diff --git a/.Rbuildignore b/.Rbuildignore index 58f456f..0bfe703 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,4 +1,5 @@ ^veupathUtils\.Rproj$ ^\.Rproj\.user$ ^\.github$ -^codecov\.yml$ \ No newline at end of file +^codecov\.yml$ +^LICENSE\.md$ diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1ac257a..0f2fe08 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,4 +1,4 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/master/examples +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help on: push: @@ -8,6 +8,8 @@ on: name: R-CMD-check +permissions: read-all + jobs: R-CMD-check: runs-on: ${{ matrix.config.os }} @@ -18,7 +20,7 @@ jobs: fail-fast: false matrix: config: - - {os: macOS-latest, r: 'release'} + - {os: macos-latest, r: 'release'} - {os: windows-latest, r: 'release'} - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} - {os: ubuntu-latest, r: 'release'} @@ -29,7 +31,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,25 +43,10 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: rcmdcheck - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_: false - run: | - Sys.setenv(TZ='EST') - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), check_dir = "check") - shell: Rscript {0} - - - name: Show testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/DESCRIPTION b/DESCRIPTION index 7c99290..3eccfd1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: veupathUtils Title: General Helper Functions for VEuPathDB Projects -Version: 2.6.5 +Version: 2.6.7 Authors@R: c(person(given = "Danielle", family = "Callan", @@ -29,7 +29,7 @@ Remotes: URL: https://github.com/VEuPathDB/veupathUtils BugReports: https://github.com/VEuPathDB/veupathUtils/issues Description: veupathUtils contains various R helper functions intended to be useful across a variety of projects, including the plot.data and microbiomeComputations packages. -License: Apache License (= 2.0) +License: Apache License (>= 2) Encoding: UTF-8 LazyData: true Roxygen: list(markdown = TRUE) diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..b62a9b5 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,194 @@ +Apache License +============== + +_Version 2.0, January 2004_ +_<>_ + +### Terms and Conditions for use, reproduction, and distribution + +#### 1. 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However, +in accepting such obligations, You may act only on Your own behalf and on Your +sole responsibility, not on behalf of any other Contributor, and only if You +agree to indemnify, defend, and hold each Contributor harmless for any liability +incurred by, or claims asserted against, such Contributor by reason of your +accepting any such warranty or additional liability. + +_END OF TERMS AND CONDITIONS_ + +### APPENDIX: How to apply the Apache License to your work + +To apply the Apache License to your work, attach the following boilerplate +notice, with the fields enclosed by brackets `[]` replaced with your own +identifying information. (Don't include the brackets!) The text should be +enclosed in the appropriate comment syntax for the file format. We also +recommend that a file or class name and description of purpose be included on +the same “printed page” as the copyright notice for easier identification within +third-party archives. + + Copyright [yyyy] [name of copyright owner] + + 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. diff --git a/R/class-Collections.R b/R/class-Collections.R index 32417ea..9ee578e 100644 --- a/R/class-Collections.R +++ b/R/class-Collections.R @@ -81,11 +81,18 @@ check_collections <- function(object) { return(TRUE) } - # check that at least one ancestorIdColumn is shared between collections + # check that at least one ancestorIdColumn is shared between collections, or there are no ancestors firstCollectionAncestorIds <- object[[1]]@ancestorIdColumns - if (!all(sapply(object, function(x) any(x@ancestorIdColumns %in% firstCollectionAncestorIds)))) { - msg <- "at least one ancestorIdColumn must be shared between collections" - errors <- c(errors, msg) + if (!!length(firstCollectionAncestorIds)) { + if (!all(sapply(object, function(x) any(x@ancestorIdColumns %in% firstCollectionAncestorIds)))) { + msg <- "at least one ancestorIdColumn must be shared between collections" + errors <- c(errors, msg) + } + } else { + if (any(sapply(object, function(x) !!length(x@ancestorIdColumns)))) { + msg <- "at least one ancestorIdColumn must be shared between collections" + errors <- c(errors, msg) + } } if (length(errors) == 0) { diff --git a/R/internal-utils.R b/R/internal-utils.R index 07c7500..d093885 100644 --- a/R/internal-utils.R +++ b/R/internal-utils.R @@ -135,6 +135,9 @@ getCollectionName <- function(collectionId, dataSourceName, ontology = NULL) { # this assumes were getting one of our own ontology download files # w columns like `iri` and `label` collectionLabel <- unique(ontology$label[ontology$iri == collectionId]) + if (collectionLabel %in% c('Kingdom','Phylum','Class','Order','Family','Genus','Species')) { + collectionLabel <- unique(paste(collectionLabel, paste0("(", ontology$parentlabel[ontology$iri == collectionId], ")"))) + } if (length(collectionLabel) == 1) { return(paste(dataSourceName, collectionLabel)) @@ -186,4 +189,4 @@ collectionsBuilder <- function(dataSources, ontology = NULL) { collections <- new("Collections", collections) return(collections) -} \ No newline at end of file +} diff --git a/R/methods-CollectionWithMetadata.R b/R/methods-CollectionWithMetadata.R index 2f40341..32b5dd9 100644 --- a/R/methods-CollectionWithMetadata.R +++ b/R/methods-CollectionWithMetadata.R @@ -153,9 +153,10 @@ setGeneric("removeIncompleteRecords", #' @aliases removeIncompleteRecords,CollectionWithMetadata-method setMethod("removeIncompleteRecords", signature("CollectionWithMetadata"), function(object, colName = character(), verbose = c(TRUE, FALSE)) { verbose <- veupathUtils::matchArg(verbose) - df <- getCollectionData(object, verbose = verbose) sampleMetadata <- getSampleMetadata(object) + # df may have had rows removed due to getCollectionData behavior. Subset sampleMetadata to match + sampleMetadata <- sampleMetadata[sampleMetadata[[object@sampleMetadata@recordIdColumn]] %in% df[[object@recordIdColumn]], ] # Remove Records with NA from data and metadata if (any(is.na(sampleMetadata[[colName]]))) { @@ -171,6 +172,7 @@ setMethod("removeIncompleteRecords", signature("CollectionWithMetadata"), functi data = sampleMetadata, recordIdColumn = object@sampleMetadata@recordIdColumn ) + validObject(object) } diff --git a/README.md b/README.md index d706de6..b3536b5 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,6 @@ -> [!CAUTION] -> Maintenance of this repository was moved to [microbiomeDB](https://github.com/microbiomeDB) on 23 May 2024. -> Please see the [new location](https://github.com/microbiomeDB/veupathUtils) for the most recent version. - - - + + [![R-CMD-check](https://github.com/VEuPathDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/VEuPathDB/veupathUtils/actions) + # veupathUtils @@ -31,7 +28,9 @@ or if they mean to also develop veupathUtils simultaneously, can use ```devtools their R session. ## Contributing -Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change. +Pull requests are welcome and should be made to the **dev** branch. + +For major changes, please open an issue first to discuss what you would like to change. Please make sure to update tests as appropriate. @@ -39,8 +38,3 @@ As a general policy, we're exporting every function that gets added here. So unl ## License [Apache 2.0](https://www.apache.org/licenses/LICENSE-2.0.txt) - -## Github Actions - - [![R-CMD-check](https://github.com/VEuPathDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/VEuPathDB/veupathUtils/actions) - diff --git a/tests/testthat/test-class-CollectionWithMetadata.R b/tests/testthat/test-class-CollectionWithMetadata.R index c784dac..df3a823 100644 --- a/tests/testthat/test-class-CollectionWithMetadata.R +++ b/tests/testthat/test-class-CollectionWithMetadata.R @@ -159,4 +159,44 @@ test_that("pruneFeatures works", { testing <- pruneFeatures(testing, veupathUtils::predicateFactory('proportionNonZero', 0.5)) expect_equal(nrow(testing@data), 200) expect_equal(ncol(testing@data), 3) +}) + +test_that("removeIncompleteRecords removes records from both metadata and data", { + nSamples <- 200 + sampleMetadataDT <- data.table::data.table( + "entity.SampleID" = 1:nSamples, + "entity.contA" = rnorm(nSamples), + "entity.contB" = rnorm(nSamples), + "entity.contC" = rnorm(nSamples) + ) + # set first 5 rows to NA + sampleMetadataDT[1:5, 2:ncol(sampleMetadataDT) ] <- NA + + df <- data.table::data.table( + "entity.SampleID" = sampleMetadataDT$entity.SampleID, + "entity.cont1" = rnorm(nSamples), + "entity.cont2" = rnorm(nSamples), + "entity.cont3" = rnorm(nSamples) + ) + # Set second 5 rows to NA + df[6:10, 2:ncol(df) ] <- NA + + sampleMetadata <- SampleMetadata( + data = sampleMetadataDT, + recordIdColumn = 'entity.SampleID' + ) + + test_collection <- CollectionWithMetadata( + name = 'test', + data = df, + sampleMetadata = sampleMetadata, + recordIdColumn = 'entity.SampleID' + ) + + result <- removeIncompleteRecords(test_collection, 'entity.contA', verbose=F) + expect_equal(nrow(result@data), nSamples-10) + expect_equal(ncol(result@data), 4) + expect_equal(nrow(result@sampleMetadata@data), nSamples-10) + expect_equal(ncol(result@sampleMetadata@data), 4) + }) \ No newline at end of file