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petermr / CEVOpen

Contentmining of Open phytochemical literature for medicinal activities
26 stars 19 forks source link

could not create full data table #91

Open tlhahsn opened 3 years ago

tlhahsn commented 3 years ago

the output i got after running ami search

C:\Users\talha>cd C:\Users\talha\CEVOpen\dictionary\eoCompound

C:\Users\talha\CEVOpen\dictionary\eoCompound>ami -p (plantcompoundpapers) search --dictionary country disease

Generic values (AMISearchTool)
================================

Specific values (AMISearchTool)
================================
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(country) search(disease)
cProject: (plantcompoundpapers)
created COMMAND: word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt search(country) search(disease)
legacy cmd> word(frequencies)xpath:@count>20~w.stopwords:pmcstop.txt_stopwords.txt
legacy cmd> search(country)
legacy cmd> search(disease)
!10.1101 .!10.21203 !10.26434 !10.26434chemrxiv.12440024.v1 PMC3365481 PMC3721410 PMC4164025 PMC4379528 PMC5686923 PMC6186079 PMC6222869 .PMC6883063 PMC6930648 PMC7006766 PMC7191900 PMC7269084 PMC7336994 PMC7412988 PMC7427108 PMC7449395 PMC7464374 .PMC7464697 PMC7469192 PMC7470146 PMC7474796 PMC7479404 PMC7488093 PMC7494105 PMC7494665 PMC7496984 PMC7499913 .PMC7503550 PMC7504212 PMC7508392 PMC7510975 PMC7513367 PMC7519196 PMC7524867 PMC7527447 PMC7527982 PMC7528132 .PMC7530510 PMC7530923 PMC7531785 PMC7542034 PMC7544953 PMC7553295 PMC7555273 PMC7558747 PMC7558993 PMC7559865 .PMC7559925 PMC7563488 PMC7564161 PMC7569807 PMC7570077 PMC7570315 PMC7570383 PMC7570746 PMC7570874 PMC7571138 .PMC7574196 PMC7574309 PMC7578979 PMC7582250 PMC7582273 PMC7582350 PMC7582661 PMC7583788 PMC7583972 PMC7586076 .PMC7586115 PMC7586119 PMC7587357 PMC7587372 PMC7587526 PMC7587584 PMC7587964 PMC7587977 PMC7588921 PMC7589128 .PMC7589259 PMC7589842 PMC7589974 PMC7590997 PMC7593249 PMC7593327 PMC7594188 PMC7596250 PMC7600465 PMC7600625 .PMC7600777 PMC7601357 PMC7601409 PMC7601815 PMC7601869 PMC7601952 PMC7602697 PMC7602794 PMC7603628 PMC7604581 .PMC7607633 PMC7607654 PMC7609408 PMC7641974 PMC7644334 PMC7647083 PMC7648075 PMC7648271 PMC7648683 PMC7648839 .PMC7652251 PMC7652730 PMC7652793 PMC7652885 PMC7653773 PMC7655048 PMC7655067 PMC7657077 PMC7659943 PMC7660698 .PMC7661141 PMC7662255 PMC7662597 PMC7662983 PMC7663017 PMC7663390 PMC7663455 PMC7663536 PMC7663620 PMC7663631 .PMC7663752 PMC7664932 PMC7666219 PMC7666564 PMC7669877 PMC7672008 PMC7674207 PMC7674627 PMC7676720 PMC7676977 .PMC7677421 PMC7680602 PMC7680756 PMC7680914 PMC7683130 PMC7684468 PMC7684603 PMC7685824 PMC7685827 PMC7688173 .PMC7689036 PMC7690256 PMC7690744 PMC7690750 PMC7690858 PMC7690868 PMC7691007 PMC7691073 PMC7691236 PMC7691295 .PMC7691503 PMC7691614 PMC7692086 PMC7692277 PMC7692298 PMC7692362 PMC7692612 PMC7692740 PMC7693031 PMC7693457 .PMC7693752 PMC7693977 PMC7694179 PMC7694502 PMC7694646 PMC7694671 PMC7695008 PMC7695023 PMC7695154 PMC7695267 .PMC7695294 PMC7695645 PMC7696031 PMC7696162 PMC7696230 PMC7696306 PMC7696458 PMC7696464 PMC7696744 PMC7696850 .PMC7697004 PMC7697102 PMC7697156 PMC7697265 