|
1
|
/**
|
|
2
|
* Copyright (C) 2015 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
6
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
7
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
8
|
*/
|
|
9
|
package eu.etaxonomy.cdm.io.specimen.abcd206.in.molecular;
|
|
10
|
|
|
11
|
import java.util.Date;
|
|
12
|
import java.util.UUID;
|
|
13
|
|
|
14
|
import org.w3c.dom.Element;
|
|
15
|
import org.w3c.dom.Node;
|
|
16
|
import org.w3c.dom.NodeList;
|
|
17
|
|
|
18
|
import eu.etaxonomy.cdm.api.application.ICdmRepository;
|
|
19
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportState;
|
|
20
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdParseUtility;
|
|
21
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.AbcdPersonParser;
|
|
22
|
import eu.etaxonomy.cdm.io.specimen.abcd206.in.SpecimenImportReport;
|
|
23
|
import eu.etaxonomy.cdm.model.agent.AgentBase;
|
|
24
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
|
25
|
import eu.etaxonomy.cdm.model.common.TimePeriod;
|
|
26
|
import eu.etaxonomy.cdm.model.molecular.DnaSample;
|
|
27
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
|
|
28
|
import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
|
|
29
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
|
30
|
import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
|
|
31
|
|
|
32
|
/**
|
|
33
|
* @author pplitzner
|
|
34
|
\* @since 15.06.2015
|
|
35
|
*
|
|
36
|
*/
|
|
37
|
public class AbcdDnaParser {
|
|
38
|
|
|
39
|
private final String prefix;
|
|
40
|
|
|
41
|
private final SpecimenImportReport report;
|
|
42
|
|
|
43
|
private final ICdmRepository cdmAppController;
|
|
44
|
|
|
45
|
public AbcdDnaParser(String prefix, SpecimenImportReport report, ICdmRepository cdmAppController) {
|
|
46
|
this.prefix = prefix;
|
|
47
|
this.report = report;
|
|
48
|
this.cdmAppController = cdmAppController;
|
|
49
|
}
|
|
50
|
|
|
51
|
public DnaSample parse(Element item, Abcd206ImportState state) {
|
|
52
|
FieldUnit fieldUnit = state.getFieldUnit(state.getDataHolder().getFieldNumber());
|
|
53
|
if (fieldUnit == null){
|
|
54
|
fieldUnit = FieldUnit.NewInstance();
|
|
55
|
}
|
|
56
|
DnaSample dnaSample = DnaSample.NewInstance();
|
|
57
|
DerivationEvent.NewSimpleInstance(fieldUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
|
|
58
|
|
|
59
|
//specimen unit
|
|
60
|
NodeList specimenUnitList = item.getElementsByTagName(prefix+"SpecimenUnit");
|
|
61
|
if(specimenUnitList.item(0)!=null && specimenUnitList.item(0) instanceof Element){
|
|
62
|
parseSpecimenUnit((Element)specimenUnitList.item(0), dnaSample);
|
|
63
|
}
|
|
64
|
NodeList unitExtensions = item.getElementsByTagName(prefix+"UnitExtension");
|
|
65
|
for(int i=0;i<unitExtensions.getLength();i++){
|
|
66
|
if(unitExtensions.item(i) instanceof Element){
|
|
67
|
Element unitExtension = (Element) unitExtensions.item(i);
|
|
68
|
NodeList ggbn = unitExtension.getElementsByTagName("ggbn:GGBN");
|
|
69
|
if(ggbn.getLength()>0){
|
|
70
|
AbcdGgbnParser ggbnParser = new AbcdGgbnParser(report, cdmAppController);
|
|
71
|
ggbnParser.parse(ggbn, dnaSample, state);
|
|
72
|
}
|
|
73
|
}
|
|
74
|
}
|
|
75
|
return dnaSample;
|
|
76
|
}
|
|
77
|
|
|
78
|
private void parseSpecimenUnit(Element item, DnaSample dnaSample) {
|
|
79
|
NodeList preparationsList = item.getElementsByTagName(prefix+"Preparations");
|
|
80
|
if(preparationsList.item(0)!=null && preparationsList.item(0) instanceof Element){
|
|
81
|
parsePreparations((Element) preparationsList.item(0), dnaSample);
|
|
82
|
}
|
|
83
|
NodeList preservationsList = item.getElementsByTagName(prefix+"Preservations");
|
|
84
|
if(preservationsList.item(0)!=null && preservationsList.item(0) instanceof Element){
|
