ro-crate 0.4.10 → 0.4.14

data/test/fixtures/ro-crate-galaxy-sortchangecase/LICENSE

@@ -0,0 +1,176 @@
+
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data/test/fixtures/ro-crate-galaxy-sortchangecase/README.md

@@ -0,0 +1,6 @@
+# Galaxy mini workflow
+
+A tiny Galaxy workflow that sorts tabular lines according to the first column
+and changes the text to upper case.
+
+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).

data/test/fixtures/ro-crate-galaxy-sortchangecase/ro-crate-metadata.json

@@ -0,0 +1,140 @@
+{
+    "@context": [
+        "https://w3id.org/ro/crate/1.1/context",
+        {
+            "TestSuite": "https://w3id.org/ro/terms/test#TestSuite",
+            "TestInstance": "https://w3id.org/ro/terms/test#TestInstance",
+            "TestService": "https://w3id.org/ro/terms/test#TestService",
+            "TestDefinition": "https://w3id.org/ro/terms/test#TestDefinition",
+            "PlanemoEngine": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "JenkinsService": "https://w3id.org/ro/terms/test#JenkinsService",
+            "TravisService": "https://w3id.org/ro/terms/test#TravisService",
+            "GithubService": "https://w3id.org/ro/terms/test#GithubService",
+            "instance": "https://w3id.org/ro/terms/test#instance",
+            "runsOn": "https://w3id.org/ro/terms/test#runsOn",
+            "resource": "https://w3id.org/ro/terms/test#resource",
+            "definition": "https://w3id.org/ro/terms/test#definition",
+            "engineVersion": "https://w3id.org/ro/terms/test#engineVersion"
+        }
+    ],
+    "@graph": [
+        {
+            "@id": "ro-crate-metadata.json",
+            "@type": "CreativeWork",
+            "about": {
+                "@id": "./"
+            },
+            "conformsTo": [
+                { "@id": "https://w3id.org/ro/crate/1.1" },
+                { "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/" }
+            ]
+        },
+        {
+            "@id": "./",
+            "@type": "Dataset",
+            "name": "sort-and-change-case",
+            "description": "sort lines and change text to upper case",
+            "license": "Apache-2.0",
+            "mainEntity": {
+                "@id": "sort-and-change-case.ga"
+            },
+            "hasPart": [
+                {
+                    "@id": "sort-and-change-case.ga"
+                },
+                {
+                    "@id": "LICENSE"
+                },
+                {
+                    "@id": "README.md"
+                },
+                {
+                    "@id": "test/test1/sort-and-change-case-test.yml"
+                }
+            ],
+            "mentions": [
+                {
+                    "@id": "#test1"
+                }
+            ]
+        },
+        {
+            "@id": "sort-and-change-case.ga",
+            "@type": [
+                "File",
+                "SoftwareSourceCode",
+                "ComputationalWorkflow"
+            ],
+            "programmingLanguage": {
+                "@id": "#galaxy"
+            },
+            "name": "sort-and-change-case"
+        },
+        {
+            "@id": "LICENSE",
+            "@type": "File"
+        },
+        {
+            "@id": "README.md",
+            "@type": "File"
+        },
+        {
+            "@id": "#galaxy",
+            "@type": "ComputerLanguage",
+            "name": "Galaxy",
+            "identifier": {
+                "@id": "https://galaxyproject.org/"
+            },
+            "url": {
+                "@id": "https://galaxyproject.org/"
+            }
+        },
+        {
+            "@id": "#test1",
+            "name": "test1",
+            "@type": "TestSuite",
+            "mainEntity": {
+                "@id": "sort-and-change-case.ga"
+            },
+            "instance": [
+                {"@id": "#test1_1"}
+            ],
+            "definition": {"@id": "test/test1/sort-and-change-case-test.yml"}
+        },
+        {
+            "@id": "#test1_1",
+            "name": "test1_1",
+            "@type": "TestInstance",
+            "runsOn": {"@id": "https://w3id.org/ro/terms/test#JenkinsService"},
+            "url": "http://example.org/jenkins",
+            "resource": "job/tests/"
+        },
+        {
+            "@id": "test/test1/sort-and-change-case-test.yml",
+            "@type": [
+                "File",
+                "TestDefinition"
+            ],
+            "conformsTo": {"@id": "https://w3id.org/ro/terms/test#PlanemoEngine"},
+            "engineVersion": ">=0.70"
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#JenkinsService",
+            "@type": "TestService",
+            "name": "Jenkins",
+            "url": {"@id": "https://www.jenkins.io"}
+        },
+        {
+            "@id": "https://w3id.org/ro/terms/test#PlanemoEngine",
+            "@type": "SoftwareApplication",
+            "name": "Planemo",
+            "url": {"@id": "https://github.com/galaxyproject/planemo"}
+        },
+        {
+            "@id": "https://about.workflowhub.eu/Workflow-RO-Crate/",
+            "@type": "CreativeWork",
+            "name": "Workflow RO-Crate Profile",
+            "version": "0.2.0"
+        }
+    ]
+}

