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

Example 1 with ExternalIdentifier

use of ambit2.base.data.substance.ExternalIdentifier 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 2 with ExternalIdentifier

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

the class SubstanceCSVReporter method processItem.

@Override
public Object processItem(SubstanceRecord item) throws AmbitException {
    try {
        Writer writer = getOutput();
        if (item.getSubstanceName() != null)
            writer.write(JSONUtils.jsonQuote(item.getSubstanceName()));
        writer.write(comma);
        writer.write(item.getSubstanceUUID());
        writer.write(comma);
        writer.write(JSONUtils.jsonQuote(item.getSubstancetype()));
        writer.write(comma);
        if (item.getPublicName() != null)
            writer.write(JSONUtils.jsonQuote(item.getPublicName()));
        writer.write(comma);
        if (item.getReferenceSubstanceUUID() != null)
            writer.write(JSONUtils.jsonQuote(item.getReferenceSubstanceUUID()));
        writer.write(comma);
        writer.write(JSONUtils.jsonQuote(item.getOwnerName()));
        writer.write(comma);
        if (item.getOwnerUUID() != null)
            writer.write(item.getOwnerUUID());
        writer.write(comma);
        if (item.getExternalids() != null) {
            for (ExternalIdentifier id : item.getExternalids()) {
                writer.write(id.getSystemDesignator());
                writer.write(":");
                writer.write(id.getSystemIdentifier());
                writer.write(" ");
            }
        } else
            writer.write(" ");
        writer.write("\n");
    } catch (Exception x) {
        logger.log(java.util.logging.Level.SEVERE, x.getMessage(), x);
    }
    return item;
}

Example 3 with ExternalIdentifier

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

the class BucketDenormalised method substance2Bucket.

protected void substance2Bucket(SubstanceRecord record, Bucket bucket, boolean hasSuffix, String suffix) {
    if (record == null)
        return;
    bucket.put(ns("name", hasSuffix, suffix), record.getSubstanceName());
    bucket.put(ns("publicname", hasSuffix, suffix), record.getPublicName());
    if (!"".equals(record.getOwnerName()))
        bucket.put(ns("owner_name", hasSuffix, suffix), record.getOwnerName());
    bucket.put(ns("s_uuid", hasSuffix, suffix), record.getSubstanceUUID());
    bucket.put(ns("substanceType", hasSuffix, suffix), record.getSubstancetype());
    bucket.put("type_s", "substance");
    bucket.put("id", record.getSubstanceUUID());
    if (record.getExternalids() != null) {
        for (ExternalIdentifier id : record.getExternalids()) if ("NM code".equals(id.getSystemDesignator())) {
            bucket.put(ns("nmcode", hasSuffix, suffix), id.getSystemIdentifier());
        }
    }
    String[] terms_substance = annotator.annotateSubstance(record);
    if (terms_substance != null) {
        String key = ns("substance_annotation", hasSuffix, suffix + "s");
        bucket.put(key, Arrays.asList(terms_substance));
    }
// bucket.put(ns("content", hasSuffix, suffix), record.getContent());
}

Example 4 with ExternalIdentifier

use of ambit2.base.data.substance.ExternalIdentifier 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;
}

Example 5 with ExternalIdentifier

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

the class BucketDenormalised method externalids2Bucket.

protected void externalids2Bucket(ExternalIdentifier id, Bucket bucket, String key, String prefix) {
    TreeSet<String> keys = new TreeSet<String>();
    IParams ids = (IParams) bucket.get(key);
    if (ids == null) {
        ids = new Params();
        bucket.put(key, ids);
        keys.add(key);
    }
    ids.put(id.getSystemDesignator(), id.getSystemIdentifier());
}