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

Example 11 with TumorType

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

the class MainTypesApi method mainTypesGet.

@ApiOperation(value = "Return all available main tumor types.", notes = "")
@ApiResponses(value = { @ApiResponse(code = 200, message = "Nested tumor types object"), @ApiResponse(code = 404, message = "Could not find maintypes"), @ApiResponse(code = 503, message = "Required data source unavailable") })
@RequestMapping(value = "", produces = { "application/json" }, method = RequestMethod.GET)
public Iterable<String> mainTypesGet(@ApiParam(value = "The version of tumor types. For example, " + VersionUtil.DEFAULT_VERSION + ". Please see the versions api documentation for released versions.") @RequestParam(value = "version", required = false) String version) {
    Version v = (version == null) ? versionUtil.getDefaultVersion() : versionUtil.getVersion(version);
    Map<String, TumorType> tumorTypes = cacheUtil.getTumorTypesByVersion(v);
    Set<TumorType> tumorTypesSet = tumorTypesUtil.flattenTumorTypes(tumorTypes, version);
    return mainTypesUtil.getMainTypesByTumorTypes(tumorTypesSet);
}

Example 12 with TumorType

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

the class TumorTypesUtilTest method getReturnedFullTumorTypeMap.

private Map<String, TumorType> getReturnedFullTumorTypeMap() throws Exception {
    Set<TumorType> tumorTypesAsPreparedForTumorTypesEndpoint = simulateFullTumorTypeApiResponse();
    HashMap<String, TumorType> returnedTumorTypeMap = new HashMap<>(tumorTypesAsPreparedForTumorTypesEndpoint.size());
    for (TumorType tumorType : tumorTypesAsPreparedForTumorTypesEndpoint) {
        returnedTumorTypeMap.put(tumorType.getCode(), tumorType);
    }
    return returnedTumorTypeMap;
}

Example 13 with TumorType

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

the class TumorTypesUtil method getAllTumorTypesFromOncoTreeNodes.

public Map<String, TumorType> getAllTumorTypesFromOncoTreeNodes(List<OncoTreeNode> oncoTreeNodes, Version version, HashMap<String, ArrayList<String>> topBraidURIsToOncotreeCodes) throws InvalidOncoTreeDataException {
    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);
        }
        // get all codes defined so far for this topbraid uri and save in history
        if (topBraidURIsToOncotreeCodes.containsKey(thisNode.getURI())) {
            // do not add this code to the history, but add any others
            HashSet<String> allButThisNode = new HashSet<String>(topBraidURIsToOncotreeCodes.get(thisNode.getURI()));
            allButThisNode.remove(thisNode.getCode());
            tumorType.setHistory(new ArrayList<String>(allButThisNode));
        } else {
            topBraidURIsToOncotreeCodes.put(thisNode.getURI(), new ArrayList<String>());
        }
        for (String topBraidURI : thisNode.getRevocations()) {
            String fullTopBraidURI = TOPBRAID_BASE_URI + topBraidURI;
            if (topBraidURIsToOncotreeCodes.containsKey(fullTopBraidURI)) {
                ArrayList<String> nodeHistory = topBraidURIsToOncotreeCodes.get(fullTopBraidURI);
                // last node is most recent for this URI
                tumorType.addRevocations(nodeHistory.get(nodeHistory.size() - 1));
            } else {
                logger.error("loadFromRepository() -- unknown topBraidURI " + fullTopBraidURI + " in revocations field for topBraidURI " + thisNode.getURI());
                throw new InvalidOncoTreeDataException("Unknown topBraidURI " + fullTopBraidURI + " in revocations field for topBraidURI " + thisNode.getURI());
            }
        }
        for (String topBraidURI : thisNode.getPrecursors()) {
            String fullTopBraidURI = TOPBRAID_BASE_URI + topBraidURI;
            if (topBraidURIsToOncotreeCodes.containsKey(fullTopBraidURI)) {
                ArrayList<String> nodeHistory = topBraidURIsToOncotreeCodes.get(fullTopBraidURI);
                // last node is most recent for this URI
                tumorType.addPrecursors(nodeHistory.get(nodeHistory.size() - 1));
            } else {
                logger.error("loadFromRepository() -- unknown topBraidURI " + fullTopBraidURI + " in precursors field for topBraidURI " + thisNode.getURI());
                throw new InvalidOncoTreeDataException("Unknown topBraidURI " + fullTopBraidURI + " in precursors field for topBraidURI " + thisNode.getURI());
            }
        }
        // now save this as onoctree code history for this topbraid uri
        topBraidURIsToOncotreeCodes.get(thisNode.getURI()).add(thisNode.getCode());
    }
    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.setExternalReference("NCI", crosswalks.get("NCI"));
            }
            if (mskConcept.getConceptIds() != null) {
                for (String mskConceptId : mskConcept.getConceptIds()) {
                    tumorType.addExternalReference("UMLS", mskConceptId.replace("MSK", "C"));
                }
            }
        }
        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;
}

