diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv
new file mode 100644
index 0000000000000000000000000000000000000000..ed2713a61ec52c577807ba50504483b63fce26c8
--- /dev/null
+++ b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/data-from-server.csv
@@ -0,0 +1,520 @@
+id,hasPredictions,hasPhenotypes
+JJS-MGP009,False,True
+JJS-DIN262,False,False
+JJS-DIN112,True,True
+JJS-DIN237,True,True
+JJS-DIN039,True,True
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+JJS-DIN224,True,True
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+JJS-DIN214,True,True
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+JJS-MGP062,False,True
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+JJS-DIN029,True,True
+JJS-MGP122,False,True
+JJS-DIN198,True,True
+JJS-MGP098,False,True
+JJS-DIN048,True,True
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+JJS-MGP160,False,True
+JJS-DIN097,True,True
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+JJS-DIN013,True,True
+JJS-DIN162,True,True
+JJS-DIN141,True,True
+JJS-DIN277,True,True
+JJS-DIN068,True,True
+JJS-MGP037,False,True
+PROTO-4,False,False
+JJS-DIN191,True,True
+PROTO-3,False,False
+JJS-MGP015,False,True
+JJS-MGP225,False,True
+JJS-MGP036,False,True
+JJS-DIN065,True,True
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+PROTO-1,False,False
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+JJS-DIN268,False,False
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diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py
new file mode 100644
index 0000000000000000000000000000000000000000..80b8ff973f6be4d599a8eebd9708435d3db68c2a
--- /dev/null
+++ b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py
@@ -0,0 +1,44 @@
+#! /usr/bin/env python
+
+import csv
+
+FIELD_ID = 'id'
+FIELD_HAS_PREDICTIONS = 'hasPredictions'
+FIELD_HAS_PHENOTYPES = 'hasPhenotypes'
+
+def loadDataFromFile(filePath):
+ file = None
+ try:
+ file = open(filePath, 'r')
+ reader = csv.DictReader(file)
+ dataList = []
+
+ for row in reader:
+ dataList.append(row)
+
+ return dataList
+ except IOError, err:
+ print 'Could not read the data from a file: ' + str(filePath)
+ raise
+ finally:
+ if file != None:
+ file.close()
+
+def addDataToTable(dataList, table):
+ table.addHeader(FIELD_ID)
+ table.addHeader(FIELD_HAS_PREDICTIONS)
+ table.addHeader(FIELD_HAS_PHENOTYPES)
+
+ for dataItem in dataList:
+ id = dataItem[FIELD_ID]
+ hasPredictions = dataItem[FIELD_HAS_PREDICTIONS]
+ hasPhenotypes = dataItem[FIELD_HAS_PHENOTYPES]
+
+ row = table.addRow()
+ row.setCell(FIELD_ID, id)
+ row.setCell(FIELD_HAS_PREDICTIONS, hasPredictions)
+ row.setCell(FIELD_HAS_PHENOTYPES, hasPhenotypes)
+
+def aggregate(parameters, table):
+ data = loadDataFromFile('TODO_FILE_TO_FILE_WITH_SERVER_DATA')
+ addDataToTable(data, table)
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py
new file mode 100644
index 0000000000000000000000000000000000000000..ed7382b3ea65c68fb7d1b086bd364600bcfd836c
--- /dev/null
+++ b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py
@@ -0,0 +1,52 @@
+#! /usr/bin/env python
+
+import urllib
+import json
+import csv
+
+FIELD_ID = 'id'
+FIELD_PREDICTIONS = 'predictions'
+FIELD_PHENOTYPES = 'phenotypes'
