*ë 4ª;;csÌdZdkZdkZdkZdklZdklZdklZ dkl Z "dfd„ƒYZ mdd e d e d „Z ½d „Z ée d dde d„ZdS(sÄPubMed.py This module provides code to work with PubMed from the NCBI. http://www.ncbi.nlm.nih.gov/PubMed/ Online documentation for linking to PubMed is available at: http://www.ncbi.nlm.nih.gov/PubMed/linking.html Classes: Dictionary Access PubMed articles using a dictionary interface. Functions: search_for Search PubMed. find_related Find related articles in PubMed. download_many Download many articles from PubMed in batch mode. N(sFile(sRequestLimiter(sNCBI(sMedlines Dictionarycs§"dZ'(ded„Z5d„Z7d„Z9d„Z;d„Z=d„Z?d„ZAd „Z Cd „Z Fd „Z Ned „Z Ud „Z RS(sMAccess PubMed using a read-only dictionary interface. Methods: f5.0cs((12||_3t|ƒ|_dS(sjDictionary(delay=5.0, parser=None) Create a new Dictionary to access PubMed. parser is an optional parser (e.g. Medline.RecordParser) object to change the results into another form. If set to None, then the raw contents of the file will be returned. delay is the number of seconds to wait between each query. N(sparsersselfsRequestLimitersdelayslimiter(sselfsdelaysparser((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys__init__(s  cs56td‚dS(NsPubMed contains lots of entries(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys__len__5scs78td‚dS(NsThis is a read-only dictionary(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysclear7scs9:td‚dS(NsThis is a read-only dictionary(sNotImplementedError(sselfskeysitem((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys __setitem__9scs;<td‚dS(NsThis is a read-only dictionary(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysupdate;scs=>td‚dS(NsYou don't need to do this...(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pyscopy=scs?@td‚dS(Ns#You don't really want to do this...(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pyskeys?scsABtd‚dS(Ns#You don't really want to do this...(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysitemsAscsCDtd‚dS(Ns#You don't really want to do this...(sNotImplementedError(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysvaluesCscsCFGHyI||WnJtj oKdSnXLdSdS(sS.has_key(id) -> booliiN(sselfsidsKeyError(sselfsid((s+/mit/seven/lib/python/Bio/Medline/PubMed.pyshas_keyFs  csBNOyP||SWnQtj oR|SnXSd‚dS(NsHow did I get here?(sselfsidsKeyErrorsfailobj(sselfsidsfailobj((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysgetNs  c s¦U\_|iiƒay+btiddd|ddddƒ}Wn$dtj o}ht |‚nXi|i t j oj|i i |ƒSnk|i ƒSdS( sÍS.__getitem__(id) -> object Return the Medline entry. id is either the Medline Unique ID or the Pubmed ID of the article. Raises a KeyError if there's an error. sdbsPubMedsidsreportsmedlarssmodestextN(sselfslimiterswaitsNCBIspmfetchsidshandlesIOErrorsxsKeyErrorsparsersNonesparsesread(sselfsidshandlesx((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys __getitem__Us+(s__doc__sNones__init__s__len__sclears __setitem__supdatescopyskeyssitemssvaluesshas_keysgets __getitem__(((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys Dictionary"s          i'iic sŸm|}dtifd„ƒY} ¢t|ƒ}£g} ¤xT¤|tjpt | ƒ|jo0¥| ƒ}©|i ƒ«|t | ƒ} ¬|} ­|tj o| |t | ƒjo®|t | ƒ} n²tid|ddd| d| ƒ} ³|i| iƒƒ´| i|iƒµ|tj o-·x#|id·r}¸||ƒqEWn¹t |iƒ| jp|i oºPnq@W»| Sd S( s›search_for(search[, batchsize][, delay][, callback_fn] [, start_id][, max_ids]) -> ids Search PubMed and return a list of the PMID's that match the criteria. search is the search string used to search the database. batchsize specifies the number of ids to return at one time. By default, it is set to 10000, the maximum. delay is the number of seconds to wait between queries (default 2). callback_fn is an optional callback function that will be called as passed a PMID as results are retrieved. start_id specifies the index of the first id to retrieve and max_ids specifies the maximum number of id's to retrieve. s ResultParsercsG}†d„ZŠd„ZŒd„ZŽeidƒZd„ZRS(Ncs2†‡tii|ƒˆg|_‰d|_dS(Ni(ssgmllibs SGMLParsers__init__sselfsidssin_body(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys__init__†s csŠ‹d|_dS(Ni(sselfsin_body(sselfs attributes((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys start_bodyŠscsŒd|_dS(Ni(sselfsin_body(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysend_bodyŒss\Dcs‹’|i o “dSn•ti|ƒ}–| o —dSnœ|ii|ƒotdt|ƒ‚n |i i |ƒdS(Ns1I expected an ID, but '%s' doesn't look like one.