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Fix PepDB NPE from the crawler #221

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Merged
labkey-jeckels merged 1 commit into from
Apr 2, 2025
Merged

Fix PepDB NPE from the crawler #221

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56 changes: 21 additions & 35 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;

/**
* User: sravani
Expand Down Expand Up @@ -729,7 +730,6 @@ public boolean handlePost(FileForm form, BindException errors) throws Exception
}
catch (Exception e)
{
e.printStackTrace();
_log.error(e.getMessage(), e);
errors.reject(null, "There was a problem uploading File: " + e.getMessage());
return false;
Expand Down Expand Up @@ -842,25 +842,18 @@ public void addNavTrail(NavTree root)
@RequiresPermission(ReadPermission.class)
public abstract class PeptideExcelExportAction extends ExportAction<Object>
{
public void printExcel(Object bean, HttpServletResponse response, BindException errors, PeptideQueryForm form)
public void printExcel(Object bean, HttpServletResponse response, BindException errors, PeptideQueryForm form) throws Exception
{
try
{
RenderContext context = new RenderContext(getViewContext());
DataRegion rgn = getDataRegion(getContainer(), form, Table.ALL_ROWS);
context.setBaseFilter(form.getFilter());
context.setBaseSort(form.getSort());
ExcelWriter ew = new ExcelWriter(()->rgn.getResults(context), rgn.getDisplayColumns());
ew.setAutoSize(true);
ew.setFilenamePrefix(form.getMessage());
ew.setSheetName(form.getMessage());
ew.setFooter(form.getMessage());
ew.renderWorkbook(getResponse());
}
catch (Exception e)
{
_log.error("PeptideExcelExportAction: ", e);
}
RenderContext context = new RenderContext(getViewContext());
DataRegion rgn = getDataRegion(getContainer(), form, Table.ALL_ROWS);
context.setBaseFilter(form.getFilter());
context.setBaseSort(form.getSort());
ExcelWriter ew = new ExcelWriter(()->rgn.getResults(context), rgn.getDisplayColumns());
ew.setAutoSize(true);
ew.setFilenamePrefix(form.getMessage());
ew.setSheetName(form.getMessage());
ew.setFooter(form.getMessage());
ew.renderWorkbook(getResponse());
}
}

Expand Down Expand Up @@ -896,7 +889,7 @@ public void export(Object bean, HttpServletResponse response, BindException erro
public class PeptideDefaultExcelExportAction extends PeptideExcelExportAction
{
@Override
public void export(Object bean, HttpServletResponse response, BindException errors)
public void export(Object bean, HttpServletResponse response, BindException errors) throws Exception
{
ViewContext ctx = getViewContext();
HttpSession session = ctx.getRequest().getSession();
Expand All @@ -911,24 +904,17 @@ public void export(Object bean, HttpServletResponse response, BindException erro
@RequiresPermission(ReadPermission.class)
public abstract class PeptideTextExportAction extends ExportAction
{
public void printText(Object bean, HttpServletResponse response, BindException errors, PeptideQueryForm form)
public void printText(Object bean, HttpServletResponse response, BindException errors, PeptideQueryForm form) throws Exception
{
try
{
RenderContext context = new RenderContext(getViewContext());
DataRegion rgn = getDataRegion(getContainer(), form, Table.ALL_ROWS);
context.setBaseFilter(form.getFilter());
context.setBaseSort(form.getSort());
RenderContext context = new RenderContext(getViewContext());
DataRegion rgn = getDataRegion(getContainer(), form, Table.ALL_ROWS);
context.setBaseFilter(form.getFilter());
context.setBaseSort(form.getSort());

try (TSVGridWriter tsv = new TSVGridWriter(()->rgn.getResults(context), rgn.getDisplayColumns()))
{
tsv.setFilenamePrefix(form.getMessage());
tsv.write(getResponse());
}
}
catch (Exception e)
try (TSVGridWriter tsv = new TSVGridWriter(()->rgn.getResults(context), rgn.getDisplayColumns()))
{
_log.error("PeptideTextExportAction: ", e);
tsv.setFilenamePrefix(Objects.toString(form.getMessage(), "peptideTextExport"));
tsv.write(getResponse());
}
}
}
Expand Down