Skip to content

Manually decode form parameters #197

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
bbimber merged 2 commits into from
Aug 27, 2025
Merged

Manually decode form parameters #197

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a1babe5
Manually decode form parameters
bbimber Aug 27, 2025
2f850c8
Manually decode form parameters
bbimber Aug 27, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

package org.labkey.genotypeassays;

import org.apache.commons.text.StringEscapeUtils;
import org.json.JSONArray;
import org.labkey.api.action.ApiResponse;
import org.labkey.api.action.ApiSimpleResponse;
Expand All @@ -37,6 +38,7 @@
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;

import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
Expand Down Expand Up @@ -130,7 +132,8 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
return null;
}

Pair<List<Integer>, List<Integer>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, form.getAlleleNames());
String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
Pair<List<Integer>, List<Integer>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
resultProperties.put("runsCreated", ret.first);
resultProperties.put("runsDeleted", ret.second);
}
Expand Down
8 changes: 8 additions & 0 deletions GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -60,6 +60,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;

public class GenotypeAssaysManager
{
Expand Down Expand Up @@ -121,13 +122,15 @@ public Pair<List<Integer>, List<Integer>> cacheAnalyses(final ViewContext ctx, f
final Map<Integer, List<Map<String, Object>>> rowHash = new HashMap<>();
final Map<Integer, Set<Integer>> toDeleteByAnalysis = new HashMap<>();

AtomicInteger records = new AtomicInteger();
TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
{
@Override
public void exec(ResultSet object) throws SQLException
{
Results rs = new ResultsImpl(object, cols);
records.getAndIncrement();

int analysisId = rs.getInt(FieldKey.fromString("analysis_id"));
String lineages = rs.getString(FieldKey.fromString("lineages"));
Expand Down Expand Up @@ -167,6 +170,11 @@ public void exec(ResultSet object) throws SQLException
}
});

if (records.get() != pks.length)
{
throw new IllegalStateException("The number of records found did not match the number supplied. This indicates a problem with the import.");
}

if (!rowHash.isEmpty())
{
processSet(SBT_LINEAGE_ASSAY_TYPE, rowHash, assayDataTable, u, ctx, toDeleteByAnalysis, ap, protocol, runsCreated);
Expand Down