diff --git a/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html b/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
index b3e7d67a3e4bc7b38466ad5bab8a808f0d3397cd..80b2085581a9cde30f82444b016923cee43181b7 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
+++ b/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
@@ -97,6 +97,19 @@ function addSequencingSamplesToProject(project, bissamps)
if (samples.length > 0)
project.children = groupedSamples;
+
+ // Get the flow lanes for each sequencing sample
+ var deferrer =
+ new actionDeferrer(
+ function() { updateDiagram(500) },
+ samples.map(function(samp) { return samp.bis.code; }));
+
+ samples.forEach(function(sample) {
+ dsu.retrieveFlowLanesForSequencingSample(sample, function(data) {
+ if (data.result) sample.flowlanes = data.result.map(function(flowlane) { return { bis : flowlane }});
+ deferrer.dependencyCompleted(sample.bis.code);
+ })
+ });
}
@@ -221,13 +234,16 @@ function updateDiagram(duration)
node.exit().transition()
.duration(duration)
- .attr("transform", translateDst)
+ .attr("transform", translateSrc)
.remove();
}
function classForNode(d) {
+ // Use whether the node has open children or not to compute the class
var cssClass = hasChildren(d) ? "node withchildren" : "node leaf";
if (d.inspected) cssClass = cssClass + " inspected";
+ if (d.flowlanes && d.flowlanes.length > 0) cssClass = cssClass + " sequenced";
+
return cssClass;
}
@@ -259,6 +275,11 @@ function hasChildren(d)
return d.children != null || d._children != null;
}
+function hasOpenChildren(d)
+{
+ return d.children != null;
+}
+
// Toggle children on click.
function toggle_open(d) {
if (!hasChildren(d)) {
@@ -303,6 +324,23 @@ function updateInspectors(duration)
.text(function(d) { return d })
.transition()
.style("opacity", "1");
+
+ var downloadTable =
+ box.append("table")
+ .attr("width", "100%")
+ .attr("class", "downloads")
+ .style("color", "steelblue");
+ downloadTable.append("caption").text("Files");
+ var downloadTableRow = downloadTable.append("tr");
+ downloadTableRow
+ .append("td")
+ .style("text-align", "left")
+ .text("metadata.tsv");
+ downloadTableRow
+ .append("td")
+ .style("border-right", "0px")
+ .style("text-align", "right")
+ .text("fastq.gz");
inspector.exit().transition()
.duration(duration)
@@ -316,15 +354,23 @@ function toggle_inspected(d) {
var index = inspected.indexOf(d)
if (index > -1) inspected.splice(index, 1);
d.inspected = false;
- d3.select(d.svgNode).attr("class", "node leaf")
+ d3.select(d.svgNode).attr("class", classForNode(d))
} else {
d.inspected = true;
inspected.push(d);
- d3.select(d.svgNode).attr("class", "node leaf inspected")
+ d3.select(d.svgNode).attr("class", classForNode(d))
+ retrieveFilesForSequencingSample(d);
}
updateInspectors(500);
}
+function retrieveFilesForSequencingSample(sequencing)
+{
+ // dsu.retrieveFastqGzDataSetsForFlowLane(sequencing, function(data) {
+ // sequencing.files = data.result;
+ // });
+}
+
/**
* Convert properties to pairs
*/
diff --git a/deep_sequencing_unit/source/html/downloader/openbis-dsu.js b/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
index e5acbfa2fe0ce77329911583dbc727794ad23fa1..80f02391801d389dfde6e4823d6218baf41fa86d 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
+++ b/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
@@ -106,6 +106,19 @@ openbis_dsu.prototype.retrieveSequencingSamplesForExperiment = function(experime
*/
openbis_dsu.prototype.retrieveFlowLanesForSequencingSample = function(sample, action)
{
+ var experimentCriteria =
+ {
+ targetEntityKind : "EXPERIMENT",
+ criteria : {
+ matchClauses :
+ [ {"@type":"AttributeMatchClause",
+ "attribute":"PROJECT",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": sample.project.bis.code
+ } ]
+ }
+ };
+
var parentCriteria =
{
targetEntityKind : "SAMPLE_PARENT",
@@ -121,7 +134,7 @@ openbis_dsu.prototype.retrieveFlowLanesForSequencingSample = function(sample, ac
var sampleCriteria =
{
- subCriterias : [ parentCriteria ],
+ subCriterias : [ experimentCriteria, parentCriteria ],
