1
|
package eu.dnetlib.data.mapreduce.hbase.propagation.country.institutionalrepositories;
|
2
|
|
3
|
import com.google.gson.Gson;
|
4
|
import com.googlecode.protobuf.format.JsonFormat;
|
5
|
import com.sun.org.apache.commons.logging.Log;
|
6
|
import com.sun.org.apache.commons.logging.LogFactory;
|
7
|
import eu.dnetlib.data.mapreduce.hbase.propagation.Value;
|
8
|
import eu.dnetlib.data.proto.*;
|
9
|
import org.apache.commons.lang3.StringUtils;
|
10
|
import org.apache.hadoop.hbase.client.Put;
|
11
|
import org.apache.hadoop.hbase.io.ImmutableBytesWritable;
|
12
|
import org.apache.hadoop.hbase.util.Bytes;
|
13
|
import org.apache.hadoop.io.Text;
|
14
|
import org.apache.hadoop.mapreduce.Reducer;
|
15
|
|
16
|
import java.io.IOException;
|
17
|
import java.util.Iterator;
|
18
|
|
19
|
import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.COUNTER_PROPAGATION;
|
20
|
import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.ONE;
|
21
|
import static eu.dnetlib.data.mapreduce.hbase.propagation.PropagationConstants.ZERO;
|
22
|
|
23
|
public class PropagationCountryFromDsOrgResultFileReducer extends Reducer<InstOrgKey, ImmutableBytesWritable,Text,Text> {
|
24
|
|
25
|
private static final Log log = LogFactory.getLog(PropagationCountryFromDsOrgResultFileReducer.class); // NOPMD by marko on 11/24/08 5:02 PM
|
26
|
|
27
|
private Text keyOut;
|
28
|
|
29
|
private Text outValue;
|
30
|
|
31
|
final static String DNETCOUNTRYSCHEMA = "dnet:countries";
|
32
|
private final static String DATA_INFO_TYPE = "propagation";
|
33
|
private final static String SCHEMA_NAME = "dnet:provenanceActions";
|
34
|
private final static String CLASS_ID = "propagation::country::instrepos";
|
35
|
private final static String SCHEMA_ID = "dnet:provenanceActions";
|
36
|
|
37
|
|
38
|
@Override
|
39
|
protected void setup(final Context context) throws IOException, InterruptedException {
|
40
|
super.setup(context);
|
41
|
keyOut = new Text("");
|
42
|
outValue = new Text();
|
43
|
|
44
|
}
|
45
|
|
46
|
private void emit(final Context context, final String key, final String data) {
|
47
|
keyOut.set(key);
|
48
|
outValue.set(data.getBytes());
|
49
|
try {
|
50
|
context.write(keyOut, outValue);
|
51
|
} catch (Exception e) {
|
52
|
e.printStackTrace();
|
53
|
throw new RuntimeException(e);
|
54
|
}
|
55
|
}
|
56
|
|
57
|
@Override
|
58
|
protected void reduce(InstOrgKey dsId, Iterable<ImmutableBytesWritable> values, Context context) {
|
59
|
|
60
|
final Iterator<ImmutableBytesWritable> it = values.iterator();
|
61
|
if(!it.hasNext()){
|
62
|
context.getCounter(COUNTER_PROPAGATION,"empty information for key").increment(1);
|
63
|
return;
|
64
|
}
|
65
|
Gson gson = new Gson();
|
66
|
Value v = gson.fromJson(Bytes.toString(it.next().get()),Value.class);
|
67
|
final String first = Bytes.toString(v.getValue().get());
|
68
|
final String trust = v.getTrust();
|
69
|
if (!(first.equals(ZERO) || first.equals(ONE))) {
|
70
|
if (dsId.getKeyType().get() == TypeProtos.Type.organization.getNumber())
|
71
|
context.getCounter(COUNTER_PROPAGATION,"First Element in reducer is not type of datasource, but the organization exists").increment(1);
|
72
|
else {
|
73
|
// context.getCounter(COUNTER_PROPAGATION,String.format("WARNINGS: First element value is %s " , first));
|
74
|
while (it.hasNext()) {
|
75
|
|
76
|
byte[] targetRowKey = gson.fromJson(Bytes.toString(it.next().get()), Value.class).getValue().get();
|
77
|
String resultId = Bytes.toString(targetRowKey);
|
78
|
if (!resultId.startsWith("50|"))
|
79
|
context.getCounter(COUNTER_PROPAGATION,"ERROR ORDERING CHECK").increment(1);
|
80
|
}
|
81
