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Merged
labkey-adam merged 7 commits into from
Feb 15, 2023
Merged

Migrate to new JSONObject/JSONArray #162

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94274c4
Migrate to new JSONObject/JSONArray
bbimber Feb 10, 2023
7277eae
Add dependency
bbimber Feb 10, 2023
49bf092
Another bugfix related to JSONObject migration
bbimber Feb 12, 2023
c52f478
Bugfix related to JSON migration
bbimber Feb 12, 2023
58938e8
Fix string cast
bbimber Feb 12, 2023
33afea0
Convert JSONObject to Map to avoid null vs. JSONObject$Null issues
bbimber Feb 12, 2023
1a3586f
Remove warnings
bbimber Feb 13, 2023
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2 changes: 1 addition & 1 deletion GenotypeAssays/resources/assay/GenotypeAssay/queries/Batches.query.xml
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Expand Up @@ -11,7 +11,7 @@
<column columnName="Hypothesis">
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="Comments">
<column columnName="comments">
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="importMethod">
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2 changes: 1 addition & 1 deletion GenotypeAssays/resources/assay/GenotypeAssay/queries/Runs.query.xml
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Expand Up @@ -7,7 +7,7 @@
<column columnName="Name">
<columnTitle>Run Name</columnTitle>
</column>
<column columnName="Comments">
<column columnName="comments">
<columnTitle>Run Description</columnTitle>
<nullable>true</nullable>
</column>
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2 changes: 1 addition & 1 deletion GenotypeAssays/resources/assay/SnpAssay/queries/Batches.query.xml
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Expand Up @@ -11,7 +11,7 @@
<column columnName="Hypothesis">
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="Comments">
<column columnName="comments">
<shownInInsertView>false</shownInInsertView>
</column>
<column columnName="importMethod">
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2 changes: 1 addition & 1 deletion GenotypeAssays/resources/assay/SnpAssay/queries/Runs.query.xml
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Expand Up @@ -7,7 +7,7 @@
<column columnName="Name">
<columnTitle>Run Name</columnTitle>
</column>
<column columnName="Comments">
<column columnName="comments">
<columnTitle>Run Description</columnTitle>
<nullable>true</nullable>
</column>
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2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java
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Expand Up @@ -16,7 +16,7 @@

package org.labkey.genotypeassays;

import org.json.old.JSONArray;
import org.json.JSONArray;
import org.labkey.api.action.ApiResponse;
import org.labkey.api.action.ApiSimpleResponse;
import org.labkey.api.action.ConfirmAction;
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7 changes: 4 additions & 3 deletions GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java
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Expand Up @@ -18,8 +18,8 @@

import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.json.old.JSONArray;
import org.json.old.JSONObject;
import org.json.JSONArray;
import org.json.JSONObject;
import org.labkey.api.assay.AssayProtocolSchema;
import org.labkey.api.assay.AssayProvider;
import org.labkey.api.assay.AssayService;
Expand All @@ -45,6 +45,7 @@
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Pair;
import org.labkey.api.view.ViewContext;
Expand Down Expand Up @@ -197,7 +198,7 @@ public Pair<List<Integer>, List<Integer>> cacheHaplotypes(final ViewContext ctx,

Set<Integer> analysisIds = new HashSet<>();
final Map<Integer, List<JSONObject>> haploMap = new HashMap<>();
for (JSONObject row : data.toJSONObjectArray())
for (JSONObject row : JsonUtil.toJSONObjectList(data))
{
Integer analysisId = row.getInt("analysisId");
analysisIds.add(analysisId);
Expand Down
5 changes: 3 additions & 2 deletions GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultGenotypeAssaysImportMethod.java
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@@ -1,7 +1,7 @@
package org.labkey.genotypeassays.assay;

import org.apache.commons.lang3.StringUtils;
import org.labkey.api.data.Container;
import org.labkey.api.gwt.client.util.StringUtils;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.laboratory.assay.AssayParser;
import org.labkey.api.laboratory.assay.DefaultAssayImportMethod;
Expand All @@ -27,12 +27,13 @@ public DefaultGenotypeAssaysImportMethod()
super(GenotypeAssaysManager.GENOTYPE_ASSAY_PROVIDER);
}

