Item 5911: Added tic area as default run scoped metric

* Item 5911 : Add new run scoped metric in qcmetricconfiguration and new column in sample file * Item 5911: Read tic area in skyline doc importer and add in samplefile table * Item 5911: new run scoped metric query and changes in qc plot panel * Item 5911: Hide/Un-hide Show All Series in a single plot checkbox in qc plot web part * Item 5911: upgrading sql scripts and module version * Item 5911: using setVisible to show/hide the checkbox * Item 5911: Include runid in view document link for run scoped metrics * Item 5911: Adding ticarea column in xml * Item 5911: sample data -adding tic area to existing sample data file * Item 5912 : automated test * Fixing automated tests and correcting typo * Item 5912: Re-arranging the order of qc metric configuration deletions on container delete * scroll down to qc plot web part * Item 5912: mouse over data point * adding wait after scroll to the view * Added wiki webpart to scroll into * Moving QC Plots webpart at the top * Removing sleep * moving qc plt webpart down after the test
nickshulman · Aug 2, 2019 · d903f72 · d903f72
1 parent c96418d
commit d903f72
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Showing 19 changed files with 233 additions and 15 deletions.
diff --git a/resources/queries/targetedms/QCRunMetric_ticArea.query.xml b/resources/queries/targetedms/QCRunMetric_ticArea.query.xml
@@ -0,0 +1,18 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="QCRunMetric_ticArea" tableDbType="NOT_IN_DB">
+                <columns>
+                    <column columnName="SampleFileId">
+                        <fk>
+                            <fkDbSchema>targetedms</fkDbSchema>
+                            <fkTable>SampleFile</fkTable>
+                            <fkColumnName>Id</fkColumnName>
+                            <fkDisplayColumnName>SampleName</fkDisplayColumnName>
+                        </fk>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>
diff --git a/resources/queries/targetedms/QCRunMetric_ticArea.sql b/resources/queries/targetedms/QCRunMetric_ticArea.sql
@@ -0,0 +1,25 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+SELECT
+  0 AS PrecursorId,
+  0 AS PrecursorChromInfoId,
+  Id AS SampleFileId,
+  'Total Ion Chromatogram Area' AS SeriesLabel,
+  NULL AS DataType,
+  TicArea AS MetricValue,
+  0.0 AS mz
+FROM SampleFile
diff --git a/resources/schemas/dbscripts/postgresql/targetedms-19.21-19.22.sql b/resources/schemas/dbscripts/postgresql/targetedms-19.21-19.22.sql
@@ -0,0 +1,22 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+WITH rootIdentity as (select EntityId as theIdentity FROM core.Containers WHERE Parent is null)
+
+INSERT INTO targetedms.QCMetricConfiguration (Container, Name,Series1Label,Series1SchemaName,Series1QueryName,Series2Label,Series2SchemaName,Series2QueryName,PrecursorScoped) VALUES
+((select theIdentity from rootIdentity), 'TIC Area','TIC Area','targetedms','QCRunMetric_ticArea',NULL , NULL , NULL , FALSE );
+
+ALTER TABLE targetedms.SampleFile ADD COLUMN TicArea DOUBLE PRECISION;
diff --git a/resources/schemas/dbscripts/sqlserver/targetedms-19.21-19.22.sql b/resources/schemas/dbscripts/sqlserver/targetedms-19.21-19.22.sql
@@ -0,0 +1,24 @@
+/*
+ * Copyright (c) 2019 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+declare @rootIdentity ENTITYID;
+select @rootIdentity = [EntityId] FROM [core].[Containers] WHERE Parent is null
+
+INSERT INTO targetedms.QCMetricConfiguration (Container, Name, Series1Label, Series1SchemaName, Series1QueryName, PrecursorScoped)
+VALUES (@rootIdentity, 'TIC Area','TIC Area','targetedms','QCRunMetric_ticArea', 0);
+
+ALTER TABLE targetedms.SampleFile ADD TicArea DOUBLE PRECISION;
diff --git a/resources/schemas/targetedms.xml b/resources/schemas/targetedms.xml
@@ -88,6 +88,7 @@
             <column columnName="InstrumentId">
                 <columnTitle>Instrument</columnTitle>
             </column>
+            <column columnName="TicArea"/>
         </columns>
     </table>
     <table tableName="Runs" tableDbType="TABLE">

diff --git a/src/org/labkey/targetedms/TargetedMSListener.java b/src/org/labkey/targetedms/TargetedMSListener.java
@@ -78,11 +78,12 @@ public void containerDeleted(Container c, User user)
         // Clean up AutoQCPing
         new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoAutoQCPing() + " WHERE Container = ?", c);
 
