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Merge branch 'develop' into fb_53306_propertyName
2 parents 11307e4 + 854c695 commit 7716d42

3 files changed

Lines changed: 45 additions & 40 deletions

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‎ms2/test/src/org/labkey/test/tests/ms2/LibraTest.java‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -26,6 +26,7 @@
2626
import org.labkey.test.categories.MS2;
2727
import org.labkey.test.components.CustomizeView;
2828
import org.labkey.test.ms2.MS2TestBase;
29+
import org.labkey.test.params.FieldKey;
2930
import org.labkey.test.util.DataRegionExportHelper;
3031
import org.labkey.test.util.DataRegionTable;
3132
import org.labkey.test.util.TextSearcher;
@@ -127,9 +128,9 @@ private void spectraCountTest()
127128
// Customize view to pull in other columns
128129
_customizeViewsHelper.openCustomizeViewPanel();
129130
_customizeViewsHelper.addColumn("TrimmedPeptide");
130-
_customizeViewsHelper.addColumn(new String[] {"Protein", "ProtSequence"});
131-
_customizeViewsHelper.addColumn(new String[] {"Protein", "BestName"});
132-
_customizeViewsHelper.addColumn(new String[] {"Protein", "Mass"});
131+
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "ProtSequence"));
132+
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "BestName"));
133+
_customizeViewsHelper.addColumn(FieldKey.fromParts("Protein", "Mass"));
133134
_customizeViewsHelper.saveDefaultView();
134135
assertTextPresent("84731", "MPEETQAQDQPMEEEEVETFAFQAEIAQLM");
135136

@@ -142,7 +143,7 @@ private void spectraCountTest()
142143
clickAndWait(Locator.linkWithText("Spectra Count Options"));
143144
click(Locator.linkWithText("Create or Edit View"));
144145
findButton("Save");
145-
_customizeViewsHelper.addFilter("Hyper", "Hyper", "Is Greater Than", "250");
146+
_customizeViewsHelper.addFilter("Hyper", "Is Greater Than", "250");
146147
assertRadioButtonSelected(Locator.radioButtonByNameAndValue("spectraConfig", "SpectraCountPeptide"));
147148
_customizeViewsHelper.saveCustomView("HyperFilter");
148149
click(Locator.radioButtonById("SpectraCountPeptideCharge"));
@@ -219,7 +220,7 @@ private void addNormalizationCount(CustomizeView customizeView)
219220
{
220221
for (int i = 1; i <= normalizationCount; i++)
221222
{
222-
customizeView.addColumn("iTRAQQuantitation/Normalized" + i, "Normalized " + i);
223+
customizeView.addColumn("iTRAQQuantitation/Normalized" + i);
223224
}
224225
}
225226

@@ -231,7 +232,7 @@ private void proteinProphetTest()
231232

232233
for (int i = 1; i <= normalizationCount; i++)
233234
{
234-
customizeView.addColumn("ProteinProphetData/ProteinGroupId/iTRAQQuantitation/Ratio" + i, "Ratio " + i);
235+
customizeView.addColumn("ProteinProphetData/ProteinGroupId/iTRAQQuantitation/Ratio" + i);
235236
}
236237
addNormalizationCount(customizeView);
237238
customizeView.saveCustomView(proteinProphetView);

‎ms2/test/src/org/labkey/test/tests/ms2/MS2Test.java‎

Lines changed: 33 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -24,10 +24,10 @@
2424
import org.labkey.test.WebTestHelper;
2525
import org.labkey.test.categories.Daily;
2626
import org.labkey.test.categories.MS2;
27+
import org.labkey.test.params.FieldKey;
2728
import org.labkey.test.util.AbstractDataRegionExportOrSignHelper.ColumnHeaderType;
2829
import org.labkey.test.util.DataRegionExportHelper;
2930
import org.labkey.test.util.DataRegionTable;
30-
import org.labkey.test.util.EscapeUtil;
3131
import org.labkey.test.util.LogMethod;
3232
import org.labkey.test.util.TextSearcher;
3333
import org.openqa.selenium.WebElement;
@@ -397,21 +397,22 @@ private void verifyFirstRun()
397397
log("Check that saved view is working");
398398
assertTextNotPresent("K.KTEENYTLVFIVDVK.A");
399399