PMC7697716 PMC7697879 PMC7698425 PMC7698523 PMC7698706 PMC7698770 .PMC7698878 PMC7698941 PMC7698964 PMC7699174 PMC7699777 PMC7699931 PMC7699947 PMC7700059 PMC7700206 PMC7700410 .PMC7700638 PMC7701093 PMC7701256 PMC7704417 PMC7707474 PMC7707481 PMC7707995 PMC7708940 PMC7711191 PMC7711696 .PMC7713432 PMC7715011 PMC7715482 PMC7717572 PMC7717613 PMC7719695 PMC7720635 PMC7721531 PMC7721540 PMC7724791 .PMC7725569 PMC7725741 PMC7728069 PMC7728153 PMC7728155 PMC7728315 PMC7728322 PMC7728332 PMC7728353 PMC7728470 .PMC7728478 PMC7728801 PMC7729004 PMC7729440 PMC7729875 PMC7729923 PMC7729994 PMC7730080 PMC7730301 PMC7730475 .PMC7730552 PMC7730595 PMC7730820 PMC7730830 PMC7731065 PMC7731202 PMC7731506 PMC7731913 PMC7732089 PMC7732400 .PMC7733000 PMC7733993 PMC7736719 !PMC7737096 PMC7738326 PMC7739878 PMC7742202 PMC7743958 PMC7744478 PMC7744551 .PMC7745032 PMC7747825 PMC7748911 PMC7751431 PMC7753128 PMC7755035 PMC7756191 PMC7756559 PMC7757906 PMC7758400 .PMC7758404 PMC7758432 PMC7758512 PMC7759553 PMC7760007 PMC7760024 PMC7760039 PMC7760081 PMC7760164 PMC7760375 .PMC7760478 PMC7760518 PMC7760624 PMC7760773 PMC7760984 PMC7761064 PMC7761148 PMC7761249 PMC7761298 PMC7761563 .PMC7761567 PMC7761800 PMC7761819 PMC7762000 PMC7762048 PMC7762054 PMC7762085 PMC7762097 PMC7762183 PMC7762190 .PMC7762226 PMC7762448 PMC7762608 PMC7763075 PMC7763091 PMC7763115 PMC7763123 PMC7763129 PMC7763292 PMC7763305 .PMC7763331 PMC7763345 PMC7763476 PMC7763512 PMC7763559 PMC7763593 PMC7763744 PMC7763825 PMC7763896 PMC7763918 .PMC7764037 PMC7764227 PMC7764658 PMC7764892 PMC7765096 PMC7765139 PMC7765155 PMC7765257 PMC7765828 PMC7765886 .PMC7765926 PMC7765930 PMC7766005 PMC7766089 PMC7766149 PMC7766153 PMC7766178 PMC7766379 PMC7766633 PMC7766674 .PMC7766725 PMC7766727 PMC7767053 PMC7767113 PMC7767136 PMC7767169 PMC7767361 PMC7767362 PMC7767399 PMC7767424 .PMC7767818 PMC7767828 PMC7768730 PMC7769628 PMC7769672 PMC7769804 PMC7769811 PMC7772181 PMC7772544 PMC7772550 .PMC7772620 PMC7773461 PMC7773473 PMC7774525 PMC7775464 PMC7777452 PMC7777528 PMC7779480 PMC7779684 PMC7779698 .PMC7781418 PMC7781944 PMC7782663 PMC7783804 PMC7785441 PMC7785522 PMC7785825 PMC7785844 PMC7785943 PMC7785955 .PMC7786132 PMC7786139 PMC7787523 PMC7787652 PMC7787816 PMC7787954 PMC7788046 PMC7788126 PMC7789504 PMC7789580 .PMC7789753 PMC7789864 PMC7791887 PMC7791912 PMC7792625 PMC7792949 PMC7793533 PMC7794673 PMC7794732 PMC7794910 .PMC7795015 PMC7795089 PMC7795161 PMC7795193 PMC7795351 PMC7795411 PMC7795503 PMC7795506 PMC7795748 PMC7795833 .PMC7796079 PMC7796276 PMC7796298 PMC7796335 PMC7796366 PMC7796387 PMC7796436 PMC7797125 PMC7797194 PMC7799430 .PMC7801105 PMC7801116 PMC7801304 PMC7801432 PMC7801735 PMC7802159 PMC7802575 PMC7803138 PMC7803143 PMC7803989 .PMC7804112 PMC7804141 PMC7804154 PMC7805276 PMC7806260 PMC7806641 PMC7807059 PMC7807802 PMC7808741 PMC7808824 .PMC7809109 PMC7809392 PMC7810277 PMC7810394 PMC7810889 PMC7811472 PMC7811550 PMC7811810 PMC7812032 PMC7812931 .PMC7813745 PMC7814569 PMC7814726 PMC7814937 PMC7815160 PMC7815396 PMC7815410 PMC7815652 PMC7816146 PMC7816844 .PMC7816845 PMC7817466 PMC7817489 PMC7818593 PMC7819315 PMC7820602 PMC7821929 PMC7822065 PMC7822123 PMC7822174 .PMC7822430 PMC7822660 PMC7823258 PMC7823385 PMC7823439 PMC7823444 PMC7823482 PMC7823506 PMC7823517 PMC7823625 .PMC7823675 PMC7823753 PMC7823792 PMC7823795 PMC7823840 PMC7823854 PMC7823993 PMC7824023 PMC7824034 PMC7824061 .PMC7824064 PMC7824111 PMC7824119 PMC7824130 PMC7824150 PMC7824169 PMC7824205 PMC7824228 PMC7824284 PMC7824362 .PMC7824416 PMC7824492 PMC7824498 PMC7824601 PMC7824676 PMC7824788 PMC7824789 PMC7824868 PMC7824881 PMC7824898 .PMC7825055 PMC7825126 PMC7825178 PMC7825240 PMC7825337 PMC7825428 PMC7825507 PMC7825567 PMC7826111 PMC7826242 .PMC7826587 PMC7826601 PMC7826859 PMC7827020 PMC7827031 PMC7827111 PMC7827182 PMC7827262 PMC7827335 PMC7827347 .PMC7827382 PMC7827440 PMC7827451 PMC7827483 PMC7827498 PMC7827524 PMC7827528 PMC7827553 PMC7827591 PMC7827611 .PMC7827728 PMC7827760 PMC7827789 PMC7827795 PMC7827828 PMC7827872 PMC7827964 PMC7828031 PMC7828129 PMC7828132 .PMC7828134 PMC7828174 PMC7828211 PMC7828301 PMC7828331 PMC7828423 PMC7828511 PMC7828711 PMC7828715 PMC7828731 .PMC7828735 PMC7828736 PMC7828774 PMC7829895 PMC7830006 PMC7830248 PMC7830311 PMC7830447 PMC7830475 PMC7830503 .PMC7830504 PMC7830528 PMC7830657 PMC7830842 PMC7830865 PMC7830912 PMC7830935 PMC7830962 PMC7830967 PMC7831036 .PMC7831324 PMC7831775 PMC7831912 PMC7831921 PMC7831927 PMC7831946 PMC7831952 PMC7831967 PMC7832193 PMC7832194 .PMC7832296 PMC7832333 PMC7832401 PMC7832499 PMC7832507 PMC7832534 PMC7832542 PMC7833040 PMC7833388 PMC7833933 .PMC7834779 PMC7835903 PMC7835970 PMC7836426 PMC7836487 PMC7838277 PMC7840253 PMC7840926 PMC7841026 PMC7841356 .PMC7841903 PMC7841945 PMC7843487 PMC7843771 PMC7845744 PMC7847758 PMC7847861 PMC7848649 PMC7848973 PMC7849236 .PMC7850368 PMC7850424 PMC7852404 PMC7853596 PMC7853604 PMC7854439 PMC7854645 PMC7854674 PMC7854675 PMC7854678 .PMC7856339 PMC7857882 PMC7858074 PMC7860093 PMC7862227 PMC7862595 PMC7864745 PMC7864906 PMC7864976 PMC7865082 .PMC7865084 PMC7865210 PMC7865227 PMC7865290 PMC7865323 PMC7865359 PMC7865499 PMC7865555 PMC7865568 PMC7865595 .PMC7865633 PMC7865715 PMC7865826 PMC7865903 PMC7865983 PMC7866000 PMC7866031 PMC7866120 PMC7866194 PMC7866218 .PMC7866295 PMC7866531 PMC7866625 PMC7866841 PMC7867005 PMC7867013 PMC7867015 PMC7867026 PMC7867105 PMC7867241 .PMC7867259 PMC7867377 PMC7868139 PMC7868585 !PMC7869076 PMC7869668 PMC7870401 PMC7871409 PMC7871548 PMC7871564 .PMC7872560 PMC7872582 PMC7872952 PMC7873959 PMC7874482 PMC7875619 PMC7876777 PMC7877615 PMC7878689 PMC7878694 .PMC7878698 PMC7878742 PMC7879783 PMC7881030 PMC7881223 PMC7882218 PMC7882510 PMC7882811 PMC7884620 PMC7885008 .PMC7885310 PMC7885413 PMC7885726 PMC7886531 PMC7887227 PMC7887249 PMC7888440 PMC7888442 PMC7888597 PMC7889342 .PMC7889936 PMC7889937 PMC7889962 PMC7890032 !PMC7890104 PMC7890384 PMC7891170 PMC7891363 PMC7891737 PMC7892566 .PMC7892686 PMC7892916 PMC7892933 PMC7892936 PMC7892944 PMC7893418 PMC7894489 PMC7894860 PMC7894928 PMC7895382 .PMC7895923 PMC7896091 PMC7896135 PMC7896843 PMC7897203 PMC7897622 PMC7897978 PMC7898454 PMC7899166 PMC7899931 .PMC7900558 PMC7900560 PMC7900702 PMC7900706 PMC7901085 PMC7901698 PMC7902047 PMC7902150 PMC7902500 PMC7902804 .PMC7902805 PMC7903152 PMC7903315 PMC7904367 PMC7904547 