diff --git a/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html b/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
index 4af8cd8dd59ce8ce0bcb3aaeb98dbb64113ab681..c2846681ecef5ddec789a8f68a9b53497193abe2 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
+++ b/deep_sequencing_unit/source/html/downloader/openbis-dendrogram.html
@@ -336,20 +336,16 @@ function updateInspectors(duration)
.data(downloadTableCaption)
.enter()
.append("caption").text(function(d) { return d; });
+
+ // We just want to see non-directories here
var downloadTableRow =
downloadTable.selectAll("tr")
- .data(function(d) { return (d.flowlanes) ? d.flowlanes : [] })
+ .data(function(d) { return (d.files) ? d.files.filter(function(file) { return !file.isDirectory }) : [] })
.enter()
- .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");
+ .append("tr")
+ .append("td")
+ .style("text-align", "left")
+ .text(function (d) { return d.pathInListing });
inspector.exit().transition()
.duration(duration)
@@ -375,9 +371,33 @@ function toggle_inspected(d) {
function retrieveFilesForSequencingSample(sequencing)
{
- // dsu.retrieveFastqGzDataSetsForFlowLane(sequencing, function(data) {
- // sequencing.files = data.result;
- // });
+ // No point getting files for a sample that hasn't been sequenced
+ if (!hasSampleBeenSequenced(sequencing)) return;
+
+ dsu.retrieveDataSetsForSequencingSample(sequencing, function(data) {
+ if (!data.result) return;
+
+ sequencing.datasets = data.result.map(function(bisds) { return {bis : bisds} });
+ sequencing.files = [];
+
+ // Get all the files and update the inspectors once all the data is avilable
+ var deferrer =
+ new actionDeferrer(
+ function() { updateInspectors(500) },
+ sequencing.datasets.map(function(ds) { return ds.bis.code; }));
+
+ sequencing.datasets.forEach(function(ds) {
+ dsu.server.listFilesForDataSet(ds.bis.code, "/", true, function(data) {
+ if (!data.result) {
+ deferrer.dependencyCompleted(ds.bis.code);
+ return;
+ }
+
+ sequencing.files = sequencing.files.concat(data.result);
+ deferrer.dependencyCompleted(ds.bis.code);
+ })
+ });
+ });
}
/**
@@ -398,9 +418,15 @@ function props_to_pairs(d)
return pairs;
}
+
+function hasSampleBeenSequenced(d)
+{
+ return (d.flowlanes && d.flowlanes.length > 0);
+}
+
function downloadTableCaption(d)
{
- return (d.flowlanes && d.flowlanes.length > 0) ? ["Files"] : ["Not Yet Sequenced"];
+ return hasSampleBeenSequenced(d) ? ["Files"] : ["Not Yet Sequenced"];
}
function enterApp()
diff --git a/deep_sequencing_unit/source/html/downloader/openbis-dsu.js b/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
index 80f02391801d389dfde6e4823d6218baf41fa86d..433db05a19a29cba1d0ec8b0ad88d02b031c92a0 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
+++ b/deep_sequencing_unit/source/html/downloader/openbis-dsu.js
@@ -102,7 +102,7 @@ openbis_dsu.prototype.retrieveSequencingSamplesForExperiment = function(experime
}
/**
- * Request the replicas for the grid
+ * Get the flow lanes for a sequencing sample.
*/
openbis_dsu.prototype.retrieveFlowLanesForSequencingSample = function(sample, action)
{
@@ -148,40 +148,9 @@ openbis_dsu.prototype.retrieveFlowLanesForSequencingSample = function(sample, ac
}
/**
- * Request the replicas for the grid
+ * Get all data sets connected to a sequencing sample
*/
-openbis_dsu.prototype.retrieveFastqGzDataSetsForFlowLane = function(flowlane, action)
+openbis_dsu.prototype.retrieveDataSetsForSequencingSample = function(sequencing, action)
{
- var flowLaneCriteria =
- {
- targetEntityKind : "SAMPLE",
- criteria : {
- 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"
- };
-
- this.server.searchForDataSets(dataSetCriteria, action);
+ this.server.listDataSetsForSample(sequencing.bis, false, action);
}
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/html/downloader/openbis-request-cache.js b/deep_sequencing_unit/source/html/downloader/openbis-request-cache.js
index 986d2882d9c9bc67ff5820092596d5f89eb7610c..5a20c8e7391a97623bea51ec8fc6665b98d7fae8 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis-request-cache.js
+++ b/deep_sequencing_unit/source/html/downloader/openbis-request-cache.js
@@ -9,6 +9,8 @@
* Be careful not to distribute it to your customers.
*
* <script type="text/javascript" src="openbis-request-cache.js"></script>
+ *
+ * To clear the cache, you can call "localStorage.clear()" in a browser console.
