bolognese 2.3.6 → 2.3.9

data/spec/find_from_format_spec.rb

@@ -1,114 +0,0 @@
-# frozen_string_literal: true
-
-require 'spec_helper'
-require 'bolognese/cli'
-
-describe Bolognese::CLI do
-  context "find_from_format_by_id", vcr: true do
-    let(:subject) do
-      described_class.new
-    end
-
-    it "crossref" do
-      id = "https://doi.org/10.7554/eLife.01567"
-      expect(subject.find_from_format_by_id(id)).to eq("crossref")
-    end
-
-    it "datacite" do
-      id = "https://doi.org/10.5061/DRYAD.8515"
-      expect(subject.find_from_format_by_id(id)).to eq("datacite")
-    end
-
-    it "medra" do
-      id = "https://doi.org/10.1392/roma081203"
-      expect(subject.find_from_format_by_id(id)).to eq("medra")
-    end
-
-    it "kisti" do
-      id = "https://doi.org/10.5012/bkcs.2013.34.10.2889"
-      expect(subject.find_from_format_by_id(id)).to eq("kisti")
-    end
-
-    it "jalc" do
-      id = "https://doi.org/10.11367/grsj1979.12.283"
-      expect(subject.find_from_format_by_id(id)).to eq("jalc")
-    end
-
-    it "op" do
-      id = "https://doi.org/10.2791/81962"
-      expect(subject.find_from_format_by_id(id)).to eq("op")
-    end
-
-    it "codemeta" do
-      id = "https://github.com/datacite/maremma"
-      expect(subject.find_from_format_by_id(id)).to eq("codemeta")
-    end
-
-    it "npm" do
-      id = "https://github.com/datacite/bracco/blob/master/package.json"
-      expect(subject.find_from_format_by_id(id)).to eq("npm")
-    end
-
-    it "schema_org" do
-      id = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/GAOC03"
-      expect(subject.find_from_format_by_id(id)).to eq("schema_org")
-    end
-  end
-
-  context "find_from_format_by_filename" do
-    let(:subject) do
-      described_class.new
-    end
-
-    it "npm" do
-      filename = "package.json"
-      expect(subject.find_from_format_by_filename(filename)).to eq("npm")
-    end
-  end
-
-  context "find_from_format_by_string" do
-    let(:subject) do
-      described_class.new
-    end
-
-    it "crossref" do
-      string = IO.read(fixture_path + 'crossref.xml').strip
-      expect(subject.find_from_format_by_string(string)).to eq("crossref")
-    end
-
-    it "datacite" do
-      string = IO.read(fixture_path + 'datacite.xml').strip
-      expect(subject.find_from_format_by_string(string)).to eq("datacite")
-    end
-
-    it "datacite namespaced" do
-      string = IO.read(fixture_path + 'ns0.xml').strip
-      expect(subject.find_from_format_by_string(string)).to eq("datacite")
-    end
-
-    it "codemeta" do
-      string = IO.read(fixture_path + 'codemeta.json').strip
-      expect(subject.find_from_format_by_string(string)).to eq("codemeta")
-    end
-
-    it "schema_org" do
-      string = IO.read(fixture_path + 'schema_org_topmed.json').strip
-      expect(subject.find_from_format_by_string(string)).to eq("schema_org")
-    end
-
-    it "ris" do
-      string = IO.read(fixture_path + 'crossref.ris').strip
-      expect(subject.find_from_format_by_string(string)).to eq("ris")
-    end
-
-    it "ris from pure" do
-      string = IO.read(fixture_path + 'pure.ris').strip
-      expect(subject.find_from_format_by_string(string)).to eq("ris")
-    end
-
-    it "bibtex" do
-      string = IO.read(fixture_path + 'crossref.bib').strip
-      expect(subject.find_from_format_by_string(string)).to eq("bibtex")
-    end
-  end
-end

