Example usage for com.mongodb BasicDBObject getString

List of usage examples for com.mongodb BasicDBObject getString

  1. HOME
  2. Java
  3. com.mongodb
  4. com.mongodb.*
  5. BasicDBObject
  6. getString

Introduction

In this page you can find the example usage for com.mongodb BasicDBObject getString.

Prototype

public String getString(final String key)

Source Link

Document

Returns the value of a field as a string

Usage

From source file:tango.plugin.filter.PostFilterSequence.java

License:Open Source License

public PostFilterSequence(BasicDBObject type, int nbCPUs, boolean verbose) {
    if (type == null || !type.containsField("postFilters"))
        return;//from  w  w  w  . jav  a  2 s  . com
    BasicDBList prefilters = (BasicDBList) type.get("postFilters");
    filters = new ArrayList<PostFilter>(prefilters.size());
    for (int i = 0; i < prefilters.size(); i++) {
        Object o = prefilters.get(i);
        if (o != null) {
            BasicDBObject data = (BasicDBObject) o;
            if (!data.getBoolean("isActivated", true)) {
                filters.add(new DummyPostFilter());
                continue;
            }
            PostFilter f = PluginFactory.getPostFilter(data.getString("method"));
            if (f != null) {
                Parameter[] parameters = f.getParameters();
                for (Parameter p : parameters)
                    p.dbGet(data);
                filters.add(f);
                f.setMultithread(nbCPUs);
                f.setVerbose(verbose);
            }
        }
    }
}

From source file:tango.plugin.filter.PreFilterSequence.java

License:Open Source License

public PreFilterSequence(BasicDBObject settings, int nbCPUs, boolean verbose) {
    if (settings == null || !settings.containsField("preFilters"))
        return;//from ww w  .  j a  va2 s  .  c  om
    BasicDBList prefilters = (BasicDBList) settings.get("preFilters");
    filters = new ArrayList<PreFilter>(prefilters.size());
    for (int i = 0; i < prefilters.size(); i++) {
        //IJ.log(i+"");
        Object o = prefilters.get(i);
        if (o != null) {
            BasicDBObject data = (BasicDBObject) o;
            //IJ.log("preFilter:"+data);
            if (!data.getBoolean("isActivated", true)) {
                filters.add(new DummyPreFilter());
                continue;
            }
            PreFilter f = PluginFactory.getPreFilter(data.getString("method"));
            if (f != null) {
                //IJ.log("preFilter loaded:"+f.getId());
                Parameter[] parameters = f.getParameters();
                for (Parameter p : parameters)
                    p.dbGet(data);
                filters.add(f);
                f.setMultithread(nbCPUs);
                f.setVerbose(verbose);
            }
        }
    }
}

From source file:tango.plugin.measurement.MeasurementSequence.java

License:Open Source License

protected void addMeasurement(Object o) {
    if (o != null) {
        BasicDBObject data = (BasicDBObject) o;
        if (!data.getBoolean("isActivated", true))
            return;
        Measurement m = PluginFactory.getMeasurement(data.getString("method"));
        if (m != null) {
            for (Parameter p : m.getParameters()) {
                //System.out.println("parameter:"+p.getClass()+ " id:"+p.getId()+ " label:"+p.getLabel());
                p.dbGet(data);/*from  w  w  w .j  av  a  2  s.  c o  m*/
            }
            Parameter[] keys = m.getKeys();
            Object kData = data.get("keys");
            if (keys != null && kData != null) {
                BasicDBObject keysData = (BasicDBObject) kData;
                for (Parameter p : keys)
                    p.dbGet(keysData);
            }
            if (m instanceof MeasurementObject) {
                mO.add((MeasurementObject) m);
            } else if (m instanceof MeasurementStructure) {
                mS.add((MeasurementStructure) m);
            }

