From a81c73ba764b90a1b14965a8b1a5cd156cd12d32 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:41:15 +0800 Subject: [PATCH 01/10] Quieten Integration tests --- test/CKAN.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/CKAN.jl b/test/CKAN.jl index 4a27c7a..76ac149 100644 --- a/test/CKAN.jl +++ b/test/CKAN.jl @@ -7,7 +7,7 @@ using ReferenceTests @testset "CKAN Demo test" begin registration_code = generate(CKAN(), "https://demo.ckan.org/dataset/gold-prices") - @testset "Integration Test" begin + @suppress @testset "Integration Test" begin eval(parse(registration_code)) @test length(collect(readdir(datadep"Gold Prices in London 1950-2008 (Monthly)"))) > 0 end @@ -21,4 +21,4 @@ end @testset "data.gov.au test" begin @test_reference "references/CKAN Hazelwood Fire.txt" generate(CKAN(), "https://data.gov.au/api/3/action/package_show?id=2016-soe-atmosphere-hourly-co-and-24h-pm2-5-concentrations-measured-during-the-hazelwood-mine-fire") -end \ No newline at end of file +end From 7906fef5fc1693d4978f018ee8f6db8be4ddad7a Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:44:19 +0800 Subject: [PATCH 02/10] quiet --- test/Figshare.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/Figshare.jl b/test/Figshare.jl index 4425590..6d5fd1a 100644 --- a/test/Figshare.jl +++ b/test/Figshare.jl @@ -10,7 +10,7 @@ using ReferenceTests @testset "Chile Activism" begin registration_code = generate(Figshare(), "https://figshare.com/articles/Youth_Activism_in_Chile_from_urban_educational_inequalities_to_experiences_of_living_together_and_solidarity/6504206") - @testset "Integration Test" begin + @suppress @testset "Integration Test" begin eval(parse(registration_code)) @test length(collect(readdir(datadep"Youth Activism in Chile from urban educational inequalities to experiences of living together and solidarity"))) > 0 end From c2958c751a5b335cea256254ecafc5de51cc6fbe Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:44:59 +0800 Subject: [PATCH 03/10] quiet --- test/GitHub.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/GitHub.jl b/test/GitHub.jl index 5b1a773..0a80ebb 100644 --- a/test/GitHub.jl +++ b/test/GitHub.jl @@ -16,7 +16,7 @@ end @testset "538 March" begin registration_code = generate(GitHub(), "https://github.com/fivethirtyeight/data/tree/master/march-madness-predictions-2015") - @testset "Integration Test" begin + @suppress @testset "Integration Test" begin eval(parse(registration_code)) @test length(collect(readdir(datadep"March Madness Predictions"))) > 0 end @@ -37,7 +37,7 @@ end @testset "Pres Camp" begin registration_code = generate(GitHub(), "https://github.com/BuzzFeedNews/presidential-campaign-contributions") - @testset "Integration Test" begin + @suppress @testset "Integration Test" begin eval(parse(registration_code)) # evaluate the new code @test length(collect(readdir(datadep"Presidential Campaign Contributions"))) > 0 end From f39cfa5d036ed08c0ff88f046c108a3a4f45ec21 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:45:43 +0800 Subject: [PATCH 04/10] quiet --- test/GitHub.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/GitHub.jl b/test/GitHub.jl index 0a80ebb..0cccf69 100644 --- a/test/GitHub.jl +++ b/test/GitHub.jl @@ -2,6 +2,8 @@ using DataDeps using DataDepsGenerators using Base.Test +using Suppressor + using ReferenceTests """ From 58afb4e0e78717048ff9f6eeada32a8cd9464edb Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:46:05 +0800 Subject: [PATCH 05/10] ssshh --- test/Figshare.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/Figshare.jl b/test/Figshare.jl index 6d5fd1a..957d5e1 100644 --- a/test/Figshare.jl +++ b/test/Figshare.jl @@ -2,7 +2,7 @@ using DataDeps using DataDepsGenerators using Base.Test using MD5 - +using Suppressor using ReferenceTests @testset "Figshare test" begin From f86d974758f54b9324af83b8c724bd30cd59ed88 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:46:22 +0800 Subject: [PATCH 06/10] ssshh --- test/CKAN.