+FIELD_HAS_PREDICTIONS = 'hasPredictions'
+FIELD_HAS_PHENOTYPES = 'hasPhenotypes'
+
+def loadDataFromServer(serverUrl):
+ url = urllib.urlopen(serverUrl)
+ return url.read().decode('utf8')
+
+def convertData(dataString):
+ jsonList = json.loads(dataString)
+ dataList = []
+
+ for jsonItem in jsonList:
+ id = jsonItem[FIELD_ID].upper()
+ hasPredictions = jsonItem[FIELD_PREDICTIONS] != None and len(jsonItem[FIELD_PREDICTIONS]) > 0
+ hasPhenotypes = jsonItem[FIELD_PHENOTYPES] != None and len(jsonItem[FIELD_PHENOTYPES]) > 0
+ dataList.append({FIELD_ID: id, FIELD_HAS_PREDICTIONS: hasPredictions, FIELD_HAS_PHENOTYPES: hasPhenotypes})
+
+ return dataList
+
+def writeDataToFile(filePath, dataList):
+ file = None
+ try:
+
+ file = open(filePath,'w')
+ writer = csv.writer(file)
+ writer.writerow([FIELD_ID, FIELD_HAS_PREDICTIONS, FIELD_HAS_PHENOTYPES]);
+
+ for dataItem in dataList:
+ id = dataItem[FIELD_ID]
+ hasPredictions = dataItem[FIELD_HAS_PREDICTIONS]
+ hasPhenotypes = dataItem[FIELD_HAS_PHENOTYPES]
+ writer.writerow([id, hasPredictions, hasPhenotypes])
+
+ except IOError as err:
+ print 'Could not write the data to a file: ' + str(filePath)
+ raise
+ finally:
+ if file != None:
+ file.close()
+
+data = loadDataFromServer('http://pubseed.theseed.org/model-prod/StrainServer.cgi?user=reviewer&pass=reviewer&method=getAllPhenotypesAndPredictions&encoding=json')
+writeDataToFile('data-from-server.csv', convertData(data))
+
diff --git a/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties
new file mode 100644
index 0000000000000000000000000000000000000000..666e00845bf9b229a7620241188b56bf4b27f581
--- /dev/null
+++ b/eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/plugin.properties
@@ -0,0 +1,4 @@
+label = Load data from UChicago DB
+class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonAggregationService
+script-path = load-data-from-file-and-put-to-table.py
+dataset-types = .*
diff --git a/eu_basynthec/source/html/browser/basynthec-browser.js b/eu_basynthec/source/html/browser/basynthec-browser.js
index 58a14caab61ac1497eef21fde2eb995c9c62f76c..b59a15e34fd63ae8d627fb038dd750b9fb8c74c3 100644
--- a/eu_basynthec/source/html/browser/basynthec-browser.js
+++ b/eu_basynthec/source/html/browser/basynthec-browser.js
@@ -5,7 +5,6 @@ var curveColors = d3.scale.category10().domain([0, 9]);
/**
* Abstract superclass for the wrapper classes.
- *
* @constructor
*/
function AbstractThingWrapper() {
@@ -108,12 +107,29 @@ AppPresenter.prototype.switchToOD600View = function()
od600InspectorView.updateView();
}
+/** This view is very similar to the OD600 view, but the data is also divided into two main groups:
+ * - strains for which there are phenotypes, predictions, and data in the openBIS database
+ * - strains for which there are phenotypes or predictions, but no data in the openBIS database
+ * (in this group strains with phenotypes and predictions should be marked green; strains with
+ * phenotypes only should be marked blue; strains with predictions only should be yellow)
+ * Information about the phenotypes and predictions is retrieved from UChicago strain database
+ * (http://pubseed.theseed.org/model-prod/StrainServer.cgi) and cached at the server-side in OpenBIS.
