Merge pull request #53 from oxinabox/ox/quiettest

Quieten Integration tests
oxinabox · Sep 13, 2018 · a76964f · a76964f
2 parents ab1cfdd + 3a3bdfb
commit a76964f
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Showing 12 changed files with 67 additions and 34 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,4 @@
 *.jl.*.cov
 *.jl.mem
 **.vscode/
+**.swp
diff --git a/test/CKAN.jl b/test/CKAN.jl
@@ -1,13 +1,13 @@
+using Base.Test
 using DataDeps
 using DataDepsGenerators
-using Base.Test
-
+using Suppressor
 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
+end
diff --git a/test/Figshare.jl b/test/Figshare.jl
@@ -2,21 +2,21 @@ using DataDeps
 using DataDepsGenerators
 using Base.Test
 using MD5
-
+using Suppressor
 using ReferenceTests
 
 @testset "Figshare test" begin
 
     @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
 
         @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/GitHub.jl b/test/GitHub.jl
@@ -2,6 +2,8 @@ using DataDeps
 using DataDepsGenerators
 using Base.Test
 
+using Suppressor
+
 using ReferenceTests
 
 """
@@ -16,7 +18,7 @@ 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 +39,7 @@ 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

diff --git 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/UCI.jl b/test/UCI.jl
@@ -1,13 +1,13 @@
 using DataDeps
 using DataDepsGenerators
 using Base.Test
-
+using 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

diff --git 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
@@ -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"],
 ))
diff --git a/test/references/Figshare Gene Diversity.txt b/test/references/Figshare Gene Diversity.txt
diff --git a/test/references/Figshare from doi.txt 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")]
+))
diff --git a/test/references/JSONLD_DOI Zenodo Gene Diversity.txt 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,
+))
diff --git a/test/references/JSONLD_Web Zenodo Gene Diversity.txt 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"],
+))