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JSchoenbachler commented
- R/get_citation.R line 5: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_citation.R#L5)
published_date = name = NULL
- R/get_citation.R line 106: Lines should not be more than 120 characters. (https://github.com/hugheylab/pmparser/blob/main/R/get_citation.R#L106)
glue(' \r\n powershell -command "Get-Content -Path {pathTmpCsv} -TotalCount {nrows + 1L} | Set-Content {pathTmpCsv2}" ',
- R/get_parsing_tables.R line 2: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_parsing_tables.R#L2)
xml_filename = NULL
- R/get_parsing_tables.R line 94: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_parsing_tables.R#L94)
r[[tableName]][, xml_filename := ac]
- R/get_pubmed_files.R line 15: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L15)
sub_dir = subDir = . = xml_filename = NULL
- R/get_pubmed_files.R line 20: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L20)
dNow[, sub_dir := subDir]}
- R/get_pubmed_files.R line 58: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L58)
md5_match = md5_computed = md5_provided = NULL
- R/get_pubmed_files.R line 61: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L61)
d[, md5_match := md5_computed == md5_provided]
- R/get_pubmed_files.R line 69: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L69)
md5_download = xml_download = f = sub_dir = xml_filename = md5_filename =
- R/get_pubmed_files.R line 70: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L70)
md5_match = NULL
- R/get_pubmed_files.R line 80: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L80)
fileInfo[, md5_download := NA_integer_]
- R/get_pubmed_files.R line 82: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L82)
fileInfo[, md5_download := xml_download]}
- R/get_pubmed_files.R line 91: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L91)
fileInfo[is.na(md5_download), md5_download := r]
- R/get_pubmed_files.R line 107: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_pubmed_files.R#L107)
fileInfo[!(md5_match), xml_download := r]
- R/get_test_standard.R line 19: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L19)
.N = pmid = N = . = step = NULL
- R/get_test_standard.R line 51: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L51)
sub_dir = .N = sample_base = NULL
- R/get_test_standard.R line 62: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L62)
dFile[, sample_base := gsub('\\.xml.*$', '', sampleBase)][]}
- R/get_test_standard.R line 92: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L92)
parsed$pmid_status = parsed$pmid_status[[2L]]
- R/get_test_standard.R line 99: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L99)
sub_dir = NULL
- R/get_test_standard.R line 106: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/get_test_standard.R#L106)
sub_dir = xml_download = xml_filename = md5_filename = NULL
- R/modify_pubmed_db.R line 41: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/modify_pubmed_db.R#L41)
processed = .N = md5_match = xml_filename = . = step = NULL
- R/parse_element.R line 149: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L149)
.N = id_type = NULL
- R/parse_element.R line 168: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L168)
pub_date = y = m = d = NULL
- R/parse_element.R line 187: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L187)
x4[, pub_date := as.Date(sprintf('%s-%s-%s', y, m, d))]
- R/parse_element.R line 201: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L201)
.N = pub_date = y = m = d = NULL
- R/parse_element.R line 214: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L214)
x4[, pub_date := as.Date(sprintf('%s-%s-%s', y, m, d))]
- R/parse_element.R line 224: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L224)
medline_date = pub_month_tmp1 = pub_month = pub_day_tmp = pub_day = pub_year =
- R/parse_element.R line 225: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L225)
pub_month_tmp2 = pub_date = date_idx = NULL
- R/parse_element.R line 242: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L242)
x2[is.na(pub_year), date_idx := regexpr('[0-9]{4}', medline_date)]
- R/parse_element.R line 244: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L244)
pub_year := as.integer(substr(medline_date, date_idx, date_idx + 3L))]
- R/parse_element.R line 245: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L245)
x2[, date_idx := NULL]
- R/parse_element.R line 253: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L253)
x2[, pub_month_tmp1 := tolower(pub_month)]
- R/parse_element.R line 256: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L256)
x3[, pub_day_tmp := pub_day]
- R/parse_element.R line 257: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L257)
x3[is.na(pub_day_tmp), pub_day_tmp := '01']
- R/parse_element.R line 259: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L259)
pub_date := as.Date(
- R/parse_element.R line 271: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L271)
.N = NULL
- R/parse_element.R line 289: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L289)
indexing_method = .N = descriptor_pos = pmid = NULL
- R/parse_element.R line 311: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L311)
x3[, descriptor_pos := 1:.N, by = pmid]
- R/parse_element.R line 313: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L313)
x3[, descriptor_pos := ai]}
- R/parse_element.R line 346: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L346)
.N = NULL
- R/parse_element.R line 373: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L373)
.N = NULL
- R/parse_element.R line 403: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L403)
.N = NULL
- R/parse_element.R line 424: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L424)
.N = accession_number = NULL
- R/parse_element.R line 441: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L441)
x5[, accession_number := unlist(lapply(x3, xml_text))]
- R/parse_element.R line 450: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L450)
.N = NULL
- R/parse_element.R line 468: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L468)
.N = abstract_pos = copyright = pmid = NULL
- R/parse_element.R line 484: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L484)
x5[, abstract_pos := 1:.N, by = pmid]
- R/parse_element.R line 486: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_element.R#L486)
x5[, abstract_pos := as.integer()]}
- R/parse_person.R line 4: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L4)
. = pmid = .N = equal_contrib = collective_name = person_pos =
- R/parse_person.R line 5: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L5)
affiliation_pos = affiliation = affil_idx = person_idx = n_affil_ids =
- R/parse_person.R line 6: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L6)
n_person_ids = n_total_ids = id_pos = NULL
- R/parse_person.R line 34: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L34)
dPerson[, equal_contrib := xml_attr(x2, 'EqualContrib')]
- R/parse_person.R line 35: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L35)
dPerson[, collective_name :=
- R/parse_person.R line 39: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L39)
