RubyGems - bolognese - Versions diffs - 2.2.0 → 2.6.1 - Mend

bolognese 2.2.0 → 2.6.1

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data/spec/fixtures/datacite-empty-sizes.xml DELETED Viewed

@@ -1,57 +0,0 @@
-<?xml version="1.0"?>
-<resource xmlns="http://datacite.org/schema/kernel-2.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-2.2 http://schema.datacite.org/meta/kernel-2.2/metadata.xsd">
-  <identifier identifierType="DOI">10.13116/c6b6060e-0648-4f88-b108-95ea00928171</identifier>
-  <creators>
-    <creator>
-      <creatorName>EvK2 CNR Committee</creatorName>
-    </creator>
-  </creators>
-  <titles>
-    <title>SHARE (Stations at High Altitude for Research on the Environment) Network</title>
-    <title titleType="Subtitle">Urdukas (Baltoro Glacier, Baltistan - Pakistan)</title>
-  </titles>
-  <publisher>EvK2 CNR Committee</publisher>
-  <publicationYear>2011</publicationYear>
-  <subjects>
-    <subject>Environmental research</subject>
-  </subjects>
-  <contributors>
-    <contributor contributorType="Funder">
-      <contributorName>EvK2 CNR Committee</contributorName>
-    </contributor>
-  </contributors>
-  <dates>
-    <date dateType="Valid">
-		</date>
-  </dates>
-  <language>en</language>
-  <resourceType resourceTypeGeneral="Dataset"/>
-  <relatedIdentifiers>
-    <relatedIdentifier relatedIdentifierType="URL" relationType="IsDocumentedBy">http://geonetwork.evk2cnr.org:8080/geonetwork/srv/en/main.home</relatedIdentifier>
-  </relatedIdentifiers>
-  <sizes>
-    <size>
-		</size>
-  </sizes>
-  <formats>
-    <format>text</format>
-  </formats>
-  <version>1.0</version>
-  <rights>
-	</rights>
-  <descriptions>
-    <description descriptionType="Abstract">The Baltoro Glacier, 62 km long, is one of the longest glaciers outside of the Polar Regions. It is located in Baltistan, in the Northern Areas of Pakistan, and runs through part of the Karakoram mountain range. In the middle of the Baltoro glacier there is the campsite of Urdukas located on the trek way to Concordia.
-This automatic weather station was installed, in June 17, 2004 on the Baltoro Glacier, more precisely on a moraine ridge close to the left glacier margin at 3926 m asl.
-Geographical coordinates:
-Latitude: 35deg 43' 41" N
-Longitude: 76deg 17' 10" EThe Urdukas AWS provides data (with a 60 minute time resolution" of the following parameters:
-- air temperature (degC)
-- atmopherich pressure (hPa)
-- relative humidity (%)
-- total precipitation (mm)
-- global solar radiation (W/m2)
-- wind speed (m/s)
-- wind direction (degree)</description>
-  </descriptions>
-</resource>

