Python Util.warning方法代碼示例

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def checkForNewRoot():
    """
    Check if ontology has a new root node.  Update this module's internal
    state if there is a new root, and return the root node if it has changed
    or not.
    """
    # Hmm, could do this the efficient but unsafe way: pick a node randomly
    # and follow its part of path upward until it ends.
    # Or could check every node and report an error if we find more than one
    # root in the list.
    # Do it the slow, safe way.
    global _rootNode

    roots = []
    for node in Iterator():
        if len(getPartOfParentsForNode(node)) == 0:
            roots.append(node)

    if len(roots) == 0:
        Util.warning(["No root node found in ontology."])
    elif len(roots) == 1:
        _rootNode = roots[0]
    else:
        message = [str(len(roots)) + " root nodes found."]
        for node in roots:
            message.append("ID: " + node.getPublicId() +
                           " Name: " + node.getComponentName())
        Util.fatalError(message)

    return _rootNode

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def __addGeneToKnowledge(geneNomen):
    """
    Add this gene to what we know about MGI genes.
    """

    name = geneNomen.getName()
    symbol = geneNomen.getSymbol()
    accession = geneNomen.getAccession()

    # accession
    if accession:
        accessionLower = accession.lower()
        if accessionLower in _nomenclatureByAnyName:
            Util.fatalError([
                "Accession " + accession +
                " occurs twice in MGI marker files."])
        _nomenclatureByAccession[accessionLower] = geneNomen
        _nomenclatureByAnyName[accessionLower] = geneNomen

    # symbol
    symbolLower = symbol.lower()
    if symbolLower in _nomenclatureByAnyName:
        Util.warning([
            "Symbol " + symbol + " occurs twice in MGI marker files.",
            "Ignoring earlier occurrence."])
    _nomenclatureByAnyName[symbolLower] = geneNomen
    _nomenclatureBySymbol[symbolLower] = geneNomen

    # name can be same as Symbol
    nameLower = name.lower()
    _nomenclatureByName[nameLower] = geneNomen
    if nameLower not in _nomenclatureByAnyName:
        _nomenclatureByAnyName[nameLower] = geneNomen

    return None

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def getCloneByNibbXdbId(nibbXdbId):
    """
    Return information about a NIBB XDB clone, given its NIBB XDB ID.

    nibbXdbId: NIBB XDB clone ID, with or without the leading NIBB:.
    """

    cloneId = Util.stripPublicIdPrefix(nibbXdbId)
    nibbXdbClone = None

    if cloneId in _clonesByNibbXdbId:
        nibbXdbClone = _clonesByNibbXdbId[cloneId]
    elif cloneId in _failedNibbXdbIds:
        pass
    else:
        # build clone from sequence and library.
        library = NibbXdbLibrary.getLibraryByNibbXdbId(cloneId)
        if library:
            sequencePage = urllib.urlopen(SEQUENCE_URL + cloneId )
            nibbXdbClone = NibbXdbClone(sequencePage, library)
            _clonesByNibbXdbId[cloneId] = nibbXdbClone
        else:
            Util.warning([
                "Failed to locate NIBB clone library for " + nibbXdbId])
            _failedNibbXdbIds.add(nibbXdbId)


    return nibbXdbClone

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def initialise(dbHost, dbName, dbUser, dbPass,
               outputDir = None, outputFilePath = None, charset = None):
    """
    Initialise the database connection.

