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Merged
labkey-jeckels merged 5 commits into from
Dec 3, 2025
Merged

Continue adopting FileLike instead of File or Path #1069

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330074d
Continue adopting FileLike instead of File or Path
labkey-jeckels Nov 17, 2025
8896f07
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Nov 19, 2025
2eb9d59
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Dec 1, 2025
e60175e
Fix HTML generation
labkey-jeckels Dec 1, 2025
55ce4ce
Merge branch 'develop' into fb_fileLike3
labkey-jeckels Dec 2, 2025
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5 changes: 2 additions & 3 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsImportTask.java
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Expand Up @@ -60,7 +60,6 @@
import org.labkey.vfs.FileLike;

import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.LineNumberReader;
import java.sql.PreparedStatement;
Expand Down Expand Up @@ -152,8 +151,8 @@ public RecordedActionSet run() throws PipelineJobException
PipelineJob job = getJob();
FileAnalysisJobSupport support = (FileAnalysisJobSupport) job;

processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger());
processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectoryFileLike(), job.getLogger(), job);
processInbreeding(job.getContainer(), job.getUser(), support.getAnalysisDirectory(), job.getLogger());
processKinship(job.getContainer(), job.getUser(), support.getAnalysisDirectory(), job.getLogger(), job);

if (GeneticCalculationsJob.isKinshipValidation())
{
Expand Down
5 changes: 3 additions & 2 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsInitTask.java
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Expand Up @@ -34,6 +34,7 @@
import org.labkey.api.util.FileType;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.writer.PrintWriters;
import org.labkey.vfs.FileLike;
import org.springframework.jdbc.BadSqlGrammarException;

import java.io.File;
Expand Down Expand Up @@ -135,9 +136,9 @@ public RecordedActionSet run() throws PipelineJobException
}
TableSelector ts = new TableSelector(pedTable, PageFlowUtil.set("Id", "Dam", "Sire", "Gender", "Species"), null, new Sort("Species, Id"));

File outputFile = new File(support.getAnalysisDirectory(), GeneticCalculationsImportTask.PEDIGREE_FILE);
FileLike outputFile = support.getAnalysisDirectory().resolveChild(GeneticCalculationsImportTask.PEDIGREE_FILE);

try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(outputFile), '\t', CSVWriter.DEFAULT_QUOTE_CHARACTER))
try (CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(outputFile.openOutputStream()), '\t', CSVWriter.DEFAULT_QUOTE_CHARACTER))
{
long count = ts.getRowCount();
if (count > 0)
Expand Down
7 changes: 4 additions & 3 deletions ehr/src/org/labkey/ehr/pipeline/GeneticCalculationsRTask.java
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Expand Up @@ -35,6 +35,7 @@
import org.labkey.api.resource.Resource;
import org.labkey.api.util.FileType;
import org.labkey.ehr.EHRModule;
import org.labkey.vfs.FileLike;

import java.io.File;
import java.util.ArrayList;
Expand Down Expand Up @@ -120,7 +121,7 @@ public RecordedAction runScript(String scriptName, String outputFileName, String
String exePath = getRPath();

String scriptPath = getScriptPath(scriptName);
File tsvFile = new File(support.getAnalysisDirectory(), GeneticCalculationsImportTask.PEDIGREE_FILE);
FileLike tsvFile = support.getAnalysisDirectory().resolveChild(GeneticCalculationsImportTask.PEDIGREE_FILE);
if (!tsvFile.exists())
throw new PipelineJobException("Unable to find TSV file at location: " + tsvFile.getPath());

Expand All @@ -132,13 +133,13 @@ public RecordedAction runScript(String scriptName, String outputFileName, String
args.add("--no-restore"); // don't restore saved objects
args.add(scriptPath);
args.add("-f");
args.add(tsvFile.getPath());
args.add(tsvFile.toNioPathForRead().toFile().getPath());

getJob().getLogger().info("Using working directory of: " + support.getAnalysisDirectory().getPath());
ProcessBuilder pb = new ProcessBuilder(args);
job.runSubProcess(pb, support.getAnalysisDirectory());

File output = new File(support.getAnalysisDirectory(), outputFileName);
FileLike output = support.getAnalysisDirectory().resolveChild(outputFileName);
if (!output.exists())
throw new PipelineJobException("Unable to find file: " + output.getPath());

Expand Down
2 changes: 0 additions & 2 deletions ehr_billing/api-src/org/labkey/api/ehr_billing/pipeline/BillingPipelineJobSupport.java
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Expand Up @@ -31,8 +31,6 @@ public interface BillingPipelineJobSupport

String getName();

File getAnalysisDir();

/*
* Returns Pair of previous matching billing run's objectId and rowId
* */
Expand Down
20 changes: 12 additions & 8 deletions ehr_billing/src/org/labkey/ehr_billing/EHR_BillingController.java
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Expand Up @@ -47,6 +47,8 @@
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.util.GUID;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.HtmlStringBuilder;
import org.labkey.api.util.Pair;
import org.labkey.api.util.URLHelper;
import org.labkey.api.view.ActionURL;
Expand All @@ -57,11 +59,12 @@
import org.labkey.api.view.WebPartView;
import org.labkey.ehr_billing.pipeline.BillingPipelineForm;
import org.labkey.ehr_billing.pipeline.BillingPipelineJob;
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.List;
Expand Down Expand Up @@ -113,12 +116,12 @@ public ApiResponse execute(BillingPipelineForm form, BindException errors)
}

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);
}
catch (PipelineValidationException | PipelineJobException e)
catch (PipelineValidationException | PipelineJobException | IOException e)
{
errors.reject(ERROR_MSG, e.getMessage());
return null;
Expand Down Expand Up @@ -146,15 +149,16 @@ public ModelAndView getConfirmView(QueryForm form, BindException errors) throws
{
Set<String> ids = DataRegionSelection.getSelected(form.getViewContext(), true);