data/spec/fixtures/aida.json

@@ -1,82 +0,0 @@
-{
-  "@context": "http://schema.org",
-  "@type": "Dataset",
-  "@id": "https://doi.org/10.23698/aida/drov",
-  "name": "Ovary data from the Visual Sweden project DROID",
-  "about": "Pathology",
-  "url": "https://doi.aida.medtech4health.se/10.23698/aida/drov",
-  "author": [{
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0003-1298-517X",
-    "givenName": "Karin",
-    "familyName": "Lindman",
-    "name": "Karin Lindman"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/",
-    "givenName": "Jerónimo",
-    "familyName": "Rose",
-    "name": "Jerónimo F. Rose"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/",
-    "givenName": "Martin",
-    "familyName": "Lindvall",
-    "name": "Martin Lindvall"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0001-7250-234X",
-    "givenName": "Caroline",
-    "familyName": "Bivik Stadler",
-    "name": "Caroline Bivik Stadler"
-  }],
-  "publisher": {
-    "@type": "Organization",
-    "name": "AIDA"
-  },
-  "copyrightYear": 2019,
-  "copyrightHolder": [{
-    "@type": "Organization",
-    "name": "Linköping University",
-    "url": "https://liu.se/"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0002-9368-0177",
-    "givenName": "Claes",
-    "familyName": "Lundström",
-    "name": "Claes Lundström"
-  }],
-  "provider": [{
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0002-0128-870X",
-    "name": "Karin Lindman",
-    "email": "Karin.Lindman@regionostergotland.se"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0002-9368-0177",
-    "name": "Claes Lundstrom",
-    "email": "claes.lundstrom@liu.se"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0001-7250-234X",
-    "givenName": "Caroline",
-    "familyName": "Bivik Stadler",
-    "name": "Caroline Bivik Stadler"
-  }, {
-    "@type": "Person",
-    "@id": "https://orcid.org/0000-0001-6443-3604",
-    "name": "Joel Hedlund",
-    "email": "joel.hedlund@liu.se"
-  }],
-  "dateCreated": "2019-01-09",
-  "datePublished": "2019-01-09",
-  "dateModified": "2019-01-09",
-  "keywords": "pathology, whole slide imaging, annotated",
-  "version": "1.0",
-  "description": "This dataset consists of 174 WSI ovary whole slide images (WSI): 158\nmalignant and 16 benign. Eight of the most common, histological definable\ntumour types were annotated: high grade serous carcinoma (HGSC), low grade\nserous carcinoma (LGSC), clear cell carcinoma (CC), endometrioid\nadenocarcinoma (EN), metastastic serous carcinoma (MS), metastatic other\n(MO), serous borderline tumor (SB) and mucinous borderline tumor (MB). Also\nnormal ovarian tissue were annotated. 11258 separate annotations were made.\nFor the benign structures only the epithelial structures, stroma and support\ntissue were annotated.\n",
-  "license": {
-    "name": "Restricted access",
-    "id": "https://datasets.aida.medtech4health.se/10.23698/aida/drov#license"
-  },
-  "citation": null
-}

data/spec/fixtures/cgimp_package.json

@@ -1,18 +0,0 @@
-{
-  "name": "fullstack_app",
-  "version": "1.0.0",
-  "main": "index.js",
-  "scripts": {
-    "start": "concurrently \"sudo -i service elasticsearch start\" \"cd backend && node --max_old_space_size=8000 server.js\" \"cd client && npm start\""
-  },
-  "keywords": [],
-  "author": "",
-  "license": "ISC",
-  "dependencies": {
-    "concurrently": "^4.1.0",
-    "d3": "^5.9.2",
-    "monk": "^6.0.6"
-  },
-  "devDependencies": {},
-  "description": ""
-}

data/spec/fixtures/cit_package.json

@@ -1,19 +0,0 @@
-{
-  "name": "CITapp",
-  "description": "Concealed Information Test app",
-  "version": "1.1.0",
-  "scripts": {
-    "test": "karma start test/karma.conf.js --single-run"
-  },
-  "devDependencies": {
-    "jasmine-core": "*",
-    "karma": "*",
-    "karma-chrome-launcher": "^2.2.0",
-    "karma-cli": "*",
-    "karma-fixture": "^0.2.6",
-    "karma-html2js-preprocessor": "*",
-    "karma-jasmine": "*",
-    "karma-phantomjs-launcher": "*",
-    "phantomjs-prebuilt": "*"
-  }
-}