data/test/fixtures/ro-crate-galaxy-sortchangecase/sort-and-change-case.ga

@@ -0,0 +1,118 @@
+{
+    "uuid": "e2a8566c-c025-4181-9e90-7ed29d4e4df1",
+    "tags": [],
+    "format-version": "0.1",
+    "name": "sort-and-change-case",
+    "version": 0,
+    "steps": {
+        "0": {
+            "tool_id": null,
+            "tool_version": null,
+            "outputs": [],
+            "workflow_outputs": [],
+            "input_connections": {},
+            "tool_state": "{}",
+            "id": 0,
+            "uuid": "5a36fad2-66c7-4b9e-8759-0fbcae9b8541",
+            "errors": null,
+            "name": "Input dataset",
+            "label": "bed_input",
+            "inputs": [],
+            "position": {
+                "top": 200,
+                "left": 200
+            },
+            "annotation": "",
+            "content_id": null,
+            "type": "data_input"
+        },
+        "1": {
+            "tool_id": "sort1",
+            "tool_version": "1.1.0",
+            "outputs": [
+                {
+                    "type": "input",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "8237f71a-bc2a-494e-a63c-09c1e65ef7c8",
+                    "label": "sorted_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "output",
+                    "id": 0
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"style\": \"\\\"alpha\\\"\", \"column\": \"\\\"1\\\"\", \"__rerun_remap_job_id__\": null, \"column_set\": \"[]\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"header_lines\": \"\\\"0\\\"\", \"order\": \"\\\"ASC\\\"\"}",
+            "id": 1,
+            "uuid": "0b6b3cda-c75f-452b-85b1-8ae4f3302ba4",
+            "errors": null,
+            "name": "Sort",
+            "post_job_actions": {},
+            "label": "sort",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Sort"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 420
+            },
+            "annotation": "",
+            "content_id": "sort1",
+            "type": "tool"
+        },
+        "2": {
+            "tool_id": "ChangeCase",
+            "tool_version": "1.0.0",
+            "outputs": [
+                {
+                    "type": "tabular",
+                    "name": "out_file1"
+                }
+            ],
+            "workflow_outputs": [
+                {
+                    "output_name": "out_file1",
+                    "uuid": "c31cd733-dab6-4d50-9fec-b644d162397b",
+                    "label": "uppercase_bed"
+                }
+            ],
+            "input_connections": {
+                "input": {
+                    "output_name": "out_file1",
+                    "id": 1
+                }
+            },
+            "tool_state": "{\"__page__\": null, \"casing\": \"\\\"up\\\"\", \"__rerun_remap_job_id__\": null, \"cols\": \"\\\"c1\\\"\", \"delimiter\": \"\\\"TAB\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}",
+            "id": 2,
+            "uuid": "9698bcde-0729-48fe-b88d-ccfb6f6153b4",
+            "errors": null,
+            "name": "Change Case",
+            "post_job_actions": {},
+            "label": "change_case",
+            "inputs": [
+                {
+                    "name": "input",
+                    "description": "runtime parameter for tool Change Case"
+                }
+            ],
+            "position": {
+                "top": 200,
+                "left": 640
+            },
+            "annotation": "",
+            "content_id": "ChangeCase",
+            "type": "tool"
+        }
+    },
+    "annotation": "",
+    "a_galaxy_workflow": "true"
+}

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/input.bed

@@ -0,0 +1,3 @@
+chr1	66999824	67210768
+chr7	48998526	50489626
+chr1	66874821	66010368

