Examples with SubstanceProperty ambit2.base.data.substance.SubstanceProperty used on opensource projects

Example 1 with SubstanceProperty

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

the class SubstancePropertyresourceTest method testCreateEntry2.

@Test
public void testCreateEntry2() throws Exception {
    EffectRecord<String, IParams, String> effect = new EffectRecord<String, IParams, String>();
    effect.setConditions(new Params());
    effect.setEndpoint("EC10");
    effect.setUnit("mg/L");
    IParams conditions = new Params();
    effect.setConditions(conditions);
    /*
	Value v = new Value();
	v.setUnits("h");
	v.setLoValue(48.0);
	effect.getConditions().put("EC_DAPHNIATOX",v);
	*/
    // System.out.println(effect);
    SubstanceProperty prop = new SubstanceProperty(null, null, effect.getEndpoint(), effect.getUnit(), null);
    String key = prop.createHashedIdentifier(effect.getConditions());
    UUID protocol_uuid = UUID.nameUUIDFromBytes("http://localhost:8080/ambit2/dataset/Method%3A+other%3A+Am.+Soc.+Test.+Mater.+%281980%29+and+U.S.+EPA+%281975%29".getBytes());
    URL url = getClass().getClassLoader().getResource("feature.rdf");
    FileRepresentation rep = new FileRepresentation(url.getFile(), MediaType.APPLICATION_RDF_XML, 0);
    testAsyncPoll(new Reference(getTestURI()), MediaType.TEXT_URI_LIST, rep, Method.POST, new Reference(String.format("http://localhost:%d/property/ECOTOX/EC_DAPHNIATOX_SECTION/EC10/%s/NOTSPECIFIED/%s", port, key.toUpperCase(), protocol_uuid)));
}

Example 2 with SubstanceProperty

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

the class CallableEndpointsBundle method getTarget.

@Override
protected SubstanceProperty getTarget(Form input) throws Exception {
    if (Method.POST.equals(method)) {
        SubstanceProperty record = new SubstanceProperty(null, null, null, "Default");
        parseForm(input, record);
        command = update_command.add;
        return record;
    } else if (Method.PUT.equals(method)) {
        command = null;
        SubstanceProperty record = new SubstanceProperty(null, null, null, "Default");
        parseForm(input, record);
        if (command != null)
            return record;
        else
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
    }
    throw new ResourceException(Status.CLIENT_ERROR_METHOD_NOT_ALLOWED);
}

Example 3 with SubstanceProperty

use of ambit2.base.data.substance.SubstanceProperty 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 4 with SubstanceProperty

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

the class CallableSubstancePropertyCreator method parseForm.

protected SubstanceProperty parseForm(Form form) throws ResourceException {
    String topCategory = null;
    ProtocolEffectRecord<String, IParams, String> detail = new ProtocolEffectRecord<String, IParams, String>();
    String endpointcategory = form.getFirstValue(_param_endpointcategory);
    try {
        topCategory = Protocol._categories.valueOf(endpointcategory.trim()).getTopCategory();
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Unsupported endpoint category");
    }
    detail.setEndpoint(form.getFirstValue(_param_name));
    if (detail.getEndpoint() == null)
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Unsupported name");
    detail.setUnit(form.getFirstValue(_param_units));
    try {
        String p_conditions = form.getFirstValue(_param_conditions);
        if (p_conditions != null) {
            JsonNode conditions = mapper.readTree(new StringReader(p_conditions));
            if (conditions instanceof ObjectNode) {
                detail.setConditions(SubstanceStudyParser.parseParams((ObjectNode) conditions));
            }
        }
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "conditions: unexpected format");
    }
    String guideline = form.getFirstValue(_param_protocol);
    if (guideline == null)
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "protocol: undefined");
    Protocol protocol = new Protocol(guideline);
    // protocol.addGuideline("Method: other: see below");
    protocol.setCategory(endpointcategory);
    protocol.setTopCategory(topCategory);
    detail.setProtocol(protocol);
    try {
        SubstanceProperty p = processor.process(detail);
        p.setIdentifier(p.createHashedIdentifier(detail.getConditions()));
        return p;
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, x.getMessage(), x);
    }
}

Example 5 with SubstanceProperty

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

the class ReadChemPropertiesByComposition method processDetail.