400+
DataRegionTable innerTable = DataRegionTable.DataRegion(getDriver()).withName(REGION_NAME_PEPTIDES).find(peptidesTable);
400401
log("Test adding a sort and a filter");
401-
peptidesTable.setFilter("Hyper", "Is Greater Than", "10.6");
402+
innerTable.setFilter("Hyper", "Is Greater Than", "10.6");
402403
assertTextNotPresent("K.RFSGTVKLK.Y");
403-
peptidesTable.setSort("Next", SortDirection.ASC);
404+
innerTable.setSort("Next", SortDirection.ASC);
404405
// Explicitly clear out the sorts, since we want to be just dealing with the ones set in Customize View
405-
peptidesTable.clearSort("Next");
406-
peptidesTable.clearSort("Scan");
406+
innerTable.clearSort("Next");
407+
innerTable.clearSort("Scan");
407408

408409
log("Test customize view");
409410
peptidesTable.clearAllFilters();
410411
_customizeViewsHelper.openCustomizeViewPanel();
411-
_customizeViewsHelper.addSort("Charge", "Z", SortDirection.DESC);
412-
_customizeViewsHelper.addSort("Mass", "CalcMH+", SortDirection.DESC);
413-
_customizeViewsHelper.addFilter("DeltaMass", "dMass", "Is Less Than", "0");
414-
_customizeViewsHelper.addColumn("NextAA", "Next AA");
412+
_customizeViewsHelper.addSort("Charge", SortDirection.DESC);
413+
_customizeViewsHelper.addSort("Mass", SortDirection.DESC);
414+
_customizeViewsHelper.addFilter("DeltaMass", "Is Less Than", "0");
415+
_customizeViewsHelper.addColumn("NextAA");
415416
_customizeViewsHelper.removeColumn("Expect");
416417
_customizeViewsHelper.removeColumn("ProteinHits");
417418
_customizeViewsHelper.saveCustomView(VIEW4);
@@ -515,8 +516,8 @@ private void verifyFirstRun()
515516
_customizeViewsHelper.openCustomizeViewPanel();
516517
_customizeViewsHelper.clearFilters();
517518
_customizeViewsHelper.clearSorts();
518-
_customizeViewsHelper.addSort("DeltaMass", "dMass", SortDirection.ASC);
519-
_customizeViewsHelper.addFilter("Mass", "CalcMH+", "Is Greater Than", "1000");
519+
_customizeViewsHelper.addSort("DeltaMass", SortDirection.ASC);
520+
_customizeViewsHelper.addFilter("Mass", "Is Greater Than", "1000");
520521
_customizeViewsHelper.addColumn("Fraction");
521522
_customizeViewsHelper.removeColumn("IonPercent");
522523
_customizeViewsHelper.saveDefaultView();
@@ -551,14 +552,14 @@ private void verifyFirstRun()
551552

552553
log("Test Protein Prophet view in Query - Peptides grouping");
553554
_customizeViewsHelper.openCustomizeViewPanel();
554-
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/Group", "Group");
555-
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/TotalNumberPeptides", "Peptides");
556-
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob");
557-
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/BestName", "Best Name");
555+
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/Group");
556+
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/TotalNumberPeptides");
557+
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/GroupProbability");
558+
_customizeViewsHelper.addColumn("ProteinProphetData/ProteinGroupId/BestName");
558559
_customizeViewsHelper.removeColumn("Mass");
559-
_customizeViewsHelper.addFilter("DeltaMass", "dMass", "Is Greater Than", "0");
560-
_customizeViewsHelper.addFilter("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob", "Is Greater Than", "0.7");
561-
_customizeViewsHelper.addSort("ProteinProphetData/ProteinGroupId/GroupProbability", "Prob", SortDirection.ASC);
560+
_customizeViewsHelper.addFilter("DeltaMass", "Is Greater Than", "0");
561+
_customizeViewsHelper.addFilter("ProteinProphetData/ProteinGroupId/GroupProbability", "Is Greater Than", "0.7");
562+
_customizeViewsHelper.addSort("ProteinProphetData/ProteinGroupId/GroupProbability", SortDirection.ASC);
562563
_customizeViewsHelper.saveCustomView(VIEW4);
563564

