
b8^8'                 @   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 d   Z d d   Z d d	   Z d d
 d  Z d S)    N)Flaskrender_templatesessionrequesturl_forredirect)MySQLc             C   s   d j  | t j d d |    S)Nz>{}
{}z.{60}z\g<0>
)formatresub)seqheader r   >/home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.py
prep_fasta
   s    r   c             C   s  | d d k r" d j  |  } n  t j j |  j d  t t j    } | d } | d } t | d   } | j	 |  Wd  QXt
 j |  j d d	 j  | |  d
 d y g  } t | d   } x | D] } | j   } t |  d k r | j d  \ }	 }
 } t j d |
  } | j i | j d  d 6| j d  d 6| j d  d 6| j d  d 6| d 6 q q WWd  QXWn t k
 rg  d f SYn Xt j |  t j |  | d f S)Nr   >z>User provided sequence
{}ztmp/pdbz.query_fastaz.blast_reportwZBLAST_CMDLINEz -query {} -out {}shellTr   	z,(....)_(.) mol:([^ ]*) length:([0-9]*) *(.*)idCode   r      Ztip   descevF)r	   ospathjoininstance_pathstruuiduuid4openwrite
subprocessrunconfigrstriplensplitr
   matchappendgroupIOErrorremove)appqueryZtmpFileNameZquery_fasta_fileZblast_report_fileZquery_fastaresultsreportlineidr   r   mr   r   r   	run_blast   s>    (


r8   c       	      C   s'  d g } |  d d k s) |  d d k r| |  d d k rQ | j  d |  d  n  |  d d k r| | j  d |  d  q| n  g  } xR | d j   D]@ \ } } d	 t |  d
 |  k r | j  d t |   q q W| r | j  d d j |  d  n  g  } xR | d j   D]@ \ } } d t |  d
 |  k r| j  d t |   qqW| r| j  d d j |  d  n  |  d rg  } x/ | D]' } | j  d | d |  d d  qW| j  d d j |  d  n  d d d d d d d j |  } d |  k r#| d 7} n  | S)z Prepare SQL from search form TrueminResz0.0maxResInfze.resolution >= ze.resolution <= compTypeArrayzidCompType[]z e.idCompType = (z OR )expClasseArrayzidExpClasse[z et.idExpClasse = r2   zMATCH (z) AGAINST ('z' IN BOOLEAN MODE)zSSELECT distinct e.idCode,e.header,e.compound,e.resolution,s.source,et.expType FROM zeexpType et, author_has_entry ae, author a, source s, entry_has_source es, entry e, sequence sq WHERE ze.idExpType=et.idExpType AND z2ae.idCode=e.idCode and ae.idAuthor=a.idAuthor AND z2es.idCode=e.idCode and es.idsource=s.idSource AND ze.idCode = sq.idCode AND z AND Znolimitz LIMIT 5000)r-   itemsr!   r   )	Z	form_data	glob_varsZtext_fieldsZANDcondsZORCondskeyvaluefieldsqlr   r   r   prep_sql4   s6    	 !!
