .text("Summary Table")
- .attr("class", "h3");
+ //d3.select("body").append("text")
+ // .text("Summary Table")
+ // .attr("class", "h3");
d3.select("body").append("text")
- .text(function (){if (withNOINDEX) {return " with NOINDEX";} return " without NOINDEX";})
- .attr("class", "h6");
+ .text(function (){if (withNOINDEX) {return " All " + clusters;} return " Without Undetermined " + clusters;})
+ .attr("class", "h3");
+
+ d3.select("body")
+ .append("p")
+ ;
var laneTableStats = d3.select("body")
.append("table")
.attr("id", "tableStats")
.attr("class", "tableStats")
;
- header = {"Lane":1, "# of Samples":1, "Average Passed Filtering (PF)":1, "Sum Raw Reads":1, "Sum PF Reads":1, "Sum Raw Bases":1,
- "Sum PF Bases":1, "Average Raw Clusters in % per Index":1, "Average PF Phred Score":1, "Average > 30 Phred Score":1 }
- // create the table header
+ header = {}
+ header["Lane"] = 1
+ header["# of Samples"] = 1
+ header["AVG Passed Filtering (PF)"] = 1
+ header["Sum Raw " + clusters] = 1
+ header["Sum PF " + clusters] = 1
+ header["Sum Raw Bases"] = 1
+ header["Sum PF Bases"] = 1
+ header["AVG Raw Clusters in % per Index"] = 1
+ header["AVG PF Phred Score"] = 1
+ header["AVG > 30 Phred Score"] = 1
+
+ // create the table header
var thead = laneTableStats.selectAll("th")
.data(d3.keys(header))
.enter().append("th")
@@ -135,8 +173,8 @@ function plotLaneTable (sumArray, withNOINDEX) {
;
// create rows
- console.log("Sumarray")
- console.log(sumArray)
+ // console.log("Sumarray")
+ // console.log(sumArray)
//sumArray.splice(1,3)
@@ -174,8 +212,8 @@ function placeholder() {
var space = d3.select("body")
.append("svg")
.attr("id", "placeholder")
- .attr("width", 1500)
- .attr("height", 50)
+ .attr("width", 0)
+ .attr("height", 100)
;
}
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 77b58f02ef9..bc7cc543b84 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
@@ -276,13 +276,15 @@ function loadData () {
dsu.retrieveSampleWithProperties(webAppContext.getEntityPermId(), function(laneResponse){
bclVersion = laneResponse.result[0].properties.BCL_VERSION
- if (bclVersion.startsWith("bcl2fastq v2")) {
- clusters = "Clusters";
- }
- else {
- clusters = "Reads";
- }
-
+ if (bclVersion !== undefined) {
+ if (bclVersion.startsWith("bcl2fastq v2")) {
+ clusters = "Clusters";
+ }
+ else {
+ clusters = "Reads";
+ }
+ }
+ else {clusters = "Reads"};
if (! isNaN(statisticsArray[0].percFilteringPass)) {
plotLaneTable(sumsWithNOINDEX, false)
// TODO: removed for now, as there is a bug
diff --git a/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/openbis-dsu.js b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/openbis-dsu.js
new file mode 100644
index 00000000000..a1cc807e5a8
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/core-plugins/illumina-qgf/1/as/webapps/openbis-dsu.js
@@ -0,0 +1,358 @@
+/**
+ * openbis-dsu.js
+ * OpenBIS-DSU API
+ *
+ * A DSU-specific API for accessing openBIS. Depends on openbis.js.
+ * @author Chandrasekhar Ramakrishnan
+ */
+
+/**
+ * The openbis_dsu object provides a dsu-specific interface to openbis.
+ *
+ * It creates objects for projects, experiments, samples, and datasets. These objects
+ * are designed to be passed on to GUI libraries (like d3). The openbis version of each
+ * object is stored in the bis variable.
