
    Ng3                         d dl Z 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 d dlmZ d dlmZmZ  ej        e          Z G d de          ZdS )    N)AnyDictIteratorList)Document)	BaseModelmodel_validatorc                      e Zd ZU dZeed<   dZeed<   dZeed<   dZ	e
ed<   d	Zeed
<   dZe
ed<   dZe
ed<   dZe
ed<   dZeed<    ed          ededefd                        ZdedefdZdedee         fdZdedee         fdZdedefdZdedee         fdZdedee         fdZd ed!edefd"Zd ed#edefd$Z d%S )&PubMedAPIWrappera(  
    Wrapper around PubMed API.

    This wrapper will use the PubMed API to conduct searches and fetch
    document summaries. By default, it will return the document summaries
    of the top-k results of an input search.

    Parameters:
        top_k_results: number of the top-scored document used for the PubMed tool
        MAX_QUERY_LENGTH: maximum length of the query.
          Default is 300 characters.
        doc_content_chars_max: maximum length of the document content.
          Content will be truncated if it exceeds this length.
          Default is 2000 characters.
        max_retry: maximum number of retries for a request. Default is 5.
        sleep_time: time to wait between retries.
          Default is 0.2 seconds.
        email: email address to be used for the PubMed API.
    parsez;https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?base_url_esearchz:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?base_url_efetch   	max_retryg?
sleep_time   top_k_resultsi,  MAX_QUERY_LENGTHi  doc_content_chars_maxzyour_email@example.comemailbefore)modevaluesreturnc                 `    	 ddl }|j        |d<   n# t          $ r t          d          w xY w|S )z7Validate that the python package exists in environment.r   Nr   zZCould not import xmltodict python package. Please install it with `pip install xmltodict`.)	xmltodictr   ImportError)clsr   r   s      `/var/www/html/ai-engine/env/lib/python3.11/site-packages/langchain_community/utilities/pubmed.pyvalidate_environmentz%PubMedAPIWrapper.validate_environment3   sZ    	'oF7OO 	 	 	B  	
 s    +queryc                     	 d |                      |d| j                           D             }|r"d                    |          d| j                 ndS # t          $ r}d| cY d}~S d}~ww xY w)z
        Run PubMed search and get the article meta information.
        See https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
        It uses only the most informative fields of article meta information.
        c                 Z    g | ](}d |d          d|d          d|d          d|d          )S )zPublished: 	Publishedz
Title: Titlez
Copyright Information: Copyright Informationz
Summary::
Summary ).0results     r   
<listcomp>z(PubMedAPIWrapper.run.<locals>.<listcomp>K   ss       
 	2f[1 2 2 /2 2*01H*I2 2 %Y/2 2      Nz

