Merge pull request #80 from simleo/update_05_links

Fix 0.5-DRAFT links

Author: stain

docs/profiles/0.5-DRAFT/process_run_crate/index.md

@@ -13,19 +13,19 @@ title: Process Run Crate
 * Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html)
 * Extends:
   - [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1)
-* JSON-LD context: <https://w3id.org/ro/terms/workflow-run>
+* JSON-LD context: <https://w3id.org/ro/terms/workflow-run/context>
 * Vocabulary terms:  <https://w3id.org/ro/terms/workflow-run#>
 
-This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
+This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
 
 
 ## Overview
 
-This profile is used to describe the execution of an _implicit_ workflow, indicating that one or more computational tools have been executed, typically generating some result files that are represented as [data entities](https://www.researchobject.org/ro-crate/1.1/data-entities.html) in the RO-Crate.
+This profile is used to describe the execution of an _implicit_ workflow, indicating that one or more computational tools have been executed, typically generating some result files that are represented as [data entities](https://www.researchobject.org/ro-crate/specification/1.1/data-entities.html) in the RO-Crate.
 
 By "implicit workflow" we mean that the composition of these tools may have been done by hand (a user executes one tool following another) or by some script that has not yet been included as part of the crate (for instance because it is an embedded part of a larger application).
 
-This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/1.1/provenance.html#software-used-to-create-files), namely a [SoftwareApplication](http://schema.org/SoftwareApplication) (the tool) and a [CreateAction](http://schema.org/CreateAction) (the execution of said tool).
+This profile requires the indication of [Software used to create files](https://www.researchobject.org/ro-crate/specification/1.1/provenance.html#software-used-to-create-files), namely a [SoftwareApplication](http://schema.org/SoftwareApplication) (the tool) and a [CreateAction](http://schema.org/CreateAction) (the execution of said tool).
 
 The following diagram shows the relationships between provenance-related entities. Note the distinction between *prospective* provenance (plans for activities, e.g., an application) and *retrospective* provenance (what actually happened, e.g. the execution of an application).
 
@@ -40,7 +40,10 @@ The following diagram shows the relationships between provenance-related entitie
 <!-- Remember to update above as well as below! -->
 
 ```json
-{ "@context": "https://w3id.org/ro/crate/1.1/context", 
+{ "@context": [
+    "https://w3id.org/ro/crate/1.1/context",
+    "https://w3id.org/ro/terms/workflow-run/context"
+  ],
   "@graph": [
     {
         "@id": "ro-crate-metadata.json",
@@ -105,7 +108,7 @@ The following diagram shows the relationships between provenance-related entitie
 }
 ```
 
-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).
+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
@@ -400,13 +403,13 @@ The use case shown here is an example of a situation where it's important to ref
 