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/CKAN.jl b/test/CKAN.jl index 76ac149..c3b37df 100644 --- a/test/CKAN.jl +++ b/test/CKAN.jl @@ -1,7 +1,7 @@ using DataDeps using DataDepsGenerators using Base.Test - +using Suppressor using ReferenceTests @testset "CKAN Demo test" begin From d70e12b3579ead452e156ddcfa2da93f58b2c97d Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Tue, 4 Sep 2018 10:46:55 +0800 Subject: [PATCH 07/10] sshhh --- test/UCI.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/UCI.jl b/test/UCI.jl index 8e36edf..d227769 100644 --- a/test/UCI.jl +++ b/test/UCI.jl @@ -1,13 +1,13 @@ using DataDeps using DataDepsGenerators using Base.Test - +usinng Suppressor using ReferenceTests @testset "UCI Air Quality" begin registration_code = generate(UCI(), "Air+Quality") - @testset "Integration Test" begin + @suppress @testset "Integration Test" begin eval(parse(registration_code)) @test length(collect(readdir(datadep"Air Quality Data Set (UCI ML Repository)"))) > 0 end From 3e6ef8c5979396ee8a56a4b5e0d16c0b4272ea49 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Wed, 5 Sep 2018 13:55:34 +0800 Subject: [PATCH 08/10] poke CI --- test/CKAN.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/CKAN.jl b/test/CKAN.jl index c3b37df..4b3593a 100644 --- a/test/CKAN.jl +++ b/test/CKAN.jl @@ -1,6 +1,6 @@ +using Base.Test using DataDeps using DataDepsGenerators -using Base.Test using Suppressor using ReferenceTests From 2c504f8f901def6630484666fc80227fe82fede3 Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Wed, 5 Sep 2018 14:00:37 +0800 Subject: [PATCH 09/10] typo --- test/UCI.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/UCI.jl b/test/UCI.jl index d227769..a68ccf9 100644 --- a/test/UCI.jl +++ b/test/UCI.jl @@ -1,7 +1,7 @@ using DataDeps using DataDepsGenerators using Base.Test -usinng Suppressor +using Suppressor using ReferenceTests @testset "UCI Air Quality" begin From 3a3bdfbdd3c0a4ec057941680bc8d53d42fbc83f Mon Sep 17 00:00:00 2001 From: Lyndon White Date: Thu, 13 Sep 2018 13:53:32 +0800 Subject: [PATCH 10/10] =update things that broken --- .gitignore | 1 + test/Figshare.jl | 2 +- test/JSONLD/JSONLD.jl | 5 +++++ test/combine.jl | 2 +- test/references/Combining Gene Diversity.txt | 11 +++++------ test/references/Figshare Gene Diversity.txt | 16 ---------------- test/references/Figshare from doi.txt | 16 ++++++++++++++++ .../JSONLD_DOI Zenodo Gene Diversity.txt | 13 +++++++++++++ .../JSONLD_Web Zenodo Gene Diversity.txt | 13 +++++++++++++ 9 files changed, 55 insertions(+), 24 deletions(-) delete mode 100644 test/references/Figshare Gene Diversity.txt create mode 100644 test/references/Figshare from doi.txt create mode 100644 test/references/JSONLD_DOI Zenodo Gene Diversity.txt create mode 100644 test/references/JSONLD_Web Zenodo Gene Diversity.txt diff --git a/.gitignore b/.gitignore index ec58498..2cdbe86 100644 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ *.jl.*.cov *.jl.mem **.vscode/ +**.swp diff --git a/test/Figshare.jl b/test/Figshare.jl index 957d5e1..4922f50 100644 --- a/test/Figshare.jl +++ b/test/Figshare.jl @@ -18,5 +18,5 @@ using ReferenceTests @test_reference "references/Figshare Chile Activism.txt" registration_code end - @test_reference "references/Figshare Gene Diversity.txt" generate(Figshare(), "10.5281/zenodo.1194927") + @test_reference "references/Figshare from doi.txt" generate(Figshare(), "10.1371/journal.pbio.2001414") end diff --git a/test/JSONLD/JSONLD.jl b/test/JSONLD/JSONLD.jl index 2102daf..d71ce48 100644 --- a/test/JSONLD/JSONLD.jl +++ b/test/JSONLD/JSONLD.jl @@ -6,12 +6,17 @@ using ReferenceTests @testset "JSON-LD Web" begin @test_reference "../references/JSONLD_Web Kaggle.txt" generate(JSONLD_Web(), "https://www.kaggle.com/stackoverflow/stack-overflow-2018-developer-survey") @test_reference "../references/JSONLD_Web Zenodo.txt" generate(JSONLD_Web(), "https://zenodo.org/record/1287281") + + @test_reference "../references/JSONLD_Web Zenodo Gene Diversity.txt" generate(JSONLD_Web(), "https://doi.org/10.5281/zenodo.1194927") + @test_reference "../references/JSONLD_Web Dataverse.txt" generate(JSONLD_Web(), "https://dataverse.harvard.edu/dataset.xhtml?persistentId=hdl:1902.1/15580") @test_reference "../references/JSONLD_Web