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Merged
labkey-jeckels merged 1 commit into from
May 12, 2026
Merged

Auto-refactor lint cleanup #262

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2 changes: 1 addition & 1 deletion ms2extensions/src/org/labkey/ms2extensions/MS2ExtensionsController.java
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Expand Up @@ -110,7 +110,7 @@ public ModelAndView getView(Object o, BindException errors)
return new HtmlView(DOM.DIV("Success!"));
}

warnings.add(0, DOM.DIV("Success, with warnings:"));
warnings.addFirst(DOM.DIV("Success, with warnings:"));
return new HtmlView(DOM.DIV(warnings.toArray(new Object[0])));
}
return new HtmlView(DOM.LK.FORM(
Expand Down
6 changes: 3 additions & 3 deletions ms2extensions/src/org/labkey/ms2extensions/PeptideCountUpdater.java
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Expand Up @@ -106,14 +106,14 @@ public String update(Container container, User user)
}

// Only allow one thread to update at a time
LOG.info("Starting to update peptide counts for " + runIds);
LOG.info("Starting to update peptide counts for {}", runIds);
try (DbScope.Transaction transaction = MS2ExtensionsModule.getSchema().getScope().ensureTransaction(LOCK))
{
// Execute the query, filtering to just the runs that need aggregates calculated
SimpleFilter filter = new SimpleFilter(new SimpleFilter.InClause(ms2RunColumn.getFieldKey(), runIds));
Collection<Map<String, Object>> results = new TableSelector(table, Arrays.asList(ms2RunColumn, totalPeptidesColumn, distinctPeptidesColumn), filter, null).getMapCollection();

LOG.info("Inserting peptide counts for " + runIds);
LOG.info("Inserting peptide counts for {}", runIds);

// Iterate through the results and insert them into the table so they're cached and fast to show
for (Map<String, Object> result : results)
Expand All @@ -123,7 +123,7 @@ public String update(Container container, User user)
Table.insert(null, MS2ExtensionsModule.getSchema().getTable("Ms2RunAggregates"), toInsert);
}
transaction.commit();
LOG.info("Finished updating peptide counts for " + runIds);
LOG.info("Finished updating peptide counts for {}", runIds);
}
}
return null;
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3 changes: 1 addition & 2 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBBaseController.java
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Expand Up @@ -26,7 +26,6 @@
import org.scharp.atlas.pepdb.model.ProteinCategory;
import org.springframework.validation.Errors;

import java.sql.SQLException;
import java.util.List;
import java.util.Map;

Expand Down Expand Up @@ -376,7 +375,7 @@ public void validate(Errors errors)
errors.reject(null, "Peptide Group Name is required.");
}

public void validateName(Errors errors) throws SQLException
public void validateName(Errors errors)
{
PeptideGroup bean = getBean();
PeptideGroup pg = PepDBManager.getPeptideGroupByName(bean);
Expand Down
53 changes: 0 additions & 53 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBContainerListener.java
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53 changes: 19 additions & 34 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBController.java
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Expand Up @@ -49,7 +49,6 @@
import org.springframework.web.servlet.ModelAndView;
import org.springframework.web.servlet.mvc.Controller;

import java.sql.SQLException;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
Expand Down Expand Up @@ -223,7 +222,7 @@ public ModelAndView getView(DisplayPeptideForm form, BindException errors) throw
errors.reject(null, "Peptide Id not found in the database.");
return new JspView<>(PAGE_INDEX, form, errors);
}
_log.debug("DisplayPeptideForm: " + form);
_log.debug("DisplayPeptideForm: {}", form);
VBox box = new VBox();
PeptideQueryForm queryform = new PeptideQueryForm();
queryform.setQueryValue(pepId);
Expand Down Expand Up @@ -419,7 +418,7 @@ public class DisplayPeptideGroupInformationAction extends SimpleViewAction<Pepti
@Override
public ModelAndView getView(PeptideAndGroupForm form, BindException errors) throws Exception
{
_log.debug("PeptideAndGroupForm: " + form.toString());
_log.debug("PeptideAndGroupForm: {}", form.toString());
PeptideGroup pg = null;
try
{
Expand Down Expand Up @@ -503,7 +502,7 @@ public class DisplayPeptidePoolInformationAction extends SimpleViewAction<Peptid
@Override
public ModelAndView getView(PeptideAndPoolForm form, BindException errors) throws Exception
{
_log.debug("PeptideAndPoolForm: " + form.toString());
_log.debug("PeptideAndPoolForm: {}", form.toString());
PeptideQueryForm queryform = new PeptideQueryForm();
TableInfo tableInfo = PepDBSchema.getInstance().getTableInfoPeptidePools();
PropertyValues pv = this.getPropertyValues();
Expand Down Expand Up @@ -570,7 +569,7 @@ public ModelAndView getView(PeptideGroupForm form, boolean reshow, BindException
}