564565
log("Test that Protein Prophet view is displayed and that it sorts and filters correctly");
@@ -621,9 +622,9 @@ private void verifyFirstRun()
621622
log("Test customize view");
622623
_customizeViewsHelper.openCustomizeViewPanel();
623624
_customizeViewsHelper.removeColumn("UniquePeptidesCount");
624-
_customizeViewsHelper.addColumn("Proteins/Protein/ProtSequence", "Protein Sequence");
625-
_customizeViewsHelper.addFilter("GroupProbability", "Prob", "Is Greater Than", "0.7");
626-
_customizeViewsHelper.addSort("ErrorRate", "Error", SortDirection.DESC);
625+
_customizeViewsHelper.addColumn("Proteins/Protein/ProtSequence");
626+
_customizeViewsHelper.addFilter("GroupProbability", "Is Greater Than", "0.7");
627+
_customizeViewsHelper.addSort("ErrorRate", SortDirection.DESC);
627628
_customizeViewsHelper.saveCustomView(VIEW4);
628629

629630
log("Test that sorting, filtering, and columns are correct");
@@ -833,13 +834,14 @@ private void validateRunGroups()
833834
setFormElement(Locator.name("name"), RUN_GROUP1_NAME2);
834835
clickButton("Submit");
835836

837+
FieldKey runGroupFK = FieldKey.fromParts("RunGroupToggle");
836838
log("Test customizing view to include the run groups");
837839
navigateToFolder(FOLDER_NAME);
838840
clickAndWait(Locator.linkWithText("MS2 Runs"));
839841
_customizeViewsHelper.openCustomizeViewPanel();
840-
_customizeViewsHelper.addColumn(new String[] { "RunGroupToggle", EscapeUtil.fieldKeyEncodePart(RUN_GROUP1_NAME2) }, RUN_GROUP1_NAME2);
841-
_customizeViewsHelper.addColumn(new String[]{"RunGroupToggle", RUN_GROUP2_NAME}, "Run Groups " + RUN_GROUP2_NAME);
842-
_customizeViewsHelper.addColumn(new String[]{"RunGroupToggle", "Default Experiment"}, "Run Groups Default Experiment");
842+
_customizeViewsHelper.addColumn(runGroupFK.child(RUN_GROUP1_NAME2));
843+
_customizeViewsHelper.addColumn(runGroupFK.child(RUN_GROUP2_NAME));
844+
_customizeViewsHelper.addColumn(runGroupFK.child("Default Experiment"));
843845
_customizeViewsHelper.applyCustomView();
844846

845847
assertTextPresent(new TextSearcher(this).setSearchTransformer(TextSearcher.TextTransformers.FIELD_LABEL),
@@ -876,8 +878,8 @@ private void validateRunGroups()
876878

877879
log("Test Customize View");
878880
_customizeViewsHelper.openCustomizeViewPanel();
879-
_customizeViewsHelper.addColumn("SeqId/Mass", "Protein Mass");
880-
_customizeViewsHelper.addFilter("SeqId/Mass", "Protein Mass", "Is Less Than", "30000");
881+
_customizeViewsHelper.addColumn("SeqId/Mass");
882+
_customizeViewsHelper.addFilter("SeqId/Mass", "Is Less Than", "30000");
881883
_customizeViewsHelper.saveCustomView(VIEW5);
882884

883885
DataRegionTable peptidesTable = new DataRegionTable("query", this);
@@ -1110,7 +1112,7 @@ private void validateCompare()
11101112
_customizeViewsHelper.openCustomizeViewPanel();
11111113
_customizeViewsHelper.addColumn("CTAGG_AVG_XCorr");
11121114
_customizeViewsHelper.removeColumn("InstanceCount");
1113-
_customizeViewsHelper.addFilter("CTAGG_AVG_XCorr", "Avg XCorr", "Is Greater Than", "10");
1115+
_customizeViewsHelper.addFilter("CTAGG_AVG_XCorr", "Is Greater Than", "10");
11141116
_customizeViewsHelper.saveCustomView();
11151117