%!	'rH   c                s  t  t d d   y? t j   j d d t j t j j   j d  d d Wn2 t k
 r } z t j	 |  WYd  d  } ~ Xn X  j
 j d d d t      f d d	      j   j
 d
 d     f d d    }   j   j
 d
 d d d d g     f d d    }   j   j
 d
 d    f d d    }   j   j
 d
 d      f d d    }   S)Ninstance_relative_configTexist_oktmpz	config.pysilentFc                 s   i  }  i  |  d <  j  j   } | j d  x( | j   D] \ } } | |  d | <q9 Wi  |  d <| j d  x( | j   D] \ } } | |  d | <q{ Wi  |  d <| j d  x( | j   D] \ } } | |  d | <q W|  S)Nr=   zSELECT * from comptyperA   zSELECT * from expClasseZexpTypeArrayz&SELECT idExptype, ExpType from expType)
connectioncursorexecutefetchall)globalscurrD   rE   )mysqlr   r   get_globalsr   s    


zcreate_app.<locals>.get_globalsZBASE_URL/c                 s`      }  d t  k r3 i d d 6d d 6d d 6} n
 t  d } t d d	   j d
 d | d |  S)N
query_dataz0.0r:   r<   r;    r2   z
index.htmltitleTITLErQ   )r   r   r(   )rC   rV   )r1   rT   r   r   index   s    	
zcreate_app.<locals>.indexz/search/methodsGETPOSTc                 s     }  t  j t d <t  j d r@ t t d d t  j d  St  j d s] t  j d j r t  j d j r t  j d j   j d  } n t  j d } | s t	 d d   j
 d	 d
 d d S| t d <t t d   St t  j |    j
 d  } g  }  j j   } | j |  } | sAt	 d d   j
 d	 d d d Sx | j   D]y } | j i | d d 6| d j   j   d 6| d j   j   d 6| d d 6| d j   j   d 6| d d 6 qNWt	 d d   j
 d	 d d t |  d  | Sd  S)!NrV   r   showZseqQueryZseqFileasciiz
error.htmlrX   rY   z No input sequence found
error_textzNo input sequence found	query_seqblastZTEXT_FIELDSz No results foundzNo results foundr   r   r   r   Zcompoundr   
resolution   sourcer   ZexpTypezsearch_output.htmlz - Blast searchcountr3   )r   formr   r   r   filesfilenamereaddecoder   r(   rH   rM   rN   rO   rP   r-   lower
capitalizer*   )rC   sequencerG   r3   rR   rsdata)r1   rT   rS   r   r   search   sL    	
zcreate_app.<locals>.searchz/blast/c                 sq   t    t d  \ }  } | r@ t d d   j d d d d St d d   j d d	 d
 t |   d |  Sd  S)Nra   z
error.htmlrX   rY   z No Blast results foundr`   zNo results foundzblast_output.htmlz - Blast searchrf   r3   )r8   r   r   r(   r*   )r3   error)r1   r   r   rb      s    zcreate_app.<locals>.blastz/show/<idCode>c                s     }  j  j   } | j d j |    } | s\ t d d   j d d d j |   Sd d   | j D } t t | | j	     } | j d	 j |    } d
 j
 d d   | j   D  | d <| j d j |    } d
 j
 d d   | j   D  | d <| j d j |    } g  | d <x6 | j   D]( } | d j t | d | d   q8Wt d d   j d d |  d | d | S)Nz+SELECT e.* from entry e where e.idCode='{}'z
error.htmlrX   rY   r`   zStructure not found ({})c             S   s   g  |  ] } | d   q S)r   r   ).0colr   r   r   
<listcomp>   s   	 z,create_app.<locals>.show.<locals>.<listcomp>zvSELECT a.author from author a, author_has_entry ae where ae.idCode='{}' and a.idAuthor = ae.idAuthor order by a.authorz, c             S   s   g  |  ] } | d   q S)r   r   )rs   Zautr   r   r   ru      s   	 Zauthor_listzvSELECT s.source from source s, entry_has_source es where es.idCode='{}' and s.idSource = es.idSource order by s.sourcec             S   s   g  |  ] } | d   q S)r   r   )rs   Zscr   r   r   ru      s   	 Zsource_listz=SELECT * from sequence s where s.idCode='{}' order by s.chain	sequencesr   r   z	show.htmlz - rQ   rp   )rM   rN   rO   r	   r   r(   descriptiondictzipZfetchoner   rP   r-   r   )r   rC   rR   ro   columnsrp   sq)r1   rT   rS   r   r   r^      s.    	&&
&zcreate_app.<locals>.show)r   __name__r   makedirsr    r   r   OSErrorsysexitr(   from_pyfiler   route)Ztest_configerZ   rq   rb   r^   r   )r1   rT   rS   r   
create_appc   s    ) />9,2r   )r   r   r
   r"   r&   flaskr   r   r   r   r   r   Zflask_mysqldbr   r   r8   rH   r   r   r   r   r   <module>   s   .'/