Examples with Params ambit2.base.data.study.Params used on opensource projects

Example 1 with Params

use of ambit2.base.data.study.Params 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 Params

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

the class SubstanceStudyReporterTest method main.

public static void main(String[] args) {
    Substance2BucketJsonReporter reporter = new Substance2BucketJsonReporter(null, null, Substance2BucketJsonReporter._JSON_MODE.substance, null, null, null);
    Reader in = null;
    try {
        OutputStreamWriter writer;
        if (args.length < 2)
            writer = new OutputStreamWriter(System.out);
        else
            writer = new OutputStreamWriter(new FileOutputStream(new File(args[1])));
        reporter.setOutput(writer);
        in = new FileReader(new File(args[0]));
        RawIteratingCSVReader reader = new RawIteratingCSVReader(in, CSVFormat.TDF) {

            protected SubstanceRecord prevrecord = null;

            protected String getRecordid(CSVRecord record) {
                return record.get(0);
            }

            protected String getExternalId(CSVRecord record) {
                return record.get(1);
            }

            protected String getExternalIdSystem(CSVRecord record) {
                return record.get(5);
            }

            protected String getAssayid(CSVRecord record) {
                return record.get(6);
            }

            protected String getSummaryActivity(CSVRecord record) {
                return record.get(3);
            }

            protected double getActivityValue(CSVRecord record) throws NumberFormatException {
                return Double.parseDouble(record.get(4));
            }

            protected String getOrthologgroup(CSVRecord record) {
                return record.get(9);
            }

            protected String getGeneSymbol(CSVRecord record) {
                return record.get(8);
            }

            protected String getSpecies(CSVRecord record) {
                return record.get(7);
            }

            @Override
            protected IStructureRecord transform(CSVRecord record) {
                SubstanceRecord substance = prevrecord;
                String id = getRecordid(record);
                if (prevrecord == null || !id.equals(prevrecord.getSubstanceName())) {
                    substance = new SubstanceRecord();
                    substance.setContent(null);
                    // substance.setSubstancetype("standardized");
                    substance.setSubstanceUUID(I5Utils.getPrefixedUUID("PC", UUID.nameUUIDFromBytes(id.getBytes())));
                    substance.setSubstanceName(id);
                    prevrecord = substance;
                }
                structureRecord = substance;
                String externalid = getExternalId(record);
                String externaldb = getExternalIdSystem(record);
                ExternalIdentifier eid = new ExternalIdentifier(externaldb, externalid);
                boolean newid = true;
                if (substance.getExternalids() == null)
                    substance.setExternalids(new ArrayList<ExternalIdentifier>());
                else
                    for (ExternalIdentifier e : substance.getExternalids()) if (e.getSystemDesignator().equals(eid.getSystemDesignator()) && e.getSystemIdentifier().equals(eid.getSystemIdentifier())) {
                        newid = false;
                        break;
                    }
                if (newid)
                    substance.getExternalids().add(eid);
                String assayid = getAssayid(record);
                Protocol p = new Protocol(String.format("%s", externalid));
                p.setTopCategory(null);
                p.setCategory(null);
                // p.addGuideline(String.format("%s_AID%s", externaldb,assayid));
                ProtocolApplication<Protocol, IParams, String, IParams, String> papp = new ProtocolApplication<Protocol, IParams, String, IParams, String>(p);
                // papp.setDocumentUUID(I5Utils.getPrefixedUUID("PC",UUID.nameUUIDFromBytes(p.getEndpoint().getBytes())));
                papp.setDocumentUUID(null);
                papp.setInterpretationResult(getSummaryActivity(record));
                papp.setReference(String.format("AID%s", assayid));
                papp.setReferenceOwner(externaldb);
                IParams params = new Params();
                params.put("gene", getGeneSymbol(record));
                params.put("taxid", "TaxId:" + getSpecies(record));
                // params.put("OG_GENE", String.format("OG%s_%s", record.get(9),	record.get(8)));
                params.put("og", "OG" + getOrthologgroup(record));
                params.put("ez", "entrez:" + record.get(2));
                papp.setParameters(params);
                try {
                    EffectRecord<String, IParams, String> effect = new EffectRecord<String, IParams, String>();
                    effect.setEndpoint("pXC50");
                    effect.setIdresult(1);
                    double value = getActivityValue(record);
                    effect.setLoValue(value);
                    effect.setUnit("nM");
                    papp.addEffect(effect);
                } catch (Exception x) {
                // x.printStackTrace();
                }
                substance.addMeasurement(papp);
                return structureRecord;
            }
        };
        int n = 0;
        IStructureRecord prevrecord = null;
        reporter.header(writer, null);
        while (reader.hasNext()) {
            IStructureRecord record = reader.nextRecord();
            if (prevrecord != null && (prevrecord != record)) {
                reporter.processItem((SubstanceRecord) prevrecord);
                writer.flush();
            }
            n++;
            prevrecord = record;
            if ((n % 100000) == 0) {
                System.err.println();
                System.err.print(n);
            } else if ((n % 10000) == 0)
                System.err.print(".");
        }
        reporter.processItem((SubstanceRecord) prevrecord);
        reporter.footer(writer, null);
        writer.flush();
    } catch (Exception x) {
        x.printStackTrace();
    } finally {
        try {
            in.close();
        } catch (Exception x) {
        }
        try {
            reporter.close();
        } catch (Exception x) {
        }
    }
}

