rof 0.0.1.pre → 1.0.4

data/spec/fixtures/vecnet-citation.json

@@ -0,0 +1,73 @@
+[{
+     "type" : "fobject",
+     "pid" : "vecnet:d217qs82g",
+     "af-model" : "Citation",
+     "rights" : {
+          "read-groups" : ["public"],
+          "edit" : ["vecnet_batchuser"]
+     },
+     "metadata" : {
+          "@context" : {
+            "dc" : "http://purl.org/dc/terms/",
+            "rdfs" : "http://www.w3.org/2000/01/rdf-schema#"
+          },
+          "dc:title" : "Molecular systematics and insecticide resistance in the major African malaria vector Anopheles funestus",
+          "dc:creator" : ["Coetzee, M.", "Koekemoer, L. L."],
+          "dc:identifier" : ["doi:10.1146/annurev-ento-120811-153628", "issn:1545-4487 (Electronic)", "issn:0066-4170 (Linking)", "23317045"],
+          "dc:description" : "Anopheles funestus is one of three major African vectors of malaria. Its distribution extends over much of the tropics and subtropics wherever suitable swampy breeding habitats are present. As with members of the Anopheles gambiae complex, An. funestus shows marked genetic heterogeneity across its range. Currently, two unnamed species are recognized in the group, with molecular and cytogenetic data indicating that more may be present. The control of malaria vectors in Africa has received increased attention in the past decade with the scaling up of insecticide-treated bed nets and indoor residual house spraying. Also in the past decade, the frequency of insecticide-resistant mosquitoes has increased exponentially. Whether this increase is in response to vector control initiatives or because of insecticide use in agriculture is debatable. In this article we examine the progress made on the systematics of the An. funestus group and review research on insecticide resistance and its mechanisms.",
+          "dc:language" : "eng",
+          "dc:type" : "Article",
+          "dc:source" : "Annual review of entomology",
+          "dc:references" : "Molecu2013",
+          "dc:bibliographicCitation" : "Annu Rev Entomol 58, 393-412. (2013)",
+          "rdfs:seeAlso" : "http://www.ncbi.nlm.nih.gov/pubmed/23317045",
+          "dc:created" : "2013",
+          "dc:modified" : {
+              "@value":"2014-03-17Z",
+              "@type":"http://www.w3.org/2001/XMLSchema#date"
+          },
+          "rdfs:domain" : "Citation"
+     },
+     "properties-meta" : {
+          "mime-type" : "text/xml"
+     },
+     "properties" : "<fields><depositor>vecnet_batchuser</depositor></fields>"
+},
+{
+     "type" : "fobject",
+     "pid" : "vecnet:h415pf50x",
+     "af-model" : "CitationFile",
+     "rights" : {
+          "read-groups" : ["registered"],
+          "edit" : ["vecnet_batchuser"]
+     },
+     "metadata" : {
+          "@context" : {
+            "dc" : "http://purl.org/dc/terms/",
+            "rdfs" : "http://www.w3.org/2000/01/rdf-schema#"
+          },
+          "dc:type" : "CitationFile",
+          "dc:dateSubmitted" : {
+              "@value" : "2014-03-17Z",
+              "@type"  : "http://www.w3.org/2001/XMLSchema#date"
+          },
+          "dc:modified" : {
+              "@value" : "2014-03-17Z",
+              "@type"  : "http://www.w3.org/2001/XMLSchema#date"
+          },
+          "dc:creator" : [ "Vecnet Batchuser", "Maureen Coetzee and Lizette L. Koekemoer" ],
+          "dc:title" : "Molecular Systematics and Insecticide Resistance in the Major African Malaria Vector Anopheles funestus"
+     },
+     "rels-ext" : {
+          "isPartOf" : ["vecnet:d217qs82g"]
+     },
+     "properties" : "<fields><depositor>vecnet_batchuser</depositor></fields>",
+     "properties-meta" : {
+          "mime-type": "text/xml"
+     },
+     "content-meta" : {
+          "mime-type": "application/pdf",
+          "label" : "5772.pdf"
+     },
+     "content-file" : "5772.pdf"
+}]

data/spec/lib/rof/access_spec.rb

@@ -0,0 +1,36 @@
+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"]})
+
+      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
+
+    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 "removes duplicates" do
+      s = Access.decode("edit=user1,user2;edit=user1")
+      expect(s).to eq({"edit" => ["user1", "user2"]})
+    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")
+    end
+  end
+end

data/spec/lib/rof/cli_spec.rb

@@ -0,0 +1,66 @@
+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\./)
+  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/",
+           "ebucore"=>"http://www.ebu.ch/metadata/ontologies/ebucore/ebucore#",
+           "foaf"=>"http://xmlns.com/foaf/0.1/",
+           "mrel"=>"http://id.loc.gov/vocabulary/relators/",
+	   "nd"=>"https://library.nd.edu/ns/terms/",
+           "rdfs"=>"http://www.w3.org/2000/01/rdf-schema#",
+           "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)
+    end
+  end
+end

data/spec/lib/rof/collection_spec.rb

@@ -0,0 +1,90 @@
+require 'spec_helper'
+
+module ROF
+  RSpec.describe Collection do
+    let!(:util) { ROF::Utility.new }
+    let!(:testobject1) { { 'owner' => 'rtillman', 'pid' => '$(first)'} } 
+    let!(:testobject2) { { 'owner' => 'rtillman', 'rights' => { 'read-groups' => [ 'public' ], 'edit' => [ 'edit']}} } 
+    let!(:testobject3) { { 'owner' => 'rtillman', "metadata" => { "dc:title" => "Extensive Reading in Japanese"} } }
+    let!(:testobject4) { { 'owner' => 'rtillman', "files" => [ '/it_is_not_there'] } }
+
+    describe 'set_required_fields' do
+    let(:obj) { ROF::Collection.set_required_fields( testobject1, util) }
+    let(:obj_rights) { ROF::Collection.set_required_fields( testobject2, util) }
+    let(:obj_metadata) { ROF::Collection.set_required_fields( testobject3, util) }
+      context 'type' do
+	subject { obj['type'] }
+	it { is_expected.to eq("fobject") }
+      end
+      context 'af-model' do
+	subject { obj['af-model'] }
+	it { is_expected.to eq("Collection") }
+      end
+      context 'rights' do
+	subject { obj_rights['rights'] }
+	it { is_expected.to eq({"read-groups"=>["public"], "edit"=>["edit"]}) }
+      end
+      context 'metadata' do
+	subject { obj_metadata['metadata'] }
+	it { is_expected.to eq({"dc:title"=>"Extensive Reading in Japanese"}) }
+      end
+      context 'pid' do
+	subject { obj['pid'] }
+	it { is_expected.to eq("$(first)") }
+      end
+      context 'properties' do
+        subject { obj['properties'] }
+        it { is_expected.to eq "<fields><depositor>batch_ingest</depositor>\n<owner>rtillman</owner>\n</fields>\n" }
+      end
+      context 'properties--meta' do
+	subject { obj['properties-meta'] }
+	it { is_expected.to eq({ 'mime-type' => 'text/xml' }) }
+      end
+      context 'rels-ext' do
+	subject { obj['rels-ext'] }
+	it { is_expected.to eq({}) }
+      end
+    end
+    describe 'mk_dest_img_name' do
+      context 'with file extension' do
+	subject { ROF::Collection.mk_dest_img_name('/opt/data/und:12345/flashcrowd.jpg', '-thumb') }
+	it { is_expected.to eq("/opt/data/und:12345/flashcrowd-thumb.jpg") }
+      end
+      context 'without file extension' do
+	subject { ROF::Collection.mk_dest_img_name('/opt/data/und:12345/flashcrowd', '-launch') }
+	it { is_expected.to eq("/opt/data/und:12345/flashcrowd-launch") }
+      end
+    end
+    describe 'make_images' do
+      it 'raises error with non-existent file' do
+	expect { ROF::Collection.make_images({}, testobject4, util)}.to raise_error(ROF::Collection::NoFile) 
+      end
+    end
+    describe 'find_file_mime' do
+      context 'jpg' do
+	subject { ROF::Collection.find_file_mime('/opt/data/und:12345/flashcrowd.jpg') }
+	it { is_expected.to eq("image/jpeg") }
+      end
+      context 'JPG' do
+	subject { ROF::Collection.find_file_mime('und:12345/flashcrowd.JPG') }
+	it { is_expected.to eq("image/jpeg") }
+      end
+      context 'GIF' do
+	subject { ROF::Collection.find_file_mime('und:12345/flashcrowd.GIF') }
+	it { is_expected.to eq("image/gif") }
+      end
+      context 'gif' do
+	subject { ROF::Collection.find_file_mime('/und:12345/flashcrowd.gif') }
+	it { is_expected.to eq("image/gif") }
+      end
+      context 'png' do
+	subject { ROF::Collection.find_file_mime('death_of_middle_class.png') }
+	it { is_expected.to eq("image/png") }
+      end
+      context 'PNG' do
+	subject { ROF::Collection.find_file_mime('death_of_middle_class.PNG') }
+	it { is_expected.to eq("image/png") }
+      end
+    end
+  end
+end

data/spec/lib/rof/compare_rof_spec.rb

@@ -0,0 +1,263 @@
+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)
+    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
+
+    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)
+    end
+
+    it "compares metadata (same) " do
+      fedora = { "metadata"=> { "@context"=> {
+            "dc"=> "http://purl.org/dc/terms/",
+            "foaf"=> "http://xmlns.com/foaf/0.1/",
+            "rdfs"=> "http://www.w3.org/2000/01/rdf-schema#",
+            "dc:dateSubmitted"=> {
+              "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+            },
+            "dc:modified"=> {
+	            "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+	          }
+          },
+          "dc:dateSubmitted"=> "2016-07-22Z",
+          "dc:modified"=> "2016-07-22Z",
+          "dc:title"=> "carmella.jpeg"
+        }}
+      bendo = { "metadata"=> {
+          "dc:dateSubmitted"=> "2016-07-22Z",
+          "dc:modified"=> "2016-07-22Z",
+          "dc:title"=> "carmella.jpeg"
+        }}
+      test_return = CompareRof.compare_metadata(fedora, bendo)
+      expect(test_return).to eq(0)
+    end
+
+    it "compares metadata (different) " do
+      fedora = { "metadata"=> { "@context"=> {
+            "dc"=> "http://purl.org/dc/terms/",
+            "foaf"=> "http://xmlns.com/foaf/0.1/",
+            "rdfs"=> "http://www.w3.org/2000/01/rdf-schema#",
+            "dc:dateSubmitted"=> {
+              "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+            },
+            "dc:modified"=> {
+	            "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+	          }
+          },
+          "dc:dateSubmitted"=> "2016-07-22Z",
+          "dc:modified"=> "2016-07-22Z",
+          "dc:title"=> "carmella.jpeg"
+        }}
+      bendo = { "metadata"=> {
+          "dc:dateSubmitted"=> "2016-07-22Z",
+          "dc:modified"=> "2016-07-23Z",
+          "dc:title"=> "carmella.jpeg"
+        }}
+      test_return = CompareRof.compare_metadata(fedora, bendo)
+      expect(test_return).to eq(1)
+    end
+
+    it "compares metadata (different types) " do
+      # dateSubmitted is a string literal in one and a date type in the other
+      fedora = { "metadata"=> { "@context"=> {
+                                  "dc"=> "http://purl.org/dc/terms/",
+                                  "foaf"=> "http://xmlns.com/foaf/0.1/",
+                                  "rdfs"=> "http://www.w3.org/2000/01/rdf-schema#",
+                                  "dc:dateSubmitted"=> {
+                                    "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+                                  },
+                                  "dc:modified"=> {
+	                                "@type"=> "http://www.w3.org/2001/XMLSchema#date"
+	                              }
+                                },
+                                "dc:dateSubmitted"=> "2016-07-22Z",
+                                "dc:modified"=> "2016-07-22Z",
+                                "dc:title"=> "carmella.jpeg"
+                              }}
+      bendo = { "metadata"=> {
+                  "@context" => {
+                    "dc"=> "http://purl.org/dc/terms/",
+                  },
+                  "dc:dateSubmitted"=> "2016-07-22Z",
+                  "dc:modified"=> "2016-07-22Z",
+                  "dc:title"=> "carmella.jpeg"
+                }}
+      test_return = CompareRof.compare_metadata(fedora, bendo)
+      expect(test_return).to eq(1)
+    end
+
+    it "compares rels-ext (same) " do
+      fedora = { "rels-ext"=> {
+		    "@context"=> {
+		      "@vocab"=> "info:fedora/fedora-system:def/relations-external#",
+	              "fedora-model"=> "info:fedora/fedora-system:def/model#",
+	              "hydra"=> "http://projecthydra.org/ns/relations#",
+	              "hasModel"=> {
+		            "@id"=> "fedora-model:hasModel",
+		            "@type"=> "@id"
+	              },
+	              "hasEditor"=> {
+	                "@id"=> "hydra:hasEditor",
+	                "@type"=> "@id"
+	              },
+	              "hasEditorGroup"=> {
+	                "@id"=> "hydra:hasEditorGroup",
+	                "@type"=> "@id"
+	              },
+	              "isPartOf"=> {
+	                "@type"=> "@id"
+	              },