+ */
+AppPresenter.prototype.switchToOD600WithPhenotypesAndPredictionsView = function()
+{
+ this.presenterMode = presenterModeTypeStrain;
+ this.hideExplanation();
+ this.toggleDisplayedVisualizations(od600StrainWithPhenotypesAndPredictionsVis);
+ dataSetInspectorView.removeAll(250);
+ od600InspectorView.updateView();
+}
+
/** Utility function to gracefully switch from one visualization to another */
AppPresenter.prototype.toggleDisplayedVisualizations = function(visToShow)
{
this.visualizationContainers.forEach(function(vis) {
if (vis == visToShow) {
- if (od600StrainVis == vis) {
+ if (od600StrainVis == vis || od600StrainWithPhenotypesAndPredictionsVis == vis) {
// So that scrolling works
vis.style("display", "block");
} else {
@@ -152,12 +168,13 @@ AppPresenter.prototype.showDataSets = function(bisDataSets) {
};
basynthec.dataSetList.sort(sortByTypeAndRegistration);
-
- model.initialize();
-
- this.refreshDataSetTypeTables();
- this.refreshStrainTables();
- this.refreshOd600StrainTables();
+
+ model.initialize(function(){
+ presenter.refreshDataSetTypeTables();
+ presenter.refreshStrainTables();
+ presenter.refreshOd600StrainTables();
+ presenter.refreshOd600StrainWithPhenotypesAndPredictionsTables();
+ });
}
AppPresenter.prototype.refreshStrainTables = function() {
@@ -180,6 +197,12 @@ AppPresenter.prototype.refreshOd600StrainTables = function() {
od600StrainView.updateView(1000);
}
+AppPresenter.prototype.refreshOd600StrainWithPhenotypesAndPredictionsTables = function() {
+ this.createVis();
+ od600StrainWithPhenotypesAndPredictionsView.updateView(1000);
+}
+
+
AppPresenter.prototype.createVis = function()
{
if (this.didCreateVis) return;
@@ -216,7 +239,13 @@ AppPresenter.prototype.createVis = function()
od600StrainVis.style("overflow-y", "scroll");
od600StrainView = new Od600StrainView();
- this.visualizationContainers = [dataSetTypeVis, strainVis, od600StrainVis];
+ od600StrainWithPhenotypesAndPredictionsVis = tableRoot.append("div").style("display", "none");
+ od600StrainWithPhenotypesAndPredictionsVis.style("width", w + "px");
+ od600StrainWithPhenotypesAndPredictionsVis.style("height",w + "px");
+ od600StrainWithPhenotypesAndPredictionsVis.style("overflow-y", "scroll");
+ od600StrainWithPhenotypesAndPredictionsView = new Od600StrainWithPhenotypesAndPredictionsView();
+
+ this.visualizationContainers = [dataSetTypeVis, strainVis, od600StrainVis, od600StrainWithPhenotypesAndPredictionsVis];
dataSetInspectorView = new DataSetInspectorView();
od600InspectorView = new Od600InspectorView();
@@ -406,11 +435,12 @@ function AppModel() {
this.dataSetsByType = { };
}
-AppModel.prototype.initialize = function() {
+AppModel.prototype.initialize = function(callback) {
this.initializeDataSetsByType();
this.initializeDataSetsByStrain();
this.initializeStrainGroups();
- this.initializeOd600Model();
+ this.initializeOd600Model();
+ this.initializeOd600WithPhenotypesAndPredictionsModel(callback);
}
/** Compute the dataSetsByType variable */
@@ -448,7 +478,7 @@ AppModel.prototype.initializeDataSetsByStrain = function() {
AppModel.prototype.initializeStrainGroups = function() {
var strains = []
for (strainName in this.dataSetsByStrain) {
- strains.push(strainName)
+ strains.push({name: strainName});
}
this.strainGroups = createStrainGroups(strains);
}
@@ -477,6 +507,57 @@ AppModel.prototype.initializeOd600Model= function() {
});
}
