Examples with ReadDataset ambit2.db.update.dataset.ReadDataset used on opensource projects

Example 1 with ReadDataset

use of ambit2.db.update.dataset.ReadDataset in project ambit-mirror by ideaconsult.

the class MetadatasetResource method getQuery.

protected IQueryRetrieval<M> getQuery(Context context, Request request, Response response, boolean IDcanBeEmpty) throws ResourceException {
    Form form = getResourceRef(request).getQueryAsForm();
    try {
        headless = Boolean.parseBoolean(form.getFirstValue("headless"));
    } catch (Exception x) {
        headless = false;
    }
    AbstractReadDataset query = null;
    structureParam = getStructureParameter();
    StringCondition condition;
    try {
        condition = StringCondition.getInstance(form.getFirstValue(QueryResource.condition));
    } catch (Exception x) {
        condition = StringCondition.getInstance(StringCondition.C_EQ);
    }
    Property property = new Property(null);
    property.setClazz(null);
    property.setLabel(null);
    property.setReference(null);
    for (search_features sf : search_features.values()) {
        Object id = form.getFirstValue(sf.name());
        if (id != null) {
            // because we are not storing full local references!
            if (search_features.feature_hassource.equals(sf)) {
                String parent = getRequest().getRootRef().toString();
                int p = id.toString().indexOf(parent);
                if (p >= 0) {
                    // yet one more hack ... should store at least prefixes
                    id = id.toString().substring(p + parent.length()).replace("/algorithm/", "").replace("/model/", "");
                }
            }
            sf.setProperty(property, id);
            if (query == null) {
                query = new QueryDatasetByFeatures(property, condition);
                ((QueryDatasetByFeatures) query).setStructure(structureParam);
            }
        }
    }
    if (query == null) {
        query = new ReadDataset();
        query.setValue(null);
    }
    Object id = request.getAttributes().get(DatasetStructuresResource.datasetKey);
    if (id != null)
        try {
            Integer idnum = new Integer(Reference.decode(id.toString()));
            dataset = (M) new SourceDataset();
            dataset.setID(idnum);
            query.setValue(dataset);
        } catch (NumberFormatException x) {
            if (id.toString().startsWith(DatasetStructuresResource.QR_PREFIX)) {
                String key = id.toString().substring(DatasetStructuresResource.QR_PREFIX.length());
                try {
                    IQueryRetrieval<M> q = (IQueryRetrieval<M>) new ReadStoredQuery(Integer.parseInt(key.toString()));
                    return q;
                } catch (NumberFormatException xx) {
                    throw new InvalidResourceIDException(id);
                }
            } else {
                dataset = (M) new SourceDataset();
                dataset.setName(id.toString());
                query.setValue(dataset);
            }
        } catch (Exception x) {
            throw new InvalidResourceIDException(id);
        }
    if (!IDcanBeEmpty && (query.getValue() == null))
        throw new ResourceException(Status.CLIENT_ERROR_BAD_REQUEST, "Empty dataset ID!");
    return query;
}

Example 2 with ReadDataset

use of ambit2.db.update.dataset.ReadDataset in project ambit-mirror by ideaconsult.

the class CallableSubstanceImporter method createReference.

@Override
protected TaskResult createReference(Connection connection) throws Exception {
    if ((importedRecord.getIdsubstance() > 0) || (importedRecord.getSubstanceUUID() != null)) {
        try {
            batch.close();
        } catch (Exception xx) {
        }
        try {
            if (file != null && file.exists())
                file.delete();
        } catch (Exception x) {
        }
        return new TaskResult(substanceReporter.getURI(importedRecord));
    } else {
        SourceDataset newDataset = dataset;
        if (newDataset.getId() <= 0) {
            ReadDataset q = new ReadDataset();
            q.setValue(newDataset);
            QueryExecutor<ReadDataset> x = new QueryExecutor<ReadDataset>();
            x.setConnection(connection);
            ResultSet rs = x.process(q);
            while (rs.next()) {
                newDataset = q.getObject(rs);
                if (newDataset.getId() > 0)
                    break;
            }
            x.closeResults(rs);
            x.setConnection(null);
        }
        if (newDataset == null || newDataset.getId() <= 0)
            throw new ResourceException(Status.SUCCESS_NO_CONTENT);
        try {
            batch.close();
        } catch (Exception xx) {
        }
        try {
            if (file != null && file.exists())
                file.delete();
        } catch (Exception x) {
        }
        return new TaskResult(datasetURIReporter.getURI(newDataset));
    }
}

