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

Example 1 with TumorType

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

the class CacheUtil method resetCache.

public void resetCache() throws FailedCacheRefreshException {
    logger.info("resetCache() -- refilling tumor types cache");
    Map<Version, Map<String, TumorType>> latestTumorTypesCache = new HashMap<>();
    ArrayList<Version> oncoTreeVersions = new ArrayList<Version>();
    ArrayList<String> failedVersions = new ArrayList<String>();
    // use this to store and look up previous oncoTree codes
    HashMap<String, ArrayList<String>> topBraidURIsToOncotreeCodes = new HashMap<String, ArrayList<String>>();
    boolean failedOncoTreeVersionsCacheRefresh = false;
    boolean failedVersionedOncoTreeNodesCacheRefresh = false;
    // update EHCache with newest versions available
    try {
        oncoTreePersistentCache.updateOncoTreeVersionsInPersistentCache();
    } catch (TopBraidException exception) {
        logger.error("resetCache() -- failed to pull versions from repository");
        failedOncoTreeVersionsCacheRefresh = true;
    }
    // attmpt to get versions from EHCache -- RuntimeException thrown when ALL options are exhausted (ehcache, topbraid, backup)
    try {
        oncoTreeVersions = oncoTreePersistentCache.getOncoTreeVersionsFromPersistentCache();
    } catch (RuntimeException e) {
        throw new FailedCacheRefreshException("No data found in specified backup cache location...");
    }
    if (!failedOncoTreeVersionsCacheRefresh) {
        try {
            oncoTreePersistentCache.backupOncoTreeVersionsPersistentCache(oncoTreeVersions);
        } catch (Exception e) {
            logger.error("Unable to backup versions EHCache");
            slackUtil.sendSlackNotification("*OncoTree Error* - OncoTreeVersionsCache backup failed." + e.getMessage());
        }
    }
    // versions are ascending by release date
    for (Version version : oncoTreeVersions) {
        Map<String, TumorType> latestTumorTypes = new HashMap<String, TumorType>();
        ArrayList<OncoTreeNode> oncoTreeNodes = new ArrayList<OncoTreeNode>();
        failedVersionedOncoTreeNodesCacheRefresh = false;
        if (version != null) {
            try {
                oncoTreePersistentCache.updateOncoTreeNodesInPersistentCache(version);
            } catch (TopBraidException e) {
                logger.error("resetCache() -- failed to pull tumor types for version '" + version.getVersion() + "' from repository : " + e.toString());
                failedVersionedOncoTreeNodesCacheRefresh = true;
            }
            // store versions for which nodes cannot be successfully loaded (either due to inaccessible data or invalid data)
            try {
                oncoTreeNodes = oncoTreePersistentCache.getOncoTreeNodesFromPersistentCache(version);
            } catch (RuntimeException e) {
                failedVersions.add(version.getVersion());
                logger.warn("resetCache() -- failed to retrieve version '" + version.getVersion() + "'");
                continue;
            }
            if (!failedVersionedOncoTreeNodesCacheRefresh) {
                try {
                    oncoTreePersistentCache.backupOncoTreeNodesPersistentCache(oncoTreeNodes, version);
                } catch (Exception e) {
                    logger.error("Unable to backup oncotree nodes EHCache");
                    slackUtil.sendSlackNotification("*OncoTree Error* - OncoTreeNodesCache backup failed." + e.getMessage());
                }
            }
            try {
                latestTumorTypes = tumorTypesUtil.getAllTumorTypesFromOncoTreeNodes(oncoTreeNodes, version, topBraidURIsToOncotreeCodes);
            } catch (InvalidOncoTreeDataException exception) {
                logger.error("Unable to get tumor types from oncotree nodes");
                failedVersions.add(version.getVersion());
                logger.warn("resetCache() -- failed to retrieve version : " + version.getVersion() + " : " + exception.toString());
                continue;
            }
        }
        latestTumorTypesCache.put(version, latestTumorTypes);
    }
    // Fail the cache refresh if required oncotree version cannot be constructed or if no versions can be constructed
    if (latestTumorTypesCache.keySet().size() == 0) {
        logger.error("resetCache() -- failed to pull a single valid OncoTree version");
        throw new FailedCacheRefreshException("Failed to refresh cache - no versions constructed");
    }
    if (failedVersions.contains(requiredOncotreeVersion)) {
        logger.error("resetCache() -- failed to pull required oncotree version: " + requiredOncotreeVersion);
        throw new FailedCacheRefreshException("Failed to refresh cache - required version not constructed");
    }
    if (failedVersions.size() > 0) {
        slackUtil.sendSlackNotification("OncoTree successfully recached `" + requiredOncotreeVersion + "`, but ran into issues with the following versions: " + String.join(", ", failedVersions));
    }
    tumorTypesCache = latestTumorTypesCache;
    // cache is filled, but indicate to endpoint that we did not successfully pull updated data from TopBraid
    if (failedOncoTreeVersionsCacheRefresh || failedVersionedOncoTreeNodesCacheRefresh) {
        throw new FailedCacheRefreshException("Failed to refresh cache - composite error");
    } else {
        dateOfLastCacheRefresh = new Date();
        logger.info("resetCache() -- successfully reset cache from repository");
    }
}