+AppModel.prototype.initializeOd600WithPhenotypesAndPredictionsModel = function(callback){
+ var model = this;
+
+ basynthec.getStrainsPhenotypesAndPredictions(function(strainDataMap){
+
+ var strainsKnownToOpenbisWithPhenotypesAndPredictions = [];
+ var strainsUnknownToOpenbisWithPhenotypesOrPredictions = [];
+
+ for(strainName in model.dataSetsByStrain){
+ var strainData = strainDataMap[strainName];
+ var strainDatasets = model.dataSetsByStrain[strainName];
+
+ var hasPhenotypesAndPredictions = strainData && strainData.hasPhenotypes && strainData.hasPredictions;
+ var hasOd600Datasets = strainDatasets && strainDatasets.dataSets.some(function(dataset){
+ return "OD600" == dataset.dataSetTypeCode;
+ });
+
+ if(hasPhenotypesAndPredictions && hasOd600Datasets){
+ strainData.isKnown = true;
+ strainsKnownToOpenbisWithPhenotypesAndPredictions.push(strainData);
+ }
+ }
+
+ for(strainName in strainDataMap){
+ var strainData = strainDataMap[strainName];
+ var strainDatasets = model.dataSetsByStrain[strainName];
+
+ var hasPhenotypesOrPredictions = strainData && (strainData.hasPhenotypes || strainData.hasPredictions);
+ var hasDatasets = strainDatasets && strainDatasets.dataSets.length > 0;
+
+ if(hasPhenotypesOrPredictions && !hasDatasets){
+ strainData.isKnown = false;
+ strainsUnknownToOpenbisWithPhenotypesOrPredictions.push(strainData);
+ }
+ }
+
+ model.od600StrainsWithPhenotypesAndPredictionsGroups = [];
+ model.od600StrainsWithPhenotypesAndPredictionsGroups.push({
+ "mainGroupName" : "Known strains with phenotypes and predictions",
+ "groups" : createStrainGroups(strainsKnownToOpenbisWithPhenotypesAndPredictions)
+ });
+ model.od600StrainsWithPhenotypesAndPredictionsGroups.push({
+ "mainGroupName" : "Unknown strains with phenotypes or predictions",
+ "groups" : createStrainGroups(strainsUnknownToOpenbisWithPhenotypesOrPredictions)
+ });
+
+ callback();
+ });
+
+}
+
AppModel.prototype.od600DataSets = function() {
return this.dataSetsByType["OD600"];
}
@@ -485,6 +566,10 @@ AppModel.prototype.od600DataSets = function() {
* A utility function that groups strains together based on strain name
*/
function createStrainGroups(strains) {
+ if(!strains || strains.length == 0){
+ return [];
+ }
+
// prefixes of strain names to be grouped togehter
var STRAIN_GROUP_PREFIXES = [ "JJS-DIN", "JJS-MGP" ];
@@ -494,19 +579,19 @@ function createStrainGroups(strains) {
var groups = STRAIN_GROUP_PREFIXES.map(
function(strainPrefix) {
var filtered = strains.filter(function(strain) {
- return strain.indexOf(strainPrefix) >= 0
+ return strain.name.indexOf(strainPrefix) >= 0
});
var groupStrains = filtered.map(function(strain) {
- return { name : strain, label : strain.substring(strainPrefix.length)};
+ return { name : strain.name, label : strain.name.substring(strainPrefix.length), data: strain};
});
return {groupName : STRAIN_GROUP_PREFIXES_DISPLAY_NAME[strainPrefix], strains : groupStrains};
});
var otherStrains = strains.filter(function(strain) {
- return false == STRAIN_GROUP_PREFIXES.some(function(prefix) { return strain.indexOf(prefix) >=0; } );
+ return false == STRAIN_GROUP_PREFIXES.some(function(prefix) { return strain.name.indexOf(prefix) >=0; } );
});
- otherStrains = otherStrains.map(function(strain) { return {name:strain, label:strain}});
+ otherStrains = otherStrains.map(function(strain) { return {name:strain.name, label:strain.name, data: strain}});
groups.push({groupName : "Other strains", strains : otherStrains});
