diff --git a/nextflow/module.properties b/nextflow/module.properties index be867ce9..e79c9076 100644 --- a/nextflow/module.properties +++ b/nextflow/module.properties @@ -5,4 +5,4 @@ Description: This module provides the functionality \ License: Apache 2.0 LicenseURL: http://www.apache.org/licenses/LICENSE-2.0 SupportedDatabases: pgsql -ManageVersion: false +ManageVersion: true diff --git a/nextflow/resources/schemas/dbscripts/nextflow.xml b/nextflow/resources/schemas/dbscripts/nextflow.xml new file mode 100644 index 00000000..01709064 --- /dev/null +++ b/nextflow/resources/schemas/dbscripts/nextflow.xml @@ -0,0 +1,28 @@ + + + + + Invocation counts to ensure unique NextFlow run names + + + + +
+ \ No newline at end of file diff --git a/nextflow/resources/schemas/dbscripts/postgresql/nextflow-0.000-25.000.sql b/nextflow/resources/schemas/dbscripts/postgresql/nextflow-0.000-25.000.sql new file mode 100644 index 00000000..5f6a43a3 --- /dev/null +++ b/nextflow/resources/schemas/dbscripts/postgresql/nextflow-0.000-25.000.sql @@ -0,0 +1,24 @@ +/* + * Copyright (c) 2025 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. + */ +CREATE SCHEMA nextflow; + +CREATE TABLE nextflow.Job +( + JobId INTEGER NOT NULL, + InvocationCount INTEGER NOT NULL, + CONSTRAINT PK_Job PRIMARY KEY (JobId), + CONSTRAINT FK_Job_JobId FOREIGN KEY (JobId) REFERENCES pipeline.StatusFiles (RowId) ON DELETE CASCADE -- Automatically clean up when a job is deleted +); diff --git a/nextflow/src/org/labkey/nextflow/NextFlowController.java b/nextflow/src/org/labkey/nextflow/NextFlowController.java index ea758886..736b8e4f 100644 --- a/nextflow/src/org/labkey/nextflow/NextFlowController.java +++ b/nextflow/src/org/labkey/nextflow/NextFlowController.java @@ -3,6 +3,7 @@ import lombok.Getter; import lombok.Setter; import org.apache.commons.lang3.StringUtils; +import org.apache.logging.log4j.Logger; import org.labkey.api.action.ApiResponse; import org.labkey.api.action.ApiSimpleResponse; import org.labkey.api.action.FormViewAction; @@ -12,7 +13,6 @@ import org.labkey.api.data.PropertyManager; import org.labkey.api.data.PropertyStore; import org.labkey.api.pipeline.PipeRoot; -import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineProvider; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.pipeline.PipelineStatusUrls; @@ -31,6 +31,7 @@ import org.labkey.api.util.Path; import org.labkey.api.util.URLHelper; import org.labkey.api.util.element.Select; +import org.labkey.api.util.logging.LogHelper; import org.labkey.api.view.HtmlView; import org.labkey.api.view.JspView; import org.labkey.api.view.NavTree; @@ -64,6 +65,8 @@ public class NextFlowController extends SpringActionController private static final DefaultActionResolver _actionResolver = new DefaultActionResolver(NextFlowController.class); public static final String NAME = "nextflow"; + protected static final Logger LOG = LogHelper.getLogger(NextFlowPipelineJob.class, "LabKey UI and API for NextFlow usage"); + public NextFlowController() { setActionResolver(_actionResolver); @@ -326,8 +329,9 @@ public boolean handlePost(AnalyzeForm form, BindException errors) throws Excepti { ViewBackgroundInfo info = getViewBackgroundInfo(); PipeRoot root = PipelineService.get().findPipelineRoot(info.getContainer()); - PipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles.stream().map(File::toPath).toList()); + NextFlowPipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles.stream().map(File::toPath).toList()); PipelineService.get().queueJob(job); + LOG.info("NextFlow job queued: {}", job.getJsonJobInfo(false)); } } diff --git a/nextflow/src/org/labkey/nextflow/NextFlowManager.java b/nextflow/src/org/labkey/nextflow/NextFlowManager.java