+ * @constructor
+ */
+function openbis_dsu(url, dssUrl) {
+ this.server = new openbis(url, dssUrl);
+}
+
+/**
+ * Request the sequencing samples for a project
+ */
+openbis_dsu.prototype.retrieveSequencingSamples = function(action)
+{
+ var sampleCriteria =
+ {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "TYPE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : "ILLUMINA_SEQUENCING"
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ this.server.searchForSamples(sampleCriteria, action);
+}
+
+
+/**
+ * Request a Sample using the code
+ */
+openbis_dsu.prototype.retrieveSample = function(sampleIdentifier, action)
+{
+ var sampleCriteria =
+ {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "CODE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : sampleIdentifier
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ this.server.searchForSamples(sampleCriteria, action);
+}
+
+
+/**
+ * Request a Sample with Properties using the code
+ */
+openbis_dsu.prototype.retrieveSampleWithPropertiesCode = function(sampleIdentifier, action)
+{
+ var sampleCriteria =
+ {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "CODE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : sampleIdentifier
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ var fetchOptions = ["PROPERTIES"];
+
+ var thisDsu = this;
+ this.server.searchForSamplesWithFetchOptions(sampleCriteria, fetchOptions, function(response){
+ response.result = thisDsu.getInitializedSamples(response.result);
+ action(response);
+ });
+}
+
+
+/**
+ * Request a Sample with Properties using the permID
+ */
+openbis_dsu.prototype.retrieveSampleWithProperties = function(samplePermId, action)
+{
+ var sampleCriteria =
+ {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "PERM_ID",
+ fieldType : "ATTRIBUTE",
+ desiredValue : samplePermId
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ var fetchOptions = ["PROPERTIES"];
+
+ var thisDsu = this;
+ this.server.searchForSamplesWithFetchOptions(sampleCriteria, fetchOptions, function(response){
+ response.result = thisDsu.getInitializedSamples(response.result);
+ action(response);
+ });
+}
+
+
+
+/**
+ * Request Parent Samples including properties
+ */
+
+openbis_dsu.prototype.retrieveSampleParents = function(samplePermId, action)
+{
+ var sampleCriteria =
+ {
+ targetEntityKind : "SAMPLE_CHILD",
+ criteria : {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ "attribute":"PERM_ID",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": samplePermId
+ }]
+ }
+ };
+
+ var parentCriteria =
+ {
+ subCriterias : [ sampleCriteria ],
+ matchClauses :
+ [
+ ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ var fetchOptions = ["PROPERTIES"];
+
+ var thisDsu = this;
+ this.server.searchForSamplesWithFetchOptions(parentCriteria, fetchOptions, function(response){
+ response.result = thisDsu.getInitializedSamples(response.result);
+ action(response);
+ });
+}
+
+
+/**
+ * Request Child Samples including properties
+ */
+
+openbis_dsu.prototype.retrieveSampleChildren = function(samplePermIds, action)
+{
+ var permIdClauses = [];
+
+ samplePermIds.forEach(function(samplePermId){
+ var clause = {"@type":"AttributeMatchClause",
+ "attribute":"PERM_ID",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": samplePermId
+ }
+ permIdClauses.push(clause)
+ });
+
+ var sampleCriteria =
+ {
+ targetEntityKind : "SAMPLE_PARENT",
+ criteria : {
+ matchClauses : permIdClauses,
+ operator : "MATCH_ANY_CLAUSES"
+ }
+ };
+
+ var childCriteria =
+ {
+ subCriterias : [ sampleCriteria ],
+ matchClauses :
+ [
+ ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ var fetchOptions = ["PROPERTIES", "PARENTS"];
+
+ var thisDsu = this;
+ this.server.searchForSamplesWithFetchOptions(childCriteria, fetchOptions, function(response){