data/spec/fixtures/datacite-example-ROR-nameIdentifiers.xml DELETED Viewed

@@ -1,125 +0,0 @@
-<?xml version="1.0"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-%s http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-    <identifier identifierType="DOI">10.48321/D1Z60Q</identifier>
-    <creators>
-        <creator>
-            <creatorName nameType="Personal">Ashwini Sukale</creatorName>
-            <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">0000-0001-9998-0117</nameIdentifier>
-            <affiliation affiliationIdentifier="05bp8ka77" affiliationIdentifierScheme="ROR"> Metadata Game Changers </affiliation>
-            <affiliation affiliationIdentifier="grid.268117.b" affiliationIdentifierScheme="GRID">Wesleyan University</affiliation>
-        </creator>
-        <creator>
-            <creatorName nameType="Personal">Erin Robinson</creatorName>
-            <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">https://orcid.org/0000-0001-9998-0114</nameIdentifier>
-            <affiliation schemeURI="https://ror.org" affiliationIdentifier="https://ror.org/05bp8ka05" affiliationIdentifierScheme="ROR"> Metadata Game Changers </affiliation>
-            <affiliation affiliationIdentifier="grid.268117.b" affiliationIdentifierScheme="GRID" schemeURI="https://grid.ac/institutes/">Wesleyan University</affiliation>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">Gump South Pacific Research Station</creatorName>
-            <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org/">https://ror.org/04sk0et52</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">University of Vic</creatorName>
-            <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org">006zjws59</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">University of Kivu</creatorName>
-            <nameIdentifier nameIdentifierScheme="ROR">http://ror.org/01qfhxr31</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">សាកលវិទ្យាល័យកម្ពុជា</creatorName>
-            <nameIdentifier nameIdentifierScheme="RORS">http://ror.org/025e3rc84</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">جامعة زاخۆ</creatorName>
-            <nameIdentifier nameIdentifierScheme="RORS" schemeURI="https://ror.org">05sd1pz50</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Personal">Ashwini S</creatorName>
-            <nameIdentifier nameIdentifierScheme="ORCID">0000-0001-9998-0117</nameIdentifier>
-        </creator>
-         <creator>
-            <creatorName nameType="Personal">Mike B</creatorName>
-            <nameIdentifier nameIdentifierScheme="ORCID"> 0000-0001-9998-0118 </nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Organizational">Gump South Pacific Research Station</creatorName>
-            <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org/">https://ror.org/04sk0et52/</nameIdentifier>
-        </creator>
-        <creator>
-            <creatorName nameType="Personal">Ashwini Sukale</creatorName>
-            <nameIdentifier schemeURI="https://orcid.org/" nameIdentifierScheme="ORCID">https://orcid.org/0000-0001-9998-0117/</nameIdentifier>
-        </creator>
-    </creators>
-    <titles>
-        <title xml:lang="en-US">Genomic Standards Consortium (GSC) Island Sampling Day: Moorea Reef to Ridges Genomic Transect</title>
-    </titles>
-    <publisher xml:lang="en-US">DMPHub</publisher>
-    <publicationYear>2022</publicationYear>
-    <contributors>
-        <contributor contributorType="Producer">
-            <contributorName nameType="Organizational"> Nawroz University </contributorName>
-            <nameIdentifier nameIdentifierScheme="ROR">04gp75d48</nameIdentifier>
-        </contributor>
-        <contributor contributorType="ProjectLeader">
-            <contributorName nameType="Personal">Neil Davies</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0001-8085-5014</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/01an7q238" affiliationIdentifierScheme="ROR"> University of California, Berkeley </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectLeader">
-            <contributorName nameType="Personal">Ramona Walls</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0001-8815-0078</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/03m2x1q45" affiliationIdentifierScheme="ROR"> University of Arizona </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectLeader">
-            <contributorName nameType="Personal">Serge Planes</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0002-5689-5371</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/02feahw73" affiliationIdentifierScheme="ROR"> French National Centre for Scientific Research </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectLeader">
-            <contributorName nameType="Personal">Chris Meyer</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0003-2501-7952</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/01pp8nd67" affiliationIdentifierScheme="ROR"> Smithsonian Institution </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectLeader">
-            <contributorName nameType="Personal">Lynn Schriml</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0001-8910-9851</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/04rq5mt64" affiliationIdentifierScheme="ROR"> University of Maryland, Baltimore </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectMember">
