DRAFT: FnO 2 CWL

package.json

@@ -5,11 +5,16 @@
   "main": "example-client.js",
   "scripts": {
     "test": "ts-mocha 'src/**/*.test.ts'",
+    "test:fno2cwl": "ts-mocha 'src/FnO2CWL.test.ts'",
+    "test:fno2cwl:watch": "ts-mocha 'src/FnO2CWL.test.ts' -w --watch-files src/FnO2CWL.test.ts",
     "build:typescript": "npx tsc index.ts",
     "setup:download-rmlmapper": "curl -L https://github.com/RMLio/rmlmapper-java/releases/download/v4.11.0/rmlmapper.jar --output rmlmapper.jar"
   },
   "author": "Lander Noterman <lander.noterman@ugent.be>",
-  "contributors": [ "Gertjan De Mulder", "Ben De Meester" ],
+  "contributors": [
+    "Gertjan De Mulder",
+    "Ben De Meester"
+  ],
   "license": "ISC",
   "dependencies": {
     "@rmlio/rmlmapper-java-wrapper": "^2.0.2",

resources/fno-cwl/example01/.ipynb_checkpoints/abstract-wf-checkpoint.cwl

@@ -0,0 +1,27 @@
+cwlVersion: v1.2
+class: Workflow
+
+
+inputs:
+  message: string
+outputs: []
+
+steps:
+  echo:
+    run: ../echo.cwl
+    in:
+      message: message
+    out: [out]
+  # Here you know you want an operation that changes the case of
+  # the previous step, but you do not have an implementation yet.
+  uppercase:
+    run:
+      class: Operation
+      inputs:
+        message: string
+      outputs:
+        uppercase_message: string
+    in:
+      message:
+        source: echo/out
+    out: [uppercase_message]

resources/fno-cwl/example01/.ipynb_checkpoints/abstract-wf.cwl-checkpoint.ttl

@@ -0,0 +1,52 @@
+@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
+@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
+@prefix cwl: <https://w3id.org/cwl/cwl#> .
+@prefix ns1: <http://commonwl.org/cwltool#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix sld: <https://w3id.org/cwl/salad#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl> a cwl:Workflow ;
+    ns1:original_cwlVersion "v1.2" ;
+    Workflow:steps <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo>,
+        <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase> ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> ;
+    cwl:run <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/uppercase_message> ;
+    cwl:run [ a cwl:Operation ;
+            cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/message> ;
+            cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/uppercase_message> ] .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/uppercase_message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> a cwl:CommandLineTool ;
+    ns1:original_cwlVersion "v1.2" ;
+    cwl:baseCommand ( "echo" ) ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> ;
+    cwl:stdout "output.txt" .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> cwl:inputBinding [ ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> cwl:outputBinding [ CommandOutputBinding:glob "output.txt" ;
+            CommandOutputBinding:outputEval "$(self[0].contents)" ;
+            cwl:loadContents true ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> sld:type xsd:string .
+
+

resources/fno-cwl/example01/.ipynb_checkpoints/echo-checkpoint.cwl

@@ -0,0 +1,18 @@
+cwlVersion: v1.2
+class: CommandLineTool
+
+baseCommand: echo
+
+stdout: output.txt
+
+inputs:
+  message:
+    type: string
+    inputBinding: {}
+outputs:
+  out:
+    type: string
+    outputBinding:
+      glob: output.txt
+      loadContents: true
+      outputEval: $(self[0].contents)

resources/fno-cwl/example01/abstract-wf.cwl

@@ -0,0 +1,30 @@
+cwlVersion: v1.2
+class: Workflow
+
+
+inputs:
+  message: string
+outputs:
+  wf_output:
+    type: string
+    outputSource: uppercase/uppercase_message
+
+steps:
+  echo:
+    run: ./echo.cwl
+    in:
+      message: message
+    out: [out]
+  # Here you know you want an operation that changes the case of
+  # the previous step, but you do not have an implementation yet.
+  uppercase:
+    run:
+      class: Operation
+      inputs:
+        message: string
+      outputs:
+        uppercase_message: string
+    in:
+      message:
+        source: echo/out
+    out: [uppercase_message]

resources/fno-cwl/example01/abstract-wf.cwl.ttl

@@ -0,0 +1,56 @@
+@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
+@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
+@prefix cwl: <https://w3id.org/cwl/cwl#> .
+@prefix ns1: <http://commonwl.org/cwltool#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix sld: <https://w3id.org/cwl/salad#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl> a cwl:Workflow ;
+    ns1:original_cwlVersion "v1.2" ;
+    Workflow:steps <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo>,
+        <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase> ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#wf_output> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> ;
+    cwl:run <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/uppercase_message> ;
+    cwl:run [ a cwl:Operation ;
+            cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/message> ;
+            cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/uppercase_message> ] .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/run/uppercase_message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#wf_output> cwl:outputSource <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/uppercase_message> ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> a cwl:CommandLineTool ;
+    ns1:original_cwlVersion "v1.2" ;
+    cwl:baseCommand ( "echo" ) ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> ;
+    cwl:stdout "output.txt" .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> cwl:inputBinding [ ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> cwl:outputBinding [ CommandOutputBinding:glob "output.txt" ;
+            CommandOutputBinding:outputEval "$(self[0].contents)" ;
+            cwl:loadContents true ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#message> sld:type xsd:string .
+
+

