ó gbc@sÅddlmZmZddlmZddlmZddlmZmZddl Z de fd„ƒYZ edd d e ƒZ d „Zd efd „ƒYZd„Zdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZdefd„ƒYZd„Zd efd!„ƒYZd"„Zd#efd$„ƒYZd%efd&„ƒYZd'„Z d(„Z!dS()iÿÿÿÿ(tskipWhiteLineIteratortmultiLineWrapper(t universalOpen(tgenericEntryIteratorGenerator(tdebugtwarningNtFileFormatErrorcBseZdZRS(s7 An error derived from the class Exception. (t__name__t __module__t__doc__(((s2lib/python2.7/site-packages/obitools/obo/parser.pyRstendEntrys^ *$tstripcCs"t|ƒ}t|ƒ}t|ƒS(sf Iterator of stanza. The stanza are the basic units of OBO files. @param inputfile: a stream of strings from an opened OBO file. @type inputfile: a stream of strings @return: a stream of stanza @rtype: a stream of aggregated strings @note: The iterator constructs stanza by aggregate strings from the OBO file. (RRt_oboEntryIterator(t inputfile((s2lib/python2.7/site-packages/obitools/obo/parser.pytstanzaIterators  tTrailingModifiercBs&eZdZejdƒZd„ZRS(s™ A class object which inherits from the class dict. Trailing modifiers can be found at the end of TaggedValue objects when they exist. s(?<=\ {)[^\]]*(\}) *( !|$)cCs\tjj|ƒ}|rX|jdƒjƒ}|GHtj|d„|jdƒDƒƒndS(Nicss'|]}|jƒjddƒVqdS(t=iN(R tsplit(t.0tx((s2lib/python2.7/site-packages/obitools/obo/parser.pys Ast,(Rt _match_bracetsearchtgroupR tdictt__init__R(tselftstringttrailing_modifiers((s2lib/python2.7/site-packages/obitools/obo/parser.pyR7s (RRR tretcompileRR(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR/scCst|ƒ}|sd}n|S(s¥ Dispatcher of trailing modifiers. @param string: a string from a TaggedValue object with a trailing modifiers signal. @type string: string @return: a class object @note: The dispatcher is currently very simple. Only one case is treated by the function. `the function returns a class object inherited from the class dict if the trailing modifiers exist, None if they don't. N(RtNone(RR((s2lib/python2.7/site-packages/obitools/obo/parser.pyttrailingModifierFactoryDs  t TaggedValuecBseeZdZejdƒZejdƒZejdƒZejdƒZd„Z d„Z d„Z RS(s1 A couple 'tag:value' of an OBOEntry. s'(("(\\"|[^"])*")|(\\"|[^"]))*?( !| {|$)s^!| !s(?<=")(\\"|[^"])*(?=")s \[[^\]]*\]c Cs=td|ƒd }d }|jddƒ\}}tjj|ƒjdƒ}td|ƒ|rñ|ddkrñt|ƒ}||djƒ}tj j|dƒ}t|ƒdkrË|djƒ}n|d}t |ƒ}|dd!}n|d krd }t d ‚n|jƒ|_ ||_ ||_||_d S( s Constructor of the class TaggedValue. @param line: a line of an OBOEntry composed of a tag and a value. @type line: string @note: The constructor separates tags from right terms. 'value' is extracted from right terms using a regular expression (value is at the beginning of the string, between quotes or not). Then, 'comment' is extracted from the rest of the string using another regular expression ('comment' is at the end of the string after a '!'. By default, 'comment' is set to None). Finally, 'trailing_modifiers' are extracted from the last string using another regular expression. The tag, the value, the comment and the trailing_modifiers are saved. stagValueParser : %st:iisExtracted value : %siÿÿÿÿs!