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Merged
labkey-jeckels merged 5 commits into from
Nov 5, 2025
Merged

Adopt FileLike for more pipeline APIs #1515

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6793888
More FileLike
labkey-jeckels Oct 21, 2025
99a3059
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 22, 2025
257ec21
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 27, 2025
7d3bd19
Minor cleanup
labkey-jeckels Oct 29, 2025
d1e820b
Merge branch 'develop' into fb_pipelineFileLike
labkey-jeckels Oct 31, 2025
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11 changes: 6 additions & 5 deletions GeneticsCore/src/org/labkey/GeneticsCore/etl/ImportGeneticsCalculationsStep.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
package org.labkey.GeneticsCore.etl;

import org.apache.commons.lang3.StringUtils;
import org.apache.xmlbeans.XmlException;
import org.jetbrains.annotations.NotNull;
import org.labkey.GeneticsCore.GeneticsCoreModule;
import org.labkey.api.data.Container;
Expand All @@ -17,6 +16,8 @@
import org.labkey.api.security.permissions.UpdatePermission;
import org.labkey.api.view.UnauthorizedException;
import org.labkey.api.writer.ContainerUser;
import org.labkey.vfs.FileLike;
import org.labkey.vfs.FileSystemLike;

import java.io.File;
import java.util.Collections;
Expand Down Expand Up @@ -64,19 +65,19 @@ public RecordedActionSet run(@NotNull PipelineJob job) throws PipelineJobExcepti
throw new PipelineJobException("Must provide the filepath to import data using the KinshipDataPath module property");
}

File pipeDir = new File(pipeDirPath);
FileLike pipeDir = FileSystemLike.wrapFile(new File(pipeDirPath));
if (!pipeDir.exists())
{
throw new PipelineJobException("Path does not exist: " + pipeDir.getPath());
}

File kinship = new File(pipeDir, "kinship.txt");
FileLike kinship = pipeDir.resolveChild("kinship.txt");
if (!kinship.exists())
{
throw new PipelineJobException("File does not exist: " + kinship.getPath());
}

File inbreeding = new File(pipeDir, "inbreeding.txt");
FileLike inbreeding = pipeDir.resolveChild("inbreeding.txt");
if (!inbreeding.exists())
{
throw new PipelineJobException("File does not exist: " + inbreeding.getPath());
Expand All @@ -94,7 +95,7 @@ public List<String> getRequiredSettings()
}

@Override
public void setSettings(Map<String, String> settings) throws XmlException
public void setSettings(Map<String, String> settings)
{

}
Expand Down
100 changes: 19 additions & 81 deletions onprc_billing/src/org/labkey/onprc_billing/pipeline/BillingTask.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.onprc_billing.pipeline;

import au.com.bytecode.opencsv.CSVWriter;
import org.apache.commons.lang3.time.DateUtils;
import org.jetbrains.annotations.NotNull;
import org.labkey.api.collections.CaseInsensitiveHashMap;
Expand All @@ -25,10 +24,8 @@
import org.labkey.api.data.DbSchema;
import org.labkey.api.data.DbScope;
import org.labkey.api.data.Results;
import org.labkey.api.data.ResultsImpl;
import org.labkey.api.data.RuntimeSQLException;
import org.labkey.api.data.SQLFragment;
import org.labkey.api.data.Selector;
import org.labkey.api.data.SimpleFilter;
import org.labkey.api.data.SqlSelector;
import org.labkey.api.data.Table;
Expand All @@ -49,10 +46,6 @@
import org.labkey.api.util.GUID;
import org.labkey.onprc_billing.ONPRC_BillingSchema;

import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
Expand Down Expand Up @@ -105,11 +98,9 @@ public List<String> getProtocolActionNames()
}

@Override
public PipelineJob.Task createTask(PipelineJob job)
public BillingTask createTask(PipelineJob job)
{
BillingTask task = new BillingTask(this, job);

return task;
return new BillingTask(this, job);
}

@Override
Expand Down Expand Up @@ -198,43 +189,6 @@ private BillingPipelineJobSupport getSupport()
return (BillingPipelineJobSupport)getJob();
}

private void writeToTsv(String fileName, List<Map<String, Object>> rows, String[] headers, String[] colNames) throws PipelineJobException
{
File csvFile = new File(getSupport().getAnalysisDir(), fileName + ".txt");
if (csvFile.exists())
throw new PipelineJobException("There is already a file with path: " + csvFile.getPath());

try
{
csvFile.createNewFile();

try (CSVWriter csv = new CSVWriter(new FileWriter(csvFile), '\t'))
{
csv.writeNext(headers);

if (!rows.isEmpty())
{
for (Map<String, Object> row : rows)
{
String[] toWrite = new String[colNames.length];
int i = 0;
for (String colName: colNames)
{
toWrite[i] = getString(row.get(colName));
i++;
}

csv.writeNext(toWrite);
}
}
}
}
catch (IOException e)
{
throw new PipelineJobException(e);
}
}

private String _invoiceId = null;

private String getOrCreateInvoiceRunRecord() throws PipelineJobException
Expand Down Expand Up @@ -312,7 +266,7 @@ private String getOrCreateInvoiceRunRecord() throws PipelineJobException
"quantity", "unitCost", "totalcost",
"rateId", "exemptionId", "creditaccountid", "comment", "transactionType", "sourceRecord", "chargeCategory"};

private void writeToInvoicedItems(List<Map<String, Object>> rows, String category, String[] colNames, String queryName, boolean allowNullProject) throws PipelineJobException
private void writeToInvoicedItems(List<Map<String, Object>> rows, String[] colNames, String queryName, boolean allowNullProject) throws PipelineJobException
{
assert colNames.length >= invoicedItemsCols.length;