Example 3 with ReadDataset

use of ambit2.db.update.dataset.ReadDataset in project ambit-mirror by ideaconsult.

the class CallableFileImport method importFile.

public TaskResult importFile(File file) throws Exception {
    try {
        // if target dataset is not defined, create new dataset
        final SourceDataset dataset = targetDataset != null ? targetDataset : datasetMeta(file);
        if (targetDataset == null)
            dataset.setId(-1);
        final BatchDBProcessor<String> batch = new BatchDBProcessor<String>() {

            /**
             */
            private static final long serialVersionUID = -7971761364143510120L;

            @Override
            public Iterator<String> getIterator(IInputState target) throws AmbitException {
                try {
                    File file = ((FileInputState) target).getFile();
                    RDFIteratingReader i = getRDFIterator(file, getReporter().getBaseReference().toString());
                    if (i == null) {
                        IIteratingChemObjectReader ni = getNanoCMLIterator(file, getReporter().getBaseReference().toString());
                        if (ni == null)
                            return super.getIterator(target);
                        else
                            return ni;
                    } else {
                        /*
			     * RDFMetaDatasetIterator datasets = null; try {
			     * datasets = new
			     * RDFMetaDatasetIterator(i.getJenaModel());
			     * datasets
			     * .setBaseReference(getReporter().getBaseReference
			     * ()); while (datasets.hasNext()) { SourceDataset d
			     * = datasets.next(); dataset.setId(d.getId());
			     * dataset.setName(d.getName());
			     * dataset.setTitle(d.getTitle());
			     * dataset.setURL(d.getURL()); } } catch (Exception
			     * x) { x.printStackTrace(); } finally { try {
			     * datasets.close();} catch (Exception x) {} }
			     */
                        return i;
                    }
                } catch (AmbitException x) {
                    throw x;
                } catch (Exception x) {
                    throw new AmbitException(x);
                }
            }

            @Override
            public void onItemProcessed(String input, Object output, IBatchStatistics stats) {
                super.onItemProcessed(input, output, stats);
                if (firstCompoundOnly && (stats.getRecords(RECORDS_STATS.RECORDS_PROCESSED) >= 1)) {
                    cancelled = true;
                    if (output != null)
                        if ((output instanceof ArrayList) && ((ArrayList) output).size() > 0) {
                            if (((ArrayList) output).get(0) instanceof IStructureRecord)
                                recordImported = (IStructureRecord) ((ArrayList) output).get(0);
                        } else if (output instanceof IStructureRecord)
                            recordImported = (IStructureRecord) output;
                }
            }
        };
        batch.setReference(dataset.getReference());
        batch.setConnection(connection);
        final RepositoryWriter writer = new RepositoryWriter();
        writer.setUseExistingStructure(isPropertyOnly());
        writer.setPropertyKey(getMatcher());
        writer.setDataset(dataset);
        final ProcessorsChain<String, IBatchStatistics, IProcessor> chain = new ProcessorsChain<String, IBatchStatistics, IProcessor>();
        chain.add(writer);
        batch.setProcessorChain(chain);
        writer.setConnection(connection);
        FileInputState fin = new FileInputState(file);
        IBatchStatistics stats = batch.process(fin);
        if (firstCompoundOnly) {
            if (recordImported == null)
                throw new Exception("No compound imported");
            if (compoundReporter == null)
                compoundReporter = new ConformerURIReporter("", null, false);
            try {
                batch.close();
            } catch (Exception xx) {
            }
            return new TaskResult(compoundReporter.getURI(recordImported));
        } else {
            ReadDataset q = new ReadDataset();
            q.setValue(dataset);
            QueryExecutor<ReadDataset> x = new QueryExecutor<ReadDataset>();
            x.setConnection(connection);
            ResultSet rs = x.process(q);
            ISourceDataset newDataset = null;
            while (rs.next()) {
                newDataset = q.getObject(rs);
                break;
            }
            x.closeResults(rs);
            x.setConnection(null);
            if (newDataset == null)
                throw new ResourceException(Status.SUCCESS_NO_CONTENT);
            if (reporter == null)
                reporter = new DatasetURIReporter<IQueryRetrieval<ISourceDataset>, ISourceDataset>();
            try {
                batch.close();
            } catch (Exception xx) {
            }
            return new TaskResult(reporter.getURI(newDataset));
        }
    } catch (ResourceException x) {
        throw x;
    } catch (Exception x) {
        throw new ResourceException(new Status(Status.SERVER_ERROR_INTERNAL, x.getMessage()));
    } finally {
        try {
            connection.close();
        } catch (Exception x) {
        }
        connection = null;
    }
}

