diff --git a/arachne-ee-zip/TestRareBloodCancersPrevalence.zip b/arachne-ee-zip/TestRareBloodCancersPrevalence.zip new file mode 100644 index 0000000..94137a0 Binary files /dev/null and b/arachne-ee-zip/TestRareBloodCancersPrevalence.zip differ diff --git a/TestRareBloodCancersPrevalence/.gitignore b/arachne-ee/TestRareBloodCancersPrevalence/.gitignore similarity index 100% rename from TestRareBloodCancersPrevalence/.gitignore rename to arachne-ee/TestRareBloodCancersPrevalence/.gitignore diff --git a/TestRareBloodCancersPrevalence/README.md b/arachne-ee/TestRareBloodCancersPrevalence/README.md similarity index 100% rename from TestRareBloodCancersPrevalence/README.md rename to arachne-ee/TestRareBloodCancersPrevalence/README.md diff --git a/TestRareBloodCancersPrevalence/RareBloodCancersPrevalence.Rproj b/arachne-ee/TestRareBloodCancersPrevalence/RareBloodCancersPrevalence.Rproj similarity index 100% rename from TestRareBloodCancersPrevalence/RareBloodCancersPrevalence.Rproj rename to arachne-ee/TestRareBloodCancersPrevalence/RareBloodCancersPrevalence.Rproj diff --git a/arachne-ee/TestRareBloodCancersPrevalence/cdm_from_environment.R b/arachne-ee/TestRareBloodCancersPrevalence/cdm_from_environment.R new file mode 100644 index 0000000..035869d --- /dev/null +++ b/arachne-ee/TestRareBloodCancersPrevalence/cdm_from_environment.R @@ -0,0 +1,154 @@ + + +cdm_from_environment <- function(write_prefix = "") { + + connection_string <- Sys.getenv("CONNECTION_STRING") + + if (connection_string == "") { + stop("CONNECTION_STRING environment variable not set.") + } + + parts <- stringr::str_split(connection_string, ":")[[1]] + port_db <- stringr::str_split(parts[4], "/")[[1]] + + # required args that need to be passed in + dbms <- Sys.getenv("DBMS_TYPE") + server <- stringr::str_remove(parts[3], "^//+") + port <- port_db[1] + dbname <- port_db[2] + username <- Sys.getenv("DBMS_USERNAME") + password <- Sys.getenv("DBMS_PASSWORD") + cdm_schema <- Sys.getenv("DBMS_SCHEMA") + write_schema <- Sys.getenv("RESULT_SCHEMA") + + + vars <- c(dbms, server, port, dbname, password, cdm_schema, write_schema) + names_vars <- c("dbms", "server", "port", "dbname", "password", "cdm_schema", "write_schema") + + for (i in seq_along(vars)) { + if (nchar(vars[i]) < 1) stop(paste(names_vars[i], "is not required but not available!")) + } + + supported_db <- c("postgresql", "sql server", "redshift", "duckdb", "snowflake") + + if (!(dbms %in% supported_db)) { + cli::cli_abort("The environment variable DBMS_TYPE must be on one of {paste(supported_db, collapse = ', ')} not `{Sys.getenv('DBMS_TYPE')}`.") + } + + if (dbms == "duckdb") { + db <- dbname + if (db == "") { + db <- "GiBleed" + } + + checkmate::assert_choice(db, CDMConnector::example_datasets()) + con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomia_dir(db)) + cdm <- CDMConnector::cdm_from_con(con, "main", "main", cdm_version = "5.3", cdm_name = db) + return(cdm) + } + + cdm_schema <- stringr::str_split(cdm_schema, "\\.")[[1]] + write_schema <- stringr::str_split(write_schema, "\\.")[[1]] + + + print(write_schema) + print(sapply(write_schema, nchar)) + + if (dbms %in% c("postgresql", "redshift")) { + + drv <- switch (dbms, + "postgresql" = RPostgres::Postgres(), + "redshift" = RPostgres::Redshift() + ) + + con <- DBI::dbConnect(drv = drv, + dbname = dbname, + host = server, + user = username, + password = password, + port = port) + + if (!DBI::dbIsValid(con)) { + cli::cli_abort("Database connection failed!") + } + + } else if (dbms == "sql server") { + + con <- DBI::dbConnect(odbc::odbc(), + Driver = "ODBC Driver 17 for SQL Server", + Server = server, + Database = dbname, + UID = username, + PWD = password, + TrustServerCertificate="yes", + Port = port) + + if (!DBI::dbIsValid(con)) { + cli::cli_abort("Database connection failed!") + } + + + } else if (dbms == "snowflake") { + con <- DBI::dbConnect(odbc::odbc(), + DRIVER = "SnowflakeDSIIDriver", + SERVER = server, + DATABASE = dbname, + UID = username, + PWD = password, + WAREHOUSE = "COMPUTE_WH_XS") # don't hardcode this + + if (!DBI::dbIsValid(con)) { + cli::cli_abort("Database connection failed!") + } + + } else { + cli::cli_abort("{dbms} is not a supported database type!") + } + + # split schemas. If write schema has a dot we need to interpret it as catalog.schema + # cdm schema should not have a dot + + # if (stringr::str_detect(Sys.getenv("WRITE_SCHEMA"), "\\.")) { + # write_schema <- stringr::str_split(write_schema, "\\.")