@Override
public AssayParser getFileParser(Container c, User u, int assayId)
{
return new DefaultGenotypeAssayParser(this, c, u, assayId);
}

public class DefaultGenotypeAssayParser extends DefaultAssayParser
public static class DefaultGenotypeAssayParser extends DefaultAssayParser
{
public DefaultGenotypeAssayParser(AssayImportMethod method, Container c, User u, int assayId)
{
Expand Down
2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/DefaultSnpAssayImportMethod.java
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@@ -1,6 +1,6 @@
package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.laboratory.assay.DefaultAssayImportMethod;
import org.labkey.api.view.ViewContext;
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2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/GenotypeAssayDataProvider.java
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@@ -1,6 +1,6 @@
package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.laboratory.NavItem;
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2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/SNPAssayDataProvider.java
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@@ -1,6 +1,6 @@
package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.laboratory.assay.AbstractAssayDataProvider;
import org.labkey.api.module.Module;
import org.labkey.api.view.ViewContext;
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2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDataProvider.java
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package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.laboratory.assay.AbstractAssayDataProvider;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.module.Module;
Expand Down
4 changes: 2 additions & 2 deletions GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPAssayDefaultImportMethod.java
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@@ -1,6 +1,6 @@
package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpProtocol;
Expand Down Expand Up @@ -72,7 +72,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>

while (rowsIter.hasNext())
{
Map<String, Object> row = new CaseInsensitiveHashMap(rowsIter.next());
Map<String, Object> row = new CaseInsensitiveHashMap<>(rowsIter.next());
appendPromotedResultFields(row, context);

helper.normalizeResultField(row, context);
Expand Down
2 changes: 1 addition & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPImportHelper.java
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Expand Up @@ -84,7 +84,7 @@ private Map<String, String> getResultValues()

TableSelector ts = new TableSelector(ti);
Map<String, Object>[] rows = ts.getMapArray();
Map<String, String> ret = new CaseInsensitiveHashMap();
Map<String, String> ret = new CaseInsensitiveHashMap<>();
for (Map<String, Object> row : rows)
{
ret.put((String)row.get("result"), (String)row.get("result"));
Expand Down
3 changes: 2 additions & 1 deletion GenotypeAssays/src/org/labkey/genotypeassays/assay/SSPPivotingImportMethod.java
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@@ -1,6 +1,6 @@
package org.labkey.genotypeassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpProtocol;
Expand Down Expand Up @@ -51,6 +51,7 @@ public JSONObject getMetadata(ViewContext ctx, ExpProtocol protocol)
return _importMethod.getMetadata(ctx, protocol);
}

@Override
public String getTooltip()
{
return "Choose this option to upload data using a template with many allele typings per row";
Expand Down
2 changes: 1 addition & 1 deletion LabPurchasing/src/org/labkey/labpurchasing/LabPurchasingDataProvider.java
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@@ -1,6 +1,6 @@
package org.labkey.labpurchasing;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.laboratory.AbstractDataProvider;
import org.labkey.api.laboratory.DetailsUrlWithoutLabelNavItem;
Expand Down
2 changes: 1 addition & 1 deletion covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java
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@@ -1,6 +1,6 @@
package org.labkey.covidseq;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.data.TableInfo;
import org.labkey.api.laboratory.AbstractDataProvider;
Expand Down
2 changes: 1 addition & 1 deletion elispot_assay/src/org/labkey/elispot_assay/ELISPOT_AssayDataProvider.java
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Expand Up @@ -15,7 +15,7 @@
*/
package org.labkey.elispot_assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.laboratory.NavItem;
Expand Down
3 changes: 2 additions & 1 deletion elispot_assay/src/org/labkey/elispot_assay/assay/AIDImportMethod.java
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Expand Up @@ -2,7 +2,7 @@

import au.com.bytecode.opencsv.CSVWriter;
import org.apache.commons.lang3.StringUtils;
import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpExperiment;
Expand Down Expand Up @@ -74,6 +74,7 @@ public String getTemplateInstructions()
return super.getTemplateInstructions() + "<br><br>This import path assumes you prepared this run by creating/saving a template from this site, which defines your plate layout and sample information. The results you enter below will be merged with that previously imported sample information using well. When you select a saved plate template using the \'Saved Sample Information\' section above, you should see a list of the samples you uploaded.";
}