index e560e413..a1b115c7 100644 --- a/nextflow/src/org/labkey/nextflow/NextFlowManager.java +++ b/nextflow/src/org/labkey/nextflow/NextFlowManager.java @@ -3,8 +3,16 @@ import org.apache.commons.lang3.StringUtils; import org.labkey.api.data.Container; import org.labkey.api.data.CoreSchema; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DbSchemaType; import org.labkey.api.data.DbScope; import org.labkey.api.data.PropertyManager; +import org.labkey.api.data.SQLFragment; +import org.labkey.api.data.SqlExecutor; +import org.labkey.api.data.SqlSelector; +import org.labkey.api.pipeline.PipelineService; +import org.labkey.api.pipeline.PipelineStatusFile; +import org.labkey.nextflow.pipeline.NextFlowPipelineJob; import org.springframework.validation.BindException; import java.nio.file.Files; @@ -27,6 +35,8 @@ public class NextFlowManager private static final String NEXTFLOW_S3_BUCKET_PATH = "s3BucketPath"; private static final String NEXTFLOW_API_KEY = "apiKey"; + public static final String SCHEMA_NAME = "nextflow"; + private static final String IS_NEXTFLOW_ENABLED = "enabled"; private static final NextFlowManager _instance = new NextFlowManager(); @@ -158,4 +168,42 @@ public void saveEnabledState(Container container, Boolean enabled) map.save(); } } + + private DbSchema getDbSchema() + { + return DbSchema.get(SCHEMA_NAME, DbSchemaType.Module); + } + + private Integer getJobId(NextFlowPipelineJob job) + { + PipelineStatusFile file = PipelineService.get().getStatusFile(job.getJobGUID()); + return file == null ? null : file.getRowId(); + } + + public int getInvocationCount(NextFlowPipelineJob job) + { + return getInvocationCount(getJobId(job)); + } + + private int getInvocationCount(int jobId) + { + Integer result = new SqlSelector(getDbSchema(), new SQLFragment("SELECT InvocationCount FROM nextflow.Job WHERE JobId = ?", jobId)).getObject(Integer.class); + return result != null ? result.intValue() : 0; + } + + public int incrementInvocationCount(NextFlowPipelineJob job) + { + int jobId = getJobId(job); + int current = getInvocationCount(jobId); + current++; + if (current == 1) + { + new SqlExecutor(getDbSchema()).execute(new SQLFragment("INSERT INTO nextflow.Job (JobId, InvocationCount) VALUES (?, ?)", jobId, current)); + } + else + { + new SqlExecutor(getDbSchema()).execute(new SQLFragment("UPDATE nextflow.Job SET InvocationCount = ? WHERE JobId = ?", current, jobId)); + } + return current; + } } diff --git a/nextflow/src/org/labkey/nextflow/NextFlowModule.java b/nextflow/src/org/labkey/nextflow/NextFlowModule.java index 46853d27..83dac6fc 100644 --- a/nextflow/src/org/labkey/nextflow/NextFlowModule.java +++ b/nextflow/src/org/labkey/nextflow/NextFlowModule.java @@ -1,6 +1,7 @@ package org.labkey.nextflow; import org.jetbrains.annotations.NotNull; +import org.jetbrains.annotations.Nullable; import org.labkey.api.data.ContainerManager; import org.labkey.api.module.ModuleContext; import org.labkey.api.module.SpringModule; @@ -40,13 +41,18 @@ protected void init() @Override public boolean hasScripts() { - return false; + return true; } @Override - public @NotNull Collection getSchemaNames() + public @Nullable Double getSchemaVersion() { - return List.of(); + return 25.000; } + @Override + public @NotNull Collection getSchemaNames() + { + return List.of(NextFlowManager.SCHEMA_NAME); + } } diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java index 8a3cd0c0..137a9dca 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java @@ -20,6 +20,7 @@ import org.labkey.api.util.StringUtilsLabKey; import org.labkey.api.util.logging.LogHelper; import org.labkey.api.view.ViewBackgroundInfo; +import