Examples with ComplexData org.openmrs.obs.ComplexData used on opensource projects

Example 6 with ComplexData

use of org.openmrs.obs.ComplexData in project openmrs-core by openmrs.

the class ObsServiceTest method saveObs_shouldCreateNewFileFromComplexDataForNewObs.

/**
 * @see ObsService#saveObs(Obs,String)
 */
@Test
public void saveObs_shouldCreateNewFileFromComplexDataForNewObs() {
    executeDataSet(COMPLEX_OBS_XML);
    ObsService os = Context.getObsService();
    ConceptService cs = Context.getConceptService();
    AdministrationService as = Context.getAdministrationService();
    // make sure the file isn't there to begin with
    File complexObsDir = OpenmrsUtil.getDirectoryInApplicationDataDirectory(as.getGlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_COMPLEX_OBS_DIR));
    File createdFile = new File(complexObsDir, "nameOfFile.txt");
    if (createdFile.exists())
        createdFile.delete();
    // the complex data to put onto an obs that will be saved
    Reader input = new CharArrayReader("This is a string to save to a file".toCharArray());
    ComplexData complexData = new ComplexData("nameOfFile.txt", input);
    // must fetch the concept instead of just new Concept(8473) because the attributes on concept are checked
    // this is a concept mapped to the text handler
    Concept questionConcept = cs.getConcept(8474);
    Obs obsToSave = new Obs(new Person(1), questionConcept, new Date(), new Location(1));
    obsToSave.setComplexData(complexData);
    try {
        os.saveObs(obsToSave, null);
        // make sure the file appears now after the save
        Assert.assertTrue(createdFile.exists());
    } finally {
        // we always have to delete this inside the same unit test because it is outside the
        // database and hence can't be "rolled back" like everything else
        createdFile.delete();
    }
}

Example 7 with ComplexData

use of org.openmrs.obs.ComplexData in project openmrs-core by openmrs.

the class ObsServiceImpl method handleExistingObsWithComplexConcept.

private void handleExistingObsWithComplexConcept(Obs obs) {
    ComplexData complexData = obs.getComplexData();
    Concept concept = obs.getConcept();
    if (null != concept && concept.isComplex() && null != complexData && null != complexData.getData()) {
        // save or update complexData object on this obs
        // this is done before the database save so that the obs.valueComplex
        // can be filled in by the handler.
        ComplexObsHandler handler = getHandler(obs);
        if (null != handler) {
            handler.saveObs(obs);
        } else {
            throw new APIException("unknown.handler", new Object[] { concept });
        }
    }
}

Example 8 with ComplexData

use of org.openmrs.obs.ComplexData in project openmrs-core by openmrs.

the class ORUR01Handler method parseObs.

/**
 * Creates the Obs pojo from the OBX message
 *
 * @param encounter The Encounter object this Obs is a member of
 * @param obx The hl7 obx message
 * @param obr The parent hl7 or message
 * @param uid unique string for this message for any error reporting purposes
 * @return Obs pojo with all values filled in
 * @throws HL7Exception if there is a parsing exception
 * @throws ProposingConceptException if the answer to this obs is a proposed concept
 * @should add comments to an observation from NTE segments
 * @should add multiple comments for an observation as one comment
 * @should add comments to an observation group
 */
private Obs parseObs(Encounter encounter, OBX obx, OBR obr, String uid) throws HL7Exception, ProposingConceptException {
    if (log.isDebugEnabled()) {
        log.debug("parsing observation: " + obx);
    }
    Varies[] values = obx.getObservationValue();
    // bail out if no values were found
    if (values == null || values.length < 1) {
        return null;
    }
    String hl7Datatype = values[0].getName();
    if (log.isDebugEnabled()) {
        log.debug("  datatype = " + hl7Datatype);
    }
    Concept concept = getConcept(obx.getObservationIdentifier(), uid);
    if (log.isDebugEnabled()) {
        log.debug("  concept = " + concept.getConceptId());
    }
    ConceptName conceptName = getConceptName(obx.getObservationIdentifier());
    if (log.isDebugEnabled()) {
        log.debug("  concept-name = " + conceptName);
    }
    Date datetime = getDatetime(obx);
    if (log.isDebugEnabled()) {
        log.debug("  timestamp = " + datetime);
    }
    if (datetime == null) {
        datetime = encounter.getEncounterDatetime();
    }
    Obs obs = new Obs();
    obs.setPerson(encounter.getPatient());
    obs.setConcept(concept);
    obs.setEncounter(encounter);
    obs.setObsDatetime(datetime);
    obs.setLocation(encounter.getLocation());
    obs.setCreator(encounter.getCreator());
    obs.setDateCreated(encounter.getDateCreated());
    // set comments if there are any
    StringBuilder comments = new StringBuilder();
    ORU_R01_OBSERVATION parent = (ORU_R01_OBSERVATION) obx.getParent();
    // iterate over all OBX NTEs
    for (int i = 0; i < parent.getNTEReps(); i++) {
        for (FT obxComment : parent.getNTE(i).getComment()) {
            if (comments.length() > 0) {
                comments.append(" ");
            }
            comments = comments.append(obxComment.getValue());
        }
    }
    // only set comments if there are any
    if (StringUtils.hasText(comments.toString())) {
        obs.setComment(comments.toString());
    }
    Type obx5 = values[0].getData();
    if ("NM".equals(hl7Datatype)) {
        String value = ((NM) obx5).getValue();
        if (value == null || value.length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        } else if ("0".equals(value) || "1".equals(value)) {
            concept = concept.hydrate(concept.getConceptId().toString());
            obs.setConcept(concept);
            if (concept.getDatatype().isBoolean()) {
                obs.setValueBoolean("1".equals(value));
            } else if (concept.getDatatype().isNumeric()) {
                try {
                    obs.setValueNumeric(Double.valueOf(value));
                } catch (NumberFormatException e) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
                }
            } else if (concept.getDatatype().isCoded()) {
                Concept answer = "1".equals(value) ? Context.getConceptService().getTrueConcept() : Context.getConceptService().getFalseConcept();
                boolean isValidAnswer = false;
                Collection<ConceptAnswer> conceptAnswers = concept.getAnswers();
                if (conceptAnswers != null && !conceptAnswers.isEmpty()) {
                    for (ConceptAnswer conceptAnswer : conceptAnswers) {
                        if (conceptAnswer.getAnswerConcept().getId().equals(answer.getId())) {
                            obs.setValueCoded(answer);
                            isValidAnswer = true;
                            break;
                        }
                    }
                }
                // answer the boolean answer concept was't found
                if (!isValidAnswer) {
                    throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.invalidAnswer", new Object[] { answer.toString(), uid }, null));
                }
            } else {
                // throw this exception to make sure that the handler doesn't silently ignore bad hl7 message
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.CannotSetBoolean", new Object[] { obs.getConcept().getConceptId() }, null));
            }
        } else {
            try {
                obs.setValueNumeric(Double.valueOf(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.notnumericConcept", new Object[] { value, concept.getConceptId(), conceptName.getName(), uid }, null), e);
            }
        }
    } else if ("CWE".equals(hl7Datatype)) {
        log.debug("  CWE observation");
        CWE value = (CWE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        log.debug("    value id = " + valueIdentifier);
        String valueName = value.getText().getValue();
        log.debug("    value name = " + valueName);
        if (isConceptProposal(valueIdentifier)) {
            if (log.isDebugEnabled()) {
                log.debug("Proposing concept");
            }
            throw new ProposingConceptException(concept, valueName);
        } else {
            log.debug("    not proposal");
            try {
                Concept valueConcept = getConcept(value, uid);
                obs.setValueCoded(valueConcept);
                if (HL7Constants.HL7_LOCAL_DRUG.equals(value.getNameOfAlternateCodingSystem().getValue())) {
                    Drug valueDrug = new Drug();
                    valueDrug.setDrugId(Integer.valueOf(value.getAlternateIdentifier().getValue()));
                    obs.setValueDrug(valueDrug);
                } else {
                    ConceptName valueConceptName = getConceptName(value);
                    if (valueConceptName != null) {
                        if (log.isDebugEnabled()) {
                            log.debug("    value concept-name-id = " + valueConceptName.getConceptNameId());
                            log.debug("    value concept-name = " + valueConceptName.getName());
                        }
                        obs.setValueCodedName(valueConceptName);
                    }
                }
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
        if (log.isDebugEnabled()) {
            log.debug("  Done with CWE");
        }
    } else if ("CE".equals(hl7Datatype)) {
        CE value = (CE) obx5;
        String valueIdentifier = value.getIdentifier().getValue();
        String valueName = value.getText().getValue();
        if (isConceptProposal(valueIdentifier)) {
            throw new ProposingConceptException(concept, valueName);
        } else {
            try {
                obs.setValueCoded(getConcept(value, uid));
                obs.setValueCodedName(getConceptName(value));
            } catch (NumberFormatException e) {
                throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.InvalidConceptId", new Object[] { valueIdentifier, valueName }, null));
            }
        }
    } else if ("DT".equals(hl7Datatype)) {
        DT value = (DT) obx5;
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), 0, 0, 0);
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TS".equals(hl7Datatype)) {
        DTM value = ((TS) obx5).getTime();
        if (value != null) {
            Date valueDate = getDate(value.getYear(), value.getMonth(), value.getDay(), value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueDate);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("TM".equals(hl7Datatype)) {
        TM value = (TM) obx5;
        if (value != null) {
            Date valueTime = getDate(0, 0, 0, value.getHour(), value.getMinute(), value.getSecond());
            obs.setValueDatetime(valueTime);
        } else {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
    } else if ("ST".equals(hl7Datatype)) {
        ST value = (ST) obx5;
        if (value == null || value.getValue() == null || value.getValue().trim().length() == 0) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        obs.setValueText(value.getValue());
    } else if ("ED".equals(hl7Datatype)) {
        ED value = (ED) obx5;
        if (value == null || value.getData() == null || !StringUtils.hasText(value.getData().getValue())) {
            log.warn("Not creating null valued obs for concept " + concept);
            return null;
        }
        // we need to hydrate the concept so that the EncounterSaveHandler
        // doesn't fail since it needs to check if it is a concept numeric
        Concept c = Context.getConceptService().getConcept(obs.getConcept().getConceptId());
        obs.setConcept(c);
        String title = null;
        if (obs.getValueCodedName() != null) {
            title = obs.getValueCodedName().getName();
        }
        if (!StringUtils.hasText(title)) {
            title = c.getName().getName();
        }
        obs.setComplexData(new ComplexData(title, value.getData().getValue()));
    } else {
        // do we need to support BIT just in case it slips thru?
        throw new HL7Exception(Context.getMessageSourceService().getMessage("ORUR01.error.UpsupportedObsType", new Object[] { hl7Datatype }, null));
    }
    return obs;
}

