rof 1.0.7 → 1.2.0

data/spec/fixtures/jsonld_to_rof/zk51vd69n1r.rof

@@ -0,0 +1,121 @@
+[
+  {
+    "type": "fobject",
+    "pid": "und:zk51vd69n1r",
+    "af-model": "Etd",
+    "metadata": {
+      "@context": {
+        "bibo": "http://purl.org/ontology/bibo/",
+        "dc": "http://purl.org/dc/terms/",
+        "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
+        "foaf": "http://xmlns.com/foaf/0.1/",
+        "hydramata-rel": "http://projecthydra.org/ns/relations#",
+        "mrel": "http://id.loc.gov/vocabulary/relators/",
+        "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
+        "nd": "https://library.nd.edu/ns/terms/",
+        "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+        "ths": "http://id.loc.gov/vocabulary/relators/",
+        "vracore": "http://purl.org/vra/",
+        "dc:dateSubmitted": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        },
+        "dc:created": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        },
+        "dc:modified": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        }
+      },
+      "dc:title": "Characterization of the Roles of ADAM17a and ADAM17b during Zebrafish Retinal Regeneration",
+      "dc:creator": [
+        "Jingling Li"
+      ],
+      "dc:title#alternate": [
+
+      ],
+      "dc:subject": [
+
+      ],
+      "dc:description#abstract": [
+        "<p>The zebrafish retina provides an excellent model to study neuronal regeneration because it possesses the inherent capacity to generate new neurons in the growing retina throughout its life and to restore any neuronal types that are lost upon injury. In response to retinal cell loss caused by injury or disease, zebrafish Müller glial cells re-enter the cell cycle to produce neuronal progenitor cells that continue to proliferate and differentiate into any retinal neuronal type that was lost. We previously demonstrated that tumor necrosis factor α (TNFα) is required and sufficient to initiate this proliferation response (Nelson et al., 2013; Conner et al., 2014). However, the activation and upstream regulator of TNFα signaling during retinal regeneration remained undetermined. </p><p>In this study, I investigated the roles of two A Disintegrin And Metalloproteases 17 (ADAM17) paralogs, ADAM17a and ADAM17b, in stimulating regeneration of the damaged zebrafish retina and TNFα processing. Reduced expression of either ADAM17 paralog significantly suppressed Müller glia cell cycle re-entry in the light-damaged retina, which indicates that both ADAM17a and ADAM17b are necessary and functionally nonredundant in initiating Müller glia proliferation during retinal regeneration. The recombinant soluble TNFα rescued Müller glia proliferation in damaged <i>adam17b</i> morphant retinas, but not <i>adam17a</i> morphant retinas. We also demonstrated that knocking down ADAM17b expression reduced TNFα processing in the light-damaged retina, which results in decreased levels the soluble form of TNFα. In contrast, the <i>adam17a</i> morphant retina did not exhibit reduced amounts of the soluble TNFα. Intravitreal injection of the soluble TNFα into light-damaged retinas rescued Müller glia proliferation in <i>adam17b</i> morphant retinas, which produced proliferating neuronal progenitor cells (NPC). However, fewer NPCs in the TNFα-rescued light-damaged <i>adam17b</i> morphant retinas committed to the <i>atoh7</i> neuronal lineage relative to control retinas and differentiated into greater numbers of amacrine cells rather than photoreceptors. Thus, ADAM17b is required to process TNFα prior to Müller glia proliferation and is necessary for NPC commitment to a neuronal lineage.</p>"
+      ],
+      "dc:rights": [
+        "All rights reserved"
+      ],
+      "dc:language": [
+
+      ],
+      "dc:date": [
+        "2017-02-13"
+      ],
+      "dc:dateSubmitted": [
+        "2017-02-14"
+      ],
+      "dc:contributor": [
+        {
+          "dc:contributor": "David R.Hyde",
+          "ms:role": "Research Director"
+        }
+      ],
+      "ms:degree": {
+        "ms:name": [
+          "Doctor of Philosophy"
+        ],
+        "ms:discipline": [
+          "Biological Sciences"
+        ],
+        "ms:level": "Doctoral Dissertation"
+      },
+      "dc:modified": "2017-02-25Z"
+    },
+    "rels-ext": {
+      "@context": {
+        "bibo": "http://purl.org/ontology/bibo/",
+        "dc": "http://purl.org/dc/terms/",
+        "ebucore": "http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
+        "foaf": "http://xmlns.com/foaf/0.1/",
+        "hydramata-rel": "http://projecthydra.org/ns/relations#",
+        "mrel": "http://id.loc.gov/vocabulary/relators/",
+        "ms": "http://www.ndltd.org/standards/metadata/etdms/1.1/",
+        "nd": "https://library.nd.edu/ns/terms/",
+        "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+        "ths": "http://id.loc.gov/vocabulary/relators/",
+        "vracore": "http://purl.org/vra/",
+        "dc:dateSubmitted": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        },
+        "dc:created": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        },
+        "dc:modified": {
+          "@type": "http://www.w3.org/2001/XMLSchema#date"
+        }
+      },
+      "hydramata-rel:hasEditor": [
+        "und:qb98mc9021z"
+      ],
+      "hydramata-rel:hasEditorGroup": [
+        "und:q524jm23g92"
+      ]
+    },
+    "rights": {
+      "read": [
+        "ljinglin"
+      ],
+      "edit": [
+        "curate_batch_user"
+      ],
+      "edit-groups": [
+        "und:q524jm23g92"
+      ],
+      "read-groups": [
+        "public"
+      ]
+    },
+    "properties-meta": {
+      "mime-type": "text/xml"
+    },
+    "properties": "<fields><depositor>curate_batch_user</depositor></fields>",
+    "bendo-item": "zk51vd69n1r"
+  }
+]

