+
    iE                        R t ^ RIt^ RIt^ RIt^ RIt^ RIHt ^ RIHtH	t	H
t
Ht ^ RIt^ RIHtHt ^ RIHt ^ RIt^ RIHt ^ RIHtHt ]P.                  ! ]4      t]P4                  ! 4       t]P8                  ! R4      t]P=                  ]4       ]P?                  ]4       ]PA                  ]PB                  4       ] ! R	 R
4      4       t"] ! R R4      4       t#] ! R R4      4       t$] ! R R4      4       t% ! R R4      t& ! R R4      t' ! R R4      t( ! R R4      t) ! R R4      t*]R8X  Ed   ^ RI+t+]+PX                  ! RR7      t-]-P]                  RRR 7       ]-P]                  R!R"R#R 7       ]-P]                  R$R%R&R'R(7       ]-P]                  R)R*R+R,R-7       ]-P]                  R.R/R+R0R-7       ]-P_                  4       t0]0Pb                  '       d   ]PA                  ]Pd                  4       ]*! 4       t3 ]3Pi                  ]0Pj                  R1]0Pl                  R27      t7]0Pp                  '       d   ]3Ps                  ]7]0Pp                  4       M(]:! ]Pv                  ! ]7Py                  4       ^R37      4       ]0Pz                  '       d:   ]3P}                  ]7]0Pz                  4      t?]P                  R4]A! ]?4       R524       R# R# R#   ]B d2   tC]P                  R6]C 24       ]P                  ! ^4        RtCACR# RtCACii ; i)7ul   
PDFx Research Helper — Academic PDF Research Tool
Wrapper around pdfx for research automation workflows.
NPath)DictListOptionalTuple)	dataclassasdict)datetime)urlparse)ThreadPoolExecutoras_completedz)%(asctime)s - %(levelname)s - %(message)sc                     a  ] tR t^!t o Rt]! ]P                  P                  R4      4      t	]! ]P                  P                  R4      4      t
]! ]P                  P                  R4      4      t^t^tRtRtRtR tV 3R	 ltR
tV tR# )ResearchConfigz"Configuration for research helper.z~/Documents/Researchz~/Documents/Research/outputz~/Documents/Research/cacheTz)(?i)(doi|https?://doi\.org/)(10\.\S+/\S+)z&(?i)(arxiv\.org/abs/)?(\d{4}\.\d{4,5})c                    V P                   P                  RRR7       V P                  P                  RRR7       V P                  P                  RRR7       R# )zCreate directories.Tparentsexist_okN)base_dirmkdir
output_dir	cache_dirselfs   &research_helper.py__post_init__ResearchConfig.__post_init__1   sG    D48dT:TD9    c                z   < V ^8  d   Qh/ S[ ;R&   S[ ;R&   S[ ;R&   S[;R&   S[;R&   S[;R&   S[;R&   S[;R&   # )	   r   r   r   max_workerstimeout_sec
verify_ssldoi_patternarxiv_pattern)r   intboolstr)format__classdict__s   "r   __annotate__ResearchConfig.__annotate__!   sm      E  N	 
 L        C  B r    N)__name__
__module____qualname____firstlineno____doc__r   ospath
expanduserr   r   r   r    r!   r"   r#   r$   r   __annotate_func____static_attributes____classdictcell__r)   s   @r   r   r   !   s     ,"'',,-CDEHBGG../LMNJ277--.JKLI KKJ DKBM:!  r   r   c                   4   a  ] tR t^<t o RtRtV 3R ltRtV tR# )PDFReferencezSingle reference from a PDF. c                >   < V ^8  d   Qh/ S[ ;R&   S[ ;R&   S[ ;R&   # )r   typevaluecontext)r'   )r(   r)   s   "r   r*   PDFReference.__annotate__<   s*      I  J	 
  r   r,   N)	r-   r.   r/   r0   r1   r?   r5   r6   r7   r8   s   @r   r:   r:   <   s     & G  r   r:   c                   R   a  ] tR t^Dt o RtRtRtRtRt^ t	Rt
RtR tV 3R ltRtV tR# )PDFMetadatazExtracted PDF metadata.r;   Nc                4    V P                   f
