Inital functions (#4)

* Adding initial functions
* add github actions
* add tests

.github/workflows/R_CMD_check_Hades.yaml

@@ -0,0 +1,171 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    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 }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - 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
+
+      - name: Install system requirements
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libssh-dev
+          Rscript -e 'install.packages("remotes")'
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - 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"'
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          install.packages("covr")
+        shell: Rscript {0}
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
+
+  Release:
+    needs: R-CMD-Check
+
+    runs-on: macOS-latest
+
+    env:
+      GH_TOKEN: ${{ secrets.GH_TOKEN }}
+
+    if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/main' }}
+
+    steps:
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Check if version has increased
+        run: |
+          echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
+
+      - name: Display new version number
+        if: ${{ env.new_version != '' }}
+        run: |
+          echo "${{ env.new_version }}"
+
+      - name: Create release
+        if: ${{ env.new_version != '' }}
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+        with:
+          tag_name: ${{ env.new_version }}
+          release_name: Release ${{ env.new_version }}
+          body: |
+            See NEWS.md for release notes.
+          draft: false
+          prerelease: false
+
+      - uses: r-lib/actions/setup-r@v2
+        if: ${{ env.new_version != '' }}
+
+      - name: Install drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          install.packages('drat')
+        shell: Rscript {0}
+
+      - name: Remove any tarballs that already exists
+        if: ${{ env.new_version != '' }}
+        run: |
+          rm -f *.tar.gz
+
+      - name: Download package tarball
+        if: ${{ env.new_version != '' }}
+        uses: actions/download-artifact@v2
+        with:
+          name: package_tarball
+
+      - name: Push to drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          bash deploy.sh
+
+      - name: Push to BroadSea
+        if: ${{ env.new_version != '' }}
+        run: |
+          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/

.github/workflows/nightly_cleanup_Hades.yml

@@ -0,0 +1,18 @@
+name: 'nightly artifacts cleanup'
+on:
+  schedule:
+    - cron: '0 1 * * *' # every night at 1 am UTC
+
+jobs:
+  remove-old-artifacts:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - name: Remove old artifacts
+      uses: c-hive/gha-remove-artifacts@v1
+      with:
+        age: '7 days'
+        # Optional inputs
+        # skip-tags: true
+        skip-recent: 1

.gitignore

@@ -4,3 +4,4 @@
 .Ruserdata
 *.tmp
 .Rprofile
+errorReportSql.txt

DESCRIPTION

@@ -1,22 +1,34 @@
 Package: CohortAlgebra
 Type: Package
-Title: Cohort Algebra to create new cohort(s) from existing cohorts.
+Title: Cohort Algebra to create new cohort(s) from existing cohorts
 Version: 0.0.1
 Date: 2022-07-07
-Author: Gowtham Rao [aut, cre]
+Authors@R: c(
+    person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
+    person("Adam", "Black", email = "[email protected]", role = c("aut")),
+    person("Observational Health Data Science and Informatics", role = c("cph"))
+  )
 Maintainer: Gowtham Rao <[email protected]>
 Description: An R package that creates new cohort(s) from previously instantiated cohorts.
 Depends:
 	DatabaseConnector (>= 5.0.0),
 	R (>= 4.1.0)
 Imports:
     checkmate,
-  	rlang,
-  	testthat
+    dplyr,
+    ParallelLogger,
+  	rlang
 Suggests:
-	testthat
+  remotes,
+  rmarkdown,
+  knitr,
+	testthat,
+	withr
+Remotes:
+  ohdsi/ParallelLogger
 License: Apache License
 RoxygenNote: 7.2.0
+VignetteBuilder: knitr
 Roxygen: list(markdown = TRUE)
 Encoding: UTF-8
 Language: en-US

NAMESPACE

@@ -1,4 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(eraFyCohorts)
+export(intersectCohorts)
+export(minusCohorts)
+import(DatabaseConnector)
 import(dplyr)
 importFrom(rlang,.data)

R/CohortAlgebra.R

@@ -17,6 +17,7 @@
 #' @keywords internal
 "_PACKAGE"
 
+#' @import DatabaseConnector
 #' @import dplyr
 #' @importFrom rlang .data
 NULL

R/CopyCohortsToTempTable.R

@@ -0,0 +1,79 @@
+# Copyright 2022 Observational Health Data Sciences and Informatics
+#
+# This file is part of CohortAlgebra
+#
+# 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.
+
+#' Get cohort ids in table
+#'
+#' @description
+#' Get cohort ids in table. This function is not exported.
+#'
+#' @template Connection
+#'
+#' @template OldToNewCohortId
+#'
+#' @template TempEmulationSchema
+#'
+#' @param sourceCohortDatabaseSchema The database schema of the source cohort table.
+#'
+#' @param sourceCohortTable         The name of the source cohort table.
+#'
+#' @param targetCohortTable         A temp table to copy the cohorts from the source table.
+#'
+#' @return
+#' NULL
+#'
+copyCohortsToTempTable <- function(connection = NULL,
+                                   oldToNewCohortId,
+                                   sourceCohortDatabaseSchema = NULL,
+                                   sourceCohortTable,
+                                   targetCohortTable = "#cohort_rows",
+                                   tempEmulationSchema = getOption("sqlRenderTempEmulationSchema")) {
+  DatabaseConnector::insertTable(
+    connection = connection,
+    tableName = "#old_to_new_cohort_id",
+    createTable = TRUE,
+    dropTableIfExists = TRUE,
+    tempTable = TRUE,
+    tempEmulationSchema = tempEmulationSchema,
+    progressBar = FALSE,
+    bulkLoad = (Sys.getenv("bulkLoad") == TRUE),
+    camelCaseToSnakeCase = TRUE,
+    data = oldToNewCohortId
+  )
+
+  sqlCopyCohort <- "
+                  DROP TABLE IF EXISTS @target_cohort_table;
+                  SELECT target.new_cohort_id cohort_definition_id,
+                          source.subject_id,
+                          source.cohort_start_date,
+                          source.cohort_end_date
+                  INTO @target_cohort_table
+                  FROM {@source_database_schema != ''} ? {@source_database_schema.@source_cohort_table} : {@source_cohort_table} source
+                  INNER JOIN #old_to_new_cohort_id target
+                  ON source.cohort_definition_id = target.old_cohort_id
+                  ;"
+
+  DatabaseConnector::renderTranslateExecuteSql(
+    connection = connection,
+    sql = sqlCopyCohort,
+    profile = FALSE,
+    progressBar = FALSE,
+    reportOverallTime = FALSE,
+    source_database_schema = sourceCohortDatabaseSchema,
+    source_cohort_table = sourceCohortTable,
+    target_cohort_table = targetCohortTable,
+    tempEmulationSchema = tempEmulationSchema
+  )
+}