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Standard TLGs For Clinical Trials Reporting
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clear up spelling errors and/or enhance pre-commit spell-check exclusions
#721
Open
pawelru
opened
7 months ago
pawelru
commented
7 months ago
Currently we have the following:
beware! long list here!
``` ❯ pre-commit run spell-check --all-files Check spelling with `spelling`...........................................Failed - hook id: spell-check - exit code: 1 - files were modified by this hook The following spelling errors were found: WORD FOUND IN ACTARM new_table.html:386 new_table.md:39 ADAE new_table.html:373 new_table.md:24 admh ael01_nollt.md:1 AE new_table.html:402,404 new_table.md:55,56 AEBODSYS new_table.html:391,393 new_table.md:44,46 AEDECOD new_table.html:391,394 new_table.md:44,47 ael ael01_nollt.md:1,19,37,46 default_tlg.md:1 AEs new_table.html:406 new_table.md:57 aesi aet01_aesi.md:1,45,69 default_tlg.md:44 aet aet01_aesi.md:1,45,69 aet01.md:1,46,71,86 aet02.md:1 aet03.md:1,24 aet04.md:1,77 aet05_all.md:1,25 aet05.md:1,25 aet10.md:1,11 default_tlg.md:19,44,104,146,213,308,350,392 AET new_table.html:359,399 new_table.md:9,52 ALBUMLS mladir.csv:2 ALBUMSI ctcdir.csv:2,36 ctcgrades.csv:2,3,4,157,158,159 ALKPHLS mladir.csv:3 ALKPHSI ctcdir.csv:3,37 ctcgrades.csv:5,6,7,8,160,161,162,163 ALTLS mladir.csv:4 ALTSI ctcdir.csv:4,38 ctcgrades.csv:9,10,11,12,164,165,166,167 AMYLASSI ctcdir.csv:5,39 ctcgrades.csv:13,14,15,16,168,169,170,171 anl aet01.md:71 ANL new_table.html:377 new_table.md:29 APTTLS mladir.csv:5 APTTSI ctcdir.csv:6,40 ctcgrades.csv:17,18,19,20,21,22,172,173,174,175,176,177 ASEV new_table.html:391,395 new_table.md:44,48 ASTLS mladir.csv:6 ASTSI ctcdir.csv:7,41 ctcgrades.csv:23,24,25,26,178,179,180,181 BANDSFLS mladir.csv:7 BANDSLS mladir.csv:8 BASOSFLS mladir.csv:9 BASOSLS mladir.csv:10 BICARBLS mladir.csv:11,12 BioConductor CONTRIBUTING.md:107 BUNLS mladir.csv:13 CALCUMLS mladir.csv:14,15 CALCUMSI ctcdir.csv:8,42 ctcgrades.csv:27,28,29,30,31,32,33,34,182,183,184,185,186,187,188,189 cfbt cfbt01.md:1,535 CHLORLS mladir.csv:16,17 CHOLESLS mladir.csv:18 CHOLESSI ctcdir.csv:14,48 ctcgrades.csv:59,60,61,62,214,215,216,217 cmt cmt01a.md:1,53,97,112 cmt02_pt.md:1,13 default_tlg.md:411 coxt coxt01.md:1 coxt02.md:1 default_tlg.md:431,446 CPKLS mladir.csv:19 CPKMBLS mladir.csv:20 CPKSI ctcdir.csv:15,49 ctcgrades.csv:63,64,65,66,218,219,220,221 CREATNLS mladir.csv:21 CREATNSI ctcdir.csv:16,50 ctcgrades.csv:67,68,69,70,222,223,224,225 CTCv ctcdir.csv:1 ctcgrades.csv:1 cutomized dmt01.md:202 DBILILS mladir.csv:22 DCSREAS dst01.md:10 dependenct CONTRIBUTING.md:101 dmt default_tlg.md:467 dmt01.md:1,30,64,108,133,158,202,240,284 DSS SECURITY.md:23 dst default_tlg.md:501 dst01.md:1,10,22,41,51 dtht default_tlg.md:520 dtht01.md:1,16,51 egt egt01.md:1,241 egt02.md:1,19 egt03.md:1,73 egt05_qtcat.md:1,79 EOSINFLS mladir.csv:23 EOSINLS mladir.csv:24 FASTGLLS mladir.csv:25,26 FASTGLSI ctcdir.csv:17,51 ctcgrades.csv:71,72,73,74,226,227,228,229,230,231,232,233 FIBLS