   / V n         R # R # Ncustom_fieldsr   s   &r   r   PDFMetadata.__post_init__O   s    %!#D &r   c                n   < V ^8  d   Qh/ S[ ;R&   S[ ;R&   S[ ;R&   S[ ;R&   S[;R&   S[ ;R&   S[;R&   # )r   titleauthorcreatorcreation_datepagesproducerrF   )r'   r%   r   )r(   r)   s   "r   r*   PDFMetadata.__annotate__D   s^      O  	 
     N     r   rE   )r-   r.   r/   r0   r1   rI   rJ   rK   rL   rM   rN   rF   r   r5   r6   r7   r8   s   @r   rB   rB   D   s7     !EFGMEHM$  r   rB   c                   >   a  ] tR t^Tt o Rt^ tRtR tV 3R ltRt	V t
R# )PDFAnalysiszComplete PDF analysis result.r;   c                   RV P                   R\        V P                  4      RV P                   Uu. uF)  pRVP                  RVP
                  RVP                  /NK+  	  upRV P                  RV P                  /# u upi )	z-Convert to dictionary for JSON serialization.sourcemetadata
referencesr=   r>   r?   text_lengthanalysis_date)	rS   r	   rT   rU   r=   r>   r?   rV   rW   )r   rs   & r   to_dictPDFAnalysis.to_dict]   s}     dkkt}}-(A !''9aiiH( 4++T//	
 		
s   /A<c                f   < V ^8  d   Qh/ S[ ;R&   S[;R&   S[S[,          ;R&   S[;R&   S[ ;R&   # )r   rS   rT   rU   rV   rW   )r'   rB   r   r:   r%   )r(   r)   s   "r   r*   PDFAnalysis.__annotate__T   sJ      K  	 
 \""     r   r,   N)r-   r.   r/   r0   r1   rV   rW   rY   r5   r6   r7   r8   s   @r   rQ   rQ   T   s      ' KM
  r   rQ   c                      a  ] tR t^ot o Rt]R 4       t]V 3R lR l4       t]V 3R lR l4       t]V 3R lR l4       t	R	t
V tR
# )PDFExtractorz$Extract metadata and text from PDFs.c                     / p  ^ RI pWR&    ^ RIHp W R&    ^ RIpVP                  V R&   V #   \         d     L.i ; i  \         d     L4i ; i  \         d     T # i ; i)z3Try to import PDF libraries in order of preference.N
pdfplumber)	PdfReaderPyPDF2pypdf)r`   ImportErrorrb   ra   rc   )libsr`   ra   rc   s       r   _try_import_pdf_libs!PDFExtractor._try_import_pdf_libsr   s     	!+	(&N	!OODM   		  		  		s,   - 
> A ;;AAAAc                L   < V ^8  d   QhRS[ RS[S[S[,          S[ 3,          /# )r   pdf_pathreturn)r'   r   r   rB   )r(   r)   s   "r   r*   PDFExtractor.__annotate__   s*      C E(;2G2L,M r   c                V   \        V 4      p V P                  4       '       g   \        RV  24      h\        P	                  4       pV'       g   \
        P                  R4       R# RV9   d   \        P                  WR,          4      # RV9   d   \        P                  WR,          4      # R# )z)Extract metadata and text from local PDF.zPDF not found: z6No PDF library available. Install pdfplumber or PyPDF2r`   rb   Nr;   )	r   existsFileNotFoundErrorr^   rf   loggererror_extract_pdfplumber_extract_pypdf2)ri   re   s   & r   extract_from_filePDFExtractor.extract_from_file   s     >  #ohZ$@AA002LLQRO 433H<>PQQ t//x.IIr   c                    < V ^8  d   QhRS[ /# r   ri   r   )r(   r)   s   "r   r*   rk      s      d r   c                ,    VP                  V 4      ;_uu_ 4       p\        VP                  P                  RR4      VP                  P                  RR4      VP                  P                  RR4      \	        VP                  P                  RR4      4      \        VP                  4      VP                  P                  RR4      VP                  '       d   \        VP                  4      M/ R7      pRP                  R	 VP                   4       4      p\        P                  R