data/spec/lib/rof/access_spec.rb

@@ -1,36 +1,43 @@
 require 'spec_helper'
 
 module ROF
-  describe "Access" do
-    it "decodes public restricted private" do
-      s = Access.decode("public", "user1")
-      expect(s).to eq({"read-groups" => ["public"], "edit" => ["user1"]})
+  RSpec.describe Access do
+    context '.decode' do
+      it 'raises an error on an unknown clause' do
+        expect { Access.decode("chicken") }.to raise_error described_class::DecodeError
+      end
+      it "decodes public restricted private" do
+        s = Access.decode("public", "user1")
+        expect(s).to eq({"read-groups" => ["public"], "edit" => ["user1"]})
 
-      s = Access.decode("restricted", "user1")
-      expect(s).to eq({"read-groups" => ["registered"], "edit" => ["user1"]})
+        s = Access.decode("restricted", "user1")
+        expect(s).to eq({"read-groups" => ["registered"], "edit" => ["user1"]})
 
-      s = Access.decode("private", "user1")
-      expect(s).to eq({"edit" => ["user1"]})
-    end
+        s = Access.decode("private", "user1")
+        expect(s).to eq({"edit" => ["user1"]})
+      end
 
-    it "handles embargos" do
-      s = Access.decode("embargo=2014-12-25", "user1")
-      expect(s).to eq({"embargo-date" => "2014-12-25"})
-    end
+      it "handles embargos" do
+        s = Access.decode("embargo=2014-12-25", "user1")
+        expect(s).to eq({"embargo-date" => "2014-12-25"})
+      end
 
-    it "handles multiple clauses" do
-      s = Access.decode("public;editgroup=group1,group2;edit=user2", "user1")
-      expect(s).to eq({"read-groups" => ["public"], "edit" => ["user1","user2"], "edit-groups" => ["group1","group2"]})
-    end
+      it "handles multiple clauses" do
+        s = Access.decode("public;editgroup=group1,group2;edit=user2", "user1")
+        expect(s).to eq({"read-groups" => ["public"], "edit" => ["user1","user2"], "edit-groups" => ["group1","group2"]})
+      end
 
-    it "removes duplicates" do
-      s = Access.decode("edit=user1,user2;edit=user1")
-      expect(s).to eq({"edit" => ["user1", "user2"]})
+      it "removes duplicates" do
+        s = Access.decode("edit=user1,user2;edit=user1")
+        expect(s).to eq({"edit" => ["user1", "user2"]})
+      end
     end
 
