B ‰°bˆã@s dZddlZddlZddlmZddlmZddlmZddl m m Z ddl mZddlmZmZGdd „d ƒZGd d „d eƒZGd d „d eƒZGdd„deƒZGdd„deƒZGdd„deƒZGdd„deƒZGdd„deƒZGdd„deƒZ Gdd„de dZ!dS)a‚Parser 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. The question is how to represent an XML file as Python objects. Some XML files returned by NCBI look like lists, others look like dictionaries, and others look like a mix of lists and dictionaries. My approach is to classify each possible element in the XML as a plain string, an integer, a list, a dictionary, or a structure. The latter is a dictionary where the same key can occur multiple times; in Python, it is represented as a dictionary where that key occurs once, pointing to a list of values found in the XML file. The parser then goes through the XML and creates the appropriate Python object for each element. The different levels encountered in the XML are preserved on the Python side. So a subelement of a subelement of an element is a value in a dictionary that is stored in a list which is a value in some other dictionary (or a value in a list which itself belongs to a list which is a value in a dictionary, and so on). Attributes encountered in the XML are stored as a dictionary in a member .attributes of each element, and the tag name is saved in a member .tag. To decide which kind of Python object corresponds to each element in the XML, the parser analyzes the DTD referred at the top of (almost) every XML file returned by the Entrez Utilities. This is preferred over a hand- written solution, since the number of DTDs is rather large and their contents may change over time. About half the code in this parser deals with parsing the DTD, and the other half with the XML itself. éN)ÚCounter)Úexpat)ÚBytesIO)Úescape)ÚurlopenÚurlparsec@s2eZdZdZd dd„Zdd„Zdd„Zd d „ZdS) Ú NoneElementz'NCBI Entrez XML element mapped to None.NcCs&||_|dkr||_n||_||_dS)zCreate a NoneElement.N)ÚtagÚkeyÚ attributes)Úselfr r r ©r ú0lib/python3.7/site-packages/Bio/Entrez/Parser.pyÚ__init__:s zNoneElement.__init__cCs"|dkr dS| d¡rdSdSdS)z(Define equality with other None objects.NTF)Ú__eq__)r Úotherr r rrCs  zNoneElement.__eq__cCs"|dkr dS| d¡rdSdSdS)zDefine non-equality.NFT)r)r rr r rÚ__ne__Ls  zNoneElement.__ne__cCs(y |j}Wntk rdSXd|S)z-Return a string representation of the object.rzNoneElement(attributes=%r))r ÚAttributeError)r r r r rÚ__repr__Us  zNoneElement.__repr__)N)Ú__name__Ú __module__Ú __qualname__Ú__doc__rrrrr r r rr7s    rc@s"eZdZdZddd„Zdd„ZdS)ÚIntegerElementz-NCBI Entrez XML element mapped to an integer.NcCs2t ||¡}||_|dkr"||_n||_||_|S)zCreate an IntegerElement.N)ÚintÚ__new__r r r )ÚclsÚvaluer r r r r r rras zIntegerElement.__new__cCs6t |¡}y |j}Wntk r(|SXd||fS)z-Return a string representation of the object.z!IntegerElement(%s, attributes=%r))rrr r)r Útextr r r rrls   zIntegerElement.__repr__)N)rrrrrrr r r rr^s rc@s"eZdZdZddd„Zdd„ZdS)Ú StringElementz+NCBI Entrez XML element mapped to a string.NcCs2t ||¡}||_|dkr"||_n||_||_|S)zCreate a StringElement.N)Ústrrr r r )rrr r r r r r rrys zStringElement.__new__cCs$t |¡}|j}|s|Sd||fS)z-Return a string representation of the object.z StringElement(%s, attributes=%r))r rr )r rr r r rr„s  zStringElement.__repr__)N)rrrrrrr r r rrvs rc@s*eZdZdZd dd„Zdd„Zdd„ZdS) Ú ListElementz)NCBI Entrez XML element mapped to a list.NcCs,||_|dkr||_n||_||_||_dS)zCreate a ListElement.N)r r r Ú allowed_tags)r r r r"r r r rrs zListElement.__init__cCs$t |¡}|j}|s|Sd||fS)z-Return a string representation of the object.zListElement(%s, attributes=%r))Úlistrr )r rr r r rršs  zListElement.