From ad6b3df44d0f3f3ceb59776752ef0e02d8d25ae2 Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 11 Dec 2012 10:09:51 +0000
Subject: [PATCH] BIS-229 SP-419 : Implemented bottom-up and top-down display.
SVN: 27906
---
.../1/as/webapps/sample-graph/html/webapp.js | 132 +++++++++++++-----
1 file changed, 94 insertions(+), 38 deletions(-)
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/sample-graph/html/webapp.js b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/sample-graph/html/webapp.js
index e1f1c561b0a..084cdc18468 100644
--- a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/sample-graph/html/webapp.js
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/sample-graph/html/webapp.js
@@ -73,53 +73,50 @@ function SampleGraphLink(sourceNode, targetNode) {
this.targetNode = targetNode;
}
+/** Break an identifier into a code and space */
+function codeAndSpaceFromIdentifier(identifier) {
+ var identifierTokens = identifier.split("/");
+ var space, code;
+ if (identifierTokens.length > 2) {
+ space = identifierTokens[1];
+ code = identifierTokens[2];
+ } else {
+ space = null;
+ code = identifierTokens[1];
+ }
+ return {space : space, code : code};
+}
+
+
/**
- * The model that manages state and implements the operations for the sample graph. This model is specific to the Flowcell type.
+ * The model that manages state and implements the operations for the sample graph.
*/
-function FlowcellGraphModel() {
+function SampleGraphModel() {
this.initializeModel();
}
-FlowcellGraphModel.prototype.initializeModel = function() {
+SampleGraphModel.prototype.initializeModel = function() {
this.sampleIdentifier = webappContext.getEntityIdentifier();
- var identifierTokens = this.sampleIdentifier.split("/");
- if (identifierTokens.length > 2) {
- this.sampleSpace = identifierTokens[1];
- this.sampleCode = identifierTokens[2];
- } else {
- this.sampleSpace = null;
- this.sampleCode = identifierTokens[1];
- }
+ var codeAndSpace = codeAndSpaceFromIdentifier(this.sampleIdentifier);
+ this.sampleSpace = codeAndSpace.space;
+ this.sampleCode = codeAndSpace.code;
this.samplePermId = webappContext.getEntityPermId();
this.sampleType = webappContext.getEntityType();
var samplesByType = {};
COLUMNS.forEach(function(column) { samplesByType[column.type] = [] });
this.samplesByType = samplesByType;
+ this.flowcellsByIdentifier = {};
}
/**
* Request the data necessary to display the graph.
*/
-FlowcellGraphModel.prototype.requestGraphData = function(callback)
+SampleGraphModel.prototype.requestGraphData = function(callback)
{
- var containerCriteria = {
- matchClauses :
- [ {"@type" : "AttributeMatchClause",
- fieldType : "ATTRIBUTE",
- attribute : "CODE",
- desiredValue : this.sampleCode
- }, {"@type" : "AttributeMatchClause",
- fieldType : "ATTRIBUTE",
- attribute : "SPACE",
- desiredValue : this.sampleSpace
- } ],
- operator : "MATCH_ALL_CLAUSES"
- };
-
var matchClauses = [ {"@type" : "AttributeMatchClause",
fieldType : "ATTRIBUTE",
attribute : "CODE",
- desiredValue : this.sampleCode + "*"
+ desiredValue : (FLOWCELL_SAMPLE_TYPE == this.sampleType) ? this.sampleCode + "*" : this.sampleCode
}];
if (this.sampleSpace) {
@@ -139,16 +136,58 @@ FlowcellGraphModel.prototype.requestGraphData = function(callback)
var lexicalParent = this;
function coalesceResult(data) {
lexicalParent.coalesceGraphData(data);
- callback();
+ lexicalParent.requestFlowcellData(callback)
}
openbisServer.searchForSamplesWithFetchOptions(sampleCriteria, ["PROPERTIES", "ANCESTORS", "DESCENDANTS"], coalesceResult);
}
+/**
+ * In most cases, we need an additional server request to get the flowcell data. Make that call here.
