Merge pull request #44 from OHDSI/develop

Capr v2 release

.Rbuildignore

@@ -9,3 +9,7 @@ compare_versions
 ^docs$
 ^extras$
 ^man-roxygen$
+^scratch$
+^work$
+^README\.Rmd$
+^pkgdown$

.github/workflows/R_CMD_check_main_weekly.yml

@@ -0,0 +1,71 @@
+on:
+ schedule:
+ - cron: '0 15 * * 6' # every Sunday at 11am UTC
+
+name: 'R check'
+
+jobs:
+ R-CMD-check-main:
+ runs-on: ${{ matrix.config.os }}
+
+ name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+ strategy:
+ fail-fast: false
+ matrix:
+ config:
+ - {os: macOS-latest, r: 'release'}
+
+ env:
+ GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+ R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+ RSPM: ${{ matrix.config.rspm }}
+ CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+ CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+ CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+ CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+ CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+ CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+ CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+ CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+ CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+ CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+ CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+ CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+ CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+ CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+ CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+ CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+ CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+ CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+ CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+ CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+ CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+ CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+ CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+ WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
+ WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
+ WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
+ WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
+
+ steps:
+ - uses: actions/checkout@v3
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ r-version: ${{ matrix.config.r }}
+
+ - uses: r-lib/actions/setup-tinytex@v2
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ args: 'c("--no-manual", "--as-cran")'
+ error-on: '"warning"'
+ check-dir: '"check"'

.gitignore

@@ -5,3 +5,5 @@ errorReportSql.txt
 *.log
 /Meta/
 work/*
+inst/doc
+scratch/

DESCRIPTION

@@ -1,68 +1,63 @@
 Package: Capr
-Title: Cohort definition Application Programming in R
-Version: 1.0.3
-Authors@R: 
- person(given = "Martin",
- family = "Lavallee",
- role = c("aut", "cre"),
- email = "mdlavallee92@gmail.com")
-Description: The CAPR package develops cohort definitions to implement across an OMOP mapped dbms. This pacakge allows 
- allows for the programmatic creation of OMOP cohorts that compile to the CIRCE-BE engine. CAPR utilizes s4 to construct
- component parts to the cohort definition (i.e. Primary Criteria, Inclusion Rules, Additional Criteria, Censoring Criteria,
- and End Strategy) and then packs them together into a Cohort Definition class. The Cohort Definition can be rendered into a 
- CIRCE-BE object that will generate ohdsiSQL to query against an OMOP dbms. CAPR adds component parts to the OMOP cohort
- definition in order to combine Concept Set Expressions with its definition logic in the same position, facilitating the 
- transition between scientific description and computational implmentation. 
+Title: Cohort Definition Application Programming in R
+Version: 2.0.0
+Authors@R: c(
+ person("Martin", "Lavallee", , "mdlavallee92@gmail.com", role = c("aut", "cre")),
+ person("Adam", "Black", , "black@ohdsi.org", role = "aut")
+ )
+Description: The Capr package provides a programming language for defining OHDSI cohort definitions in R. 
+ The functions in Capr allow for the programmatic creation of OHDSI concept sets and cohorts that can be serialized 
+ to Atlas/CIRCE-BE compatible json files or to OHDSI-SQL. Capr functions can be used to create, save, and load 
+ component parts to a cohort definition allowing R programmers to easily reuse cohort logic. Capr provides tools
+ to create a large number of OHDSI cohorts programmatically while also helping bridge the gap between human readable
+ descriptions of clinical phenotypes and their computational implmentation. 
 License: Apache License 2.0
 URL: https://ohdsi.github.io/Capr, https://github.com/OHDSI/Capr
 BugReports: https://github.com/OHDSI/Capr/issues
 Encoding: UTF-8
-LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Depends: 
  R (>= 3.5.0),
- CirceR (>= 1.0.0),
- DatabaseConnector (>= 2.4.2),
- magrittr (>= 1.5.0)
 Imports: 
+ magrittr (>= 1.5.0),
  jsonlite,
- RJSONIO,
  methods,
  purrr,
  rlang,
- uuid,
- SqlRender,
  dplyr,
  checkmate,
  tibble,
- withr,
  readr,
- utils,
  stringr,
  glue,
- cli
+ cli,
+ digest,
+ fs,
+ lubridate,
+ DBI,
+ DatabaseConnector,
+ SqlRender
 Suggests:
- testthat (>= 3.0.0),
- knitr,
- rmarkdown
-Remotes:
- ohdsi/CirceR
+ testthat (>= 3.0.0),
+ knitr,
+ rmarkdown,
+ CohortGenerator,
+ CirceR,
+ Eunomia
+VignetteBuilder: knitr
+Additional_repositories: https://OHDSI.github.io/drat
+Config/testthat/edition: 3
 Collate: 
  'Capr.R'
- 'LowLevelClasses.R'
- 'LowLevelUtilityFn.R'
- 'LowLevelBuildLangFn.R'
- 'LowLevelCoercionFn.R'
- 'LowLevelCreateFn.R'
- 'LowLevelLoadFn.R'
- 'LowLevelSaveFn.R'
- 'UserAttributeEdit.R'
- 'UserCommands.R'
- 'UserConceptLookupFn.R'
- 'UserCreateAttributeFn.R'
- 'UserCreateDomainFn.R'
- 'UserCreateFn.R'
- 'UserEditFn.R'
+ 'conceptSet.R'
+ 'attributes-concept.R'
+ 'attributes-logic.R'
+ 'query.R'
+ 'window.R'
+ 'criteria.R'
+ 'attributes-nested.R'
+ 'attributes-op.R'
+ 'exit.R'
+ 'cohort.R'
+ 'collectCodesetId.R'
  'utils.R'
-VignetteBuilder: knitr
-Config/testthat/edition: 3