[[1]] + # if (length(write_schema) != 2) { + # cli::cli_abort("write_schema can have at most one period (.)!") + # } + # + # stopifnot(nchar(write_schema[1]) > 0, nchar(write_schema[2]) > 0) + # write_schema <- c(catalog = write_schema[1], schema = write_schema[2]) + # } else { + # write_schema <- c(schema = Sys.getenv("WRITE_SCHEMA")) + # } + # + # if (write_prefix != "") { + # if (dbms != "snowflake") { + # write_schema <- c(write_schema, prefix = write_prefix) + # } + # } + + # add prefix + if (write_prefix != "") { + if (length(write_schema) == 1) { + write_schema <- c(schema = write_schema, prefix = write_prefix) + } else if (length(write_schema) == 2) { + write_schema <- c(catalog = write_schema[1], + schema = write_schema[2], + prefix = write_prefix) + } + } else if (length(write_schema) == 2) { + write_schema <- c(catalog = write_schema[1], schema = write_schema[2]) + } + + cdm <- CDMConnector::cdm_from_con( + con = con, + cdm_schema = cdm_schema, + write_schema = write_schema, + cdm_version = "5.3", + cdm_name = Sys.getenv("DATA_SOURCE_NAME", unset = "unnamed_cdm")) + + if (length(names(cdm)) == 0) { + cli::cli_abort("CDM object creation failed!") + } + + return(cdm) +} diff --git a/arachne-ee/TestRareBloodCancersPrevalence/main.R b/arachne-ee/TestRareBloodCancersPrevalence/main.R new file mode 100644 index 0000000..153ae79 --- /dev/null +++ b/arachne-ee/TestRareBloodCancersPrevalence/main.R @@ -0,0 +1,168 @@ +library(CDMConnector) +library(IncidencePrevalence) +library(dplyr) +library(log4r) +setwd(file.path(getwd(), "TestRareBloodCancersPrevalence")) +print(getwd()) +print(list.files()) +# source("arachne-ee/TestRareBloodCancersPrevalence/cdm_from_environment.R") +source("cdm_from_environment.R") + +# database metadata and connection details ----- +# The name/ acronym for the database +db_name <- Sys.getenv("DATA_SOURCE_NAME") %>% + tolower() %>% + stringr::str_replace_all(" ", "_") %>% + stringr::str_replace_all("\\(|\\)", "") + +# Set output folder location ----- +# the path to a folder where the results from this analysis will be saved +# output_folder <- here::here("results") # does not work with execution engine +output_folder <- "/results" + +# create cdm reference ---- +# con <- DBI::dbConnect(duckdb::duckdb(), eunomia_dir()) +# cdm <- cdm_from_con(con, "main", "main") + +# cdm <- cdm_from_environment(write_prefix = "dw_") +prefix <- paste0("tmp", as.integer(Sys.time()) %% 1000, "_") +cdm <- cdm_from_environment(prefix) + +# check database connection +# running the next line should give you a count of your person table +n <- cdm$person %>% + tally() %>% + pull(n) + +print(paste(n, "persons in the CDM person table")) + +print(paste("Database connection class:", class(attr(cdm, "dbcon")))) + +# create directory if it does not already exist ---- +if (!file.exists(output_folder)) { + dir.create(output_folder, recursive = TRUE) +} + +# start log ---- +log_file <- paste0(output_folder, "/log.txt") +logger <- create.logger() +logfile(logger) <- log_file +level(logger) <- "INFO" + +# tables --- +table_outcome <-"outcome" +table_dpop_sex <- "dpop_sex" +table_ph <- "dpop_ph" +table_age <- "dpop_age" +table_point_prev <- "point_prev" +table_period_prev <- "period_prev" + +# instantiate outcome cohorts ---- +info(logger, "INSTANTIATE OUTCOME COHORTS") + +outcome_cohorts <- readCohortSet(here::here("outcomeCohorts")) %>% + slice(1:2) # for testing + +info(logger, "- getting outcomes") + +cdm <- generateCohortSet(cdm, + outcome_cohorts, + name = table_outcome, + overwrite = TRUE) + +total_subjects <- cohort_count(cdm[[table_outcome]]) %>% + summarise(total = sum(number_subjects)) %>% + pull(total) + +print(paste("total subjects with outcomes:", total_subjects)) + +# get