3
]u`'                 @   sz   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   sD  |d dkrdj |}tjj| jdttj  }|d }|d }t|d}|j	| W d Q R X t
j| jd d	j || d
d yg }t|dr}xj|D ]b}|j }t|dkr|jd\}	}
}tjd|
}|j|jd|jd|jd|jd|d qW W d Q R X W n tk
r&   g d
fS X tj| tj| |dfS )Nr   >z>User provided sequence
{}ztmp/pdbz.query_fastaz.blast_reportwZBLAST_CMDLINEz -query {} -out {}T)shellr   	z,(....)_(.) mol:([^ ]*) length:([0-9]*) *(.*)         )idCoder   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rZ| d dkr<|j d| d   | d dkrZ|j d| d   g }x>|d j D ].\}}d	t| d
 | krl|j dt|  qlW |r|j ddj| d  g }x>|d j D ].\}}dt| d
 | kr|j dt|  qW |r|j ddj| d  | d rpg }x,|D ]$}|j d| d | d  d  q0W |j ddj| d  dd d d d d dj| }d| kr|d7 }|S )z Prepare SQL from search form TrueminResz0.0maxResInfze.resolution >= ze.resolution <= compTypeArrayzidCompType[]z e.idCompType = (z OR )expClasseArrayzidExpClasse[z et.idExpClasse = r2   zMATCH (z) AGAINST ('z' IN BOOLEAN MODE)zSSELECT distinct e.idCode,e.header,e.compound,e.resolution,s.source,et.expType FROM zeexpType et, author_has_entry ae, author a, source s, entry_has_source es, entry e, sequence sq WHERE ze.idExpType=et.idExpType AND z2ae.idCode=e.idCode and ae.idAuthor=a.idAuthor AND z2es.idCode=e.idCode and es.idsource=s.idSource AND ze.idCode = sq.idCode AND z AND Znolimitz LIMIT 5000)r-   itemsr!   r   )	Z	form_data	glob_varsZtext_fieldsZANDcondsZORCondskeyvaluefieldsqlr   r   r   prep_sql4   s6    

$	"
rH   c                s   t tdd y.tj jdd tjtjj jddd W n, tk
rf } ztj	| W Y d d }~X nX  j
jddd t fdd	 jd
 fdd} jdddgd fdd} jd fdd} jd fdd} S )NT)instance_relative_config)exist_oktmpz	config.pyF)silentc                 s   i } i | d<  j j }|jd x |j D ]\}}|| d |< q*W i | d< |jd x |j D ]\}}|| d |< q^W i | d< |jd x |j D ]\}}|| d |< qW | 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/pypdb/c                 sB    } dt krdddd}nt d }td jd ||  jd d	S )
N
query_dataz0.0r<    )r:   r;   r2   z
index.htmlTITLEEXT_URL)titlerU   rQ   ext_url)r   r   r(   )rC   rU   )r1   rT   r   r   index   s    
zcreate_app.<locals>.indexz/pypdb/search/GETPOST)methodsc           	      s   } t jtd< t jd r:t jd tdt jd d S t jd sPt jd jrt jd jrrt jd j j	d}n
t jd }|st
d	 jd
 d ddS |td< t jd td S tt j|  jd }g }jj }|j|}|s t
d	 jd
 d ddS xZ|j D ]N}|j|d |d j j |d j j |d |d j j |d d q
W t
d jd
 d t|| jd dS d S )NrU   r   rX   show)r   ZseqQueryZseqFileasciiz
error.htmlrW   z No input sequence foundzNo input sequence found)rY   
error_text	query_seqblastZTEXT_FIELDSz No results foundzNo results foundr   r   r   r      r   )r   r   Zcompound
resolutionsourceZexpTypezsearch_output.htmlz - Blast search)rY   countr3   rZ   )r   formr   r   r(   r   filesfilenamereaddecoder   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/pypdb/blast/c                 sX   t  td \} }|r.td jd d ddS td jd d t| |  jd	 d
S d S )Nrb   z
error.htmlrW   z No Blast results foundzNo results found)rY   ra   zblast_output.htmlz - Blast searchrX   )rY   rg   r3   rZ   )r8   r   r   r(   r*   )r3   error)r1   r   r   rc      s    zcreate_app.<locals>.blastz/pypdb/show/<idCode>c                s$   }j j }|jdj| }|s>td jd dj| dS d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< x,|j D ] }|d jt|d |d  qW td jd d |  || jd dS )Nz+SELECT e.* from entry e where e.idCode='{}'z
error.htmlrW   zStructure not found ({}))rY   ra   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   )rt   Zautr   r   r   rv      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   )rt   Zscr   r   r   rv      s    Zsource_listz=SELECT * from sequence s where s.idCode='{}' order by s.chain	sequencesr   r   z	show.htmlz - rX   )rY   rQ   rq   rZ   )rM   rN   rO   r	   r   r(   descriptiondictzipZfetchoner   rP   r-   r   )r   rC   rR   rp   columnsrq   sq)r1   rT   rS   r   r   r_      s0    
 zcreate_app.<locals>.show)r   __name__r   makedirsr    r   r   OSErrorsysexitr(   from_pyfiler   route)Ztest_configer[   rr   rc   r_   r   )r1   rT   rS   r   
create_appc   s    ":r   )N)r   r   r
   r"   r&   flaskr   r   r   r   r   r   Zflask_mysqldbr   r   r8   rH   r   r   r   r   r   <module>   s    '/