\        V4       RV P                   24       W43uuRRR4       #   + '       g   i     R# ; i  \         d%   p\        P                  RT 24       Ru Rp?# Rp?ii ; i)zExtract using pdfplumber.Titler;   AuthorCreatorCreationDateProducerrI   rJ   rK   rL   rM   rN   rF   

c              3   T   "   T F  qP                  4       ;'       g    R x  K   	  R# 5i)r;   Nextract_text.0pages   & r   	<genexpr>3PDFExtractor._extract_pdfplumber.<locals>.<genexpr>   s%      #:C$%%'--2-)s   ((
Extracted  chars from Nzpdfplumber extraction failed: rm   )openrB   rT   getr'   lenrM   dictjoinrp   infoname	Exceptionrq   )ri   r`   pdfrT   textes   &&    r   rr    PDFExtractor._extract_pdfplumber   s.   	**c&,,**7B7<<++Hb9LL,,Y;"%cll&6&6~r&J"Kcii. \\--j"=8;$s||"4" {{ #:=))#  jT<OP~% +***&  	LL9!=>O	s;   E$ D*E
E$ E!	E$ !E$ $F/FFFc                    < V ^8  d   QhRS[ /# rw   r   )r(   r)   s   "r   r*   rk      s      $ r   c                    \        V R4      ;_uu_ 4       pV! V4      pVP                  ;'       g    / p\        VP                  RR4      VP                  RR4      VP                  RR4      \	        VP                  RR4      4      \        VP                  4      VP                  RR4      \        V4      R7      pR	P                  R
 VP                   4       4      p\        P                  R\        V4       RV P                   24       WV3uuRRR4       #   + '       g   i     R# ; i  \         d%   p\        P                  RT 24       Ru Rp?# Rp?ii ; i)zExtract using PyPDF2.rbz/Titler;   z/Authorz/Creatorz/CreationDatez	/Producerr~   r   c              3   @   "   T F  qP                  4       x  K  	  R # 5irD   r   r   s   & r   r   /PDFExtractor._extract_pypdf2.<locals>.<genexpr>   s      #4@D%%''Ls   r   r   NzPyPDF2 extraction failed: rm   )r   rT   rB   r   r'   r   rM   r   r   rp   r   r   r   rq   )ri   ra   freadermetarT   r   r   s   &&      r   rs   PDFExtractor._extract_pypdf2   s   	h%%"1 ,,"&((8R088Ir2 HHZ4"%dhh&C"Dfll+!XXk26"&t* {{ #4:LL#  jT<OP~+ &%%%,  	LL5aS9:O	s;   D- C8D
D- D*	$D- *D- -E8EEEr,   N)r-   r.   r/   r0   r1   staticmethodrf   rt   rr   rs   r6   r7   r8   s   @r   r^   r^   o   sV     . .  ,  4  r   r^   c                      a  ] tR t^t o Rt]P                  ! R4      t]P                  ! R4      t]P                  ! R4      t	]P                  ! R]P                  4      t]V 3R lR l4       tRtV tR	# )
ReferenceExtractorz!Extract references from PDF text.z:(?i)(doi|https?://doi\.org/)(10\.\S+?(?=\s|$|[,;.]|/]|\)))zB((?:https?://)?(?:www\.)?arxiv\.org/(?:abs|pdf)/)?(\d{4}\.\d{4,5})zfhttps?://(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&/=]*)zhttps?://\S+\.pdf(?:\?|$|\s)c                6   < V ^8  d   QhRS[ RS[S[,          /# )r   r   rj   )r'   r   r:   )r(   r)   s   "r   r*   ReferenceExtractor.__annotate__   s      / / /l); /r   c                  a . p\         P                  P                  V 4       F|  pVP                  ^4      P	                  R4      p\        RRV 2V \        ^ VP                  4       ^2,
          4      VP                  4       ^2,            R7      pVP                  V4       K~  	  \         P                  P                  V 4       Fm  pVP                  ^4      p\        RRV 2V \        ^ VP                  4       ^2,
          4      VP                  4       ^2,            R7      pVP                  V4       Ko  	  \         P                  P                  V 4       Fx  pVP                  ^ 4      P	                  4       o\        RSV \        ^ VP                  4       ^2,
