# Copyright 2018 Observational Health Data Sciences and Informatics
#
# This file is part of hivTestStudyCharacterization
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# making cohorts the primitive way, not using insertCohortDefinitionSetInPackage
# and cohort.csv, etc.
library(tidyverse)
readRenviron('.env')
OhdsiRTools::insertCohortDefinitionInPackage(
# fileName = "settings.csv",
# cat inst/settings/settings.csv
# "cohortId","atlasId","name","fullName"
# 987654321,1769961,"Male50plus","Male > 50"
definitionId = 1769961,
name = "Male50plus",
baseUrl = Sys.getenv("WebAPIBaseUrl"),# "http://18.213.176.21:80/WebAPI"
generateStats = FALSE
)
# add second cohort def at some point
# cohort 2:
# HIV patients when HIV onset > age 18
# cohort 3:
# patients with HIV lab test
# temporarily use any, ldl measure table record
# don't use settings.csv or cohorts.csv
#
# # Generate CSV of cohort names and IDs for the package
#
# cohortCsv <-
# "cohortId,cohortName,cohortSql
# 1,Male50plus,Male50plus.sql
# "
# #2,ConditionCount,ConditionCount.sql
#
# writeLines(cohortCsv, "inst/settings/cohorts.csv")
# Insert cohort definitions from ATLAS into package -----------------------
# couldn't get the Set version of insertCohortDefinition<Set>InPackage with
# /inst/settings/settings.csv:
# "cohortId","atlasId","name","fullName"
# 987654321,1769961,"Male50plus","Male > 50"
# OhdsiRTools::insertCohortDefinitionSetInPackage(
# fileName = "settings.csv",
# baseUrl = Sys.getenv("WebAPIBaseUrl"),# "http://18.213.176.21:80/WebAPI"
# insertTableSql = TRUE,
# insertCohortCreationR = TRUE,
# generateStats = FALSE,
# packageName="hivTestStudy")
# Inserting cohort: Male50plus
# Error in readChar(fileName, file.info(fileName)$size) :
# invalid 'nchars' argument
# In addition: Warning message:
# In file(con, "rb") :
# file("") only supports open = "w+" and open = "w+b": using the former
# so, don't need settings.csv, and loading from single public ATLAS/WebAPI cohort def:
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