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Merged
labkey-jeckels merged 5 commits into from
Nov 5, 2025
Merged

Adopt FileLike for more pipeline APIs #614

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954bfb4
More file path improvements, mostly around pipeline jobs
labkey-jeckels Oct 18, 2025
63e5560
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 22, 2025
263af1e
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 27, 2025
9812c2e
More appendPath and other cleanup
labkey-jeckels Oct 29, 2025
2578968
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 31, 2025
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36 changes: 19 additions & 17 deletions nirc_ehr/test/src/org.labkey.test/tests.nirc_ehr/NIRC_EHRTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,12 +18,14 @@

import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.experimental.categories.Category;
import org.labkey.api.reader.Readers;
import org.labkey.api.util.FileUtil;
import org.labkey.remoteapi.CommandException;
import org.labkey.remoteapi.SimplePostCommand;
import org.labkey.remoteapi.core.SaveModulePropertiesCommand;
Expand Down Expand Up @@ -100,8 +102,8 @@ public class NIRC_EHRTest extends AbstractGenericEHRTest implements PostgresOnly
private static final String departedAnimalId = "H6767";
private static final String aliveAnimalId = "A4545";

private String[] weightFields = {"Id", "date", "enddate", "project", "weight", FIELD_QCSTATELABEL, FIELD_OBJECTID, FIELD_LSID, "_recordid", "performedby"};
private Object[] weightData1 = {getExpectedAnimalIDCasing("TESTSUBJECT1"), EHRClientAPIHelper.DATE_SUBSTITUTION, null, null, "12", EHRQCState.IN_PROGRESS.label, null, null, "_recordID", 1004};
private final String[] weightFields = {"Id", "date", "enddate", "project", "weight", FIELD_QCSTATELABEL, FIELD_OBJECTID, FIELD_LSID, "_recordid", "performedby"};
private final Object[] weightData1 = {getExpectedAnimalIDCasing("TESTSUBJECT1"), EHRClientAPIHelper.DATE_SUBSTITUTION, null, null, "12", EHRQCState.IN_PROGRESS.label, null, null, "_recordID", 1004};

DateTimeFormatter _dateFormat = DateTimeFormatter.ofPattern("yyyy-MM-dd");

Expand All @@ -115,7 +117,7 @@ public static void setupProject() throws Exception
@Override
public void importStudy()
{
File path = new File(TestFileUtils.getLabKeyRoot(), getModulePath() + "/resources/referenceStudy");
File path = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse(getModulePath() + "/resources/referenceStudy"));
importFolderByPath(path, getContainerPath(), 1);
path = TestFileUtils.getSampleData("nirc_ehr/study");
importFolderByPath(path, getContainerPath(), 2);
Expand Down Expand Up @@ -278,7 +280,7 @@ private void doSetup() throws Exception
private void populateEHRTables()
{
goToEHRFolder();
File fileName = new File(TestFileUtils.getLabKeyRoot(), getModulePath() + "/resources/data/observation_types.tsv");
File fileName = FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse(getModulePath() + "/resources/data/observation_types.tsv"));
ImportDataCommand command = new ImportDataCommand("ehr", "observation_types");
command.setFile(fileName);
try
Expand Down Expand Up @@ -697,7 +699,7 @@ public void testClinicalObservation()

goToEHRFolder();
waitAndClickAndWait(Locator.linkWithText("Active Clinical Cases"));
ParticipantViewPage reportPage = new AnimalHistoryPage(getDriver()).clickCategoryTab("Clinical")
ParticipantViewPage<?> reportPage = new AnimalHistoryPage<>(getDriver()).clickCategoryTab("Clinical")
.clickReportTab("All Clinical Cases");
table = reportPage.getActiveReportDataRegion();
Assert.assertEquals("Case not closed correctly ", LocalDateTime.now().format(_dateFormat) + " 00:00", table.getDataAsText(0, "enddate"));
Expand Down Expand Up @@ -893,7 +895,7 @@ public void testDeathNecropsyForm() throws IOException, CommandException
// The 'button' is actually a link tag.
WebElement submitButton = Locator.tagWithText("a", "Submit").findWhenNeeded(submitForReview);
scrollIntoView(submitButton);
doAndWaitForPageToLoad(() -> submitButton.click());
doAndWaitForPageToLoad(submitButton::click);

stopImpersonating();

Expand All @@ -918,7 +920,7 @@ public void testDeathNecropsyForm() throws IOException, CommandException
verifyRowCreated("study", "weight", aliveAnimalId, 1);

log("Verify animal is marked as dead");
AnimalHistoryPage historyPage = AnimalHistoryPage.beginAt(this);
AnimalHistoryPage<?> historyPage = AnimalHistoryPage.beginAt(this);
historyPage.searchSingleAnimal(aliveAnimalId);
waitForText(WAIT_FOR_PAGE, "Dead");
waitForText("23 kg"); //checking latest weight is updated.
Expand Down Expand Up @@ -997,15 +999,15 @@ public void testClinicalCasesWorkflow()
_ext4Helper.selectComboBoxItem(Ext4Helper.Locators.formItemWithLabelContaining("Ordered By:"), NIRC_VET_NAME);
waitAndClick(bulkEditWindow.append(Ext4Helper.Locators.ext4Button("Submit")));