          4      VP                  4       ^2,            R7      pVP                  V4       Kz  	  \         P                  P                  V 4       F  pVP                  ^ 4      P	                  R4      o\        ;QJ d    V3R lV 4       F  '       g   K   R	M	  R
M! V3R lV 4       4      '       d   Ke  \        RSV \        ^ VP                  4       ^2,
          4      VP                  4       ^2,            R7      pVP                  V4       K  	  \        P                  R\!        V4       R24       V# )z&Extract all reference types from text.z.,;)doizhttps://doi.org/)r=   r>   r?   arxivzhttps://arxiv.org/abs/r   c              3   @   <"   T F  qP                   S8H  x  K  	  R # 5irD   )r>   )r   rX   urls   & r   r   8ReferenceExtractor.extract_references.<locals>.<genexpr>  s     :z!ww#~zs   TFr   r   z references)r   DOI_PATTERNfinditergroupstripr:   maxstartendappendARXIV_PATTERNPDF_EXTENSION_PATTERNURL_PATTERNanyrp   r   r   )r   rU   matchr>   refarxiv_idr   s   &     @r   extract_references%ReferenceExtractor.extract_references   s>    
 (33<<TBEKKN((0E(0SEKKM"$45eiik"nEC
 c" C (55>>tDE{{1~H.xj9SEKKM"$45eiik"nEC
 c" E (==FFtLE++a.&&(CSEKKM"$45eiik"nEC
 c" M (33<<TBE++a.&&v.C3:z:333:z:::" Qb(8!9%))+b.I
 !!#& C 	jZ 1=>r   r,   N)r-   r.   r/   r0   r1   recompiler   r   r   
IGNORECASEr   r   r   r6   r7   r8   s   @r   r   r      sa     +**Z[KJJdeM**qK JJ'FV/ /r   r   c                   ^   a  ] tR tRt o RtV 3R lR ltRV 3R lR lltV 3R lR	 ltR
tV t	R# )PDFDownloaderi   zDownload referenced PDFs.c                    < V ^8  d   QhRS[ /# r   configr   )r(   r)   s   "r   r*   PDFDownloader.__annotate__#        ~ r   c                    Wn         R # rD   r   r   r   s   &&r   __init__PDFDownloader.__init__#      r   Nc                b   < V ^8  d   QhRS[ S[,          RS[S[,          RS[S[S[3,          /# )r   rU   r   rj   )r   r:   r   r   r   r'   )r(   r)   s   "r   r*   r   &  s5      \(: !)$;?S>r   c           
         T;'       g    V P                   P                  R,          pVP                  RRR7       V Uu. uF  q3P                  R8X  g   K  VNK  	  pp\        P                  R\        V4       R24       / p\        V P                   P                  R7      ;_uu_ 4       pV Uu/ uF   pVP                  V P                  Wr4      VbK"  	  pp\        V4       F4  p	W,          p V	P                  4       p
V
'       d   WVP                  &   K4  K6  	  R
R
R
4       V# u upi u upi   \         d1   p\        P                  RTP                   R	T 24        R
p?K  R
p?ii ; i  + '       g   i     T# ; i)zBDownload all PDF references. Returns mapping of URL -> local path.	downloadsTr   r   zDownloading z PDFs...r    Failed to download : N)r   r   r   r=   rp   r   r   r   r    submit_download_singler   resultr>   r   rq   )r   rU   r   rX   pdf_refsresultsexecutorr   futuresfuture
local_pathr   s   &&&         r   download_pdfsPDFDownloader.download_pdfs&  sX     GG4;;#9#9K#G
5)=z!VVu_AAz=l3x=/:;DKK,C,CDD $#C  5 5sGL#  
 'w/oI!'J!-7		* "	 0 E ' >
 ! ILL#6syykA3!GHHI ED sS   D$D$*E,/&D)E,.&D.E,)E,.E)	9%E$	E,$E)	)E,,E=	c                <   < V ^8  d   QhRS[ RS[RS[S[,          /# )r   r   r   rj   )r:   r   r   r'   )r(   r)   s   "r   r*   r   A  s'      L d xPS} r   c                    \         P                  ! VP                  V P                  P                  V P                  P