    The outputDir and outputFilePath parameters are optional and are
    only needed if you are updating the code.  outputDir is deprecated.
    Use outputFilePath instead.

    charset should be set to "latin1" if you are having difficulties
            writing non-ASCII characters.
    """

    global _dbConn, _outputFile

    # PYTHON Connection
    _dbConn = MySQLdb.connect(
        user = dbUser, passwd = dbPass, host = dbHost, db = dbName,
        charset = charset, unix_socket = '/tmp/mysql.sock' )
    
    # JYTHON Connection
    #dbUrl = "jdbc:mysql://" + dbHost + "/" + dbName
    #dbDriver = "org.gjt.mm.mysql.Driver"
    
    #_dbConn = zxJDBC.connect(dbUrl, dbUser, dbPass, dbDriver)
    
    """
    try :
    # if called from command line with .login CLASSPATH setup right,this works
        _dbConn = zxJDBC.connect(dbUrl, dbUser, dbPass, dbDriver)
    except:
    # if called from Apache or account where the .login has not set CLASSPATH
    # need to use run-time CLASSPATH Hacker
        try :
            jarLoad = classPathHacker()
            a = jarLoad.addFile("/net/homehost/export/home/mwicks/Downloads/JarRegenerateDerivedData/lib/mm.mysql-2.0.14-bin.jar")
            _dbConn = zxJDBC.connect(dbUrl, dbUser, dbPass, dbDriver)
        except :
            sys.exit ("still failed \n%s" % (sys.exc_info()))
    """


    # Output dir only defined if producing SQL.
    if outputDir != None:
        # Open single output file to hold all generated SQL.
        fileName = outputDir + "/" + "db.sql"
        _outputFile = open(fileName, "w")
        Util.warning([
            "The 'outputDir' parameter to 'DbAccess.initialise()' has been "
            "deprecated.",
            "Please use the 'outputFilePath' parameter instead."
            ])
    elif outputFilePath != None:
        # Open single output file to hold all generated SQL.
        _outputFile = open(outputFilePath, "w")
    else:
        _outputFile = None

    return

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def _processWithdrawns(withdrawn):
    """
    Process withdrawn nomenclature from the marker file.  Withdrawn
    nomenclature forms a graph that terminates at valid gene names.
    The names in the graph become synonyms for the gene names at the
    end of the graph.

    withdrawn: Dictionary indexed by lower case withdrawn symbol.
               Each entry is a list of GeneNomenclature objects
               for that symbol.
    """
    # Walk through withdrawn nomenclature, collating them and adding them
    # to the known nomenclature.
    for symbolLower, withdrawnNomens in withdrawn.iteritems():
        processedNomens = sets.Set()
        horizon = sets.Set(withdrawnNomens)
        geneNomens = sets.Set()
        while len(horizon) > 0:
            withdrawnNomen = horizon.pop()
            geneSymbol = withdrawnNomen.getReplacementSymbol()
            geneSymbolLower = geneSymbol.lower()
            geneNomen = _nomenclatureByAnyName.get(geneSymbolLower)
            if geneNomen:
                geneNomens.add(geneNomen)
            else:
                nextGeneration = withdrawn.get(geneSymbolLower)
                if nextGeneration:
                    for nextNomen in nextGeneration:
                        if nextNomen not in processedNomens:
                            horizon.add(nextNomen)
                        elif _verbose:
                            Util.warning([
                                "Cirucular withdrawn list for symbol '" +
                                symbolLower + "'",
                                "Loop starts at symbol: '" +
                                nextNomen.getSymbol() + "'"
                                "       ends at Symbol: '" +
                                withdrawnNomen.getSymbol() + "'"])

                elif _verbose:
                    Util.warning([
                        "MGI Withdrawn symbol '" + symbolLower +
                        "' leads to a dead end at symbol '" +
                        geneSymbol + "'."])
            processedNomens.add(withdrawnNomen)

        if len(geneNomens) > 0:
            if symbolLower not in _nomenclatureByWithdrawnName:
                _nomenclatureByWithdrawnName[symbolLower] = geneNomens
            else:
                _nomenclatureByWithdrawnName[symbolLower] += geneNomens

    return

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def writeStageReport(reportTree, outputDir, format, reportType,
                     togetherness):
    """
    Write stage specific reports, one for each stage.
    """
    if format == XML and togetherness == CONCATENATED:
        # Reject outright any request for concatenated XML stage reports.
        # There is not enough memory on my machine to produce these.
        Util.warning([
            "You have requested an XML report that would include a separate",
            "tree for each stage, all in the same XML file.  This is a",
            "reasonable request, but past experience indicates that there",
            "is not enough memory on most workstations to build such a large",
            "XML file.  Therefore, THE REQUESTED REPORT WILL NOT BE GENERATED."])
        return None