denominator cohorts ----- +info(logger, "GETTING DENOMINATOR COHORTS") +info(logger, "- getting denominator - primary and sex") + +cdm <- generateDenominatorCohortSet( + cdm = cdm, + name = table_dpop_sex, + cohortDateRange = c(as.Date("2010-01-01"), as.Date("2024-01-01")), + sex = c("Male", "Female", "Both"), + daysPriorObservation = 365, + overwrite = TRUE +) + +info(logger, "- getting denominator - prior history") + +cdm <- generateDenominatorCohortSet( + cdm = cdm, + name = table_ph, + cohortDateRange = c(as.Date("2010-01-01"), as.Date("2024-01-01")), + daysPriorObservation = c(0, 1095), + overwrite = TRUE +) + +info(logger, "- getting denominator - age_gr") + +cdm <- generateDenominatorCohortSet( + cdm = cdm, + name = table_age, + cohortDateRange = c(as.Date("2010-01-01"), as.Date("2024-01-01")), + ageGroup = list( + # age_gr_1 + c(0, 9), c(10, 19), c(20, 29), c(30, 39), c(40, 49), + c(50, 59), c(60, 69), c(70, 79), c(80, 89), + c(90, 99), c(100, 150), + # age_gr_2 + c(0, 44), c(45, 64), c(65, 150) + ), + daysPriorObservation = 365, + overwrite = TRUE +) + +# estimate prevalence ----- +denominators <- c( + table_dpop_sex, + table_ph, + table_age +) + +prevalence_estimates <- list() + +for (i in seq_along(denominators)) { + + info(logger, paste0("- getting point prevalence for ", denominators[i])) + # debugonce(estimatePointPrevalence) + prevalence_estimates[[paste0("point_prevalence_", denominators[[i]])]] <- estimatePointPrevalence( + cdm = cdm, + denominatorTable = denominators[i], + outcomeTable = table_outcome, + interval = "years", + temporary = FALSE + ) + + info(logger, paste0("- getting period prevalence for ", denominators[i])) + + + prevalence_estimates[[paste0("period_prevalence_", denominators[[i]])]] <- estimatePeriodPrevalence( + cdm = cdm, + denominatorTable = denominators[i], + outcomeTable = table_outcome, + completeDatabaseIntervals = TRUE, + fullContribution = c(TRUE, FALSE), + interval = "years", + temporary = FALSE + ) +} + +# gather results and export ----- +info(logger, "ZIPPING RESULTS") +exportIncidencePrevalenceResults( + result = prevalence_estimates, + zipName = paste0(c(db_name, "C1_001_Results", format(Sys.Date(), format="%Y%m%d")), collapse = "_"), + outputFolder = output_folder +) + +cdm_disconnect(cdm) + +print("-- Thank you for running the study!") +print("-- If all has worked, there should now be a zip folder with your results in the output folder to share") + + diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_broad_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/acute_ll_narrow_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/aml_broad_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_broad_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/aml_broad_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_broad_2y.json diff --git 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arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/aml_narrow_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_broad_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_narrow_2y.json 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arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/chronic_ll_narrow_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/death.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/death.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/death.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/death.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_w_fl3b_5y.json 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TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/dlbc_wo_fl3b_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_w_fl3b_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/fl_wo_fl3b_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/gi_bleed_all.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/gi_bleed_all.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/gi_bleed_all.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/gi_bleed_all.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_broad_end.