|
85
|
parsePreservations((Element) preservationsList.item(0), dnaSample);
|
|
86
|
}
|
|
87
|
}
|
|
88
|
|
|
89
|
private void parsePreparations(Element item, DnaSample dnaSample) {
|
|
90
|
NodeList preparationList = item.getElementsByTagName(prefix+"preparation");
|
|
91
|
for(int i=0;i<preparationList.getLength();i++){
|
|
92
|
Node node = preparationList.item(i);
|
|
93
|
if(node instanceof Element){
|
|
94
|
DerivationEvent derivedFrom = dnaSample.getDerivedFrom();
|
|
95
|
|
|
96
|
String preparationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationType"));
|
|
97
|
//preparation materials
|
|
98
|
String preparationMaterials = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preparationMaterials"));
|
|
99
|
derivedFrom.setDescription(preparationMaterials);
|
|
100
|
//preparation actor
|
|
101
|
NodeList preparationAgentList = ((Element) node).getElementsByTagName(prefix+"preparationAgent");
|
|
102
|
if(preparationAgentList.item(0)!=null && preparationAgentList.item(0) instanceof Element){
|
|
103
|
AgentBase<?> preparationAgent = parsePreparationAgent((Element)preparationAgentList.item(0));
|
|
104
|
derivedFrom.setActor(preparationAgent);
|
|
105
|
}
|
|
106
|
//preparation date
|
|
107
|
Date preparationDate = AbcdParseUtility.parseFirstDate(((Element) node).getElementsByTagName(prefix+"preparationDate"));
|
|
108
|
derivedFrom.setTimeperiod(TimePeriod.NewInstance(preparationDate, null));
|
|
109
|
//sample designation
|
|
110
|
NodeList sampleDesignationsList = ((Element) node).getElementsByTagName(prefix+"sampleDesignations");
|
|
111
|
if(sampleDesignationsList.item(0)!=null && sampleDesignationsList.item(0) instanceof Element){
|
|
112
|
parseSampleDesignations((Element)sampleDesignationsList.item(0), dnaSample);
|
|
113
|
}
|
|
114
|
}
|
|
115
|
}
|
|
116
|
}
|
|
117
|
|
|
118
|
/**
|
|
119
|
* @param item
|
|
120
|
* @param dnaSample
|
|
121
|
*/
|
|
122
|
private void parseSampleDesignations(Element item, DnaSample dnaSample) {
|
|
123
|
NodeList sampleDesignationList = item.getElementsByTagName(prefix+"sampleDesignation");
|
|
124
|
for(int i=0;i<sampleDesignationList.getLength();i++){
|
|
125
|
dnaSample.addIdentifier(sampleDesignationList.item(i).getTextContent(), (DefinedTerm)cdmAppController.getTermService().find(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc")));
|
|
126
|
}
|
|
127
|
|
|
128
|
}
|
|
129
|
|
|
130
|
private AgentBase<?> parsePreparationAgent(Element item) {
|
|
131
|
AgentBase<?> agentBase = null;
|
|
132
|
NodeList personList = item.getElementsByTagName(prefix+"Person");
|
|
133
|
if(personList.item(0)!=null && personList.item(0) instanceof Element){
|
|
134
|
agentBase = new AbcdPersonParser(prefix,report, cdmAppController).parse((Element)personList.item(0));
|
|
135
|
}
|
|
136
|
return agentBase;
|
|
137
|
}
|
|
138
|
|
|
139
|
private void parsePreservations(Element item, DnaSample dnaSample) {
|
|
140
|
NodeList preservationList = item.getElementsByTagName(prefix+"preservation");
|
|
141
|
for(int i=0;i<preservationList.getLength();i++){
|
|
142
|
Node node = preservationList.item(i);
|
|
143
|
if(node instanceof Element){
|
|
144
|
PreservationMethod preservation = PreservationMethod.NewInstance();
|
|
145
|
dnaSample.setPreservation(preservation);
|
|
146
|
|
|
147
|
String preservationType = AbcdParseUtility.parseFirstTextContent(((Element) node).getElementsByTagName(prefix+"preservationType"));
|
|
148
|
|
|
149
|
Double preservationTemperature = AbcdParseUtility.parseFirstDouble(((Element) node).getElementsByTagName(prefix+"preservationTemperature"), report);
|
|
150
|
preservation.setTemperature(preservationTemperature);
|
|
151
|
}
|
|
152
|
}
|
|
153
|
}
|
|
154
|
|
|
155
|
|
|
156
|
}
|