Example 14 with TumorType

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

the class TumorTypesUtil method addTumorTypeToRows.

private void addTumorTypeToRows(TumorType tumorType, List<String> rows, List<String> parents) {
    List<String> row = new ArrayList<>();
    String oncotreeCode = StringUtils.defaultString(tumorType.getCode()).trim();
    // only 7 levels of headers. Abort the attemp to render the spreadsheet and throw an exception.
    if (parents.size() > 7) {
        throw new RuntimeException("OncoTree depth for code " + oncotreeCode + " exceeds max representation. Depth cannot be > 7");
    }
    String displayName = StringUtils.defaultString(tumorType.getName()).trim() + " (" + oncotreeCode + ")";
    row.addAll(parents);
    row.add(displayName);
    // Need to pad for the primary - quinternary columns if all parents are not present
    for (int i = 6; i > parents.size(); i--) {
        row.add("");
    }
    row.add(StringUtils.defaultString(tumorType.getMainType()));
    row.add(StringUtils.defaultString(tumorType.getColor()));
    // TODO enum or something
    if (tumorType.getExternalReferences().containsKey("NCI")) {
        row.add(StringUtils.defaultString(StringUtils.join(tumorType.getExternalReferences().get("NCI"), ",")));
    } else {
        row.add("");
    }
    // TODO enum or something
    if (tumorType.getExternalReferences().containsKey("UMLS")) {
        row.add(StringUtils.defaultString(StringUtils.join(tumorType.getExternalReferences().get("UMLS"), ",")));
    } else {
        row.add("");
    }
    // add revocations and precursors to history column
    List<String> combinedHistory = new ArrayList<String>();
    combinedHistory.addAll(tumorType.getHistory());
    combinedHistory.addAll(tumorType.getRevocations());
    combinedHistory.addAll(tumorType.getPrecursors());
    // do not display a code in its own history (e.g. PTCL)
    combinedHistory.removeAll(Collections.singletonList(tumorType.getCode()));
    row.add(StringUtils.defaultString(StringUtils.join(combinedHistory, ",")));
    rows.add(StringUtils.join(row, "\t"));
    // Prepare for next recursive call
    Map<String, TumorType> children = tumorType.getChildren();
    if (children.size() > 0) {
        parents.add(displayName);
        for (String code : children.keySet()) {
            TumorType child = children.get(code);
            addTumorTypeToRows(child, rows, parents);
        }
        parents.remove(parents.size() - 1);
    }
}

Example 15 with TumorType

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

the class TumorTypesUtil method getTsvFromTumorTypes.

private String getTsvFromTumorTypes(Map<String, TumorType> tumorTypes) {
    List<String> rows = new ArrayList<>();
    for (String code : tumorTypes.keySet()) {
        TumorType tumorType = tumorTypes.get(code);
        // skip the root node, "TISSUE". Just add it's children
        Map<String, TumorType> children = tumorType.getChildren();
        for (String childCode : children.keySet()) {
            addTumorTypeToRows(children.get(childCode), rows, new ArrayList<String>());
        }
    }
    Collections.sort(rows);
    rows.add(0, TSV_HEADER);
    return StringUtils.join(rows, "\n") + "\n";
}