/**
 * Hack for merging dataset properties with substances; This is not
 * necessarily correct, as the substance may have many components!
 *
 * @param target
 * @param detail
 * @return
 * @throws Exception
 */
public SubstanceRecord processDetail(SubstanceRecord target, IStructureRecord detail) throws Exception {
    for (Property p : detail.getRecordProperties()) {
        if (p.getName().indexOf("#explanation") > 0)
            continue;
        else if (p.getName().indexOf("Error") >= 0)
            continue;
        else if (p.getName().indexOf("Alert for") == 0)
            continue;
        else if (p.getName().indexOf("For a better assessment") >= 0)
            continue;
        Protocol._categories category = Protocol._categories.SUPPORTING_INFO_SECTION;
        if (p.getLabel().endsWith("Carcinogenicity"))
            category = Protocol._categories.TO_CARCINOGENICITY_SECTION;
        else if (p.getLabel().endsWith("Mutagenicity"))
            category = Protocol._categories.TO_GENETIC_IN_VITRO_SECTION;
        else if (p.getLabel().endsWith("Dissociation_constant_pKa"))
            category = Protocol._categories.PC_DISSOCIATION_SECTION;
        else if (p.getLabel().endsWith("Octanol-water_partition_coefficient_Kow"))
            category = Protocol._categories.PC_PARTITION_SECTION;
        else if (p.getLabel().endsWith("Acute_toxicity_to_fish_lethality"))
            category = Protocol._categories.EC_FISHTOX_SECTION;
        else if (p.getLabel().endsWith("Eye_irritation_corrosion"))
            category = Protocol._categories.TO_EYE_IRRITATION_SECTION;
        else if (p.getLabel().endsWith("SkinIrritationCorrosion"))
            category = Protocol._categories.TO_SKIN_IRRITATION_SECTION;
        else if (p.getLabel().endsWith("SkinSensitisation"))
            category = Protocol._categories.TO_SENSITIZATION_SECTION;
        else if (p.getLabel().endsWith("PersistenceBiodegradation"))
            category = Protocol._categories.TO_BIODEG_WATER_SCREEN_SECTION;
        else if (p.getLabel().endsWith("Genotoxicity"))
            category = Protocol._categories.TO_GENETIC_IN_VITRO_SECTION;
        else if (p.getLabel().endsWith("ReproductiveToxicity"))
            category = Protocol._categories.TO_REPRODUCTION_SECTION;
        else if (p.getLabel().endsWith("DevelopmentalToxicity"))
            category = Protocol._categories.TO_DEVELOPMENTAL_SECTION;
        else if (p.getLabel().endsWith("Sensitisation"))
            category = Protocol._categories.TO_SENSITIZATION_SECTION;
        else if (p.getLabel().endsWith("Respiratory_sensitisation"))
            category = Protocol._categories.TO_REPEATED_INHAL_SECTION;
        SubstanceProperty sp = new SubstanceProperty("TOX", category.name().replace("_SECTION", ""), p.getName(), p.getUnits(), p.getReference());
        sp.setEnabled(true);
        if (p.getReference().getType().equals(_type.Dataset))
            sp.setStudyResultType(_r_flags.experimentalresult);
        else
            sp.setStudyResultType(_r_flags.estimatedbycalculation);
        if (detail.getRecordProperty(p) != null) {
            target.setRecordProperty(sp, detail.getRecordProperty(p));
        /*
				 * Object value = target.getProperty(sp); if (value == null)
				 * target.setProperty(sp, detail.getProperty(p)); else { if
				 * (value instanceof MultiValue) { IValue v = new
				 * Value(detail.getProperty(p)); ((MultiValue) value).add(v); }
				 * else { MultiValue v = new MultiValue(); IValue vo = new
				 * Value(value); v.add(vo); vo = new
				 * Value(detail.getProperty(p)); v.add(vo);
				 * target.setProperty(sp, v); }
				 * 
				 * }
				 */
        }
    }
    return target;
}