Added query and example for CQ1

docs/sparql/cq1.py

@@ -0,0 +1,109 @@
+"""\
+This script contains the SPARQL query for Competency Question 1 "What
+container images (e.g., Docker) were used by the run?". The discussion on
+https://github.com/ResearchObject/workflow-run-crate/issues/9 resulted in
+"""
+
+import rdflib
+from pathlib import Path
+
+CRATE = Path("workflow_run_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	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#>
+PREFIX	wikidata: <https://www.wikidata.org/wiki/>
+
+SELECT ?execution ?container ?container_additional_type ?type_of_container ?type_of_container_type ?container_registry ?container_name ?container_tag ?container_sha256 ?container_platform ?container_arch
+WHERE   {
+    # This first part is just matching
+    # Workflow RO-Crates and its main entity
+    ?rocratejson
+        a s:CreativeWork ;
+        dcterms:conformsTo ?rocrateprofile ;
+        s:about ?rootdataset .
+    ?rootdataset a s:Dataset .
+    FILTER (
+        STRSTARTS(str(?rocrateprofile), str(rocrate:))
+    ) .
+    ?rocratejson dcterms:conformsTo ?wfcrateprofile .
+    FILTER (
+        ?wfcrateprofile = wfhprofile: || STRSTARTS(str(?wfcrateprofile), str(wfcrate:))
+    ) .
+    ?rootdataset
+        s:mainEntity ?main_entity .
+    ?main_entity
+        a bs:ComputationalWorkflow ;
+        dcterms:conformsTo ?bsworkflowprofile .
+    FILTER (
+        STRSTARTS(str(?bsworkflowprofile), str(bswfprofile:))
+    ) .
+
+    # We are taking here only the first 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 wrterm:containerImage ?container .
+    ?container
+        a wrterm:ContainerImage ;
+        s:additionalType ?container_additional_type .
+    OPTIONAL {
+        ?container
+            s:softwareRequirements ?container_type ;
+            s:applicationCategory ?type_of_container .
+        ?container_type
+            a s:SoftwareApplication ;
+            s:applicationCategory ?type_of_container_type .
+        FILTER(
+            STRSTARTS(str(?type_of_container), str(wikidata:)) &&
+            STRSTARTS(str(?type_of_container_type), str(wikidata:))
+        ) .
+    }
+    OPTIONAL {
+        ?container wrterm:registry ?container_registry .
+    }
+    OPTIONAL {
+        ?container s:name ?container_name .
+    }
+    OPTIONAL {
+        ?container wrterm:tag ?container_tag .
+    }
+    OPTIONAL {
+        ?container wrterm:sha256 ?container_sha256 .
+    }
+    OPTIONAL {
+        ?container
+            a s:SoftwareApplication ;
+            s:operatingSystem ?container_platform .
+    }
+    OPTIONAL {
+        ?container
+            a s:SoftwareApplication ;
+            s:processorRequirements ?container_arch .
+    }
+}
+"""
+
+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}")