data/spec/fixtures/citeproc-no-author.json

@@ -1,26 +0,0 @@
-{
-    "type": "post-weblog",
-    "id": "https://doi.org/10.5438/4k3m-nyvg",
-    "DOI": "10.5438/4k3m-nyvg",
-    "URL": "https://blog.datacite.org/eating-your-own-dog-food",
-    "title": "Eating your own Dog Food",
-    "container-title": "DataCite Blog",
-    "publisher": "DataCite",
-    "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
-    "categories": [
-        "Phylogeny",
-        "Malaria",
-        "Parasites",
-        "Taxonomy",
-        "Mitochondrial genome",
-        "Africa",
-        "Plasmodium"
-    ],
-    "issued": {
-        "date-parts": [
-            [
-                2016, 12, 20
-            ]
-        ]
-    }
-}

data/spec/fixtures/citeproc-no-categories.json

@@ -1,21 +0,0 @@
-{
-    "type": "post-weblog",
-    "id": "https://doi.org/10.5072/4k3m-nyvg",
-    "DOI": "10.5072/4k3m-nyvg",
-    "URL": "https://blog.datacite.org/eating-your-own-dog-food",
-    "title": "Eating your own Dog Food",
-    "container-title": "DataCite Blog",
-    "publisher": "DataCite",
-    "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
-    "issued": {
-        "date-parts": [
-            [
-                2016, 12, 20
-            ]
-        ]
-    },
-    "author": [{
-        "family": "Fenner",
-        "given": "Martin"
-    }]
-}

data/spec/fixtures/citeproc.json

@@ -1,36 +0,0 @@
-{
-    "type": "post-weblog",
-    "id": "https://doi.org/10.5438/4k3m-nyvg",
-    "DOI": "10.5438/4k3m-nyvg",
-    "URL": "https://blog.datacite.org/eating-your-own-dog-food",
-    "title": "Eating your own Dog Food",
-    "container-title": "DataCite Blog",
-    "publisher": "DataCite",
-    "abstract": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...",
-    "categories": [
-        "Phylogeny",
-        "Malaria",
-        "Parasites",
-        "Taxonomy",
-        "Mitochondrial genome",
-        "Africa",
-        "Plasmodium"
-    ],
-    "issued": {
-        "date-parts": [
-            [
-                2016, 12, 20
-            ]
-        ]
-    },
-    "author": [{
-        "family": "Fenner",
-        "given": "Martin",
-        "literal": "Fenner, Martin"
-    }],
-    "translator": [{
-        "family": "Ross",
-        "given": "Cody",
-        "literal": "Ross, Cody"
-    }]
-}

data/spec/fixtures/codemeta.json

@@ -1,86 +0,0 @@
-{
-	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
-	"@type": "SoftwareSourceCode",
-	"agents": [{
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"email": "jones@nceas.ucsb.edu",
-		"name": "Matt Jones",
-		"affiliation": "NCEAS",
-		"mustBeCited": true,
-		"isMaintainer": true,
-		"isRightsHolder": true,
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": [
-				"originator",
-				"resourceProvider"
-			]
-		}
-	}, {
-		"@id": "http://orcid.org/0000-0002-2192-403X",
-		"@type": "person",
-		"email": "slaughter@nceas.ucsb.edu",
-		"name": "Peter Slaughter",
-		"affiliation": "NCEAS",
-		"mustBeCited": true,
-		"isMaintainer": false,
-		"isRightsHolder": false,
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": "contributor"
-		}
-	}, {
-		"@type": "organization",
-		"email": "info@ucop.edu",
-		"name": "University of California, Santa Barbara",
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": "copyrightHolder"
-		}
-	}],
-	"depends": {
-		"@type": "URL",
-		"@value": "https://github.com/ropensci/datapack"
-	},
-	"identifier": "http://dx.doi.org/10.5063/F1M61H5X",
-	"codeRepository": "https://github.com/DataONEorg/rdataone",
-	"controlledTem": "software",
-	"datePublished": "2016-05-27",
-	"dateModified": "2016-05-27",
-	"dateCreated": "2016-05-27",
-	"description": "Provides read and write access to data and metadata from the DataONE network of data repositories.Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository.Users can also insert and update data objects on repositories that support these methods.",
-	"downloadLink": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz",
-	"funding": "National Science Foundation grant #012345678",
-	"isAutomatedBuild": false,
-	"issueTracker": "https://github.com/DataONEorg/rdataone/issues",
-	"licenseId": "Apache-2.0",
-	"publisher": "https://cran.r-project.org",
-	"tags": [
-		"data sharing",
-		"data repository",
-		"DataONE"
-	],
-	"title": "R Interface to the DataONE REST API",
-	"version": "2.0.0",
-	"uploadedBy": {
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"email": "mbjones@nceas.ucsb.edu",
-		"name": "Matt Jones"
-	},
-	"programmingLanguage": {
-		"name": "R",
-		"version": "> 3.1.1",
-		"URL": "https://www.r-project.org"
-	},
-	"readme": "https://github.com/DataONEorg/rdataone/README.md",
-	"relatedPublications": "ISBN:0201703726",
-	"relationship": {
-		"relationshipType": "isPartOf",
-		"relatedIdentifier": "urn:uuid:F1A0A7AF-ECF3-4C7D-B675-7C6949963995",
-		"relatedIdentifierType": "UUID"
-	},
-	"softwarePaperCitationIdentifiers": "http://doi.org/0000/0000",
-	"zippedCode": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz"
-}