{ituse_termtconsiders>user_term is a deprecated tag, you should instead use considerN(RRRR!t _match_valueRRtlenR t_split_commentR tDeprecationWarningtvaluettagR R( RtlineRtcommentR*trigthR)tlvaluetextra((s2lib/python2.7/site-packages/obitools/obo/parser.pyRgs,       cCs t|jƒS(N(tstrR)(R((s2lib/python2.7/site-packages/obitools/obo/parser.pyt__str__žscCsdt|ƒS(Ns"""%s"""(R0(R((s2lib/python2.7/site-packages/obitools/obo/parser.pyt__repr__¡s( RRR RRR%R't_match_quotedStringt_match_bracketRR1R2(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR!]s 7 t NameValuecBseZdZd„ZRS(sb A couple 'name:value' inherited from the class TaggedValue. Used to manage name tags. cCsF|jddƒ\}}|jƒ|_d|_d|_d|_dS(NR"itname(RR R)R*RR R(RR+R*R-((s2lib/python2.7/site-packages/obitools/obo/parser.pyRªs   (RRR R(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR5¥stDefValuecBseZdZd„ZRS(s` A couple 'def:value' inherited from the class TaggedValue. Used to manage def tags. cCs•tj||ƒtjj|jƒjdƒ}|jj|dƒ}|jddƒ}tjj|ƒjdƒ}d|_||_t |ƒ|_ dS(s‰ Constructor of the class DefValue. @param line: a line of an OBOEntry composed of a tag named 'def' and a value. @type line: string @note: The constructor calls the TaggedValue constructor. A regular expression is used to extract the 'definition' from TaggedValue.value (definition is a not quoted TaggedValue.value). A regular expression is used to extract 'dbxrefs' from the aggedValue.value without the definition (dbxrefs are between brackets and definition can be so). Definition is saved as the new value of the DefValue. dbxrefs are saved. its t tdefN( R!RR3RR)RtreplaceR4R*t xrefFactorytdbxrefs(RR+t definitiont cleanvalueR=((s2lib/python2.7/site-packages/obitools/obo/parser.pyR¼s  (RRR R(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR7·st SynonymValuecBs8eZdZejdƒZd„Zd„Zd„ZRS(s° A couple 'synonym:value' inherited from the class TaggedValue. Used to manage synonym tags, exact_synonym tags, broad_synonym tags and narrow_synonym tags. s(?<="")[^\[]*(?=\[|$)c Csñtj||ƒtjj|jƒjdƒ}|jj|dƒ}|jddƒ}ttj j|ƒjdƒj ƒj ƒƒ}|tddddgƒ@}||}t |ƒd ksÆt d ƒ‚|rÛ|jƒ}nd}|jd kr td ‚d |_d}n|jdkr5td‚d |_d}n|jdkr_td‚d |_d}n|jdkr€d |_d}n|jd ks¢t d|jƒ‚tjj|ƒjdƒ}||_t|ƒ|_||_t|ƒ|_dS(s” Constructor of the class SynonymValue. @param line: a line of an OBOEntry composed of a tag named 'synonym' or 'exact_synonym' or 'broad_synonym' or 'narrow_synonym' and a value. @type line: string @note: SynonymValue is composed of a tag, a value, a scope, a list of types and dbxrefs. The constructor calls the TaggedValue constructor. A regular expression is used to extract 'definition' from TaggedValue.value (definition is a not quoted TaggedValue.value). Definition is saved as the new value of the class SynonymValue. A regular expression is used to extract 'attributes' from the rest of the string. Attributes may contain an optional