( sselfsin_bodysstringsstripsdatas _not_pmid_ressearchs SyntaxErrorsreprsidssappend(sselfsdata((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys handle_datas   (s__init__s start_bodysend_bodysrescompiles _not_pmid_res handle_data(((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys ResultParser}s    smsdoptsdsdispmaxs dispstartiN(ssgmllibs SGMLParsers ResultParsersRequestLimitersdelayslimitersidssmax_idssNoneslensparserswaitsstart_idsstarts batchsizesmaxsNCBIspmqtyssearchshsfeedsreadsextends callback_fnsid(ssearchs batchsizesdelays callback_fnsstart_idsmax_idssidslimitersparsers ResultParsersidssmaxsstartsh((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys search_forms,% #   '' $ csœ½ÃÄdtifd„ƒY}â|ƒ}ãt|ƒtgƒjoäti|dƒ}nåti |dƒ}æ|i |i ƒƒç|i SdS(sœfind_related(pmid) -> ids Search PubMed for a list of citations related to pmid. pmid can be a PubMed ID, a MEDLINE UID, or a list of those. s ResultParsercsGÄÌd„ZÐd„ZÒd„ZÔeidƒZÕd„ZRS(Ncs2ÌÍtii|ƒÎg|_Ïd|_dS(Ni(ssgmllibs SGMLParsers__init__sselfsidssin_id(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys__init__Ìs csÐÑd|_dS(Ni(sselfsin_id(sselfs attributes((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysstart_idÐscsÒÓd|_dS(Ni(sselfsin_id(sself((s+/mit/seven/lib/python/Bio/Medline/PubMed.pysend_idÒss\DcscÕÖ|i o ×dSnÜ|ii|ƒoÝtdt|ƒ‚nà|ii|ƒdS(Ns1I expected an ID, but '%s' doesn't look like one.( sselfsin_ids _not_pmid_ressearchsdatas SyntaxErrorsreprsidssappend(sselfsdata((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys handle_dataÕs  (s__init__sstart_idsend_idsrescompiles _not_pmid_res handle_data(((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys ResultParserÄs    s,spmidN(ssgmllibs SGMLParsers ResultParsersparserstypespmidsstringsjoinsNCBIs pmneighborshsfeedsreadsids(spmids ResultParsersparsersh((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys find_related½s f120.0f5.0iôc sòéõú|djp |djoûtd‚nüt|ƒ}ý|} d}  x” |o‰ |t|ƒjo t|ƒ}ndi || ƒ}| o|i |ƒn|i ƒy»t iddd|d d d d ƒ}|iƒ} titi|ƒƒ} !d} "x("| iƒtj o#| d} q5W$| |jo %t‚n&ti|ƒ}Wny'tj oj(|djo7+|idƒ} ,|tj o-|| ƒnn1|d }2d} 3qZnX4| d} 8ti||ƒ} 9d}:xW:doL;| iƒ} <| tjo=Pn>|||| ƒ?|d}q:WA||}E| d jo ||jo.F|d }G||jo H|}nnqZWdS(sdownload_many(ids, callback_fn, broken_fn=None, delay=120.0, batchsize=500) Download many records from PubMed. ids is a list of either the Medline Unique ID or the PubMed ID's of the articles. Each time a record is downloaded, callback_fn is called with the text of the record. broken_fn is an optional function that is called with the id of records that were not able to be downloaded. delay is the number of seconds to wait between requests. batchsize is the number of records to request each time. iôis#batchsize must be between 1 and 500is,sdbsPubMedsidsreportsmedlarssmodestextiN("s batchsizes ValueErrorsRequestLimitersdelayslimiterscurrent_batchsizes nsuccessessidsslensjoinsid_strswaits faildelaysNCBIspmfetchshandlesreadsresultssMedlinesIteratorsFiles StringHandlesitersnum_idssnextsNonesIOErrorspopsids broken_fnsparsersidnumsrecs callback_fn(sidss callback_fns broken_fnsdelays faildelays batchsizesparsersidnumsid_strs nsuccessessitersnum_idssidsrecslimiterscurrent_batchsizesresultsshandle((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys download_manyés`     '          (s__doc__sstringsressgmllibsBiosFilesBio.WWWsRequestLimitersNCBIsMedlines DictionarysNones search_fors find_relateds download_many( sFiles download_manysRequestLimiters find_relateds search_forsresNCBIsstrings DictionarysMedlinessgmllib((s+/mit/seven/lib/python/Bio/Medline/PubMed.pys?s    KP ,