From ba1bf394daebd51b6caaa4d4e170d3418a2f1a15 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Thu, 23 May 2024 11:31:29 -0400 Subject: [PATCH 01/12] change references to github org from veupath to mbio --- DESCRIPTION | 6 +++--- README.md | 8 ++++---- man/veupathUtils-package.Rd | 6 +++--- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7c99290..74e54cd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: veupathUtils -Title: General Helper Functions for VEuPathDB Projects +Title: General Helper Functions for MicrobiomeDB Projects Version: 2.6.5 Authors@R: c(person(given = "Danielle", @@ -26,8 +26,8 @@ Depends: jsonlite Remotes: zdk123/SpiecEasi -URL: https://github.com/VEuPathDB/veupathUtils -BugReports: https://github.com/VEuPathDB/veupathUtils/issues +URL: https://github.com/microbiomeDB/veupathUtils +BugReports: https://github.com/microbiomeDB/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) Encoding: UTF-8 diff --git a/README.md b/README.md index e256a75..182a4dc 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ # veupathUtils -veupathUtils is an R package which provides helper functions for solving common problems in the VEuPathDB project. +veupathUtils is an R package which provides helper functions for solving common problems in the MicrobiomeDB project. ## Installation Use the R package [remotes](https://cran.r-project.org/web/packages/remotes/index.html) to install veupathUtils. From the R command prompt: ```R -remotes::install_github('VEuPathDB/veupathUtils') +remotes::install_github('microbiomeDB/veupathUtils') ``` ## Usage @@ -15,7 +15,7 @@ This package is primarily intended for use as a dependency in other R packages. dependent package must follow these steps: 1. add ```veupathUtils``` to the ```Imports``` section of the dependent package's ```DESCRIPTION``` file. 2. add a ```Remotes``` section to the dependent package's ```DESCRIPTION``` file. -3. add ```VEuPathDB/veupathUtils``` to the ```Remotes``` section of the dependent package's ```DESCRIPTION``` file. +3. add ```microbiomeDB/veupathUtils``` to the ```Remotes``` section of the dependent package's ```DESCRIPTION``` file. 4. add ```#' @import veupathUtils``` to the dependent package's package-level documentation file (usually called ```{mypackage}-package.R```). 5. run ```devtools::document()```. @@ -35,5 +35,5 @@ As a general policy, we're exporting every function that gets added here. So unl ## Github Actions - [![R-CMD-check](https://github.com/VEuPathDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/VEuPathDB/veupathUtils/actions) + [![R-CMD-check](https://github.com/microbiomeDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/microbiomeDB/veupathUtils/actions) diff --git a/man/veupathUtils-package.Rd b/man/veupathUtils-package.Rd index 73c3547..d60a5da 100644 --- a/man/veupathUtils-package.Rd +++ b/man/veupathUtils-package.Rd @@ -4,15 +4,15 @@ \name{veupathUtils-package} \alias{veupathUtils} \alias{veupathUtils-package} -\title{veupathUtils: General Helper Functions for VEuPathDB Projects} +\title{veupathUtils: General Helper Functions for MicrobiomeDB Projects} \description{ veupathUtils contains various R helper functions intended to be useful across a variety of projects, including the plot.data and microbiomeComputations packages. } \seealso{ Useful links: \itemize{ - \item \url{https://github.com/VEuPathDB/veupathUtils} - \item Report bugs at \url{https://github.com/VEuPathDB/veupathUtils/issues} + \item \url{https://github.com/microbiomeDB/veupathUtils} + \item Report bugs at \url{https://github.com/microbiomeDB/veupathUtils/issues} } } From f0cdfbb3a7a783e470d39d5ce63e817ce95eb267 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Tue, 28 May 2024 22:00:04 -0400 Subject: [PATCH 02/12] make sure we can differentiate relative and absolute abundance collections --- R/internal-utils.