-            <contributorName nameType="Personal">Scott Tighe</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0002-3988-0741</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/0155zta11" affiliationIdentifierScheme="ROR"> University of Vermont </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectMember">
-            <contributorName nameType="Personal">Pier Luigi Buttigieg</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0002-4366-3088</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/02h2x0161" affiliationIdentifierScheme="ROR"> GEOMAR Helmholtz Centre for Ocean Research Kiel </affiliation>
-        </contributor>
-        <contributor contributorType="ProjectMember">
-            <contributorName nameType="Personal">Raïssa Meyer</contributorName>
-            <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="https://orcid.org/">https://orcid.org/0000-0002-2996-719X</nameIdentifier>
-            <affiliation affiliationIdentifier="https://ror.org/032e6b942" affiliationIdentifierScheme="ROR"> Alfred Wegener Institute for Polar and Marine Research </affiliation>
-        </contributor>
-        <contributor contributorType="Sponsor">
-            <contributorName nameType="Organizational">University of Greenland (https://www.uni.gl/)</contributorName>
-            <nameIdentifier nameIdentifierScheme="ROR" schemeURI="https://ror.org/">https://ror.org/00t5j6b61</nameIdentifier>
-        </contributor>
-    </contributors>
-    <language>en-US</language>
-    <resourceType resourceTypeGeneral="OutputManagementPlan">Data Management Plan</resourceType>
-    <descriptions>
-        <description xml:lang="en-US" descriptionType="Abstract"> &lt;p&gt;Here we describe a project that supports the mission of the Genomic Standards Consortium (GSC) and contributes to the “Ocean Biomolecular Observations Network” (OBON) and the “Ocean Best Practice System” (OBPS - Omics Task Team), flagship programs of the UN Ocean Decade of Ocean Science for Sustainable Development. The project serves as a test case for two related infrastructure projects that aim to improve standards, policies, and best practices in sample collection: Sampling Nature (SN) Research Coordination Network and the Internet of Samples (iSamples).&lt;/p&gt;  &lt;p&gt;&lt;strong&gt;The project’s primary goal (first paper) is methodologica&lt;/strong&gt;l: (i) to demonstrate the value of genomic standards for both genomic research and secondary interdisciplinary research, (ii) to highlight the importance of data curation workflows that follow FAIR+CARE principles maximizing the potential for appropriate reuse of data and material samples, (iii) to illustrate the challenges that remain in implementing those standards - including ethical, legal, and social aspects, and (iv) to demonstrate some of the tools, infrastructures, and best-practices available for overcoming these challenges. This paper will include all the elements of a data paper (primary publication of the initial data collected), but with broader discussion around it as a use case for metadata standards and best practices in multi-omic sampling.&lt;/p&gt;  &lt;p&gt;&lt;strong&gt;The project’s secondary goal (second paper) is to address research questions including&lt;/strong&gt;: (1) To what extent can one day of environmental sampling, and subsequent multi-omic analyses, characterize the ecological state of an island (coupled marine-terrestrial ecosystem)? (2) To what extent might such surveys serve as baselines for futuromic study (future analysis of biomolecules from the material samples archived), and (3) if repeated, could these surveys help address long-term changes in genomic biodiversity? (4) How does marine and terrestrial eDNA change across a transect? Moorea is one of the most well-described biotas in the world and has one of the longest and most intensive time-series of ecological data, particularly for coral reef ecosystems. It thus serves as a powerful calibration site for such a study.&lt;/p&gt;  &lt;p&gt;&lt;br&gt;&lt;strong&gt;The project’s broader impact goal is public outreach &lt;/strong&gt;– if possible engage local citizen scientists/schools, ideally through Fare Natura (ecomuseum at entrance to the Opunohu Valley. (Also perhaps local Associations that might be interested, e.g., Te Pu Atitia). Sampling Nature will produce an outreach videos based on this Island Sampling Day.&lt;/p&gt; </description>
-    </descriptions>
-    <fundingReferences>
-        <fundingReference>
-            <funderName>Genomic Standards Consortium</funderName>
-        </fundingReference>
-    </fundingReferences>
-    <relatedIdentifiers>
-        <relatedIdentifier relationType="IsMetadataFor" relatedIdentifierType="URL"> https://dmptool.org/api/v2/plans/74309.pdf </relatedIdentifier>
-        <relatedIdentifier relationType="Cites" relatedIdentifierType="URL"> https://n2t.net/ark:/21547/EBW2 </relatedIdentifier>
-        <relatedIdentifier relationType="Cites" relatedIdentifierType="URL"> https://docs.google.com/document/d/1EYgEEUroMBiTNc5Px11_44G-B17JtTgyssyNkK3hV_U/edit#heading=h.ckwz8v2yry1q </relatedIdentifier>
-    </relatedIdentifiers>
-</resource>

