From ecee7b69908fbbf7c291e06ee3ed95b078640b1c Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Mon, 26 Nov 2012 14:47:29 +0000
Subject: [PATCH] BIS-263 SP-400 : Retrieve sample information from the AS.
SVN: 27768
---
.../1/as/webapps/bottom-up/html/openbis.js | 19 +++
.../1/as/webapps/bottom-up/html/webapp.js | 135 ++++++++++++++++--
.../1/as/webapps/bottom-up/plugin.properties | 2 +-
.../sample-bottom-up-data/plugin.properties | 3 +
.../sample-bottom-up-data/sample-bottom-up.py | 8 ++
5 files changed, 154 insertions(+), 13 deletions(-)
create mode 100644 deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/plugin.properties
create mode 100644 deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/sample-bottom-up.py
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/openbis.js b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/openbis.js
index 36c5c3e7219..86fe7a99717 100644
--- a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/openbis.js
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/openbis.js
@@ -231,6 +231,25 @@ openbis.prototype.searchForSamples = function(searchCriteria, action) {
});
}
+/**
+ * See ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService.searchForSamples(String, SearchCriteria, EnumSet<SampleFetchOption>)
+ *
+ * @method
+ */
+openbis.prototype.searchForSamplesWithFetchOptions = function(searchCriteria, fetchOptions, action) {
+ ajaxRequest({
+ url: this.generalInfoServiceUrl,
+ data: {
+ "method" : "searchForSamples",
+ "params" : [
+ this.sessionToken,
+ searchCriteria,
+ fetchOptions ]
+ },
+ success: action
+ });
+}
+
/**
* See ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService.searchForDataSets(String, SearchCriteria)
*
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/webapp.js b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/webapp.js
index 1760dfe166a..9b2e71293b8 100644
--- a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/webapp.js
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/html/webapp.js
@@ -1,3 +1,15 @@
+//
+// BEGIN CONFIGURATION PARAMTERS
+//
+// The following parameters must be configured for the webapp
+
+// The name of the dss
+var DSS_NAME = "DSS1";
+
+var FLOWCELL_SAMPLE_TYPE = "FLOWCELL";
+
+// END CONFIGURATION PARAMTERS
+
/// The openbisServer we use for our data
var webappContext = new openbisWebAppContext();
@@ -26,9 +38,57 @@ function SampleGraphModel() {
SampleGraphModel.prototype.initializeModel = function() {
this.sampleIdentifier = webappContext.getEntityIdentifier();
+ var identifierTokens = this.sampleIdentifier.split("/");
+ this.sampleSpace = identifierTokens[1];
+ this.sampleCode = identifierTokens[2];
this.samplePermId = webappContext.getEntityPermId();
}
+/**
+ * Request the data necessary to display the graph. This variant uses an aggregation service
+ */
+SampleGraphModel.prototype.requestGraphDataFromAggregationService = function(callback)
+{
+ var parameters = {'FLOWCELL_PERM_ID' : this.samplePermId};
+
+ openbisServer.createReportFromAggregationService(DSS_NAME, "sample-bottom-up-data", parameters, callback);
+}
+
+/**
+ * Request the data necessary to display the graph.
+ */
+SampleGraphModel.prototype.requestGraphData = function(callback)
+{
+ var containerCriteria = {
+ matchClauses :
+ [ {"@type" : "AttributeMatchClause",
+ fieldType : "ATTRIBUTE",
+ attribute : "TYPE",
+ desiredValue : FLOWCELL_SAMPLE_TYPE
+ }, {"@type" : "AttributeMatchClause",
+ fieldType : "ATTRIBUTE",
+ attribute : "CODE",
+ desiredValue : this.sampleCode
+ }, {"@type" : "AttributeMatchClause",
+ fieldType : "ATTRIBUTE",
+ attribute : "SPACE",
+ desiredValue : this.sampleSpace
+ } ],
+ operator : "MATCH_ALL_CLAUSES"
+ };
+
+ var sampleCriteria = {
+ subCriterias :
+ [ {"@type" : "SearchSubCriteria",
+ criteria : containerCriteria,
+ targetEntityKind : "SAMPLE_CONTAINER"
+ } ]
+ };
+
+ openbisServer.searchForSamplesWithFetchOptions(sampleCriteria, ["PROPERTIES", "ANCESTORS", "DESCENDANTS"], callback);
+}
+
+
/**
* The presenter that shows the model.