+ response.result = thisDsu.getInitializedSamples(response.result);
+ action(response);
+ });
+}
+
+/**
+ * Get the data sets for a sample specified by sample permId
+ */
+openbis_dsu.prototype.retrieveDataSetsForSampleWithPermIds = function(samplePermIds, action)
+{
+ var clauses = [];
+
+ samplePermIds.forEach(function(samplePermId){
+ var clause = {"@type":"AttributeMatchClause",
+ "attribute":"PERM_ID",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": samplePermId
+ }
+ clauses.push(clause)
+ });
+
+ var sampleCriteria =
+ {
+ targetEntityKind : "SAMPLE",
+ criteria : {
+ matchClauses : clauses,
+ operator: "MATCH_ANY_CLAUSES"
+ }
+ };
+
+ var dataSetCriteria =
+ {
+ subCriterias : [ sampleCriteria ],
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "TYPE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : "FASTQ_GZ"
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ this.server.searchForDataSets(dataSetCriteria, action)
+}
+
+
+
+/**
+ * Get the data sets for a sample specified by sample identifier
+ */
+openbis_dsu.prototype.retrieveDataSetsForSample = function(sampleIdentifier, action)
+{
+ var sampleIdentifierTokens = sampleIdentifier.split("/");
+ var sampleCriteria =
+ {
+ targetEntityKind : "SAMPLE",
+ criteria : {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ "attribute":"CODE",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": sampleIdentifierTokens[2]
+ }]
+ }
+ };
+
+ var dataSetCriteria =
+ {
+ subCriterias : [ sampleCriteria ],
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ attribute : "TYPE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : "FASTQ_GZ"
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ this.server.searchForDataSets(dataSetCriteria, action)
+}
+
+/**
+ * Get all data sets connected to a sequencing sample
+ */
+openbis_dsu.prototype.retrieveDataSetsForSequencingSample = function(sequencing, action)
+{
+ this.server.listDataSetsForSample(sequencing.bis, false, action);
+}
+
+openbis_dsu.prototype.getInitializedSamples = function(result) {
+ //
+ // Fill Map that uses as key the sample @id and value the sample object
+ //
+ var samplesById = {};
+
+ function storeSamplesById(originalSample)
+ {
+ var stack = [originalSample];
+
+ var referredSample = null;
+ while (referredSample = stack.pop()) {
+ if (isNaN(referredSample)) {
+ samplesById[referredSample["@id"]] = referredSample;
+ if (referredSample.parents) {
+ for(var i = 0, len = referredSample.parents.length; i < len; ++i) {
+ stack.push(referredSample.parents[i]);
+ }
+ }
+ if (referredSample.children) {
+ for(var i = 0, len = referredSample.children.length; i < len; ++i) {
+ stack.push(referredSample.children[i]);
+ }
+ }
+ }
+ }
+ }
+
+ for(var i = 0; i < result.length; i++) {
+ var sampleOrId = result[i];
+ storeSamplesById(sampleOrId);
+ }
+
+ //
+ // Fix Result List
+ //
+ function fixSamples(result)
+ {
+ for(var i = 0; i < result.length; i++)
+ {
+ var sampleOrId = result[i];
+ if (isNaN(sampleOrId))
+ {
+ sampleOrId = samplesById[sampleOrId["@id"]];
+ } else
+ {
+ sampleOrId = samplesById[sampleOrId];
+ }
+ result[i] = sampleOrId;
+
+
+ //Fill Parents
+ if(sampleOrId.parents) {
+ for(var j = 0; j < sampleOrId.parents.length; j++) {
+ var parentOrId = sampleOrId.parents[j];
+ if(!isNaN(parentOrId)) { //If is an Id get the reference
+ sampleOrId.parents[j] = samplesById[parentOrId];
+ }
+ }
+ fixSamples(sampleOrId.parents);
+ }
+
+ //Fill Children
+ if(sampleOrId.children) {
+ for(var j = 0; j < sampleOrId.children.length; j++) {
+ var childOrId = sampleOrId.children[j];
+ if(!isNaN(childOrId)) { //If is an Id get the reference
+ sampleOrId.children[j] = samplesById[childOrId];
+ }
+ }
+ fixSamples(sampleOrId.children);
+ }
+ }
+ }
+
+ fixSamples(result);
+
+ return result;
+ }
--
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