ó
{™xTc           @   sš   d  d l  m Z d  d l m Z d  d l Z d  d l m Z d  d l m Z d  d l Z d „  Z	 d „  Z
 d e f d	 „  ƒ  YZ d
 e f d „  ƒ  YZ d S(   iÿÿÿÿ(   t   division(   t   SorryN(   t   slots_getstate_setstate(   t   parseStringc         C   s!   |  j  | ƒ } | d j d j S(   Ni    (   t   getElementsByTagNamet
   childNodest   data(   t   xml_nodet	   node_namet   child_nodes(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   get_node_data	   s    c         C   sö   t  |  t ƒ rB y t |  ƒ }  WqB t k
 r> t d ƒ ‚ qB Xn  d } t j i t |  ƒ d 6d d 6d d 6d d	 6ƒ } t j j	 | | ƒ j
 ƒ  } t | ƒ } | j d
 ƒ } t | ƒ d k rÐ t d ƒ ‚ n  t | ƒ d k sè t ‚ t | d ƒ S(   Ns   PubMed IDs must be integers.s8   http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgit   idt   fullt   rettypet   PubMedt   dbt   xmlt   retmodet   PubmedArticlei    s   No article with PMID %s found.i   (   t
   isinstancet   strt   intt
   ValueErrorR   t   urllibt	   urlencodet   libtbxt   utilst   urlopent   readR   R   t   lent   AssertionErrort   article(   t   pmidt   urlt   paramst   resultt   xmlrect   articles(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   get_pubmed_xml   s$    	t   authorc           B   s/   e  Z d  d g Z d „  Z d „  Z d „  Z RS(   t	   last_namet   initialsc         C   s:   t  | d ƒ j d ƒ |  _ t  | d ƒ j d ƒ |  _ d  S(   Nt   LastNames   utf-8t   Initials(   R
   t   encodeR(   R)   (   t   selfR   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   __init__$   s    c         C   s   d |  j  |  j f j ƒ  S(   Ns   %s %s(   R(   R)   t   strip(   R-   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   __str__(   s    c         C   sE   d } x% t  |  j ƒ D] } | d | 7} q Wd |  j | f j ƒ  S(   Nt    s   %s.s   %s, %s(   t   listR)   R(   R/   (   R-   R)   t   i(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   bibtex+   s    (   t   __name__t
   __module__t	   __slots__R.   R0   R4   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyR'   "   s   		R   c           B   sA   e  Z d  d d d d d d d g Z d „  Z d	 „  Z d
 „  Z RS(   t   authorst   titlet   yeart   journalt   volumet   pagesR    t   doic         C   sH  | j  d ƒ } g  |  _ x$ | D] } |  j j t | ƒ ƒ q Wt | d ƒ j d ƒ |  _ t | d ƒ j d ƒ |  _ t | d ƒ j d ƒ |  _ t | d ƒ j d ƒ |  _	 t | d ƒ j d ƒ |  _
 t | d ƒ j d ƒ |  _ d  |  _ | j  d	 ƒ } xH | D]@ } | j d
 ƒ } | d k r | j d j j d ƒ |  _ q q Wd  S(   Nt   Authort   ArticleTitles   utf-8t   Yeart	   MedlineTAt   Volumet
   MedlinePgnt   PMIDt	   ArticleIdt   IdTypeR>   i    (   R   R8   t   appendR'   R
   R,   R9   R:   R;   R<   R=   R    t   NoneR>   t   getAttributeR   R   (   R-   R$   R8   t   author_xml_nodet   article_idsR   t   id_type(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyR.   4   s     		c         C   s±   d } |  j  d  k	 r% d |  j  } n  d j d d |  j d d j g  |  j D] } t | ƒ ^ qK ƒ d |  j d	 |  j d
 |  j d |  j	 d |  j
 d | d |  j d g ƒ S(   NRI   s   "%s"s   
s
   citation {s     article_id = %ss     authors = %ss   , s     title = %ss     journal = %ss     volume = %ss     pages = %ss     year = %ss     doi_id = %ss     pmid = %st   }(   R>   RI   t   joinR    R8   R   R9   R;   R<   R=   R:   (   R-   R>   t   a(    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   as_phenix_citationF   s    
,





c      	   C   sx   d j  d |  j d d j  g  |  j D] } | j ƒ  ^ q# ƒ d |  j d |  j d |  j d |  j d	 |  j d
 g ƒ S(   Ns   
s   @Article{%s,s     Author = {%s},s    and s     Year = {%s},s     Title = {%s},s     Journal = {%s},s     Volume = {%s},s     Pages = {%s},RN   (	   RO   R    R8   R4   R:   R9   R;   R<   R=   (   R-   RP   (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   as_bibtex_citationW   s    
,




(   R5   R6   R7   R.   RQ   RR   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyR   1   s
   		(   t
   __future__R    t   libtbx.utilsR   R   R   t   xml.dom.minidomR   R   R
   R&   R'   R   (    (    (    sI   /public2/ftp/pub/ccp4/6.5/ccp4-6.5/lib/py2/iotbx/bioinformatics/pubmed.pyt   <module>   s   		