synonym scope and an optional list of synonym types. The scope is extracted from attributes or set by default to 'RELATED'. It is saved as the scope of the class. The types are the rest of the attributes and are saved as the list of types of the class. For deprecated tags 'exact_synonym', 'broad_synonym' and 'narrow_synonym', tag is set to 'synonym' and scope is set respectively to 'EXACT', 'BROAD' and 'NARROW'. A regular expression is used to extract 'dbxrefs' from the TaggedValue.value without the definition (dbxrefs are between brackets and definition can be so). dbxrefs are saved. iR8s R9tRELATEDtEXACTtBROADtNARROWisOnly one synonym scope allowedt exact_synonyms9exact_synonym is a deprecated tag use instead synonym tagtsynonymt broad_synonyms9broad_synonym is a deprecated tag use instead synonym tagtnarrow_synonyms:narrow_synonym is a deprecated tag use instead synonym tagtsystematic_synonymt SYSTEMATICs%s synonym type is not managedN(R!RR3RR)RR;tsetR@t _match_scopeR RR&tAssertionErrortpopR*R(R4R<R=tscopetlistttypes( RR+R>R?t attributestscopesRQROR=((s2lib/python2.7/site-packages/obitools/obo/parser.pyRçs@-            "  cCs||j|jko{|j|jko{|j|jko{|j|jko{|j|jko{|j|jko{|j|jkS(N(R)R=RORQR R*R(Rtb((s2lib/python2.7/site-packages/obitools/obo/parser.pyt__eq__Bs$$$c CsWtd„d„|j|jt|jƒ|jt|jƒ|j|jgDƒdƒdS(NcSs||S(N((Rty((s2lib/python2.7/site-packages/obitools/obo/parser.pytIscss|]}t|ƒVqdS(N(thash(Rtz((s2lib/python2.7/site-packages/obitools/obo/parser.pys IsiiiI€( treduceR R)t frozensetR=RORQR*R(R((s2lib/python2.7/site-packages/obitools/obo/parser.pyt__hash__Hs  ( RRR RRRLRRUR\(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR@ßs  [ t XrefValuecBseZdZd„ZRS(sj A couple 'xref:value' inherited from the class TaggedValue. Used to manage xref tags. cCsftj||ƒt|jƒ|_|jdkrMtd|j‚d|_n|jdksbt‚dS(Nt xref_analogtxref_unks/%s is a deprecated tag use instead sysnonym tagtxref(R^R_(R!RR<R)R*R(RM(RR+((s2lib/python2.7/site-packages/obitools/obo/parser.pyRXs  (RRR R(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR]RstRelationshipValuecBseZdZd„ZRS(sj A couple 'xref:value' inherited from the class TaggedValue. Used to manage xref tags. cCsttj||ƒ|jjddƒ}t|ƒdkrN|d}|d}nd}|d}||_||_dS(Niiitis_a(R!RR)RRR&t relationship(RR+R)Rctterm((s2lib/python2.7/site-packages/obitools/obo/parser.pyRns    (RRR R(((s2lib/python2.7/site-packages/obitools/obo/parser.pyRahstNamespaceValuecBseZd„ZRS(cCstj||ƒdS(N(R!R(RR+((s2lib/python2.7/site-packages/obitools/obo/parser.pyR…s(RRR(((s2lib/python2.7/site-packages/obitools/obo/parser.pyRe„st RemarkValuecBseZd„ZRS(cCsYtj||ƒ|jjddƒ\}}|jƒ}|jƒ}||_||_dS(NR"i(R!RR)RR tlabel(RR+RgR)((s2lib/python2.7/site-packages/obitools/obo/parser.pyR‰s    (RRR(((s2lib/python2.7/site-packages/obitools/obo/parser.pyRfˆscCs^|dd!dks&|dd!dkr0t|ƒS|dd!dkrMt|ƒS|dd!d krs|dd !d ks¬|dd !d ks¬|dd !dks¬|dd !dkr¶t|ƒS|dd!dkrÓt|ƒS|dd!dkrðt|ƒS|dd!dks)|dd!dks)|dd!dkr3t|ƒS|dd!dkrPt|ƒSt|ƒSdS(sú A function used to dispatch lines of an OBOEntry between the class TaggedValue and its inherited classes. @param line: a line of an OBOEntry composed of a tag and a value. @type line: string @return: a class object ii t namespaceisdefault-namespaceiR:iRFitsynonymtypedefi RERGRHiR`R6itintersection_ofitunion_ofi RcitremarkN(ReR7R@R]R5RaRfR!