@Override
public AssayParser getFileParser(Container c, User u, int assayId)
{
return new Parser(this, c, u, assayId);
Expand Down
23 changes: 12 additions & 11 deletions elispot_assay/src/org/labkey/elispot_assay/assay/DefaultImportMethod.java
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Expand Up @@ -7,8 +7,8 @@
import org.apache.commons.math3.stat.inference.TestUtils;
import org.apache.logging.log4j.Level;
import org.jetbrains.annotations.Nullable;
import org.json.old.JSONArray;
import org.json.old.JSONObject;
import org.json.JSONArray;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.data.ConvertHelper;
Expand All @@ -21,6 +21,7 @@
import org.labkey.api.query.BatchValidationException;
import org.labkey.api.query.ValidationException;
import org.labkey.api.security.User;
import org.labkey.api.util.JsonUtil;
import org.labkey.api.view.ViewContext;

import java.text.DecimalFormat;
Expand Down Expand Up @@ -106,12 +107,12 @@ protected List<Map<String, Object>> calculatePositivity(List<Map<String, Object>
{
String delim = "/";

JSONObject runProperties = context.getRunProperties();
List<Map<String, Object>> newRows = new ArrayList<Map<String, Object>>();
Map<String, List<Double>> negWellMap = new CaseInsensitiveHashMap<List<Double>>();
Map<String, String> sampleKeyToNegCtlKey = new HashMap<String, String>();
Map<String, Object> runProperties = context.getRunProperties();
List<Map<String, Object>> newRows = new ArrayList<>();
Map<String, List<Double>> negWellMap = new CaseInsensitiveHashMap<>();
Map<String, String> sampleKeyToNegCtlKey = new HashMap<>();

Map<String, List<Map<String, Object>>> map = new CaseInsensitiveHashMap<List<Map<String, Object>>>();
Map<String, List<Map<String, Object>>> map = new CaseInsensitiveHashMap<>();
for (Map<String, Object> row : rows)
{
//build a map of rows, grouped by id/date/peptide
Expand All @@ -123,7 +124,7 @@ protected List<Map<String, Object>> calculatePositivity(List<Map<String, Object>

List<Map<String, Object>> foundRows = map.get(key);
if (foundRows == null)
foundRows = new ArrayList<Map<String, Object>>();
foundRows = new ArrayList<>();

foundRows.add(row);
map.put(key, foundRows);
Expand Down Expand Up @@ -169,14 +170,14 @@ protected List<Map<String, Object>> calculatePositivity(List<Map<String, Object>
}
}

Integer minspots = runProperties.containsKey(MIN_SPOTS_FIELD) ? Integer.valueOf(runProperties.getInt(MIN_SPOTS_FIELD)) : null;
Integer minspots = runProperties.get(MIN_SPOTS_FIELD) != null ? Integer.valueOf(runProperties.get(MIN_SPOTS_FIELD).toString()) : null;
if (minspots == null)
{
minspots = 0;
runProperties.put(MIN_SPOTS_FIELD, minspots);
}

Double threshold = runProperties.containsKey(THRESHOLD_FIELD) ? runProperties.getDouble(THRESHOLD_FIELD) : null;
Double threshold = runProperties.get(THRESHOLD_FIELD) != null ? Double.parseDouble(runProperties.get(THRESHOLD_FIELD).toString()) : null;
if (threshold == null)
{
threshold = 0.05;
Expand Down Expand Up @@ -295,7 +296,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl

SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
Map<String, Double> negCtlCounts = new HashMap<String, Double>();
for (JSONObject row : rawResults.toJSONObjectArray())
for (JSONObject row : JsonUtil.toJSONObjectList(rawResults))
{
for (String prop : resultDefaults.keySet())
{
Expand Down
2 changes: 1 addition & 1 deletion flowassays/src/org/labkey/flowassays/FlowAssaysDataProvider.java
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Expand Up @@ -15,7 +15,7 @@
*/
package org.labkey.flowassays;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.data.ContainerManager;
import org.labkey.api.laboratory.AbstractDataProvider;
Expand Down
4 changes: 2 additions & 2 deletions flowassays/src/org/labkey/flowassays/assay/DefaultFlowImportMethod.java
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@@ -1,6 +1,6 @@
package org.labkey.flowassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpProtocol;
Expand Down Expand Up @@ -64,7 +64,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>