@Override
public boolean handlePost(PeptideGroupForm form, BindException errors) throws Exception
public boolean handlePost(PeptideGroupForm form, BindException errors)
{
PeptideGroup bean = form.getBean();
PeptideGroup dbBean = PepDBManager.getPeptideGroupByID(bean.getPeptide_group_id());
Expand All @@ -583,15 +582,8 @@ public boolean handlePost(PeptideGroupForm form, BindException errors) throws Ex
@Override
public void validateCommand(PeptideGroupForm form, Errors errors)
{
try
{
form.validate(errors);
form.validateName(errors);
}
catch (SQLException e)
{
errors.reject(null, "There's something wrong with database when trying to get all the existing groups.");
}
form.validate(errors);
form.validateName(errors);
}

@Override
Expand Down Expand Up @@ -632,7 +624,7 @@ public ModelAndView getView(PeptideGroupForm form, boolean reshow, BindException
}

@Override
public boolean handlePost(PeptideGroupForm form, BindException errors) throws Exception
public boolean handlePost(PeptideGroupForm form, BindException errors)
{
PeptideGroup group = form.getBean();
group = PepDBManager.insertGroup(getContainer(), getUser(), group);
Expand All @@ -644,15 +636,8 @@ public boolean handlePost(PeptideGroupForm form, BindException errors) throws Ex
@Override
public void validateCommand(PeptideGroupForm form, Errors errors)
{
try
{
form.validate(errors);
form.validateName(errors);
}
catch (SQLException e)
{
errors.reject(null, "There's something wrong with database when trying to get all the existing groups.");
}
form.validate(errors);
form.validateName(errors);
}

@Override
Expand Down Expand Up @@ -867,7 +852,7 @@ public void export(Object bean, HttpServletResponse response, BindException erro
ViewContext ctx = getViewContext();
HttpSession session = ctx.getRequest().getSession();
PeptideQueryForm form = (PeptideQueryForm) session.getAttribute("PEPTIDE_QUERY_FORM");
_log.info("Form " + form.getMessage() + " had filter : " + form.getFilter());
_log.info("Form {} had filter : {}", form.getMessage(), form.getFilter());
printExcel(form);
}
}
Expand Down Expand Up @@ -963,7 +948,7 @@ protected GridView getGridViewByGroup(PeptideQueryForm form, PropertyValues pv)
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewGroupPeptides();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for peptideGroup." + PepDBSchema.COLUMN_PEPTIDE_GROUP_ID + ": " + form);
_log.debug("Creating a Filter for peptideGroup." + PepDBSchema.COLUMN_PEPTIDE_GROUP_ID + ": {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PEPTIDE_GROUP_ID), Integer.parseInt(form.getQueryValue()));
if (form.getLabId() != null)
sFilter.addCondition(FieldKey.fromParts(PepDBSchema.COLUMN_PEPTIDE_ID_IN_GROUP), form.getLabId());
Expand Down Expand Up @@ -995,7 +980,7 @@ protected GridView getGridViewByPool(PeptideQueryForm form, PropertyValues pv) t
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewPoolPeptides();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for peptidePool." + PepDBSchema.COLUMN_PEPTIDE_POOL_ID + ": " + form);
_log.debug("Creating a Filter for peptidePool." + PepDBSchema.COLUMN_PEPTIDE_POOL_ID + ": {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PEPTIDE_POOL_ID), Integer.parseInt(form.getQueryValue()));
Sort sort = new Sort(PepDBSchema.COLUMN_PEPTIDE_ID);
form.setFilter(sFilter);
Expand All @@ -1020,7 +1005,7 @@ protected GridView getGridViewByParentPool(PeptideQueryForm form, PropertyValues
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewPoolDetails();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for parent peptidePool." + PepDBSchema.COLUMN_PARENT_POOL_ID + ": " + form);
_log.debug("Creating a Filter for parent peptidePool." + PepDBSchema.COLUMN_PARENT_POOL_ID + ": {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PARENT_POOL_ID), Integer.parseInt(form.getQueryValue()));
Sort sort = new Sort(PepDBSchema.COLUMN_PEPTIDE_POOL_ID);
form.setFilter(sFilter);
Expand All @@ -1042,7 +1027,7 @@ protected GridView getGridViewBySequence(PeptideQueryForm form, PropertyValues p
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewGroupPeptides();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for peptideSequence." + PepDBSchema.COLUMN_PEPTIDE_SEQUENCE + ": " + form);
_log.debug("Creating a Filter for peptideSequence." + PepDBSchema.COLUMN_PEPTIDE_SEQUENCE + ": {}", form);
SimpleFilter sFilter = new SimpleFilter();