Example 3 with Params

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

the class CallableSubstancePropertyCreatorTest method testCreateSubstanceProperty.

@Test
public void testCreateSubstanceProperty() throws Exception {
    Form form = new Form();
    form.add("endpointcategory", Protocol._categories.ZETA_POTENTIAL_SECTION.name());
    form.add("name", "ZETA POTENTIAL");
    form.add("unit", "mV");
    form.add("protocol", "Method: other: no data");
    Params p = new Params();
    Value v = new Value();
    v.setLoValue(4.26);
    p.put("pH", v);
    Assert.assertEquals("{\"pH\":{\"loValue\":4.26}}", p.toString());
    try {
        PropertyURIReporter reporter = new PropertyURIReporter(new Reference("http://localhost:8081/ambit2"));
        CallableSubstancePropertyCreator callable = new CallableSubstancePropertyCreator(reporter, Method.POST, form, null, null);
        TaskResult task = callable.call();
        Assert.assertTrue(task.getUri().startsWith("http://localhost:8081/ambit2/property/P-CHEM/ZETA_POTENTIAL_SECTION/ZETA+POTENTIAL/A597EBC063D7A5A605B9535656E09149A72F0C23"));
    // "http://localhost:8081/ambit2/property/P-CHEM/ZETA_POTENTIAL_SECTION/ZETA+POTENTIAL/945DEEC24F876DEE6116F92646EF729107F5B5FD"
    } catch (Exception x) {
        throw x;
    } finally {
    }
}

Example 4 with Params

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

the class CallableSubstancePropertyCreatorTest method testCreateSubstanceProperty_TO_BIODEG_WATER_SCREEN_SECTION.