while (rowsIter.hasNext())
{
Map<String, Object> row = new CaseInsensitiveHashMap(rowsIter.next());
Map<String, Object> row = new CaseInsensitiveHashMap<>(rowsIter.next());
appendPromotedResultFields(row, context);

helper.normalizePopulationField(row, "population", context);
Expand Down
14 changes: 7 additions & 7 deletions flowassays/src/org/labkey/flowassays/assay/FlowImportHelper.java
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@@ -1,10 +1,10 @@
package org.labkey.flowassays.assay;

import org.json.old.JSONObject;
import org.apache.commons.lang3.StringUtils;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.TableInfo;
import org.labkey.api.data.TableSelector;
import org.labkey.api.gwt.client.util.StringUtils;
import org.labkey.api.laboratory.assay.ImportContext;
import org.labkey.flowassays.FlowAssaysSchema;

Expand All @@ -28,10 +28,10 @@ public FlowImportHelper()

public void normalizePopulationField(Map<String, Object> row, String populationField, ImportContext context)
{
if (!row.containsKey(populationField))
if (!row.containsKey(populationField) || row.get(populationField) == null)
return;

String population = StringUtils.trimToNull((String) row.get(populationField));
String population = row.get(populationField) == null ? null : StringUtils.trimToNull(row.get(populationField).toString());
if (population == null)
return;

Expand Down Expand Up @@ -79,7 +79,7 @@ public String guessPopulation(String population)

public Map<String, String> getGuessedValues(Map<String, String> allowable)
{
Map<String, String> guesses = new CaseInsensitiveHashMap();
Map<String, String> guesses = new CaseInsensitiveHashMap<>();
for (String key : allowable.keySet())
{
String guess = key.replaceAll(" ", "");
Expand All @@ -103,7 +103,7 @@ private Map<String, String> getResultValues()
TableInfo ti = FlowAssaysSchema.getInstance().getTable(FlowAssaysSchema.TABLE_POPULATIONS);
TableSelector ts = new TableSelector(ti);
Map<String, Object>[] rows = ts.getMapArray();
Map<String, String> ret = new CaseInsensitiveHashMap();
Map<String, String> ret = new CaseInsensitiveHashMap<>();
for (Map<String, Object> row : rows)
{
ret.put((String)row.get(NAME_FIELD), (String)row.get(NAME_FIELD));
Expand Down Expand Up @@ -159,6 +159,6 @@ public static JSONObject applyDefaultMetadata(JSONObject meta)

private static JSONObject getJsonObject(JSONObject parent, String key)
{
return parent.containsKey(key) ? parent.getJSONObject(key): new JSONObject();
return parent.has(key) ? parent.getJSONObject(key): new JSONObject();
}
}
2 changes: 1 addition & 1 deletion flowassays/src/org/labkey/flowassays/assay/FlowPivotingImportMethod.java
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package org.labkey.flowassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.data.Container;
import org.labkey.api.exp.api.ExpProtocol;
import org.labkey.api.laboratory.assay.AssayImportMethod;
Expand Down
2 changes: 1 addition & 1 deletion flowassays/src/org/labkey/flowassays/assay/ICSDataProvider.java
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package org.labkey.flowassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.laboratory.assay.AbstractAssayDataProvider;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.module.Module;
Expand Down
2 changes: 1 addition & 1 deletion flowassays/src/org/labkey/flowassays/assay/ImmunophenotypingDataProvider.java
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package org.labkey.flowassays.assay;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.laboratory.assay.AbstractAssayDataProvider;
import org.labkey.api.laboratory.assay.AssayImportMethod;
import org.labkey.api.module.Module;
Expand Down
2 changes: 1 addition & 1 deletion mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
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@@ -1,6 +1,6 @@
package org.labkey.mgap.columnTransforms;

import org.json.old.JSONObject;
import org.json.JSONObject;
import org.labkey.api.collections.CaseInsensitiveHashMap;
import org.labkey.api.data.ColumnInfo;
import org.labkey.api.data.DbSchema;
Expand Down
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