mladir.csv:27 FIBSI ctcdir.csv:18,52 ctcgrades.csv:75,76,77,78,234,235,236,237 FREELS mladir.csv:66,67 funs chevron_tlg-methods.md:613,635 GGTLS mladir.csv:28 GGTSI ctcdir.csv:19,53 ctcgrades.csv:79,80,81,82,238,239,240,241 GLUCSI ctcdir.csv:20,54 ctcgrades.csv:83,84,85,86,242,243,244,245,246,247 HCRITLS mladir.csv:29,30 HDLLS mladir.csv:31 HGBLS mladir.csv:32,33 HGBSI ctcdir.csv:21,55 ctcgrades.csv:87,88,89,90,91,92,248,249,250,251,252,253 HPTSI ctcdir.csv:22,56 ctcgrades.csv:93,254 ifneeded utils.md:1 infs cfbt01.md:535 egt01.md:241 lbt01.md:487 lbl mht01.md:67 lbt lbt01.md:1,241,487 lbt04.md:1,55,64,118 lbt05.md:1,61 lbt06.md:1 lbt07.md:1,50 lbt14.md:1,96,196,291,386,419,521,806,839,946 lbt15.md:1,55,109,163,217,271 LDHLS mladir.csv:34 LDLLS mladir.csv:35 LIPASESI ctcdir.csv:23,57 ctcgrades.csv:94,95,96,97,255,256,257,258 LYMPHFLS mladir.csv:36,37 LYMPHLS mladir.csv:38,39 LYMPHSI ctcdir.csv:24,58 ctcgrades.csv:98,99,100,101,102,103,259,260,261,262,263,264 MAGNESSI ctcdir.csv:25,59 ctcgrades.csv:104,105,106,107,108,109,110,265,266,267,268,269,270,271 MCHCLS mladir.csv:40,41 MCHLS mladir.csv:42,43 MCVLS mladir.csv:44,45 medconcept aet01.md:86 mhbodsys mht01.md:67 mhdecod mht01.md:67 mht mht01.md:1,34,67 MONOSFLS mladir.csv:46 MONOSLS mladir.csv:47 NEUTRFLS mladir.csv:48,49 NEUTRLS mladir.csv:50,51 NEUTRSI ctcdir.csv:26,60 ctcgrades.csv:111,112,113,114,272,273,274,275 nollt ael01_nollt.md:1,19,37,46 default_tlg.md:1 PARAMCD ctcdir.csv:1 ctcgrades.csv:1 mladir.csv:1 parametrize dtht01.md:51 PCI SECURITY.md:25 pdt pdt01.md:1,38,51 pdt02.md:1,24,41 PHOSATLS mladir.csv:52,53 PHOSATSI ctcdir.csv:61 ctcgrades.csv:276,277,278,279 PII SECURITY.md:25 PLATELS mladir.csv:54,55 PLATESI ctcdir.csv:27,62 ctcgrades.csv:115,116,117,118,280,281,282,283 POTASLS mladir.csv:56,57 POTASSI ctcdir.csv:28,63 ctcgrades.csv:119,120,121,122,123,124,125,284,285,286,287,288,289,290 PTINRLS mladir.csv:58 PTINRSI ctcdir.csv:29,64 ctcgrades.csv:126,127,128,291,292,293 PTTLS mladir.csv:59 PTTSI ctcdir.csv:30,65 ctcgrades.csv:129,130,131,132,133,134,294,295,296,297,298,299 qtcat egt05_qtcat.md:1,79 RBCLS mladir.csv:60,61 recommedations CONTRIBUTING.md:97 rmpt rmpt01.md:1,15,55 rmpt03.md:1,21,79 rmpt04.md:1,15,43 rmpt05.md:1,17,49 rmpt06.md:1,27,55 rspt rspt01.md:1,23,75,118,161,210,280 sexualized CODE_OF_CONDUCT.md:31 socio CODE_OF_CONDUCT.md:6 SODIUMLS mladir.csv:62,63 SODIUMSI ctcdir.csv:31,66 ctcgrades.csv:135,136,137,138,139,140,141,142,300,301,302,303,304,305,306 summaryvars dmt01.md:284 TBILILS mladir.csv:70 tinyverse CONTRIBUTING.md:97 tlg new_table.html:364 new_table.md:14 TPROTLS mladir.csv:71,72 TRIGLS mladir.csv:73 TRIGSI ctcdir.csv:33,68 ctcgrades.csv:147,148,149,150,311,312,313,314 TSHLS mladir.csv:74 ttet ttet01.md:1,47,134,217 UI CONTRIBUTING.md:77 upvote CONTRIBUTING.md:39 URACIDLS mladir.csv:75 URACIDSI ctcdir.csv:34,69 ctcgrades.csv:151,315,316 vst vst01.md:1,535 vst02.md:1,28 WBCLS mladir.csv:76,77 WBCSI ctcdir.csv:35,70 ctcgrades.csv:152,153,154,155,156,317,318,319,320,321 ```
Currently we have the following:
beware! long list here!