-    it "encodes" do
-      s = Access.encode({"read-groups" => ["public"], "edit" => ["user1","user2"], "edit-groups" => ["group1","group2"]})
-      expect(s).to eq("readgroup=public;edit=user1,user2;editgroup=group1,group2")
+    context '.encode' do
+      it "converts a Hash to a String" do
+        s = Access.encode({"read-groups" => ["public"], "edit" => ["user1","user2"], "edit-groups" => ["group1","group2"]})
+        expect(s).to eq("readgroup=public;edit=user1,user2;editgroup=group1,group2")
+      end
     end
   end
 end

data/spec/lib/rof/cli_spec.rb

@@ -2,68 +2,91 @@ require 'spec_helper'
 require 'stringio'
 
 describe ROF::CLI do
-  it "ingests an array of items" do
-    items = [{"pid" => "test:1",
-              "type" => "fobject"},
-             {"pid" => "test:2",
-              "type" => "fobject"}]
-    output = StringIO.new
-    ROF::CLI.ingest_array(items, [], output)
-    expect(output.string).to match(/1\. Verifying test:1 \.\.\.ok\..*\n2\. Verifying test:2 \.\.\.ok\./)
+  describe '.ingest_array' do
+    it "ingests an array of items" do
+      items = [{"pid" => "test:1",
+                "type" => "fobject"},
+               {"pid" => "test:2",
+                "type" => "fobject"}]
+      output = StringIO.new
+      ROF::CLI.ingest_array(items, [], output)
+      expect(output.string).to match(/1\. Verifying test:1 \.\.\.ok\..*\n2\. Verifying test:2 \.\.\.ok\./)
+    end
+  end
+
+  describe '.osf_to_rof' do
+    let(:outfile) { double(write: true) }
+    let(:data_from_file) { [:data_from_file] }
+    let(:rof_data) { [{ "rof" => "true" }] }
+    let(:config) { {} }
+    let(:project_file) { File.join(GEM_ROOT, 'spec/fixtures/for_utility_load_items_from_json_file/single_item.json') }
+    it 'loads the JSON file, calls the translator then writes the output as JSON' do
+      expect(ROF::Utility).to receive(:load_items_from_json_file).with(project_file, outfile).and_return(data_from_file)
+      expect(ROF::Translators::OsfToRof).to receive(:call).with(data_from_file[0], config).and_return(rof_data)
+      described_class.osf_to_rof(project_file, config, outfile)
+      expect(outfile).to have_received(:write).with(JSON.pretty_generate(rof_data))
+    end
   end
 