+        //Clean up QC enabled metrics
+        new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoQCEnabledMetrics() + " WHERE Container = ?", c);
+
         // Clean up Metric Configurations
         new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoQCMetricConfiguration() + " WHERE Container = ?", c);
 
-        //Clean up QC enabled metrics
-        new SqlExecutor(TargetedMSManager.getSchema()).execute("DELETE FROM " + TargetedMSManager.getTableInfoQCEnabledMetrics() + " WHERE Container = ?", c);
 
         BlibSpectrumReader.clearBlibCache(c);
     }

diff --git a/src/org/labkey/targetedms/TargetedMSManager.java b/src/org/labkey/targetedms/TargetedMSManager.java
@@ -1947,8 +1947,10 @@ public List<QCMetricConfiguration> getEnabledQCMetricConfigurations(Container co
                         "Series1QueryName, " +
                         "Series2Label, " +
                         "Series2SchemaName, " +
-                        "Series2QueryName " +
-                      "FROM qcMetricsConfig WHERE Enabled = TRUE";
+                        "Series2QueryName, " +
+                        "PrecursorScoped " +
+                      "FROM qcMetricsConfig " +
+                      "WHERE Enabled = TRUE ";
 
         QuerySchema query = DefaultSchema.get(user, container).getSchema(TargetedMSSchema.SCHEMA_NAME);
         return QueryService.get().selector(query, sql).getArrayList(QCMetricConfiguration.class);

diff --git a/src/org/labkey/targetedms/TargetedMSModule.java b/src/org/labkey/targetedms/TargetedMSModule.java
@@ -208,7 +208,7 @@ public String getName()
     @Override
     public double getVersion()
     {
-        return 19.21;
+        return 19.22;
     }
 
     @Override

diff --git a/src/org/labkey/targetedms/model/QCMetricConfiguration.java b/src/org/labkey/targetedms/model/QCMetricConfiguration.java
@@ -27,6 +27,7 @@ public class QCMetricConfiguration
     private String _series2Label;
     private String _series2SchemaName;
     private String _series2QueryName;
+    private boolean _precursorScoped;
 
     public int getId()
     {
@@ -107,13 +108,24 @@ public void setSeries2QueryName(String series2QueryName)
         _series2QueryName = series2QueryName;
     }
 
+    public boolean isPrecursorScoped()
+    {
+        return _precursorScoped;
+    }
+
+    public void setPrecursorScoped(boolean precursorScoped)
+    {
+        _precursorScoped = precursorScoped;
+    }
+
     public JSONObject toJSON(){
         JSONObject jsonObject = new JSONObject();
         jsonObject.put("id", _id);
         jsonObject.put("name", _name);
         jsonObject.put("series1Label",      _series1Label);
         jsonObject.put("series1SchemaName", _series1SchemaName);
         jsonObject.put("series1QueryName",  _series1QueryName);
+        jsonObject.put("precursorScoped",  _precursorScoped);
         if(_series2Label != null){
             jsonObject.put("series2Label",      _series2Label);
         }

diff --git a/src/org/labkey/targetedms/parser/SampleFile.java b/src/org/labkey/targetedms/parser/SampleFile.java
@@ -31,6 +31,7 @@ public class SampleFile extends SkylineEntity
     private String _skylineId;
     private Date _acquiredTime;
     private Date _modifiedTime;
+    private Double _ticArea;
 
     private List<Instrument> _instrumentInfoList;
     private boolean _skip;
@@ -115,4 +116,13 @@ public void setInstrumentInfoList(List<Instrument> instrumentInfoList)
         _instrumentInfoList = instrumentInfoList;
     }
 
+    public Double getTicArea()
+    {
+        return _ticArea;
+    }
+
+    public void setTicArea(Double ticArea)
+    {
+        _ticArea = ticArea;
+    }
 }
diff --git a/src/org/labkey/targetedms/parser/SkylineDocumentParser.java b/src/org/labkey/targetedms/parser/SkylineDocumentParser.java
@@ -916,6 +916,7 @@ private SampleFile readSampleFile(XMLStreamReader reader) throws XMLStreamExcept
 
         sampleFile.setAcquiredTime(XmlUtil.readDateAttribute(reader, "acquired_time"));
         sampleFile.setModifiedTime(XmlUtil.readDateAttribute(reader, "modified_time"));
+        sampleFile.setTicArea(XmlUtil.readDoubleAttribute(reader,"tic_area"));
 
