Examples with Node ambit2.smarts.Node used on opensource projects

Example 1 with Node

use of ambit2.smarts.Node in project ambit-mirror by ideaconsult.

the class SubstanceLookupTest method verifyResponseJSON.

public boolean verifyResponseJSON(String uri, MediaType media, InputStreamReader reader) throws Exception {
    // JsonNode node = parseResponseJSON(uri, media, in);
    SubstanceStudyParser p = new SubstanceStudyParser(reader);
    int i = 0;
    while (p.hasNext()) {
        Object o = p.next();
        Assert.assertTrue(o instanceof SubstanceRecord);
        Assert.assertEquals(testUUID, ((SubstanceRecord) o).getSubstanceUUID());
        System.out.println(o);
        i++;
    }
    return i == 1;
}

Example 2 with Node

use of ambit2.smarts.Node 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 3 with Node

use of ambit2.smarts.Node in project ambit-mirror by ideaconsult.

the class SubstanceStudyParser method parseReliability.

// ProtocolApplicationAnnotated
protected void parseReliability(ObjectNode node, ProtocolApplication record) {
    if (node == null)
        return;
    ReliabilityParams reliability = new ReliabilityParams();
    JsonNode jn = node.get(_FIELDS_RELIABILITY.r_isUsedforMSDS.name());
    try {
        reliability.setIsUsedforMSDS(jn.asBoolean());
    } catch (Exception x) {
    }
    jn = node.get(_FIELDS_RELIABILITY.r_isRobustStudy.name());
    try {
        reliability.setIsRobustStudy(jn.asBoolean());
    } catch (Exception x) {
    }
    jn = node.get(_FIELDS_RELIABILITY.r_isUsedforClassification.name());
    try {
        reliability.setIsUsedforClassification(jn.asBoolean());
    } catch (Exception x) {
    }
    jn = node.get(_FIELDS_RELIABILITY.r_purposeFlag.name());
    try {
        reliability.setPurposeFlag(jn.textValue());
    } catch (Exception x) {
    }
    jn = node.get(_FIELDS_RELIABILITY.r_studyResultType.name());
    try {
        reliability.setStudyResultType(jn.textValue());
    } catch (Exception x) {
    }
    jn = node.get(_FIELDS_RELIABILITY.r_value.name());
    try {
        reliability.setValue(jn.textValue());
    } catch (Exception x) {
    }
    record.setReliability(reliability);
}

Example 4 with Node

use of ambit2.smarts.Node in project ambit-mirror by ideaconsult.

the class SubstanceStudyParser method parseTextValueProteomics.

public static IParams parseTextValueProteomics(ObjectMapper dx, String t) {
    IParams nonzero = null;
    if (t != null && t.startsWith("{")) {
        IParams proteomics = SubstanceStudyParser.parseConditions(dx, t.toString());
        Iterator i = proteomics.keySet().iterator();
        nonzero = new Params();
        while (i.hasNext()) {
            Object p = i.next();
            try {
                Value node = (Value) proteomics.get(p);
                if (node != null && (node.getLoValue() != null) && (node.getLoValue() instanceof Double) && ((Double) node.getLoValue()) > 0) {
                    nonzero.put(p, node.getLoValue());
                }
            } catch (Exception x) {
                x.printStackTrace();
            }
        }
    }
    return nonzero;
}

Example 5 with Node

use of ambit2.smarts.Node in project ambit-mirror by ideaconsult.

the class SubstanceStudyParser method parseSubstance.

public SubstanceRecord parseSubstance(JsonNode node) {
    if (node == null)
        return null;
    SubstanceRecord record = new SubstanceRecord();
    record.setSubstanceName(node.get(SubstanceRecord.jsonSubstance.name.name()).textValue());
    record.setSubstanceUUID(node.get(SubstanceRecord.jsonSubstance.i5uuid.name()).textValue());
    record.setOwnerName(node.get(SubstanceRecord.jsonSubstance.ownerName.name()).textValue());
    record.setOwnerUUID(node.get(SubstanceRecord.jsonSubstance.ownerUUID.name()).textValue());
    record.setPublicName(node.get(SubstanceRecord.jsonSubstance.publicname.name()).textValue());
    record.setSubstancetype(node.get(SubstanceRecord.jsonSubstance.substanceType.name()).textValue());
    record.setFormat(node.get(SubstanceRecord.jsonSubstance.format.name()).textValue());
    JsonNode subnode = node.get(SubstanceRecord.jsonSubstance.externalIdentifiers.name());
    if (subnode instanceof ArrayNode) {
        ArrayNode ids = (ArrayNode) subnode;
        List<ExternalIdentifier> extids = new ArrayList<ExternalIdentifier>();
        record.setExternalids(extids);
        for (int i = 0; i < ids.size(); i++) {
            if (ids.get(i) instanceof ObjectNode) {
                extids.add(new ExternalIdentifier(((ObjectNode) ids.get(i)).get("type").textValue(), ((ObjectNode) ids.get(i)).get("id").textValue()));
            }
        }
    }
    subnode = node.get(SubstanceRecord.jsonSubstance.referenceSubstance.name());
    if (subnode != null) {
        record.setReferenceSubstanceUUID(subnode.get(SubstanceRecord.jsonSubstance.i5uuid.name()).textValue());
    }
    return record;
}