From 7449305c9cb14642bc5c4896b4b6586243bbbaf6 Mon Sep 17 00:00:00 2001 From: Joel Nitta Date: Fri, 3 Jun 2022 09:18:07 +0900 Subject: [PATCH 1/4] Skip biomartr-tools test until switch to duckdb --- tests/testthat/test-biomartr-tools.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-biomartr-tools.R b/tests/testthat/test-biomartr-tools.R index 3d2ed0c..2ca3814 100644 --- a/tests/testthat/test-biomartr-tools.R +++ b/tests/testthat/test-biomartr-tools.R @@ -5,6 +5,7 @@ library(testthat) # RUNNING context('Testing \'biomartr-tools\'') test_that('check_connection() works', { + skip("skip until switch to duckdb") with_mock( `url_exists` = function(...) FALSE, expect_error(restez:::check_connection()) From a54f40b5d2c6619e61b06ceea1e763b79c3f99a5 Mon Sep 17 00:00:00 2001 From: Joel Nitta Date: Fri, 3 Jun 2022 09:18:45 +0900 Subject: [PATCH 2/4] Don't hard-code version in README --- README.Rmd | 4 ---- 1 file changed, 4 deletions(-) diff --git a/README.Rmd b/README.Rmd index de30334..17d576d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -122,10 +122,6 @@ restez_disconnect() Want to contribute? Check the [contributing page](https://ropensci.github.io/restez/CONTRIBUTING.html). -## Version - -Release version 1. - ## Licence MIT From 8e890485201b125b565028587d45df0c54a0f7c5 Mon Sep 17 00:00:00 2001 From: Joel Nitta Date: Fri, 3 Jun 2022 09:19:16 +0900 Subject: [PATCH 3/4] Update NEWS --- NEWS.md | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/NEWS.md b/NEWS.md index 7b0dd2f..6169cc0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,18 @@ -# restez (in development) +# restez 1.1.0 + +## Bug fixes + +* Fix bug where single extremely long sequence caused db_create() to die (#14) + +## New features + +* Add ability to filter database by accession number upon creation (#25) + +## Other + +* Change maintainer to [Joel Nitta](https://github.com/joelnitta) + +# restez 1.0.1 ## Bug fixes From ec892db8a8ebdb9743f50231a389fd58d737ffbc Mon Sep 17 00:00:00 2001 From: Joel Nitta Date: Fri, 3 Jun 2022 09:19:54 +0900 Subject: [PATCH 4/4] Bump version --- DESCRIPTION | 2 +- README.md | 94 +++++++++++++++++++++++++-------------------------- codemeta.json | 4 +-- 3 files changed, 49 insertions(+), 51 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e3f26e4..cc8df8a 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: restez Type: Package Title: Create and Query a Local Copy of 'GenBank' in R -Version: 1.0.3 +Version: 1.1.0 Authors@R: c( person( given = "Joel H.", diff --git a/README.md b/README.md index 51cfbe9..9d65712 100644 --- a/README.md +++ b/README.md @@ -89,7 +89,7 @@ no longer available.) # Warning: running these examples may take a few minutes library(restez) #> ------------- -#> restez v1.0.3 +#> restez v1.1.0 #> ------------- #> Remember to restez_path_set() and, then, restez_connect() # choose a location to store GenBank files @@ -117,11 +117,11 @@ id <- sample(list_db_ids(), 1) # sequences seq <- gb_sequence_get(id)[[1]] str(seq) -#> chr "GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGCCAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACG"| __truncated__ +#> chr "AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGAAGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGT"| __truncated__ # definitions def <- gb_definition_get(id)[[1]] print(def) -#> [1] "Unidentified clone B27 DNA sequence from ocean beach sand" +#> [1] "Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence" # organisms org <- gb_organism_get(id)[[1]] print(org) @@ -129,44 +129,46 @@ print(org) # or whole records rec <- gb_record_get(id)[[1]] cat(rec) -#> LOCUS