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The client-side library for Java developers is a separate JAR from the LabKey Server code base. It can be used by any Java program, including another Java web application.
/*
* Copyright (c) 2017-2018 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.labkey.remoteapi.experiment;
import org.apache.commons.logging.LogFactory;
import org.labkey.remoteapi.ResponseObject;
import org.labkey.remoteapi.query.DateParser;
import org.labkey.remoteapi.query.Filter;
import org.labkey.remoteapi.query.SelectRowsResponse;
import java.text.ParseException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
public class LineageNode extends ResponseObject
{
private final String _lsid;
private final Integer _id;
private final String _name;
private final String _container;
private final String _url;
private final String _type;
private final String _cpasType;
private final String _expType;
private final Date _created;
private final String _createdBy;
private final Date _modified;
private final String _modifiedBy;
private final String _comment;
// query reference
private final String _schemaName;
private final String _queryName;
private final List _pkFilters;
private final Map _properties;
private List _parents;
private List _children;
public LineageNode(String lsid, Map map)
{
super(map);
_lsid = lsid;
_id = ((Number)map.getOrDefault("id", -1)).intValue();
_name = (String)map.get("name");
_container = (String)map.get("container");
_type = (String)map.get("type");
_cpasType = (String)map.get("cpasType");
_expType = (String)map.get("expType");
_url = (String)map.get("url");
Date created = null;
Date modified = null;
DateParser dateParser = new DateParser();
try
{
String createdStr = (String) map.get("created");
if (createdStr != null && createdStr.length() > 0)
created = dateParser.parse(createdStr);
String modifiedStr = (String) map.get("modified");
if (modifiedStr != null && modifiedStr.length() > 0)
modified = dateParser.parse(modifiedStr);
}
catch (ParseException e)
{
//just log it--if it doesn't parse, we can't fix it up
LogFactory.getLog(SelectRowsResponse.class).warn("Failed to parse date: " + e.getMessage(), e);
}
_created = created;
_modified = modified;
_createdBy = (String) map.get("createdBy");
_modifiedBy = (String)map.get("modifiedBy");
_comment = (String)map.get("comment");
// query row ref
_schemaName = (String)map.get("schemaName");
_queryName = (String)map.get("queryName");
_pkFilters = createPkFilters((List>)map.get("pkFilters"));
_properties = (Map)map.getOrDefault("properties", Collections.emptyMap());
}
void fixup(Map nodes)
{
_children = fixupEdges(nodes, (List>) getAllProperties().get("children"));
_parents = fixupEdges(nodes, (List>) getAllProperties().get("parents"));
}
List createPkFilters(List> filters)
{
if (filters == null)
return Collections.emptyList();
List result = new ArrayList<>(filters.size());
for (Map filter : filters)
{
String fieldKey = (String)filter.get("fieldKey");
Object value = filter.get("value");
result.add(new Filter(fieldKey, value, Filter.Operator.EQUAL));
}
return Collections.unmodifiableList(result);
}
List fixupEdges(Map nodes, List> edges)
{
List fixedEdges = new ArrayList<>();
for (Map edge : edges)
{
String role = (String)edge.get("role");
String lsid = (String)edge.get("lsid");
fixedEdges.add(new Edge(role, nodes.get(lsid)));
}
return fixedEdges;
}
public String getLsid()
{
return _lsid;
}
public Integer getId()
{
return _id;
}
public String getName()
{
return _name;
}
public String getUrl()
{
return _url;
}
/**
* The namespace portion of the LSID.
* Examples include:
*
* - Sample
* - The type for a Sample.
*
*
- GeneralAssayRun
* - The type for a Standard (formerly called General) assay run
*
* - AssayRunTSVData
* - The type for the Data output file of an assay run
*
* - GeneralAssayResultRow
* - The type for an individual assay result row of a Standard assay. (requires provenance module)
*
*/
public String getType()
{
return _type;
}
/**
* The CPAS type of the object as an LSID.
* For a Sample node, the CPAS type is the LSID of the Sample Type.
* For a Data in a DataClass, the CPAS type is the LSID of the Data Class.
* For a run, the CPAS type is the LSID of the run's protocol.
*/
public String getCpasType()
{
return _cpasType;
}
/**
* The Experiment type of the object.
*
* - Data
* - A file or a data in a DataClass
*
* - Material
* - A sample in a Sample Type
*
* - ExperimentRun
* - An experiment run, e.g. a derivation or an assay import
*
*/
public String getExpType()
{
return _expType;
}
/**
* Container entity ID of the object.
*/
public String getContainer()
{
return _container;
}
public Date getCreated()
{
return _created;
}
public String getCreatedBy()
{
return _createdBy;
}
public Date getModified()
{
return _modified;
}
public String getModifiedBy()
{
return _modifiedBy;
}
public String getComment()
{
return _comment;
}
public String getSchemaName()
{
return _schemaName;
}
public String getQueryName()
{
return _queryName;
}
public List getPkFilters()
{
return _pkFilters;
}
public Map getProperties()
{
return _properties;
}
public List getParents()
{
return _parents;
}
public List getChildren()
{
return _children;
}
void dump(int indent, StringBuilder sb, Set seen)
{
indent(indent, sb).append("> ").append(getName()).append(" (").append(getId()).append(")");
if (seen.contains(getLsid()))
{
sb.append(" **\n");
return;
}
sb.append("\n");
seen.add(getLsid());
indent(indent+1, sb).append("lsid: ").append(getLsid()).append("\n");
indent(indent+1, sb).append("type: ").append(getType()).append("\n");
indent(indent+1, sb).append("exp: ").append(getExpType()).append("\n");
indent(indent+1, sb).append("cpas: ").append(getCpasType()).append("\n");
indent(indent+1, sb).append("url: ").append(getUrl()).append("\n");
if (getComment() != null)
indent(indent+1, sb).append("comment: ").append(getComment()).append("\n");
if (getSchemaName() != null)
indent(indent+1, sb).append("schemaName: ").append(getSchemaName()).append("\n");
if (getQueryName() != null)
indent(indent+1, sb).append("queryName: ").append(getQueryName()).append("\n");
if (getPkFilters() != null && getPkFilters().size() > 0)
indent(indent + 1, sb).append("pkFilters: ").append(getPkFilters().stream().map(f -> f.getColumnName() + "=" + f.getValue()).collect(Collectors.joining(", ", "[", "]"))).append("\n");
if (!getProperties().isEmpty())
indent(indent+1, sb).append("properties: ").append(getProperties()).append("\n");
indent(indent+1, sb).append("parents:");
if (_parents.isEmpty())
sb.append(" (none)");
sb.append("\n");
for (Edge edge : _parents)
{
indent(indent+2, sb).append("role: ").append(edge.getRole()).append("\n");
edge.getNode().dump(indent+3, sb, seen);
}
indent(indent+1, sb).append("children:");
if (_children.isEmpty())
sb.append(" (none)");
sb.append("\n");
for (Edge edge : _children)
{
indent(indent+2, sb).append("role: ").append(edge.getRole()).append("\n");
edge.getNode().dump(indent+3, sb, seen);
}
}
StringBuilder indent(int indent, StringBuilder sb)
{
for (int i = 0; i < indent; i++)
sb.append(" ");
return sb;
}
public static class Edge
{
private final String role;
private final LineageNode node;
Edge(String role, LineageNode node)
{
this.role = role;
this.node = node;
}
public String getRole()
{
return role;
}
public LineageNode getNode()
{
return node;
}
}
}