use of ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty in project ambit-mirror by ideaconsult.
the class SubstanceDatasetResource method getPropertyProcessors.
protected IProcessor getPropertyProcessors(final boolean removeIdentifiers, final boolean removeStringProperties) {
IQueryRetrieval<ProtocolEffectRecord<String, String, String>> queryP = getEffectQuery();
MasterDetailsProcessor<SubstanceRecord, ProtocolEffectRecord<String, String, String>, IQueryCondition> effectReader = new MasterDetailsProcessor<SubstanceRecord, ProtocolEffectRecord<String, String, String>, IQueryCondition>(queryP) {
/**
*/
private static final long serialVersionUID = -7354966336095750101L;
ProtocolEffectRecord2SubstanceProperty processor = new ProtocolEffectRecord2SubstanceProperty();
@Override
public SubstanceRecord process(SubstanceRecord target) throws Exception {
if (target == null || target.getSubstanceUUID() == null)
return target;
else
return super.process(target);
}
@Override
protected SubstanceRecord processDetail(SubstanceRecord master, ProtocolEffectRecord<String, String, String> detail) throws Exception {
if (master.getIdsubstance() <= 0)
return master;
if (detail != null) {
if (detail.getTextValue() != null && detail.getTextValue().toString().startsWith("{")) {
JsonNode node = dx.readTree(new StringReader(detail.getTextValue().toString()));
List<String> guideline = detail.getProtocol().getGuideline();
ILiteratureEntry ref = LiteratureEntry.getInstance(guideline == null ? null : guideline.size() == 0 ? null : guideline.get(0), guideline == null ? null : guideline.size() == 0 ? null : guideline.get(0));
Iterator<Entry<String, JsonNode>> i = node.fields();
while (i.hasNext()) {
Entry<String, JsonNode> val = i.next();
SubstanceProperty key = new SubstanceProperty(detail.getProtocol().getTopCategory(), detail.getProtocol().getCategory(), val.getKey(), detail.getUnit(), ref);
try {
key.setStudyResultType(_r_flags.valueOf(detail.getStudyResultType().replace(":", "").replace("_", "").replace(" ", "").replace("-", "").replace(")", "").replace("(", "")));
} catch (Exception x) {
key.setStudyResultType(null);
}
key.setExtendedURI(true);
key.setIdentifier(detail.getSampleID() + "/" + val.getKey());
groupProperties.add(key);
if (val.getValue().get(EffectRecord._fields.loValue.name()) != null) {
Number num = val.getValue().get(EffectRecord._fields.loValue.name()).asDouble();
master.setRecordProperty(key, num);
key.setClazz(Number.class);
} else {
master.setRecordProperty(key, val.getValue().textValue());
key.setClazz(String.class);
}
}
} else {
boolean isTextValue = ((detail.getLoValue() == null) && (detail.getUpValue() == null));
if (isTextValue && removeStringProperties)
return master;
/*
* JsonNode conditions = detail.getConditions() == null
* ? null : dx.readTree(new StringReader(
* detail.getConditions()));
*
* PropertyAnnotations ann = new PropertyAnnotations();
*
* Iterator<Entry<String, JsonNode>> i = conditions ==
* null ? null : conditions.getFields();
*
* if (i != null) while (i.hasNext()) { Entry<String,
* JsonNode> val = i.next(); if (val.getValue()
* instanceof NullNode) continue;
*
* if (val.getValue().getTextValue() == null) try {
* PropertyAnnotation a = new PropertyAnnotation();
* String unit =
* val.getValue().get(EffectRecord._fields.unit.name())
* == null ? null :
* val.getValue().get(EffectRecord._fields
* .unit.name()).asText(); a.setPredicate(val.getKey());
* if (unit == null)
* a.setObject(val.getValue().get(EffectRecord
* ._fields.loValue.name()) .asText()); else {
* a.setObject(String.format("%s %s",
* val.getValue().get(
* EffectRecord._fields.loValue.name()).asText(),
* unit)); } ann.add(a); } catch (Exception x) { } else
* { PropertyAnnotation a = new PropertyAnnotation();
* a.setPredicate(val.getKey());
* a.setObject(val.getValue().getTextValue());
* ann.add(a); }
*
* }
*/
ProtocolEffectRecord<String, IParams, String> effect = new ProtocolEffectRecord<String, IParams, String>();
ProtocolEffectRecord2SubstanceProperty.copyEffectRecordValues(detail, effect);
try {
JsonNode conditions = detail.getConditions() == null ? null : dx.readTree(new StringReader(detail.getConditions()));
if (conditions instanceof ObjectNode) {
effect.setConditions(SubstanceStudyParser.parseParams((ObjectNode) conditions));
}
} catch (Exception x) {
logger.log(Level.FINE, x.getMessage());
}
SubstanceProperty key = processor.process(effect);
key.setIdentifier(key.createHashedIdentifier(effect.getConditions()));
Object oldValue = master.getRecordProperty(key);
groupProperties.add(key);
/*
* if (isTextValue) { //textvalue if (oldValue == null)
* master.setProperty(key, detail.getTextValue()); else
* { master.setProperty(key, String.format( "%s, %s",
* oldValue instanceof Number ? nf.format((Number)
* oldValue) : oldValue .toString(),
* detail.getTextValue())); }
* key.setClazz(String.class); } else { //numeric
*/
Value value = processValue(detail, isTextValue);
if (value != null)
ProtocolEffectRecord2SubstanceProperty.addValues(master, key, value, oldValue);
// }
}
}
return master;
}
};
return effectReader;
}
use of ambit2.core.io.study.ProtocolEffectRecord2SubstanceProperty in project ambit-mirror by ideaconsult.
the class CallableSubstancePropertyCreatorTest method testCreateSubstancePropertyFromRDF.
@Test
public void testCreateSubstancePropertyFromRDF() throws Exception {
URL url = getClass().getClassLoader().getResource("feature.rdf");
File file = new File(url.getFile());
Assert.assertTrue(file.exists());
try {
PropertyURIReporter reporter = new PropertyURIReporter(new Reference("http://localhost:8081/ambit2"));
CallableSubstancePropertyCreator callable = new CallableSubstancePropertyCreator(reporter, Method.POST, file, MediaType.APPLICATION_RDF_XML, null, null);
TaskResult task = callable.call();
ProtocolEffectRecord2SubstanceProperty p = new ProtocolEffectRecord2SubstanceProperty();
ProtocolEffectRecord<String, IParams, String> effect = new ProtocolEffectRecord<String, IParams, String>();
Protocol protocol = new Protocol(null);
Protocol._categories category = Protocol._categories.EC_DAPHNIATOX_SECTION;
protocol.setCategory(category.name());
protocol.setTopCategory(category.getTopCategory());
protocol.addGuideline("http://localhost:8080/ambit2/dataset/Method%3A+other%3A+Am.+Soc.+Test.+Mater.+%281980%29+and+U.S.+EPA+%281975%29");
effect.setProtocol(protocol);
effect.setEndpoint("EC10");
effect.setUnit("mg/L");
effect.setConditions(new Params());
/*
* Value value = new Value(); value.setLoValue(48.0);
* value.setUnits("h"); effect.getConditions().put("Exposure",
* value);
*/
SubstanceProperty prop = p.process(effect);
prop.setIdentifier(prop.createHashedIdentifier(effect.getConditions()));
Assert.assertEquals(reporter.getURI(prop), task.getUri());
} catch (Exception x) {
throw x;
} finally {
}
}
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