From 0e4993d10da6a695e56fcbe59cfee8cf58f128e7 Mon Sep 17 00:00:00 2001 From: Luis Roberto Mercado Diaz Date: Mon, 6 May 2024 12:46:52 -0400 Subject: [PATCH] Updated Support in the files and documents. --- code/lib/Loading_PudMed.py | 2 +- .../Loading_PudMed.cpython-311.pyc | Bin 11092 -> 11092 bytes code/step1_data_collection.py | 16 +-- esearch.dtd | 103 ++++++++++++++++++ 4 files changed, 112 insertions(+), 9 deletions(-) create mode 100644 esearch.dtd diff --git a/code/lib/Loading_PudMed.py b/code/lib/Loading_PudMed.py index 43916a5..31104b5 100644 --- a/code/lib/Loading_PudMed.py +++ b/code/lib/Loading_PudMed.py @@ -13,7 +13,7 @@ import time sys.path.append('lib') -import lib.Medline +from Bio import Medline import os date = startTime = datetime.now().strftime("%Y_%m_%d_%H_%M_%S") diff --git a/code/lib/__pycache__/Loading_PudMed.cpython-311.pyc b/code/lib/__pycache__/Loading_PudMed.cpython-311.pyc index 4786d65e0c0caaf3989365c9d91a0a9dc257b7b3..8f0ff861105a8459c5fdcf4f477c92fa227c55e1 100644 GIT binary patch delta 1070 zcmY+CT}TvB6oBWB?(EL)j_!}TtFG*-yY7ry?HUT1nHj4XTIMh8i!RRi$F56v+)6Y0 zA&9_->^vA0VG%|c1TGN;J=RMvJxI_z)k8=x5%kp0L-&kkbeQ|iopaAQbAImD$kvGT zNRsRvlMlk7$@q#?PQI-~mweW=BjZdu38xa3PfJOO=QPV~5scNA@oUBK$z9T-+SUoj zZLqZ?=Sk9)bn{#{r;67&)xOTNQ?_;_=~4MXPH}*r%sLceSo<_JJu|1}uaZ$h9C?F} z3qlpMr2%k@1H=KUmw9aZ?Yx7OP1yY>N+xH@|GZ&6Co6L^{s5l%rJ? zQGuvt=wg4golT`@)YQC2YfxQ_!1QPs5rKQfRedsU_ahX<0S3iMJ-9bhX~G>QKo2t* zRy~)=r04=|L)8&PJK`v!18lA!OHFnylFCx1nJ8fRD^|9_@9!aa<({@azbGwnYXln$ z9iD>{9`DL*VSd^3nJ;*-WQB3BTzHc#zsRqZ_7e{lY6v}Q?~Fcg@Vx^x0lY74?_%mj zUhJUV5c5R_DaP8Vrx6`2G&MJ+(HLsu42s7r(6F4zX{;2p1$}sU5^)OAj~GOpMhw6c z-x%?N)89-sq0^ruck?g(9XNnr6-m;BV>Aj`qces*r)$$Jy)0c&Y!nMNe_&WOT}#o4 z>D@lV^*}IYws~~VMA)^!-Wo*H1@;b^LcM4-lz$)Cy;Y?GxuRg$XVw8 zOm1i`L8oJg6Nqud5MmK=2Qkd>n4@@!c4`-KCqjj??l6`3t$5+B(pqHBxS(?;Yt9|Y t>g#0F`aZhsMfhoJ%VgDDT5G2p?0~SPe+9Mvg3I@g`|p7-^;3oD_XpMe;x+&P delta 1106 zcmYk5O-vI(6o7ZO?QVZ4v}=_LHMH2$E>;CmOwbto0Yid+fROZ{R(6q^{^)G$4`S5B zc=8~52aFu7i2)6Ip(dV;2M>DC#6&J`;?09ZFUG{EiHYwm6@A(L^5)IFnfEiZIJ`LQ zo%4F#0?Llh9b?HU?^^a{Dn7YN%z9FGjcH=GCRHN}y5qDLn6ySL*TPqSpi`4)nIO#L zzbqG6sxIXdh5dr&ye??2SrKRPUzU_#69)y=4Iy^AGQ~z1b61wcc1a51Ja2@sYk;}I zaP@>dWT+w35qyMNgzD#hSad~LEqr&~XG&$peOqLK%2w}Qu`@`kS_o?iVMMRWOy{|D zHlwABI**XKnLr`&^@J!qu3NV=PU=QNg0Kmp)^I=RRw(VHQ2@LPVai4+mrL`DdNUsi&y%)P7um=%UYJ| zDs##k(e_|chI@g8{T93V99}kdR^G2}U<&1FN_|>?#weO%{{Y_yj{2y(2h9_rtDE;i zM}2I>ln>}yHj~$vQ`$gI4xY}R()ni8c^g7itQ<|p*^-XgSXJn!$peIgghPY@!ePP@ zn6E$16z~MMu_v%QShC$s-l;qdc2gIAG^E%S>ZNJNYUfOM$MB7 zLr?S3@qfiOT|E~@^)tmxA#cikhk7_KaMNZKxhgGpVPwTws`^stO{N=EzOW@+K~>~~ zm3N^9k%iz!Qw;g2sg1?qLsKwmwRVi$?D=#~=NVFMnS4=||2xD$E004YybT*V5_U06 zEFGB^**^HWzK_LVZ#0S9o{0{yHh2+j4kpQgk~1ZJOfRma1;3*W%n!lXdEDq$Y#KL$ zM7$h2O6#u>t`e>xFw5!__!y5mDNfaa7u}agN|X~Hf<1`>x-TR)bgd#oH=&Pkf-p#! zAj}Yk5Dx`T7tyK-car9WdUe)g8ELF4@Jj9STld0~&79m+y)NKuZAn-T_sDBylV8rA hxq?>8>bv+nPSBG#KEbipOK#<@Q2k)3^^~1F{s2|H_0j+U diff --git a/code/step1_data_collection.py b/code/step1_data_collection.py index 35538d6..e01710c 100644 --- a/code/step1_data_collection.py +++ b/code/step1_data_collection.py @@ -33,16 +33,16 @@ ld = literature_data_collection(email, output_dir, document_output_dir, api_key=api_key) ########### word query based literature data collection ################# -gap=9000 -batch = 400 -w2d_starting_point = 2 +# gap=9000 +# batch = 400 +# w2d_starting_point = 2 -search_results, _word_end_point = ld.word_based_query_fit(year = years, user_term=word_query) -print('The number of avaliable abstracts :', _word_end_point, 'for ', word_query) +# search_results, _word_end_point = ld.word_based_query_fit(year = years, user_term=word_query) +# print('The number of avaliable abstracts :', _word_end_point, 'for ', word_query) -if int(sys.argv[2])==0: - word_end_point = _word_end_point -ld.collecting_doc_using_word_based_query(year = years, user_term=word_query, gap = gap, starting = gap*w2d_starting_point, ixs = w2d_starting_point, test_end_point=word_end_point) +# if int(sys.argv[2])==0: +# word_end_point = _word_end_point +# ld.collecting_doc_using_word_based_query(year = years, user_term=word_query, gap = gap, starting = gap*w2d_starting_point, ixs = w2d_starting_point, test_end_point=word_end_point) ########### gene name-query based literature data collection ################# query_full=ld.text_open('./data/gene_name_info/query_full_name.txt') diff --git a/esearch.dtd b/esearch.dtd new file mode 100644 index 0000000..bd11e35 --- /dev/null +++ b/esearch.dtd @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +