oxinabox · oxinabox · Oct 31, 2018 · Oct 25, 2018 · Oct 26, 2018 · Oct 27, 2018
diff --git a/README.md b/README.md
@@ -188,22 +188,13 @@ Example of use:
 ```
 
 
-### `DataOneV1()` - API Based
-
-https://releases.dataone.org/online/api-documentation-v1.2.0/
-
-Data repositories like DataDryad, support version 1 API of the DataOne. 
-
-Data Repositories:
-* DataDryad: `generate(DataOneV1(), "https://datadryad.org/resource/doi:10.5061/dryad.74699", "Wild Crop Genomics")`
-
-
 
 ### `DataOneV2`
 
 https://releases.dataone.org/online/api-documentation-v2.0/apis/index.html
 
-Supports DataOne API version 2. There are differences in the API structure in each of them, hence are accounted for, separately:
+Supports DataOne API version 2.
+There are differences in the API structure for each repository each of them, hence are accounted for, separately:
 
 Data Repositories:
 * Knowledge Network for Biocomplexity `KnowledgeNetworkforBiocomplexity()`: `generate(KnowledgeNetworkforBiocomplexity(), "https://knb.ecoinformatics.org/knb/d1/mn/v2/object/doi:10.5063/F1T43R7N")`

diff --git a/src/APIs/DataOneV1.jl b/src/APIs/DataOneV1.jl
diff --git a/src/APIs/Figshare.jl b/src/APIs/Figshare.jl
@@ -2,6 +2,9 @@ struct Figshare <: DataRepo
 end
 
 base_url(::Figshare) = "https://api.figshare.com/v2/articles"
+# Note: Unlike other generators, FigShare base_url is sometimes a "directory" and sometimes a file
+# But it is OK, because Figshare also overloads all the functions that use `base_url`
+# Most importantly `mainpage_url`
 
 description(repo::Figshare, mainpage) = mainpage["description"]
 
@@ -49,7 +52,7 @@ function mainpage_url(repo::Figshare, dataname)
         return JSON.parse(text_only(getpage(url).root)), url
     elseif match_figshare(dataname)!= nothing
         identifier = match_figshare(dataname)
-        url = base_url(repo) * "/" *identifier
+        url = joinpath(base_url(repo), identifier)
         return JSON.parse(text_only(getpage(url).root)), url
     else
         throw(GeneratorError(repo))

diff --git a/src/APIs/GitHub.jl b/src/APIs/GitHub.jl
@@ -1,7 +1,7 @@
 struct GitHub <: DataRepo
 end
 
-base_url(::GitHub) = "https://github.com"
+base_url(::GitHub) = "https://github.com/"
 
 git_repo_page_url(page) = base_url(GitHub()) * getattr(first(eachmatch(sel"strong[itemprop=\"name\"] a", page.root)), "href")
 

diff --git a/src/DataDepsGenerators.jl b/src/DataDepsGenerators.jl
@@ -7,7 +7,7 @@ using Dates
 using InteractiveUtils: subtypes
 
 export generate, citation_text, remove_cite_version
-export UCI, GitHub, DataDryad, DataOneV1, DataOneV2, CKAN, DataCite, Figshare, JSONLD_Web, JSONLD_DOI
+export UCI, GitHub, DataDryad, DataOneV2, CKAN, DataCite, Figshare, JSONLD_Web, JSONLD_DOI
 
 
 
@@ -38,7 +38,6 @@ include("misc_extractors.jl")
 include("APIs/UCI.jl")
 include("APIs/GitHub.jl")
 include("APIs/DataDryad.jl")
-include("APIs/DataOneV1.jl")
 include("APIs/DataOneV2/DataOneV2.jl")
 include("APIs/CKAN.jl")
 include("APIs/DataCite.jl")

diff --git a/src/generate.jl b/src/generate.jl
@@ -116,7 +116,7 @@ function mainpage_url(repo::DataRepo, dataname)
     if startswith(dataname, "http")
         url = dataname
     else # not a URL
-        url = joinpath(base_url(repo), dataname)
+        url = base_url(repo) * dataname
     end
     getpage(url), url
 end

diff --git a/test/DataDryad.jl b/test/DataDryad.jl
@@ -4,6 +4,9 @@ using Test
 using ReferenceTests
 
 @testset "DataDryad test" begin
+    # Via URL
+    @test_reference "references/DataDryad Ecology.txt" generate(DataDryad(), "https://datadryad.org/resource/doi:10.5061/dryad.74699")
+    #Via DOI
     @test_reference "references/DataDryad Ecology.txt" generate(DataDryad(), "https://datadryad.org/resource/doi:10.5061/dryad.74699")
 
     #Checking files with multiple files available for download

diff --git a/test/DataOneV1.jl b/test/DataOneV1.jl
diff --git a/test/combine.jl b/test/combine.jl
@@ -6,7 +6,7 @@ using ReferenceTests
 @testset "Combining test" begin
     @test_reference "references/Combining Ecology.txt" remove_cite_version(generate("10.5061/dryad.74699"))
 
-    @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 Plasticity.txt" remove_cite_version(generate("http://dx.doi.org/10.5061/dryad.f9s4424"))
 
     @test_reference "references/Combining Stack Overflow.txt" generate("https://www.kaggle.com/stackoverflow/stack-overflow-2018-developer-survey")
 

diff --git a/test/references/Combining Ecology.txt b/test/references/Combining Ecology.txt
@@ -2,17 +2,17 @@ register(DataDep(
     "Data from Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation",
     """
 	Dataset: Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation
-	Website: http://dx.doi.org/10.5061/dryad.74699
-	Author: von Wettberg, Eric J. B. et al.
