Examples with ILiteratureEntry ambit2.base.data.ILiteratureEntry used on opensource projects

Example 1 with ILiteratureEntry

use of ambit2.base.data.ILiteratureEntry 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;
}

Example 2 with ILiteratureEntry

use of ambit2.base.data.ILiteratureEntry in project ambit-mirror by ideaconsult.

the class CallableFileImport method datasetMeta.

protected SourceDataset datasetMeta(File file) {
    String title = properties == null ? null : properties.get("title");
    title = title == null ? fileDescription : ("".equals(title.trim()) ? fileDescription : title.trim());
    String source = properties == null ? null : properties.get(AbstractDataset._props.source.name());
    source = source == null ? fileDescription : source;
    String license = properties == null ? null : properties.get(AbstractDataset._props.license.name());
    license = license == null ? ISourceDataset.license.Unknown.getURI() : license;
    String rightsHolder = properties == null ? null : properties.get(AbstractDataset._props.rightsHolder.name());
    rightsHolder = rightsHolder == null ? "Unknown" : rightsHolder;
    String seeAlso = properties == null ? null : properties.get(AbstractDataset._props.seeAlso.name());
    String publisher = seeAlso == null ? client == null ? "File uploaded by user" : (client.getUser() == null ? client.getAddress() : client.getUser().getIdentifier() == null ? client.getAddress() : client.getUser().getIdentifier()) : seeAlso;
    ILiteratureEntry reference = LiteratureEntry.getInstance(source, publisher);
    reference.setType(_type.Dataset);
    SourceDataset dataset = new SourceDataset(title, reference);
    dataset.setLicenseURI(license);
    dataset.setrightsHolder(rightsHolder);
    return dataset;
}

Example 3 with ILiteratureEntry

use of ambit2.base.data.ILiteratureEntry in project ambit-mirror by ideaconsult.

the class DXParser method verifyDXProperty.

protected Property verifyDXProperty(Property property, Object value, ILiteratureEntry reference) throws AmbitException {
    property.setReference(reference);
    String[] split = property.getName().split("\\.");
    JsonNode endpoint = (split.length > 1) ? dxRoot.get(json_fields.endpoints.name()).get(split[1]) : null;
    JsonNode superEndpoint = endpoint == null ? null : endpoint.get("super");
    JsonNode species = (split.length > 2) ? dxRoot.get(json_fields.species.name()).get(split[2]) : null;
    if (species == null)
        return null;
    JsonNode ontology = null;
    PropertyAnnotations pa = new PropertyAnnotations();
    if (species != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("species");
        a.setObject(split[2]);
        pa.add(a);
    }
    if (superEndpoint != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("DX Superendpoint");
        a.setObject(superEndpoint.textValue());
        pa.add(a);
        try {
            ontology = dxRoot.get(json_fields.endpoints.name()).get(superEndpoint.textValue()).get(json_fields.ot.name());
        } catch (Exception x) {
            logger.log(Level.WARNING, x.getClass().getName() + " " + superEndpoint);
        }
    }
    if (endpoint != null) {
        PropertyAnnotation a = new PropertyAnnotation();
        a.setPredicate("DX endpoint");
        a.setObject(split[1]);
        pa.add(a);
        try {
            if (endpoint.get(json_fields.ot.name()) != null)
                ontology = endpoint.get(json_fields.ot.name());
        } catch (Exception x) {
            logger.log(Level.WARNING, x.getClass().getName() + " " + endpoint);
        }
    }
    if (ontology != null)
        property.setLabel(ontology.textValue());
    for (PropertyAnnotation a : categories) pa.add(a);
    property.setAnnotations(pa);
    return property;
}

Example 4 with ILiteratureEntry

use of ambit2.base.data.ILiteratureEntry in project ambit-mirror by ideaconsult.

the class AbstractPropertyRetrieval method getObject.

/*
 WARNING: No enum const class ambit2.db.search.property.AbstractPropertyRetrieval$_PROPERTY_TYPE.
 java.lang.IllegalArgumentException: No enum const class ambit2.db.search.property.AbstractPropertyRetrieval$_PROPERTY_TYPE.
         at java.lang.Enum.valueOf(Enum.java:214)
         at ambit2.db.search.property.AbstractPropertyRetrieval$_PROPERTY_TYPE.valueOf(AbstractPropertyRetrieval.java:104)
         at ambit2.db.search.property.AbstractPropertyRetrieval.getObject(AbstractPropertyRetrieval.java:164)
         at ambit2.db.search.property.AbstractPropertyRetrieval.getObject(AbstractPropertyRetrieval.java:141)
         at ambit2.db.search.property.AbstractPropertyRetrieval.getObject(AbstractPropertyRetrieval.java:45)
         at ambit2.db.DbReader$1.next(DbReader.java:159)
         at ambit2.db.processors.AbstractBatchProcessor.process(AbstractBatchProcessor.java:105)
         at ambit2.db.reporters.QueryAbstractReporter.process(QueryAbstractReporter.java:115)
         at ambit2.rest.AbstractObjectConvertor.process(AbstractObjectConvertor.java:41)
         at ambit2.rest.AbstractObjectConvertor.process(AbstractObjectConvertor.java:17)
         at ambit2.rest.query.QueryResource.getRepresentation(QueryResource.java:183)
         at ambit2.rest.AbstractResource.get(AbstractResource.java:98)
         at org.restlet.resource.ServerResource.doHandle(ServerResource.java:519)
         at org.restlet.resource.ServerResource.doNegotiatedHandle(ServerResource.java:579)
         at org.restlet.resource.ServerResource.doConditionalHandle(ServerResource.java:258)
         at org.restlet.resource.ServerResource.handle(ServerResource.java:818)
	