org.labkey.nextflow.NextFlowManager; import java.io.BufferedWriter; import java.io.File; @@ -59,25 +60,24 @@ public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, Path super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getFileName().toString(), config, inputFiles, false, false); this.config = config; setLogFile(log); - LOG.info("NextFlow job queued: {}", getJsonJobInfo(null)); } - protected JSONObject getJsonJobInfo(Long invocationCount) + public JSONObject getJsonJobInfo(boolean includeInvocationCount) { JSONObject result = new JSONObject(); result.put("user", getUser().getEmail()); result.put("container", getContainer().getPath()); result.put("filePath", getLogFilePath().getParent().toString()); - result.put("runName", getNextFlowRunName(invocationCount)); + result.put("runName", getNextFlowRunName(includeInvocationCount)); result.put("configFile", getConfig().getFileName().toString()); return result; } - protected String getNextFlowRunName(Long invocationCount) + protected String getNextFlowRunName(boolean includeInvocationCount) { PipelineStatusFile file = PipelineService.get().getStatusFile(getJobGUID()); String result = file == null ? "Unknown" : ("LabKeyJob" + file.getRowId()); - result += invocationCount == null ? "" : ("_" + invocationCount); + result += includeInvocationCount ? ("_" + NextFlowManager.get().getInvocationCount(this)) : ""; return result; } diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java index 2749796f..1a64acc9 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java @@ -2,9 +2,6 @@ import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.NotNull; -import org.labkey.api.data.ContainerManager; -import org.labkey.api.data.DbSequence; -import org.labkey.api.data.DbSequenceManager; import org.labkey.api.exp.XarFormatException; import org.labkey.api.pipeline.AbstractTaskFactory; import org.labkey.api.pipeline.AbstractTaskFactorySettings; @@ -40,8 +37,6 @@ public class NextFlowRunTask extends WorkDirectoryTask public static final String ACTION_NAME = "NextFlow"; - private static final DbSequence INVOCATION_SEQUENCE = DbSequenceManager.get(ContainerManager.getRoot(), NextFlowRunTask.class.getName()); - public NextFlowRunTask(Factory factory, PipelineJob job) { super(factory, job); @@ -54,9 +49,9 @@ public NextFlowRunTask(Factory factory, PipelineJob job) // NextFlow requires a unique job name for every execution. Increment a counter to append as a suffix to // ensure uniqueness - long invocationCount = INVOCATION_SEQUENCE.next(); - INVOCATION_SEQUENCE.sync(); - NextFlowPipelineJob.LOG.info("Starting to execute NextFlow: {}", getJob().getJsonJobInfo(invocationCount)); + NextFlowManager.get().incrementInvocationCount(getJob()); + + NextFlowPipelineJob.LOG.info("Starting to execute NextFlow: {}", getJob().getJsonJobInfo(true)); SecurityManager.TransformSession session = null; boolean success = false; @@ -83,10 +78,10 @@ public NextFlowRunTask(Factory factory, PipelineJob job) File dir = getJob().getLogFile().getParentFile(); getJob().runSubProcess(secretsPB, dir); - ProcessBuilder executionPB = new ProcessBuilder(getArgs(invocationCount)); + ProcessBuilder executionPB = new ProcessBuilder(getArgs()); getJob().runSubProcess(executionPB, dir); log.info("Job Finished"); - NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo(invocationCount)); + NextFlowPipelineJob.LOG.info("Finished executing NextFlow: {}", getJob().getJsonJobInfo(true)); RecordedAction action = new RecordedAction(ACTION_NAME); for (Path inputFile : getJob().getInputFilePaths()) @@ -110,7 +105,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job) } if (!success) { - NextFlowPipelineJob.LOG.info("Failed executing NextFlow: {}", getJob().getJsonJobInfo(invocationCount)); + NextFlowPipelineJob.LOG.info("Failed executing NextFlow: {}", getJob().getJsonJobInfo(true)); } } } @@ -176,7 +171,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException } - private @NotNull List getArgs(long invocationCount) throws PipelineJobException + private @NotNull List getArgs() throws PipelineJobException { NextFlowConfiguration config = NextFlowManager.get().getConfiguration(); Path configFile = getJob().getConfig(); @@ -201,7 +196,7 @@ private boolean hasAwsSection(Path configFile) throws PipelineJobException args.add("-c"); args.add(configFile.toAbsolutePath().toString()); args.add("-name"); - args.add(getJob().getNextFlowRunName(invocationCount)); + args.add(getJob().getNextFlowRunName(true)); return args; } diff --git a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicFileImporter.java b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicFileImporter.java index 2a65f28d..9048e16c 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicFileImporter.java +++ b/panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicFileImporter.java @@ -16,6 +16,7 @@ import org.labkey.api.pipeline.PipelineService; import org.labkey.api.query.BatchValidationException; import org.labkey.api.security.User; +import org.labkey.api.targetedms.TargetedMSService; import org.labkey.api.writer.VirtualFile; import org.labkey.panoramapublic.pipeline.CopyExperimentPipelineJob; @@ -25,6 +26,7 @@ import java.nio.file.Paths; import java.util.List; import java.util.Objects; +import java.util.Optional; /** * This importer does a file move instead of copy to the temp directory and creates a symlink in place of the original @@ -90,6 +92,7 @@ public void process(@Nullable PipelineJob job, FolderImportContext ctx, VirtualF PanoramaPublicSymlinkManager.get().moveAndSymLinkDirectory(expJob, ctx.getContainer(), sourceFiles, targetFiles, log); alignDataFileUrls(expJob.getUser(), ctx.getContainer(), log); + updateSkydDataIds(expJob.getUser(), ctx.getContainer(), log); } } @@ -154,6 +157,78 @@ private void alignDataFileUrls(User user, Container targetContainer, Logger log) } } + /** + * Fixes incorrect skydDataId reference in TargetedMSRun. This happens when the relative locations of the sky.zip + * and .skyd file are non-standard in the folder being copied. + * + * When a sky.zip file or its exploded folder are moved, post-import, so that the relative locations of sky.zip and + * its corresponding .skyd file are non-standard, two ExpData rows are created for the skyd file in the Panorama Public + * copy pipeline job. + * The first ExpData (linked to the ExpRun) is created during XAR import. + * The second ExpData (not linked to the ExpRun) is created in the SkylineDocumentParser.parseChromatograms() method. + * Normally, while running the copy pipeline job, SkylineDocumentParser.parseChromatograms() does not have to create + * a new ExpData, since an ExpData with the expected path already exists. + * Having 2 ExpDatas causes: + * 1. The skydDataId in TargetedMSRun references an ExpData not linked to the ExpRun. It refers to a file in the + * 'export' directory which gets deleted after folder import. + * 2. FK violations during cleanup (CopyExperimentFinalTask.cleanupExportDirectory()) prevents deletion of ExpData + * corresponding to the skydDataId + * + * This method finds a match and updates skydDataId in TargetedMSRun in the case where the skyDataId is not linked + * to the ExpRun. + */ + private void updateSkydDataIds(User user, Container targetContainer, Logger log) throws BatchValidationException, ImportException + { + log.info("Updating skydDataIds in folder: " + targetContainer.getPath()); + + boolean