B
    £b8^8'  ã               @   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 )é    N)ÚFlaskÚrender_templateÚsessionÚrequestÚurl_forÚredirect)ÚMySQLc             C   s   d  |t dd| ¡¡S )Nz>{}
{}z.{60}z\g<0>
)ÚformatÚreÚsub)ÚseqÚheader© r   ú>/home/dbw00/public_html/py_pdb_browser/pdb_browser/__init__.pyÚ
prep_fasta
   s    r   c          
   C   sD  |d dkrd  |¡}tj | jd¡tt ¡ ƒ }|d }|d }t|dƒ}| 	|¡ W d Q R X t
j| jd d	  ||¡ d
d yŠg }t|dƒr}xj|D ]b}| ¡ }t|ƒdkrš| d¡\}	}
}t d|
¡}| | d¡| d¡| d¡| d¡|dœ¡ qšW W d Q R X W n tk
r&   g d
fS X t |¡ t |¡ |dfS )Nr   ú>z>User provided sequence
{}ztmp/pdbz.query_fastaz.blast_reportÚwZBLAST_CMDLINEz -query {} -out {}T)ÚshellÚré   ú	z,(....)_(.) mol:([^ ]*) length:([0-9]*) *(.*)é   é   é   )ÚidCoder   ZtipZdescÚevF)r	   ÚosÚpathÚjoinÚinstance_pathÚstrÚuuidZuuid4ÚopenÚwriteÚ
subprocessÚrunÚconfigÚrstripÚlenÚsplitr
   ÚmatchÚappendÚgroupÚIOErrorÚremove)ÚappÚqueryZtmpFileNameZquery_fasta_fileZblast_report_fileZquery_fastaÚresultsZreportÚlineÚidr   r   Úmr   r   r   Ú	run_blast   s<    




r5   c       	      C   s”  dg}| d dks| d dkrZ| d dkr<|  d| d  ¡ | d dkrZ|  d| d  ¡ g }x>|d  ¡ D ].\}}d	t|ƒ d
 | krl|  dt|ƒ ¡ qlW |rº|  dd |¡ d ¡ g }x>|d  ¡ D ].\}}dt|ƒ d
 | krÌ|  dt|ƒ ¡ qÌW |r|  dd |¡ d ¡ | d rpg }x,|D ]$}|  d| d | d  d ¡ q0W |  dd |¡ d ¡ dd |¡ }d| kr|d7 }|S )z Prepare SQL from search form ÚTrueÚminResz0.0ÚmaxResÚInfze.resolution >= ze.resolution <= ÚcompTypeArrayzidCompType[ú]z e.idCompType = ú(z OR ú)ÚexpClasseArrayzidExpClasse[z et.idExpClasse = r0   zMATCH (z) AGAINST ('z' IN BOOLEAN MODE)aR  SELECT distinct e.idCode,e.header,e.compound,e.resolution,s.source,et.expType FROM expType et, author_has_entry ae, author a, source s, entry_has_source es, entry e, sequence sq WHERE e.idExpType=et.idExpType AND ae.idCode=e.idCode and ae.idAuthor=a.idAuthor AND es.idCode=e.idCode and es.idsource=s.idSource AND e.idCode = sq.idCode AND z AND Znolimitz LIMIT 5000)r+   Úitemsr    r   )	Z	form_dataÚ	glob_varsZtext_fieldsZANDcondsZORCondsÚkeyÚvalueZfieldÚsqlr   r   r   Úprep_sql4   s6    

$	
rD   c          
      s"  t tdd‰ y.tjˆ jdd tjtj ˆ jd¡dd W n, tk
rf } zt 	|¡ W d d }~X Y nX ˆ j
jddd tˆ ƒ‰‡fdd	„‰ˆ  ˆ j
d
 d ¡‡ ‡fdd„ƒ}ˆ jˆ j
d
 d ddgd‡ ‡‡fdd„ƒ}ˆ  ˆ j
d
 d ¡‡ fdd„ƒ}ˆ  ˆ j
d
 d ¡‡ ‡‡fdd„ƒ}ˆ S )NT)Zinstance_relative_config)Úexist_okZtmpz	config.pyF)Zsilentc                 s®   i } i | d< ˆ j  ¡ }| d¡ x | ¡ D ]\}}|| d |< q*W i | d< | d¡ x | ¡ D ]\}}|| d |< q^W i | d< | d¡ x | ¡ D ]\}}|| d |< q’W | S )Nr:   zSELECT * from comptyper>   zSELECT * from expClasseZexpTypeArrayz&SELECT idExptype, ExpType from expType)Ú
connectionÚcursorÚexecuteÚfetchall)ÚglobalsÚcurrA   rB   )Úmysqlr   r   Úget_globalsr   s    



zcreate_app.<locals>.get_globalsZBASE_URLú/c                 s:   ˆƒ } dt krddddœ}nt d }tdˆ jd || dS )	NÚ
query_dataz0.0r9   Ú )r7   r8   r0   z
index.htmlÚTITLE)ÚtitlerO   rJ   )r   r   r&   )r@   rO   )r/   rM   r   r   Úindex‡   s    
zcreate_app.<locals>.indexz/search/ZGETZPOST)Úmethodsc           
      sf  ˆƒ } t jtd< t jd r0ttdt jd dƒS t jd sFt jd jr¢t jd jrht jd  ¡  d¡}n
t jd }|sŽt	dˆ j
d	 d
 ddS |td< ttdƒƒS tt j| ˆ j
d ƒ}g }ˆj ¡ }| |¡}|sêt	dˆ j
d	 d ddS xX| ¡ D ]L}| |d |d  ¡  ¡ |d  ¡  ¡ |d |d  ¡  ¡ |d dœ¡ qôW t	dˆ j
d	 d t|ƒ|dS d S )NrO   r   Úshow)r   ZseqQueryZseqFileÚasciiz
error.htmlrQ   z No input sequence foundzNo input sequence found)rR   Ú
error_textÚ	query_seqÚblastZTEXT_FIELDSz No results foundzNo results foundr   r   r   r   é   r   )r   r   ZcompoundZ
resolutionÚsourceZexpTypezsearch_output.htmlz - Blast search)rR   Úcountr1   )r   Zformr   r   r   ÚfilesÚfilenameÚreadÚdecoder   r&   rD   rF   rG   rH   rI   r+   ÚlowerÚ
capitalizer(   )r@   ZsequencerC   r1   rK   ÚrsÚdata)r/   rM   rL   r   r   Úsearchœ   sJ    




zcreate_app.<locals>.searchz/blast/c                 sP   t ˆ td ƒ\} }|r.tdˆ jd d ddS tdˆ jd d t| ƒ| d	S d S )
NrX   z
error.htmlrQ   z No Blast results foundzNo results found)rR   rW   zblast_output.htmlz - Blast search)rR   r\   r1   )r5   r   r   r&   r(   )r1   Úerror)r/   r   r   rY   Õ   s    zcreate_app.<locals>.blastz/show/<idCode>c                s  ˆƒ }ˆj  ¡ }| d | ¡¡}|s>tdˆ jd d | ¡dS dd„ |jD ƒ}tt|| 	¡ ƒƒ}| d | ¡¡}d	 
d
d„ | ¡ D ƒ¡|d< | d | ¡¡}d	 
dd„ | ¡ D ƒ¡|d< | d | ¡¡}g |d< x,| ¡ D ] }|d  t|d |d ƒ¡ qÚW tdˆ jd d |  ||dS )Nz+SELECT e.* from entry e where e.idCode='{}'z
error.htmlrQ   zStructure not found ({}))rR   rW   c             S   s   g | ]}|d  ‘qS )r   r   )Ú.0Úcolr   r   r   ú
<listcomp>ô   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   )rg   Zautr   r   r   ri   ÷   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   )rg   Zscr   r   r   ri   ù   s    Zsource_listz=SELECT * from sequence s where s.idCode='{}' order by s.chainÚ	sequencesr   r   z	show.htmlz - )rR   rJ   rd   )rF   rG   rH   r	   r   r&   ZdescriptionÚdictÚzipZfetchoner   rI   r+   r   )r   r@   rK   rc   Úcolumnsrd   Zsq)r/   rM   rL   r   r   rU   é   s.    
 zcreate_app.<locals>.show)r   Ú__name__r   Úmakedirsr   r   r   ÚOSErrorÚsysÚexitr&   Zfrom_pyfiler   Zroute)Ztest_configÚerS   re   rY   rU   r   )r/   rM   rL   r   Ú
create_appc   s    ",9 $rt   )N)r   rq   r
   r!   r$   Zflaskr   r   r   r   r   r   Zflask_mysqldbr   r   r5   rD   rt   r   r   r   r   Ú<module>   s    '/