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/output_exp.bed

@@ -0,0 +1,3 @@
+CHR1	66874821	66010368
+CHR1	66999824	67210768
+CHR7	48998526	50489626

data/test/fixtures/ro-crate-galaxy-sortchangecase/test/test1/sort-and-change-case-test.yml

@@ -0,0 +1,8 @@
+- doc: test with a small input
+  job:
+    bed_input:
+      class: File
+      path: input.bed
+  outputs:
+    uppercase_bed:
+      path: output_exp.bed

data/test/fixtures/sparse_directory_crate/ro-crate-preview.html

@@ -1,66 +1,67 @@
 <!DOCTYPE html>
 <html>
 <head>
-  <title>New RO-Crate</title>
-  <script type="application/ld+json">{
-  "@context": "https://w3id.org/ro/crate/1.1/context",
-  "@graph": [
-    {
-      "@id": "ro-crate-metadata.jsonld",
-      "@type": "CreativeWork",
-      "about": {
-        "@id": "./"
-      }
-    },
-    {
-      "@id": "ro-crate-preview.html",
-      "@type": "CreativeWork",
-      "about": {
-        "@id": "./"
-      }
-    },
-    {
-      "@id": "./",
-      "@type": "Dataset",
-      "hasPart": [
-        {
-          "@id": "fish/"
-        }
-      ]
-    },
-    {
-      "@id": "fish/",
-      "@type": "Dataset"
-    }
-  ]
-}</script>
-  <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
-  <meta name="keywords" content="RO-Crate">
+    <title>New RO-Crate</title>
+    <script type="application/ld+json">{
+        "@context": "https://w3id.org/ro/crate/1.0/context",
+        "@graph": [
+            {
+                "@id": "ro-crate-metadata.jsonld",
+                "@type": "CreativeWork",
+                "about": {
+                    "@id": "./"
+                }
+            },
+            {
+                "@id": "ro-crate-preview.html",
+                "@type": "CreativeWork",
+                "about": {
+                    "@id": "./"
+                }
+            },
+            {
+                "@id": "./",
+                "@type": "Dataset",
+                "hasPart": [
+                    {
+                        "@id": "listed_file.txt"
+                    }
+                ]
+            },
+            {
+                "@id": "listed_file.txt",
+                "@type": "File"
+            }
+        ]
+    }</script>
+    <meta name="generator" content="https://github.com/fbacall/ro-crate-ruby">
+    <meta name="keywords" content="RO-Crate">
 </head>
 <body>
-  <h1>New RO-Crate</h1>
-  
-  <p>
-    
-  </p>
-  <dl>
-    
-    
-    
-    
-  </dl>
+<h1>New RO-Crate</h1>
+Some stuff has been added here blablabla
 
-  <h2>Contents</h2>
-  <ul>
-    
-      <li id="__data_entity_fish/">
-        
-          <strong>fish/</strong>
-        
-        
-        
-      </li>
-    
-  </ul>
+<p>
+
+</p>
+<dl>
+
+
+
+
+</dl>
+
+<h2>Contents</h2>
+<ul>
+
+    <li id="__data_entity_listed_file.txt">
+
+        <strong>listed_file.txt</strong>
+
+
+
+    </li>
+
+</ul>
 </body>
-</html>
+</html>

data/test/fixtures/workflow-0.2.0/ro-crate-metadata.jsonld

@@ -123,7 +123,7 @@
         },
         {
             "@id": "workflow/workflow.knime",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -161,7 +161,7 @@
         },
         {
             "@id": "tools/RetroPath2.cwl",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wfdesc:Workflow"
             },
@@ -188,7 +188,7 @@
         },
         {
             "@id": "workflow/workflow.svg",
-            "@type": "ImageObject",
+            "@type": ["File", "ImageObject"],
             "additionalType": {"@id": "roterms:Sketch"},
             "encodingFormat": "image/svg+xml",
             "description": "Diagram of RetroPath2.0 workflow",
@@ -201,7 +201,7 @@
         },
         {
             "@id": "Dockerfile",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "url": {
                 "@id": "https://hub.docker.com/r/ibisba/retropath2/"
             },
@@ -220,7 +220,7 @@
         },
         {
             "@id": "test/test.sh",
-            "@type": "SoftwareSourceCode",
+            "@type": ["File", "SoftwareSourceCode"],
             "additionalType": {
                 "@id": "wf4ever:Script"
             },