var sortFunction = sortByProp("name")
@@ -647,6 +732,72 @@ Od600StrainView.prototype.updateView = function(duration)
.text(function(d) { return d.label });
}
+/**
+ * The view for the OD600 strains with phenotypes and predictions
+ *
+ * @constructor
+ */
+function Od600StrainWithPhenotypesAndPredictionsView(){
+}
+
+Od600StrainWithPhenotypesAndPredictionsView.prototype.updateView = function(duration)
+{
+ var mainGroupDiv = od600StrainWithPhenotypesAndPredictionsVis.selectAll("div.strainsMainGroup").data(model.od600StrainsWithPhenotypesAndPredictionsGroups)
+ .enter().append("div").attr("class", "strainsMainGroup");
+
+ mainGroupDiv.append("h2").text(function(d) { return d.mainGroupName });
+
+ var strainDiv = mainGroupDiv.selectAll("div.strains").data(function(d){ return d.groups; })
+ .enter().append("div").attr("class", "strains");
+
+ strainDiv.append("h3").text(function(d) { return d.groupName });
+ strainDiv.append("table").selectAll("tr").data(function(d) {
+ // Group the different sets of strains differently
+ if (d.groupName.indexOf("Other") == 0) return d.strains.reduce(groupBy(3), []);
+ if (d.groupName.indexOf("JJS-MGP") == 0) return d.strains.reduce(groupBy(10), []);
+
+ // Group the JJS-DIn strains by runs
+ return d.strains.reduce(groupByRuns(10), []) })
+ .enter()
+ .append("tr")
+ .selectAll("td").data(function(d) { return d })
+ .enter()
+ .append("td")
+ .attr("class", function(d){
+ if(d.data.isKnown){
+ return "known";
+ }else{
+ return "unknown";
+ }
+ })
+ .on("click", function(d){
+ if(d.data.isKnown){
+ return toggleOd600Inspected.call(this, d);
+ }
+ })
+ .text(function(d) { return d.label })
+ .style("color", function(d){
+ if(d.data.isKnown){
+ return "black";
+ }else{
+ if(d.data.hasPhenotypes && d.data.hasPredictions){
+ return "green";
+ }else if(d.data.hasPhenotypes){
+ return "blue";
+ }else if(d.data.hasPredictions){
+ return "red";
+ }
+ }
+ });
+
+ var legend = od600StrainWithPhenotypesAndPredictionsVis.append("div");
+ legend.append("h3").style("font-style","italic").text("Legend");
+ var legendList = legend.append("ul");
+ legendList.append("li").append("span").text("strain with phenotypes and predictions").style("color","green");
+ legendList.append("li").append("span").text("strain with phenotypes only").style("color","blue");
+ legendList.append("li").append("span").text("strain with predictions only").style("color","red");
+}
+
/**
* The view that shows data sets.
*
@@ -932,6 +1083,9 @@ function props_to_pairs(d)
var pairs = [];
var dataSetStrains = basynthec.getStrains({properties:d});
+ dataSetStrains = dataSetStrains.map(function(strain){
+ return { name : strain };
+ });
var strainGroups = createStrainGroups(dataSetStrains);
strainGroups.forEach(function(group) {
diff --git a/eu_basynthec/source/html/browser/basynthec-style.css b/eu_basynthec/source/html/browser/basynthec-style.css
index d4c9d209a40f2d8871353b03c4b58b4fcbd9b0a9..ee552870b0a4812edcc9a577f5c2ce072475e884 100644
--- a/eu_basynthec/source/html/browser/basynthec-style.css
+++ b/eu_basynthec/source/html/browser/basynthec-style.css
@@ -1,6 +1,10 @@
body { font: 14px "Trebuchet MS", sans-serif; }
h1 { font: 16px; }
+h2 {
+ font-family: "Verdana", sans-serif;
+ color: #222;
+}
h3 { font: 12px; }
.strains { padding-bottom: 10px; }
@@ -9,11 +13,6 @@ h3 { font: 12px; }
border-collapse: collapse;
}
-.strains h2 {
- font-family: "Verdana", sans-serif;