Window msgWindow = new Window.WindowFinder(this.getDriver()).withTitle("Set Values").waitFor();
Window<?> msgWindow = new Window.WindowFinder(this.getDriver()).withTitle("Set Values").waitFor();
msgWindow.clickButton("Yes", 0);

submitForm("Submit Final", "Finalize Form");

log("Completing today's Medication Schedule");
goToEHRFolder();
waitAndClickAndWait(Locator.linkWithText("Today's Medication/Treatment Schedule"));
AnimalHistoryPage animalHistoryPage = new AnimalHistoryPage<>(getDriver());
AnimalHistoryPage<?> animalHistoryPage = new AnimalHistoryPage<>(getDriver());
DataRegionTable scheduleTable = animalHistoryPage.getActiveReportDataRegion();
Assert.assertEquals("Incorrect number of rows", 4, scheduleTable.getDataRowCount());
scheduleTable.link(0, "treatmentRecord").click();
Expand All @@ -1026,7 +1028,7 @@ public void testClinicalCasesWorkflow()
clickAndWait(Locator.linkWithText("Active Clinical Cases"));

//Click on 'Case Update' link
AnimalHistoryPage historyPage = new AnimalHistoryPage<>(getDriver());
AnimalHistoryPage<?> historyPage = new AnimalHistoryPage<>(getDriver());
DataRegionTable activeClinicalCases = historyPage.getActiveReportDataRegion();
activeClinicalCases.link(0, "caseCheck").click();
switchToWindow(2);
Expand Down Expand Up @@ -1089,7 +1091,7 @@ public void testLookupPage() throws Exception

EHRLookupPage ehrLookupPage = new EHRLookupPage(this);
QueryGrid grid = ehrLookupPage.getQueryGrid();
checker().verifyEquals("Missing look up tables", countLines(TestFileUtils.getLabKeyRoot() + getModulePath() + "/resources/data/editable_lookups.tsv") - 1, grid.getRecordCount());
checker().verifyEquals("Missing look up tables", countLines(FileUtil.appendPath(TestFileUtils.getLabKeyRoot(), org.labkey.api.util.Path.parse(getModulePath() + "/resources/data/editable_lookups.tsv"))) - 1, grid.getRecordCount());

clickAndWait(Locator.linkWithText("Age Class"));
checker().verifyEquals("Navigated to incorrect schema", "ehr_lookups", getUrlParam("schemaName"));
Expand Down Expand Up @@ -1163,7 +1165,7 @@ public void testBehavioralCases()
log("Verify reports and schedule");
goToEHRFolder();
waitAndClickAndWait(Locator.linkWithText("Active Behavior Cases"));
AnimalHistoryPage animalHistoryPage = new AnimalHistoryPage<>(getDriver());
AnimalHistoryPage<?> animalHistoryPage = new AnimalHistoryPage<>(getDriver());
DataRegionTable activeCase = animalHistoryPage.getActiveReportDataRegion();
Assert.assertEquals("Behavioral case did not get created", 2, activeCase.getDataRowCount());

Expand Down Expand Up @@ -1230,9 +1232,9 @@ public void testBehavioralCases()
Assert.assertEquals("Case was not closed", 1, activeCase.getDataRowCount());
}

private int countLines(String filePath) throws Exception
private int countLines(File file) throws Exception
{
try (BufferedReader reader = Readers.getReader(new File(filePath)))
try (BufferedReader reader = Readers.getReader(file))
{
int count = 0;
while (reader.readLine() != null)
Expand Down Expand Up @@ -1262,7 +1264,7 @@ private void verifyOrchardFileGenerated(String animalId)
Files.walkFileTree(orchardFileLocation.toPath(), new SimpleFileVisitor<>()
{
@Override
public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IOException
public @NotNull FileVisitResult visitFile(@NotNull Path file, @NotNull BasicFileAttributes attrs)
{
// Check if the file name starts with "orchardFile"
if (file.getFileName().toString().startsWith(prefix))
Expand All @@ -1281,7 +1283,7 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
}
catch (IOException e)
{
e.printStackTrace();
log("Error while traversing the directory: " + e.getMessage());
}

if (largestTimestamp[0].equals("0"))
Expand All @@ -1290,7 +1292,7 @@ public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) throws IO
}

File orchardFile = new File(orchardFileLocation + "/orchardFile" + largestTimestamp[0] + ".txt");
waitFor(() -> orchardFile.exists(), WAIT_FOR_PAGE);
waitFor(orchardFile::exists, WAIT_FOR_PAGE);
Assert.assertTrue("Edited animal is not present in the orchard file",
TestFileUtils.getFileContents(orchardFile).contains(animalId));
}
Expand Down