bolognese 0.10.20 → 0.10.21
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- checksums.yaml +4 -4
- data/Gemfile.lock +3 -3
- data/lib/bolognese/author_utils.rb +4 -1
- data/lib/bolognese/readers/datacite_reader.rb +1 -1
- data/lib/bolognese/version.rb +1 -1
- data/spec/fixtures/datacite_malformed_creator.xml +52 -0
- data/spec/fixtures/gtex.xml +1 -0
- data/spec/readers/datacite_reader_spec.rb +8 -0
- metadata +3 -2
checksums.yaml
CHANGED
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@@ -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:
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3
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+
metadata.gz: 2233cdf85f7a47f0fa6f92ea880af3c4f565ad0c4b98308aa939940c27a6d7f7
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4
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+
data.tar.gz: 7f1a426c3c54522173c39cd1c333429c55e2fff2348759646f8f5ea8fda6d808
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 585fd910b3e5e6175888b1cdcdadc7d37967f57f9ec4f316d70d8343d96f1cff5fa875308e38712916d9cf87a56c55288ba2cc0b00f2e3b28766c84d6428f059
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7
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+
data.tar.gz: e2403467fe285adaa8237dd13f3bd16600648e969ddf27618b1803977bea07335aad2d4116646468b9398d6d13f7ad310569fafb27738ecd6e490e53728db743
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data/Gemfile.lock
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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PATH
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2
2
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remote: .
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3
3
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specs:
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4
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-
bolognese (0.10.
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4
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+
bolognese (0.10.21)
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5
5
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activesupport (>= 4.2.5, < 6)
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6
6
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benchmark_methods (~> 0.7)
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7
7
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bibtex-ruby (~> 4.1)
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@@ -78,7 +78,7 @@ GEM
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78
78
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loofah (2.2.2)
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79
79
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crass (~> 1.0.2)
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80
80
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nokogiri (>= 1.5.9)
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81
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-
maremma (4.0.
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81
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+
maremma (4.0.10)
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82
82
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activesupport (>= 4.2.5, < 6)
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83
83
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addressable (>= 2.3.6)
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84
84
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builder (~> 3.2, >= 3.2.2)
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@@ -94,7 +94,7 @@ GEM
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94
94
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multi_json (1.13.1)
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95
95
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multipart-post (2.0.0)
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96
96
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namae (0.11.3)
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|
97
|
-
nokogiri (1.8.
|
|
97
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+
nokogiri (1.8.3)
|
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98
98
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mini_portile2 (~> 2.3.0)
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99
99
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oj (2.18.5)
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100
100
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postrank-uri (1.0.23)
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@@ -11,7 +11,10 @@ module Bolognese
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11
11
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}
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12
12
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13
13
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def get_one_author(author)
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14
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-
if author.fetch("
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14
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+
if author.fetch("creatorName", nil).is_a?(Array)
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15
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+
# malformed XML
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16
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+
return nil
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17
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+
elsif author.fetch("type", nil).present?
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15
18
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type = author.fetch("type").titleize
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16
19
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elsif author.fetch("creatorName", nil).is_a?(Hash)
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17
20
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type = author.dig("creatorName", "nameType") == "Organizational" ? "Organization" : "Person"
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@@ -109,7 +109,7 @@ module Bolognese
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109
109
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"url" => options.fetch(:url, nil),
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110
110
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"title" => title,
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111
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"alternate_name" => alternate_name,
|
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112
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-
"author" => get_authors(meta.dig("creators", "creator")),
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112
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+
"author" => get_authors(Array.wrap(meta.dig("creators", "creator"))),
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113
113
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"editor" => get_authors(Array.wrap(meta.dig("contributors", "contributor")).select { |r| r["contributorType"] == "Editor" }),
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114
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"container_title" => container_title,
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115
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"publisher" => meta.fetch("publisher", nil),
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data/lib/bolognese/version.rb
CHANGED
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@@ -0,0 +1,52 @@
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1
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+
<?xml version="1.0" encoding="UTF-8"?>
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2
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+
<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
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3
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+
<identifier identifierType="DOI">10.25670/oi2018-001on</identifier>
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4
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<titles>
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5
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<title xml:lang="sl">Učinkovitost kanabinoidov pri zdravljenju raka</title>
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6
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+
<title xml:lang="sl" titleType="Subtitle">mit ali resnica</title>
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7
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+
<title xml:lang="en" titleType="TranslatedTitle">Therapeutic Efficacy of Cannabinoids in Cancer Treatment</title>
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8
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+
<title xml:lang="en" titleType="Subtitle">Myth or Fact</title>
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9
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+
</titles>
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10
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+
<creators>
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11
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+
<creator>
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12
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+
<creatorName nameType="Personal">Grošelj, Blaž</creatorName>
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13
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+
<givenName>Blaž</givenName>
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14
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+
<familyName>Grošelj</familyName>
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15
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+
<affiliation>Onkološki inštitut Ljubljana</affiliation>
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16
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+
<creatorName nameType="Personal">Oražem, Miha </creatorName>
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17
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+
<givenName>Miha</givenName>
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18
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+
<familyName>Oražem</familyName>
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19
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+
<affiliation>Onkološki inštitut Ljubljana</affiliation>
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20
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+
<creatorName nameType="Personal">Kovač, Viljem</creatorName>
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21
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<givenName>Viljem</givenName>
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22
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+
<familyName>Kovač</familyName>
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23
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+
<affiliation>Onkološki inštitut Ljubljana</affiliation>
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24
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+
</creator>
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25
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+