Figshare.txt" generate(JSONLD_Web(), "https://figshare.com/articles/_shows_examples_of_coordinated_and_uncoordinated_motion_for_dangerous_and_non_dangerous_crowd_behavior_/186003") end @testset "JSON-LD DOI" begin + @test_reference "../references/JSONLD_DOI Zenodo Gene Diversity.txt" generate(JSONLD_DOI(), "https://doi.org/10.5281/zenodo.1194927") + @test_reference "../references/JSONLD_DOI Figshare.txt" generate(JSONLD_DOI(), "10.1371/journal.pbio.2001414") @test_reference "../references/JSONLD_DOI PBIO.txt" generate(JSONLD_DOI(), "https://data.datacite.org/10.1371/journal.pbio.2001414") diff --git a/test/combine.jl b/test/combine.jl index 19f3d36..574908c 100644 --- a/test/combine.jl +++ b/test/combine.jl @@ -8,7 +8,7 @@ using ReferenceTests @test_reference "references/Combining Plasticity.txt" remove_cite_version(generate("https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.f9s4424")) - @test_reference "references/Combining Gene Diversity.txt" remove_cite_version(generate("10.5281/zenodo.1194927")) + @test_reference "references/Combining Gene Diversity.txt" remove_cite_version(generate("https://doi.org/10.5281/zenodo.1194927")) @test_reference "references/Combining Stack Overflow.txt" generate("https://www.kaggle.com/stackoverflow/stack-overflow-2018-developer-survey") diff --git a/test/references/Combining Gene Diversity.txt b/test/references/Combining Gene Diversity.txt index b25974c..bbc2c8f 100644 --- a/test/references/Combining Gene Diversity.txt +++ b/test/references/Combining Gene Diversity.txt @@ -1,16 +1,15 @@ register(DataDep( - "Supplemental Material For "Overcoming Challenges In Variant Calling Exploring Sequence Diversity In Candidate Genes For Plant Development In Perennial Ryegrass (Lolium Perenne)"", + "Supplemental Material for "Overcoming challenges in variant calling exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)"", """ - Dataset: Supplemental Material For "Overcoming Challenges In Variant Calling: Exploring Sequence Diversity In Candidate Genes For Plant Development In Perennial Ryegrass (Lolium Perenne)" - Website: https://figshare.com/articles/Supplemental_Material_for_Overcoming_challenges_in_variant_calling_exploring_sequence_diversity_in_candidate_genes_for_plant_development_in_perennial_ryegrass_Lolium_perenne_/5969383 + Dataset: Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)" + Website: https://doi.org/10.5281/zenodo.1194927 Author: Elisabeth Veeckman - Date of Publication: 2019-03-09T00:00:00Z + Date of Publication: March 9, 2019 License: https://creativecommons.org/licenses/by/4.0 Supplemental materials to the manuscript. Please cite this dataset: Veeckman, E. (2019). Supplemental Material For ‘Overcoming Challenges In Variant Calling: Exploring Sequence Diversity In Candidate Genes For Plant Development In Perennial Ryegrass (Lolium Perenne)’ [Data set]. Zenodo. https://doi.org/10.5281/zenodo.1194927 """, - Any["https://ndownloader.figshare.com/files/10703311", "https://ndownloader.figshare.com/files/10703314"], - [(md5, "a167841695f0349fe3ce0c8858eaf452"), (md5, "b951ef090d8bd8a037df7d466da1f848")] + String["https://zenodo.org/api/files/056ac4e4-94e1-4bad-8efa-d95f0691a92f/3. AnnotatedVariants_503TargetGenes_736Genotypes_SnpEff.csv.zip", "https://zenodo.org/api/files/056ac4e4-94e1-4bad-8efa-d95f0691a92f/5. CAP3contigs_503CandidateGenes.fasta.zip"], )) \ No newline at end of file diff --git a/test/references/Figshare Gene Diversity.txt b/test/references/Figshare Gene Diversity.txt deleted file mode 100644 index 7902c12..0000000 --- a/test/references/Figshare Gene Diversity.txt +++ /dev/null @@ -1,16 +0,0 @@ -register(DataDep( - "Supplemental Material for "Overcoming challenges in variant calling exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)"", - """ - Dataset: Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)" - Website: https://figshare.com/articles/Supplemental_Material_for_Overcoming_challenges_in_variant_calling_exploring_sequence_diversity_in_candidate_genes_for_plant_development_in_perennial_ryegrass_Lolium_perenne_/5969383 - Author: Elisabeth Veeckman - Date of Publication: 