         List<Instrument> instrumentList = new ArrayList<>();
         sampleFile.setInstrumentInfoList(instrumentList);

diff --git a/test/sampledata/TargetedMS/SProCoPTutorial.zip b/test/sampledata/TargetedMS/SProCoPTutorial.zip
diff --git a/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java b/test/src/org/labkey/test/components/targetedms/QCPlotsWebPart.java
@@ -237,7 +237,8 @@ public enum MetricType
         LHRATIO("Light/Heavy Ratio", false),
         TPAREARATIO("Transition/Precursor Area Ratio", true),
         TPAREAS("Transition & Precursor Areas", true),
-        MASSACCURACTY("Mass Accuracy", true);
+        MASSACCURACY("Mass Accuracy", true),
+        TICAREA("TIC Area", true);
 
         private String _text;
         private boolean _hasData;
@@ -784,4 +785,15 @@ protected Checkbox findQCPlotTypeCheckbox(QCPlotType plotType)
             return plotTypeCheckboxes.get(plotType);
         }
     }
+
+    public Locator.XPathLocator getBubble()
+    {
+        return Locator.byClass("hopscotch-bubble-container");
+    }
+
+    public Locator.XPathLocator getBubbleContent()
+    {
+        Locator.XPathLocator hopscotchBubble = Locator.byClass("hopscotch-bubble-container");
+        return hopscotchBubble.append(Locator.byClass("hopscotch-bubble-content").append(Locator.byClass("hopscotch-content")));
+    }
 }
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCSummaryTest.java
@@ -232,7 +232,7 @@ public void testShowAutoQC()
         waitForElements(Locator.tagWithClass("div", "sample-file-item"), 6);
         tempStringList01.put("Q_Exactive_08_23_2013_JGB_58", "27");
         tempStringList01.put("Q_Exactive_08_23_2013_JGB_51", "26");
-        tempStringList01.put("Q_Exactive_08_23_2013_JGB_37", "29");
+        tempStringList01.put("Q_Exactive_08_23_2013_JGB_37", "31");
         tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_58", "Acquired Date/Time: 2013-08-27 14:45"));
         tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_51", "Acquired Date/Time: 2013-08-27 03:19"));
         tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_37", "Acquired Date/Time: 2013-08-26 04:27"));
@@ -293,10 +293,12 @@ public void testShowAutoQC()
         tempStringList01.clear();
         tempStringList01.put("Q_Exactive_08_23_2013_JGB_58", "2");
         tempStringList01.put("Q_Exactive_08_23_2013_JGB_51", "4");
+        tempStringList01.put("Q_Exactive_08_23_2013_JGB_37", "1");
 
         tempStringList02.clear();
         tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_58", "Full Width at Half Maximum (FWHM) 1 1 0 0 0 0"));
         tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_51", "Peak Area 0 2 0 0 0 0"));
+        tempStringList02.add(Arrays.asList("Q_Exactive_08_23_2013_JGB_37", "TIC Area 0 1 0 0 0 0"));
         validateSampleFile(0, tempStringList01, tempStringList02);
 
         removeAllGuideSets();

diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSQCTest.java
@@ -28,6 +28,7 @@
 import org.labkey.test.categories.DailyB;
 import org.labkey.test.categories.MS2;
 import org.labkey.test.components.ext4.RadioButton;
+import org.labkey.test.components.html.SiteNavBar;
 import org.labkey.test.components.targetedms.GuideSet;
 import org.labkey.test.components.targetedms.QCAnnotationTypeWebPart;
 import org.labkey.test.components.targetedms.QCAnnotationWebPart;
@@ -55,7 +56,6 @@
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.CUSUMm;
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.LeveyJennings;
 import static org.labkey.test.components.targetedms.QCPlotsWebPart.QCPlotType.MovingRange;
@@ -155,6 +155,8 @@ public class TargetedMSQCTest extends TargetedMSTest
                     "\n" +
                     "    return testLegends();";
 
+    private final PortalHelper portalHelper = new PortalHelper(this);
+
     @Override
     protected String getProjectName()
     {
@@ -364,7 +366,7 @@ public void testQCPlotLogMessages()
         qcPlotsWebPart.checkAllPlotTypes(true);
 