``` ❯ pre-commit run spell-check --all-files Check spelling with `spelling`...........................................Failed - hook id: spell-check - exit code: 1 - files were modified by this hook The following spelling errors were found: WORD FOUND IN ACTARM new_table.html:386 new_table.md:39 ADAE new_table.html:373 new_table.md:24 admh ael01_nollt.md:1 AE new_table.html:402,404 new_table.md:55,56 AEBODSYS new_table.html:391,393 new_table.md:44,46 AEDECOD new_table.html:391,394 new_table.md:44,47 ael ael01_nollt.md:1,19,37,46 default_tlg.md:1 AEs new_table.html:406 new_table.md:57 aesi aet01_aesi.md:1,45,69 default_tlg.md:44 aet aet01_aesi.md:1,45,69 aet01.md:1,46,71,86 aet02.md:1 aet03.md:1,24 aet04.md:1,77 aet05_all.md:1,25 aet05.md:1,25 aet10.md:1,11 default_tlg.md:19,44,104,146,213,308,350,392 AET new_table.html:359,399 new_table.md:9,52 ALBUMLS mladir.csv:2 ALBUMSI ctcdir.csv:2,36 ctcgrades.csv:2,3,4,157,158,159 ALKPHLS mladir.csv:3 ALKPHSI ctcdir.csv:3,37 ctcgrades.csv:5,6,7,8,160,161,162,163 ALTLS mladir.csv:4 ALTSI ctcdir.csv:4,38 ctcgrades.csv:9,10,11,12,164,165,166,167 AMYLASSI ctcdir.csv:5,39 ctcgrades.csv:13,14,15,16,168,169,170,171 anl aet01.md:71 ANL new_table.html:377 new_table.md:29 APTTLS mladir.csv:5 APTTSI ctcdir.csv:6,40 ctcgrades.csv:17,18,19,20,21,22,172,173,174,175,176,177 ASEV new_table.html:391,395 new_table.md:44,48 ASTLS mladir.csv:6 ASTSI ctcdir.csv:7,41 ctcgrades.csv:23,24,25,26,178,179,180,181 BANDSFLS mladir.csv:7 BANDSLS mladir.csv:8 BASOSFLS mladir.csv:9 BASOSLS mladir.csv:10 BICARBLS mladir.csv:11,12 BioConductor CONTRIBUTING.md:107 BUNLS mladir.csv:13 CALCUMLS mladir.csv:14,15 CALCUMSI ctcdir.csv:8,42 ctcgrades.csv:27,28,29,30,31,32,33,34,182,183,184,185,186,187,188,189 cfbt cfbt01.md:1,535 CHLORLS mladir.csv:16,17 CHOLESLS mladir.csv:18 CHOLESSI ctcdir.csv:14,48 ctcgrades.csv:59,60,61,62,214,215,216,217 cmt cmt01a.md:1,53,97,112 cmt02_pt.md:1,13 default_tlg.md:411 coxt coxt01.md:1 coxt02.md:1 default_tlg.md:431,446 CPKLS mladir.csv:19 CPKMBLS mladir.csv:20 CPKSI ctcdir.csv:15,49 ctcgrades.csv:63,64,65,66,218,219,220,221 CREATNLS mladir.csv:21 CREATNSI ctcdir.csv:16,50 ctcgrades.csv:67,68,69,70,222,223,224,225 CTCv ctcdir.csv:1 ctcgrades.csv:1 cutomized dmt01.md:202 DBILILS mladir.csv:22 DCSREAS dst01.md:10 dependenct CONTRIBUTING.md:101 dmt default_tlg.md:467 dmt01.md:1,30,64,108,133,158,202,240,284 DSS SECURITY.md:23 dst default_tlg.md:501 dst01.md:1,10,22,41,51 dtht default_tlg.md:520 dtht01.md:1,16,51 egt egt01.md:1,241 egt02.md:1,19 egt03.md:1,73 egt05_qtcat.md:1,79 EOSINFLS mladir.csv:23 EOSINLS mladir.csv:24 FASTGLLS mladir.csv:25,26 FASTGLSI ctcdir.csv:17,51 ctcgrades.csv:71,72,73,74,226,227,228,229,230,231,232,233 FIBLS mladir.csv:27 FIBSI ctcdir.csv:18,52 ctcgrades.csv:75,76,77,78,234,235,236,237 FREELS mladir.csv:66,67 funs chevron_tlg-methods.md:613,635 GGTLS