Expand All @@ -323,7 +277,7 @@ private void writeToInvoicedItems(List<Map<String, Object>> rows, String categor
TableInfo invoicedItems = ONPRC_BillingSchema.getInstance().getSchema().getTable(ONPRC_BillingSchema.TABLE_INVOICED_ITEMS);
for (Map<String, Object> row : rows)
{
CaseInsensitiveHashMap toInsert = new CaseInsensitiveHashMap();
CaseInsensitiveHashMap<Object> toInsert = new CaseInsensitiveHashMap<>();
toInsert.put("container", getJob().getContainer().getId());
toInsert.put("createdby", getJob().getUser().getUserId());
toInsert.put("created", new Date());
Expand Down Expand Up @@ -373,24 +327,6 @@ private void writeToInvoicedItems(List<Map<String, Object>> rows, String categor
}
}

private String getString(Object val)
{
if (val == null)
{
return "";
}
else if (val instanceof Date)
{
return _dateFormat.format(val);
}
else if (val instanceof Number)
{
return val.toString();
}

return val.toString();
}

private void leaseFeeProcessing(Container ehrContainer) throws PipelineJobException
{
getJob().getLogger().info("Caching Lease Fees");
Expand Down Expand Up @@ -434,7 +370,7 @@ private void leaseFeeProcessing(Container ehrContainer) throws PipelineJobExcept

getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Lease Fees", colNames, queryName, false);
writeToInvoicedItems(rows, colNames, queryName, false);
getJob().getLogger().info("Finished Caching Lease Fees");
}

Expand Down Expand Up @@ -467,20 +403,22 @@ private List<Map<String, Object>> getRowList(Container c, String schemaName, Str
ts.setNamedParameters(params);

final List<Map<String, Object>> rows = new ArrayList<>();
ts.forEach(new Selector.ForEachBlock<>()
try (Results results = ts.getResults())
{
@Override
public void exec(ResultSet object) throws SQLException
while (results.next())
{
Results rs = new ResultsImpl(object, colKeys);
Map<String, Object> ret = new HashMap<>();
for (FieldKey fk : colKeys.keySet())
for (Map.Entry<FieldKey, ColumnInfo> entry: colKeys.entrySet())
{
ret.put(fk.toString(), rs.getObject(fk));
ret.put(entry.getKey().toString(), entry.getValue().getValue(results));
}
rows.add(ret);
}
});
}
catch (SQLException e)
{
throw new RuntimeSQLException(e);
}

return rows;
}
Expand Down Expand Up @@ -531,7 +469,7 @@ private void perDiemProcessing(Container ehrContainer) throws PipelineJobExcepti
List<Map<String, Object>> rows = getRowList(ehrContainer, "onprc_billing", queryName, colNames, params);
getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Per Diems", colNames, queryName, false);
writeToInvoicedItems(rows, colNames, queryName, false);
getJob().getLogger().info("Finished Caching Per Diem Fees");
}

Expand Down Expand Up @@ -583,7 +521,7 @@ private void slaPerDiemProcessing() throws PipelineJobException
List<Map<String, Object>> rows = getRowList(slaContainer, "onprc_billing", queryName, colNames, params);
getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Small Lab Animal Per Diems", colNames, queryName, false);
writeToInvoicedItems(rows, colNames, queryName, false);
getJob().getLogger().info("Finished Caching Per Diem Fees");
}

Expand Down Expand Up @@ -629,7 +567,7 @@ private void proceduresProcessing(Container ehrContainer) throws PipelineJobExce
List<Map<String, Object>> rows = getRowList(ehrContainer, "onprc_billing", queryName, colNames, params);
getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Procedure Fees", colNames, queryName, false);
writeToInvoicedItems(rows, colNames, queryName, false);
getJob().getLogger().info("Finished Caching Procedure Fees");
}

Expand Down Expand Up @@ -675,7 +613,7 @@ private void labworkProcessing(Container ehrContainer) throws PipelineJobExcepti
List<Map<String, Object>> rows = getRowList(ehrContainer, "onprc_billing", queryName, colNames, params);
getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Labwork Fees", colNames, queryName, false);
writeToInvoicedItems(rows, colNames, queryName, false);
getJob().getLogger().info("Finished Caching Labwork Fees");
}

Expand Down Expand Up @@ -718,7 +656,7 @@ private void miscChargesProcessing(Container ehrContainer) throws PipelineJobExc
List<Map<String, Object>> rows = getRowList(ehrContainer, "onprc_billing", MISC_CHARGES_QUERY, colNames, params);
getJob().getLogger().info(rows.size() + " rows found");

writeToInvoicedItems(rows, "Other Charges", colNames, MISC_CHARGES_QUERY, true);
writeToInvoicedItems(rows, colNames, MISC_CHARGES_QUERY, true);

getJob().getLogger().info("Finished Caching Other Charges");
}
Expand Down