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Merged
labkey-adam merged 2 commits into from
Feb 18, 2026
+81 −99
Merged

Avoid NPE when bad queryKey is provided #252

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34bfebd
Avoid NPE when bad queryKey is provided
labkey-adam Feb 17, 2026
48081c4
Show bogus queryKey error
labkey-adam Feb 17, 2026
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122 changes: 60 additions & 62 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBBaseController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -157,87 +157,85 @@ public void setLabId(String labId)
this.labId = labId;
}

public boolean validate(Errors errors) throws SQLException
public boolean validate(Errors errors)
{
if(getQueryKey() == null || StringUtils.trimToNull(getQueryKey()) == null)
errors.reject(null, "The Search Criteria must be entered.");
String qValue = getQueryValue();
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_PARENT_SEQUENCE))
if (getQueryKey() != null)
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Parent Sequence must be entered.");
}
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_CHILD_SEQUENCE))
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Child Sequence must be entered.");
}
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_GROUP_ID))
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Peptide Group must be selected to get peptides in a group.");
/*
if(StringUtils.trimToNull(getLabId()) == null)
errors.reject(null, "Peptide Number must be entered.");
*/
}
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_POOL_ID))
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Peptide Pool Name must be selected to get peptides in a pool.");
}
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_PROTEIN_CAT_ID))
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Protein Category must be selected to get peptides in a protein category.");
else
switch (getQueryKey())
{
ProteinCategory pc = PepDBManager.getProCatByID(Integer.parseInt(getQueryValue()));
if(pc.getProtein_cat_desc().trim().contains("-"))
case PepDBSchema.COLUMN_PARENT_SEQUENCE ->
{
if(StringUtils.trimToNull(getAAStart()) != null || StringUtils.trimToNull(getAAEnd()) != null)
errors.reject(null,"When you select a hyphanated Protein Category : "+pc.getProtein_cat_desc()+" AAStart & AAEnd values are not allowed.");
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Parent Sequence must be entered.");
}
else
case PepDBSchema.COLUMN_CHILD_SEQUENCE ->
{
if(StringUtils.trimToNull(getAAStart()) != null && validateInteger(getAAStart().trim()) == null)
errors.reject(null, "AAStart must be an Integer.");
if(StringUtils.trimToNull(getAAEnd()) != null && validateInteger(getAAEnd().trim()) == null)
errors.reject(null, "AAEnd must be an Integer.");
if(StringUtils.trimToNull(getAAStart()) != null && validateInteger(getAAStart().trim()) != null
&& StringUtils.trimToNull(getAAEnd()) != null && validateInteger(getAAEnd().trim()) != null
&& validateInteger(getAAStart().trim()) > validateInteger(getAAEnd().trim()))
errors.reject(null, "AAStart must be less than or equal to AAEnd.");
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Child Sequence must be entered.");
}
}
}
if (getQueryKey() != null && getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_ID))
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Peptide Id range must be entered.");
if (qValue != null && !qValue.isEmpty())
{
if (!(qValue.matches("\\d+-\\d+")))
case PepDBSchema.COLUMN_PEPTIDE_GROUP_ID ->
{
errors.reject(null, "To get the peptides in the range you should specify the Range of numbers.\n" +
"The format for specify the range of peptide is <number>-<number> Example would be 30-100");
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Peptide Group must be selected to get peptides in a group.");
}
else
case PepDBSchema.COLUMN_PEPTIDE_POOL_ID ->
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Peptide Pool Name must be selected to get peptides in a pool.");
}
case PepDBSchema.COLUMN_PROTEIN_CAT_ID ->
{
String[] range = qValue.split("-");
if (Integer.parseInt(range[0]) > Integer.parseInt(range[1]))
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "Protein Category must be selected to get peptides in a protein category.");
else
{
errors.reject(null, "The minimum value which is before '-' should be less than the max value which is after '-'.\n");

