fix formatting

ResearchObject · Jan 16, 2023 · a110f03 · a110f03
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diff --git a/docs/profiles/0.1-DRAFT/process_run_crate.md b/docs/profiles/0.1-DRAFT/process_run_crate.md
@@ -35,7 +35,7 @@ This profile requires the indication of [Software used to create files](https://
     {
         "@id": "./",
         "@type": "Dataset",
-        "conformsTo": { "@id": "https://w3id.org/ro/wfrun/process/0.1" },
+        "conformsTo": {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
         "hasPart": [
             {"@id": "pics/2017-06-11%2012.56.14.jpg"},
             {"@id": "pics/sepia_fence.jpg"}
@@ -92,8 +92,6 @@ This profile requires the indication of [Software used to create files](https://
 Note that the command line shown in the action's `description` is not directly re-executable, as file paths are not required to match the RO-Crate locations. For a more structural and reproducible description of tool executions, see [Workflow Run Crate](workflow_run_crate).
 
 
-
-
 ## Requirements
 
 <table>
@@ -110,7 +108,7 @@ Note that the command line shown in the action's `description` is not directly r
   <tr>
    <td>conformsTo</td>
    <td>MUST</td>
-   <td>MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, e.g. <code>{"@id": "https://w3id.org/ro/wfrun/process/0.1"}</code>
+   <td>MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, e.g. <code>{"@id": "https://w3id.org/ro/wfrun/process/0.1"}</code></td>
   </tr>
 
   <tr>
@@ -160,7 +158,7 @@ Note that the command line shown in the action's `description` is not directly r
   <tr>
    <td>@id</td>
    <td>MUST</td>
-   <td>A unique identifier for the execution, e.g. <code>"urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1"</code>, <code>"#f99a8e6c"</code>. MAY be an absolute URI, e.g. <a href="http://example.com/runs/846756b228c1">http://example.com/runs/846756b228c1</a>. The use of randomly generated <a href="https://datatracker.ietf.org/doc/html/rfc4122">UUIDs</a> (type 4) is RECOMMENDED. SHOULD be listed under <a href="http://schema.org/mentions">mentions</a> of the [root data entity](https://www.researchobject.org/ro-crate/1.1/root-data-entity.html).</td>
+   <td>A unique identifier for the execution, e.g. <code>"urn:uuid:50ec5c76-1f7a-4130-8ef6-846756b228c1"</code>, <code>"#f99a8e6c"</code>. MAY be an absolute URI, e.g. <a href="http://example.com/runs/846756b228c1">http://example.com/runs/846756b228c1</a>. The use of randomly generated <a href="https://datatracker.ietf.org/doc/html/rfc4122">UUIDs</a> (type 4) is RECOMMENDED. SHOULD be listed under <a href="http://schema.org/mentions">mentions</a> of the <a href="https://www.researchobject.org/ro-crate/1.1/root-data-entity.html">root data entity</a>.</td>
   </tr>
 
   <tr>

diff --git a/docs/profiles/0.1-DRAFT/provenance_run_crate.md b/docs/profiles/0.1-DRAFT/provenance_run_crate.md
@@ -32,7 +32,7 @@ The following diagram shows the relationships between all provenance-related ent
 ## Example Metadata File (`ro-crate-metadata.json`)
 
 ```json
-{ "@context": "https://w3id.org/ro/crate/1.1/context", 
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
   "@graph": [
     {
         "@id": "ro-crate-metadata.json",
@@ -47,10 +47,10 @@ The following diagram shows the relationships between all provenance-related ent
         "@id": "./",
         "@type": "Dataset",
         "conformsTo": [
-            { "@id": "https://w3id.org/ro/wfrun/process/0.1" },
-            { "@id": "https://w3id.org/ro/wfrun/workflow/0.1" },
-            { "@id": "https://w3id.org/ro/wfrun/provenance/0.1" },
-            { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}            
+            {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
+            {"@id": "https://w3id.org/ro/wfrun/workflow/0.1"},
+            {"@id": "https://w3id.org/ro/wfrun/provenance/0.1"},
+            {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
         ],
         "hasPart": [
             {"@id": "packed.cwl"},
@@ -72,7 +72,7 @@ The following diagram shows the relationships between all provenance-related ent
         "@type": "CreativeWork",
         "name": "Workflow Run Crate",
         "version": "0.1"
-    },    
+    },
     {   "@id": "https://w3id.org/ro/wfrun/provenance/0.1",
         "@type": "CreativeWork",
         "name": "Provenance Run Crate",
@@ -321,6 +321,7 @@ The following diagram shows the relationships between all provenance-related ent
         "value": "True"
     }
 ]
+}
 ```
 
 
@@ -448,7 +449,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_
   <tr>
    <td>conformsTo</td>
    <td>MUST</td>
-   <td>Array MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, and SHOULD also reference versioned permalinks for <a href="https://w3id.org/ro/wfrun/process/0.1">Process Run Crate</a>, <a href="https://w3id.org/ro/wfrun/workflow/0.1">Workflow Run Crate</a> and <a href="https://w3id.org/workflowhub/workflow-ro-crate/1.0">Workflow RO-Crate</a>.
+   <td>Array MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, and SHOULD also reference versioned permalinks for <a href="https://w3id.org/ro/wfrun/process/0.1">Process Run Crate</a>, <a href="https://w3id.org/ro/wfrun/workflow/0.1">Workflow Run Crate</a> and <a href="https://w3id.org/workflowhub/workflow-ro-crate/1.0">Workflow RO-Crate</a>.</td>
   </tr>
 
   <tr>

diff --git a/docs/profiles/0.1-DRAFT/workflow_run_crate.md b/docs/profiles/0.1-DRAFT/workflow_run_crate.md
@@ -21,10 +21,10 @@ This profile is a combination of [Process Run Crate](process_run_crate) and [Wor
 Some workflows have multiple inputs/outputs that, in conformance with the [Bioschemas ComputationalWorkflow profile](https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE) are defined as [FormalParameter](https://bioschemas.org/types/FormalParameter/1.0-RELEASE) entities. It is OPTIONAL to include these definitions on a `ComputationalWorkflow`. A data entity or `PropertyValue` that realizes a `FormalParameter` definition SHOULD refer to it via [exampleOfWork](https://schema.org/exampleOfWork); additionally, if the data entity or `PropertyValue` is an illustrative example of the parameter, the latter MAY refer back to the former using the reverse property [workExample](https://schema.org/workExample). This links the `input` of a `ComputationalWorkflow` to the `object` of a `CreateAction`, and the `output` of a `ComputationalWorkflow` to the `result` of a `CreateAction`. An `object` item that does not match a slot in the workflow's input interface (e.g., a [configuration file](process_run_crate#referencing-configuration-files) read from a predefined path) MUST NOT refer to a `FormalParameter` of the `ComputationalWorkflow` via `exampleOfWork`. A `FormalParameter` that maps to a `PropertyValue` SHOULD have a subclass of [DataType](https://schema.org/DataType) (e.g., [Integer](https://schema.org/Integer)) &mdash; or [PropertyValue](https://schema.org/PropertyValue), in the case of dictionary-like structured types &mdash; as its `additionalType`. See [CWL parameter mapping](/workflow-run-crate/cwl_param_mapping) for an example.
 
 
-## Example
+## Example Metadata File (`ro-crate-metadata.json`)
 
 ```json
-{ "@context": "https://w3id.org/ro/crate/1.1/context", 
+{ "@context": "https://w3id.org/ro/crate/1.1/context",
   "@graph": [
     {
         "@id": "ro-crate-metadata.json",
@@ -39,9 +39,9 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc
         "@id": "./",
         "@type": "Dataset",
         "conformsTo": [
-            { "@id": "https://w3id.org/ro/wfrun/process/0.1" },
-            { "@id": "https://w3id.org/ro/wfrun/workflow/0.1" },
-            { "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}            
+            {"@id": "https://w3id.org/ro/wfrun/process/0.1"},
+            {"@id": "https://w3id.org/ro/wfrun/workflow/0.1"},
+            {"@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"}
         ],
         "hasPart": [
             {"@id": "Galaxy-Workflow-Hello_World.ga"},
@@ -201,6 +201,7 @@ Some workflows have multiple inputs/outputs that, in conformance with the [Biosc
         "name": "Workflow Execution Summary of Hello World"
     }
 ]
+}
 ```
 
 
@@ -222,7 +223,7 @@ This profile inherits the requirements of [Process Run Crate](process_run_crate)
   <tr>
    <td>conformsTo</td>
    <td>MUST</td>
-   <td>Array MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, and SHOULD also reference versioned permalinks for <a href="https://w3id.org/ro/wfrun/process/0.1">Process Run Crate</a> and <a href="https://w3id.org/workflowhub/workflow-ro-crate/1.0">Workflow RO-Crate</a>.
+   <td>Array MUST reference a <code>CreativeWork</code> entity with an <code>@id</code> URI that is consistent with the versioned <em>Permalink</em> of this document, and SHOULD also reference versioned permalinks for <a href="https://w3id.org/ro/wfrun/process/0.1">Process Run Crate</a> and <a href="https://w3id.org/workflowhub/workflow-ro-crate/1.0">Workflow RO-Crate</a>.</td>
   </tr>
 
   <tr>