+	              "isEditorOf"=> {
+	                "@id"=> "hydra:isEditorOf",
+	                "@type"=> "@id"
+	              },
+	              "hasMember"=> {
+	                "@type"=> "@id"
+	              }
+	            },
+	            "isPartOf"=> [
+		      "und:dev00149x01"
+	            ]
+	}}
+        bendo = { "rels-ext"=> {
+	            "isPartOf"=> [
+		      "und:dev00149x01"
+	            ]
+	}}
+      test_return = CompareRof.compare_rels_ext(fedora, bendo)
+      expect(test_return).to eq(0)
+    end
+
+    it "compares rels-ext (different) " do
+      fedora = { "rels-ext"=> {
+		    "@context"=> {
+		      "@vocab"=> "info:fedora/fedora-system:def/relations-external#",
+	              "fedora-model"=> "info:fedora/fedora-system:def/model#",
+	              "hydra"=> "http://projecthydra.org/ns/relations#",
+	              "hasModel"=> {
+		            "@id"=> "fedora-model:hasModel",
+		            "@type"=> "@id"
+	              },
+	              "hasEditor"=> {
+	                "@id"=> "hydra:hasEditor",
+	                "@type"=> "@id"
+	              },
+	              "hasEditorGroup"=> {
+	                "@id"=> "hydra:hasEditorGroup",
+	                "@type"=> "@id"
+	              },
+	              "isPartOf"=> {
+	                "@type"=> "@id"
+	              },
+	              "isEditorOf"=> {
+	                "@id"=> "hydra:isEditorOf",
+	                "@type"=> "@id"
+	              },
+	              "hasMember"=> {
+	                "@type"=> "@id"
+	              }
+	            },
+	            "isPartOf"=> [
+		      "und:dev00149x01"
+	            ]
+	}}
+        bendo = { "rels-ext"=> {
+	            "isPartOf"=> [
+		      "und:dev00148x01"
+	            ]
+	}}
+      test_return = CompareRof.compare_rels_ext(fedora, bendo)
+      expect(test_return).to eq(1)
+    end
+
+    it "compares everything else (same) " do
+      fedora = {
+	        "pid"=> "und:dev00149w5f",
+                "type"=> "fobject",
+                "af-model"=> "Collection",
+                "properties-meta"=> {
+	          "mime-type"=> "text/xml"
+	       },
+               "properties"=> "<fields><depositor>batch_ingest</depositor>\n\t\t\t\t<owner>rtillman</owner></fields>\n",
+	       "content-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+	       "thumbnail-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+	       "bendo-item"=> "dev00149w5f"
+       }
+      bendo = {
+               "properties-meta"=> {
+	          "mime-type"=> "text/xml"
+	       },
+               "properties"=> "<fields><depositor>batch_ingest</depositor>\n\t\t\t\t<owner>rtillman</owner></fields>\n",
+	       "content-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+               "af-model"=> "Collection",
+	       "pid"=> "und:dev00149w5f",
+	       "thumbnail-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+               "type"=> "fobject",
+	       "bendo-item"=> "dev00149w5f"
+	}
+      test_return = CompareRof.compare_everything_else(fedora, bendo, {})
+      expect(test_return).to eq(0)
+    end
+
+    it "compares everything else (differenet) " do
+      fedora = {
+	        "pid"=> "und:dev00149w5f",
+                "type"=> "fobject",
+                "af-model"=> "Collection",
+                "properties-meta"=> {
+	          "mime-type"=> "text/xml"
+	       },
+               "properties"=> "<fields><depositor>batch_ingest</depositor>\n\t\t\t\t<owner>msuhovec</owner></fields>\n",
+	       "content-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+	       "thumbnail-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+	       "bendo-item"=> "dev00149w5f"
+       }
+      bendo = {
+               "properties-meta"=> {
+	          "mime-type"=> "text/xml"
+	       },
+               "properties"=> "<fields><depositor>batch_ingest</depositor>\n\t\t\t\t<owner>rtillman</owner></fields>\n",
+	       "content-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+               "af-model"=> "Collection",
+	       "pid"=> "und:dev00149w5f",
+	       "thumbnail-meta"=> {
+	         "mime-type"=> "image/jpeg"
+	       },
+               "type"=> "fobject",
+	       "bendo-item"=> "dev00149w5f"
+	}
+      test_return = CompareRof.compare_everything_else(fedora, bendo, {})
+      expect(test_return).to eq(1)
+    end
+  end
+end