-  it "retrieves a fedora object and converts it to ROF" do
-    expected_output = {
-      "pid" => "und:dev0012829m",
-      "type" => "fobject",
-      "af-model" => "GenericFile",
-      "rels-ext" => {
-        "@context"=> ROF::RelsExtRefContext,
-        "@id" => "und:dev0012829m",
-        "isPartOf"=> "und:dev00128288"
-      },
-      "rights" => {
-        "read-groups" => ["registered"],
-        "edit" => ["dbrower"]
-      },
-      "properties" => "<fields>\n<depositor>batch_ingest</depositor>\n<owner>dbrower</owner>\n</fields>\n",
-      "properties-meta" => {"mime-type" => "text/xml"},
-      "metadata" => {
-	 "@context"=> {
-           "bibo"=>"http://purl.org/ontology/bibo/",
-           "dc"=>"http://purl.org/dc/terms/",
-           "ms" => 'http://www.ndltd.org/standards/metadata/etdms/1.1/',
-           "ebucore"=>"http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
-           "foaf"=>"http://xmlns.com/foaf/0.1/",
-           'hydramata-rel' => 'http://projecthydra.org/ns/relations#',
-           "mrel"=>"http://id.loc.gov/vocabulary/relators/",
-	   "nd"=>"https://library.nd.edu/ns/terms/",
-           "rdfs"=>"http://www.w3.org/2000/01/rdf-schema#",
-           'ths' => 'http://id.loc.gov/vocabulary/relators/',
-           "vracore"=>"http://purl.org/vra/",
-           "dc:dateSubmitted" => {"@type" => "http://www.w3.org/2001/XMLSchema#date"},
-           "dc:created"=>{"@type"=>"http://www.w3.org/2001/XMLSchema#date"},
-           "dc:modified" => {"@type" => "http://www.w3.org/2001/XMLSchema#date"}
-        },
-        "@id" => "info:fedora/und:dev0012829m",
-        "dc:dateSubmitted" => "2016-04-12Z",
-        "dc:modified" => "2016-04-12Z",
-        "dc:title" => "bonnie+chauncey"
-      },
-      "bendo-item" => "dev0012826k",
-      "characterization-meta" => {"mime-type"=>"text/xml"},
-      "content-meta" => {"label"=>"bonnie+chauncey", "mime-type"=>"application/octet-stream", "URL"=>"http://libvirt9.library.nd.edu:14000/item/dev0012826k/bonnie+chauncey"},
-      "thumbnail-meta" => {"label"=>"File Datastream", "mime-type"=>"image/png"},
-    }
-    pid = 'und:dev0012829m'
-    config = {}
-    fedora = {}
-    fedora[:url] = 'http://localhost:8080/fedora'
-    fedora[:user] = 'fedoraAdmin'
-    fedora[:password] = 'fedoraAdmin'
-    VCR.use_cassette("fedora_to_rof1") do
-      fedora_data =  ROF::FedoraToRof.GetFromFedora(pid, fedora, config)
-      expect(fedora_data).to eq(expected_output)
+  describe '.fedora_to_rof' do
+    let(:outfile) { double(write: true) }
+    let(:pids) { [1, 2, 3] }
+    let(:rof_data) { [{ "rof" => "true" }] }
+    let(:config) { {} }
+    it 'calls the translator then writes the output as JSON' do
+      expect(ROF::Translators::FedoraToRof).to receive(:call).with(pids, config).and_return(rof_data)
+      described_class.fedora_to_rof(pids, config, outfile)
+      expect(outfile).to have_received(:write).with(JSON.pretty_generate(rof_data))
+    end
+  end
+
+  describe '.csv_to_rof' do
+    let(:outfile) { double(write: true) }
+    let(:csv) { "1,2,3" }
+    let(:rof_data) { [{ "rof" => "true" }] }
+    let(:config) { {} }
+    it 'calls the translator then writes the output as JSON' do
+      expect(ROF::Translators::CsvToRof).to receive(:call).with(csv, config).and_return(rof_data)
+      described_class.csv_to_rof(csv, config, outfile)
+      expect(outfile).to have_received(:write).with(JSON.pretty_generate(rof_data))
+    end
+  end
+
+  describe '.jsonld_to_rof' do
+    let(:outfile) { double(write: true) }
+    let(:jsonld) { double('JSON-LD') }
+    let(:rof_data) { [{ "rof" => "true" }] }
+    let(:config) { {} }
+    it 'calls the translator then writes the output as JSON' do
+      expect(ROF::Translators::JsonldToRof).to receive(:call).with(jsonld, config).and_return(rof_data)
+      described_class.jsonld_to_rof(jsonld, config, outfile)
+      expect(outfile).to have_received(:write).with(JSON.pretty_generate(rof_data))
+    end
+  end
+
+  describe '.with_outfile_handling' do
+    let(:writer) { double(close: true) }
+    context 'when given a string' do
+      let(:outfile) { '/hello/world' }
+      it 'will open a file' do
+        expect(File).to receive(:open).with('/hello/world', 'w').and_return(writer)
+        expect {|b| described_class.with_outfile_handling(outfile, &b) }.to yield_with_args(writer)
+        expect(writer).to have_received(:close)
+      end
+    end
+    context 'when given nil' do
+      let(:outfile) { nil }
+      it 'will write to /dev/null' do
+        expect(File).to receive(:open).with('/dev/null', 'w').and_return(writer)
+        expect {|b| described_class.with_outfile_handling(outfile, &b) }.to yield_with_args(writer)
+        expect(writer).to have_received(:close)
+      end
+    end
+    context 'when given something else' do
+      it 'will assume it is can be "written" to' do
+        expect {|b| described_class.with_outfile_handling(writer, &b) }.to yield_with_args(writer)
+        expect(writer).to have_received(:close)
+      end
     end
   end
 end

