ó
£b8^c           @   s¥   d  d l  Z  d  d l Z d  d l Z d  d l Z d  d l Z d  d l m Z m Z m Z m	 Z	 m
 Z
 m Z d  d l m Z d „  Z d „  Z d „  Z d d „ Z d S(   iÿÿÿÿN(   t   Flaskt   render_templatet   sessiont   requestt   url_fort   redirect(   t   MySQLc         C   s   d j  | t j d d |  ƒ ƒ S(   Ns   >{}
{}s   .{60}s   \g<0>
(   t   formatt   ret   sub(   t   seqt   header(    (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt
   prep_fasta
   s    c      
   C   s¾  | d d k r" d j  | ƒ } n  t j j |  j d ƒ t t j ƒ  ƒ } | d } | d } t | d ƒ  } | j	 | ƒ Wd  QXt
 j |  j d d	 j  | | ƒ d
 t ƒyÒ g  } t | d ƒ · } x­ | D]¥ } | j ƒ  } t | ƒ d k rÏ | j d ƒ \ }	 }
 } t j d |
 ƒ } | j i | j d ƒ d 6| j d ƒ d 6| j d ƒ d 6| j d ƒ d 6| d 6ƒ qÏ qÏ WWd  QXWn t k
 r™g  t f SXt j | ƒ t j | ƒ | t f S(   Ni    t   >s   >User provided sequence
{}s   tmp/pdbs   .query_fastas   .blast_reportt   wt   BLAST_CMDLINEs    -query {} -out {}t   shellt   ri   s   	s,   (....)_(.) mol:([^ ]*) length:([0-9]*) *(.*)t   idCodei   R	   i   t   tipi   t   desct   ev(   R   t   ost   patht   joint   instance_patht   strt   uuidt   uuid4t   opent   writet
   subprocesst   runt   configt   Truet   rstript   lent   splitR   t   matcht   appendt   groupt   IOErrort   removet   False(   t   appt   queryt   tmpFileNamet   query_fasta_filet   blast_report_filet   query_fastat   resultst   reportt   linet   idR   R   t   m(    (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt	   run_blast   s>    (


c   	      C   s'  d g } |  d d k s) |  d d k r| |  d d k rQ | j  d |  d ƒ n  |  d d k r| | j  d |  d ƒ q| n  g  } xR | d j ƒ  D]@ \ } } d	 t | ƒ d
 |  k r“ | j  d t | ƒ ƒ q“ q“ W| rþ | j  d d j | ƒ d ƒ n  g  } xR | d j ƒ  D]@ \ } } d t | ƒ d
 |  k r| j  d t | ƒ ƒ qqW| r€| j  d d j | ƒ d ƒ n  |  d rãg  } x/ | D]' } | j  d | d |  d d ƒ q—W| j  d d j | ƒ d ƒ n  d d d d d d d j | ƒ } d |  k r#| d 7} n  | S(   s    Prepare SQL from search form R"   t   minRess   0.0t   maxRest   Infs   e.resolution >= s   e.resolution <= t   compTypeArrays   idCompType[t   ]s    e.idCompType = t   (s    OR t   )t   expClasseArrays   idExpClasse[s    et.idExpClasse = R-   s   MATCH (s   ) AGAINST ('s   ' IN BOOLEAN MODE)sS   SELECT distinct e.idCode,e.header,e.compound,e.resolution,s.source,et.expType FROM se   expType et, author_has_entry ae, author a, source s, entry_has_source es, entry e, sequence sq WHERE s   e.idExpType=et.idExpType AND s2   ae.idCode=e.idCode and ae.idAuthor=a.idAuthor AND s2   es.idCode=e.idCode and es.idsource=s.idSource AND s   e.idCode = sq.idCode AND s    AND t   nolimits    LIMIT 5000(   R'   t   itemsR   R   (	   t	   form_datat	   glob_varst   text_fieldst   ANDcondst   ORCondst   keyt   valuet   fieldt   sql(    (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt   prep_sql4   s6    	 !!