(R+((s2lib/python2.7/site-packages/obitools/obo/parser.pyttaggedValueFactory’s*   &     tXrefcBs8eZdZejdƒZd„Zd„Zd„ZRS(s” A xref object of an OBOentry. It may be the 'dbxrefs' of SynonymValue and DefValue objects or the 'value' of XrefValue objects. s +(?=["{])cCsÐ|dkrd}d}ntjj|dƒ}|d}d}d}t|ƒdkr±|d}tjj|ƒ}|dk r¢|jdƒ}|j |dƒnt |ƒ}n||_ ||_ ||_ dS(NR8ii(RRnt __splitdata__RR&R!R3RRR;R t referencet descriptionR(RtreftdataRqRR/((s2lib/python2.7/site-packages/obitools/obo/parser.pyRÉs"       cCs4|j|jko3|j|jko3|j|jkS(N(RpRqR(RRT((s2lib/python2.7/site-packages/obitools/obo/parser.pyRUÝs$cCs3td„d„|j|j|jgDƒdƒdS(NcSs||S(N((RRV((s2lib/python2.7/site-packages/obitools/obo/parser.pyRWâscss|]}t|ƒVqdS(N(RX(RRY((s2lib/python2.7/site-packages/obitools/obo/parser.pys âsiiiI€(RZRpRqR(R((s2lib/python2.7/site-packages/obitools/obo/parser.pyR\ás( RRR RRRoRRUR\(((s2lib/python2.7/site-packages/obitools/obo/parser.pyRnÁs   cCs]|jƒ}|ddkrOg|dd!jdƒD]}t|jƒƒ^q3St|ƒSdS(s# Dispatcher of xrefs. @param string: a string (between brackets) from an inherited TaggedValue object with a dbxrefs signal (actually, the signal can only be found into SynonymValue and DefValue objects) or a string (without brackets) from a XrefValue object. @type string: string @return: a class object @note: The dispatcher treats differently the strings between brackets (from SynonymValue and DefValue objects) and without brackets (from XrefValue objects). it[iiÿÿÿÿRN(R RRn(RR((s2lib/python2.7/site-packages/obitools/obo/parser.pyR<çs 3tOBOEntrycBs;eZdZejdƒZd„Zd„ZeeƒZRS(sª An entry of an OBOFile. It can be a header (without a stanza name) or a stanza (with a stanza name between brackets). It inherits from the class dict. s(?<=^\[)[^\]]*(?=\])cCs¼|ddk|_|jdƒ}|jse|djƒdd!|_|d}|jƒg|dR‚RhR6R,talt_idsRbtsynonymstsubsetstxrefsRcRkRjR„R™R…R$(((s2lib/python2.7/site-packages/obitools/obo/parser.pyR€(sL                   cCs3tj|ƒ}|dkr%t|ƒSt|ƒSdS(s Dispatcher of stanza. @param stanza: a stanza composed of several lines. @type stanza: text @return: an C{OBOTerm} | C{OBOEntry} instance @note: The dispatcher treats differently the stanza which are OBO "Term" and the others. RN(RuR~R€(Rvt stanzaType((s2lib/python2.7/site-packages/obitools/obo/parser.pytOBOEntryFactory©s   ccs6t|ƒ}x#|D]}t|ƒt|ƒVqWdS(N(RRR£(tfiletentrieste((s2lib/python2.7/site-packages/obitools/obo/parser.pytOBOEntryIterator½s   ("tobitools.utilsRRRtobitools.format.genericparserRtloggingRRRt ExceptionRtTrueR RRRR tobjectR!R5R7R@R]RaReRfRmRnR<RuR€R£R§(((s2lib/python2.7/site-packages/obitools/obo/parser.pyts2     H(s /& &