mladir.csv:28 GGTSI ctcdir.csv:19,53 ctcgrades.csv:79,80,81,82,238,239,240,241 GLUCSI ctcdir.csv:20,54 ctcgrades.csv:83,84,85,86,242,243,244,245,246,247 HCRITLS mladir.csv:29,30 HDLLS mladir.csv:31 HGBLS mladir.csv:32,33 HGBSI ctcdir.csv:21,55 ctcgrades.csv:87,88,89,90,91,92,248,249,250,251,252,253 HPTSI ctcdir.csv:22,56 ctcgrades.csv:93,254 ifneeded utils.md:1 infs cfbt01.md:535 egt01.md:241 lbt01.md:487 lbl mht01.md:67 lbt lbt01.md:1,241,487 lbt04.md:1,55,64,118 lbt05.md:1,61 lbt06.md:1 lbt07.md:1,50 lbt14.md:1,96,196,291,386,419,521,806,839,946 lbt15.md:1,55,109,163,217,271 LDHLS mladir.csv:34 LDLLS mladir.csv:35 LIPASESI ctcdir.csv:23,57 ctcgrades.csv:94,95,96,97,255,256,257,258 LYMPHFLS mladir.csv:36,37 LYMPHLS mladir.csv:38,39 LYMPHSI ctcdir.csv:24,58 ctcgrades.csv:98,99,100,101,102,103,259,260,261,262,263,264 MAGNESSI ctcdir.csv:25,59 ctcgrades.csv:104,105,106,107,108,109,110,265,266,267,268,269,270,271 MCHCLS mladir.csv:40,41 MCHLS mladir.csv:42,43 MCVLS mladir.csv:44,45 medconcept aet01.md:86 mhbodsys mht01.md:67 mhdecod mht01.md:67 mht mht01.md:1,34,67 MONOSFLS mladir.csv:46 MONOSLS mladir.csv:47 NEUTRFLS mladir.csv:48,49 NEUTRLS mladir.csv:50,51 NEUTRSI ctcdir.csv:26,60 ctcgrades.csv:111,112,113,114,272,273,274,275 nollt ael01_nollt.md:1,19,37,46 default_tlg.md:1 PARAMCD ctcdir.csv:1 ctcgrades.csv:1 mladir.csv:1 parametrize dtht01.md:51 PCI SECURITY.md:25 pdt pdt01.md:1,38,51 pdt02.md:1,24,41 PHOSATLS mladir.csv:52,53 PHOSATSI ctcdir.csv:61 ctcgrades.csv:276,277,278,279 PII SECURITY.md:25 PLATELS mladir.csv:54,55 PLATESI ctcdir.csv:27,62 ctcgrades.csv:115,116,117,118,280,281,282,283 POTASLS mladir.csv:56,57 POTASSI ctcdir.csv:28,63 ctcgrades.csv:119,120,121,122,123,124,125,284,285,286,287,288,289,290 PTINRLS mladir.csv:58 PTINRSI ctcdir.csv:29,64 ctcgrades.csv:126,127,128,291,292,293 PTTLS mladir.csv:59 PTTSI ctcdir.csv:30,65 ctcgrades.csv:129,130,131,132,133,134,294,295,296,297,298,299 qtcat egt05_qtcat.md:1,79 RBCLS mladir.csv:60,61 recommedations CONTRIBUTING.md:97 rmpt rmpt01.md:1,15,55 rmpt03.md:1,21,79 rmpt04.md:1,15,43 rmpt05.md:1,17,49 rmpt06.md:1,27,55 rspt rspt01.md:1,23,75,118,161,210,280 sexualized CODE_OF_CONDUCT.md:31 socio CODE_OF_CONDUCT.md:6 SODIUMLS mladir.csv:62,63 SODIUMSI ctcdir.csv:31,66 ctcgrades.csv:135,136,137,138,139,140,141,142,300,301,302,303,304,305,306 summaryvars dmt01.md:284 TBILILS mladir.csv:70 tinyverse CONTRIBUTING.md:97 tlg new_table.html:364 new_table.md:14 TPROTLS mladir.csv:71,72 TRIGLS mladir.csv:73 TRIGSI ctcdir.csv:33,68 ctcgrades.csv:147,148,149,150,311,312,313,314 TSHLS mladir.csv:74 ttet ttet01.md:1,47,134,217 UI CONTRIBUTING.md:77 upvote CONTRIBUTING.md:39 URACIDLS mladir.csv:75 URACIDSI ctcdir.csv:34,69 ctcgrades.csv:151,315,316 vst vst01.md:1,535 vst02.md:1,28 WBCLS mladir.csv:76,77 WBCSI ctcdir.csv:35,70 ctcgrades.csv:152,153,154,155,156,317,318,319,320,321 ```