    reportDir = (outputDir + "/" +
                 FORMATS[format][FORMAT_SUBDIRECTORY] + "/ByStage/" +
                 REPORT_TYPES[reportType][REPORT_TYPE_NAME])
    reportFile = None

    if togetherness == CONCATENATED:
        # Open one report file.
        fileName = (reportDir + "/AllStages" +
                    REPORT_TYPES[reportType][REPORT_TYPE_NAME] + "." +
                    FORMATS[format][FORMAT_EXTENSION])
        reportFile = _openReportFile(fileName, reportTree, format)
        reportFile.addReportHeader()

    for stage in Stages.SequenceIterator():

        if togetherness == SEPARATE:
            # open report file for each stage
            fileName = (reportDir + "/" + stage.getName() +
                        REPORT_TYPES[reportType][REPORT_TYPE_NAME] +
                        "." + FORMATS[format][FORMAT_EXTENSION])
            reportFile = _openReportFile(fileName, reportTree, format)
            reportFile.addReportHeader()

        if reportType == GROUPS_EMBEDDED:
            _writeStageGroupsEmbeddedReport(reportTree, reportFile, stage, format)
        elif reportType == GROUPS_TRAILING:
            _writeStageGroupsTrailingReport(reportTree, reportFile, stage)

        if togetherness == SEPARATE:
            reportFile.closeReportFile()
        else:
            reportFile.addPageBreak()

    if togetherness == CONCATENATED:
        reportFile.closeReportFile()

    return

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def _addGeneToKnowledge(gene):
    """
    Add this gene to what we know about Xenbase genes.
    """

    # Accession
    accessionLower = gene.getAccession().lower()
    if accessionLower in _geneByAccession:
        Util.fatalError([
            "Accession ID '" + gene.getAccession() +
            "' occurs more than once in Xenbase gene file."])
    else:
        _geneByAccession[accessionLower] = gene
        _addToByAnyName(gene.getAccession(), gene)

    # Symbol
    symbolLower = gene.getSymbol().lower()
    if symbolLower in _geneBySymbol:
        Util.fatalError([
            "Gene Symbol '" + gene.getSymbol() +
            "' occurs more than once in Xenbase gene file."])
    else:
        _geneBySymbol[symbolLower] = gene
        _addToByAnyName(gene.getSymbol(), gene)

    # Name
    nameLower = gene.getName().lower()
    if nameLower != symbolLower:
        if nameLower in _geneByName:
            Util.fatalError([
                "Gene Name '" + gene.getName() +
                "' occurs more than once in Xenbase gene file."])
        else:
            _geneByName[nameLower] = gene
            _addToByAnyName(gene.getName(), gene)

    # Synonyms
    for syn in gene.getSynonyms():
        synLower = syn.lower()
        if synLower == symbolLower:
            if _verbose:
                Util.warning([
                    "Synonym '" + syn + "' same as symbol. Ignoring synonym."])
        else:
            if synLower not in _geneBySynonym:
                _geneBySynonym[synLower] = []
            _geneBySynonym[synLower].append(gene)

    return None

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def __readGenes(markerFileName):
    """
    Read lines from marker file saving information about genes.
    """

    markerFile = open(markerFileName, "r")
    __verifyStaticFileSection(markerFile, _MGI_MF_EXPECTED_HEADER,
                              "MGI marker file header not as expected")