*/
@@ -47,14 +107,16 @@ SampleGraphPresenter.prototype.initializePresenter = function()
// Create a div to house the tree visualization and the inspectors
this.root = d3.select("#root");
+ this.rootLabel = d3.select("#root-label");
+ this.rootLabel.text(this.model.sampleIdentifier);
this.didCreateVis = true;
}
/**
- * Display the data returned by the server
+ * Display the table data returned by the server
*/
-SampleGraphPresenter.prototype.showGraph = function(data)
+SampleGraphPresenter.prototype.showGraphTable = function(data)
{
if (data.error) {
console.log(data.error);
@@ -74,6 +136,59 @@ SampleGraphPresenter.prototype.showGraph = function(data)
showTableData(table);
}
+/**
+ * Display the sample returned by the server
+ */
+SampleGraphPresenter.prototype.showGraphSamples = function(data)
+{
+ if (data.error) {
+ console.log(data.error);
+ this.root.append("p").text("Could not retrieve data.");
+ return;
+ }
+
+ // This will show the object in the log -- helpful for debugging
+ // console.log(data.result);
+ var tableData = data.result;
+
+ // Display the rows in a table
+ var table = this.root.selectAll("table").data([tableData]);
+ // Code under enter is run if there is no HTML element for a data element
+ table.enter().append("table").attr("class", "table");
+ this.showEntityTableHeader(table);
+ this.showEntityTableData(table);
+}
+
+/**
+ * Construct the table header.
+ */
+SampleGraphPresenter.prototype.showEntityTableHeader = function(table)
+{
+ var header = table.selectAll("thead").data(function(d) { return [["Identifier", "Multiplex"]] });
+ header.enter().append("thead");
+ var headerRows = header.selectAll("tr").data(function(d) { return [d] });
+ headerRows.enter().append("tr");
+ var headerData = headerRows.selectAll("th").data(function(d) { return d; });
+ headerData.enter().append("th");
+ headerData.text(function (d) { return d})
+}
+
+/**
+ * Construct the table data.
+ */
+SampleGraphPresenter.prototype.showEntityTableData = function(table)
+{
+ var tableBody = table.selectAll("tbody").data(function(d) { return d });
+ tableBody.enter().append("tbody");
+ var dataRows = tableBody.selectAll("tr").data(function(d) { return [d] });
+ dataRows.enter().append("tr").on("click", function (d) { presenter.selectEntity(d); });
+ dataRows.exit().remove();
+
+ var dataData = dataRows.selectAll("td").data(function(d) { console.log(d); return [d.identifier, "" + d.parents[0]["@id"] + " " + d.parents[0].identifier] });
+ dataData.enter().append("td");
+ dataData.text(function (d) { return d });
+}
+
SampleGraphPresenter.prototype.selectEntity = function(d) {
}
@@ -117,23 +232,19 @@ function showTableData(table)
}
-function displayRoot(data)
+function displayGraphTable(data)
{
- presenter.showGraph(data)
+ presenter.showGraphTable(data)
}
-/**
- * Request samples matching some criteria from the server and show them in the Page.
- */
-function listRootLevelEntities()
+function displayGraphSamples(data)
{
- var parameters = {requestKey : 'ROOT'};
-
- openbisServer.createReportFromAggregationService("DSS1", "ipad-read-service-v1", parameters, displayRoot);
+ presenter.showGraphSamples(data)
}
function enterApp(data)
{
presenter = new SampleGraphPresenter(model);
- listRootLevelEntities();
+ //model.requestGraphDataFromAggregationService(displayGraphTable);
+ model.requestGraphData(displayGraphSamples);
}
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/plugin.properties b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/plugin.properties
index 51f90650dc0..9b2c6c383ec 100644
--- a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/plugin.properties
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/as/webapps/bottom-up/plugin.properties
@@ -4,4 +4,4 @@ webapp-folder = html
label = Bottom-Up Graph
sorting = 1
openbisui-contexts = sample-details-view
-sample-entity-types = .*
+sample-entity-types = FLOWCELL
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/plugin.properties b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/plugin.properties
new file mode 100644
index 00000000000..4420c9f866f
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/plugin.properties
@@ -0,0 +1,3 @@
+label = Sample Bottom Up Data
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
+script-path = sample-bottom-up.py
\ No newline at end of file
diff --git a/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/sample-bottom-up.py b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/sample-bottom-up.py
new file mode 100644
index 00000000000..a698d3c98f5
--- /dev/null
+++ b/deep_sequencing_unit/source/core-plugins/ngs-sample-overview-graph/1/dss/reporting-plugins/sample-bottom-up-data/sample-bottom-up.py
@@ -0,0 +1,8 @@
+"""An aggregation service that aggregates data for the sample-bottom-up display"""
+
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+
+def aggregate(parameters, table_builder):
+ table_builder.addHeader("TEST")
+ row = table_builder.addRow()
+ row.setCell("TEST", "TEST")
--
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