Example 4 with ReadDataset

use of ambit2.db.update.dataset.ReadDataset in project ambit-mirror by ideaconsult.

the class CallableFinder method getDataset.

protected SourceDataset getDataset(SourceDataset dataset) {
    QueryExecutor exec = new QueryExecutor();
    Connection connection = null;
    try {
        ReadDataset q = new ReadDataset();
        q.setPage(0);
        q.setPageSize(1);
        q.setValue(dataset);
        DBConnection dbc = new DBConnection(context);
        connection = dbc.getConnection();
        exec.setConnection(connection);
        ResultSet rs = exec.process(q);
        while (rs.next()) {
            dataset = q.getObject(rs);
        }
        try {
            exec.closeResults(rs);
        } catch (Exception x) {
        }
        ;
    } catch (Exception x) {
    // if failed will return the original dataset
    } finally {
        try {
            exec.close();
        } catch (Exception x) {
        }
        ;
        try {
            connection.close();
        } catch (Exception x) {
        }
        ;
    }
    return dataset;
}

Example 5 with ReadDataset

use of ambit2.db.update.dataset.ReadDataset in project ambit-mirror by ideaconsult.

the class DbStructureWriter method writeDataset.

protected void writeDataset(IStructureRecord structure) throws SQLException, AmbitException, OperationNotSupportedException {
    if (getDataset() == null)
        setDataset(new SourceDataset("Default"));
    if (getDataset().getID() <= 0) {
        if (readDatasetQuery == null)
            readDatasetQuery = new ReadDataset();
        readDatasetQuery.setValue(getDataset());
        readDatasetQuery.setCondition(StringCondition.getInstance(StringCondition.C_EQ));
        readDatasetQuery.setPageSize(2);
        readDatasetQuery.setPage(0);
        ResultSet rs = null;
        try {
            rs = queryexec.process(readDatasetQuery);
            // should be 1 only
            int record = 0;
            while (rs.next()) {
                SourceDataset d = readDatasetQuery.getObject(rs);
                getDataset().setID(d.getID());
                record++;
            }
            if (record > 1)
                // smth is wrong
                getDataset().setID(-1);
        } catch (Exception x) {
            getDataset().setID(-1);
        }
    }
    datasetAddStruc.setObject(structure);
    datasetAddStruc.setGroup(dataset);
    try {
        exec.process(datasetAddStruc);
    } catch (Exception x) {
        logger.log(Level.SEVERE, String.format("Error %s adding structure /compound/%d/conformer/%d to dataset [%d] %s", x.getMessage(), structure.getIdchemical(), structure.getIdstructure(), dataset.getId(), dataset.getName()));
        throw new AmbitException(x);
    }
    propertyWriter.setDataset(dataset);
}