ó ´ZÄIc@s˝dZddlZddlmZdefd„ƒYZdefd„ƒYZde fd „ƒYZ d e fd „ƒYZ d e fd „ƒYZde fd„ƒYZddd„ƒYZdS(sœParser for XML results returned by NCBI's Entrez Utilities. This parser is used by the read() function in Bio.Entrez, and is not intended be used directly. i˙˙˙˙N(texpattIntegerElementcBseZRS((t__name__t __module__(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR,st StringElementcBseZRS((RR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR.stUnicodeElementcBseZRS((RR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR0st ListElementcBseZRS((RR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR2stDictionaryElementcBseZRS((RR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR4stStructureElementcBseZd„Zd„ZRS(cCs>tj|ƒx!|D]}tj||gƒqW||_dS(N(tdictt__init__t __setitem__tlistkeys(tselftkeystkey((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR :s  cCs:||jkr#||j|ƒntj|||ƒdS(N(R tappendR R (R Rtvalue((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR ?s(RRR R (((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR9s t DataHandlercBsGeZd„Zd„Zd„Zd„Zd„Zd„Zd„ZRS(cCsUg|_g|_g|_g|_g|_g|_i|_g|_||_dS(N( tstackterrorstintegerststringstlistst dictionariest structurestitemstdtd_dir(R R((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR Gs        cCs~tjƒ|_|jjtjƒ|j|j_|j|j_|j |j_ |j |j_ |jj |ƒd|_|jS(s2Set up the parser and let it parse the XML resultsN(Rt ParserCreatetparsertSetParamEntityParsingtXML_PARAM_ENTITY_PARSING_ALWAYSt startElementtStartElementHandlert endElementtEndElementHandlert characterstCharacterDataHandlertexternal_entity_ref_handlertExternalEntityRefHandlert ParseFiletNonetobject(R thandle((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pytrunRs cCsŘd|_||jkr$tƒ}n||jkr?tƒ}n||jkrdt|j|ƒ}nÜ||jkrt|dƒ}|d=t|dƒ}|d=|dkrštƒ}nB|d krÚtddgƒ}n!|d krňtƒ}n t ƒ}||_ ||_ n0||j |j |jkr:||_dSd}|dkrÄ||_|rmt|ƒ|_nt|jƒd krÄ|jd }y|j|ƒWqÁtk r˝|||RR@((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR"‡sD         cCs|j|7_dS(N(R6(R R6((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR$°scs$|jƒdkr&|jj|ƒdS|dkr…|tjjtjjdtjjtjj ddfffkr…|j j|ƒdSxl|dtjj tjj fkró|dtjj tjj fkrót|dƒdkró|dd}qˆW|dtjjtjjfkr*|jj|ƒdS|dtjj tjj fkr‚|dtjjtjjfkr‚|jj|ƒdSg‰g‰‡‡‡fd†‰ˆ|ƒtˆƒdkrätˆƒdkrä|jj|ƒn<tˆƒdkr |jj|ƒn|jjiˆ|6ƒdS( s*This callback function is called for each element declaration: encountered in a DTD. The purpose of this function is to determine whether this element should be regarded as a string, integer, list dictionary, structure, or error.tERRORNtItemiiicső|d\}}}|dkr€|tjjtjjfkrbx=|D]}ˆj|dƒqDWqńxŒ|D]}ˆ|ƒqiWnq|jƒdkrń|tjjtjjfkrŔˆj|ƒqń|tjjtjjfkrńˆj|ƒqńndS(NiiRE( R)RtmodeltXML_CQUANT_PLUStXML_CQUANT_REPRtuppertXML_CQUANT_NONEtXML_CQUANT_OPT(RGt quantifierR>tchildrentchild(tcounttmultipletsingle(s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyRPčs      ((RJRRRRGtXML_CTYPE_MIXEDRIR)tXML_CTYPE_NAMERKRt XML_CTYPE_SEQtXML_CTYPE_CHOICERLR<tXML_CTYPE_EMPTYRRHRRRtupdate(R R>RG((RPRQRRs„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyt elementDeclłsH    $c CsŤtjj|ƒ\}}tjj|j|ƒ}yt|ƒ}Wn9tk r{d||||j|f} t| ƒ‚nX|jj |ƒ} |j | _ | j |ƒdS(s°The purpose of this function is to load the DTD locally, instead of downloading it from the URL specified in the XML. Using the local DTD results in much faster parsing. If the DTD is not found locally, we try to download it. In practice, this may fail though, if the XML relies on many interrelated DTDs. If new DTDs appear, putting them in Bio/Entrez/DTDs will allow the parser to see them.sźUnable to load DTD file %s. Bio.Entrez uses NCBI's DTD files to parse XML files returned by NCBI Entrez. Though most of NCBI's DTD files are included in the Biopython distribution, sometimes you may find that a particular DTD file is missing. In such a case, you can download the DTD file from NCBI and install it manually. Usually, you can find missing DTD files at either http://www.ncbi.nlm.nih.gov/dtd/ or http://eutils.ncbi.nlm.nih.gov/entrez/query/DTD/ If you cannot find %s there, you may also try to search for it with a search engine such as Google. Please save %s in the directory %s in order for Bio.Entrez to find it. Alternatively, you can save %s in the directory Bio/Entrez/DTDs in the Biopython distribution, and reinstall Biopython. Please also inform the Biopython developers by sending an email to biopython-dev@biopython.org to inform us about this missing DTD, so that we can include it with the next release of Biopython. i( tostpathtsplittjoinRtopentIOErrorRBRtExternalEntityParserCreateRYtElementDeclHandlerR(( R tcontexttbasetsystemIdtpublicIdtlocationtfilenameR[R+tmessageR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyR&s   ( RRR R,R R"R$RYR&(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyREs ) )  N((t__doc__tos.pathRZt xml.parsersRtintRR7RtunicodeRtlistRR RRR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.pyt s