StringBuilder msg = new StringBuilder("You have selected " + ids.size() + " billing runs to delete. This will also delete: <p>");
for (String m : EHR_BillingManager.get().deleteBillingRuns(getUser(),getContainer(), ids, true))
HtmlStringBuilder msg = HtmlStringBuilder.of("You have selected ").append(ids.size()).append(" billing runs to delete. This will also delete: ");
msg.startTag("p");
for (HtmlString m : EHR_BillingManager.get().deleteBillingRuns(getUser(),getContainer(), ids, true))
{
msg.append(m).append("<br>");
msg.append(m).append(msg.startTag("br"));
}

msg.append("<p>Are you sure you want to do this?");
msg.startTag("p").append("Are you sure you want to do this?");

return new HtmlView(msg.toString());
return new HtmlView(msg.getHtmlString());
}

@Override
Expand Down
11 changes: 6 additions & 5 deletions ehr_billing/src/org/labkey/ehr_billing/EHR_BillingManager.java
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Expand Up @@ -36,6 +36,7 @@
import org.labkey.api.query.QueryUpdateServiceException;
import org.labkey.api.security.User;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.util.HtmlString;

import java.sql.SQLException;
import java.util.ArrayList;
Expand All @@ -60,7 +61,7 @@ public static EHR_BillingManager get()
return _instance;
}

public List<String> deleteBillingRuns(User user, Container container, Collection<String> pks, boolean testOnly) throws QueryUpdateServiceException, BatchValidationException, InvalidKeyException
public List<HtmlString> deleteBillingRuns(User user, Container container, Collection<String> pks, boolean testOnly) throws QueryUpdateServiceException, BatchValidationException, InvalidKeyException
{
TableInfo invoice = EHR_BillingSchema.getInstance().getSchema().getTable(EHR_BillingSchema.TABLE_INVOICE);
TableInfo invoiceRuns = QueryService.get().getUserSchema(user, container,EHR_BillingSchema.NAME).getTable(EHR_BillingSchema.TABLE_INVOICE_RUNS);
Expand All @@ -75,17 +76,17 @@ public List<String> deleteBillingRuns(User user, Container container, Collection
SimpleFilter miscChargesFilter = new SimpleFilter(FieldKey.fromString("invoiceId"), pks, CompareType.IN);

//perform the work
List<String> ret = new ArrayList<>();
List<HtmlString> ret = new ArrayList<>();
if (testOnly)
{
TableSelector tsInvItems = new TableSelector(invoicedItems, invoiceIdFilter, null);
ret.add(tsInvItems.getRowCount() + " records from invoiced items");
ret.add(HtmlString.of(tsInvItems.getRowCount() + " records from invoiced items"));

TableSelector tsInvoice = new TableSelector(invoice, invoiceRunIdFilter, null);
ret.add(tsInvoice.getRowCount() + " records from invoice");
ret.add(HtmlString.of(tsInvoice.getRowCount() + " records from invoice"));

TableSelector tsMiscCharges2 = new TableSelector(miscCharges, miscChargesFilter, null);
ret.add(tsMiscCharges2.getRowCount() + " invoice records from misc charges will be removed from the deleted invoice, which means they will be picked up by the next billing period. They are not deleted.");
ret.add(HtmlString.of(tsMiscCharges2.getRowCount() + " invoice records from misc charges will be removed from the deleted invoice, which means they will be picked up by the next billing period. They are not deleted."));
}
else
{
Expand Down
22 changes: 8 additions & 14 deletions ehr_billing/src/org/labkey/ehr_billing/pipeline/BillingPipelineJob.java
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Expand Up @@ -30,8 +30,10 @@
import org.labkey.api.util.Pair;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.ViewBackgroundInfo;
import org.labkey.vfs.FileLike;

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

Expand All @@ -41,31 +43,29 @@
*/
public class BillingPipelineJob extends PipelineJob implements BillingPipelineJobSupport
{
private File _analysisDir;
private BillingPipelineForm _form;

// For serialization
protected BillingPipelineJob() {}

public BillingPipelineJob(Container c, User user, ActionURL url, PipeRoot pipeRoot, File analysisDir, BillingPipelineForm form)
public BillingPipelineJob(Container c, User user, ActionURL url, PipeRoot pipeRoot, FileLike analysisDir, 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)
public static FileLike createAnalysisDir(PipeRoot pipeRoot, String name) throws IOException
{
String trialName = FileUtil.makeLegalName(name);
File analysisDir = new File(pipeRoot.getRootPath(), trialName);
FileLike analysisDir = pipeRoot.getRootFileLike().resolveChild(trialName);
int suffix = 0;
while (analysisDir.exists())
{
suffix++;
trialName = FileUtil.makeLegalName(name) + "." + suffix;
analysisDir = new File(pipeRoot.getRootPath(), trialName);
analysisDir = pipeRoot.getRootFileLike().resolveChild(trialName);
}

analysisDir.mkdirs();
Expand All @@ -86,7 +86,7 @@ public ActionURL getStatusHref()
}

@Override
public TaskPipeline getTaskPipeline()
public TaskPipeline<?> getTaskPipeline()
{
return PipelineJobService.get().getTaskPipeline(new TaskId(BillingPipelineJob.class));
}
Expand Down Expand Up @@ -115,12 +115,6 @@ public String getName()
return _form.getProtocolName();
}

@Override
public File getAnalysisDir()
{
return _analysisDir;
}

@Override
public Pair<String,String> getPreviousInvoice()
{
Expand Down