 ## Representing environment variable settings
 
-The behavior of some applications may be modified by setting appropriate environment variables. These are different from ordinary application inputs in that they are part of the environment in which the process runs, rather than parameters supplied through a command line or a graphical interface. To represent the fact that an environment variable was set to a certain value during the execution of an action, use the `environment` property from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace, making it point to a `PropertyValue` that describes the setting:
+The behavior of some applications may be modified by setting appropriate environment variables. These are different from ordinary application inputs in that they are part of the environment in which the process runs, rather than parameters supplied through a command line or a graphical interface. To represent the fact that an environment variable was set to a certain value during the execution of an action, use the `environment` property from the [workflow-run](https://w3id.org/ro/terms/workflow-run#https://w3id.org/ro/terms/workflow-run/context) ro-terms namespace, making it point to a `PropertyValue` that describes the setting:
 
 ```json
 {
     "@context": [
         "https://w3id.org/ro/crate/1.1/context",
-        "https://w3id.org/ro/terms/workflow-run"
+        "https://w3id.org/ro/terms/workflow-run/context"
     ],
     "@graph": [
         ...

docs/profiles/0.5-DRAFT/provenance_run_crate/index.md

@@ -13,23 +13,23 @@ title: Provenance Run Crate
 * Profile Crate: [ro-crate-metadata.json](ro-crate-metadata.json) [ro-crate-preview.html](ro-crate-preview.html)
 * Extends:
   - [Workflow Run Crate](https://w3id.org/ro/wfrun/workflow/0.5-DRAFT)
-* JSON-LD context: <https://w3id.org/ro/terms/workflow-run>
+* JSON-LD context: <https://w3id.org/ro/terms/workflow-run/context>
 * Vocabulary terms:  <https://w3id.org/ro/terms/workflow-run#>
 
-This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
+This profile uses terminology from the [RO-Crate 1.1 specification](https://w3id.org/ro/crate/1.1), and [extends it](https://www.researchobject.org/ro-crate/specification/1.1/appendix/jsonld.html#extending-ro-crate) with additional terms from the [workflow-run](https://github.com/ResearchObject/ro-terms/tree/master/workflow-run) ro-terms namespace.
 
 
 ## Overview
 
-This profile extends [Workflow Run Crate](workflow_run_crate) with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs.
+This profile extends [Workflow Run Crate](../workflow_run_crate) with specifications to describe internal details of the workflow run, such as step executions and intermediate outputs.
 
-A Provenance Run Crate MUST record the details of *tool* executions orchestrated by the workflow through additional [CreateAction](http://schema.org/CreateAction) entities, each of which MUST refer to an entity representing the tool itself via [instrument](http://schema.org/instrument) as specified in [Process Run Crate](process_run_crate). Entities representing the tools MAY reference formal parameter definitions via `input` and `output` (and `environment`, in the case of [environment variables](workflow_run_crate#environment-variables-as-formal-parameters)) as specified in [Workflow Run Crate](workflow_run_crate). The workflow MUST refer to the orchestrated tools via [hasPart](http://schema.org/hasPart) (the usage of `hasPart` for this purpose follows the Bioschemas [ComputationalWorkflow profile](http://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)).
+A Provenance Run Crate MUST record the details of *tool* executions orchestrated by the workflow through additional [CreateAction](http://schema.org/CreateAction) entities, each of which MUST refer to an entity representing the tool itself via [instrument](http://schema.org/instrument) as specified in [Process Run Crate](../process_run_crate). Entities representing the tools MAY reference formal parameter definitions via `input` and `output` (and `environment`, in the case of [environment variables](../workflow_run_crate#environment-variables-as-formal-parameters)) as specified in [Workflow Run Crate](../workflow_run_crate). The workflow MUST refer to the orchestrated tools via [hasPart](http://schema.org/hasPart) (the usage of `hasPart` for this purpose follows the Bioschemas [ComputationalWorkflow profile](http://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE)).
 
 The crate SHOULD also record *step* executions via [ControlAction](http://schema.org/ControlAction) instances, each of which MUST reference: a [HowToStep](http://schema.org/HowToStep) instance representing the step via `instrument`; the `CreateAction` representing the corresponding tool run via `object`. The workflow MUST reference any `HowToStep` instances that represent its steps via [step](http://schema.org/step). Each `HowToStep` instance MUST reference the entity that represents its corresponding tool via [workExample](http://schema.org/workExample), and MAY indicate its position in the execution order via [position](http://schema.org/position). In addition to `File`, `SoftwareSourceCode` and `ComputationalWorkflow`, a workflow that points to step metadata via `step` MUST have a type of [HowTo](http://schema.org/HowTo).
 
 The crate MAY also include an [OrganizeAction](http://schema.org/OrganizeAction) representing the execution of the workflow *engine* (e.g. cwltool), which MUST point to: an entity representing the workflow engine (e.g. a [SoftwareApplication](http://schema.org/SoftwareApplication)) via `instrument`; the `CreateAction` that represents the workflow run via `result`; the `ControlAction` instances representing the step executions via `object`.
 
-The tool that implements a step can in turn be a workflow (*nested workflow* or *subworkflow*): in this case, it MUST be represented as a `ComputationalWorkflow`, and all of the above directions apply to it recursively. If the subworkflow is described in a section of the main workflow (e.g. as in [packed CWL workflows](https://www.commonwl.org/v1.2/CommandLineTool.html#Packed_documents)), rather than in a file of its own, it SHOULD be added to the crate as a [contextual entity](https://www.researchobject.org/ro-crate/1.1/contextual-entities.html): in this case, its type list MUST NOT include `File`.
+The tool that implements a step can in turn be a workflow (*nested workflow* or *subworkflow*): in this case, it MUST be represented as a `ComputationalWorkflow`, and all of the above directions apply to it recursively. If the subworkflow is described in a section of the main workflow (e.g. as in [packed CWL workflows](https://www.commonwl.org/v1.2/CommandLineTool.html#Packed_documents)), rather than in a file of its own, it SHOULD be added to the crate as a [contextual entity](https://www.researchobject.org/ro-crate/specification/1.1/contextual-entities.html): in this case, its type list MUST NOT include `File`.
 
 The following diagram shows the relationships between all provenance-related entities. Note the distinction between *prospective* provenance (plans for activities, e.g. a workflow) and *retrospective* provenance (what actually happened, e.g. the execution of a workflow).
 
@@ -45,7 +45,10 @@ The following diagram shows the relationships between all provenance-related ent
 
 
 ```json
-{ "@context": "https://w3id.org/ro/crate/1.1/context",
+{ "@context": [
+    "https://w3id.org/ro/crate/1.1/context",
+    "https://w3id.org/ro/terms/workflow-run/context"
+  ],
   "@graph": [
     {
         "@id": "ro-crate-metadata.json",
@@ -392,7 +395,7 @@ Note that the `workflow-run` terms are not part of the standard RO-Crate context
 {
     "@context": [
         "https://w3id.org/ro/crate/1.1/context",
-        "https://w3id.org/ro/terms/workflow-run"
+        "https://w3id.org/ro/terms/workflow-run/context"
     ],
     "@graph": [...]
 }
@@ -436,12 +439,12 @@ A workflow engine may support configuration through a configuration file. In thi
 ...
 ```
 
-See also the [section on referencing configuration files of executed tools](process_run_crate#referencing-configuration-files).
+See also the [section on referencing configuration files of executed tools](../process_run_crate#referencing-configuration-files).
 
 
 ## Tool wrapper dependencies
 
-In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`:
+In some workflow systems (e.g., CWL, Galaxy), tools are typically wrappers for an executable written in a scripting programming language. This MAY be represented by listing the wrapped tool and its dependencies as described in [Specifying software dependencies](../process_run_crate#specifying-software-dependencies). The wrapped tool can be highlighted by using `mainEntity`:
 