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_2y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_2y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_2y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_2y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_5y.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_5y.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_5y.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_5y.json diff --git a/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_end.json b/arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_end.json similarity index 100% rename from TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_end.json rename to arachne-ee/TestRareBloodCancersPrevalence/outcomeCohorts/mm_narrow_end.json diff --git a/create_zipfiles.R b/create_zipfiles.R new file mode 100644 index 0000000..ca19881 --- /dev/null +++ b/create_zipfiles.R @@ -0,0 +1,24 @@ + + +testnames <- list.files(here::here("arachne-ee")) + +for (i in seq_along(testnames)) { + message(paste("writing ", testnames[i])) + withr::with_dir(here::here("arachne-ee"), { + filenames <- list.files(testnames[i], full.names = T) + zip(zipfile = paste0("../arachne-ee-zip/", testnames[i]), files = filenames) + }) +} + + + + +testnames <- list.files(here::here("darwin-ee")) + +for (i in seq_along(testnames)) { + message(paste("writing ", testnames[i])) + withr::with_dir(here::here("arachne-ee"), { + filenames <- list.files(testnames[i], full.names = T) + zip(zipfile = paste0("../darwin-ee-zip/", testnames[i]), files = filenames) + }) +} diff --git a/TestCDMConnector/cdm_from_environment.R b/darwin-ee/TestCDMConnector/cdm_from_environment.R similarity index 100% rename from TestCDMConnector/cdm_from_environment.R rename to darwin-ee/TestCDMConnector/cdm_from_environment.R diff --git a/TestCDMConnector/execution-config.yml b/darwin-ee/TestCDMConnector/execution-config.yml similarity index 100% rename from TestCDMConnector/execution-config.yml rename to darwin-ee/TestCDMConnector/execution-config.yml diff --git a/TestCDMConnector/main.R b/darwin-ee/TestCDMConnector/main.R similarity index 100% rename from TestCDMConnector/main.R rename to darwin-ee/TestCDMConnector/main.R diff --git a/TestCDMConnector/readme.md b/darwin-ee/TestCDMConnector/readme.md similarity index 100% rename from TestCDMConnector/readme.md rename to darwin-ee/TestCDMConnector/readme.md diff --git a/TestDatabaseConnector/execution-config.yml b/darwin-ee/TestDatabaseConnector/execution-config.yml similarity index 100% rename from TestDatabaseConnector/execution-config.yml rename to darwin-ee/TestDatabaseConnector/execution-config.yml diff --git a/TestDatabaseConnector/main.R b/darwin-ee/TestDatabaseConnector/main.R similarity index 100% rename from TestDatabaseConnector/main.R rename to darwin-ee/TestDatabaseConnector/main.R diff --git a/TestDatabaseConnector/readme.md b/darwin-ee/TestDatabaseConnector/readme.md similarity index 100% rename from TestDatabaseConnector/readme.md rename to darwin-ee/TestDatabaseConnector/readme.md diff --git a/TestOnboarding/Dockerfile b/darwin-ee/TestOnboarding/Dockerfile similarity index 100% rename from TestOnboarding/Dockerfile rename to darwin-ee/TestOnboarding/Dockerfile diff --git a/TestOnboarding/codeToRun.R b/darwin-ee/TestOnboarding/codeToRun.R similarity index 100% rename from TestOnboarding/codeToRun.R rename to darwin-ee/TestOnboarding/codeToRun.R diff --git a/TestOnboarding/execution-config.yml b/darwin-ee/TestOnboarding/execution-config.yml similarity index 100% rename from TestOnboarding/execution-config.yml rename to darwin-ee/TestOnboarding/execution-config.yml diff --git a/TestOnboarding/readme.md b/darwin-ee/TestOnboarding/readme.md similarity index 100% rename from TestOnboarding/readme.md rename to darwin-ee/TestOnboarding/readme.md diff --git a/darwin-ee/Untitled/.gitignore b/darwin-ee/Untitled/.gitignore new file mode 100644 index 0000000..b3ab1f8 --- /dev/null +++ b/darwin-ee/Untitled/.gitignore @@ -0,0 +1,10 @@ +.Rproj.user +.Rhistory +.RData +.Ruserdata +postgresql-42.2.18.jar +CodeToRun_local.R +Results/CPRD GOLD/* +*.zip +*log.txt +.Rprofile diff --git a/darwin-ee/Untitled/README.md b/darwin-ee/Untitled/README.md new file mode 100644 index 0000000..1d60a7f --- /dev/null +++ b/darwin-ee/Untitled/README.md @@ -0,0 +1,40 @@ +# C1-001: Rare Blood Cancers + +Study Status: Started + +- Analytics use case(s): **-** +- Study type: Off-the-shelf; prevalence +- Tags: **-** +- Study lead: Edward Burn, Marti Catala +- Study start date: **-** +- Study end date: **-** +- Protocol: **-** +- Publications: **-** +- Results explorer: **-** + +## Instructions to run +1) Download this entire repository (you can download as a zip folder using Code -> Download ZIP, or you can use GitHub Desktop). +2) Open the project RareBloodCancersPrevalence.Rproj in RStudio (when inside the project, you will see its name on the top-right of your RStudio session) +3) Open the CodeToRun.R file - this is the only file you should need to interact with. +- Install the latest versions of IncidencePrevalence (by uncommenting and running line 4). Because IncidencePrevalence is currently a private package, please see the instructions below on installing a private package. +- Add your database specific parameters (name of database, schema name with OMOP data, schema name to write results, table name stem for results to be saved in the result schema). +- Create a connection to the via CDMConnector (see https://odyosg.github.io/CDMConnector/articles/DBI_connection_examples.html for connection examples for different dbms). +- Choose whether to run as a test (TRUE/ FALSE - if TRUE we'll run the analysis for one denominator cohort and one outcome to quickly get an idea if the full analysis code should run without a problem). +- Run the source analysis line which will start the analysis. Once completed, the results should be in your output folder. + +## Installing a private package +Once your username has been added to the private GitHub repo you will be able to install once you have your Github PAT set up. If you do not already have this, you can set this up by: +### In GitHub +- Click on your username/ profile picture +- Go to Settings +- Choose Developer Settings +- In the left sidebar, choose Personal access tokens +- Choose Generate new token +- Provide a name and description for your token, +- Choose Generate token +- Copy the token you are given to your clipboard +### In RStudio +- usethis::edit_r_environ() +- GITHUB_PAT = '.....' +- restart RStudio +- Now you can run: remotes::install_github("....") diff --git a/darwin-ee/Untitled/RareBloodCancersPrevalence.Rproj b/darwin-ee/Untitled/RareBloodCancersPrevalence.Rproj new file mode 100644 index 0000000..ffefba4 --- /dev/null +++ b/darwin-ee/Untitled/RareBloodCancersPrevalence.Rproj @@ -0,0 +1,13 @@ +Version: 1.0 + +RestoreWorkspace: No +SaveWorkspace: No +AlwaysSaveHistory: No + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX diff --git a/TestRareBloodCancersPrevalence/cdm_from_environment.R b/darwin-ee/Untitled/cdm_from_environment.R similarity index 100% rename from TestRareBloodCancersPrevalence/cdm_from_environment.R rename to darwin-ee/Untitled/cdm_from_environment.R diff --git a/TestRareBloodCancersPrevalence/execution-config.yml b/darwin-ee/Untitled/execution-config.yml similarity index 100% rename from TestRareBloodCancersPrevalence/execution-config.yml rename to darwin-ee/Untitled/execution-config.yml diff --git a/TestRareBloodCancersPrevalence/main.R b/darwin-ee/Untitled/main.R similarity index 100% rename from TestRareBloodCancersPrevalence/main.R rename to darwin-ee/Untitled/main.R diff --git a/darwin-ee/Untitled/outcomeCohorts/acute_ll_broad_2y.json b/darwin-ee/Untitled/outcomeCohorts/acute_ll_broad_2y.json new file mode 100644 index 0000000..7b37dba --- /dev/null +++ b/darwin-ee/Untitled/outcomeCohorts/acute_ll_broad_2y.json @@ -0,0 +1,714 @@ +{ + "ConceptSets": [ + { + "id": 0, + "name": "acute_ll broad", + "expression": { + "items": [ + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "278453007", + "CONCEPT_ID": 4081867, + "CONCEPT_NAME": "Acute biphenotypic