         // if metric has negative values and we pick log y-axis scale, we should revert to linear scale and show message
-        qcPlotsWebPart.setMetricType(QCPlotsWebPart.MetricType.MASSACCURACTY);
+        qcPlotsWebPart.setMetricType(QCPlotsWebPart.MetricType.MASSACCURACY);
         qcPlotsWebPart.setScale(QCPlotsWebPart.Scale.LOG);
         assertEquals("Unexpected number of plots with invalid log scale.", 3, qcPlotsWebPart.getLogScaleInvalidCount());
         assertEquals("Unexpected number of plots with invalid log scale.", 0, qcPlotsWebPart.getLogScaleWarningCount());
@@ -662,6 +664,42 @@ public void testCombinedPlots()
         qcPlotsWebPart.resetInitialQCPlotFields();
     }
 
+    @Test
+    public void testRunScopedMetric()
+    {
+        new SiteNavBar(getDriver()).enterPageAdminMode();
+        portalHelper.moveWebPart("QC Plots", PortalHelper.Direction.UP);
+        String acquiredDate = "2013-08-09 11:39:00";
+        PanoramaDashboard qcDashboard = new PanoramaDashboard(this);
+        QCPlotsWebPart qcPlotsWebPart = qcDashboard.getQcPlotsWebPart();
+
+        log("Verifying TIC Area QC Plots");
+        qcPlotsWebPart.setMetricType(QCPlotsWebPart.MetricType.TICAREA);
+        qcPlotsWebPart.waitForPlots(1, true);
+        String ticPlotSVGText = qcPlotsWebPart.getSVGPlotText("tiledPlotPanel-2-precursorPlot0");
+        assertFalse(ticPlotSVGText.isEmpty());
+
+        log("Verifying Show All Series Checkbox");
+        assertElementNotVisible(Locator.tagContainingText("label", "Show All Series in a Single Plot"));
+        qcPlotsWebPart.setMetricType(QCPlotsWebPart.MetricType.RETENTION);
+        assertElementVisible(Locator.tagContainingText("label", "Show All Series in a Single Plot"));
+
+        log("Verifying tic_area information in hover plot");
+        qcPlotsWebPart.setMetricType(QCPlotsWebPart.MetricType.TICAREA);
+        qcPlotsWebPart.waitForPlots(1, true);
+        mouseOver(qcPlotsWebPart.getPointByAcquiredDate(acquiredDate));
+        waitForElement(qcPlotsWebPart.getBubble());
+        String ticAreahoverText = waitForElement(qcPlotsWebPart.getBubbleContent()).getText();
+        assertTrue("Wrong header present", ticAreahoverText.contains("Total Ion Chromatogram Area"));
+        assertTrue("Wrong Link present", ticAreahoverText.contains("VIEW DOCUMENT"));
+        assertFalse("peptide should not be present", ticAreahoverText.contains("peptide"));
+        assertFalse("View Chromatogram link should not be present", ticAreahoverText.contains("VIEW CHROMATOGRAM"));
+
+        log("Moving QC Plots Webpart down");
+        portalHelper.moveWebPart("QC Plots", PortalHelper.Direction.DOWN);
+        portalHelper.exitAdminMode();
+    }
+
     private void testEachCombinedPlots(QCPlotsWebPart.QCPlotType plotType)
     {
         log("Testing combined plot for " + plotType.getLongLabel());

diff --git a/webapp/TargetedMS/js/QCPlotHelperBase.js b/webapp/TargetedMS/js/QCPlotHelperBase.js
@@ -241,6 +241,7 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
                 {
                     var data = this.processPlotDataRow(row, fragment, seriesType, metricProps);
                     this.fragmentPlotData[fragment].data.push(data);
+                    this.fragmentPlotData[fragment].precursorScoped = metricProps.precursorScoped;
                     this.setSeriesMinMax(this.fragmentPlotData[fragment], data);
                     allPlotDateValues.push(data.fullDate);
                 }, this);

diff --git a/webapp/TargetedMS/js/QCPlotHelperWrapper.js b/webapp/TargetedMS/js/QCPlotHelperWrapper.js
@@ -56,7 +56,11 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperWrapper", {
                 {
                     ids.push(id + '_plotType_' + j);
                 }
-                this.addPlotsToPlotDiv(ids, this.precursors[i] + ", " + precursorInfo.mz, this.plotDivId, 'qc-plot-wp');
+
+                precursorInfo.precursorScoped ?
+                        this.addPlotsToPlotDiv(ids, this.precursors[i] + ", " + precursorInfo.mz, this.plotDivId, 'qc-plot-wp'):
+                        this.addPlotsToPlotDiv(ids, this.precursors[i], this.plotDivId, 'qc-plot-wp');
+
                 var plotIndex = 0;
                 // add a new panel for each plot so we can add the title to the frame
                 if (this.showLJPlot())