 ```json
 {
@@ -512,7 +515,7 @@ The values of `propertyID` SHOULD be URLs that univocally identify the quantity.
 
 ## Requirements
 
-The requirements of this profile are those of [Workflow Run Crate](workflow_run_crate) plus the ones listed below.
+The requirements of this profile are those of [Workflow Run Crate](../workflow_run_crate) plus the ones listed below.
 
 <table>
 
@@ -544,7 +547,7 @@ The requirements of this profile are those of [Workflow Run Crate](workflow_run_
   <tr>
    <td>hasPart</td>
    <td>MUST</td>
-   <td>Identifiers of the <em>tools</em> (including subworkflows) orchestrated by this workflow, represented as specified in the <a href="process_run_crate#requirements">Process Run Crate requirements</a> under "SoftwareApplication". The referenced tools MAY also incude formal parameter definitions via <code>input</code> and <code>output</code> as specified in <a href="workflow_run_crate">Workflow Run Crate</a>. In the case of subworkflows, the type MUST include <code>ComputationalWorkflow</code></td>
+   <td>Identifiers of the <em>tools</em> (including subworkflows) orchestrated by this workflow, represented as specified in the <a href="../process_run_crate#requirements">Process Run Crate requirements</a> under "SoftwareApplication". The referenced tools MAY also incude formal parameter definitions via <code>input</code> and <code>output</code> as specified in <a href="../workflow_run_crate">Workflow Run Crate</a>. In the case of subworkflows, the type MUST include <code>ComputationalWorkflow</code></td>
   </tr>
 
   <tr>