leukemia", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "413440007", + "CONCEPT_ID": 4189936, + "CONCEPT_NAME": "Acute lymphoblastic leukemia - category", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "371012000", + "CONCEPT_ID": 4153344, + "CONCEPT_NAME": "Acute lymphoblastic leukemia, transitional pre-B-cell", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "91857003", + "CONCEPT_ID": 134305, + "CONCEPT_NAME": "Acute lymphoid leukemia", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "12301000132103", + "CONCEPT_ID": 36712834, + "CONCEPT_NAME": "Acute lymphoid leukemia relapse", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "110007008", + "CONCEPT_ID": 4003188, + "CONCEPT_NAME": "Adult T-cell leukemia/lymphoma", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "721310007", + "CONCEPT_ID": 36717161, + "CONCEPT_NAME": "Aggressive natural killer-cell leukemia", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "277571004", + "CONCEPT_ID": 4173963, + "CONCEPT_NAME": "B-cell acute lymphoblastic leukemia", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "783744003", + "CONCEPT_ID": 37204838, + "CONCEPT_NAME": "B-lymphoblastic leukemia lymphoma BCR-ABL1-like", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450920005", + "CONCEPT_ID": 42872925, + "CONCEPT_NAME": "B lymphoblastic leukemia / lymphoma - category", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450949002", + "CONCEPT_ID": 42872954, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma, no ICD-O subtype", + "DOMAIN_ID": 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"CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "838344002", + "CONCEPT_ID": 3654651, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with hypodiploidy", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450954006", + "CONCEPT_ID": 42872959, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with hypodiploidy (Hypodiploid ALL)", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "785825000", + "CONCEPT_ID": 37206196, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with iAMP21", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450956008", + "CONCEPT_ID": 42872961, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(1;19)(q23;p13.3); E2A-PBX1 (TCF3-PBX1)", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "838343008", + "CONCEPT_ID": 3654650, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(1;19)(Q23;P13.3); E2A-PBX1 (TCF3/PBX1)", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "838342003", + "CONCEPT_ID": 3654649, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(12;21) (p13;q22); TEL/AML1 (ETV6-RUNX1)", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450952005", + "CONCEPT_ID": 42872957, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1)", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "838340006", + "CONCEPT_ID": 3654647, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(5;14)(q31;q32); IL3-IGH", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450955007", + "CONCEPT_ID": 42872960, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(5;14)(q31;q32); IL3-IGH", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450950002", + "CONCEPT_ID": 42872955, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(9;22)(q34;q11.2); BCR-ABL1", + "DOMAIN_ID": "Observation", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "723889003", + "CONCEPT_ID": 37109936, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(9:22) (q34;q11.2); BCR-ABL 1", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Clinical Finding", + "CONCEPT_CODE": "838341005", + "CONCEPT_ID": 3654648, + "CONCEPT_NAME": "B lymphoblastic leukemia lymphoma with t(v;11q23); MLL rearranged", + "DOMAIN_ID": "Condition", + "INVALID_REASON": "V", + "INVALID_REASON_CAPTION": "Valid", + "STANDARD_CONCEPT": "S", + "STANDARD_CONCEPT_CAPTION": "Standard", + "VOCABULARY_ID": "SNOMED" + } + }, + { + "concept": { + "CONCEPT_CLASS_ID": "Morph Abnormality", + "CONCEPT_CODE": "450951003", + "CONCEPT_ID": 42872956, + "CONCEPT_NAME": "B lymphoblastic 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