§
    æ˜ºh  ã                   ó¦   — 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 )é    N)ÚAnyÚDictÚIteratorÚList)ÚDocument)Ú	BaseModelÚroot_validatorc                   óv  — 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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 )$Ú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.
    Úparsez;https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?Úbase_url_esearchz:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?Úbase_url_efetché   Ú	max_retrygš™™™™™É?Ú
sleep_timeé   Útop_k_resultsi,  ÚMAX_QUERY_LENGTHiÐ  Údoc_content_chars_maxzyour_email@example.comÚemailÚvaluesÚreturnc                 ó`   — 	 ddl }|j        |d<   n# t          $ r t          d¦  «        ‚w xY w|S )z7Validate that the python package exists in environment.r   Nr   zZCould not import xmltodict python package. Please install it with `pip install xmltodict`.)Ú	xmltodictr   ÚImportError)Úclsr   r   s      úl/var/www/html/services/rag-service/venv/lib/python3.11/site-packages/langchain_community/utilities/pubmed.pyÚvalidate_environmentz%PubMedAPIWrapper.validate_environment3   sZ   € ð	ØÐÐÐà'œoˆF�7‰OˆOøÝð 	ð 	ð 	ÝðBñô ð ð	øøøð
 ˆs   ‚ ‘+Úqueryc                 óà   — 	 d„ |                       |d| j        …         ¦  «        D ¦   «         }|r"d                     |¦  «        d| j        …         ndS # t          $ r}d|› �cY d}~S d}~ww xY w)zá
        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                 óZ   — g | ](}d |d         › d|d         › d|d         › d|d         › �‘Œ)S )zPublished: Ú	Publishedz
Title: ÚTitlez
Copyright Information: úCopyright Informationz
Summary::
ÚSummary© )Ú.0Úresults     r   ú
<listcomp>z(PubMedAPIWrapper.run.<locals>.<listcomp>J   ss   € ð ð ð ð
 ð	2˜f [Ô1ð 2ð 2Ø  œ/ð2ð 2à*0Ð1HÔ*Ið2ð 2ð % YÔ/ð2ð 2ðð ð ó    Nz

zNo good PubMed Result was foundzPubMed exception: )Úloadr   Újoinr   Ú	Exception)Úselfr   ÚdocsÚexs       r   ÚrunzPubMedAPIWrapper.runA   s°   € ð	-ðð ð
 #Ÿiši¨Ð.E°Ô0EÐ.EÔ(FÑGÔGðñ ô ˆDð ð7�—’˜DÑ!Ô!Ð"> DÔ$>Ð">Ô?Ð?à6ðøõ
 ð 	-ð 	-ð 	-Ø,¨Ð,Ð,Ð,Ð,Ð,Ð,Ð,Ð,øøøøð	-øøøs   ‚AA Á
A-ÁA(Á"A-Á(A-c              #   ó´  K  — | j         dz   t          t          j                             |¦  «        h¦  «        z   d| j        › d�z   }t          j                             |¦  «        }|                     ¦   «          	                    d¦  «        }t          j        |¦  «        }|d         d         }|d         d         D ]}|                      ||¦  «        V — ŒdS )	zŽ
        Search PubMed for documents matching the query.
        Return an iterator of dictionaries containing the document metadata.
        zdb=pubmed&term=z&retmode=json&retmax=z&usehistory=yúutf-8ÚesearchresultÚwebenvÚidlistN)r   ÚstrÚurllibr   Úquoter   ÚrequestÚurlopenÚreadÚdecodeÚjsonÚloadsÚretrieve_article)r.   r   Úurlr(   ÚtextÚ	json_textr5   Úuids           r   Ú	lazy_loadzPubMedAPIWrapper.lazy_load[   sê   è è € ð Ô!Øñ å•6”<×%Ò% eÑ,Ô,Ð-Ñ.Ô.ñ/ð H dÔ&8ÐGÐGÐGñHð 	õ ”×'Ò'¨Ñ,Ô,ˆØ�{Š{‰}Œ}×#Ò# GÑ,Ô,ˆÝ”J˜tÑ$Ô$ˆ	à˜?Ô+¨HÔ5ˆØ˜_Ô-¨hÔ7ð 	5ð 	5ˆCØ×'Ò'¨¨VÑ4Ô4Ð4Ð4Ð4Ð4ð	5ð 	5r*   c                 óF   — t          |                      |¦  «        ¦  «        S )z‰
        Search PubMed for documents matching the query.
        Return a list of dictionaries containing the document metadata.
