Examples of SampleObject

eu.planets_project.pp.plato.model.SampleObject
Encapsulates a sample record that we want to use for testing and evaluating Alternatives. At the moment, this data will be uploaded and saved through this object. Later we will want to allow references to repository data. @author Christoph Becker
eu.scape_project.planning.model.SampleObject
Encapsulates a sample record that we want to use for testing and evaluating Alternatives. At the moment, this data will be uploaded and saved through this object. Later we will want to allow references to repository data. @author Christoph Becker
whitedb.holder.SampleObject

Examples of eu.scape_project.planning.model.SampleObject

     * Determines if there is at least one sample with format info.
     * 
     * @return true if a sample with format info is available
     */
    public boolean isMimetypeAvailable() {
        SampleObject sample = getSampleWithFormat();
        return isFormatInfoAvailable() && sample.getFormatInfo().getMimeType() != null
            && !"".equals(sample.getFormatInfo().getMimeType());
    }

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Examples of eu.scape_project.planning.model.SampleObject

            setProgramOutputForAlternative(a, msg, false);
        }


        if (action instanceof IMigrationAction) {
            IMigrationAction migrationAction = (IMigrationAction) action;
            SampleObject record = experimentStatus.getNextSample();
            while (record != null) {
                if (record.isDataExistent()) {
                    MigrationResult migrationResult = null;


                    try {
                        DigitalObject workflow = a.getExperiment().getWorkflow();
                        if (workflow != null) {

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Examples of eu.scape_project.planning.model.SampleObject

     * @param sampleObj
     *            Experiment sample object.
     */
    public void updateSelectedDetailedExperimentInfo(Object alt, Object sampleObj) {
        Alternative alternative = (Alternative) alt;
        SampleObject sampleObject = (SampleObject) sampleObj;


        selectedDetailedExperimentInfo = alternative.getExperiment().getDetailedInfo().get(sampleObject);
    }

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Examples of eu.scape_project.planning.model.SampleObject

     * @param sampleObj
     *            SampleObject corresponding to the next file-upload.
     */
    public void updateDataForNextUpload(Object alt, Object sampleObj) {
        Alternative alternative = (Alternative) alt;
        SampleObject sampleObject = (SampleObject) sampleObj;


        alternativeForNextUpload = alternative;
        sampleObjectForNextUpload = sampleObject;
    }

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Examples of eu.scape_project.planning.model.SampleObject

     * @param sampleObj
     *            SampleObject of the wanted result file.
     */
    public void downloadResultFile(Object alt, Object sampleObj) {
        Alternative alternative = (Alternative) alt;
        SampleObject sampleObject = (SampleObject) sampleObj;


        DigitalObject resultFile = null;


        try {
            resultFile = runExperiments.fetchResultFile(alternative, sampleObject);
        } catch (StorageException e) {
            log.error("Exception at trying to fetch result file for alternative " + alternative.getName()
                + "and sample " + sampleObject.getFullname(), e);
            facesMessages.addError("Unable to fetch result file. Please try again.");
        }


        if (resultFile != null) {
            downloader.download(resultFile);
        } else {
            log.debug("No result file exists for alternative " + alternative.getName() + " and sample "
                + sampleObject.getFullname() + ".");
        }
    }

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Examples of eu.scape_project.planning.model.SampleObject

     * @param sampleObj
     *            Sample the file was uploaded for.
     */
    public void removeResultFile(Object alt, Object sampleObj) {
        Alternative alternative = (Alternative) alt;
        SampleObject sampleObject = (SampleObject) sampleObj;


        runExperiments.removeResultFile(alternative, sampleObject);
    }

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Examples of eu.scape_project.planning.model.SampleObject


        samplesToRemove.clear();
    }


    public SampleObject addSample(String filename, String contentType, byte[] data) throws PlanningException {
        SampleObject sample = new SampleObject(filename);
        sample.setFullname(filename);
        sample.setContentType(contentType);


        ByteStream bsData = new ByteStream();
        bsData.setData(data);
        sample.setData(bsData);


        digitalObjectManager.moveDataToStorage(sample);
        addedBytestreams.add(sample.getPid());
        plan.getSampleRecordsDefinition().addRecord(sample);


        // identify format of newly uploaded samples
        if (shouldCharacterise(sample)) {
            characteriseFits(sample);
        }


        log.debug("Content-Type: " + sample.getContentType());
        log.debug("Size of samples Array: " + plan.getSampleRecordsDefinition().getRecords().size());
        log.debug("FileName: " + sample.getFullname());
        log.debug("Length of File: " + sample.getData().getSize());
        log.debug("added SampleObject: " + sample.getFullname());
        log.debug("JHove initialized: " + (sample.getJhoveXMLString() != null));


        return sample;
    }

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Examples of eu.scape_project.planning.model.SampleObject


        /*
         * map sample records to uploads and their xcdlDescriptions, if present
         */
        for (String key : tempUploads.keySet()) {
            SampleObject rec = records.get(key);
            if (rec != null) {
                DigitalObject result = tempUploads.get(key);
                getResults().put(rec, result);
            }
        }


        /*
         * map sample records to detailedInfos
         */
        for (String key : tempDetailedInfos.keySet()) {
            SampleObject rec = records.get(key);
            if (rec != null) {
                getDetailedInfo().put(rec, tempDetailedInfos.get(key));
            }
        }

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Examples of eu.scape_project.planning.model.SampleObject

        experiment.setDescription("Description");
        experiment.setSettings("Settings");
        experiment.setWorkflow(generateDigitalObject());


        Map<SampleObject, DetailedExperimentInfo> detailedInfo = experiment.getDetailedInfo();
        SampleObject sample1 = new SampleObject("Short name");
        DetailedExperimentInfo experimentInfo1 = new DetailedExperimentInfo();
        experimentInfo1.setSuccessful(true);
        experimentInfo1.setCpr("Cpr");
        experimentInfo1.setProgramOutput("Program output");
        experimentInfo1.getMeasurements().put("key", new Measurement("Measure id", "Value"));

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Examples of eu.scape_project.planning.model.SampleObject

    }


    private SampleObject parseSample(Element sample) {


        String uid = sample.attributeValue("uid");
        SampleObject sampleObject = new SampleObject(uid);
        sampleObject.setFullname(uid);
        List<Element> mimes = new ArrayList<Element>();
        List<Element> size = new ArrayList<Element>();
        List<Element> records = sample.elements("record");


        for (Element rec : records) {
            if (rec.attributeValue("name").equals("mimetype")) {
                mimes.add(rec);
            }


            if (rec.attributeValue("name").equals("size")) {
                size.add(rec);
            }
        }


        if (mimes.size() > 1) {
            sampleObject.setContentType("Conflict");
        } else if (mimes.size() == 1) {
            Element mimetype = (Element) mimes.get(0);
            sampleObject.setContentType(mimetype.attributeValue("value"));
        }


        if (size.size() == 1) {
            Element s = (Element) size.get(0);
            sampleObject.setSizeInBytes(Long.parseLong(s.attributeValue("value")));
        }


        FormatInfo info = this.getFormatInfo(sample, sampleObject.getContentType());
        sampleObject.setFormatInfo(info);


        return sampleObject;
    }

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