ProteinCategory pc = PepDBManager.getProCatByID(Integer.parseInt(getQueryValue()));
if (pc.getProtein_cat_desc().trim().contains("-"))
{
if (StringUtils.trimToNull(getAAStart()) != null || StringUtils.trimToNull(getAAEnd()) != null)
errors.reject(null, "When you select a hyphanated Protein Category : " + pc.getProtein_cat_desc() + " AAStart & AAEnd values are not allowed.");
}
else
{
if (StringUtils.trimToNull(getAAStart()) != null && validateInteger(getAAStart().trim()) == null)
errors.reject(null, "AAStart must be an Integer.");
if (StringUtils.trimToNull(getAAEnd()) != null && validateInteger(getAAEnd().trim()) == null)
errors.reject(null, "AAEnd must be an Integer.");
if (StringUtils.trimToNull(getAAStart()) != null && validateInteger(getAAStart().trim()) != null
&& StringUtils.trimToNull(getAAEnd()) != null && validateInteger(getAAEnd().trim()) != null
&& validateInteger(getAAStart().trim()) > validateInteger(getAAEnd().trim()))
errors.reject(null, "AAStart must be less than or equal to AAEnd.");
}
}
}
case PepDBSchema.COLUMN_PEPTIDE_ID ->
{
if (StringUtils.trimToNull(qValue) == null)
errors.reject(null, "The Peptide Id range must be entered.");
if (qValue != null && !qValue.isEmpty())
{
if (!(qValue.matches("\\d+-\\d+")))
{
errors.reject(null, "To get the peptides in the range you should specify the Range of numbers.\n" +
"The format for specify the range of peptide is <number>-<number> Example would be 30-100");
}
else
{
String[] range = qValue.split("-");
if (Integer.parseInt(range[0]) > Integer.parseInt(range[1]))
{
errors.reject(null, "The minimum value which is before '-' should be less than the max value which is after '-'.\n");
}
}
}
}
}
}
if(errors != null && errors.getErrorCount() >0)
return false;
return true;
return errors == null || !errors.hasErrors();
}

}

public static class DisplayPeptideForm
Expand Down
58 changes: 21 additions & 37 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,6 @@
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.DetailsView;
import org.labkey.api.view.GridView;
import org.labkey.api.view.HttpView;
import org.labkey.api.view.InsertView;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
Expand Down Expand Up @@ -170,44 +169,29 @@ public class GetPeptidesAction extends SimpleViewAction<PeptideQueryForm>
@Override
public ModelAndView getView(PeptideQueryForm form, BindException errors) throws Exception
{
if (!form.validate(errors))
if (form.validate(errors))
{
return new JspView<>(PAGE_PEPTIDE_GROUP_SELECT, form, errors);
}
PropertyValues pv = this.getPropertyValues();
ViewContext ctx = getViewContext();
HttpSession session = ctx.getRequest().getSession(true);
session.setAttribute("QUERY_FORM", form);
GridView gridView = new GridView(new DataRegion(), (BindException) null);
if (form.getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_GROUP_ID))
{
gridView = getGridViewByGroup(form, pv);
}
if (form.getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_POOL_ID))
{
gridView = getGridViewByPool(form, pv);
}
if (form.getQueryKey().equals(PepDBSchema.COLUMN_PROTEIN_CAT_ID))
{
gridView = getGridViewByProtein(form, pv);
}
if (form.getQueryKey().equals(PepDBSchema.COLUMN_PEPTIDE_SEQUENCE))
{
gridView = getGridViewBySequence(form, pv);
}
if (form.getQueryKey().equals(PepDBSchema.COLUMN_PARENT_SEQUENCE))
{
gridView = getGridViewByParent(form, pv);
}
if (form.getQueryKey().equals(PepDBSchema.COLUMN_CHILD_SEQUENCE))
{
gridView = getGridViewByChild(form, pv);
}
if (gridView == null)
{
HttpView.redirect(new ActionURL(SearchForPeptidesAction.class, getContainer()));
PropertyValues pv = this.getPropertyValues();
GridView gridView = switch (form.getQueryKey())
{
case PepDBSchema.COLUMN_PEPTIDE_GROUP_ID -> getGridViewByGroup(form, pv);
case PepDBSchema.COLUMN_PEPTIDE_POOL_ID -> getGridViewByPool(form, pv);
case PepDBSchema.COLUMN_PROTEIN_CAT_ID -> getGridViewByProtein(form, pv);
case PepDBSchema.COLUMN_PEPTIDE_SEQUENCE -> getGridViewBySequence(form, pv);
case PepDBSchema.COLUMN_PARENT_SEQUENCE -> getGridViewByParent(form, pv);
case PepDBSchema.COLUMN_CHILD_SEQUENCE -> getGridViewByChild(form, pv);
default -> null;
};
if (gridView != null)
{
ViewContext ctx = getViewContext();
HttpSession session = ctx.getRequest().getSession(true);
session.setAttribute("QUERY_FORM", form);
return gridView;
}
errors.reject(null, "Unrecognized queryKey: " + form.getQueryKey());
}
return gridView;
return new JspView<>(PAGE_PEPTIDE_GROUP_SELECT, form, errors);
}

@Override
Expand Down