PMC7904875 PMC7905195 PMC7905319 PMC7906523 PMC7906577 .PMC7906619 PMC7907014 PMC7907592 PMC7907610 PMC7907617 PMC7907656 !PMC7907736 PMC7907780 PMC7907819 PMC7908259 .PMC7908345 PMC7908520 PMC7908993 PMC7909085 PMC7909086 PMC7909252 PMC7909524 PMC7909537 PMC7909549 PMC7909571 .PMC7910186 PMC7910824 PMC7910874 PMC7910889 PMC7910900 PMC7910941 PMC7910992 PMC7911005 PMC7911048 PMC7911230 .PMC7911256 PMC7911284 PMC7911329 PMC7911374 PMC7911470 PMC7911552 PMC7911596 PMC7911640 PMC7911646 PMC7911737 .PMC7911790 PMC7911824 PMC7911848 PMC7911922 PMC7911936 PMC7911977 PMC7912135 PMC7912141 PMC7912171 PMC7912186 .PMC7912234 PMC7912241 PMC7912315 PMC7912402 PMC7912415 PMC7912489 PMC7912629 PMC7912663 PMC7912694 PMC7912713 .PMC7912742 PMC7912826 PMC7912845 PMC7912874 PMC7912945 PMC7913007 PMC7913021 PMC7913058 PMC7913150 PMC7913229 .PMC7913287 PMC7913349 PMC7913558 PMC7913593 PMC7913636 PMC7913645 PMC7913911 PMC7913913 PMC7913918 PMC7913996 .PMC7914077 PMC7914480 PMC7914517 PMC7914639 PMC7914665 PMC7914685 PMC7914768 PMC7914860 PMC7914917 PMC7915050 .PMC7915066 PMC7915169 PMC7915315 PMC7915326 PMC7915501 PMC7915531 PMC7915647 PMC7915666 PMC7915728 PMC7915730 .PMC7915747 PMC7915774 PMC7915777 PMC7915782 PMC7915875 PMC7915883 PMC7915920 PMC7915956 PMC7915976 PMC7916075 .PMC7916253 PMC7916406 PMC7916408 PMC7916527 PMC7916587 PMC7916618 PMC7916649 PMC7916669 PMC7916811 PMC7916812 .PMC7916838 PMC7916865 PMC7916866 PMC7917091 PMC7917099 PMC7917617 PMC7917634 PMC7917646 PMC7917748 PMC7917779 .PMC7917799 PMC7917821 PMC7917892 PMC7917915 PMC7918049 PMC7918315 PMC7918357 PMC7918405 PMC7918410 PMC7918425 .PMC7918447 PMC7918514 PMC7918609 PMC7918618 PMC7918631 PMC7918658 PMC7918731 PMC7918792 PMC7918836 PMC7918939 .PMC7919017 PMC7919373 PMC7919478 PMC7919652 PMC7919663 PMC7919692 PMC7919894 PMC7920288 PMC7921287 PMC7921925 .PMC7921944 PMC7921978 PMC7922068 PMC7922108 PMC7922127 PMC7922180 PMC7922199 PMC7922265 PMC7922288 PMC7922318 .PMC7922350 PMC7922420 PMC7922507 PMC7922566 PMC7922708 PMC7922777 PMC7922796 PMC7922861 PMC7922862 PMC7922906 .PMC7922931 PMC7922938 PMC7922956 PMC7922983 PMC7922985 PMC7922987 PMC7922995 PMC7922997 PMC7923116 PMC7923153 .PMC7923163 PMC7923240 PMC7923270 PMC7923285 PMC7923287 PMC7923348 PMC7923432 PMC7924326 PMC7924333 PMC7924754 .PMC7924882 PMC7925044 PMC7925305 PMC7925997 PMC7926303 PMC7926421 PMC7926423 PMC7926453 PMC7926491 PMC7926721 .PMC7926748 PMC7926860 PMC7926895 PMC7927013 PMC7929365 !PMC7929692 PMC7930237 PMC7930249 PMC7930286 PMC7931196 .PMC7931376 PMC7932998 PMC7933046 PMC7933694 PMC7934435 PMC7935503 PMC7935522 PMC7936408 !PMC7943801 !PMC7943927 .WSW> Cannot read stopword stream: /org/contentmine/ami/wordutil, ami3, version 2020/08/09_09/54-NEXT-SNAPSHOT/pmcstop.txt
WSW> Cannot read stopword stream: /org/contentmine/ami/wordutil, ami3, version 2020/08/09_09/54-NEXT-SNAPSHOT/stopwords.txt