Example 9 with ComplexData

use of org.openmrs.obs.ComplexData in project openmrs-core by openmrs.

the class ImageHandler method getObs.

/**
 * Currently supports all views and puts the Image file data into the ComplexData object
 *
 * @see org.openmrs.obs.ComplexObsHandler#getObs(org.openmrs.Obs, java.lang.String)
 */
@Override
public Obs getObs(Obs obs, String view) {
    File file = getComplexDataFile(obs);
    // Raw image
    if (ComplexObsHandler.RAW_VIEW.equals(view)) {
        BufferedImage img = null;
        try {
            img = ImageIO.read(file);
        } catch (IOException e) {
            log.error("Trying to read file: " + file.getAbsolutePath(), e);
        }
        ComplexData complexData = new ComplexData(file.getName(), img);
        String mimeType = null;
        // Image MIME type
        try {
            FileImageInputStream imgStream = new FileImageInputStream(file);
            Iterator<ImageReader> imgReader = ImageIO.getImageReaders(imgStream);
            imgStream.close();
            if (imgReader.hasNext()) {
                mimeType = "image/" + imgReader.next().getFormatName().toLowerCase();
            } else {
                log.warn("MIME type of " + file.getAbsolutePath() + " is not known");
            }
        } catch (FileNotFoundException e) {
            log.error("Image " + file.getAbsolutePath() + " was not found", e);
        } catch (IOException e) {
            log.error("Trying to determine MIME type of " + file.getAbsolutePath(), e);
        }
        // If the mimetype is still null, determine it via getFileMimeType()
        mimeType = mimeType != null ? mimeType : OpenmrsUtil.getFileMimeType(file);
        complexData.setMimeType(mimeType);
        obs.setComplexData(complexData);
    } else {
        // NOTE: if adding support for another view, don't forget to update supportedViews list above
        return null;
    }
    return obs;
}

Example 10 with ComplexData

use of org.openmrs.obs.ComplexData in project openmrs-core by openmrs.

the class BinaryStreamHandler method getObs.

/**
 * Returns the same ComplexData for all views. The title is the original filename, and the data
 * is the raw byte[] of data (If the view is set to "download", all commas and whitespace are
 * stripped out of the filename to fix an issue where the browser wasn't handling a filename
 * with whitespace properly) Note that if the method cannot find the file associated with the
 * obs, it returns the obs with the ComplexData = null
 *
 * @see ComplexObsHandler#getObs(Obs, String)
 */
@Override
public Obs getObs(Obs obs, String view) {
    ComplexData complexData = null;
    File file = null;
    // Raw stream
    if (ComplexObsHandler.RAW_VIEW.equals(view)) {
        try {
            file = getComplexDataFile(obs);
            String[] names = obs.getValueComplex().split("\\|");
            String originalFilename = names[0];
            originalFilename = originalFilename.replace(",", "").replace(" ", "");
            if (file.exists()) {
                FileInputStream fileInputStream = new FileInputStream(file);
                complexData = new ComplexData(originalFilename, fileInputStream);
            } else {
                log.error("Unable to find file associated with complex obs " + obs.getId());
            }
        } catch (Exception e) {
            throw new APIException("Obs.error.while.trying.get.binary.complex", null, e);
        }
    } else {
        // NOTE: if adding support for another view, don't forget to update supportedViews list above
        return null;
    }
    Assert.notNull(complexData, "Complex data must not be null");
    // Get the Mime Type and set it
    String mimeType = OpenmrsUtil.getFileMimeType(file);
    complexData.setMimeType(mimeType);
    obs.setComplexData(complexData);
    return obs;
}