11161118
log("Check filtering and columns were added correctly");
@@ -1246,17 +1248,18 @@ private void validateContainerFilter()
12461248
DataRegionTable dataTable = viewQueryData("ms2", "XTandemPeptides");
12471249
dataTable.setContainerFilter(DataRegionTable.ContainerFilterType.CURRENT_AND_SUBFOLDERS);
12481250

1251+
FieldKey runGroupsFk = FieldKey.fromParts("Fraction", "Run", "ExperimentRunLSID", "RunGroups");
12491252
_customizeViewsHelper.openCustomizeViewPanel();
1250-
_customizeViewsHelper.addColumn(new String[]{"Fraction", "Run", "ExperimentRunLSID", "RunGroups"});
1253+
_customizeViewsHelper.addColumn(runGroupsFk);
12511254
_customizeViewsHelper.applyCustomView();
12521255
assertNotEquals("All rows should have a value for the run group", 0, dataTable.getDataRowCount());
12531256

12541257
// validate a single run group with the expected label
1255-
Set<String> runGroups = new HashSet<>(dataTable.getColumnDataAsText("RunGroups"));
1258+
Set<String> runGroups = new HashSet<>(dataTable.getColumnDataAsText(runGroupsFk));
12561259
assertEquals("Incorrect number of run groups", 1, runGroups.size());
12571260
assertEquals("Invalid run group label", RUN_GROUP3_NAME, runGroups.iterator().next());
12581261

1259-
dataTable.setFilter("Fraction/Run/ExperimentRunLSID/RunGroups", "Is Blank");
1262+
dataTable.setFilter(runGroupsFk, "Is Blank");
12601263
assertEquals("All rows should have a value for the run group", 0, dataTable.getDataRowCount());
12611264
}
12621265
}

‎ms2/test/src/org/labkey/test/tests/ms2/SequestImportTest.java‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
import org.labkey.test.categories.Daily;
2525
import org.labkey.test.categories.MS2;
2626
import org.labkey.test.components.CustomizeView;
27+
import org.labkey.test.params.FieldKey;
2728
import org.labkey.test.util.DataRegionTable;
2829
import org.labkey.test.util.FileBrowserHelper;
2930
import org.labkey.test.util.LogMethod;
@@ -38,8 +39,8 @@ public class SequestImportTest extends BaseWebDriverTest
3839
{
3940
private static final String PROJECT_NAME = "SequestImport" + TRICKY_CHARACTERS_FOR_PROJECT_NAMES;
4041

41-
private static final String[] TOTAL_PEPTIDES_FIELD_KEY = {"PeptideCounts", "TotalPeptides"};
42-
private static final String[] UNIQUE_PEPTIDES_FIELD_KEY = {"PeptideCounts", "DistinctPeptides"};
42+
private static final FieldKey TOTAL_PEPTIDES_FIELD_KEY = FieldKey.fromParts("PeptideCounts", "TotalPeptides");
43+
private static final FieldKey UNIQUE_PEPTIDES_FIELD_KEY = FieldKey.fromParts("PeptideCounts", "DistinctPeptides");
4344

4445
@Override
4546
protected String getProjectName()
@@ -69,8 +70,8 @@ private void verifyRunGrid()
6970
viewsHelper.addColumn(UNIQUE_PEPTIDES_FIELD_KEY);
7071

7172
// Add a filter so that we can check the values were calculated and shown correctly
72-
viewsHelper.addFilter(TOTAL_PEPTIDES_FIELD_KEY, "Total Peptides", "Equals", "2");
73-
viewsHelper.addFilter(UNIQUE_PEPTIDES_FIELD_KEY, "Distinct Peptides", "Equals", "1");
73+
viewsHelper.addFilter(TOTAL_PEPTIDES_FIELD_KEY, "Equals", "2");
74+
viewsHelper.addFilter(UNIQUE_PEPTIDES_FIELD_KEY, "Equals", "1");
7475
viewsHelper.saveDefaultView();
7576

7677
// Make sure that our run is still showing

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