__repr__cCs4|j}|jdk r&||jkr&td|ƒ‚| |¡dS)z-Append an element to the list, checking tags.NzUnexpected item '%s' in list)r r"Ú ValueErrorÚappend)r rr r r rÚstore¢s zListElement.store)N)rrrrrrr&r r r rr!s r!c@s*eZdZdZd dd„Zdd„Zdd„ZdS) ÚDictionaryElementz0NCBI Entrez XML element mapped to a dictionaray.NcCsL||_|dkr||_n||_||_||_||_|rHx|D] }g||<q8WdS)zCreate a DictionaryElement.N)r r r r"Ú repeated_tags)r r Úattrsr"r(r r r rr­s zDictionaryElement.__init__cCs$t |¡}|j}|s|Sd||fS)z-Return a string representation of the object.zDictElement(%s, attributes=%r))Údictrr )r rr r r rr»s  zDictionaryElement.__repr__cCsX|j}|j}|jdk r,||jkr,td|ƒ‚|jrL||jkrL|| |¡n|||<dS)z.Add an entry to the dictionary, checking tags.Nz"Unexpected item '%s' in dictionary)r r r"r$r(r%)r rr r r r rr&Ãs zDictionaryElement.store)NN)rrrrrrr&r r r rr'ªs r'c@s eZdZdZdd„Zdd„ZdS)Ú NotXMLErrorzFailed to parse file as XML.cCs ||_dS)zInitialize the class.N)Úmsg)r Úmessager r rrÒszNotXMLError.__init__cCs d|jS)z)Return a string summary of the exception.zZFailed to parse the XML data (%s). Please make sure that the input data are in XML format.)r,)r r r rÚ__str__ÖszNotXMLError.__str__N)rrrrrr.r r r rr+Ïsr+c@s eZdZdZdd„Zdd„ZdS)ÚCorruptedXMLErrorzCorrupted XML.cCs ||_dS)zInitialize the class.N)r,)r r-r r rrászCorruptedXMLError.__init__cCs d|jS)z)Return a string summary of the exception.zZFailed to parse the XML data (%s). Please make sure that the input data are not corrupted.)r,)r r r rr.åszCorruptedXMLError.__str__N)rrrrrr.r r r rr/Þsr/c@s eZdZdZdd„Zdd„ZdS)ÚValidationErrora_XML tag found which was not defined in the DTD. Validating parsers raise this error if the parser finds a tag in the XML that is not defined in the DTD. Non-validating parsers do not raise this error. The Bio.Entrez.read and Bio.Entrez.parse functions use validating parsers by default (see those functions for more information). cCs ||_dS)zInitialize the class.N)Úname)r r1r r rröszValidationError.__init__cCs d|jS)z)Return a string summary of the exception.zžFailed to find tag '%s' in the DTD. 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ÚERRORNr„r rrxécss|]}|dVqdS)rkNr )Ú.0Úchildr r rú Asz*DataHandler.elementDecl..css|]}|dVqdS)rkNr )r£r¤r r rr¥Nscs²|dd…\}}}|dkrd|tjjtjjfkrLx2|D]}ˆ |d¡q4Wq®x`|D] }ˆ|ƒqRWnJ| ¡dkr®|tjjtjjfkrˆ |¡n|tjjtjjfkr®ˆ |¡dS)Nrxrkr¡)rÚmodelÚXML_CQUANT_PLUSÚXML_CQUANT_REPr%ÚupperÚXML_CQUANT_NONEÚXML_CQUANT_OPT)r¦Z quantifierr Úchildrenr¤)Úcountr Úsingler rr­^s$       z&DataHandler.elementDecl..count)r©rWÚaddrr¦ZXML_CTYPE_MIXEDr¨ZXML_CTYPE_NAMErªrVZ XML_CTYPE_SEQZXML_CTYPE_CHOICEr«rmZXML_CTYPE_EMPTYr‹rRr§rzrSrT)r r1r¦r¬r"r(r )r­r r®rÚ elementDeclsT        zDataHandler.elementDeclcCsttj tj|¡}yt|dƒ}Wntk r2YnX|Stj tj|¡}yt|dƒ}Wntk rjYnX|SdS)zOpen specified DTD file.ÚrbN)r@rArBrKrEÚopenÚFileNotFoundErrorÚglobal_dtd_dir)r ÚfilenamerArir r rÚ open_dtd_fileszDataHandler.open_dtd_filecCsttj tj|¡}yt|dƒ}Wntk r2YnX|Stj tj|¡}yt|dƒ}Wntk rjYnX|SdS)zOpen specified XSD file.r±N)r@rArBrKrGr²r³Úglobal_xsd_dir)r rµrArir r rr}‘szDataHandler.open_xsd_filecCs\tj tj|¡}yt|dƒ}Wn&tk rDt d||f¡YnX|  |¡|  ¡dS)zSave DTD file to cache.ÚwbzFailed to save %s at %sN) r@rArBrKrEr²ÚOSErrorÚwarningsÚwarnÚwriter€)r rµrrArir r rÚ save_dtd_file£s zDataHandler.save_dtd_filecCs\tj tj|¡}yt|dƒ}Wn&tk rDt d||f¡YnX|  |¡|  ¡dS)zSave XSD file to cache.r¸zFailed to save %s at %sN) r@rArBrKrGr²r¹rºr»r¼r€)r rµrrArir r rr®s zDataHandler.save_xsd_filec Cs8t|ƒ}|jdkr|}n`|jdkrjy|jd}Wntk rHd}YnXtj |¡}| d¡d|}ntd|jƒ‚|j  |¡tj  |¡\}} |  | ¡} | súy t |ƒ} Wn&t k rÔtd| |fƒd‚YnX|  ¡} |  ¡| | | ¡t| ƒ} |j |¡} |j| _|  | ¡|  ¡|j ¡|j|j_d S) a¾Handle external entity reference in order to cache DTD locally. 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