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Merged
labkey-kevink merged 3 commits into from
Jun 8, 2021
Merged

43246: Lineage query NPE while processing an UploadedFile #20

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763958f
Issue 43246: Lineage query NPE while processing an UploadedFile
labkey-kevink Jun 7, 2021
ecacde2
support multiple seeds and additional properties of the lineage node
labkey-kevink Jun 7, 2021
cb368d1
change version back to 1.4.0-SNAPSHOT
labkey-kevink Jun 8, 2021
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5 changes: 5 additions & 0 deletions labkey-client-api/CHANGELOG.md
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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,10 @@
# The LabKey Remote API Library for Java - Change Log

## version 1.4.0-SNAPSHOT
*Released*: TBD
* Issue 43246: Lineage query NPE while processing an UploadedFile
* Additional lineage options and support additional properties in response

## version 1.3.2
*Released* : 05 November 2020
* Fix `selectedMetadataInputFormat` serialization
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109 changes: 65 additions & 44 deletions labkey-client-api/src/org/labkey/remoteapi/experiment/LineageCommand.java
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Original file line numberDiff line numberDiff line change
Expand Up@@ -19,71 +19,70 @@
import org.labkey.remoteapi.Command;
import org.labkey.remoteapi.Connection;

import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;


public class LineageCommand extends Command<LineageResponse>
{
// One of rowId or LSID required
private final Integer _rowId;
private final String _lsid;
// One or more LSIDs are required
private final List<String> _lsids;

// Optional parameters below
private final Boolean _parents;
private final Boolean _children;
private final Integer _depth;
private final String _expType;
private final String _cpasType;
private final Boolean _includeProperties;
private final Boolean _includeInputsAndOutputs;
private final Boolean _includeRunSteps;

private LineageCommand(/*@Nullable*/ Integer rowId, /*@Nullable*/ String lsid, Boolean parents, Boolean children, Integer depth, String cpasType, String expType)
private LineageCommand(
List<String> lsids, Boolean parents, Boolean children, Integer depth, String cpasType, String expType,
Boolean includeProperites, Boolean includeInputsAndOutputs, Boolean includeRunSteps)
{
super("experiment", "lineage");
if (rowId == null && lsid == null)
throw new IllegalArgumentException("One of rowId or lsid required");
if (lsids == null || lsids.isEmpty())
throw new IllegalArgumentException("One or more starting LSIDs required");

if (lsid != null && rowId != null)
throw new IllegalArgumentException("Only one of rowId or lsid allowed");

_rowId = rowId;
_lsid = lsid;
_lsids = lsids;
_depth = depth;
_parents = parents;
_children = children;
_expType = expType;
_cpasType = cpasType;
_includeProperties = includeProperites;
_includeInputsAndOutputs = includeInputsAndOutputs;
_includeRunSteps = includeRunSteps;
}

public static final class Builder
{
private final Integer _rowId;
private final String _lsid;
private final List<String> _lsids;

private Integer _depth;
private Boolean _parents;
private Boolean _children;
private String _expType;
private String _cpasType;
private Boolean _includeProperties;
private Boolean _includeInputsAndOutputs;
private Boolean _includeRunSteps;

public Builder(String lsid)
{
this(lsid, null);
this(Arrays.asList(lsid));
}

public Builder(Integer rowId)
public Builder(List<String> lsids)
{
this(null, rowId);
}

public Builder(String lsid, Integer rowId)
{
if (lsid == null && rowId == null)
throw new IllegalArgumentException("One of rowId or lsid required");

if (lsid != null && rowId != null)
throw new IllegalArgumentException("Only one of rowId or lsid allowed");
if (lsids == null || lsids.isEmpty())
throw new IllegalArgumentException("One or more starting LSIDs required");

_rowId = rowId;
_lsid = lsid;
_lsids = lsids;
}

public Builder setDepth(Integer depth)
Expand DownExpand Up@@ -116,9 +115,29 @@ public Builder setCpasType(String cpasType)
return this;
}

public Builder setIncludeProperties(Boolean includeProperties)
{
_includeProperties = includeProperties;
return this;
}

public Builder setIncludeInputsAndOutputs(Boolean includeInputsAndOutputs)
{
_includeInputsAndOutputs = includeInputsAndOutputs;
return this;
}

public Builder setIncludeRunSteps(Boolean includeRunSteps)
{
_includeRunSteps = includeRunSteps;
return this;
}

public LineageCommand build()
{
return new LineageCommand(_rowId, _lsid, _parents, _children, _depth, _cpasType, _expType);
return new LineageCommand(
_lsids, _parents, _children, _depth, _cpasType, _expType,
_includeProperties, _includeInputsAndOutputs, _includeRunSteps);
}
}

Expand All@@ -130,10 +149,7 @@ protected LineageResponse createResponse(String text, int statusCode, String con
public Map<String, Object> getParameters()
{
Map<String,Object> params = new HashMap<>();
if (null != _rowId)
params.put("rowId", _rowId);
if (null != _lsid)
params.put("lsid", _lsid);
params.put("lsids", _lsids);
if (null != _parents)
params.put("parents", _parents);
if (null != _children)
Expand All@@ -144,6 +160,12 @@ public Map<String, Object> getParameters()
params.put("expType", _expType);
if (null != _cpasType)
params.put("cpasType", _cpasType);
if (null != _includeProperties)
params.put("includeProperties", _includeProperties);
if (null != _includeInputsAndOutputs)
params.put("includeInputsAndOutputs", _includeInputsAndOutputs);
if (null != _includeRunSteps)
params.put("includeRunSteps", _includeRunSteps);

return params;
}
Expand All@@ -152,28 +174,27 @@ public Map<String, Object> getParameters()
@Override
public LineageCommand copy()
{
return new LineageCommand(_rowId, _lsid, _parents, _children, _depth, _cpasType, _expType);
return new LineageCommand(_lsids, _parents, _children, _depth, _cpasType, _expType,
_includeProperties, _includeInputsAndOutputs, _includeRunSteps);
}

public static void main(String[] args) throws Exception
{
String url = "http://localhost:8080/labkey";
String folderPath = "/bl";
String folderPath = "/AssayImportProvenance Test";
String user = "kevink@labkey.com";
String password = "xxxxxx";

String lsid = null;
Integer rowId = 7523;
Boolean parents = false;
Boolean children = null;
String lsid = "urn:lsid:labkey.com:GeneralAssayRun.Folder-4780:40166791-3d3f-1039-a854-9b7575483a25";

Builder builder = new Builder(lsid, rowId);
if (parents != null)
builder.setParents(parents);
if (children != null)
builder.setChildren(children);
LineageCommand cmd = new Builder(lsid)
.setParents(false)
.setChildren(true)
.setIncludeProperties(true)
.setIncludeInputsAndOutputs(true)
.setIncludeRunSteps(true)
.build();

LineageCommand cmd = builder.build();
Connection conn = new Connection(url, user, password);
LineageResponse resp = cmd.execute(conn, folderPath);
System.out.println(resp.dump());
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