Example 2 with TumorType

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

the class CacheUtilTest method assertNoPrecursorsInChildren.

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

Example 3 with TumorType

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

the class OncotreeTestConfig method setupExpectedTumorTypeMap.

private Map<String, TumorType> setupExpectedTumorTypeMap() throws Exception {
    String[] rawTestValueSource = getRawTestValueSource();
    final int valuesPerCase = 6;
    if (rawTestValueSource.length % valuesPerCase != 0) {
        throw new Exception("Error : malformed rawTestValueSource");
    }
    final int caseCount = rawTestValueSource.length / valuesPerCase;
    if (caseCount < 1) {
        throw new Exception("Error : no test cases defined in rawTestValueSource");
    }
    Map<String, TumorType> expectedTumorTypeMap = new HashMap<>(caseCount + 1);
    for (int pos = 0; pos < rawTestValueSource.length; pos = pos + valuesPerCase) {
        TumorType nextType = new TumorType();
        String code = rawTestValueSource[pos];
        if (code != null && code.trim().length() > 0) {
            nextType.setCode(code.trim());
        } else {
            fail("Error : list of expected oncotree codes contains a node with no code");
        }
        String name = rawTestValueSource[pos + 1];
        if (name != null && name.trim().length() > 0) {
            nextType.setName(name.trim());
        }
        String mainType = rawTestValueSource[pos + 2];
        if (mainType != null && mainType.trim().length() > 0) {
            nextType.setMainType(mainType.trim());
        }
        String color = rawTestValueSource[pos + 3];
        if (color != null && color.trim().length() > 0) {
            nextType.setColor(color.trim());
        }
        String parentCode = rawTestValueSource[pos + 4];
        if (parentCode != null && parentCode.trim().length() > 0) {
            nextType.setParent(parentCode.trim());
        }
        expectedTumorTypeMap.put(code, nextType);
    }
    return expectedTumorTypeMap;
}

Example 4 with TumorType

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

the class TumorTypesTxtApi method tumorTypesTxtGet.

@Deprecated
@ApiOperation(value = "Tumor Types in plain text format.", notes = "Return all available tumor types.", response = Void.class)
@ApiResponses(value = { @ApiResponse(code = 200, message = "Tumor types text file."), @ApiResponse(code = 404, message = "Could not find tumor types text file"), @ApiResponse(code = 503, message = "Required data source unavailable") })
@RequestMapping(value = "", produces = { TEXT_PLAIN_VALUE }, method = RequestMethod.GET)
public InputStreamResource tumorTypesTxtGet(@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) {
    Map<String, TumorType> tumorTypes = new HashMap<>();
    Version v = (version == null) ? versionUtil.getDefaultVersion() : versionUtil.getVersion(version);
    tumorTypes = cacheUtil.getTumorTypesByVersion(v);
    InputStream inputStream = tumorTypesUtil.getTumorTypeInputStream(tumorTypes);
    InputStreamResource inputStreamResource = new InputStreamResource(inputStream);
    return inputStreamResource;
}

Example 5 with TumorType

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

the class TumorTypesUtilTest method testFullOncoTreeCodeListByCode.