*/
var original_ajax_request_func = ajaxRequest;
diff --git a/deep_sequencing_unit/source/html/downloader/openbis.js b/deep_sequencing_unit/source/html/downloader/openbis.js
index 8daf9bdee3376d61bda7b45850a2ff42df6e28e7..4815067191df066a9075b6216132e12003db8de4 100644
--- a/deep_sequencing_unit/source/html/downloader/openbis.js
+++ b/deep_sequencing_unit/source/html/downloader/openbis.js
@@ -63,7 +63,7 @@ openbis.prototype.login = function(username, password, action) {
url: this.generalInfoServiceUrl,
data: { "method" : "tryToAuthenticateForAllServices",
"params" : [ username, password ]
- },
+ },
success:
function(data) {
openbisObj.sessionToken = data.result;
@@ -71,7 +71,7 @@ openbis.prototype.login = function(username, password, action) {
action(data)
},
error: function() {
- alert("Login failed")
+ alert("Login failed")
}
});
}
@@ -90,7 +90,7 @@ openbis.prototype.isSessionActive = function(action) {
url: this.generalInfoServiceUrl,
data: { "method" : "isSessionActive",
"params" : [ this.sessionToken ]
- },
+ },
success: action
});
}
@@ -105,7 +105,7 @@ openbis.prototype.logout = function(action) {
url: this.generalInfoServiceUrl,
data: { "method" : "logout",
"params" : [ this.sessionToken ]
- },
+ },
success: action
});
}
@@ -115,7 +115,7 @@ openbis.prototype.listProjects = function(action) {
url: this.generalInfoServiceUrl,
data: { "method" : "listProjects",
"params" : [ this.sessionToken ]
- },
+ },
success: action
});
}
@@ -125,7 +125,7 @@ openbis.prototype.listExperiments = function(projects, experimentType, action) {
url: this.generalInfoServiceUrl,
data: { "method" : "listExperiments",
"params" : [ this.sessionToken, projects, experimentType ]
- },
+ },
success: action
});
}
@@ -160,24 +160,34 @@ openbis.prototype.searchForDataSets = function(searchCriteria, action) {
});
}
- openbis.prototype.listFilesForDataSet = function(dataSetCode, path, recursive, action) {
- ajaxRequest({
- url: this.dssUrl,
- data: { "method" : "listFilesForDataSet",
- "params" : [ this.sessionToken, dataSetCode, path, recursive ]
- },
- success: action
- });
+openbis.prototype.listDataSetsForSample = function(sample, restrictToDirectlyConnected, action) {
+ ajaxRequest({
+ url: this.generalInfoServiceUrl,
+ data: { "method" : "listDataSetsForSample",
+ "params" : [ this.sessionToken, sample, restrictToDirectlyConnected ]
+ },
+ success: action
+ });
+}
+
+openbis.prototype.listFilesForDataSet = function(dataSetCode, path, recursive, action) {
+ ajaxRequest({
+ url: this.dssUrl,
+ data: { "method" : "listFilesForDataSet",
+ "params" : [ this.sessionToken, dataSetCode, path, recursive ]
+ },
+ success: action
+ });
}
openbis.prototype.getDownloadUrlForFileForDataSet = function(dataSetCode, filePath, action) {
- ajaxRequest({
- url: openbis.dssUrl,
- data: { "method" : "getDownloadUrlForFileForDataSet",
- "params" : [ this.sessionToken, dataSetCode, filePath ]
- },
- success: action
- });
+ ajaxRequest({
+ url: openbis.dssUrl,
+ data: { "method" : "getDownloadUrlForFileForDataSet",
+ "params" : [ this.sessionToken, dataSetCode, filePath ]
+ },
+ success: action
+ });
}
openbis.prototype.listQueries = function(action) {
diff --git a/deep_sequencing_unit/source/html/downloader/tree.css b/deep_sequencing_unit/source/html/downloader/tree.css
index cfb774fe829a7b1128291da2eeac5a8fd43c7ba6..66ee9ed7c86c7b5b48885b3dfc700fa869c62302 100644
--- a/deep_sequencing_unit/source/html/downloader/tree.css
+++ b/deep_sequencing_unit/source/html/downloader/tree.css
@@ -69,9 +69,9 @@ div.inspector {
table.downloads {
font-family: "Trebuchet MS", sans-serif;
- font-size: 18px;
- font-variant: small-caps;
+ font-size: 14px;
table-layout: fixed;
+ padding: 0px;
}
/*
@@ -80,9 +80,13 @@ table.downloads {
}
*/
+.downloads tr {
+ border-bottom: 2px solid #FFFFFF;
+}
+
.downloads td {
width: 50%;
- border-right: 2px solid #FFFFFF;
+ border-bottom: 2px solid #FFFFFF;
}
.downloads td:hover {