        }
    }
}

From source file:tango.plugin.sampler.SampleRunner.java

License:Open Source License

private static Object3D[][][] runCell(Cell cell, int nbSamples) {
    BasicDBList sampleChannels = cell.getExperiment().getSampleChannels();
    int nbSampleChannels = sampleChannels.size();
    Object3D[][][] objects = new Object3D[nbSampleChannels][nbSamples][];
    for (int i = 0; i < nbSampleChannels; i++) {
        BasicDBObject sampleSettings = (BasicDBObject) sampleChannels.get(i);
        Sampler s = PluginFactory.getSampler(sampleSettings.getString("method"));
        for (Parameter p : s.getParameters())
            p.dbGet(sampleSettings);/*from w w  w.j av  a  2  s.c  o m*/
        s.initSampler(cell.getRawImages(), cell.getSegmentedImages());
        for (int j = 0; j < nbSamples; j++)
            objects[i][j] = s.getSample();
    }
    return objects;
}

From source file:tango.plugin.segmenter.NucleusSegmenterRunner.java

License:Open Source License

public NucleusSegmenterRunner(BasicDBObject settings, int nbCPUs, boolean verbose) {
    if (settings == null)
        return;/*from   w ww  .  j  a v a  2s .c o  m*/
    Object o = settings.get("segmentation");
    if (o != null) {
        BasicDBObject data = (BasicDBObject) o;

        segmenter = PluginFactory.getNucleiSegmenter(data.getString("method"));
        if (segmenter != null) {
            Parameter[] parameters = segmenter.getParameters();
            for (Parameter p : parameters)
                p.dbGet(data);
            segmenter.setMultithread(nbCPUs);
            segmenter.setVerbose(verbose);
        }
    }
}

From source file:tango.plugin.segmenter.SpotSegmenterRunner.java

License:Open Source License

public SpotSegmenterRunner(BasicDBObject type, int nbCPUs, boolean verbose) {
    if (type == null)
        return;//from   ww  w.j  ava 2 s  .c  om
    Object o = type.get("segmentation");
    if (o != null) {
        BasicDBObject data = (BasicDBObject) o;
        segmenter = PluginFactory.getSpotSegmenter(data.getString("method"));
        if (segmenter != null) {
            Parameter[] parameters = segmenter.getParameters();
            for (Parameter p : parameters)
                p.dbGet(data);
            segmenter.setMultithread(nbCPUs);
            segmenter.setVerbose(verbose);
        }
    }
}

From source file:uk.ac.ebi.eva.server.ws.StudyWSServer.java

License:Apache License

@RequestMapping(value = "/{study}/files", method = RequestMethod.GET)
//    @ApiOperation(httpMethod = "GET", value = "Retrieves all the files from a study", response = QueryResponse.class)
public QueryResponse getFilesByStudy(@PathVariable("study") String study,
        @RequestParam("species") String species, HttpServletResponse response)
        throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
    initializeQueryOptions();/* w  ww . java2s.  c  o  m*/

    StudyDBAdaptor studyMongoDbAdaptor = DBAdaptorConnector.getStudyDBAdaptor(species);
    VariantSourceDBAdaptor variantSourceDbAdaptor = DBAdaptorConnector.getVariantSourceDBAdaptor(species);

    QueryResult idQueryResult = studyMongoDbAdaptor.findStudyNameOrStudyId(study, queryOptions);
    if (idQueryResult.getNumResults() == 0) {
        QueryResult queryResult = new QueryResult();
        queryResult.setErrorMsg("Study identifier not found");
        response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
        return setQueryResponse(queryResult);
    }

    BasicDBObject id = (BasicDBObject) idQueryResult.getResult().get(0);
    QueryResult finalResult = variantSourceDbAdaptor
            .getAllSourcesByStudyId(id.getString(DBObjectToVariantSourceConverter.STUDYID_FIELD), queryOptions);
    finalResult.setDbTime(finalResult.getDbTime() + idQueryResult.getDbTime());

    return setQueryResponse(finalResult);
}

From source file:uk.ac.ebi.eva.server.ws.StudyWSServer.java

License:Apache License

@RequestMapping(value = "/{study}/view", method = RequestMethod.GET)
//    @ApiOperation(httpMethod = "GET", value = "The info of a study", response = QueryResponse.class)
public QueryResponse getStudy(@PathVariable("study") String study,
        @RequestParam(name = "species") String species, HttpServletResponse response)
        throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
    initializeQueryOptions();//w  ww .  ja  v a2 s . c om