@Test
public void testFullOncoTreeCodeListByCode() throws Exception {
    int failureCount = 0;
    StringBuilder failureReport = new StringBuilder();
    Map<String, TumorType> returnedTumorTypeMap = getReturnedFullTumorTypeMap();
    for (String oncoTreeCode : expectedTumorTypeMap.keySet()) {
        TumorType expectedTumorType = expectedTumorTypeMap.get(oncoTreeCode);
        TumorType returnedTumorType = returnedTumorTypeMap.get(oncoTreeCode);
        if (expectedTumorType == null || returnedTumorType == null) {
            if (expectedTumorType == null) {
                failureReport.append(oncoTreeCode + " : no values in expected tumor type hash (internal error)\n");
                failureCount = failureCount + 1;
            }
            if (returnedTumorType == null) {
                failureReport.append(oncoTreeCode + " : tumor type expected but not returned from tumorTypesUtil\n");
                failureCount = failureCount + 1;
            }
        } else {
            String expectedCode = expectedTumorType.getCode();
            String returnedCode = returnedTumorType.getCode();
            if (!testValuesMatch(expectedCode, returnedCode)) {
                failureReport.append(makeMismatchMessage(oncoTreeCode, "code", returnedCode, expectedCode));
                failureCount = failureCount + 1;
            }
            String expectedName = expectedTumorType.getName();
            String returnedName = returnedTumorType.getName();
            if (!testValuesMatch(expectedName, returnedName)) {
                failureReport.append(makeMismatchMessage(oncoTreeCode, "name", returnedName, expectedName));
                failureCount = failureCount + 1;
            }
            String expectedMainType = expectedTumorType.getMainType();
            String returnedMainType = returnedTumorType.getMainType();
            if (expectedMainType == null || returnedMainType == null) {
                if (expectedMainType == null && returnedMainType != null) {
                    if (returnedMainType != null && returnedMainType.trim().length() != 0) {
                        failureReport.append(oncoTreeCode + " : expected MainType is null, and returned MainType is non-null\n");
                        failureCount = failureCount + 1;
                    }
                }
                if (returnedMainType == null && expectedMainType != null) {
                    if (expectedMainType != null && expectedMainType.trim().length() != 0) {
                        failureReport.append(oncoTreeCode + " : retunred MainType is null, and expected MainType is non-null\n");
                        failureCount = failureCount + 1;
                    }
                }
            } else {
                if (!testValuesMatch(expectedMainType, returnedMainType)) {
                    failureReport.append(makeMismatchMessage(oncoTreeCode, "mainType", returnedMainType, expectedMainType));
                    failureCount = failureCount + 1;
                }
            }
            String expectedColor = expectedTumorType.getColor();
            String returnedColor = returnedTumorType.getColor();
            if (!testValuesMatch(expectedColor, returnedColor)) {
                failureReport.append(makeMismatchMessage(oncoTreeCode, "color", returnedColor, expectedColor));
                failureCount = failureCount + 1;
            }
            String expectedParent = expectedTumorType.getParent();
            String returnedParent = returnedTumorType.getParent();
            if (!testValuesMatch(expectedParent, returnedParent)) {
                failureReport.append(makeMismatchMessage(oncoTreeCode, "parent", returnedParent, expectedParent));
                failureCount = failureCount + 1;
            }
        // TODO: add checks for children, level, tissue
        }
    }
    // TODO: scan for differences between sets of TumorTypes
    if (failureCount > 0) {
        fail(Integer.toString(failureCount) + " failed test conditions. Details follow... " + failureReport.toString());
    }
    return;
}