    # now pointing at first data row; read until you have read all the
    # marker data
    withdrawn = {} # indexed by lower case symbol
    markerLine = "Bogus"
    while markerLine not in [None, "", "\n"]:
        # read until end of markers
        markerLine = markerFile.readline()
        markerType = markerLine[_MGI_MF_TYPE_COL:_MGI_MF_TRAILER_COL].strip()

        if markerType in ["Gene", "DNA Segment"]:
            symbol = markerLine[_MGI_MF_SYMBOL_COL:_MGI_MF_STATUS_COL].strip()
            name   = markerLine[_MGI_MF_NAME_COL:_MGI_MF_TYPE_COL].strip()
            accession = (
                markerLine[_MGI_MF_ACCESSION_COL:_MGI_MF_LOCATION_COL].strip())
            if accession == "NULL":
                accession = None
            nomen = GeneNomenclature(symbol, name, accession, markerType)
            if nomen.isWithdrawn():
                if nomen.getSymbol() == nomen.getReplacementSymbol():
                    if _verbose:
                        Util.warning([
                            "Ignoring self-referential withdrawn MGI record " +
                            "for symbol '" + nomen.getSymbol() + "'"])
                else:
                    symbolLower = symbol.lower()
                    if symbolLower in withdrawn:
                        withdrawn[symbolLower].append(nomen)
                    else:
                        withdrawn[symbolLower] = [nomen]
            else:
                __addGeneToKnowledge(nomen)

    markerFile.close()

    # Add withdrawn nomenclature
    _processWithdrawns(withdrawn)

    return

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def getGeneNomenclature(anyName):
    """
    Return the GeneNomenclature object that the given string maps to.
    Returns None if string does not map to any gene.

    anyName can be a gene name, gene symbol, accesion number, or gene
    synonym.  It is case insensitive.
    """
    anyNameLower = anyName.lower()
    geneNomen = _nomenclatureByAnyName.get(anyNameLower)
    if geneNomen:
        if not geneNomen.isGene():
            Util.warning([
                "'" + anyName + "' refers to a " + geneNomen.getMarkerType() +
                " at MGI, which is not a gene."])
    else:
        # Name is not recognised in names, accessions, symbols, or
        # synonyms that map to one entry.
        # Check if string maps to a synonym that maps to multiple entries
        multipleSyns = _nomenclatureBySynonym.get(anyNameLower)
        if multipleSyns:
            message = [
                "The string '" + anyName +
                "' is a synonym that maps to multiple " +
                "entries at MGI."]
            for synNomen in multipleSyns:
                message.append(synNomen.getSymbol())
            message.append("Returning none as can't tell which one to pick.")
            Util.warning(message)
        else:
            # Check if string maps to a withdrawn name that maps to multiple
            # entries.
            multipleSyns = _nomenclatureByWithdrawnName.get(anyNameLower)
            if multipleSyns:
                message = [
                    "The string '" + anyName + "' is a withdrawn name that " +
                    "maps to multiple entries at MGI."]
                for synNomen in multipleSyns:
                    message.append(synNomen.getSymbol())
                message.append(
                    "Returning none as can't tell which one to pick.")
                Util.warning(message)
            else:
                Util.warning([
                    "The string '" + anyName + "' matches no genes at MGI."])

    return geneNomen

# 需要導入模塊: from hgu import Util [as 別名]
# 或者: from hgu.Util import warning [as 別名]
def getGeneByAnyName(anyName):
    """
    Return the Xenbase Gene object that the given string maps to.
    Returns None if string does not map to any gene.

    anyName can be a gene name, gene symbol, accesion number, or gene
    synonym.  It is case insensitive.
    """
    anyNameLower = anyName.lower()
    gene = _geneByAnyName.get(anyNameLower)
    if gene == None:
        if anyNameLower in _geneBySynonym:
            if len(_geneBySynonym[anyNameLower]) > 1:
                Util.warning([
                    "'" + anyName + "' is a synonym for multiple genes.",
                    "Can't resolve which one so returning None."])
            else:
                gene = _geneBySynonym[anyNameLower][0]

    if gene == None and _verbose:
        Util.warning([
            "The string '" + anyName + "' matches no genes at Xenbase."])

    return gene