/**
 * @throws Exception
 */
@Test
public void testCreateSubstanceProperty_TO_BIODEG_WATER_SCREEN_SECTION() throws Exception {
    Form form = new Form();
    form.add("endpointcategory", Protocol._categories.TO_BIODEG_WATER_SCREEN_SECTION.name());
    form.add("name", "% Degradation");
    form.add("unit", "%");
    form.add("protocol", "Method: other: no data");
    Params p = new Params();
    Value v = new Value();
    v.setUnits("d");
    v.setLoValue(7.0);
    p.put("Sampling time", v);
    form.add("conditions", p.toString());
    Assert.assertEquals("{\"Sampling time\":{\"loValue\":7,\"unit\":\"d\"}}", p.toString());
    try {
        PropertyURIReporter reporter = new PropertyURIReporter(new Reference("http://localhost:8081/ambit2"));
        CallableSubstancePropertyCreator callable = new CallableSubstancePropertyCreator(reporter, Method.POST, form, null, null);
        TaskResult task = callable.call();
        Assert.assertTrue(task.getUri().startsWith("http://localhost:8081/ambit2/property/ENV+FATE/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/3CF77D9EFE4E74744E691BF4880B4EF728B16FAE"));
    // /d4cd0dab-cf4c-3a22-ad92-fab40844c786
    /*
			 * "http://localhost:8080/ambit2/property/ENV+FATE/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/5FA6EFD4E83BEC47B626C6149DBBD3907084187F/1f255895-eb7d-37dc-8eb8-bc9580d8be25"
			 * :{
			 * 
			 * "type":"Feature", "title":"% Degradation", "units":"%",
			 * "isNominal":false, "isNumeric":false, "isMultiValue":true,
			 * "sameAs"
			 * :"http://www.opentox.org/echaEndpoints.owl#TO_BIODEG_WATER_SCREEN"
			 * , "isModelPredictionFeature":false,
			 * "creator":"Method: other: see below", "order":1087, "source":{
			 * "URI"
			 * :"http://localhost:8080/ambit2/dataset/Method%3A+other%3A+see+below"
			 * , "type":"Dataset" }, "annotation":[ { "p" : "Sampling time", "o"
			 * : "7.0 d"}]
			 * 
			 * },
			 */
    // http://localhost:8081/ambit2/property/P-CHEM/TO_BIODEG_WATER_SCREEN_SECTION/%25+Degradation/8C9DF1AF60CA3D8706C0156361E97E0DF4391C10/1f255895-eb7d-37dc-8eb8-bc9580d8be25
    } catch (Exception x) {
        throw x;
    } finally {
    }
}

Example 5 with Params

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

the class CompoundLookup method createQuery.