errors = false; + ExperimentService expService = ExperimentService.get(); + List runs = expService.getExpRuns(targetContainer, null, null); + + TargetedMSService tmsService = TargetedMSService.get(); + for (ExpRun run : runs) + { + var targetedmsRun = tmsService.getRunByLsid(run.getLSID(), targetContainer); + if (targetedmsRun == null) continue; + + var skydDataId = targetedmsRun.getSkydDataId(); + if (skydDataId == null) continue; + + var skydData = expService.getExpData(skydDataId); + if (skydData == null) + { + log.error("Could not find a row for skydDataId " + skydDataId + " for run " + targetedmsRun.getFileName()); + errors = true; + } + else if (skydData.getRun() == null) + { + // skydData is not associated with an ExpRun. Find an ExpData associated with the ExpRun that matches + // the skydName and update the skydDataId on the run. + String skydName = skydData.getName(); + Optional matchingData = run.getAllDataUsedByRun().stream() + .filter(data -> Objects.equals(skydName, data.getName())) + .findFirst(); + + if (matchingData.isPresent()) + { + ExpData data = matchingData.get(); + log.debug("Updating skydDataId for run " + targetedmsRun.getFileName() + " to " + data.getRowId()); + tmsService.updateSkydDataId(targetedmsRun, data, user); + } + else + { + log.error("Could not find matching skyData for run " + targetedmsRun.getFileName()); + errors = true; + } + } + } + + if (errors) + { + throw new ImportException("Could not update skydDataIds"); + } + } + public static class Factory extends AbstractFolderImportFactory { @Override diff --git a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java index 4c93fbea..622a5181 100644 --- a/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java +++ b/panoramapublic/src/org/labkey/panoramapublic/query/ExperimentAnnotationsTableInfo.java @@ -162,7 +162,10 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep .at(src, PageFlowUtil.staticResourceUrl("_images/plus.gif"))), HtmlString.NBSP) .appendTo(out); - pageConfig.addHandler(spanId, "click", "viewExperimentDetails(this,'" + container.getPath() + "', '" + id + "','" + detailsPage + "')"); + pageConfig.addHandler(spanId, "click", "viewExperimentDetails(this," + + PageFlowUtil.jsString(container.getPath()) + + ", " + id + ", " + + PageFlowUtil.jsString(detailsPage) + ")"); } super.renderGridCellContents(ctx, out); } diff --git a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMoveSkyDocTest.java b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMoveSkyDocTest.java index a469f8de..05c5f9dd 100644 --- a/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMoveSkyDocTest.java +++ b/panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicMoveSkyDocTest.java @@ -58,9 +58,46 @@ public void testExperimentCopy() moveDocument(SKY_FILE_2, targetFolder, 2); goToProjectFolder(projectName, targetFolder); - log("Importing " + SKY_FILE_3 + " in folder " + skyDocSourceFolder); + log("Importing " + SKY_FILE_3 + " in folder " + targetFolder); importData(SKY_FILE_3, 3); + // Test moving the sky.zip to a subdirectory in the file root, while the .skyd remains in the original location. + // + // If the sky.zip file and the .skyd file are not in their typical relative locations, the skydDataId in + // TargetedMSRun has to be updated after the folder is copied to Panorama Public. Without the update the + // copy pipeline job fails. + // Example: + // ------------------------- + // BEFORE MOVE: + // SmallMolLibA.sky.zip + // SmallMolLibA + // - SmallMolLibA.sky + // - SmallMolLibA.skyd + // ------------------------- + // AFTER MOVE: + // - SkylineFiles + // - SmallMolLibA.sky.zip (new location after move) + // SmallMolLibA + // - SmallMolLibA.sky + // - SmallMolLibA.skyd + // This results in: + // Two ExpData rows created for the .skyd file in folder copy on Panorama Public. + // 1. @files/export/.../Run/SkylineFiles/SmallMolLibA/SmallMolLibA.skyd + // 2. @files/SmallMolLibA/SmallMolLibA.skyd + // #1 is set as the skydDataId in TargetedMSRuns, but it is not linked to the ExpRun (runId is null) + // #2 is linked to the ExpRun. This is the ExpData that skydDataId in TargetedMSRun *should* refer to. + // This situation causes two problems + // 1. ExpData cleanup in CopyExperimentFinalTask fails due to FK violation - cannot delete ExpData #1 since + // skydDataId in TargetedMSRun points to it. + // 2. Even if we were not cleaning up ExpData referring to files in the 'export' directory, chromatogram data + // would become unavailable since the "export" directory gets deleted after folder import. + // + // PanoramaPublicFileImporter.updateSkydDataId() fixes the skydDataId, if required. + String subDir = "SkylineFiles"; + log("Moving " + SKY_FILE_3 + " to sub directory " + subDir + " in the Files browser"); + // Move the .sky.zip file to a subdirectory + moveSkyZipToSubDir(SKY_FILE_3, subDir); + log("Creating and submitting an experiment"); String experimentTitle = "Experiment to test moving Skyline documents from other folders"; var expWebPart = createExperimentCompleteMetadata(experimentTitle); @@ -75,6 +112,15 @@ public void testExperimentCopy() verifyRunFilePathRoot(SKY_FILE_1, PANORAMA_PUBLIC, panoramaCopyFolder); verifyRunFilePathRoot(SKY_FILE_2, PANORAMA_PUBLIC, panoramaCopyFolder); verifyRunFilePathRoot(SKY_FILE_3, PANORAMA_PUBLIC, panoramaCopyFolder); + + // Verify that we can view chromatograms for the Skyline document that was moved to a subdirectory. + goToDashboard(); + clickAndWait(Locator.linkContainingText(SKY_FILE_3)); + clickAndWait(Locator.linkContainingText("2 replicates")); + clickAndWait(Locator.linkContainingText("FU2_2017_0915_RJ_05_1ab_30").index(0)); + assertTextPresent("Sample File Summary"); + assertTextPresent("Total Ion Chromatogram"); + assertTextNotPresent("Unable to load chromatogram"); } private void moveDocument(String skylineDocName, String targetFolder, int jobCount) @@ -96,6 +142,18 @@ private void moveDocument(String skylineDocName, String targetFolder, int jobCou verifyRunFilePathRoot(skylineDocName, getProjectName(), targetFolder); } + private void moveSkyZipToSubDir(String documentName, String subDir) + { + portalHelper.goToModule("FileContent"); + waitForText(documentName); + if (!_fileBrowserHelper.fileIsPresent(subDir)) + { + _fileBrowserHelper.createFolder(subDir); + } + _fileBrowserHelper.moveFile(documentName, subDir); + } + + private void verifyRunFilePathRoot(String skylineDocName, String projectName, String targetFolder) { // Verify that exp.run filePathRoot is set to the target folder diff --git a/panoramapublic/webapp/PanoramaPublic/js/dropDownUtil.js b/panoramapublic/webapp/PanoramaPublic/js/dropDownUtil.js index 08af5147..cb4252d3 100644 --- a/panoramapublic/webapp/PanoramaPublic/js/dropDownUtil.js +++ b/panoramapublic/webapp/PanoramaPublic/js/dropDownUtil.js @@ -66,12 +66,13 @@ viewExperimentDetails = function (obj, experimentContainer, id, detailsPageURL) var results; if(object.rows[rowNum][type] != null) { - if(object.rows[rowNum][type].length > 500) + let description = object.rows[rowNum][type]; + if(description.length > 500) { - results = object.rows[rowNum][type].substring(0,500)+"...more."; + results = LABKEY.Utils.encodeHtml(description.substring(0,500)) +"...more."; } else { - results =object.rows[rowNum][type]; + results = LABKEY.Utils.encodeHtml(description); } } else {results = null;}