data/spec/fixtures/datacite-example-affiliation.xml DELETED Viewed

@@ -1,114 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.2/metadata.xsd">
-  <identifier identifierType="DOI">10.5072/example-full</identifier>
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-      <creatorName nameType="Personal">Miller, Elizabeth</creatorName>
-      <givenName>Elizabeth</givenName>
-      <familyName>Miller</familyName>
-      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID">0000-0001-5000-0007</nameIdentifier>
-      <affiliation affiliationIdentifier="https://ror.org/04wxnsj81" affiliationIdentifierScheme="ROR">DataCite</affiliation>
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-      <creatorName nameType="Personal">Carberry, Josiah</creatorName>
-      <givenName>Josiah</givenName>
-      <familyName>Carberry</familyName>
-      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID">0000-0002-1825-0097</nameIdentifier>
-      <affiliation affiliationIdentifier="https://ror.org/05gq02987" affiliationIdentifierScheme="ROR">Brown University</affiliation>
-      <affiliation affiliationIdentifier="grid.268117.b" affiliationIdentifierScheme="GRID" schemeURI="https://grid.ac/institutes/">Wesleyan University</affiliation>
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-    <creator>
-      <creatorName nameType="Organizational">The Psychoceramics Study Group</creatorName>
-      <affiliation affiliationIdentifier="https://ror.org/05gq02987" affiliationIdentifierScheme="ROR">Brown University</affiliation>
-    </creator>
-  </creators>
-  <titles>
-    <title xml:lang="en-US">Full DataCite XML Example</title>
-    <title xml:lang="en-US" titleType="Subtitle">Demonstration of DataCite Properties.</title>
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-  <publisher xml:lang="en">DataCite</publisher>
-  <publicationYear>2014</publicationYear>
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-    <relatedIdentifier relatedIdentifierType="URL" relationType="HasMetadata" relatedMetadataScheme="citeproc+json" schemeURI="https://github.com/citation-style-language/schema/raw/master/csl-data.json">https://data.datacite.org/application/citeproc+json/10.5072/example-full</relatedIdentifier>
-    <relatedIdentifier relatedIdentifierType="arXiv" relationType="IsReviewedBy" resourceTypeGeneral="Text">arXiv:0706.0001</relatedIdentifier>
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-  <descriptions>
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-      XML example of all DataCite Metadata Schema v4.2 properties.
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-      <geoLocationPlace>Atlantic Ocean</geoLocationPlace>
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data/spec/fixtures/datacite-example-ancientdates-v4.3.xml DELETED Viewed

@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.3/metadata.xsd">
-	<identifier identifierType="DOI">10.5072/0945113</identifier>
-	<creators>
-		<creator>
-			<creatorName nameType="Personal">Augustus</creatorName>
-			<nameIdentifier schemeURI="http://www.isni.org/" nameIdentifierScheme="ISNI">0000000121227317</nameIdentifier>
-		</creator>
-	</creators>
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-		<title xml:lang="en">Silver Denarius of Augustus, Emerita, 25 BC - 23 BC 1969.222.1267</title>
-	</titles>
-	<publisher xml:lang="en">American Numismatic Society</publisher>
-	<publicationYear>2010</publicationYear>
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-		<date dateType="Created" dateInformation="from 25 BC to 23 BC">-0024/-0022</date>
-	</dates>
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data/spec/fixtures/datacite-example-complicated-tba.xml DELETED Viewed

@@ -1,56 +0,0 @@
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-      <creatorName>つまらないものですが</creatorName>
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data/spec/fixtures/datacite-example-complicated-v3.0.xml DELETED Viewed