resources/fno-cwl/example01/concrete-wf.cwl

@@ -0,0 +1,25 @@
+cwlVersion: v1.2
+class: Workflow
+
+
+inputs:
+  message: string
+outputs:
+  wf_output:
+    type: string
+    outputSource: uppercase/uppercase_message
+
+steps:
+  echo:
+    run: ./echo.cwl
+    in:
+      message: message
+    out: [out]
+  # Here you know you want an operation that changes the case of
+  # the previous step, but you do not have an implementation yet.
+  uppercase:
+    run: ./uppercase.cwl
+    in:
+      message:
+        source: echo/out
+    out: [uppercase_message]

resources/fno-cwl/example01/concrete-wf.cwl.ttl

@@ -0,0 +1,64 @@
+@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
+@prefix ExpressionTool: <https://w3id.org/cwl/cwl#ExpressionTool/> .
+@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
+@prefix cwl: <https://w3id.org/cwl/cwl#> .
+@prefix ns1: <http://commonwl.org/cwltool#> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix sld: <https://w3id.org/cwl/salad#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl> a cwl:Workflow ;
+    ns1:original_cwlVersion "v1.2" ;
+    Workflow:steps <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo>,
+        <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase> ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#wf_output> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo/out> ;
+    cwl:run <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#message> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase> cwl:in <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase/message> ;
+    cwl:out <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase/uppercase_message> ;
+    cwl:run <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase/message> cwl:source <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#echo/out> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#wf_output> cwl:outputSource <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#uppercase/uppercase_message> ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl> a cwl:CommandLineTool ;
+    ns1:original_cwlVersion "v1.2" ;
+    cwl:baseCommand ( "echo" ) ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> ;
+    cwl:stdout "output.txt" .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#message> cwl:inputBinding [ ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/echo.cwl#out> cwl:outputBinding [ CommandOutputBinding:glob "output.txt" ;
+            CommandOutputBinding:outputEval "$(self[0].contents)" ;
+            cwl:loadContents true ] ;
+    sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl> a cwl:ExpressionTool ;
+    ns1:original_cwlVersion "v1.2" ;
+    ExpressionTool:expression """${ return {"uppercase_message": inputs.message.toUpperCase()}; }
+""" ;
+    cwl:cwlVersion cwl:v1.2 ;
+    cwl:inputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl#message> ;
+    cwl:outputs <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl#uppercase_message> ;
+    cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl#message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/uppercase.cwl#uppercase_message> sld:type xsd:string .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/concrete-wf.cwl#message> sld:type xsd:string .
+
+

resources/fno-cwl/example01/cwl2fno-composition-mappings_result.ttl

@@ -0,0 +1,42 @@
+@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
+@prefix Workflow:             <https://w3id.org/cwl/cwl#Workflow/> .
+@prefix cwl:                  <https://w3id.org/cwl/cwl#> .
+@prefix ex:                   <http://example.org/> .
+@prefix fno:                  <https://w3id.org/function/ontology#> .
+@prefix fnoc:                 <https://w3id.org/function/vocabulary/composition#> .
+@prefix ns1:                  <http://commonwl.org/cwltool#> .
+@prefix rdf:                  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs:                 <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix sld:                  <https://w3id.org/cwl/salad#> .
+@prefix xsd:                  <http://www.w3.org/2001/XMLSchema#> .
+
+<file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/sparql/cwl2fno-composition-mappings.rq#workflowComposition>
+        rdf:type         fnoc:Composition ;
+        fnoc:composedOf  [ fnoc:mapFrom  [ ex:source      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> ;
+                                           ex:sourceTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo>
+                                         ] ;
+                           fnoc:mapTo    [ ex:sink      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> ;
+                                           ex:sinkTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase>
+                                         ]
+                         ] ;
+        fnoc:composedOf  [ fnoc:mapFrom  [ ex:source      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo/out> ;
+                                           ex:sourceTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#echo>
+                                         ] ;
+                           fnoc:mapTo    [ ex:sink      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/message> ;
+                                           ex:sinkTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase>
+                                         ]
+                         ] ;
+        fnoc:composedOf  [ fnoc:mapFrom  [ ex:source      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/uppercase_message> ;
+                                           ex:sourceTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl>
+                                         ] ;
+                           fnoc:mapTo    [ ex:sink      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#wf_output> ;
+                                           ex:sinkTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl>
+                                         ]
+                         ] ;
+        fnoc:composedOf  [ fnoc:mapFrom  [ ex:source      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#uppercase/uppercase_message> ;
+                                           ex:sourceTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl>
+                                         ] ;
+                           fnoc:mapTo    [ ex:sink      <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl#wf_output> ;
+                                           ex:sinkTool  <file:///Users/gertjandm/Git/KNoWS/projects/WORKFLOWS/fno-cwl/paper/example01/abstract-wf.cwl>
+                                         ]
+                         ] .