matchClauses :
[ {"@type":"AttributeMatchClause",
attribute : "TYPE",
@@ -137,24 +150,36 @@ openbis_dsu.prototype.retrieveFlowLanesForSequencingSample = function(sample, ac
/**
* Request the replicas for the grid
*/
-openbis_dsu.prototype.retrieveDataSetsForFlowLane = function(flowlane, action)
+openbis_dsu.prototype.retrieveFastqGzDataSetsForFlowLane = function(flowlane, action)
{
var flowLaneCriteria =
{
targetEntityKind : "SAMPLE",
criteria : {
- matchClauses :
- [ {"@type":"AttributeMatchClause",
- "attribute":"CODE",
- "fieldType":"ATTRIBUTE",
- "desiredValue": flowlane.code
- } ]
+ matchClauses : [
+ {"@type":"AttributeMatchClause",
+ "attribute":"CODE",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": flowlane.bis.code
+ }, {"@type":"AttributeMatchClause",
+ "attribute":"SPACE",
+ "fieldType":"ATTRIBUTE",
+ "desiredValue": flowlane.project.bis.spaceCode
+ }
+ ]
}
};
var dataSetCriteria =
{
subCriterias : [ flowLaneCriteria ],
+ matchClauses : [
+ {"@type":"AttributeMatchClause",
+ attribute : "TYPE",
+ fieldType : "ATTRIBUTE",
+ desiredValue : "FASTQ_GZ"
+ }
+ ],
operator : "MATCH_ALL_CLAUSES"
};
diff --git a/deep_sequencing_unit/source/html/downloader/openbis.js b/deep_sequencing_unit/source/html/downloader/openbis.js
index 7e1d4131e3b1419a8953e80c90d23983b345aaef..8daf9bdee3376d61bda7b45850a2ff42df6e28e7 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis.js
+++ b/deep_sequencing_unit/source/html/downloader/openbis.js
@@ -197,3 +197,34 @@ openbis.prototype.executeQuery = function(queryId, parameterBindings, action) {
success: action
});
}
+
+/**
+ * A utility class for deferring an action until all of some kind of action has completed
+ *
+ * @argument dependencies An array of the keys for the dependencies.
+ */
+function actionDeferrer(pendingAction, dependencies) {
+ this.pendingAction = pendingAction;
+ this.dependencies = {};
+ var newme = this;
+ dependencies.forEach(function(key) {
+ newme.dependencies[key] = false;
+ });
+}
+
+/**
+ * Note that a dependency completed. Execute the pending action if appropriate.
+ */
+actionDeferrer.prototype.dependencyCompleted = function(key) {
+ this.dependencies[key] = true;
+ var shouldExecute = true;
+ for (prop in this.dependencies) {
+ if (false == this.dependencies[prop]) {
+ shouldExecute = false;
+ break;
+ }
+ }
+ if (shouldExecute) {
+ this.pendingAction();
+ }
+}
diff --git a/deep_sequencing_unit/source/html/downloader/tree.css b/deep_sequencing_unit/source/html/downloader/tree.css
index 2eda3c8c67aec20de9c23f67732a24c6f27526cd..cfb774fe829a7b1128291da2eeac5a8fd43c7ba6 100644
--- a/deep_sequencing_unit/source/html/downloader/tree.css
+++ b/deep_sequencing_unit/source/html/downloader/tree.css
@@ -1,26 +1,37 @@
.node circle {
- fill: #fff;
- stroke: steelblue;
- stroke-width: 1.5px;
+ fill: #fff;
+ stroke: steelblue;
+ stroke-width: 1.5px;
}
.node {
- font: 12px "Verdana", sans-serif;
+ font: 12px "Verdana", sans-serif;
+ z-index: 1;
+ cursor: pointer;
}
.link {
- fill: none;
- stroke: #ccc;
- stroke-width: 1.5px;
+ fill: none;
+ stroke: #ccc;
+ stroke-width: 1.5px;
+ z-index: -1;
}
g.withchildren:hover {
opacity: 0.5;
- color: #AAA;
+ font-weight: bold;
+}
+
+.leaf text {
+ fill: #999;
+}
+
+.sequenced text{
+ fill: black;
}
g.leaf:hover {
- font-weight: bold
+ font-weight: bold;
}
.inspected {
@@ -28,10 +39,6 @@ g.leaf:hover {
}
/* Inspector */
-.inspector {
- font-family: "Trebuchet MS", sans-serif;
- font-size: 12px;
-}
div.inspector {
font: 12px "Verdana", sans-serif;
@@ -52,4 +59,33 @@ div.inspector {
.close:hover {
opacity: 0.5;
color: #AAA;
+ cursor: pointer;
+}
+
+.downloads {
+ color: steelblue;
+ background-color: #E3E3E3;
+}
+
+table.downloads {
+ font-family: "Trebuchet MS", sans-serif;
+ font-size: 18px;
+ font-variant: small-caps;
+ table-layout: fixed;
+}
+
+/*
+.downloads caption {
+ text-align: left;
+}
+*/
+
+.downloads td {
+ width: 50%;
+ border-right: 2px solid #FFFFFF;
+}
+
+.downloads td:hover {
+ cursor: pointer;
+ font-weight: bold;
}
\ No newline at end of file