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/internal-utils.R b/R/internal-utils.R index 07c7500..6c2c0e9 100644 --- a/R/internal-utils.R +++ b/R/internal-utils.R @@ -135,6 +135,7 @@ 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]) + collectionLabel <- paste(collectionLabel, "(", ontology$parentlabel[ontology$iri == collectionId], ")") if (length(collectionLabel) == 1) { return(paste(dataSourceName, collectionLabel)) @@ -186,4 +187,4 @@ collectionsBuilder <- function(dataSources, ontology = NULL) { collections <- new("Collections", collections) return(collections) -} \ No newline at end of file +} From e21e9ddd12890599476fa0d5673288ec601fc9b5 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Wed, 29 May 2024 11:30:03 -0400 Subject: [PATCH 03/12] make sure collection labels are unique once parent labels are added --- R/internal-utils.R | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/R/internal-utils.R b/R/internal-utils.R index 6c2c0e9..666601e 100644 --- a/R/internal-utils.R +++ b/R/internal-utils.R @@ -135,7 +135,10 @@ 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]) - collectionLabel <- paste(collectionLabel, "(", ontology$parentlabel[ontology$iri == collectionId], ")") + if (collectionLabel %in% c('Kingdom','Phylum','Class','Order','Family','Genus','Species')) { + collectionLabel <- unique(paste(collectionLabel, paste0("(", ontology$parentlabel[ontology$iri == collectionId], ")"))) + } + print(collectionLabel) if (length(collectionLabel) == 1) { return(paste(dataSourceName, collectionLabel)) From cd2dbfcc70eadf13f77203f0487332520e237b3c Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Wed, 29 May 2024 22:43:25 -0400 Subject: [PATCH 04/12] update readme --- README.md | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 182a4dc..033c1ae 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ + + [![R-CMD-check](https://github.com/microbiomeDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/microbiomeDB/veupathUtils/actions) + + # veupathUtils veupathUtils is an R package which provides helper functions for solving common problems in the MicrobiomeDB project. @@ -24,7 +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. @@ -32,8 +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/microbiomeDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/microbiomeDB/veupathUtils/actions) - From 322e7dc6efce58215cae973cd5c3cda6adaf4d2a Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Wed, 29 May 2024 23:09:12 -0400 Subject: [PATCH 05/12] increment version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 74e54cd..b3dafea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: veupathUtils Title: General Helper Functions for MicrobiomeDB Projects -Version: 2.6.5 +Version: 2.6.6 Authors@R: c(person(given = "Danielle", family = "Callan", From fb920437ab97f8cc0805385aaf4368ced8381152 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Thu, 30 May 2024 09:14:23 -0400 Subject: [PATCH 06/12] update github actions workflow --- .github/workflows/R-CMD-check.yaml | 33 +++++++++--------------------- 1 file changed, 10 insertions(+), 23 deletions(-) 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")' From fb4026636c9af16c146e981127a961666076f6f1 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Thu, 30 May 2024 09:14:45 -0400 Subject: [PATCH 07/12] add license --- DESCRIPTION | 2 +- LICENSE.md | 194 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 195 insertions(+), 1 deletion(-) create mode 100644 LICENSE.md diff --git a/DESCRIPTION b/DESCRIPTION index b3dafea..440209c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -29,7 +29,7 @@ Remotes: URL: https://github.com/microbiomeDB/veupathUtils BugReports: https://github.com/microbiomeDB/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. Definitions + +“License” shall mean the terms and conditions for use, reproduction, and +distribution as defined by Sections 1 through 9 of this document. + +“Licensor” shall mean the copyright owner or entity authorized by the copyright +owner that is granting the License. + +“Legal Entity” shall mean the union of the acting entity and all other entities +that control, are controlled by, or are under common control with that entity. +For the purposes of this definition, “control” means **(i)** the power, direct or +indirect, to cause the direction or management of such entity, whether by +contract or otherwise, or **(ii)** ownership of fifty percent (50%) or more of the +outstanding shares, or **(iii)** beneficial ownership of such entity. + +“You” (or “Your”) shall mean an individual or Legal Entity exercising +permissions granted by this License. + +“Source” form shall mean the preferred form for making modifications, including +but not limited to software source code, documentation source, and configuration +files. + +“Object” form shall mean any form resulting from mechanical transformation or +translation of a Source form, including but not limited to compiled object code, +generated documentation, and conversions to other media types. + +“Work” shall mean the work of authorship, whether in Source or Object form, made +available under the License, as indicated by a copyright notice that is included +in or attached to the work (an example is provided in the Appendix below). + +“Derivative Works” shall mean any work, whether in Source or Object form, that +is based on (or derived from) the Work and for which the editorial revisions, +annotations, elaborations, or other modifications represent, as a whole, an +original work of authorship. For the purposes of this License, Derivative Works +shall not include works that remain separable from, or merely link (or bind by +name) to the interfaces of, the Work and Derivative Works thereof. + +“Contribution” shall mean any work of authorship, including the original version +of the Work and any modifications or additions to that Work or Derivative Works +thereof, that is intentionally submitted to Licensor for inclusion in the Work +by the copyright owner or by an individual or Legal Entity authorized to submit +on behalf of the copyright owner. For the purposes of this definition, +“submitted” means any form of electronic, verbal, or written communication sent +to the Licensor or its representatives, including but not limited to +communication on electronic mailing lists, source code control systems, and +issue tracking systems that are managed by, or on behalf of, the Licensor for +the purpose of discussing and improving the Work, but excluding communication +that is conspicuously marked or otherwise designated in writing by the copyright +owner as “Not a Contribution.” + +“Contributor” shall mean Licensor and any individual or Legal Entity on behalf +of whom a Contribution has been received by Licensor and subsequently +incorporated within the Work. + +#### 2. Grant of Copyright License + +Subject to the terms and conditions of this License, each Contributor hereby +grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, +irrevocable copyright license to reproduce, prepare Derivative Works of, +publicly display, publicly perform, sublicense, and distribute the Work and such +Derivative Works in Source or Object form. + +#### 3. Grant of Patent License + +Subject to the terms and conditions of this License, each Contributor hereby +grants to You a perpetual, worldwide, non-exclusive, no-charge, royalty-free, +irrevocable (except as stated in this section) patent license to make, have +made, use, offer to sell, sell, import, and otherwise transfer the Work, where +such license applies only to those patent claims licensable by such Contributor +that are necessarily infringed by their Contribution(s) alone or by combination +of their Contribution(s) with the Work to which such Contribution(s) was +submitted. If You institute patent litigation against any entity (including a +cross-claim or counterclaim in a lawsuit) alleging that the Work or a +Contribution incorporated within the Work constitutes direct or contributory +patent infringement, then any patent licenses granted to You under this License +for that Work shall terminate as of the date such litigation is filed. + +#### 4. Redistribution + +You may reproduce and distribute copies of the Work or Derivative Works thereof +in any medium, with or without modifications, and in Source or Object form, +provided that You meet the following conditions: + +* **(a)** You must give any other recipients of the Work or Derivative Works a copy of +this License; and +* **(b)** You must cause any modified files to carry prominent notices stating that You +changed the files; and +* **(c)** You must retain, in the Source form of any Derivative Works that You distribute, +all copyright, patent, trademark, and attribution notices from the Source form +of the Work, excluding those notices that do not pertain to any part of the +Derivative Works; and +* **(d)** If the Work includes a “NOTICE” text file as part of its distribution, then any +Derivative Works that You distribute must include a readable copy of the +attribution notices contained within such NOTICE file, excluding those notices +that do not pertain to any part of the Derivative Works, in at least one of the +following places: within a NOTICE text file distributed as part of the +Derivative Works; within the Source form or documentation, if provided along +with the Derivative Works; or, within a display generated by the Derivative +Works, if and wherever such third-party notices normally appear. The contents of +the NOTICE file are for informational purposes only and do not modify the +License. You may add Your own attribution notices within Derivative Works that +You distribute, alongside or as an addendum to the NOTICE text from the Work, +provided that such additional attribution notices cannot be construed as +modifying the License. + +You may add Your own copyright statement to Your modifications and may provide +additional or different license terms and conditions for use, reproduction, or +distribution of Your modifications, or for any such Derivative Works as a whole, +provided Your use, reproduction, and distribution of the Work otherwise complies +with the conditions stated in this License. + +#### 5. Submission of Contributions + +Unless You explicitly state otherwise, any Contribution intentionally submitted +for inclusion in the Work by You to the Licensor shall be under the terms and +conditions of this License, without any additional terms or conditions. +Notwithstanding the above, nothing herein shall supersede or modify the terms of +any separate license agreement you may have executed with Licensor regarding +such Contributions. + +#### 6. Trademarks + +This License does not grant permission to use the trade names, trademarks, +service marks, or product names of the Licensor, except as required for +reasonable and customary use in describing the origin of the Work and +reproducing the content of the NOTICE file. + +#### 7. Disclaimer of Warranty + +Unless required by applicable law or agreed to in writing, Licensor provides the +Work (and each Contributor provides its Contributions) on an “AS IS” BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, +including, without limitation, any warranties or conditions of TITLE, +NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You are +solely responsible for determining the appropriateness of using or +redistributing the Work and assume any risks associated with Your exercise of +permissions under this License. + +#### 8. Limitation of Liability + +In no event and under no legal theory, whether in tort (including negligence), +contract, or otherwise, unless required by applicable law (such as deliberate +and grossly negligent acts) or agreed to in writing, shall any Contributor be +liable to You for damages, including any direct, indirect, special, incidental, +or consequential damages of any character arising as a result of this License or +out of the use or inability to use the Work (including but not limited to +damages for loss of goodwill, work stoppage, computer failure or malfunction, or +any and all other commercial damages or losses), even if such Contributor has +been advised of the possibility of such damages. + +#### 9. Accepting Warranty or Additional Liability + +While redistributing the Work or Derivative Works thereof, You may choose to +offer, and charge a fee for, acceptance of support, warranty, indemnity, or +other liability obligations and/or rights consistent with this License. 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. From 62c0f66e3c5d1b1ef0c06927eb389a71fd62fcd9 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Thu, 30 May 2024 09:14:59 -0400 Subject: [PATCH 08/12] update r build ignore --- .Rbuildignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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$ From cba987acf8eea99a2cd84d15b3bb939706bc07f4 Mon Sep 17 00:00:00 2001 From: Danielle Callan Date: Wed, 5 Jun 2024 11:46:54 -0400 Subject: [PATCH 09/12] allow collections list to have no ancestor ids for all collections --- R/class-Collections.R | 15 +++++++++++---- R/internal-utils.R | 5 ++--- 2 files changed, 13 insertions(+), 7 deletions(-) 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 666601e..d093885 100644 --- a/R/internal-utils.R +++ b/R/internal-utils.R @@ -136,9 +136,8 @@ getCollectionName <- function(collectionId, dataSourceName, ontology = NULL) { # 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], ")"))) - } - print(collectionLabel) + collectionLabel <- unique(paste(collectionLabel, paste0("(", ontology$parentlabel[ontology$iri == collectionId], ")"))) + } if (length(collectionLabel) == 1) { return(paste(dataSourceName, collectionLabel)) From bbeb36e32e2b4dc2c0fe959acb6ff2d00e6f4ba4 Mon Sep 17 00:00:00 2001 From: asizemore Date: Thu, 12 Sep 2024 17:16:57 -0400 Subject: [PATCH 10/12] sync records in sampleMetadata with those in df after possible removal --- R/methods-CollectionWithMetadata.R | 4 +- .../test-class-CollectionWithMetadata.R | 40 +++++++++++++++++++ 2 files changed, 43 insertions(+), 1 deletion(-) 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/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 From 1f8445bb3fa9239957aeeb980b5290944c8b15ff Mon Sep 17 00:00:00 2001 From: asizemore Date: Fri, 20 Sep 2024 08:32:19 -0400 Subject: [PATCH 11/12] version to 2.6.7 --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 440209c..77c09f5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: veupathUtils Title: General Helper Functions for MicrobiomeDB Projects -Version: 2.6.6 +Version: 2.6.7 Authors@R: c(person(given = "Danielle", family = "Callan", From 29c61c2a6ac60caf54870b11115846e826a97c97 Mon Sep 17 00:00:00 2001 From: asizemore Date: Fri, 18 Oct 2024 18:14:47 -0400 Subject: [PATCH 12/12] change refs from MicrobiomeDB to VEuPathDB --- DESCRIPTION | 6 +++--- README.md | 8 ++++---- man/veupathUtils-package.Rd | 6 +++--- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 77c09f5..3eccfd1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: veupathUtils -Title: General Helper Functions for MicrobiomeDB Projects +Title: General Helper Functions for VEuPathDB Projects Version: 2.6.7 Authors@R: c(person(given = "Danielle", @@ -26,8 +26,8 @@ Depends: jsonlite Remotes: zdk123/SpiecEasi -URL: https://github.com/microbiomeDB/veupathUtils -BugReports: https://github.com/microbiomeDB/veupathUtils/issues +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) Encoding: UTF-8 diff --git a/README.md b/README.md index 033c1ae..b3536b5 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ - [![R-CMD-check](https://github.com/microbiomeDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/microbiomeDB/veupathUtils/actions) + [![R-CMD-check](https://github.com/VEuPathDB/veupathUtils/workflows/R-CMD-check/badge.svg)](https://github.com/VEuPathDB/veupathUtils/actions) # veupathUtils -veupathUtils is an R package which provides helper functions for solving common problems in the MicrobiomeDB project. +veupathUtils is an R package which provides helper functions for solving common problems in the VEuPathDB project. ## Installation Use the R package [remotes](https://cran.r-project.org/web/packages/remotes/index.html) to install veupathUtils. From the R command prompt: ```R -remotes::install_github('microbiomeDB/veupathUtils') +remotes::install_github('VEuPathDB/veupathUtils') ``` ## Usage @@ -19,7 +19,7 @@ This package is primarily intended for use as a dependency in other R packages. dependent package must follow these steps: 1. add ```veupathUtils``` to the ```Imports``` section of the dependent package's ```DESCRIPTION``` file. 2. add a ```Remotes``` section to the dependent package's ```DESCRIPTION``` file. -3. add ```microbiomeDB/veupathUtils``` to the ```Remotes``` section of the dependent package's ```DESCRIPTION``` file. +3. add ```VEuPathDB/veupathUtils``` to the ```Remotes``` section of the dependent package's ```DESCRIPTION``` file. 4. add ```#' @import veupathUtils``` to the dependent package's package-level documentation file (usually called ```{mypackage}-package.R```). 5. run ```devtools::document()```. diff --git a/man/veupathUtils-package.Rd b/man/veupathUtils-package.Rd index d60a5da..73c3547 100644 --- a/man/veupathUtils-package.Rd +++ b/man/veupathUtils-package.Rd @@ -4,15 +4,15 @@ \name{veupathUtils-package} \alias{veupathUtils} \alias{veupathUtils-package} -\title{veupathUtils: General Helper Functions for MicrobiomeDB Projects} +\title{veupathUtils: General Helper Functions for VEuPathDB Projects} \description{ veupathUtils contains various R helper functions intended to be useful across a variety of projects, including the plot.data and microbiomeComputations packages. } \seealso{ Useful links: \itemize{ - \item \url{https://github.com/microbiomeDB/veupathUtils} - \item Report bugs at \url{https://github.com/microbiomeDB/veupathUtils/issues} + \item \url{https://github.com/VEuPathDB/veupathUtils} + \item Report bugs at \url{https://github.com/VEuPathDB/veupathUtils/issues} } }