    StudyDBAdaptor studyMongoDbAdaptor = DBAdaptorConnector.getStudyDBAdaptor(species);

    QueryResult idQueryResult = studyMongoDbAdaptor.findStudyNameOrStudyId(study, queryOptions);
    if (idQueryResult.getNumResults() == 0) {
        QueryResult queryResult = new QueryResult();
        queryResult.setErrorMsg("Study identifier not found");
        response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
        return setQueryResponse(queryResult);
    }

    BasicDBObject id = (BasicDBObject) idQueryResult.getResult().get(0);
    QueryResult finalResult = studyMongoDbAdaptor
            .getStudyById(id.getString(DBObjectToVariantSourceConverter.STUDYID_FIELD), queryOptions);
    finalResult.setDbTime(finalResult.getDbTime() + idQueryResult.getDbTime());

    return setQueryResponse(finalResult);
}

From source file:uk.ac.ebi.variation.eva.server.ws.StudyWSServer.java

License:Apache License

@GET
@Path("/{study}/files")
//    @ApiOperation(httpMethod = "GET", value = "Retrieves all the files from a study", response = QueryResponse.class)
public Response getFilesByStudy(@PathParam("study") String study, @QueryParam("species") String species)
        throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
    try {/*from www.  j  a va 2s .c om*/
        checkParams();
    } catch (VersionException | SpeciesException ex) {
        return createErrorResponse(ex.toString());
    }

    StudyDBAdaptor studyMongoDbAdaptor = DBAdaptorConnector.getStudyDBAdaptor(species);
    VariantSourceDBAdaptor variantSourceDbAdaptor = DBAdaptorConnector.getVariantSourceDBAdaptor(species);

    QueryResult idQueryResult = studyMongoDbAdaptor.findStudyNameOrStudyId(study, queryOptions);
    if (idQueryResult.getNumResults() == 0) {
        QueryResult queryResult = new QueryResult();
        queryResult.setErrorMsg("Study identifier not found");
        return createOkResponse(queryResult);
    }

    BasicDBObject id = (BasicDBObject) idQueryResult.getResult().get(0);
    QueryResult finalResult = variantSourceDbAdaptor
            .getAllSourcesByStudyId(id.getString(DBObjectToVariantSourceConverter.STUDYID_FIELD), queryOptions);
    finalResult.setDbTime(finalResult.getDbTime() + idQueryResult.getDbTime());

    return createOkResponse(finalResult);
}

From source file:uk.ac.ebi.variation.eva.server.ws.StudyWSServer.java

License:Apache License

@GET
@Path("/{study}/view")
//    @ApiOperation(httpMethod = "GET", value = "The info of a study", response = QueryResponse.class)
public Response getStudy(@PathParam("study") String study, @QueryParam("species") String species)
        throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
    try {//w  w w .j  av a  2 s.  co m
        checkParams();
    } catch (VersionException | SpeciesException ex) {
        return createErrorResponse(ex.toString());
    }

    StudyDBAdaptor studyMongoDbAdaptor = DBAdaptorConnector.getStudyDBAdaptor(species);

    QueryResult idQueryResult = studyMongoDbAdaptor.findStudyNameOrStudyId(study, queryOptions);
    if (idQueryResult.getNumResults() == 0) {
        QueryResult queryResult = new QueryResult();
        queryResult.setErrorMsg("Study identifier not found");
        return createOkResponse(queryResult);
    }

    BasicDBObject id = (BasicDBObject) idQueryResult.getResult().get(0);
    QueryResult finalResult = studyMongoDbAdaptor
            .getStudyById(id.getString(DBObjectToVariantSourceConverter.STUDYID_FIELD), queryOptions);
    finalResult.setDbTime(finalResult.getDbTime() + idQueryResult.getDbTime());

    return createOkResponse(finalResult);
}