AF298103 647 bp DNA linear UNA 23-NOV-2000 -#> DEFINITION Unidentified clone B27 DNA sequence from ocean beach sand. -#> ACCESSION AF298103 -#> VERSION AF298103.1 +#> LOCUS AF298113 633 bp DNA linear UNA 23-NOV-2000 +#> DEFINITION Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence. +#> ACCESSION AF298113 +#> VERSION AF298113.1 #> KEYWORDS . #> SOURCE unidentified #> ORGANISM unidentified #> unclassified sequences. -#> REFERENCE 1 (bases 1 to 647) +#> REFERENCE 1 (bases 1 to 633) #> AUTHORS Naviaux,R.K. #> TITLE Sand DNA: a multigenomic library on the beach #> JOURNAL Unpublished -#> REFERENCE 2 (bases 1 to 647) +#> REFERENCE 2 (bases 1 to 633) #> AUTHORS Naviaux,R.K. #> TITLE Direct Submission #> JOURNAL Submitted (21-AUG-2000) Medicine, University of California, San #> Diego School of Medicine, 200 West Arbor Drive, San Diego, CA #> 92103-8467, USA #> FEATURES Location/Qualifiers -#> source 1..647 +#> source 1..633 #> /organism="unidentified" #> /mol_type="genomic DNA" #> /db_xref="taxon:32644" -#> /clone="B27" +#> /clone="E16S17" #> /note="anonymous environmental sample sequence from ocean #> beach sand" +#> rRNA <1..>633 +#> /product="SSU ribosomal RNA" #> ORIGIN -#> 1 gatcccgacc ttgatgctgt tcaagggcgg caacgtcgag gcgaccaagg tcggggcact -#> 61 gtcgaagagc cagctcgcgg catttctcga cagcaatctc tgagcgcgac gcgcgccgcc -#> 121 gtcatgtggc gctcatcacg aaaacttcgt cacacggggt agacgccccc tgaggcgcgt -#> 181 gttaggtttt tcatacaccg gcgcactcgc gccgtcctca ccttcatccg tacccagcac -#> 241 acgcttgctc acgcccatac ccgtgcggtc gtcatgaccg tcgaccgtgc tgcccgccag -#> 301 tccgcctctt ggattgctta atgaacctca cagagttgaa acagaaaacc gccccggagc -#> 361 tgctcgagct gtcgcaggag ctcggcatcg agggcatggc ccgctcgcgc aagcaggacg -#> 421 tgatcttcgc gatcctgaag aaccaggcga agaagggcga ggacatctac ggcgacggcg -#> 481 tgctcgaaat ccttcaggac ggattcggct tnctgcgctc gtctgacagc ttctacctgg -#> 541 ccgggcccga cgacatttac gtnagtccna gccanatccg ccgcttnggc tgncaccggn -#> 601 nnaccgtggt tggaaagata aggcttcaaa ggagggaagc gctcttt +#> 1 aattcggctt ggttaccttg ttacgacttc accccagtca tgaaccacaa agtggtgagc +#> 61 gacctcccga aggttagtct acccacttct tttgcaaccc actcccatgg tgtgacgggc +#> 121 ggtgtgtaca aggcccggga acgtattcac cgtagcaatg ctgatctacg attactagcg +#> 181 attccaactt catgcagtcg agttgcagac tgcaatccgg actaagaact gctttgtggg +#> 241 attggctccc cctcgcgggt tagcgaccct ctgtacagcc cattgtagca cgtgtgtagc +#> 301 ccagcccata agggccatga tgacttgacg tcatccccac cttcctccgg tttgtcaccg +#> 361 gcagtctcct tagagttccc accattacgt gctggcaact aaggacaang gttgcgctcg +#> 421 ttgcgggact taacccaaca tctcacgaca cgagctgacg acagccatgc agcacctgtg +#> 481 taacggcccg aangcggcac catctctggt aaccttccat tacatgtcaa atccaggtaa +#> 541 ggttctgcgc gttgcatcga attaaaccac atgctccact gcttgtgcgg gccccccgtc +#> 601 aatttctttg agtttaatct tgcgaccgta ctt #> // ``` @@ -176,34 +178,34 @@ cat(rec) # use the entrez_* wrappers to access GB data res <- entrez_fetch(db = 'nucleotide', id = id, rettype = 'fasta') cat(res) -#> >AF298103.1 Unidentified clone B27 DNA sequence from ocean beach sand -#> GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGC -#> CAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACGCGCGCCGCCGTCATGTGGCGCTCATCACG -#> AAAACTTCGTCACACGGGGTAGACGCCCCCTGAGGCGCGTGTTAGGTTTTTCATACACCGGCGCACTCGC -#> GCCGTCCTCACCTTCATCCGTACCCAGCACACGCTTGCTCACGCCCATACCCGTGCGGTCGTCATGACCG -#> TCGACCGTGCTGCCCGCCAGTCCGCCTCTTGGATTGCTTAATGAACCTCACAGAGTTGAAACAGAAAACC -#> GCCCCGGAGCTGCTCGAGCTGTCGCAGGAGCTCGGCATCGAGGGCATGGCCCGCTCGCGCAAGCAGGACG -#> TGATCTTCGCGATCCTGAAGAACCAGGCGAAGAAGGGCGAGGACATCTACGGCGACGGCGTGCTCGAAAT -#> CCTTCAGGACGGATTCGGCTTNCTGCGCTCGTCTGACAGCTTCTACCTGGCCGGGCCCGACGACATTTAC -#> GTNAGTCCNAGCCANATCCGCCGCTTNGGCTGNCACCGGNNNACCGTGGTTGGAAAGATAAGGCTTCAAA -#> GGAGGGAAGCGCTCTTT +#> >AF298113.1 Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence +#> AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGA +#> AGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGA +#> ACGTATTCACCGTAGCAATGCTGATCTACGATTACTAGCGATTCCAACTTCATGCAGTCGAGTTGCAGAC +#> TGCAATCCGGACTAAGAACTGCTTTGTGGGATTGGCTCCCCCTCGCGGGTTAGCGACCCTCTGTACAGCC +#> CATTGTAGCACGTGTGTAGCCCAGCCCATAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGG +#> TTTGTCACCGGCAGTCTCCTTAGAGTTCCCACCATTACGTGCTGGCAACTAAGGACAANGGTTGCGCTCG +#> TTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCTGTGTAACGGCCCG +#> AANGCGGCACCATCTCTGGTAACCTTCCATTACATGTCAAATCCAGGTAAGGTTCTGCGCGTTGCATCGA +#> ATTAAACCACATGCTCCACTGCTTGTGCGGGCCCCCCGTCAATTTCTTTGAGTTTAATCTTGCGACCGTA +#> CTT # if the id is not in the local database # these wrappers will search online via the rentrez package res <- entrez_fetch(db = 'nucleotide', id = c('S71333.1', id), rettype = 'fasta') #> [1] id(s) are unavailable locally, searching online. cat(res) -#> >AF298103.1 Unidentified clone B27 DNA sequence from ocean beach sand -#> GATCCCGACCTTGATGCTGTTCAAGGGCGGCAACGTCGAGGCGACCAAGGTCGGGGCACTGTCGAAGAGC -#> CAGCTCGCGGCATTTCTCGACAGCAATCTCTGAGCGCGACGCGCGCCGCCGTCATGTGGCGCTCATCACG -#> AAAACTTCGTCACACGGGGTAGACGCCCCCTGAGGCGCGTGTTAGGTTTTTCATACACCGGCGCACTCGC -#> GCCGTCCTCACCTTCATCCGTACCCAGCACACGCTTGCTCACGCCCATACCCGTGCGGTCGTCATGACCG -#> TCGACCGTGCTGCCCGCCAGTCCGCCTCTTGGATTGCTTAATGAACCTCACAGAGTTGAAACAGAAAACC -#> GCCCCGGAGCTGCTCGAGCTGTCGCAGGAGCTCGGCATCGAGGGCATGGCCCGCTCGCGCAAGCAGGACG -#> TGATCTTCGCGATCCTGAAGAACCAGGCGAAGAAGGGCGAGGACATCTACGGCGACGGCGTGCTCGAAAT -#> CCTTCAGGACGGATTCGGCTTNCTGCGCTCGTCTGACAGCTTCTACCTGGCCGGGCCCGACGACATTTAC -#> GTNAGTCCNAGCCANATCCGCCGCTTNGGCTGNCACCGGNNNACCGTGGTTGGAAAGATAAGGCTTCAAA -#> GGAGGGAAGCGCTCTTT +#> >AF298113.1 Unidentified clone E16S17 SSU ribosomal RNA gene, partial sequence +#> AATTCGGCTTGGTTACCTTGTTACGACTTCACCCCAGTCATGAACCACAAAGTGGTGAGCGACCTCCCGA +#> AGGTTAGTCTACCCACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGA +#> ACGTATTCACCGTAGCAATGCTGATCTACGATTACTAGCGATTCCAACTTCATGCAGTCGAGTTGCAGAC +#> TGCAATCCGGACTAAGAACTGCTTTGTGGGATTGGCTCCCCCTCGCGGGTTAGCGACCCTCTGTACAGCC +#> CATTGTAGCACGTGTGTAGCCCAGCCCATAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCGG +#> TTTGTCACCGGCAGTCTCCTTAGAGTTCCCACCATTACGTGCTGGCAACTAAGGACAANGGTTGCGCTCG +#> TTGCGGGACTTAACCCAACATCTCACGACACGAGCTGACGACAGCCATGCAGCACCTGTGTAACGGCCCG +#> AANGCGGCACCATCTCTGGTAACCTTCCATTACATGTCAAATCCAGGTAAGGTTCTGCGCGTTGCATCGA +#> ATTAAACCACATGCTCCACTGCTTGTGCGGGCCCCCCGTCAATTTCTTTGAGTTTAATCTTGCGACCGTA +#> CTT #> #> >S71333.1 alpha 1,3 galactosyltransferase [New World monkeys, mermoset lymphoid cell line B95.8, mRNA Partial, 1131 nt] #> ATGAATGTCAAAGGAAAAGTAATTCTGTCGATGCTGGTTGTCTCAACTGTGATTGTTGTGTTTTGGGAAT @@ -231,10 +233,6 @@ restez_disconnect() Want to contribute? Check the [contributing page](https://ropensci.github.io/restez/CONTRIBUTING.html). -## Version - -Release version 1. - ## Licence MIT diff --git a/codemeta.json b/codemeta.json index 73e3f18..8124731 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,7 +8,7 @@ "codeRepository": "https://github.com/ropensci/restez", "issueTracker": "https://github.com/ropensci/restez/issues", "license": "https://spdx.org/licenses/MIT", - "version": "1.0.3", + "version": "1.1.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", @@ -195,7 +195,7 @@ }, "SystemRequirements": null }, - "fileSize": "1657.315KB", + "fileSize": "1657.388KB", "citation": [ { "@type": "ScholarlyArticle",