10.1101 !w.10.21203 !w10.26434 !w10.26434chemrxiv.12440024.v1 !wPMC3365481 PMC3721410 PMC4164025 PMC4379528 PMC5686923 PMC6186079 PMC6222869 .PMC6883063 PMC6930648 PMC7006766 PMC7191900 PMC7269084 PMC7336994 PMC7412988 PMC7427108 PMC7449395 PMC7464374 .PMC7464697 PMC7469192 PMC7470146 PMC7474796 PMC7479404 PMC7488093 PMC7494105 PMC7494665 PMC7496984 PMC7499913 .PMC7503550 PMC7504212 PMC7508392 PMC7510975 PMC7513367 PMC7519196 PMC7524867 PMC7527447 PMC7527982 PMC7528132 .PMC7530510 PMC7530923 PMC7531785 PMC7542034 PMC7544953 PMC7553295 PMC7555273 PMC7558747 PMC7558993 PMC7559865 .PMC7559925 PMC7563488 PMC7564161 PMC7569807 PMC7570077 PMC7570315 PMC7570383 PMC7570746 PMC7570874 PMC7571138 .PMC7574196 PMC7574309 PMC7578979 PMC7582250 PMC7582273 PMC7582350 PMC7582661 PMC7583788 PMC7583972 PMC7586076 .PMC7586115 PMC7586119 PMC7587357 PMC7587372 PMC7587526 PMC7587584 PMC7587964 PMC7587977 PMC7588921 PMC7589128 .PMC7589259 PMC7589842 PMC7589974 PMC7590997 PMC7593249 PMC7593327 PMC7594188 PMC7596250 PMC7600465 PMC7600625 .PMC7600777 PMC7601357 PMC7601409 PMC7601815 PMC7601869 PMC7601952 PMC7602697 PMC7602794 PMC7603628 PMC7604581 .PMC7607633 PMC7607654 PMC7609408 PMC7641974 PMC7644334 PMC7647083 PMC7648075 PMC7648271 PMC7648683 PMC7648839 .PMC7652251 PMC7652730 PMC7652793 PMC7652885 PMC7653773 PMC7655048 PMC7655067 PMC7657077 PMC7659943 PMC7660698 .PMC7661141 PMC7662255 PMC7662597 PMC7662983 PMC7663017 PMC7663390 PMC7663455 PMC7663536 PMC7663620 PMC7663631 .PMC7663752 PMC7664932 PMC7666219 PMC7666564 PMC7669877 PMC7672008 PMC7674207 PMC7674627 PMC7676720 PMC7676977 .PMC7677421 PMC7680602 PMC7680756 PMC7680914 PMC7683130 PMC7684468 PMC7684603 PMC7685824 PMC7685827 PMC7688173 .PMC7689036 PMC7690256 PMC7690744 PMC7690750 PMC7690858 PMC7690868 PMC7691007 PMC7691073 PMC7691236 PMC7691295 .PMC7691503 PMC7691614 PMC7692086 PMC7692277 PMC7692298 PMC7692362 PMC7692612 PMC7692740 PMC7693031 PMC7693457 .PMC7693752 PMC7693977 PMC7694179 PMC7694502 PMC7694646 PMC7694671 PMC7695008 PMC7695023 PMC7695154 PMC7695267 .PMC7695294 PMC7695645 PMC7696031 PMC7696162 PMC7696230 PMC7696306 PMC7696458 PMC7696464 PMC7696744 PMC7696850 .PMC7697004 PMC7697102 PMC7697156 PMC7697265 PMC7697716 PMC7697879 PMC7698425 PMC7698523 PMC7698706 PMC7698770 .PMC7698878 PMC7698941 PMC7698964 PMC7699174 PMC7699777 PMC7699931 PMC7699947 PMC7700059 PMC7700206 PMC7700410 .PMC7700638 PMC7701093 PMC7701256 PMC7704417 PMC7707474 PMC7707481 PMC7707995 PMC7708940 PMC7711191 PMC7711696 .PMC7713432 PMC7715011 PMC7715482 PMC7717572 PMC7717613 PMC7719695 PMC7720635 PMC7721531 PMC7721540 PMC7724791 .PMC7725569 PMC7725741 PMC7728069 PMC7728153 PMC7728155 PMC7728315 PMC7728322 PMC7728332 PMC7728353 PMC7728470 .PMC7728478 PMC7728801 PMC7729004 PMC7729440 PMC7729875 PMC7729923 PMC7729994 PMC7730080 PMC7730301 PMC7730475 .PMC7730552 PMC7730595 PMC7730820 PMC7730830 PMC7731065 PMC7731202 PMC7731506 PMC7731913 PMC7732089 PMC7732400 .PMC7733000 PMC7733993 PMC7736719 PMC7737096 !wPMC7738326 PMC7739878 PMC7742202 PMC7743958 PMC7744478 PMC7744551 .PMC7745032 PMC7747825 PMC7748911 PMC7751431 PMC7753128 PMC7755035 PMC7756191 PMC7756559 PMC7757906 PMC7758400 .PMC7758404 PMC7758432 PMC7758512 PMC7759553 PMC7760007 PMC7760024 PMC7760039 PMC7760081 PMC7760164 PMC7760375 .PMC7760478 PMC7760518 PMC7760624 PMC7760773 PMC7760984 PMC7761064 PMC7761148 PMC7761249 PMC7761298 PMC7761563 .PMC7761567 PMC7761800 PMC7761819 PMC7762000 PMC7762048 PMC7762054 PMC7762085 PMC7762097 PMC7762183 PMC7762190 .PMC7762226 PMC7762448 PMC7762608 PMC7763075 PMC7763091 PMC7763115 PMC7763123 PMC7763129 PMC7763292 PMC7763305 .PMC7763331 PMC7763345 PMC7763476 PMC7763512 PMC7763559 PMC7763593 PMC7763744 PMC7763825 PMC7763896 PMC7763918 .PMC7764037 PMC7764227 PMC7764658 PMC7764892 PMC7765096 PMC7765139 PMC7765155 PMC7765257 PMC7765828 PMC7765886 .PMC7765926 PMC7765930 PMC7766005 PMC7766089 PMC7766149 PMC7766153 PMC7766178 PMC7766379 PMC7766633 PMC7766674 .PMC7766725 PMC7766727 PMC7767053 PMC7767113 PMC7767136 PMC7767169 PMC7767361 PMC7767362 PMC7767399 PMC7767424 .PMC7767818 PMC7767828 PMC7768730 PMC7769628 PMC7769672 PMC7769804 PMC7769811 PMC7772181 PMC7772544 PMC7772550 .PMC7772620 PMC7773461 PMC7773473 PMC7774525 PMC7775464 PMC7777452 PMC7777528 PMC7779480 PMC7779684 PMC7779698 .PMC7781418 PMC7781944 PMC7782663 PMC7783804 PMC7785441 PMC7785522 PMC7785825 PMC7785844 PMC7785943 PMC7785955 .PMC7786132 PMC7786139 PMC7787523 PMC7787652 PMC7787816 PMC7787954 PMC7788046 PMC7788126 PMC7789504 PMC7789580 .PMC7789753 PMC7789864 PMC7791887 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7791887\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7791887\scholarly.html
PMC7791912 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7791912\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7791912\scholarly.html
PMC7792625 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7792625\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7792625\scholarly.html
PMC7792949 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7792949\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7792949\scholarly.html
PMC7793533 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7793533\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7793533\scholarly.html
PMC7794673 [Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7794673\scholarly.html
[Fatal Error] scholarly.html:1:1: Content is not allowed in prolog.
Cannot create scholarlyHtmlElement: java.lang.RuntimeException: cannot parse/read file: C:\Users\talha\CEVOpen\dictionary\eoCompound\(plantcompoundpapers)\PMC7794673\scholarly.html
PMC7794732 PMC7794910 .PMC7795015 PMC7795089 PMC7795161 PMC7795193 PMC7795351 PMC7795411 PMC7795503 PMC7795506 PMC7795748 PMC7795833 .PMC7796079 PMC7796276 PMC7796298 PMC7796335 PMC7796366 PMC7796387 PMC7796436 PMC7797125 PMC7797194 PMC7799430 .PMC7801105 PMC7801116 PMC7801304 PMC7801432 PMC7801735 PMC7802159 PMC7802575 PMC7803138 PMC7803143 PMC7803989 .PMC7804112 PMC7804141 PMC7804154 PMC7805276 PMC7806260 PMC7806641 PMC7807059 PMC7807802 PMC7808741 PMC7808824 .PMC7809109 PMC7809392 PMC7810277 PMC7810394 PMC7810889 PMC7811472 PMC7811550 PMC7811810 PMC7812032 PMC7812931 .PMC7813745 PMC7814569 PMC7814726 PMC7814937 PMC7815160 PMC7815396 PMC7815410 PMC7815652 PMC7816146 PMC7816844 .PMC7816845 PMC7817466 PMC7817489 PMC7818593 PMC7819315 PMC7820602 PMC7821929 PMC7822065 PMC7822123 PMC7822174 .PMC7822430 PMC7822660 PMC7823258 PMC7823385 PMC7823439 PMC7823444 PMC7823482 PMC7823506 PMC7823517 PMC7823625 .PMC7823675 PMC7823753 PMC7823792 PMC7823795 PMC7823840 PMC7823854 PMC7823993 PMC7824023 PMC7824034 PMC7824061 .PMC7824064 PMC7824111 PMC7824119 PMC7824130 