U
    »îaÛ'  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 5 Q R X t
j| jd d	  ||¡ d
d z†g }t|dƒn}|D ]b}| ¡ }t|ƒdkr˜| d¡\}	}
}t d|
¡}| | d¡| d¡| d¡| d¡|dœ¡ q˜W 5 Q R X W n tk
r&   g d
f Y 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   sD    

ÿýûÿ


r5   c           	      C   sˆ  dg}| d dks| d dkrZ| d dkr<|  d| d  ¡ | d dkrZ|  d| d  ¡ g }|d  ¡ D ].\}}d	t|ƒ d
 | krj|  dt|ƒ ¡ qj|r¶|  dd |¡ d ¡ g }|d  ¡ D ].\}}dt|ƒ d
 | krÆ|  dt|ƒ ¡ qÆ|r|  dd |¡ d ¡ | d rdg }|D ]$}|  d| d | d  d ¡ q&|  dd |¡ d ¡ dd |¡ }d| kr„|d7 }|S )z Prepare SQL from search form ÚTrueÚminResú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   s:    
"û
rE   c              
      sú   t tdd‰ z.tjˆ jdd tjtj ˆ jd¡dd W n, tk
rf } zt 	|¡ W 5 d }~X Y nX ˆ j
jddd tˆ ƒ‰‡fdd	„‰ˆ  d
¡‡ ‡fdd„ƒ}ˆ jdddgd‡ ‡‡fdd„ƒ}ˆ  d¡‡ fdd„ƒ}ˆ  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¡ | ¡ D ]\}}|| d |< q(i | d< | d¡ | ¡ D ]\}}|| d |< qXi | d< | d¡ | ¡ D ]\}}|| d |< qˆ| S )Nr;   zSELECT * from comptyper?   zSELECT * from expClasseZexpTypeArrayz&SELECT idExptype, ExpType from expType)Ú
connectionÚcursorÚexecuteÚfetchall)ÚglobalsÚcurrB   rC   )Úmysqlr   r   Úget_globalsr   s    



zcreate_app.<locals>.get_globalsz/pypdb/c                     sB   ˆƒ } dt krddddœ}nt d }tdˆ jd || ˆ jd d	S )
NÚ
query_datar8   r:   Ú )r7   r9   r0   z
index.htmlÚTITLEÚEXT_URL)ÚtitlerO   rK   Úext_url)r   r   r&   )rA   rO   )r/   rN   r   r   Úindex‡   s    ýûzcreate_app.<locals>.indexz/pypdb/search/ZGETZPOST)Úmethodsc               
      s‚  ˆƒ } t jtd< t jd r:tˆ jd tdt jd d ƒS t jd sPt jd jr¶t jd jrrt jd  ¡  	d¡}n
t jd }|s˜t
d	ˆ jd
 d ddS |td< tˆ jd tdƒ ƒS tt j| ˆ jd ƒ}g }ˆj ¡ }| |¡}|s t
d	ˆ jd
 d ddS | ¡ D ]N}| |d |d  ¡  ¡ |d  ¡  ¡ |d |d  ¡  ¡ |d dœ¡ qt
dˆ jd
 d t|ƒ|ˆ jd dS d S )NrO   r   rR   Úshow)r   ZseqQueryZseqFileÚasciiú
error.htmlrQ   z No input sequence foundzNo input sequence found©rS   Z
error_textÚ	query_seqÚblastZTEXT_FIELDSz No results foundúNo results foundr   r   r   r   é   r   )r   r   ZcompoundZ
resolutionÚsourceZexpTypezsearch_output.htmlú - Blast search©rS   Úcountr1   rT   )r   Zformr   r   r&   r   ÚfilesÚfilenameÚreadÚdecoder   rE   rG   rH   rI   rJ   r+   ÚlowerÚ
capitalizer(   )rA   ZsequencerD   r1   rL   ÚrsÚdata©r/   rN   rM   r   r   Úsearch   sV    

 
ý

ýúÿûzcreate_app.<locals>.searchz/pypdb/blast/c                     sX   t ˆ td ƒ\} }|r.tdˆ jd d ddS tdˆ jd d t| ƒ| ˆ jd	 d
S d S )Nr[   rY   rQ   z No Blast results foundr]   rZ   zblast_output.htmlr`   rR   ra   )r5   r   r   r&   r(   )r1   Úerror)r/   r   r   r\   ×   s    ýûzcreate_app.<locals>.blastz/pypdb/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< | ¡ D ] }|d  t|d |d ƒ¡ qØtdˆ jd d |  ||ˆ jd dS )Nz+SELECT e.* from entry e where e.idCode='{}'rY   rQ   zStructure not found ({})rZ   c                 S   s   g | ]}|d  ‘qS ©r   r   )Ú.0Zcolr   r   r   Ú
<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 rn   r   )ro   Zautr   r   r   rp   ú   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 rn   r   )ro   Zscr   r   r   rp   ü   s     Zsource_listz=SELECT * from sequence s where s.idCode='{}' order by s.chainÚ	sequencesr   r   z	show.htmlz - rR   )rS   rK   rj   rT   )rG   rH   rI   r	   r   r&   ZdescriptionÚdictÚzipZfetchoner   rJ   r+   r   )r   rA   rL   ri   Úcolumnsrj   Zsqrk   r   r   rW   ì   s4    
ýûzcreate_app.<locals>.show)r   Ú__name__r   Úmakedirsr   r   r   ÚOSErrorÚsysÚexitr&   Zfrom_pyfiler   Zroute)Ztest_configÚerU   rl   r\   rW   r   rk   r   Ú
create_appc   s$    9r{   )N)r   rx   r
   r!   r$   Zflaskr   r   r   r   r   r   Zflask_mysqldbr   r   r5   rE   r{   r   r   r   r   Ú<module>   s    '/