-	Date of Publication: 2018-02-27T21:46:38
+	Website: https://datadryad.org/resource/doi:10.5061/dryad.74699
+	Author: Eric J. B. Von Wettberg et al.
+	Date of Publication: February 27, 2018
 	License: https://creativecommons.org/publicdomain/zero/1.0/
 
 	Domesticated species are impacted in unintended ways during domestication and breeding. Changes in the nature and intensity of selection impart genetic drift, reduce diversity, and increase the frequency of deleterious alleles. Such outcomes constrain our ability to expand the cultivation of crops into environments that differ from those under which domestication occurred. We address this need in chickpea, an important pulse legume, by harnessing the diversity of wild crop relatives. We document an extreme domestication-related genetic bottleneck and decipher the genetic history of wild populations. We provide evidence of ancestral adaptations for seed coat color crypsis, estimate the impact of environment on genetic structure and trait values, and demonstrate variation between wild and cultivated accessions for agronomic properties. A resource of genotyped, association mapping progeny functionally links the wild and cultivated gene pools and is an essential resource chickpea for improvement, while our methods inform collection of other wild crop progenitor species.
 
-	Please cite this paper: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L. B., Moenga, S. M., … Cook, D. R. (2018). Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications, 9(1). doi:10.1038/s41467-018-02867-z
+	Please cite this paper: von Wettberg EJB, Chang PL, Başdemir F, Carrasquila-Garcia N, Korbu L, Moenga SM, Bedada G, Greenlon A, Moriuchi KS, Suryawanshi V, Cordeiro MA, Noujdina NV, Dinegde KN, Abbas Shah Sani SG, Getahun T, Vance L, Bergmann E, Lindsay D, Mamo BE, Warschefsky EJ, Dacosta-Calheiros E, Marques E, Yilmaz MA, Cakmak AM, Rose J, Migneault A, Krieg CP, Saylak S, Temel H, Friesen ML, Silor E, Akhmetov Z, Ozelik H, Kholova J, Can C, Gaur P, Yildirim M, Sharma H, Vadez V, Tesfaye K, Woldemedhin AF, Tar'an B, Aydogan A, Bukun B, Penmetsa RV, Berger J, Kahraman A, Nuzhdin SV, Cook DR (2018) Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation. Nature Communications 9: 649.  https://doi.org/10.1038/s41467-018-02867-z
 
 	Please cite this dataset: Von Wettberg, E. J. B., Chang, P. L., Başdemir, F., Carrasquila-Garcia, N., Korbu, L., Moenga, S. M., … Cook, D. R. (2018). Data from: Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.74699
 	""",
-	Any["/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"],
-	[(md5, "3c837a0a41e01966a0f037beb7db43b8")]
+	Any["https://datadryad.org/bitstream/handle/10255/dryad.166590/draft_dryad_upload_dec2017.xls?sequence=1"],
+	[(md5, "efc75490db3444d3708b3e9ccd030d38")]
 ))
diff --git a/test/references/Combining Plasticity.txt b/test/references/Combining Plasticity.txt
@@ -2,9 +2,9 @@ register(DataDep(
     "Data from Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta",
     """
 	Dataset: Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta
-	Website: https://datadryad.org/mn/object/http://dx.doi.org/10.5061/dryad.f9s4424
-	Author: Wagner, Maggie R., Mitchell-Olds, Thomas
-	Date of Publication: 2018-03-02T20:35:36
+	Website: http://dx.doi.org/10.5061/dryad.f9s4424
+	Author: Maggie R. Wagner, Thomas Mitchell-Olds
+	Date of Publication: March 2, 2018
 	License: https://creativecommons.org/publicdomain/zero/1.0/
 
 	Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection (“adaptive plasticity”) or disfavored (“nonadaptive” plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.
@@ -14,6 +14,6 @@ register(DataDep(
 
 	Please cite this dataset: Wagner, M. R., & Mitchell-Olds, T. (2018). Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta [Data set]. Dryad Digital Repository. https://doi.org/10.5061/dryad.f9s4424
 	""",
-	Any["/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"],
-	[(md5, "aea52e9cdb6c4069720bc709415e479f"), (md5, "2abd4c62b7263eba8c74ce2bcb25790f"), (md5, "783d619e042bfe516b6ffd34dc97b5df")]
+	Any["https://datadryad.org/bitstream/handle/10255/dryad.173251/raw_data.zip?sequence=1", "https://datadryad.org/bitstream/handle/10255/dryad.173251/README.txt?sequence=2", "https://datadryad.org/bitstream/handle/10255/dryad.173252/GSplasticity_code.R?sequence=1"],
+	[(md5, "898237b1dd8306be586ffc036ebda768"), (md5, "af502ff7111868c548cc7923a9193673")]
 ))
diff --git a/test/references/DataOneV1 Drought.txt b/test/references/DataOneV1 Drought.txt
diff --git a/test/references/DataOneV1 Ecology.txt b/test/references/DataOneV1 Ecology.txt