PMC7824150 PMC7824169 PMC7824205 PMC7824228 PMC7824284 PMC7824362 .PMC7824416 PMC7824492 PMC7824498 PMC7824601 PMC7824676 PMC7824788 PMC7824789 PMC7824868 PMC7824881 PMC7824898 .PMC7825055 PMC7825126 PMC7825178 PMC7825240 PMC7825337 PMC7825428 PMC7825507 PMC7825567 PMC7826111 PMC7826242 .PMC7826587 PMC7826601 PMC7826859 PMC7827020 PMC7827031 PMC7827111 PMC7827182 PMC7827262 PMC7827335 PMC7827347 .PMC7827382 PMC7827440 PMC7827451 PMC7827483 PMC7827498 PMC7827524 PMC7827528 PMC7827553 PMC7827591 PMC7827611 .PMC7827728 PMC7827760 PMC7827789 PMC7827795 PMC7827828 PMC7827872 PMC7827964 PMC7828031 PMC7828129 PMC7828132 .PMC7828134 PMC7828174 PMC7828211 PMC7828301 PMC7828331 PMC7828423 PMC7828511 PMC7828711 PMC7828715 PMC7828731 .PMC7828735 PMC7828736 PMC7828774 PMC7829895 PMC7830006 PMC7830248 PMC7830311 PMC7830447 PMC7830475 PMC7830503 .PMC7830504 PMC7830528 PMC7830657 PMC7830842 PMC7830865 PMC7830912 PMC7830935 PMC7830962 PMC7830967 PMC7831036 .PMC7831324 PMC7831775 PMC7831912 PMC7831921 PMC7831927 PMC7831946 PMC7831952 PMC7831967 PMC7832193 PMC7832194 .PMC7832296 PMC7832333 PMC7832401 PMC7832499 PMC7832507 PMC7832534 PMC7832542 PMC7833040 PMC7833388 PMC7833933 .PMC7834779 PMC7835903 PMC7835970 PMC7836426 PMC7836487 PMC7838277 PMC7840253 PMC7840926 PMC7841026 PMC7841356 .PMC7841903 PMC7841945 PMC7843487 PMC7843771 PMC7845744 PMC7847758 PMC7847861 PMC7848649 PMC7848973 PMC7849236 .PMC7850368 PMC7850424 PMC7852404 PMC7853596 PMC7853604 PMC7854439 PMC7854645 PMC7854674 PMC7854675 PMC7854678 .PMC7856339 PMC7857882 PMC7858074 PMC7860093 PMC7862227 PMC7862595 PMC7864745 PMC7864906 PMC7864976 PMC7865082 .PMC7865084 PMC7865210 PMC7865227 PMC7865290 PMC7865323 PMC7865359 PMC7865499 PMC7865555 PMC7865568 PMC7865595 .PMC7865633 PMC7865715 PMC7865826 PMC7865903 PMC7865983 PMC7866000 PMC7866031 PMC7866120 PMC7866194 PMC7866218 .PMC7866295 PMC7866531 PMC7866625 PMC7866841 PMC7867005 PMC7867013 PMC7867015 PMC7867026 PMC7867105 PMC7867241 .PMC7867259 PMC7867377 PMC7868139 PMC7868585 PMC7869076 !wPMC7869668 PMC7870401 PMC7871409 PMC7871548 PMC7871564 .PMC7872560 PMC7872582 PMC7872952 PMC7873959 PMC7874482 PMC7875619 PMC7876777 PMC7877615 PMC7878689 PMC7878694 .PMC7878698 PMC7878742 PMC7879783 PMC7881030 PMC7881223 PMC7882218 PMC7882510 PMC7882811 PMC7884620 PMC7885008 .PMC7885310 PMC7885413 PMC7885726 PMC7886531 PMC7887227 PMC7887249 PMC7888440 PMC7888442 PMC7888597 PMC7889342 .PMC7889936 PMC7889937 PMC7889962 PMC7890032 PMC7890104 !wPMC7890384 PMC7891170 PMC7891363 PMC7891737 PMC7892566 .PMC7892686 PMC7892916 PMC7892933 PMC7892936 PMC7892944 PMC7893418 PMC7894489 PMC7894860 PMC7894928 PMC7895382 .PMC7895923 PMC7896091 PMC7896135 PMC7896843 PMC7897203 PMC7897622 PMC7897978 PMC7898454 PMC7899166 PMC7899931 .PMC7900558 PMC7900560 PMC7900702 PMC7900706 PMC7901085 PMC7901698 PMC7902047 PMC7902150 PMC7902500 PMC7902804 .PMC7902805 PMC7903152 PMC7903315 PMC7904367 PMC7904547 PMC7904875 PMC7905195 PMC7905319 PMC7906523 PMC7906577 .PMC7906619 PMC7907014 PMC7907592 PMC7907610 PMC7907617 PMC7907656 PMC7907736 !wPMC7907780 PMC7907819 PMC7908259 .PMC7908345 PMC7908520 PMC7908993 PMC7909085 PMC7909086 PMC7909252 PMC7909524 PMC7909537 PMC7909549 Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.base/java.util.Arrays.copyOf(Arrays.java:3536)