boolean sequenceIsEmpty = true;
Expand Down Expand Up @@ -1093,7 +1078,7 @@ protected GridView getGridViewByProtein(PeptideQueryForm form, PropertyValues pv
.getTableInfoViewGroupPeptides();
form.setTInfo(tableInfo);
String title = "Peptides in Protein Category " + pc.getProtein_cat_desc();
_log.debug("Creating a Filter for proteinCategory." + PepDBSchema.COLUMN_PROTEIN_CAT_ID + ": " + form);
_log.debug("Creating a Filter for proteinCategory." + PepDBSchema.COLUMN_PROTEIN_CAT_ID + ": {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PROTEIN_CAT_ID), Integer.parseInt(form.getQueryValue()));
if (form.getAAEnd() == null && form.getAAStart() != null)
{
Expand Down Expand Up @@ -1131,7 +1116,7 @@ protected GridView getGridViewByParentId(PeptideQueryForm form, PropertyValues p
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewParentChildDetails();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for parentID. : " + form);
_log.debug("Creating a Filter for parentID. : {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PARENT_ID), Integer.parseInt(form.getQueryValue()));
Sort sort = new Sort(PepDBSchema.COLUMN_CHILD_ID);
form.setFilter(sFilter);
Expand All @@ -1154,7 +1139,7 @@ protected GridView getGridViewByParent(PeptideQueryForm form, PropertyValues pv)
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewParentChildDetails();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for parentSequence. : " + form);
_log.debug("Creating a Filter for parentSequence. : {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_PARENT_SEQUENCE), form.getQueryValue().trim().toUpperCase());
Sort sort = new Sort(PepDBSchema.COLUMN_CHILD_ID);
form.setFilter(sFilter);
Expand All @@ -1177,7 +1162,7 @@ protected GridView getGridViewByChildId(PeptideQueryForm form, PropertyValues pv
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewParentChildDetails();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for childID. : " + form);
_log.debug("Creating a Filter for childID. : {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_CHILD_ID), Integer.parseInt(form.getQueryValue()));
Sort sort = new Sort(PepDBSchema.COLUMN_PARENT_ID);
form.setFilter(sFilter);
Expand All @@ -1200,7 +1185,7 @@ protected GridView getGridViewByChild(PeptideQueryForm form, PropertyValues pv)
TableInfo tableInfo = PepDBSchema.getInstance()
.getTableInfoViewParentChildDetails();
form.setTInfo(tableInfo);
_log.debug("Creating a Filter for childID. : " + form);
_log.debug("Creating a Filter for childID. : {}", form);
SimpleFilter sFilter = new SimpleFilter(FieldKey.fromParts(PepDBSchema.COLUMN_CHILD_SEQUENCE), form.getQueryValue().trim().toUpperCase());
Sort sort = new Sort(PepDBSchema.COLUMN_PARENT_ID);
form.setFilter(sFilter);
Expand Down
9 changes: 4 additions & 5 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBManager.java
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Expand Up @@ -23,7 +23,6 @@
import org.scharp.atlas.pepdb.model.ProteinCategory;
import org.scharp.atlas.pepdb.model.Source;

import java.sql.SQLException;
import java.util.HashMap;

/**
Expand Down Expand Up @@ -203,13 +202,13 @@ public static PeptidePool[] getPoolsForPeptide(String peptideId)
return pools;
}

public static PeptideGroup insertGroup(Container c, User user, PeptideGroup pg) throws SQLException
public static PeptideGroup insertGroup(Container c, User user, PeptideGroup pg)
{
PeptideGroup resultGroup = Table.insert(user, PepDBSchema.getInstance().getTableInfoPeptideGroups(), pg);
return resultGroup;
}

public static PeptideGroup updatePeptideGroup(User user,PeptideGroup pg) throws SQLException
public static PeptideGroup updatePeptideGroup(User user,PeptideGroup pg)
{
return Table.update(user, PepDBSchema.getInstance().getTableInfoPeptideGroups(),pg,pg.getPeptide_group_id());
}
Expand Down Expand Up @@ -284,7 +283,7 @@ public static Peptides getPeptideById(Integer peptideId)
return new TableSelector(tInfo, sFilter, null).getObject(Peptides.class);
}

public static Peptides[] getParentPeptides(Peptides p) throws SQLException
public static Peptides[] getParentPeptides(Peptides p)
{
TableInfo tInfo = schema.getTableInfoPeptides();
String sql = "select * from pepdb.peptides where peptides.protein_cat_id = ? and ? between peptides.amino_acid_start_pos-2 and peptides.amino_acid_end_pos\n" +
Expand All @@ -293,7 +292,7 @@ public static Peptides[] getParentPeptides(Peptides p) throws SQLException
return peptides;
}

public static Peptides[] getHyphanatedParents(Peptides p) throws SQLException
public static Peptides[] getHyphanatedParents(Peptides p)
{
String sql = "select * from "+schema.getTableInfoPeptides()+" where peptides.protein_cat_id = ? " +
" and peptides.peptide_sequence LIKE '%"+p.getPeptide_sequence()+"%' " +
Expand Down
3 changes: 0 additions & 3 deletions pepdb/src/org/scharp/atlas/pepdb/PepDBModule.java
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Expand Up @@ -4,7 +4,6 @@
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.data.DbSchema;
import org.labkey.api.module.DefaultModule;
import org.labkey.api.module.ModuleContext;
Expand Down Expand Up @@ -72,8 +71,6 @@ public boolean hasScripts()
@Override
public void doStartup(ModuleContext moduleContext)
{
// add a container listener so we'll know when our container is deleted:
ContainerManager.addContainerListener(new PepDBContainerListener());
}
@Override
@NotNull
Expand Down
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