        )ÚlistrE   ©r.   r   s     r   r+   zPubMedAPIWrapper.loado   s   € õ
 �D—N’N 5Ñ)Ô)Ñ*Ô*Ð*r*   Údocc                 óN   — |                      d¦  «        }t          ||¬¦  «        S )Nr%   )Úpage_contentÚmetadata)Úpopr   )r.   rI   Úsummarys      r   Ú_dict2documentzPubMedAPIWrapper._dict2documentv   s&   € Ø—'’'˜)Ñ$Ô$ˆÝ W°sÐ;Ñ;Ô;Ð;r*   c              #   ój   K  — |                       |¬¦  «        D ]}|                      |¦  «        V — Œd S ©N)r   )rE   rO   )r.   r   Úds      r   Úlazy_load_docszPubMedAPIWrapper.lazy_load_docsz   sJ   è è € Ø—’ e�Ñ,Ô,ð 	)ð 	)ˆAØ×%Ò% aÑ(Ô(Ð(Ð(Ð(Ð(ð	)ð 	)r*   c                 óH   — t          |                      |¬¦  «        ¦  «        S rQ   )rG   rS   rH   s     r   Ú	load_docszPubMedAPIWrapper.load_docs~   s!   € Ý�D×'Ò'¨eÐ'Ñ4Ô4Ñ5Ô5Ð5r*   rD   r5   c                 ó  — | j         dz   |z   dz   |z   }d}	 	 t          j                             |¦  «        }n‚# t          j        j        $ 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Œ£|                     ¦   «                              d¦  «        }|                      |¦  «        }|                      ||¦  «        S )Nzdb=pubmed&retmode=xml&id=z&webenv=r   Ti­  zToo Many Requests, waiting for z.2fz seconds...é   é   r3   )r   r8   r:   r;   ÚerrorÚ	HTTPErrorÚcoder   Úprintr   ÚtimeÚsleepr<   r=   r   Ú_parse_article)	r.   rD   r5   rA   Úretryr(   ÚeÚxml_textÚ	text_dicts	            r   r@   z!PubMedAPIWrapper.retrieve_article�   sS  € àÔ Ø)ñ*àñð ñð ñ	ð 	ð ˆð	ðÝœ×/Ò/°Ñ4Ô4�ØøÝ”<Ô)ð ð ð Ø”6˜S’=�= U¨T¬^Ò%;Ð%;õ ðHØ'+¤ÐGðHð Hð Hñô ð õ ”J˜tœÑ/Ô/Ð/Ø�O”O qÑ(�O”OØ˜Q‘J�E�Eà�Gð �E�E�E�Eøøøøðøøøð		ð$ —;’;‘=”=×'Ò'¨Ñ0Ô0ˆØ—J’J˜xÑ(Ô(ˆ	Ø×"Ò" 3¨	Ñ2Ô2Ð2s   ˜8 ¸B6ÁA B1Â1B6rc   c                 ó6  — 	 |d         d         d         d         }n$# t           $ r |d         d         d         }Y nw xY w|                     di ¦  «                             dg ¦  «        }d	„ |D ¦   «         }|rd
                     |¦  «        n^t          |t          ¦  «        r|nGt          |t
          ¦  «        r1d
                     d„ |                     ¦   «         D ¦   «         ¦  «        nd}|                     di ¦  «        }d                     |                     dd¦  «        |                     dd¦  «        |                     dd¦  «        g¦  «        }||                     dd¦  «        ||                     di ¦  «                             dd¦  «        |dœS )NÚPubmedArticleSetÚPubmedArticleÚMedlineCitationÚArticleÚPubmedBookArticleÚBookDocumentÚAbstractÚAbstractTextc                 óD   — g | ]}d |v ¯d|v ¯
|d         › d|d          › �‘ŒS )z#textz@Labelz: r&   )r'   Útxts     r   r)   z3PubMedAPIWrapper._parse_article.<locals>.<listcomp>©   sG   € ð 
ð 
ð 
àØ˜#ˆ~ˆ~ (¨c / /ð �8Œ}Ð.Ð.  G¤Ð.Ð.à"1 / /r*   ú
c              3   ó4   K  — | ]}t          |¦  «        V — Œd S )N)r7   )r'   Úvalues     r   ú	<genexpr>z2PubMedAPIWrapper._parse_article.<locals>.<genexpr>µ   s(   è è € ÐMÐM¨U�c %™jœjÐMÐMÐMÐMÐMÐMr*   zNo abstract availableÚArticleDateú-ÚYearÚ ÚMonthÚDayÚArticleTitleÚCopyrightInformation)rD   r#   r"   r$   r%   )ÚKeyErrorÚgetr,   Ú
isinstancer7   Údictr   )	r.   rD   rc   ÚarÚabstract_textÚ	summariesrN   Úa_dÚpub_dates	            r   r_   zPubMedAPIWrapper._parse_article¡   sÎ  € ð	TØÐ-Ô.¨Ô?Ð@QÔRØôˆBˆBøõ ð 	Tð 	Tð 	TØÐ-Ô.Ð/BÔCÀNÔSˆBˆBˆBð	TøøøàŸš˜z¨2Ñ.Ô.×2Ò2°>À2ÑFÔFˆð
ð 
à$ð
ñ 
ô 
ˆ	ð ð
ˆD�IŠI�iÑ Ô Ð õ ˜m­SÑ1Ô1ð��õ " -µÑ6Ô6ð1�D—I’IÐMÐM°m×6JÒ6JÑ6LÔ6LÐMÑMÔMÑMÔMÐMà0ð 	ð �fŠf�] BÑ'Ô'ˆØ—8’8Ø�WŠW�V˜RÑ Ô  #§'¢'¨'°2Ñ"6Ô"6¸¿ºÀÀrÑ8JÔ8JÐKñ
ô 
ˆð
 Ø—V’V˜N¨BÑ/Ô/Ø!Ø%'§V¢V¨J¸Ñ%;Ô%;×%?Ò%?Ø&¨ñ&ô &ð ð
ð 
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s   ‚ �>½>N) Ú__name__Ú
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