                  R7      pVP                  ^8w  d2   \        P                  RVP                   RVP                   24       R# \        VP                  4      p\        VP                  4      P                  ;'       g    RpW%,          pVP                  VP                  4       \        P                  RV 24       \!        V4      #   \"         d1   p\        P%                  RTP                   RT 24        Rp?R# Rp?ii ; i)zDownload a single PDF.)timeoutverifyr   r   Nzdocument.pdfzDownloaded: zDownload error for )requestsr   r>   r   r!   r"   status_coderp   warningr   r   r3   r   write_bytescontentr   r'   r   rq   )r   r   r   respparsedfilenameoutput_pathr   s   &&&     r   r   PDFDownloader._download_singleA  s   	<<		//{{--D 3&!4SYYKr$BRBRASTU cii(FFKK(--??H$/K##DLL1KK,xj12{## 	LL.syykA3?@	s%   BD :D 
AD E%E		Er   rD   )
r-   r.   r/   r0   r1   r   r   r   r6   r7   r8   s   @r   r   r      s&     #  6 r   r   c                   Z   a  ] tR tRt o RtV 3R lR ltV 3R lR ltV 3R lR ltR	tV t	R
# )LinkValidatoria  zCheck for broken links.c                    < V ^8  d   QhRS[ /# r   r   )r(   r)   s   "r   r*   LinkValidator.__annotate__d  r   r   c                    Wn         R # rD   r   r   s   &&r   r   LinkValidator.__init__d  r   r   c                L   < V ^8  d   QhRS[ S[,          RS[S[S[3,          /# )r   rU   rj   )r   r:   r   r'   r&   )r(   r)   s   "r   r*   r   g  s(      l); S$Y r   c           
        V Uu. uF  q"P                   R9   g   K  VNK  	  pp\        P                  R\        V4       R24       / p\	        V P
                  P                  R7      ;_uu_ 4       pV Uu/ uF   pVP                  V P                  V4      VbK"  	  pp\        V4       F*  pWx,          p VP                  4       p	WVP                  &   K,  	  RRR4       V# u upi u upi   \         d?   p
\        P                  RTP                   RT
 24       RYFP                  &    Rp
?
K  Rp
?
ii ; i  + '       g   i     T# ; i)	zECheck if all URLs are still live. Returns mapping of URL -> is_valid.zValidating z URLs...r   zValidation error for r   FN)r   r   r   r   )r=   rp   r   r   r   r   r    r   _validate_singler   r   r>   r   rq   )r   rU   rX   url_refsr   r   r   r   r   is_validr   s   &&         r   validate_linksLinkValidator.validate_linksg  s(   )Vz!VV7U-UAAzVk#h-9:DKK,C,CDD $#C  5 5s;S@#  
 'w/o/%}}H)1CII&	 0 E ' W
 ! /LL#82aS!IJ).GII&/ ED sR   C C 0D65&C%D64C*D6%D6*D3	53D.	(D6.D3	3D66E	c                &   < V ^8  d   QhRS[ RS[/# )r   r   rj   )r:   r&   )r(   r)   s   "r   r*   r   ~  s      L T r   c                     \         P                  ! VP                  V P                  P                  V P                  P
                  RR7      pVP                  R8  #   \         d     R# i ; i)z#Check if a single URL is reachable.T)r   r   allow_redirects  F)r   headr>   r   r!   r"   r   r   )r   r   r   s   && r   r   LinkValidator._validate_single~  s^    		==		//{{-- $	D ##c)) 		s   AA A,+A,r   N)
r-   r.   r/   r0   r1   r   r   r   r6   r7   r8   s   @r   r   r   a  s&     !  . r   r   c                   x   a  ] tR tRt o RtRV 3R lR lltRV 3R lR lltV 3R lR	 ltRV 3R
 lR lltRt	V t
R# )ResearchHelperr   z.Main orchestration for PDF research workflows.Nc                0   < V ^8  d   QhRS[ S[,          /# r   )r   r   )r(   r)   s   "r   r*   ResearchHelper.__annotate__  s     4 4x7 4r   c                    T;'       g    \        4       V n        \        4       V n        \	        4       V n        \        V P                  4      V n        \        V P                  4      V n	        R # rD   )