zNo good PubMed Result was foundzPubMed exception: )loadr   joinr   	Exception)selfr!   docsexs       r   runzPubMedAPIWrapper.runB   s    	- 
 #ii.E0E.E(FGG  D 7D!!">D$>">??6
  	- 	- 	-,,,,,,,,,	-s   AA 
A-A("A-(A-c              #     K   | j         dz   t          t          j                            |          h          z   d| j         dz   }t          j                            |          }|                                	                    d          }t          j        |          }|d         d         }|d         d         D ]}|                     ||          V  dS )	z
        Search PubMed for documents matching the query.
        Return an iterator of dictionaries containing the document metadata.
        zdb=pubmed&term=z&retmode=json&retmax=z&usehistory=yutf-8esearchresultwebenvidlistN)r   strurllibr   quoter   requesturlopenreaddecodejsonloadsretrieve_article)r0   r!   urlr*   text	json_textr7   uids           r   	lazy_loadzPubMedAPIWrapper.lazy_load\   s       ! 6<%%e,,-../ Hd&8GGGH 	 '',,{{}}##G,,Jt$$	?+H5_-h7 	5 	5C''V444444	5 	5r,   c                 F    t          |                     |                    S )z
        Search PubMed for documents matching the query.
        Return a list of dictionaries containing the document metadata.
        )listrG   r0   r!   s     r   r-   zPubMedAPIWrapper.loadp   s    
 DNN5))***r,   docc                 N    |                     d          }t          ||          S )Nr'   )page_contentmetadata)popr   )r0   rK   summarys      r   _dict2documentzPubMedAPIWrapper._dict2documentw   s&    '')$$Ws;;;;r,   c              #   j   K   |                      |          D ]}|                     |          V  d S N)r!   )rG   rQ   )r0   r!   ds      r   lazy_load_docszPubMedAPIWrapper.lazy_load_docs{   sJ      e,, 	) 	)A%%a((((((	) 	)r,   c                 H    t          |                     |                    S rS   )rI   rU   rJ   s     r   	load_docszPubMedAPIWrapper.load_docs   s!    D''e'44555r,   rF   r7   c                    | j         dz   |z   dz   |z   }d}	 	 t          j                            |          }n# t          j        j        $ rj}|j        dk    rS|| j        k     rHt          d| j	        dd           t          j        | j	                   | xj	        d	z  c_	        |d
z  }n|Y d }~nd }~ww xY w|                                                    d          }|                     |          }|                     ||          S )Nzdb=pubmed&retmode=xml&id=z&webenv=r   Ti  zToo Many Requests, waiting for z.2fz seconds...      r5   )r   r:   r<   r=   error	HTTPErrorcoder   printr   timesleepr>   r?   r   _parse_article)	r0   rF   r7   rC   retryr*   exml_text	text_dicts	            r   rB   z!PubMedAPIWrapper.retrieve_article   sS    )*  	 	 	//44<)   6S==UT^%;%; H'+GH H H   Jt///OOq(OOQJEEG EEEE		$ ;;==''00JJx((	""3	222s   8 B6A B11B6re   c                 6   	 |d         d         d         d         }n$# t           $ r |d         d         d         }Y nw xY w|                    di                               dg           }d	 |D             }|rd
                    |          n^t          |t                    r|nGt          |t
                    r1d
                    d |                                D                       nd}|                    di           }d                    |                    dd          |                    dd          |                    dd          g          }||                    dd          ||                    di                               dd          |dS )NPubmedArticleSetPubmedArticleMedlineCitationArticlePubmedBookArticleBookDocumentAbstractAbstractTextc                 D    g | ]}d |v d|v 
|d          d|d           S )z#textz@Labelz: r(   )r)   txts     r   r+   z3PubMedAPIWrapper._parse_article.<locals>.<listcomp>   sG     
 
 
#~~(c// 8}..G.."1//r,   
c              3   4   K   | ]}t          |          V  d S )N)r9   )r)   values     r   	<genexpr>z2PubMedAPIWrapper._parse_article.<locals>.<genexpr>   s(      MMUc%jjMMMMMMr,   zNo abstract availableArticleDate-Year MonthDayArticleTitleCopyrightInformation)rF   r%   r$   r&   r'   )KeyErrorgetr.   
isinstancer9   dictr   )	r0   rF   re   arabstract_text	summariesrP   a_dpub_dates	            r   ra   zPubMedAPIWrapper._parse_article   s   	T-.?@QRBB  	T 	T 	T-./BCNSBBB	Tz2..22>2FF
 
$
 
 
	 
DIIi    mS11 "-661DIIMMm6J6J6L6LMMMMMM0 	 ff]B''88WWVR  #'''2"6"6r8J8JK
 

 VVNB//!%'VVJ%;%;%?%?&& & 
 
 	
s    >>N)!__name__
__module____qualname____doc__r   __annotations__r   r9   r   r   intr   floatr   r   r   r   r	   classmethodr   r    r3   r   r   rG   r   r-   r   rQ   rU   rW   rB   ra   r(   r,   r   r   r      s2         ( JJJ 	F c    XOSWWWIsJ M3c!%3%%%)E3)))_(###$ 3    [ $#- - - - - -45s 5x~ 5 5 5 5(+# +$t* + + + +<$ <8 < < < <)C )HX,> ) ) ) )6s 6tH~ 6 6 6 63C 3 3 3 3 3 3@'
# '
$ '
4 '
 '
 '
 '
 '
 '
r,   r   )r@   loggingr_   urllib.errorr:   urllib.parseurllib.requesttypingr   r   r   r   langchain_core.documentsr   pydanticr   r	   	getLoggerr   loggerr   r(   r,   r   <module>r      s                   , , , , , , , , , , , , - - - - - - / / / / / / / /		8	$	$z
 z
 z
 z
 z
y z
 z
 z
 z
 z
r,   