+ */
+SampleGraphModel.prototype.requestFlowcellData = function(callback) {
+ if (FLOWCELL_SAMPLE_TYPE == this.sampleType) {
+ callback();
+ return;
+ }
+
+ // Collect the Flowcell code and spaces
+ var flowlaneIds = [];
+ this.samplesByType[FLOWLANE_SAMPLE_TYPE].forEach(function(flowlane) {
+ var flowcellId = flowlane.identifier.split(":")[0];
+ var codeAndSpace = codeAndSpaceFromIdentifier(flowcellId);
+ flowlaneIds.push(codeAndSpace);
+ });
+
+ var matchClauses = [];
+ flowlaneIds.forEach(function(cs) {
+ matchClauses.push({"@type" : "AttributeMatchClause",
+ fieldType : "ATTRIBUTE",
+ attribute : "CODE",
+ desiredValue : cs.code
+ })
+ })
+
+ var sampleCriteria = {
+ matchClauses : matchClauses,
+ operator : "MATCH_ANY_CLAUSES"
+ };
+
+ var lexicalParent = this;
+ function coalesceResult(data) {
+ lexicalParent.coalesceGraphData(data);
+ callback();
+ }
+
+ openbisServer.searchForSamplesWithFetchOptions(sampleCriteria, ["PROPERTIES"], coalesceResult);
+
+};
+
+
/**
* Request the data necessary to display the graph.
*/
-FlowcellGraphModel.prototype.coalesceGraphData = function(data, callback) {
+SampleGraphModel.prototype.coalesceGraphData = function(data, callback) {
var samples = data.result;
var nodesById = {};
@@ -170,6 +209,9 @@ FlowcellGraphModel.prototype.coalesceGraphData = function(data, callback) {
node.arrayIndex = sampleTypeArray.length;
sampleTypeArray.push(node);
}
+ if (FLOWCELL_SAMPLE_TYPE == node.sampleType) {
+ lexicalParent.flowcellsByIdentifier[node.identifier] = node;
+ }
if (sample.parents) sample.parents.forEach(convertSampleToNode);
if (sample.children) sample.children.forEach(convertSampleToNode);
@@ -178,35 +220,49 @@ FlowcellGraphModel.prototype.coalesceGraphData = function(data, callback) {
function resolveParents(sample) {
// This is just a nodeId, it will be resolved elsewhere
if (isPureId(sample)) return;
+ if (!sample.parents) return;
sample.parents.forEach(resolveParents);
var node = nodeForSample(sample);
node.parents = sample.parents.map(nodeForSample);
+ node.parents.forEach(function(p) { p.children = [node]});
}
function resolveChildren(sample) {
// This is just a nodeId, it will be resolved elsewhere
if (isPureId(sample)) return;
+ if (!sample.children) return;
sample.children.forEach(resolveChildren);
var node = nodeForSample(sample);
node.children = sample.children.map(nodeForSample);
+ node.children.forEach(function(p) { p.parents = [node]});
}
samples.forEach(convertSampleToNode);
samples.forEach(resolveParents);
samples.forEach(resolveChildren);
- // The parents of the flowlanes should become the parents of the flow cell
- var flowcell = this.samplesByType[FLOWCELL_SAMPLE_TYPE][0];
- if (flowcell) {
- var flowlaneParents = []
- this.samplesByType[FLOWLANE_SAMPLE_TYPE].forEach(function(d) { flowlaneParents = flowlaneParents.concat(d.parents); });
- this.samplesByType[FLOWCELL_SAMPLE_TYPE][0].parents = flowlaneParents;
- this.samplesByType[FLOWLANE_SAMPLE_TYPE].forEach(function(d) { d.parents = [flowcell]});
- }
+ // The parents of the flowlanes should become the parents of the flowcell and the
+ // flowcell should become the parent of the flowlanes.
+ var flowcellsByIdentifier = this.flowcellsByIdentifier;
+ this.samplesByType[FLOWLANE_SAMPLE_TYPE].forEach(function(flowlane) {
+ var flowcellId = flowlane.identifier.split(":")[0];
+ var flowcell = flowcellsByIdentifier[flowcellId];
+ if (flowcell) {
+ var parents = flowcell.parents;
+ parents = parents.concat(flowlane.parents);
+ flowcell.parents = parents;
+ flowcell.children.push(flowlane);
+ flowlane.parents.forEach(function(parent) {
+ var children = parent.children;
+ children.splice(children.indexOf(flowlane), 1, flowcell);
+ })
+ flowlane.parents = [flowcell];
+ }
+ });
}
@@ -563,7 +619,7 @@ function clickedTopDown() {
/// The model that manages state and implements the operations
var model;
-model = new FlowcellGraphModel();
+model = new SampleGraphModel();
// The presenter tranlsates the model into visual elements
var presenter;
--
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