use of ambit2.base.data.SubstanceRecord 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;
}
use of ambit2.base.data.SubstanceRecord 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) {
}
}
}
use of ambit2.base.data.SubstanceRecord in project ambit-mirror by ideaconsult.
the class CallableSubstanceBundle method getTarget.
@Override
protected SubstanceRecord getTarget(Form input) throws Exception {
if (Method.POST.equals(method)) {
SubstanceRecord record = new SubstanceRecord();
record = parseForm(input, record);
command = update_command.add;
return record;
} else if (Method.PUT.equals(method)) {
command = null;
SubstanceRecord record = new SubstanceRecord();
record = 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);
}
use of ambit2.base.data.SubstanceRecord 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;
}
use of ambit2.base.data.SubstanceRecord 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;
}
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