r   r   r^   	extractorr   ref_extractorr   
downloaderr   	validatorr   s   &&r   r   ResearchHelper.__init__  sH    00 0%/1'4&t{{3r   c                2   < V ^8  d   QhRS[ RS[RS[RS[/# )r   
pdf_sourcer   r   rj   )r'   r&   rQ   )r(   r)   s   "r   r*   r    s+      c  #'4?r   c                   \         P                  RV 24       V P                  P                  V4      w  rEV'       g   \	        RV 24      hV P
                  P                  V4      pV'       dO   V P                  P                  V4      pV F-  pVP                  V9   g   K  WxP                  ,          Vn
        K/  	  \        TTTV'       d   \        V4      M^ \        P                  ! 4       P                  4       R7      p	V	# )zTComplete PDF analysis: extract metadata + references + optionally text & validation.zAnalyzing: zFailed to extract from )rS   rT   rU   rV   rW   )rp   r   r  rt   RuntimeErrorr  r   r  r   r>   validrQ   r   r
   now	isoformat)
r   r	  r   r   rT   r   rU   
validationr   analysiss
   &&&&      r   analyze_pdfResearchHelper.analyze_pdf  s     	k*./ 99*E!8EFF ''::4@
 66zBJ!99
* *99 5CI " !%1D	q",,.224
 r   c                &   < V ^8  d   QhRS[ RS[/# )r   r  output_file)rQ   r'   )r(   r)   s   "r   r*   r    s     8 8k 8 8r   c                4   \        V4      pVP                  P                  RRR7       \        VR4      ;_uu_ 4       p\        P
                  ! VP                  4       V^R7       RRR4       \        P                  RV 24       R#   + '       g   i     L*; i)zSave analysis to JSON file.Tr   windentNzSaved analysis to )	r   parentr   r   jsondumprY   rp   r   )r   r  r  r   r   s   &&&  r   save_analysisResearchHelper.save_analysis  sq    ;'   =+s##qIIh&&(!A6 $ 	(67 $#s   (BB	c                R   < V ^8  d   QhRS[ RS[S[,          RS[S[S[3,          /# )r   r  r   rj   )rQ   r   r'   r   )r(   r)   s   "r   r*   r    s5     J J J,4SMJEI#s(^Jr   c                    V'       d   \        V4      MV P                  P                  R,          pV P                  P	                  VP
                  V4      # )z-Download all PDFs referenced in the analysis.pdfs)r   r   r   r  r   rU   )r   r  r   outputs   &&& r   download_referenced_pdfs'ResearchHelper.download_referenced_pdfs  s>     &0j!T[[5K5Kf5T,,X-@-@&IIr   )r   r  r  r  r  rD   )FF)r-   r.   r/   r0   r1   r   r  r  r"  r6   r7   r8   s   @r   r   r     s8     84 4 <8 8J J Jr   r   __main__zPDF Research Helper)descriptionr   zPDF file path or URL)helpz-oz--outputzOutput JSON filez-dz
--downloadDIRz%Download referenced PDFs to directory)metavarr&  z-cz--check-links
store_truezValidate all URLs)actionr&  z-vz	--verbosezVerbose loggingF)r   r   r  zDownloaded z PDFszError: )Fr1   r2   sysr  loggingpathlibr   typingr   r   r   r   r   dataclassesr   r	   r
   r   urllib.parser   concurrent.futuresr   r   	getLoggerr-   rp   StreamHandlerhandler	Formatter	formattersetFormatter
addHandlersetLevelINFOr   r:   rB   rQ   r^   r   r   r   r   argparseArgumentParserparseradd_argument
parse_argsargsverboseDEBUGhelperr  r   check_linksr  r!  r  printdumpsrY   downloadr"  r   r   r   r   r   rq   exitr,   r   r   <module>rI     s  
 
 
    . . 	 )   ! ? 
		8	$



!IJ	   Y    '    : : :4    $ $ $ 
 
 
4i i`: :B: :B( (^6J 6Jz z$$1FGF
$:;
j/AB
lE@gh
olI\]
k,EVWD|||&F%%HH++ & 
 ;;;  4;;7$**X--/:; ===77$--PIKK+c)n%5U;< A H  wqc]#s%   39K -AK 7K K9&K44K9