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Merged
labkey-jeckels merged 2 commits into from
May 27, 2026
+2 −390
Merged

Remove chromatogram crawler job #1218

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2343d36
Remove chromatogram crawler job
labkey-jeckels May 26, 2026
422235a
Merge branch 'develop' into fb_removeChromatogramCrawler
labkey-jeckels May 27, 2026
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47 changes: 0 additions & 47 deletions src/org/labkey/targetedms/TargetedMSController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,6 @@
import org.labkey.api.action.SimpleErrorView;
import org.labkey.api.action.SimpleViewAction;
import org.labkey.api.action.SpringActionController;
import org.labkey.api.admin.AdminUrls;
import org.labkey.api.analytics.AnalyticsService;
import org.labkey.api.attachments.DocumentConversionService;
import org.labkey.api.attachments.SvgSource;
Expand Down Expand Up @@ -106,7 +105,6 @@
import org.labkey.api.module.ModuleProperty;
import org.labkey.api.pipeline.LocalDirectory;
import org.labkey.api.pipeline.PipeRoot;
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineService;
import org.labkey.api.pipeline.PipelineUrls;
import org.labkey.api.pipeline.PipelineValidationException;
Expand Down Expand Up @@ -141,7 +139,6 @@
import org.labkey.api.security.SecurityManager;
import org.labkey.api.security.User;
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.ApplicationAdminPermission;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.UpdatePermission;
Expand All @@ -151,7 +148,6 @@
import org.labkey.api.targetedms.TargetedMSUrls;
import org.labkey.api.targetedms.model.QCMetricConfiguration;
import org.labkey.api.targetedms.model.SampleFileInfo;
import org.labkey.api.util.ButtonBuilder;
import org.labkey.api.util.ConfigurationException;
import org.labkey.api.util.ContainerContext;
import org.labkey.api.util.DOM;
Expand Down Expand Up @@ -229,7 +225,6 @@
import org.labkey.targetedms.parser.list.ListDefinition;
import org.labkey.targetedms.parser.skyaudit.AuditLogEntry;
import org.labkey.targetedms.parser.speclib.SpeclibReaderException;
import org.labkey.targetedms.pipeline.ChromatogramCrawlerJob;
import org.labkey.targetedms.query.ChromatogramDisplayColumnFactory;
import org.labkey.targetedms.query.ConflictResultsManager;
import org.labkey.targetedms.query.GroupChromatogramsTableInfo;
Expand Down Expand Up @@ -327,7 +322,6 @@
import static org.labkey.api.util.DOM.Attribute.height;
import static org.labkey.api.util.DOM.Attribute.href;
import static org.labkey.api.util.DOM.Attribute.id;
import static org.labkey.api.util.DOM.Attribute.method;
import static org.labkey.api.util.DOM.Attribute.src;
import static org.labkey.api.util.DOM.Attribute.style;
import static org.labkey.api.util.DOM.Attribute.width;
Expand Down Expand Up @@ -548,47 +542,6 @@ public static void addDashboardTab(String tab, Container c, String... includeWeb
}
}

public static class ChromatogramCrawlerForm
{
}

@RequiresPermission(ApplicationAdminPermission.class)
public class ChromatogramCrawlerAction extends FormViewAction<ChromatogramCrawlerForm>
{
@Override
public void validateCommand(ChromatogramCrawlerForm target, Errors errors)
{
}

@Override
public ModelAndView getView(ChromatogramCrawlerForm form, boolean reshow, BindException errors)
{
return new HtmlView("Chromatogram Crawler", DIV("Crawl all containers under the parent " + getContainer().getPath(),
DOM.LK.FORM(at(method, "POST"),
new ButtonBuilder("Start Crawl").submit(true).build())));
}

@Override
public boolean handlePost(ChromatogramCrawlerForm form, BindException errors) throws Exception
{
PipelineJob job = new ChromatogramCrawlerJob(getViewBackgroundInfo(), PipelineService.get().getPipelineRootSetting(ContainerManager.getRoot()));
PipelineService.get().queueJob(job);
return true;
}

@Override
public URLHelper getSuccessURL(ChromatogramCrawlerForm form)
{
return urlProvider(PipelineUrls.class).urlBegin(getContainer());
}

@Override
public void addNavTrail(NavTree root)
{
urlProvider(AdminUrls.class).addAdminNavTrail(root, "Chromatogram Crawler", getClass(), getContainer());
}
}

// ------------------------------------------------------------------------
// Action to create a Raw Data tab
// ------------------------------------------------------------------------
Expand Down
10 changes: 2 additions & 8 deletions src/org/labkey/targetedms/TargetedMSModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -46,14 +46,11 @@
import org.labkey.api.protein.search.ProteinSearchForm;
import org.labkey.api.query.QueryView;
import org.labkey.api.security.permissions.AdminPermission;
import org.labkey.api.security.permissions.ApplicationAdminPermission;
import org.labkey.api.settings.AdminConsole;
import org.labkey.api.settings.OptionalFeatureFlag;
import org.labkey.api.settings.OptionalFeatureService;
import org.labkey.api.targetedms.TargetedMSService;
import org.labkey.api.usageMetrics.UsageMetricsService;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.BaseWebPartFactory;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
Expand Down Expand Up @@ -380,12 +377,12 @@ public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Po
String inclSubFolders = (String)portalCtx.get("includeSubfolders");
if(!StringUtils.isBlank(inclSubFolders))
{
form.setIncludeSubfolders(Boolean.valueOf(inclSubFolders));
form.setIncludeSubfolders(Boolean.parseBoolean(inclSubFolders));
}
String hideIncludeSubfolder = (String)portalCtx.get("hideIncludeSubfolder");
if(!StringUtils.isBlank(hideIncludeSubfolder))
{
form.setHideIncludeSubfolders(Boolean.valueOf(hideIncludeSubfolder));
form.setHideIncludeSubfolders(Boolean.parseBoolean(hideIncludeSubfolder));
}
return new ModificationSearchWebPart(form);
}
Expand Down Expand Up @@ -651,9 +648,6 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
TargetedMSListener listener = new TargetedMSListener();
ContainerManager.addContainerListener(listener);

ActionURL chromatogramURL = new ActionURL(TargetedMSController.ChromatogramCrawlerAction.class, ContainerManager.getRoot());
AdminConsole.addLink(AdminConsole.SettingsLinkType.Premium, "Targeted MS Chromatogram Crawler", chromatogramURL, ApplicationAdminPermission.class);

FileContentService fcs = FileContentService.get();
if(null != fcs)
{
Expand Down
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