
    dhZ                         S SK r S SKrS SKrS SKrS SKrS SKrS SKJrJ	r	J
r
Jr  S SKJr  S SKJrJr  \R"                  " \5      r " S S\5      rg)    N)AnyDictIteratorList)Document)	BaseModelmodel_validatorc                      \ rS rSr% Sr\\S'   Sr\\S'   Sr	\\S'   Sr
\\S	'   S
r\\S'   Sr\\S'   Sr\\S'   Sr\\S'   Sr\\S'   Sr\\S'   \" SS9\S\S\4S j5       5       rS\S\4S jrS\S\\   4S jrS\S\\   4S jrS\S\4S  jrS\S\\   4S! jrS\S\\   4S" jr S#\S$\S\4S% jr!S#\S&\S\4S' jr"S(r#g))*PubMedAPIWrapper   a  
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.
    api_key: API key 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 api_keybefore)modevaluesreturnc                 `     SSK nUR                  US'   U$ ! [         a    [        S5      ef = f)z7Validate that the python package exists in environment.r   Nr   zZCould not import xmltodict python package. Please install it with `pip install xmltodict`.)	xmltodictr   ImportError)clsr   r   s      \/var/www/html/shao/venv/lib/python3.13/site-packages/langchain_community/utilities/pubmed.pyvalidate_environment%PubMedAPIWrapper.validate_environment5   sB    	'ooF7O   	B 	s    -queryc                     U R                  USU R                   5       Vs/ sH  nSUS    SUS    SUS    SUS	    3PM     nnU(       a  S
R                  U5      SU R                   $ S$ s  snf ! [         a  nSU 3s SnA$ SnAff = f)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.
NzPublished: 	Publishedz
Title: Titlez
Copyright Information: Copyright Informationz
Summary::
Summaryz

zNo good PubMed Result was foundzPubMed exception: )loadr   joinr   	Exception)selfr%   resultdocsexs        r"   runPubMedAPIWrapper.runD   s    	- #ii.E0E0E(FG
 HF	 f[12 3 /* +**01H*I)J K$Y/02 H    D!">D$>$>? 7  	-'t,,	-s4    A3 #A.&A3 ,A3 .A3 3
B=BBBc              #     #    U R                   S-   [        [        R                  R	                  U5      15      -   SU R
                   S3-   nU R                  S:w  a  USU R                   3-  n[        R                  R                  U5      nUR                  5       R                  S5      n[        R                  " U5      nUS   S   nUS   S	    H  nU R                  Xv5      v   M     g
7f)zv
Search PubMed for documents matching the query.
Return an iterator of dictionaries containing the document metadata.
zdb=pubmed&term=z&retmode=json&retmax=z&usehistory=yr   	&api_key=utf-8esearchresultwebenvidlistN)r   strurllibr   quoter   r   requesturlopenreaddecodejsonloadsretrieve_article)r.   r%   urlr/   text	json_textr8   uids           r"   	lazy_loadPubMedAPIWrapper.lazy_load^   s      !! 6<<%%e,-./ &d&8&8%9GH 	 <<2Yt||n--C'',{{}##G,JJt$	?+H5_-h7C''44 8s   C,C.c                 6    [        U R                  U5      5      $ )zq
Search PubMed for documents matching the query.
Return a list of dictionaries containing the document metadata.
)listrH   r.   r%   s     r"   r+   PubMedAPIWrapper.loadt   s    
 DNN5)**    docc                 6    UR                  S5      n[        X!S9$ )Nr*   )page_contentmetadata)popr   )r.   rO   summarys      r"   _dict2documentPubMedAPIWrapper._dict2document{   s    '')$W;;rN   c              #   ^   #    U R                  US9 H  nU R                  U5      v   M     g 7fN)r%   )rH   rU   )r.   r%   ds      r"   lazy_load_docsPubMedAPIWrapper.lazy_load_docs   s+     e,A%%a(( -s   +-c                 2    [        U R                  US95      $ rX   )rK   rZ   rL   s     r"   	load_docsPubMedAPIWrapper.load_docs   s    D''e'455rN   rG   r8   c                    U R                   S-   U-   S-   U-   nU R                  S:w  a  USU R                   3-  nSn  [        R                  R	                  U5      n UR                  5       R                  S5      nU R                  U5      nU R!                  X5      $ ! [        R
                  R                   a  nUR                  S:X  ah  X@R                  :  aY  [        SU R                  S S	35        [        R                  " U R                  5        U =R                  S
-  sl
        US-  n S nAO
UeS nAff = fGM  )Nzdb=pubmed&retmode=xml&id=z&webenv=r   r5   r   i  zToo Many Requests, waiting for z.2fz seconds...      r6   )r   r   r;   r=   r>   error	HTTPErrorcoder   printr   timesleepr?   r@   r   _parse_article)	r.   rG   r8   rD   retryr/   exml_text	text_dicts	            r"   rC   !PubMedAPIWrapper.retrieve_article   s8     )*  	 	 <<2Yt||n--C//4 ;;=''0JJx(	""322! <<)) 66S=U^^%; ''+s&;;H JJt/OOq(OQJEG	 s   B   D=>A3D86D88D=rl   c                     US   S   S   S   nUR                  S0 5      R                  S/ 5      nU Vs/ sH   nS	U;   d  M  S
U;   d  M  US
    SUS	    3PM"     nnU(       a  SR                  U5      OS[        U[        5      (       a  UO<[        U[
        5      (       a&  SR                  S UR                  5        5       5      OSnUR                  S0 5      nSR                  UR                  SS5      UR                  SS5      UR                  SS5      /5      n	UUR                  SS5      U	UR                  S0 5      R                  SS5      US.$ ! [          a    US   S   S   n GN`f = fs  snf )NPubmedArticleSetPubmedArticleMedlineCitationArticlePubmedBookArticleBookDocumentAbstractAbstractTextz#textz@Labelz: 
c              3   6   #    U H  n[        U5      v   M     g 7f)N)r:   ).0values     r"   	<genexpr>2PubMedAPIWrapper._parse_article.<locals>.<genexpr>   s     M6LUc%jj6Ls   zNo abstract availableArticleDate-Yearr   MonthDayArticleTitleCopyrightInformation)rG   r(   r'   r)   r*   )KeyErrorgetr,   
isinstancer:   dictr   )
r.   rG   rl   arabstract_texttxt	summariesrT   a_dpub_dates
             r"   rh   PubMedAPIWrapper._parse_article   s   	T-.?@QRB
 z2.22>2F %
$#~ /"*c/ /s8}oRG~.$ 	 
  IIi  mS11  "-66 IIMm6J6J6LMM0 	 ff]B'88#$r"
 VVNB/!%'VVJ%;%?%?&& 
 	
=  	T-./BCNSB	T
s"   E 	E4E4E4E10E1 N)$__name__
__module____qualname____firstlineno____doc__r   __annotations__r   r:   r   r   intr   floatr   r   r   r   r   r	   classmethodr   r#   r2   r   r   rH   r   r+   r   rU   rZ   r]   rC   rh   __static_attributes__r   rN   r"   r   r      s\   * J 	F c  XOSWIsJ M3c!%3%)E3)GS(#$ 3   $- - -45s 5x~ 5,+# +$t* +<$ <8 <)C )HX,> )6s 6tH~ 6 3C  3  3  3D+
# +
$ +
4 +
rN   r   )rA   loggingrf   urllib.errorr;   urllib.parseurllib.requesttypingr   r   r   r   langchain_core.documentsr   pydanticr   r	   	getLoggerr   loggerr   r   rN   r"   <module>r      sA          , , - /			8	$D
y D
rN   