bolognese 0.13.1 → 0.13.2
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/bolognese/readers/schema_org_reader.rb +2 -0
- data/lib/bolognese/version.rb +1 -1
- data/lib/bolognese/writers/schema_org_writer.rb +1 -0
- data/spec/fixtures/gtex.xml +4 -1
- data/spec/fixtures/schema_org_topmed.json +4 -0
- data/spec/readers/datacite_reader_spec.rb +1 -0
- data/spec/readers/schema_org_reader_spec.rb +1 -0
- data/spec/writers/schema_org_writer_spec.rb +2 -0
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
|
3
|
+
metadata.gz: d80546e87d2832b4408b869a0b9dbe8cd6fd47b718fa96cb4680187e37266361
|
4
|
+
data.tar.gz: 5266faafe16fd6750af63857bc6029232e7a0ff45dba74114283bbdd45c536fc
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5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 1f427e13c17577fbc48d309c1dfc37916cd4e8f8567c3b7da97074fad49631e88463e4e007c8c915db51de09e24359db7930a1e5d3604a550d2bfde5eb6d7715
|
7
|
+
data.tar.gz: bc0b392d86d63786ffd1e175440ad866b6ca1eb68cf313feb290f2f7b48721357fdf84c52929b0e3d544c93cce7f39c96954deeae140ad7ad4b7c71532425572
|
data/Gemfile.lock
CHANGED
@@ -92,6 +92,8 @@ module Bolognese
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|
92
92
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"alternate_identifier" => alternate_identifier,
|
93
93
|
"b_url" => normalize_id(meta.fetch("url", nil)),
|
94
94
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"content_url" => Array.wrap(meta.fetch("contentUrl", nil)).unwrap,
|
95
|
+
"content_size" => meta.fetch("contenSize", nil),
|
96
|
+
"content_format" => Array.wrap(meta.fetch("encodingFormat", nil) || meta.fetch("fileFormat", nil)).unwrap,
|
95
97
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"title" => meta.fetch("name", nil),
|
96
98
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"author" => author,
|
97
99
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"editor" => editor,
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data/lib/bolognese/version.rb
CHANGED
@@ -19,6 +19,7 @@ module Bolognese
|
|
19
19
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"keywords" => keywords.present? ? Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.join(", ") : nil,
|
20
20
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"inLanguage" => language,
|
21
21
|
"contentSize" => content_size,
|
22
|
+
"encodingFormat" => content_format,
|
22
23
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"dateCreated" => date_created,
|
23
24
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"datePublished" => date_published,
|
24
25
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"dateModified" => date_modified,
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data/spec/fixtures/gtex.xml
CHANGED
@@ -58,7 +58,10 @@
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|
58
58
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<relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>
|
59
59
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<relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier>
|
60
60
|
<relatedIdentifier relationType="IsPartOf" relatedIdentifierType="URL">https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663</relatedIdentifier>
|
61
|
-
</relatedIdentifiers>
|
61
|
+
</relatedIdentifiers>
|
62
|
+
<formats>
|
63
|
+
<format>application/tar</format>
|
64
|
+
</formats>
|
62
65
|
<sizes>
|
63
66
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<size>15.7M</size>
|
64
67
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</sizes>
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@@ -643,6 +643,7 @@ describe Bolognese::Metadata, vcr: true do
|
|
643
643
|
expect(subject.keywords).to eq(["gtex", "annotation", "phenotype", "gene regulation", "transcriptomics"])
|
644
644
|
expect(subject.date_published).to eq("2017")
|
645
645
|
expect(subject.is_supplement_to).to eq("id"=>"https://doi.org/10.1038/nmeth.4407", "type"=>"CreativeWork")
|
646
|
+
expect(subject.content_format).to eq("application/tar")
|
646
647
|
expect(subject.content_size).to eq("15.7M")
|
647
648
|
expect(subject.container_title).to eq("GTEx")
|
648
649
|
expect(subject.publisher).to eq("GTEx")
|
@@ -186,6 +186,7 @@ describe Bolognese::Metadata, vcr: true do
|
|
186
186
|
expect(subject.keywords).to eq(["topmed", "whole genome sequencing"])
|
187
187
|
expect(subject.date_published).to eq("2017-11-30")
|
188
188
|
expect(subject.publisher).to eq("TOPMed")
|
189
|
+
expect(subject.references).to eq("id"=>"https://doi.org/10.23725/2g4s-qv04", "type"=>"Dataset")
|
189
190
|
expect(subject.funding).to eq("id"=>"https://doi.org/10.13039/100000050", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)", "type"=>"Organization")
|
190
191
|
end
|
191
192
|
end
|
@@ -133,6 +133,7 @@ describe Bolognese::Metadata, vcr: true do
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|
133
133
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expect(json["@id"]).to eq("https://doi.org/10.25491/9hx8-ke93")
|
134
134
|
expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium")
|
135
135
|
expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.25491/9hx8-ke93")
|
136
|
+
expect(json["encodingFormat"]).to eq("application/tar")
|
136
137
|
expect(json["contentSize"]).to eq("15.7M")
|
137
138
|
expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz")
|
138
139
|
expect(json["includedInDataCatalog"]).to eq("@id"=>"https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663", "@type"=>"DataCatalog", "name"=>"GTEx")
|
@@ -253,6 +254,7 @@ describe Bolognese::Metadata, vcr: true do
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|
253
254
|
expect(json["contentUrl"]).to eq(["s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram"])
|
254
255
|
expect(json["schemaVersion"]).to eq("http://datacite.org/schema/kernel-4")
|
255
256
|
expect(json["publisher"]).to eq("@type"=>"Organization", "name"=>"TOPMed")
|
257
|
+
expect(json["citation"]).to eq("@id"=>"https://doi.org/10.23725/2g4s-qv04", "@type"=>"Dataset")
|
256
258
|
expect(json["funding"]).to eq("@id"=>"https://doi.org/10.13039/100000050", "@type"=>"Organization", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)")
|
257
259
|
expect(json["provider"]).to eq("@type"=>"Organization", "name"=>"DataCite")
|
258
260
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
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|
1
1
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--- !ruby/object:Gem::Specification
|
2
2
|
name: bolognese
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.13.
|
4
|
+
version: 0.13.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Martin Fenner
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2018-08-
|
11
|
+
date: 2018-08-28 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: maremma
|