data/spec/lib/rof/compare_rof_spec.rb

@@ -1,26 +1,37 @@
 require 'spec_helper'
 
 module ROF
-  describe "Compare ROF" do
-    it "compares rights metadata different read-groups" do
-      fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
-      bendo = { "rights"=> {"read-groups"=> ["private"], "edit"=> ["rtillman"]}}
-      test_return = CompareRof.compare_rights(fedora, bendo, {})
-      expect(test_return).to eq(1)
+  describe CompareRof do
+    describe '.fedora_vs_bendo' do
+      it 'is a convenience method' do
+        expect_any_instance_of(described_class).to receive(:error_count)
+        fedora = [:f]
+        bendo = [:b]
+        described_class.fedora_vs_bendo(fedora, bendo)
+      end
     end
 
-    it "compares rights metadata same read-groups" do
-      fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
-      bendo = { "rights"=> {"read-groups"=> ["public"], "edit"=> ["rtillman"]}}
-      test_return = CompareRof.compare_rights(fedora, bendo, {})
-      expect(test_return).to eq(0)
-    end
+    describe '#compare_rights' do
+      it "compares rights metadata different read-groups" do
+        fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
+        bendo = { "rights"=> {"read-groups"=> ["private"], "edit"=> ["rtillman"]}}
+        test_return = described_class.new(fedora, bendo).error_count
+        expect(test_return).to eq(1)
+      end
 
-    it "compares rights metadata with different groups" do
-      fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
-      bendo = { "rights"=> {"edit"=> ["rtillman"]}}
-      test_return = CompareRof.compare_rights(fedora, bendo, {})
-      expect(test_return).to eq(1)
+      it "compares rights metadata same read-groups" do
+        fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
+        bendo = { "rights"=> {"read-groups"=> ["public"], "edit"=> ["rtillman"]}}
+        test_return = described_class.new(fedora, bendo).error_count
+        expect(test_return).to eq(0)
+      end
+
+      it "compares rights metadata with different groups" do
+        fedora = { "rights"=> { "read-groups"=> ["public"], "edit"=> ["rtillman"]}}
+        bendo = { "rights"=> {"edit"=> ["rtillman"]}}
+        test_return = described_class.new(fedora, bendo).error_count
+        expect(test_return).to eq(1)
+      end
     end
 
     it "compares metadata (same) " do
@@ -44,7 +55,7 @@ module ROF
           "dc:modified"=> "2016-07-22Z",
           "dc:title"=> "carmella.jpeg"
         }}
-      test_return = CompareRof.compare_metadata(fedora, bendo)
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(0)
     end
 
@@ -69,7 +80,7 @@ module ROF
           "dc:modified"=> "2016-07-23Z",
           "dc:title"=> "carmella.jpeg"
         }}
-      test_return = CompareRof.compare_metadata(fedora, bendo)
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(1)
     end
 
@@ -98,7 +109,7 @@ module ROF
                   "dc:modified"=> "2016-07-22Z",
                   "dc:title"=> "carmella.jpeg"
                 }}
-      test_return = CompareRof.compare_metadata(fedora, bendo)
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(1)
     end
 
@@ -140,7 +151,7 @@ module ROF
 		      "und:dev00149x01"
 	            ]
 	}}
-      test_return = CompareRof.compare_rels_ext(fedora, bendo)
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(0)
     end
 
@@ -182,7 +193,7 @@ module ROF
 		      "und:dev00148x01"
 	            ]
 	}}
-      test_return = CompareRof.compare_rels_ext(fedora, bendo)
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(1)
     end
 
@@ -219,7 +230,7 @@ module ROF
                "type"=> "fobject",
 	       "bendo-item"=> "dev00149w5f"
 	}
-      test_return = CompareRof.compare_everything_else(fedora, bendo, {})
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(0)
     end
 
@@ -256,7 +267,7 @@ module ROF
                "type"=> "fobject",
 	       "bendo-item"=> "dev00149w5f"
 	}
-      test_return = CompareRof.compare_everything_else(fedora, bendo, {})
+      test_return = described_class.new(fedora, bendo).error_count
       expect(test_return).to eq(1)
     end
   end