data/spec/fixtures/codemeta_v2.json

@@ -1,86 +0,0 @@
-{
-	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
-	"@type": "SoftwareSourceCode",
-	"authors": [{
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"email": "jones@nceas.ucsb.edu",
-		"name": "Matt Jones",
-		"affiliation": "NCEAS",
-		"mustBeCited": true,
-		"isMaintainer": true,
-		"isRightsHolder": true,
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": [
-				"originator",
-				"resourceProvider"
-			]
-		}
-	}, {
-		"@id": "http://orcid.org/0000-0002-2192-403X",
-		"@type": "person",
-		"email": "slaughter@nceas.ucsb.edu",
-		"name": "Peter Slaughter",
-		"affiliation": "NCEAS",
-		"mustBeCited": true,
-		"isMaintainer": false,
-		"isRightsHolder": false,
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": "contributor"
-		}
-	}, {
-		"@type": "organization",
-		"email": "info@ucop.edu",
-		"name": "University of California, Santa Barbara",
-		"role": {
-			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
-			"roleCode": "copyrightHolder"
-		}
-	}],
-	"depends": {
-		"@type": "URL",
-		"@value": "https://github.com/ropensci/datapack"
-	},
-	"identifier": "http://dx.doi.org/10.5063/F1M61H5X",
-	"codeRepository": "https://github.com/DataONEorg/rdataone",
-	"controlledTem": "software",
-	"datePublished": "2016-05-27",
-	"dateModified": "2016-05-27",
-	"dateCreated": "2016-05-27",
-	"description": "Provides read and write access to data and metadata from the DataONE network of data repositories.Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository.Users can also insert and update data objects on repositories that support these methods.",
-	"downloadLink": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz",
-	"funding": "National Science Foundation grant #012345678",
-	"isAutomatedBuild": false,
-	"issueTracker": "https://github.com/DataONEorg/rdataone/issues",
-	"licenseId": "Apache-2.0",
-	"publisher": "https://cran.r-project.org",
-	"tags": [
-		"data sharing",
-		"data repository",
-		"DataONE"
-	],
-	"name": "R Interface to the DataONE REST API",
-	"version": "2.0.0",
-	"uploadedBy": {
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"email": "mbjones@nceas.ucsb.edu",
-		"name": "Matt Jones"
-	},
-	"programmingLanguage": {
-		"name": "R",
-		"version": "> 3.1.1",
-		"URL": "https://www.r-project.org"
-	},
-	"readme": "https://github.com/DataONEorg/rdataone/README.md",
-	"relatedPublications": "ISBN:0201703726",
-	"relationship": {
-		"relationshipType": "isPartOf",
-		"relatedIdentifier": "urn:uuid:F1A0A7AF-ECF3-4C7D-B675-7C6949963995",
-		"relatedIdentifierType": "UUID"
-	},
-	"softwarePaperCitationIdentifiers": "http://doi.org/0000/0000",
-	"zippedCode": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz"
-}