%!	'c            sh  t  t d t ƒ‰  y? t j ˆ  j d t ƒt j t j j ˆ  j d ƒ d t ƒWn  t k
 rs } t	 j
 | ƒ n Xˆ  j j d d t ƒt ˆ  ƒ ‰ ‡ f d †  ‰ ˆ  j ˆ  j d d ƒ ‡  ‡ f d	 †  ƒ } ˆ  j ˆ  j d d
 d d d g ƒ‡  ‡ ‡ f d †  ƒ } ˆ  j ˆ  j d d ƒ ‡  f d †  ƒ } ˆ  j ˆ  j d d ƒ ‡  ‡ ‡ f d †  ƒ } ˆ  S(   Nt   instance_relative_configt   exist_okt   tmps	   config.pyt   silentc             sß   i  }  i  |  d <ˆ  j  j ƒ  } | j d ƒ x( | j ƒ  D] \ } } | |  d | <q9 Wi  |  d <| j d ƒ x( | j ƒ  D] \ } } | |  d | <q{ Wi  |  d <| j d ƒ x( | j ƒ  D] \ } } | |  d | <q½ W|  S(   NR;   s   SELECT * from comptypeR?   s   SELECT * from expClasset   expTypeArrays&   SELECT idExptype, ExpType from expType(   t
   connectiont   cursort   executet   fetchall(   t   globalst   curRG   RH   (   t   mysql(    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt   get_globalsr   s    


t   BASE_URLt   /c             s`   ˆ ƒ  }  d t  k r3 i d d 6d d 6d d 6} n
 t  d } t d d	 ˆ  j d
 d | d |  ƒS(   Nt
   query_datas   0.0R8   R:   R9   t    R-   s
   index.htmlt   titlet   TITLERU   (   R   R   R!   (   RC   R[   (   R,   RX   (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt   index‡   s    	
s   /search/t   methodst   GETt   POSTc       	      sü  ˆ ƒ  }  t  j t d <t  j d r@ t t d d t  j d ƒƒ St  j d s] t  j d j rÚ t  j d j rŒ t  j d j ƒ  j d ƒ } n t  j d } | sÀ t	 d d ˆ  j
 d	 d
 d d ƒS| t d <t t d ƒ ƒ St t  j |  ˆ  j
 d ƒ } g  } ˆ j j ƒ  } | j | ƒ } | sAt	 d d ˆ  j
 d	 d d d ƒSx‡ | j ƒ  D]y } | j i | d d 6| d j ƒ  j ƒ  d 6| d j ƒ  j ƒ  d 6| d d 6| d j ƒ  j ƒ  d 6| d d 6ƒ qNWt	 d d ˆ  j
 d	 d d t | ƒ d  | ƒSd  S(!   NR[   R   t   showt   seqQueryt   seqFilet   asciis
   error.htmlR]   R^   s    No input sequence foundt
   error_texts   No input sequence foundt	   query_seqt   blastt   TEXT_FIELDSs    No results founds   No results foundi    i   R   i   t   compoundi   t
   resolutioni   t   sourcei   t   expTypes   search_output.htmls    - Blast searcht   countR2   (   R   t   formR   R   R   t   filest   filenamet   readt   decodeR   R!   RK   RQ   RR   RS   RT   R'   t   lowert
   capitalizeR$   (   RC   t   sequenceRJ   R2   RV   t   rst   data(   R,   RX   RW   (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt   searchœ   sL    	
s   /blast/c             sq   t  ˆ  t d ƒ \ }  } | r@ t d d ˆ  j d d d d ƒSt d d ˆ  j d d	 d
 t |  ƒ d |  ƒSd  S(   NRh   s
   error.htmlR]   R^   s    No Blast results foundRg   s   No results founds   blast_output.htmls    - Blast searchRo   R2   (   R7   R   R   R!   R$   (   R2   t   error(   R,   (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyRi   Õ   s    s   /show/<idCode>c   
         s­  ˆ ƒ  } ˆ j  j ƒ  } | j d j |  ƒ ƒ } | s\ t d d ˆ  j d d d j |  ƒ ƒSg  | j D] } | d ^ qf } t t | | j	 ƒ  ƒ ƒ } | j d j |  ƒ ƒ } d	 j
 g  | j ƒ  D] } | d ^ qÂ ƒ | d
 <| j d j |  ƒ ƒ } d	 j
 g  | j ƒ  D] } | d ^ q
ƒ | d <| j d j |  ƒ ƒ } g  | d <x6 | j ƒ  D]( }	 | d j t |	 d |	 d ƒ ƒ qVWt d d ˆ  j d d |  d | d | ƒS(   Ns+   SELECT e.* from entry e where e.idCode='{}'s
   error.htmlR]   R^   Rg   s   Structure not found ({})i    sv   SELECT a.author from author a, author_has_entry ae where ae.idCode='{}' and a.idAuthor = ae.idAuthor order by a.authors   , t   author_listsv   SELECT s.source from source s, entry_has_source es where es.idCode='{}' and s.idSource = es.idSource order by s.sourcet   source_lists=   SELECT * from sequence s where s.idCode='{}' order by s.chaint	   sequencesi   i   s	   show.htmls    - RU   Ry   (   RQ   RR   RS   R   R   R!   t   descriptiont   dictt   zipt   fetchoneR   RT   R'   R   (
   R   RC   RV   Rx   t   colt   columnsRy   t   autt   sct   sq(   R,   RX   RW   (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyRc   é   s.    	 00
&(   R    t   __name__R"   R   t   makedirsR   R   R   t   OSErrort   syst   exitR!   t   from_pyfileR+   R   t   route(   t   test_configt   eR_   Rz   Ri   Rc   (    (   R,   RX   RW   s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt
   create_appc   s    ),;9)/(   R   R‹   R   R   R   t   flaskR    R   R   R   R   R   t   flask_mysqldbR   R   R7   RK   t   NoneR‘   (    (    (    s>   /home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyt   <module>   s   .		'	/