        at java.base/java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:228)
        at java.base/java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:582)
        at java.base/java.lang.StringBuffer.append(StringBuffer.java:307)
        at nu.xom.Element.writeStartTag(Unknown Source)
        at nu.xom.Element.toXML(Unknown Source)
        at org.contentmine.graphics.html.HtmlFactory.parseLegacyHtmlToWellFormedXML(HtmlFactory.java:763)
        at org.contentmine.graphics.html.HtmlFactory.parseRawHtml(HtmlFactory.java:676)
        at org.contentmine.graphics.html.HtmlFactory.parse(HtmlFactory.java:660)
        at org.contentmine.graphics.html.HtmlFactory.parse(HtmlFactory.java:651)
        at org.contentmine.cproject.args.DefaultArgProcessor.getScholarlyHtmlElement(DefaultArgProcessor.java:1349)
        at org.contentmine.cproject.files.CTree.ensureScholarlyHtmlElement(CTree.java:1268)
        at org.contentmine.cproject.args.DefaultArgProcessor.extractPSectionElements(DefaultArgProcessor.java:1332)
        at org.contentmine.ami.plugins.AMIArgProcessor.ensureSectionElements(AMIArgProcessor.java:263)
        at org.contentmine.ami.plugins.AMIArgProcessor.runRunMethodsOnChosenArgOptions(AMIArgProcessor.java:234)
        at org.contentmine.cproject.args.DefaultArgProcessor.runAndOutput(DefaultArgProcessor.java:1263)
        at org.contentmine.ami.plugins.word.WordPluginOption.run(WordPluginOption.java:34)
        at org.contentmine.ami.plugins.CommandProcessor.runLegacyPluginOptions(CommandProcessor.java:296)
        at org.contentmine.ami.tools.AbstractAMISearchTool.runLegacyCommandProcessor(AbstractAMISearchTool.java:222)
        at org.contentmine.ami.tools.AMISearchTool.runLegacyCommandProcessor(AMISearchTool.java:304)
        at org.contentmine.ami.tools.AMISearchTool.runProjectSearch(AMISearchTool.java:247)
        at org.contentmine.ami.tools.AMISearchTool.processProject(AMISearchTool.java:232)
        at org.contentmine.ami.tools.AbstractAMISearchTool.runSpecifics(AbstractAMISearchTool.java:172)
        at org.contentmine.ami.tools.AbstractAMITool.runCommands(AbstractAMITool.java:197)
        at org.contentmine.ami.tools.AbstractAMITool.call(AbstractAMITool.java:177)
        at org.contentmine.ami.tools.AbstractAMITool.call(AbstractAMITool.java:45)
        at picocli.CommandLine.executeUserObject(CommandLine.java:1933)
        at picocli.CommandLine.access$1100(CommandLine.java:145)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2332)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2326)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2291)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2159)

as the result i got the text file but could not create full data table and cooccurrence folder

petermr commented 3 years ago

The project name should not be in parentheses:

-p (plantcompoundpapers)

should be 

-p plantcompoundpapers

Your project should be a simple directory name

petermr commented 3 years ago

and you should not be running the project in the dictionary directory.