Examples with TumorType org.mskcc.oncotree.model.TumorType used on opensource projects

Example 6 with TumorType

use of org.mskcc.oncotree.model.TumorType in project oncotree by cBioPortal.

the class TumorTypesUtil method setDepthAndTissue.

private void setDepthAndTissue(TumorType tumorType, int depth, String tissue) {
    if (tumorType != null) {
        tumorType.setLevel(new Integer(depth));
        if (depth == 1) {
            tissue = tumorType.getName();
        }
        tumorType.setTissue(tissue);
        for (TumorType childTumorType : tumorType.getChildren().values()) {
            setDepthAndTissue(childTumorType, depth + 1, tissue);
        }
    }
}

Example 7 with TumorType

use of org.mskcc.oncotree.model.TumorType in project oncotree by cBioPortal.

the class TumorTypesUtil method findTumorType.

private List<TumorType> findTumorType(TumorType allTumorTypes, TumorType currentTumorType, List<TumorType> matchedTumorTypes, String key, String keyword, Boolean exactMatch, Boolean includeParent) throws InvalidQueryException {
    Map<String, TumorType> childrenTumorTypes = currentTumorType.getChildren();
    Boolean match = false;
    Map<String, List<String>> externalReferences = currentTumorType.getExternalReferences();
    if (includeParent == null) {
        includeParent = false;
    }
    if (exactMatch == null) {
        exactMatch = true;
    }
    switch(key) {
        case "code":
            if (exactMatch) {
                match = currentTumorType.getCode() == null ? false : currentTumorType.getCode().equalsIgnoreCase(keyword);
            } else {
                match = currentTumorType.getCode() == null ? false : StringUtils.containsIgnoreCase(currentTumorType.getCode(), keyword);
            }
            break;
        case "color":
            if (exactMatch) {
                match = currentTumorType.getColor() == null ? false : currentTumorType.getColor().equalsIgnoreCase(keyword);
            } else {
                match = currentTumorType.getColor() == null ? false : StringUtils.containsIgnoreCase(currentTumorType.getColor(), keyword);
            }
            break;
        case "name":
            if (exactMatch) {
                match = currentTumorType.getName() == null ? false : currentTumorType.getName().equalsIgnoreCase(keyword);
            } else {
                match = currentTumorType.getName() == null ? false : StringUtils.containsIgnoreCase(currentTumorType.getName(), keyword);
            }
            break;
        case "nci":
            if (exactMatch) {
                match = externalReferences.containsKey("NCI") ? ListUtil.hasMatchingElementIgnoreCase(externalReferences.get("NCI"), keyword) : false;
            } else {
                match = externalReferences.containsKey("NCI") ? ListUtil.hasElementWhichContainsStringIgnoreCase(externalReferences.get("NCI"), keyword) : false;
            }
            break;
        case "umls":
            if (exactMatch) {
                match = externalReferences.containsKey("UMLS") ? ListUtil.hasMatchingElementIgnoreCase(externalReferences.get("UMLS"), keyword) : false;
            } else {
                match = externalReferences.containsKey("UMLS") ? ListUtil.hasElementWhichContainsStringIgnoreCase(externalReferences.get("UMLS"), keyword) : false;
            }
            break;
        case "maintype":
            if (exactMatch) {
                match = currentTumorType == null ? false : (currentTumorType.getMainType() == null ? false : currentTumorType.getMainType().equals(keyword));
            } else {
                match = currentTumorType == null ? false : (currentTumorType.getMainType() == null ? false : StringUtils.containsIgnoreCase(currentTumorType.getMainType(), keyword));
            }
            break;
        case "level":
            try {
                Integer keywordAsInteger = Integer.parseInt(keyword);
                match = currentTumorType == null ? false : (currentTumorType.getLevel() == null ? false : (currentTumorType.getLevel() == null ? false : currentTumorType.getLevel().equals(keywordAsInteger)));
            } catch (NumberFormatException e) {
                throw new InvalidQueryException("'" + keyword + "' is not a valid level.  Level must be an integer.");
            }
            break;
        default:
            // we should never get here because we have already checked if this is a valid key
            throw new InvalidQueryException(buildInvalidQueryTypeError(key));
    }
    if (match) {
        TumorType tumorType = new TumorType();
        tumorType.setCode(currentTumorType.getCode());
        tumorType.setColor(currentTumorType.getColor());
        tumorType.setName(currentTumorType.getName());
        tumorType.setMainType(currentTumorType.getMainType());
        tumorType.setExternalReferences(currentTumorType.getExternalReferences());
        tumorType.setTissue(currentTumorType.getTissue());
        // the results of search operations are flat lists of TumorTypes .. no nested children so do not setChildren()
        tumorType.setParent(currentTumorType.getParent());
        tumorType.setHistory(currentTumorType.getHistory());
        tumorType.setRevocations(currentTumorType.getRevocations());
        tumorType.setPrecursors(currentTumorType.getPrecursors());
        tumorType.setLevel(currentTumorType.getLevel());
        matchedTumorTypes.add(tumorType);
        if (includeParent) {
            String code = currentTumorType.getParent();
            List<TumorType> parentTumorTypes = findTumorType(allTumorTypes, allTumorTypes, new ArrayList<TumorType>(), "code", code, true, true);
            if (parentTumorTypes != null && parentTumorTypes.size() > 0) {
                TumorType parentNode = parentTumorTypes.get(0);
                matchedTumorTypes.add(parentNode);
                if (parentNode.getParent() != null) {
                    matchedTumorTypes = findTumorType(allTumorTypes, allTumorTypes, matchedTumorTypes, "code", parentNode.getParent(), true, true);
                }
            }
        }
    }
    if (childrenTumorTypes.size() > 0) {
        Iterator it = childrenTumorTypes.entrySet().iterator();
        while (it.hasNext()) {
            Map.Entry pair = (Map.Entry) it.next();
            matchedTumorTypes = findTumorType(allTumorTypes, (TumorType) pair.getValue(), matchedTumorTypes, key, keyword, exactMatch, includeParent);
        }
    }
    return new ArrayList<>(new LinkedHashSet<>(matchedTumorTypes));
}

Example 8 with TumorType

use of org.mskcc.oncotree.model.TumorType in project oncotree by cBioPortal.

the class TumorTypesUtil method initTumorType.

private TumorType initTumorType(OncoTreeNode oncoTreeNode, Version version) throws InvalidOncoTreeDataException {
    // we do not have level or tissue
    TumorType tumorType = new TumorType();
    tumorType.setMainType(oncoTreeNode.getMainType());
    tumorType.setCode(oncoTreeNode.getCode());
    tumorType.setName(oncoTreeNode.getName());
    tumorType.setColor(oncoTreeNode.getColor());
    tumorType.setParent(oncoTreeNode.getParentCode());
    // do not copy history, revocations, or precursors
    return tumorType;
}

Example 9 with TumorType

use of org.mskcc.oncotree.model.TumorType in project oncotree by cBioPortal.

the class CacheUtilTest method assertNoRevocationsInChildren.

private void assertNoRevocationsInChildren(Map<String, TumorType> tumorTypes) {
    for (TumorType tumorType : tumorTypes.values()) {
        assertEquals("Node " + tumorType.getCode() + " name: " + tumorType.getName() + " has revocations", 0, tumorType.getRevocations().size());
        assertNoRevocationsInChildren(tumorType.getChildren());
    }
}

Example 10 with TumorType

use of org.mskcc.oncotree.model.TumorType in project oncotree by cBioPortal.

the class TumorTypesUtil method loadFromRepository.

private static Map<String, TumorType> loadFromRepository(Version version) throws InvalidOncoTreeDataException {
    List<OncoTreeNode> oncoTreeNodes = oncoTreeRepository.getOncoTree(version);
    Map<String, TumorType> allNodes = new HashMap<>();
    HashSet<String> rootNodeCodeSet = new HashSet<>();
    HashSet<String> duplicateCodeSet = new HashSet<>();
    // construct basic nodes
    for (OncoTreeNode thisNode : oncoTreeNodes) {
        logger.debug("OncoTreeNode: code='" + thisNode.getCode() + "', name='" + thisNode.getName() + "'");
        TumorType tumorType = initTumorType(thisNode, version);
        String thisNodeCode = tumorType.getCode();
        if (allNodes.containsKey(thisNodeCode)) {
            duplicateCodeSet.add(thisNodeCode);
        }
        allNodes.put(thisNodeCode, tumorType);
        if (hasNoParent(tumorType)) {
            rootNodeCodeSet.add(thisNodeCode);
        }
    }
    validateOncoTreeOrThrowException(rootNodeCodeSet, duplicateCodeSet, allNodes);
    // also set NCI and UMLS codes
    for (TumorType tumorType : allNodes.values()) {
        String thisNodeCode = tumorType.getCode();
        MSKConcept mskConcept = mskConceptCache.get(thisNodeCode);
        if (mskConcept != null) {
            HashMap<String, List<String>> crosswalks = mskConcept.getCrosswalks();
            if (crosswalks != null && crosswalks.containsKey("NCI")) {
                tumorType.setNCI(crosswalks.get("NCI"));
            }
            List<String> umlsIds = new ArrayList<String>();
            if (mskConcept.getConceptIds() != null) {
                for (String mskConceptId : mskConcept.getConceptIds()) {
                    umlsIds.add(mskConceptId.replace("MSK", "C"));
                }
            }
            tumorType.setUMLS(umlsIds);
            tumorType.setHistory(new ArrayList(mskConcept.getHistory()));
        }
        if (rootNodeCodeSet.contains(thisNodeCode)) {
            // root node has no parent
            continue;
        }
        TumorType parent = allNodes.get(tumorType.getParent());
        parent.addChild(tumorType);
    }
    // set depth and tissue properties (root has tissue = null)
    String rootCode = rootNodeCodeSet.iterator().next();
    TumorType rootNode = allNodes.get(rootCode);
    setDepthAndTissue(rootNode, 0, null);
    // now that all children have a path of references to them from the root, return only the root node.
    allNodes.clear();
    allNodes.put(rootCode, rootNode);
    return allNodes;
}