/*
	 */
@Override
protected IQueryRetrieval<IStructureRecord> createQuery(Context context, Request request, Response response) throws ResourceException {
    // parse params
    Object id = null;
    try {
        id = getRequest().getAttributes().get(resourceKey);
        if (id == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No structure identifier");
        text = Reference.decode(id.toString().trim());
        if ("".equals(text))
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty query");
    } catch (Exception x) {
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, String.format("Invalid structure identifier", id));
    }
    id = null;
    try {
        id = getRequest().getAttributes().get(representationKey);
        if (id == null)
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No structure representation");
        rep_id = NCISearchProcessor.METHODS.valueOf(Reference.decode(id.toString()));
    } catch (Exception x) {
        rep_id = null;
    }
    Form form = getParams();
    try {
        Object bundleURI = OpenTox.params.bundle_uri.getFirstValue(form);
        Integer idbundle = bundleURI == null ? null : getIdBundle(bundleURI, request);
        SubstanceEndpointsBundle bundle = new SubstanceEndpointsBundle(idbundle);
        bundles = new SubstanceEndpointsBundle[1];
        bundles[0] = bundle;
    } catch (Exception x) {
        bundles = null;
    }
    try {
        includeMol = "true".equals(form.getFirstValue("mol"));
    } catch (Exception x) {
        includeMol = false;
    }
    try {
        headless = Boolean.parseBoolean(form.getFirstValue("headless"));
    } catch (Exception x) {
        headless = false;
    }
    boolean casesens = "true".equals(form.getFirstValue(QueryResource.caseSensitive)) ? true : false;
    String scparam = form.getFirstValue(QueryResource.condition);
    setCondition(StringCondition.C_EQ);
    if (scparam != null)
        for (STRING_CONDITION sc : STRING_CONDITION.values()) {
            if (scparam.equals(sc.getSQL())) {
                setCondition(sc.getSQL());
                break;
            }
        }
    boolean retrieveProperties = "true".equals(form.getFirstValue(QueryResource.returnProperties)) ? true : false;
    String url = null;
    IQueryRetrieval<IStructureRecord> query = null;
    if (isInchiKey(text))
        try {
            String inchikey = getFirstParam(form);
            if ((inchikey == null) || (inchikey.trim().length() != 27))
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid InChI Key");
            QueryStructure q = new QueryStructure();
            q.setChemicalsOnly(true);
            q.setFieldname(ExactStructureSearchMode.inchikey);
            q.setValue(inchikey.trim());
            searchType = _searchtype.inchikey;
            query = q;
        } catch (ResourceException x) {
            throw x;
        } catch (Exception x) {
            throw new ResourceException(Status.SERVER_ERROR_BAD_GATEWAY, String.format("%s %s", url, x.getMessage()), x);
        }
    else if (isURL(text))
        try {
            url = getFirstParam(form);
            if (url == null)
                throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "No search parameter!");
            Object q = CallableQueryProcessor.getQueryObject(new Reference(url), getRequest().getRootRef(), getApplication().getContext(), getCookies(), getAgent(), getRequest().getResourceRef().toString());
            if (q == null) {
                throw new ResourceException(Status.SERVER_ERROR_NOT_IMPLEMENTED, "TODO: retrieve compounds from foreign urls");
            } else if (q instanceof AbstractStructureQuery) {
                query = (IQueryRetrieval<IStructureRecord>) q;
            }
        } catch (ResourceException x) {
            throw x;
        } catch (Exception x) {
            throw new ResourceException(Status.SERVER_ERROR_BAD_GATEWAY, String.format("%s %s", url, x.getMessage()), x);
        }
    else {
        if (isSearchParam(text)) {
            text = getFirstParam(form);
            text_multi = getValuesArray(form);
        }
        Object idcompound = isAmbitID(text);
        // query
        if (idcompound != null) {
            switch(searchType) {
                case ambitid:
                    IStructureRecord record = new StructureRecord();
                    record.setIdchemical(((Integer) idcompound).intValue());
                    QueryStructureByID q = new QueryStructureByID();
                    q.setPageSize(1);
                    q.setChemicalsOnly(true);
                    q.setValue(record);
                    query = q;
                    break;
                case inchikey:
                    String inchikey = idcompound.toString();
                    if ((inchikey == null) || (inchikey.trim().length() != 27))
                        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Invalid InChI Key");
                    QueryStructure q1 = new QueryStructure();
                    q1.setChemicalsOnly(true);
                    q1.setFieldname(ExactStructureSearchMode.inchikey);
                    q1.setValue(inchikey.trim());
                    searchType = _searchtype.inchikey;
                    query = q1;
                    break;
                default:
                    query = null;
                    break;
            }
        } else if ((text_multi != null) && (text_multi.length > 1)) {
            query = getMultiTextQuery(null, casesens, retrieveProperties, text_multi);
        } else if ((text == null) || "".equals(text)) {
            throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST);
        } else if (CASProcessor.isValidFormat(text)) {
            // number
            if (CASNumber.isValid(text.trim())) {
                searchType = _searchtype.cas;
                query = getTextQuery(Property.getCASInstance(), casesens, retrieveProperties, text);
            }
        } else if (EINECS.isValidFormat(text)) {
            // we'd better not search for invalid numbers
            if (EINECS.isValid(text.trim())) {
                searchType = _searchtype.einecs;
                query = getTextQuery(Property.getEINECSInstance(), casesens, retrieveProperties, text);
            }
        } else {
            if ("".equals(text)) {
            // if inchi
            } else if (isInChI(text)) {
                QueryStructure q = new QueryStructure();
                q.setChemicalsOnly(true);
                q.setFieldname(ExactStructureSearchMode.inchi);
                q.setValue(text);
                query = q;
            } else if (isMol(text)) {
                String[] inchi = mol2inchi(text);
                QueryStructure q = new QueryStructure();
                q.setChemicalsOnly(true);
                q.setFieldname(ExactStructureSearchMode.inchi);
                // eventually search by inchikey?
                q.setValue(inchi[0]);
                query = q;
            } else
                try {
                    // inchi, inchikey
                    String[] inchi = smiles2inchi(text.trim());
                    QueryStructure q = new QueryStructure();
                    q.setChemicalsOnly(true);
                    q.setFieldname(ExactStructureSearchMode.inchi);
                    // eventually search by inchikey?
                    q.setValue(inchi[0]);
                    query = q;
                } catch (InvalidSmilesException x) {
                    query = null;
                // otherwise this was valid smiles, but inchi failed!
                } catch (CDKException x) {
                    casesens = true;
                    query = null;
                } catch (Exception x) {
                    casesens = true;
                    query = null;
                }
        }
    }
    if (query == null)
        query = getTextQuery(null, casesens, retrieveProperties, text);
    setPaging(form, query);
    setTemplate(createTemplate(form));
    setGroupProperties(context, request, response);
    return query;
}