Added implementation for CQ11

docs/sparql/cq11.py

@@ -0,0 +1,147 @@
+"""\
+This script contains the SPARQL query for Competency Question 11 "How
+were workflow parameters used in tool runs?". The discussion on
+https://github.com/ResearchObject/workflow-run-crate/issues/25 resulted
+in the specification on describing parameter connection added with pull
+requests https://github.com/ResearchObject/workflow-run-crate/pull/13 ,
+https://github.com/ResearchObject/workflow-run-crate/pull/34 and
+https://github.com/ResearchObject/workflow-run-crate/pull/35 .
+"""
+
+import rdflib
+from pathlib import Path
+
+CRATE = Path("crate")
+
+g = rdflib.Graph()
+g.parse(CRATE/"ro-crate-metadata.json")
+
+QUERY = """\
+PREFIX	dcterms: <http://purl.org/dc/terms/>
+PREFIX	s: <http://schema.org/>
+PREFIX	bs: <https://bioschemas.org/>
+PREFIX	bswf: <https://bioschemas.org/ComputationalWorkflow#>
+PREFIX	bswfprofile: <https://bioschemas.org/profiles/ComputationalWorkflow/>
+PREFIX	rocrate: <https://w3id.org/ro/crate/>
+PREFIX	wfcrate: <https://w3id.org/workflowhub/workflow-ro-crate/>
+PREFIX	wfhprofile: <https://about.workflowhub.eu/Workflow-RO-Crate/>
+PREFIX	wrterm: <https://w3id.org/ro/terms/workflow-run#>
+
+SELECT DISTINCT ?execution  ?formal_parameter ?formal_parameter_name ?step ?step_source_name ?step_formal_parameter ?step_formal_parameter_name  ?input ?additional_type ?input_value
+WHERE   {
+    # This first part is just matching
+    # Workflow RO-Crates and its main entity
+    ?rocratejson
+        a s:CreativeWork ;
+        dcterms:conformsTo ?rocrateprofile ;
+        dcterms:conformsTo ?wfcrateprofile ;
+        s:about ?rootdataset .
+    ?rootdataset a s:Dataset .
+    FILTER (
+        STRSTARTS(str(?rocrateprofile), str(rocrate:))
+    )
+    FILTER (
+        ?wfcrateprofile = wfhprofile: || STRSTARTS(str(?wfcrateprofile), str(wfcrate:))
+    )
+    ?rootdataset
+        s:mainEntity ?main_entity .
+    ?main_entity
+        a bs:ComputationalWorkflow ;
+        dcterms:conformsTo ?bsworkflowprofile ;
+        bswf:input ?formal_parameter ;
+        s:step ?step .
+    FILTER (
+        STRSTARTS(str(?bsworkflowprofile), str(bswfprofile:))
+    )
+    ?formal_parameter
+        a bs:FormalParameter ;
+        s:name ?formal_parameter_name .
+    
+    # We are taking here only one execution
+    {
+        SELECT  ?execution
+        WHERE   {
+            ?rootdataset s:mentions ?execution .
+            ?execution
+                a s:CreateAction ;
+                s:instrument ?main_entity .
+        }
+        LIMIT 1
+    }
+
+    # We are assuming the workflow is the original, instead of a derivation
+    ?execution s:object ?input .
+    ?input s:exampleOfWork ?formal_parameter .
+    ?parameter_connection
+        a wrterm:ParameterConnection ;
+        wrterm:sourceParameter ?formal_parameter ;
+        wrterm:targetParameter ?step_formal_parameter .
+    ?step_formal_parameter
+        a bs:FormalParameter ;
+        s:name ?step_formal_parameter_name .
+    ?step_source
+        a s:SoftwareApplication ;
+        s:name ?step_source_name ;
+        bswf:input ?step_formal_parameter .
+    ?step
+        a s:HowToStep ;
+        s:workExample ?step_source .
+
+    # Now the details about the input
+    ?formal_parameter
+        s:additionalType ?additional_type .
+    {
+        # A file, which is a schema.org MediaObject
+        BIND ( "File" AS ?additional_type )
+        ?input
+            a s:MediaObject ;
+            s:name ?input_value .
+    } UNION {
+        # A directory, which is a schema.org Dataset
+        BIND ( "Dataset" AS ?additional_type )
+        ?input
+            a s:Dataset ;
+            s:name ?input_value .
+        FILTER EXISTS { 
+            # subquery to determine it is not an empty Dataset
+            SELECT ?dircomp
+            WHERE { 
+                ?input
+                    s:hasPart+ ?dircomp .
+                ?dircomp
+                    a s:MediaObject .
+            }
+        }
+    } UNION {
+        # A single property value, which can be either Integer, Text, Boolean or Float
+        VALUES (?additional_type) { ( "Integer" ) ( "Text" ) ( "Boolean" ) ( "Float" ) }
+        ?input
+            a s:PropertyValue ;
+            s:value ?input_value .
+    } UNION {
+        # A combination of files or directories or property values
+        BIND ( "Collection" AS ?additional_type )
+        VALUES ( ?leaf_type ) { ( s:Integer ) ( s:Text ) ( s:Boolean ) ( s:Float ) ( s:MediaObject ) ( s:Dataset ) }
+        ?input
+            a s:Collection ;
+            s:hasPart+ ?component .
+        ?component
+            a ?leaf_type .
+        OPTIONAL {
+            ?component s:name ?input_value .
+        }
+        OPTIONAL {
+            ?component s:alternateName ?input_value .
+        }
+        OPTIONAL {
+            ?component s:value ?input_value .
+        }
+    }
+}
+"""
+
+qres = g.query(QUERY)
+for i_row, row in enumerate(qres):
+    print(f"\nTuple {i_row}")
+    for key, val in row.asdict().items():
+        print(f"{key} => {val}")