- color: #222;
-}
-
.strains td {
font-family: "Verdana", sans-serif;
font-size: 12px;
@@ -29,6 +28,10 @@ h3 { font: 12px; }
cursor: pointer;
}
+.strains td.unknown:hover {
+ cursor: auto;
+}
+
.datasetsummarytable {
font-family: "Verdana", sans-serif;
}
diff --git a/eu_basynthec/source/html/browser/index.html b/eu_basynthec/source/html/browser/index.html
index 70a3421411dff301e4bc6174ae905785d7b750fb..780de5d2ad41035ba108f9f6f0063e7c6a13edef 100644
--- a/eu_basynthec/source/html/browser/index.html
+++ b/eu_basynthec/source/html/browser/index.html
@@ -54,6 +54,9 @@ $(document).ready(function() {
$("#groupradio3").change(function(event){
presenter.switchToOD600View();
});
+ $("#groupradio4").change(function(event){
+ presenter.switchToOD600WithPhenotypesAndPredictionsView();
+ });
$('#login-form').submit(function() {
$("#login-failed").hide();
@@ -106,10 +109,11 @@ $(document).ready(function() {
<input type="radio" name="groupgroup" id="groupradio1" checked> <label for="groupradio1">Data Set Type</label>
<input type="radio" name="groupgroup" id="groupradio2"> <label for="groupradio2">Strains</label>
<input type="radio" name="groupgroup" id="groupradio3"> <label for="groupradio3">OD600</label>
+ <input type="radio" name="groupgroup" id="groupradio4"> <label for="groupradio4">OD600 with phenotypes and predictions</label>
</div>
</div>
</div>
</body>
-</html>
\ No newline at end of file
+</html>
diff --git a/eu_basynthec/source/html/browser/openbis-basynthec.js b/eu_basynthec/source/html/browser/openbis-basynthec.js
index 943efa54e12637cc28572a07c82e6545644b8ee7..6ba6f51ca10cfd3d126882befc46834cf28c6077 100644
--- a/eu_basynthec/source/html/browser/openbis-basynthec.js
+++ b/eu_basynthec/source/html/browser/openbis-basynthec.js
@@ -60,4 +60,22 @@ openbis_basynthec.prototype.getStrains = function(dataSet)
{
return [];
}
-}
\ No newline at end of file
+}
+
+openbis_basynthec.prototype.getStrainsPhenotypesAndPredictions = function(action){
+ this.server.createReportFromAggregationService("DSS1","chicago", null, function(response){
+ var result = [];
+
+ if(response.result && response.result.rows){
+ $.each(response.result.rows, function(index, row){
+ result[row[0].value] = {
+ "name" : row[0].value,
+ "hasPhenotypes" : row[1].value && row[1].value.toUpperCase() == "TRUE",
+ "hasPredictions" : row[2].value && row[2].value.toUpperCase() == "TRUE"
+ }
+ });
+ }
+
+ action(result);
+ });
+}
diff --git a/eu_basynthec/source/html/browser/openbis.js b/eu_basynthec/source/html/browser/openbis.js
index e35025bfb4377979b4dfef992b07bb0153ace058..3039e3488be7a3d357d1d448a8318f134393cb67 100644
--- a/eu_basynthec/source/html/browser/openbis.js
+++ b/eu_basynthec/source/html/browser/openbis.js
@@ -310,6 +310,20 @@ openbis.prototype.executeQuery = function(queryId, parameterBindings, action) {
});
}
+/**
+ * See ch.systemsx.cisd.openbis.plugin.query.shared.api.v1.IQueryApiServer.createReportFromAggregationService(String, String, String, Map<String, String>)
+ *
+ * @method
+ */
+openbis.prototype.createReportFromAggregationService = function(dataStoreCode, serviceKey, parameters, action) {
+ ajaxRequest({
+ url: this.queryServiceUrl,
+ data: { "method" : "createReportFromAggregationService",
+ "params" : [ this.sessionToken, dataStoreCode, serviceKey, parameters ] },
+ success: action
+ });
+}
+
/**
* A utility class for deferring an action until all of some kind of action has completed
*