ro-crate 0.4.10 → 0.4.14
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- checksums.yaml +4 -4
- data/Gemfile.lock +13 -13
- data/README.md +39 -0
- data/lib/ro_crate/model/crate.rb +48 -6
- data/lib/ro_crate/model/data_entity.rb +21 -8
- data/lib/ro_crate/model/directory.rb +5 -7
- data/lib/ro_crate/model/entity.rb +41 -4
- data/lib/ro_crate/model/entry.rb +2 -2
- data/lib/ro_crate/model/file.rb +6 -4
- data/lib/ro_crate/model/metadata.rb +9 -1
- data/lib/ro_crate/model/organization.rb +1 -1
- data/lib/ro_crate/model/preview.rb +3 -15
- data/lib/ro_crate/model/preview_generator.rb +40 -0
- data/lib/ro_crate/model/remote_entry.rb +1 -12
- data/lib/ro_crate/reader.rb +61 -23
- data/lib/ro_crate/writer.rb +4 -4
- data/lib/ro_crate.rb +2 -1
- data/ro_crate.gemspec +3 -3
- data/test/crate_test.rb +58 -3
- data/test/directory_test.rb +21 -21
- data/test/entity_test.rb +117 -3
- data/test/fixtures/biobb_hpc_workflows-condapack.zip +0 -0
- data/test/fixtures/conflicting_data_directory/info.txt +1 -0
- data/test/fixtures/conflicting_data_directory/nested.txt +1 -0
- data/test/fixtures/misc_data_entity_crate/ro-crate-metadata.json +33 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE +176 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md +6 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json +140 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga +118 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed +3 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed +3 -0
- data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml +8 -0
- data/test/fixtures/sparse_directory_crate/ro-crate-preview.html +60 -59
- data/test/fixtures/workflow-0.2.0/ro-crate-metadata.jsonld +5 -5
- data/test/fixtures/workflow-0.2.0.zip +0 -0
- data/test/reader_test.rb +110 -58
- data/test/test_helper.rb +5 -1
- data/test/writer_test.rb +70 -2
- metadata +26 -8
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# Galaxy mini workflow
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A tiny Galaxy workflow that sorts tabular lines according to the first column
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and changes the text to upper case.
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This RO-Crate is based on an [example from the Life Monitor repository](https://github.com/crs4/life_monitor/tree/8437be177822d0e2b3fed30db094b91c2fc14391/interaction_experiments/data/crates/ro-crate-galaxy-sortchangecase).
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{
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"@context": [
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"https://w3id.org/ro/crate/1.1/context",
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{
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"TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
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"TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
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"TestService": "https://w3id.org/ro/terms/test#TestService",
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"TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
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"PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
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"JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
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"TravisService": "https://w3id.org/ro/terms/test#TravisService",
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"GithubService": "https://w3id.org/ro/terms/test#GithubService",
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"instance": "https://w3id.org/ro/terms/test#instance",
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"runsOn": "https://w3id.org/ro/terms/test#runsOn",
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"resource": "https://w3id.org/ro/terms/test#resource",
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"definition": "https://w3id.org/ro/terms/test#definition",
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"engineVersion": "https://w3id.org/ro/terms/test#engineVersion"
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}
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],
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"@graph": [
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{
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"@id": "ro-crate-metadata.json",
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"@type": "CreativeWork",
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"about": {
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"@id": "./"
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},
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"conformsTo": [
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{ "@id": "https://w3id.org/ro/crate/1.1" },
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{ "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
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]
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},
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{
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"@id": "./",
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"@type": "Dataset",
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"name": "sort-and-change-case",
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"description": "sort lines and change text to upper case",
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"license": "Apache-2.0",
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"mainEntity": {
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"@id": "sort-and-change-case.ga"
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},
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"hasPart": [
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{
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"@id": "sort-and-change-case.ga"
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},
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{
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"@id": "LICENSE"
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},
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{
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"@id": "README.md"
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},
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{
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"@id": "test/test1/sort-and-change-case-test.yml"
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}
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],
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"mentions": [
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{
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"@id": "#test1"
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}
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]
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},
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{
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"@id": "sort-and-change-case.ga",
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"@type": [
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"File",
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"SoftwareSourceCode",
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"ComputationalWorkflow"
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],
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"programmingLanguage": {
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"@id": "#galaxy"
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},
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"name": "sort-and-change-case"
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},
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{
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"@id": "LICENSE",
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"@type": "File"
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},
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{
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"@id": "README.md",
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"@type": "File"
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},
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{
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"@id": "#galaxy",
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"@type": "ComputerLanguage",
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"name": "Galaxy",
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"identifier": {
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"@id": "https://galaxyproject.org/"
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},
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"url": {
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"@id": "https://galaxyproject.org/"
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}
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},
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{
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"@id": "#test1",
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"name": "test1",
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"@type": "TestSuite",
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"mainEntity": {
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"@id": "sort-and-change-case.ga"
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},
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"instance": [
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{"@id": "#test1_1"}
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],
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"definition": {"@id": "test/test1/sort-and-change-case-test.yml"}
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},
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{
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"@id": "#test1_1",
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"name": "test1_1",
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"@type": "TestInstance",
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"runsOn": {"@id": "https://w3id.org/ro/terms/test#JenkinsService"},
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"url": "http://example.org/jenkins",
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"resource": "job/tests/"
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},
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{
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"@id": "test/test1/sort-and-change-case-test.yml",
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"@type": [
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"File",
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"TestDefinition"
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],
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"conformsTo": {"@id": "https://w3id.org/ro/terms/test#PlanemoEngine"},
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"engineVersion": ">=0.70"
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},
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{
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"@id": "https://w3id.org/ro/terms/test#JenkinsService",
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"@type": "TestService",
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"name": "Jenkins",
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"tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
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"tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
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|
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|
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|
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|
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Binary file
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