</creators>
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26
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+
<publisher>Onkološki inštitut Ljubljana</publisher>
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27
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+
<publicationYear>2018</publicationYear>
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28
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+
<resourceType resourceTypeGeneral="Text">Journal Article</resourceType>
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29
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+
<subjects>
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30
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+
<subject subjectScheme="DDC">610 Medical sciences; Medicine</subject>
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31
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+
<subject xml:lang="en">cancer</subject>
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32
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+
<subject xml:lang="en">cannabinoids</subject>
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|
33
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+
</subjects>
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34
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+
<dates>
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35
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+
<date dateType="Issued">2018-06-20</date>
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36
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+
</dates>
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37
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+
<relatedIdentifiers>
|
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38
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+
<relatedIdentifier relatedIdentifierType="ISSN" relationType="IsPartOf">1581-3215</relatedIdentifier>
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39
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+
</relatedIdentifiers>
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40
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+
<descriptions>
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41
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+
<description xml:lang="en" descriptionType="Other">The use of cannabis derivatives (cannabinoids) in oncology is sometimes indicated in the symptomatic treatment of nausea and vomiting, in pain management and in some neuropsychiatric disorders. In the recent years, there has been a growing interest in determining the anticancer effects of cannabinoids. Based on our clinical experience, we know that many patients use cannabinoids, among them also those with the aim of curing their disease. But despite the extensive and convincing data on the anticancer properties of cannabinoids from in vitro studies on cell cultures and studies on animal models, these properties have not (yet) been confirmed in a clinical trial. This paper summarises the currently available data on the potential of cannabinoid use in the clinical practice of oncology.</description>
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42
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+
<description descriptionType="SeriesInformation" xml:lang="sl">Onkologija, leto XXII, št. 1, junij 2018</description>
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43
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+
<description descriptionType="SeriesInformation" xml:lang="en">Onkologija, Volume XXII, No. 1, June 2018</description>
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44
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+
</descriptions>
|
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45
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+
<language>sl</language>
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46
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+
<formats>
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47
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+
<format>pdf</format>
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48
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+
</formats>
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49
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+
<rightsList>
|
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50
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+
<rights rightsURI="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license (CC BY 4.0)</rights>
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51
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+
</rightsList>
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52
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+
</resource>
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data/spec/fixtures/gtex.xml
CHANGED
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@@ -57,6 +57,7 @@
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57
57
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<relatedIdentifier relationType="Documents" relatedIdentifierType="URL">http://identifiers.org/dbgap:phs000424.v7.p2</relatedIdentifier>
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58
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<relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>
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59
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<relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier>
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60
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+
<relatedIdentifier relationType="IsPartOf" relatedIdentifierType="URL">https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663</relatedIdentifier>
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60
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</relatedIdentifiers>
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61
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<sizes>
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62
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<size>15.7M</size>
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@@ -435,6 +435,14 @@ describe Bolognese::Metadata, vcr: true do
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435
435
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expect(subject.errors).to eq("4:0: ERROR: Element '{http://datacite.org/schema/kernel-4}creators': Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ).")
|
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436
436
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end
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437
437
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438
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+
it "malformed creator" do
|
|
439
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+
input = fixture_path + "datacite_malformed_creator.xml"
|
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440
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+
subject = Bolognese::Metadata.new(input: input, regenerate: false)
|
|
441
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+
expect(subject.author).to be_nil
|
|
442
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+
expect(subject.valid?).to be false
|
|
443
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+
expect(subject.errors).to eq("16:0: ERROR: Element '{http://datacite.org/schema/kernel-4}creatorName': This element is not expected. Expected is ( {http://datacite.org/schema/kernel-4}affiliation ).")
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444
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+
end
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445
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+
|
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438
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it "dissertation" do
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439
447
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input = "10.3204/desy-2014-01645"
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440
448
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subject = Bolognese::Metadata.new(input: input)
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metadata
CHANGED
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@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: bolognese
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3
3
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version: !ruby/object:Gem::Version
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4
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-
version: 0.10.
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4
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+
version: 0.10.21
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5
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platform: ruby
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6
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authors:
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7
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- Martin Fenner
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8
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autorequire:
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9
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bindir: bin
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10
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cert_chain: []
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11
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-
date: 2018-06-
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11
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+
date: 2018-06-21 00:00:00.000000000 Z
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12
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dependencies:
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13
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- !ruby/object:Gem::Dependency
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14
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name: maremma
|
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@@ -555,6 +555,7 @@ files:
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555
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- spec/fixtures/datacite.json
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556
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- spec/fixtures/datacite.xml
|
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557
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- spec/fixtures/datacite_dataset.xml
|
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558
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+
- spec/fixtures/datacite_malformed_creator.xml
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558
559
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- spec/fixtures/datacite_missing_creator.xml
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559
560
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- spec/fixtures/datacite_software.json
|
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560
561
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- spec/fixtures/datacite_software_missing_comma.json
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