@@ -1,48 +0,0 @@
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-			<creatorName>Smith, John</creatorName>
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-		<creator>
-			<creatorName>つまらないものですが</creatorName>
-			<nameIdentifier nameIdentifierScheme="ISNI" schemeURI="http://isni.org/isni/">0000000134596520</nameIdentifier>
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-	<titles>
-		<title>Właściwości rzutowań podprzestrzeniowych</title>
-		<title titleType="TranslatedTitle">Translation of Polish titles</title>
-	</titles>
-	<publisher>Springer</publisher>
-	<publicationYear>2010</publicationYear>
-	<subjects>
-		<subject subjectScheme="DDC">830 German &amp; related literatures</subject>
-		<subject>Polish Literature</subject>
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-			<contributorName>Doe, John</contributorName>
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data/spec/fixtures/datacite-example-complicated-v4.0.xml DELETED Viewed

@@ -1,54 +0,0 @@
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-  <titles>
-    <title>Właściwości rzutowań podprzestrzeniowych</title>
-    <title titleType="TranslatedTitle">Translation of Polish titles</title>
-  </titles>
-  <publisher>Springer</publisher>
-  <publicationYear>2010</publicationYear>
-  <subjects>
-    <subject subjectScheme="DDC">830 German &amp; related literatures</subject>
-    <subject>Polish Literature</subject>
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-      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-5393-1421</nameIdentifier>
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-  <language>GER</language>
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data/spec/fixtures/datacite-example-complicated-v4.1.xml DELETED Viewed

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-    <title titleType="TranslatedTitle">Translation of Polish titles</title>
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data/spec/fixtures/datacite-example-dissertation-v4.4.xml DELETED Viewed

@@ -1,56 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.4/metadata.xsd">
-  <identifier identifierType="DOI">10.5072/100044</identifier>
-  <creators>
-    <creator>
-      <creatorName nameType="Personal">Luo, R</creatorName>
-    </creator>
-    <creator>
-      <creatorName nameType="Personal">Liu, B</creatorName>
-    </creator>
-    <creator>
-      <creatorName nameType="Personal">Xie, Y</creatorName>
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-    <creator>
-      <creatorName nameType="Personal">Li, Z</creatorName>
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-    <title xml:lang="en">
-      Software and supporting material for "SOAPdenovo2: An empirically improved memory-efficient short read de novo assembly"
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-  <publisher xml:lang="en">GigaScience Database</publisher>
-  <publicationYear>2012</publicationYear>
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-    <subject xml:lang="en">Computer Program</subject>
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-    <date dateType="Available">2012-12-13</date>
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-    <size>31 MB</size>
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-  <descriptions>
-    <description xml:lang="en" descriptionType="Abstract">
-      SOAPdenovo2 is the latest de novo genome assembly package from BGI's SOAP (short oligonucleotide analysis package) suite of tools (homepage here: http://soap.genomics.org.cn/). Compared to SOAPdenovo1, this new version has the advantage of a new
-      algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closure, and is optimized for large genomes. Using new
-      sequencing data from the YH (Homo sapiens) diploid genome - the first sequenced Han Chinese individual, an updated assembly was produced (see dataset here: doi:10.5524/100038), with the N50 scores for the contig and scaffold being 3-fold and 50-fold
-      longer, respectively, than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 times lower during the point of largest memory consumption. Benchmarking with Assemblathon1 and GAGE datasets
-      shows that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo1 and is competitive to other assemblers on both assembly length and accuracy. In order to facilitate readers to repeat and recreate these findings, configured packages with the
-      compressed pipelines containing all of the necessary shell scripts and tools are available from the BGI FTP server (ftp://public.genomics.org.cn/BGI/SOAPdenovo2). The latest version of SOAPdenovo2 is available from Sourceforge:
-      http://soapdenovo2.sourceforge.net/ These pipelines will also soon be made available from our data platform as Galaxy workflows: http://galaxy.cbiit.cuhk.edu.hk/
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