 */
public Property getObject(ResultSet rs, Property p) throws AmbitException {
    try {
        if (p == null) {
            p = Property.getInstance(rs.getString("name"), rs.getString("title"), rs.getString("url"));
        } else {
            p.setName(rs.getString("name"));
        // !!!!!!!!!!!!!!!!!! update the rest
        }
        try {
            p.setOrder(rs.getInt("order"));
        } catch (Exception x) {
        }
        p.setId(rs.getInt("idproperty"));
        p.setUnits(rs.getString("units"));
        p.setLabel(rs.getString("comments"));
        p.getReference().setId(rs.getInt("idreference"));
        try {
            String type = rs.getString("idtype");
            String[] types = null;
            if (type != null && !"".equals(type)) {
                types = type.split(",");
                for (String t : types) try {
                    p.setClazz(_PROPERTY_TYPE.valueOf(t).getClazz());
                } catch (Exception x) {
                    logger.log(Level.WARNING, x.getMessage(), t);
                }
            }
        } catch (Exception x) {
            logger.log(Level.FINE, x.getMessage(), x);
        }
        try {
            p.setNominal(rs.getBoolean("islocal"));
        } catch (Exception x) {
            p.setNominal(false);
        }
        try {
            String _type = rs.getString("type");
            if (_type != null)
                p.getReference().setType(ILiteratureEntry._type.valueOf(_type));
        } catch (Exception x) {
        }
        PropertyAnnotation<String> a = null;
        for (ANNOTATIONS_TABLE f : ANNOTATIONS_TABLE.values()) try {
            String value = rs.getString(f.name());
            if (value == null)
                break;
            if (a == null)
                a = new PropertyAnnotation<String>();
            f.setValue(a, value);
        } catch (Exception x) {
        }
        if (a != null) {
            if (p.getAnnotations() == null)
                p.setAnnotations(new PropertyAnnotations());
            p.getAnnotations().add(a);
        }
        return p;
    } catch (SQLException x) {
        throw new AmbitException(x);
    }
}

Example 5 with ILiteratureEntry

use of ambit2.base.data.ILiteratureEntry in project ambit-mirror by ideaconsult.

the class PropertiesByDataset method getObject.

@Override
public Property getObject(ResultSet rs) throws AmbitException {
    try {
        Property p = Property.getInstance(rs.getString(2), rs.getString(4), rs.getString(5));
        p.setId(rs.getInt(1));
        p.setUnits(rs.getString(3));
        p.setLabel(rs.getString(7));
        p.getReference().setId(rs.getInt(6));
        try {
            p.setOrder(rs.getInt("order"));
        } catch (Exception x) {
        }
        try {
            String type = rs.getString(8);
            if (type != null) {
                String[] types = type.split(",");
                for (// TODO support multiple types per property
                String t : // TODO support multiple types per property
                types) p.setClazz(_PROPERTY_TYPE.valueOf(t).getClazz());
            }
        } catch (Exception x) {
        }
        try {
            p.setNominal(rs.getBoolean(9));
        } catch (Exception x) {
            p.setNominal(false);
        }
        try {
            String _type = rs.getString(10);
            if (_type != null)
                p.getReference().setType(ILiteratureEntry._type.valueOf(_type));
        } catch (Exception x) {
        }
        PropertyAnnotation<String> a = null;
        for (ANNOTATIONS_TABLE f : ANNOTATIONS_TABLE.values()) try {
            String value = rs.getString(f.name());
            if (value == null)
                break;
            if (a == null)
                a = new PropertyAnnotation<String>();
            f.setValue(a, value);
        } catch (Exception x) {
        }
        if (a != null) {
            if (p.getAnnotations() == null)
                p.setAnnotations(new PropertyAnnotations());
            p.getAnnotations().add(a);
        }
        return p;
    } catch (SQLException x) {
        throw new AmbitException(x);
    }
}