2019-03-09T00:00:00Z - License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) - - Supplemental materials to the manuscript. - - Please cite this dataset: Veeckman, Elisabeth (2019): Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)". Zenodo. Fileset. - """, - Any["https://ndownloader.figshare.com/files/10703311", "https://ndownloader.figshare.com/files/10703314"], - [(md5, "a167841695f0349fe3ce0c8858eaf452"), (md5, "b951ef090d8bd8a037df7d466da1f848")] -)) \ No newline at end of file diff --git a/test/references/Figshare from doi.txt b/test/references/Figshare from doi.txt new file mode 100644 index 0000000..494e5f9 --- /dev/null +++ b/test/references/Figshare from doi.txt @@ -0,0 +1,16 @@ +register(DataDep( + "Identifiers for the 21st century How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data", + """ + Dataset: Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data + Website: https://figshare.com/articles/Identifiers_for_the_21st_century_How_to_design_provision_and_reuse_persistent_identifiers_to_maximize_utility_and_impact_of_life_science_data/5156008 + Author: Julie A. McMurry et al. + Date of Publication: 2017-06-29T17:29:50Z + License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/) + + In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines. + + Please cite this dataset: McMurry, Julie A.; Juty, Nick; Blomberg, Niklas; Burdett, Tony; Conlin, Tom; Conte, Nathalie; et al. (2017): Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLOS Biology. Fileset. + """, + Any["https://ndownloader.figshare.com/files/8792425", "https://ndownloader.figshare.com/files/8792437", "https://ndownloader.figshare.com/files/8792482", "https://ndownloader.figshare.com/files/8792491", "https://ndownloader.figshare.com/files/8792503", "https://ndownloader.figshare.com/files/8792536", "https://ndownloader.figshare.com/files/8792545"], + [(md5, "5066bf01417f85028a09a2f4dadcbefe"), (md5, "5c3867e33c0d30952a884f1373ce3e21"), (md5, "47c7de1501dcba5d2571efc262a5cf3b"), (md5, "e9846e7297fa503771dbb6d352b31f99"), (md5, "0c46b3705abca5b99265736dcb18bf4d"), (md5, "a1220bb16027568a988ca21b86f5db1a"), (md5, "d21886f4ea8844823a03217284c34cc8")] +)) \ No newline at end of file diff --git a/test/references/JSONLD_DOI Zenodo Gene Diversity.txt b/test/references/JSONLD_DOI Zenodo Gene Diversity.txt new file mode 100644 index 0000000..d934015 --- /dev/null +++ b/test/references/JSONLD_DOI Zenodo Gene Diversity.txt @@ -0,0 +1,13 @@ +register(DataDep( + "Supplemental Material For "Overcoming Challenges In Variant Calling Exploring Sequence Diversity In Candidate Genes For Plant Development In Perennial Ryegrass (Lolium Perenne)"", + """ + Dataset: Supplemental Material For "Overcoming Challenges In Variant Calling: Exploring Sequence Diversity In Candidate Genes For Plant Development In Perennial Ryegrass (Lolium Perenne)" + Website: https://doi.org/10.5281/zenodo.1194927 + Author: Elisabeth Veeckman + Date of Publication: March 9, 2019 + License: https://creativecommons.org/licenses/by/4.0 + + Supplemental materials to the manuscript. + """, + missing, +)) \ No newline at end of file diff --git a/test/references/JSONLD_Web Zenodo Gene Diversity.txt b/test/references/JSONLD_Web Zenodo Gene Diversity.txt new file mode 100644 index 0000000..2f33d87 --- /dev/null +++ b/test/references/JSONLD_Web Zenodo Gene Diversity.txt @@ -0,0 +1,13 @@ +register(DataDep( + "Supplemental Material for "Overcoming challenges in variant calling exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)"", + """ + Dataset: Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)" + Website: https://doi.org/10.5281/zenodo.1194927 + Author: Elisabeth Veeckman + Date of Publication: March 9, 2019 + License: https://creativecommons.org/licenses/by/4.0/ + + Supplemental materials to the manuscript. + """, + String["https://zenodo.org/api/files/056ac4e4-94e1-4bad-8efa-d95f0691a92f/3. AnnotatedVariants_503TargetGenes_736Genotypes_SnpEff.csv.zip", "https://zenodo.org/api/files/056ac4e4-94e1-4bad-8efa-d95f0691a92f/5. CAP3contigs_503CandidateGenes.fasta.zip"], +)) \ No newline at end of file