data/spec/fixtures/crosscite.json

@@ -1,63 +0,0 @@
-{
-    "id": "https://doi.org/10.5281/zenodo.48440",
-    "doi": "10.5281/zenodo.48440",
-    "identifiers": [
-      {
-        "identifierType": "DOI",
-        "Identifier": "https://doi.org/10.5281/zenodo.48440"
-      },
-      {
-        "identifierType": "URL",
-        "Identifier": "http://zenodo.org/record/48440"
-      }
-    ],
-    "types":{
-        "resourceTypeGeneral": "Software",
-        "resourceType": "Software",
-        "schemaOrg": "SoftwareSourceCode",
-        "citeproc": "other",
-        "bibtex": "misc",
-        "ris": "COMP"
-    },
-    "creators": [{
-        "type": "Person",
-        "name": "Kristian Garza",
-        "givenName": "Kristian",
-        "familyName": "Garza"
-    }],
-    "titles": [{
-        "title": "Analysis Tools for Crossover Experiment of UI using Choice Architecture"
-    }],
-    "publisher": "Zenodo",
-    "subjects": [
-        {
-          "subject": "choice architecture" 
-        },
-        {
-          "subject": "crossover experiment"
-        },
-        {
-          "subject": "hci"
-        }    
-    ],
-    "dates": {
-        "date": "2016-03-27",
-        "dateType": "Issued"
-    },
-    "publication_year": "2016",
-    "rights_list": [{
-            "rights": "Open Access"
-        },
-        {
-            "rightsUri": "https://creativecommons.org/licenses/by-nc-sa/4.0",
-            "rights": "Creative Commons Attribution-NonCommercial-ShareAlike"
-        }
-    ],
-    "descriptions": [{
-        "descriptionType": "Abstract",
-        "description": "This tools are used to analyse the data produced by the Crosssover Experiment I designed to test Choice Architecture techniques as UI interventions in a SEEk4Science data catalogue. It contains:\n\n- Data structures for the experimental data.<br>\n- Visualisation functions<br>\n- Analysis functions\n\n## Installation\n\n- R<br>\n- python<br>\n- ipython 4\n\nClone and use.\n\n## Usage\n\n<br>\n```python<br>\nsource('parallel_plot.r')<br>\nwith(z, parallelset(trt,response, freq=count, alpha=0.2))<br>\n```\n\n<br>\n## Contributing\n\n1. Fork it!<br>\n2. Create your feature branch: `git checkout -b my-new-feature`<br>\n3. Commit your changes: `git commit -am 'Add some feature'`<br>\n4. Push to the branch: `git push origin my-new-feature`<br>\n5. Submit a pull request :D\n\n<br>\n## License\n\nThis work supports my PhD Thesis at University of Manchester."
-    }],
-    "schema_version": "http://datacite.org/schema/kernel-4",
-    "agency": "datacite",
-    "state": "findable"
-}

data/spec/fixtures/crossref.bib

@@ -1,14 +0,0 @@
-@article{Sankar_2014,
-  doi = {10.7554/elife.01567},
-  url = {http://elifesciences.org/lookup/doi/10.7554/eLife.01567},
-  year = 2014,
-  month = {feb},
-  publisher = {{eLife} Sciences Organisation, Ltd.},
-  volume = {3},
-  author = {Martial Sankar and Kaisa Nieminen and Laura Ragni and Ioannis Xenarios and Christian S Hardtke},
-  title = {Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth},
-  abstract = {Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale.},
-  journal = {eLife},
-  issn = {2050-084X},
-  copyright = {http://creativecommons.org/licenses/by/3.0/}
- }

data/spec/fixtures/crossref.ris

@@ -1,15 +0,0 @@
-TY  - JOUR
-T1  - Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth
-T2  - eLife
-SN  - 2050084X
-AU  - Sankar, Martial
-AU  - Nieminen, Kaisa
-AU  - Ragni, Laura
-AU  - Xenarios, Ioannis
-AU  - Hardtke, Christian S
-DO  - 10.7554/eLife.01567
-UR  - http://elifesciences.org/lookup/doi/10.7554/eLife.01567
-AB  - Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale.
-PY  - 2014
-VL  - 3
-ER  -