dPerson[, person_pos := 1:.N, by = pmid]
- R/parse_person.R line 41: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L41)
dPerson[, person_pos := ai]}
- R/parse_person.R line 50: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L50)
dAffil[, affiliation_pos := seq_len(.N), by = cols]
- R/parse_person.R line 69: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L69)
dAffil[, affil_idx := 1:.N]
- R/parse_person.R line 74: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L74)
dAffil[, affil_idx := NULL]
- R/parse_person.R line 75: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L75)
dAffilId[, affil_idx := NULL]
- R/parse_person.R line 98: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L98)
dPerson[, person_idx := 1:.N]
- R/parse_person.R line 102: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L102)
dPerson[, person_idx := NULL]
- R/parse_person.R line 103: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L103)
dAllId[, person_idx := NULL]
- R/parse_person.R line 108: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L108)
x10[is.na(n_affil_ids), n_affil_ids := 0]
- R/parse_person.R line 109: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L109)
x10[, n_person_ids := n_total_ids - n_affil_ids]
- R/parse_person.R line 114: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L114)
dAllId[, id_pos := seq_len(.N), by = cols]
- R/parse_person.R line 116: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_person.R#L116)
dPersonId[, id_pos := NULL]
- R/parse_pubmed_xml.R line 11: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_pubmed_xml.R#L11)
status = xml_filename = parseFunc = NULL
- R/parse_pubmed_xml.R line 34: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_pubmed_xml.R#L34)
if (isEmpty(tableSuffix)) dPmid[, xml_filename := NULL]
- R/parse_pubmed_xml.R line 60: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/parse_pubmed_xml.R#L60)
xml_filename = filenameNow = NULL
- R/utilities.R line 2: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/utilities.R#L2)
status = xml_filename = NULL
- R/utilities.R line 9: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/utilities.R#L9)
. = xml_filename = NULL
- R/utilities.R line 77: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/utilities.R#L77)
. = xml_filename = step = NULL
- R/utilities.R line 128: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/R/utilities.R#L128)
paste_ = function(...) {
- data-raw/clickhouse/compare_postgres_clickhouse.R line 6: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L6)
for(table in tables){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 6: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L6)
for(table in tables){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 9: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L9)
for(colname in colnames(dtP)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 9: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L9)
for(colname in colnames(dtP)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 10: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L10)
if(inherits(dtP[[colname]], 'Date')){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 10: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L10)
if(inherits(dtP[[colname]], 'Date')){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 17: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L17)
for(colname in colnames(dtC)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 17: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L17)
for(colname in colnames(dtC)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 18: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L18)
# if(inherits(dtC[[colname]], 'Date') || (colname == 'version' && table != 'pmid_status')){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 19: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L19)
if(inherits(dtC[[colname]], 'Date')){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 19: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L19)
if(inherits(dtC[[colname]], 'Date')){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 27: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L27)
if(isTRUE(allEq)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 27: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L27)
if(isTRUE(allEq)){
- data-raw/clickhouse/compare_postgres_clickhouse.R line 36: Trailing blank lines are superfluous. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/compare_postgres_clickhouse.R#L36)
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 1: There should be a space between right parenthesis and an opening curly brace. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L1)
createClickhouseFromPostgres = function(pgDbName = 'pmdbclick', clDbName = 'pmdbclick', chunkSize = 15000L){
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 15: Lines should not be more than 120 characters. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L15)
parseNames = c(parseNames, list(citation = data.table::data.table(citing_pmid = as.integer(), cited_pmid = as.integer()),
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 16: Lines should not be more than 120 characters. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L16)
citation_version = data.table::data.table(md5_computed = as.character(), pmparser_version = as.character(), datetime_processed = as.POSIXct(as.character()))))
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 29: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L29)
if(!(tableName %in% verExclude)) colNamesDT[,version := NULL]
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 29: Commas should always have a space after. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L29)
if(!(tableName %in% verExclude)) colNamesDT[,version := NULL]
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 30: Put spaces around all infix operators. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L30)
colOrder = paste(colnames(colNamesDT), collapse=', ')
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 33: Place a space before left parenthesis, except in a function call. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L33)
for(rowOff in 0:(totalRows %/% chunkSize)) {
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 36: Lines should not be more than 120 characters. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L36)
dTable = data.table::as.data.table(DBI::dbGetQuery(pCon, glue('SELECT * FROM {`tableName`} ORDER BY {`colOrder`} LIMIT {`chunkSize`} OFFSET {`off`}')))
- data-raw/clickhouse/create_clickhouse_from_postgres.R line 47: Trailing blank lines are superfluous. (https://github.com/hugheylab/pmparser/blob/main/data-raw/clickhouse/create_clickhouse_from_postgres.R#L47)
- tests/testthat/test_get_pubmed_files.R line 31: Variable and function name style should be camelCase. (https://github.com/hugheylab/pmparser/blob/main/tests/testthat/test_get_pubmed_files.R#L31)
fileInfo[, md5_match := as.numeric(md5_match)]
- vignettes/data_dictionary.Rmd line 13: Only use single-quotes. (https://github.com/hugheylab/pmparser/blob/main/vignettes/data_dictionary.Rmd#L13)
comment = "#>"