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Merged
labkey-jeckels merged 3 commits into from
Dec 3, 2025
Merged

Continue adopting FileLike instead of File or Path #1556

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cb932cb
Continue adopting FileLike instead of File or Path
labkey-jeckels Nov 17, 2025
a286c20
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Nov 19, 2025
9dfd3b6
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Dec 3, 2025
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6 changes: 4 additions & 2 deletions onprc_billing/src/org/labkey/onprc_billing/ONPRC_BillingController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -43,11 +43,13 @@
import org.labkey.onprc_billing.notification.BillingValidationNotification;
import org.labkey.onprc_billing.pipeline.BillingPipelineJob;
import org.labkey.onprc_billing.security.ONPRCBillingAdminPermission;
import org.labkey.vfs.FileLike;
import org.springframework.validation.BindException;
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;

import java.io.File;
import java.io.IOException;
import java.util.Date;
import java.util.HashMap;
import java.util.Map;
Expand All @@ -68,14 +70,14 @@ public ONPRC_BillingController()
public static class RunBillingPipelineAction extends MutatingApiAction<BillingPipelineForm>
{
@Override
public ApiResponse execute(BillingPipelineForm form, BindException errors) throws PipelineJobException
public ApiResponse execute(BillingPipelineForm form, BindException errors) throws IOException
{
Map<String, Object> resultProperties = new HashMap<>();

try
{
PipeRoot pipelineRoot = PipelineService.get().findPipelineRoot(getContainer());
File analysisDir = BillingPipelineJob.createAnalysisDir(pipelineRoot, form.getProtocolName());
FileLike analysisDir = BillingPipelineJob.createAnalysisDir(pipelineRoot, form.getProtocolName());
PipelineService.get().queueJob(new BillingPipelineJob(getContainer(), getUser(), getViewContext().getActionURL(), pipelineRoot, analysisDir, form));

resultProperties.put("success", true);
Expand Down
30 changes: 10 additions & 20 deletions onprc_billing/src/org/labkey/onprc_billing/pipeline/BillingPipelineJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,8 +30,9 @@
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.onprc_billing.ONPRC_BillingController;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.io.IOException;
import java.util.Calendar;
import java.util.Date;

Expand All @@ -42,33 +43,30 @@
*/
public class BillingPipelineJob extends PipelineJob implements BillingPipelineJobSupport
{
private File _analysisDir;
private ONPRC_BillingController.BillingPipelineForm _form;

// For deserialization
public BillingPipelineJob()
{
}

public BillingPipelineJob(Container c, User user, ActionURL url, PipeRoot pipeRoot, File analysisDir, ONPRC_BillingController.BillingPipelineForm form)
public BillingPipelineJob(Container c, User user, ActionURL url, PipeRoot pipeRoot, FileLike analysisDir, ONPRC_BillingController.BillingPipelineForm form)
{
super(null, new ViewBackgroundInfo(c, user, url), pipeRoot);

_analysisDir = analysisDir;
setLogFile(new File(analysisDir, FileUtil.makeFileNameWithTimestamp("billingPipeline", "log")));
setLogFile(analysisDir.resolveChild(FileUtil.makeFileNameWithTimestamp("billingPipeline", "log")));
_form = form;
}

public static File createAnalysisDir(PipeRoot pipeRoot, String name) throws PipelineValidationException
public static FileLike createAnalysisDir(PipeRoot pipeRoot, String name) throws PipelineValidationException, IOException
{
String trialName = FileUtil.makeLegalName(name);
File analysisDir = new File(pipeRoot.getRootPath(), trialName);
FileLike analysisDir = pipeRoot.resolvePathToFileLike(trialName);
int suffix = 0;
while (analysisDir.exists())
{
suffix++;
trialName = FileUtil.makeLegalName(name) + "." + suffix;
analysisDir = new File(pipeRoot.getRootPath(), trialName);
analysisDir = pipeRoot.resolvePathToFileLike(trialName);
}

analysisDir.mkdirs();
Expand All @@ -89,23 +87,21 @@ public ActionURL getStatusHref()
}

@Override
public TaskPipeline getTaskPipeline()
public TaskPipeline<?> getTaskPipeline()
{
return PipelineJobService.get().getTaskPipeline(new TaskId(BillingPipelineJob.class));
}

@Override
public Date getStartDate()
{
Date ret = _form.getStartDate() == null ? null : DateUtils.truncate(_form.getStartDate(), Calendar.DATE);
return ret;
return _form.getStartDate() == null ? null : DateUtils.truncate(_form.getStartDate(), Calendar.DATE);
}

@Override
public Date getEndDate()
{
Date ret = _form.getEndDate() == null ? null : DateUtils.truncate(_form.getEndDate(), Calendar.DATE);
return ret;
return _form.getEndDate() == null ? null : DateUtils.truncate(_form.getEndDate(), Calendar.DATE);
}

@Override
Expand All @@ -119,10 +115,4 @@ public String getName()
{
return _form.getProtocolName();
}

@Override
public File getAnalysisDir()
{
return _analysisDir;
}
}
2 changes: 0 additions & 2 deletions onprc_billing/src/org/labkey/onprc_billing/pipeline/BillingPipelineJobSupport.java
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Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,4 @@ public interface BillingPipelineJobSupport
String getComment();

String getName();

File getAnalysisDir();
}