|
}
|
82
|
}
|
83
|
|
84
|
|
85
|
|
86
|
//ensure we are dealing with an institutional repository
|
87
|
if (first.equals(ONE)) {
|
88
|
context.getCounter(COUNTER_PROPAGATION,"institutional datasource").increment(1);
|
89
|
if(!it.hasNext()){
|
90
|
context.getCounter(COUNTER_PROPAGATION,"no information apart of type of datasource").increment(1);
|
91
|
return;
|
92
|
}
|
93
|
|
94
|
final String country = Bytes.toString(gson.fromJson(Bytes.toString(it.next().get()),Value.class).getValue().get()); // need to update the information for the country to each element in the iterator
|
95
|
if(country.trim().length() != 2){
|
96
|
context.getCounter(COUNTER_PROPAGATION,"second element in reducer is not country").increment(1);
|
97
|
return;
|
98
|
}
|
99
|
|
100
|
boolean propagate = true;
|
101
|
while(it.hasNext()) {
|
102
|
|
103
|
byte[] targetRowKey = gson.fromJson(Bytes.toString(it.next().get()),Value.class).getValue().get();
|
104
|
String resultId = Bytes.toString(targetRowKey);
|
105
|
|
106
|
if (!resultId.startsWith(("50|"))) {
|
107
|
if(!resultId.equalsIgnoreCase(country)) {
|
108
|
context.getCounter(COUNTER_PROPAGATION, String.format("resultId expected in ordering was not found. First country %s, second country %s", country, resultId)).increment(1);
|
109
|
//throw new RuntimeException("Problem in country values of institutional repositories" + targetRowKey);
|
110
|
propagate = false;
|
111
|
}
|
112
|
|
113
|
}else{
|
114
|
if (propagate){
|
115
|
OafProtos.Oaf oafUpdate = getOafCountry(resultId, country,trust);
|
116
|
emit(context, resultId, JsonFormat.printToString(oafUpdate));
|
117
|
|
118
|
context.getCounter(COUNTER_PROPAGATION, String.format(" added country %s to product from repo %s",country, StringUtils.substringBefore( resultId,"::"))).increment(1);
|
119
|
}
|
120
|
|
121
|
}
|
122
|
|
123
|
}
|
124
|
} else {
|
125
|
context.getCounter(COUNTER_PROPAGATION,"not allowed dsType institutional datasource").increment(1);
|
126
|
}
|
127
|
|
128
|
|
129
|
|
130
|
}
|
131
|
|
132
|
private FieldTypeProtos.DataInfo.Builder getDataInfo(String trust) {
|
133
|
FieldTypeProtos.DataInfo.Builder builder = FieldTypeProtos.DataInfo.newBuilder()
|
134
|
.setInferred(true)
|
135
|
.setProvenanceaction(
|
136
|
FieldTypeProtos.Qualifier.newBuilder()
|
137
|
.setClassid(CLASS_ID)
|
138
|
.setClassname("Propagation of country information from datasources belonging to institutional repositories")
|
139
|
.setSchemeid(SCHEMA_ID)
|
140
|
.setSchemename(SCHEMA_NAME))
|
141
|
.setInferenceprovenance(DATA_INFO_TYPE)
|
142
|
.setTrust(trust);
|
143
|
return builder;
|
144
|
|
145
|
}
|
146
|
|
147
|
private OafProtos.Oaf getOafCountry(String resultId, String countryValue, String trust) {
|
148
|
|
149
|
final FieldTypeProtos.Qualifier.Builder country = FieldTypeProtos.Qualifier.newBuilder()
|
150
|
.setClassid(countryValue)
|
151
|
.setClassname(countryValue)
|
152
|
.setSchemeid(DNETCOUNTRYSCHEMA)
|
153
|
.setSchemename(DNETCOUNTRYSCHEMA);
|
154
|
country.setDataInfo(getDataInfo(trust));
|
155
|
|
156
|
final ResultProtos.Result.Metadata.Builder metadata = ResultProtos.Result.Metadata.newBuilder().addCountry(country);
|
157
|
final ResultProtos.Result.Builder result = ResultProtos.Result.newBuilder().setMetadata(metadata);
|
158
|
final OafProtos.OafEntity.Builder entity = OafProtos.OafEntity.newBuilder()
|
159
|
.setType(TypeProtos.Type.result)
|
160
|
.setId(resultId)
|
161
|
.setResult(result);
|
162
|
|
163
|
return OafProtos.Oaf.newBuilder()
|
164
|
.setKind(KindProtos.Kind.entity)
|
165
|
.setEntity(entity)
|
166
|
.build();
|
167
|
}
|
168
|
|
169
|
|
170
|
}
|