release: 🔖 version 0.4.0

crs4 · Oct 24, 2024 · 8d1809a · 8d1809a
2 parents 6512923 + 61cf551
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diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "roc-validator"
-version = "0.3.0"
+version = "0.4.0"
 description = "A Python package to validate RO-Crates"
 authors = [
     "Marco Enrico Piras <[email protected]>",

diff --git a/rocrate_validator/profiles/provenance-run-crate/may/0_computational_workflow.ttl b/rocrate_validator/profiles/provenance-run-crate/may/0_computational_workflow.ttl
@@ -0,0 +1,63 @@
+# Copyright (c) 2024 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix dct: <http://purl.org/dc/terms/> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
+@prefix codemeta: <https://codemeta.github.io/terms/> .
+@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
+
+provenance-run-crate:ProvRCComputationalWorkflowOptional a sh:NodeShape ;
+    sh:name "Provenance Run Crate ComputationalWorkflow MAY" ;
+    sh:description "Optional properties of the Provenance Run Crate ComputationalWorkflow" ;
+    sh:targetClass bioschemas:ComputationalWorkflow ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "ComputationalWorkflow connection" ;
+        sh:description "ComputationalWorkflow may have a connection property" ;
+        sh:path wfrun:connection ;
+        sh:minCount 1 ;
+        sh:message "ComputationalWorkflow may have a connection property" ;
+    ] .
+
+
+provenance-run-crate:ProvRCComputationalWorkflowHowToOptional a sh:NodeShape ;
+    sh:name "Provenance Run Crate ComputationalWorkflow / HowTo MAY" ;
+    sh:description "Optional properties of a Provenance Run Crate ComputationalWorkflow that is also a HowTo" ;
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:prefixes ro-crate:sparqlPrefixes ;
+        sh:select """
+            SELECT ?this
+            WHERE {
+                ?this a bioschemas:ComputationalWorkflow .
+                ?this a schema:HowTo .
+            }
+        """
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "ComputationalWorkflow buildInstructions" ;
+        sh:description "A ComputationalWorkflow / HowTo MAY have a buildInstructions pointing to a File" ;
+        sh:path codemeta:buildInstructions ;
+        sh:class schema:MediaObject ;
+        sh:minCount 1 ;
+        sh:message "A ComputationalWorkflow / HowTo MAY have a buildInstructions pointing to a File" ;
+    ] .
diff --git a/rocrate_validator/profiles/provenance-run-crate/may/0_tool.ttl b/rocrate_validator/profiles/provenance-run-crate/may/0_tool.ttl
@@ -0,0 +1,83 @@
+# Copyright (c) 2024 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
+
+provenance-run-crate:ProvRCToolOptional a sh:NodeShape ;
+    sh:name "ProvRC tool MAY" ;
+    sh:description "Optional properties of a Provenance Run Crate tool" ;
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:prefixes ro-crate:sparqlPrefixes ;
+        sh:select """
+            SELECT ?this
+            WHERE {
+                { ?this a schema:SoftwareApplication } UNION
+                { ?this a schema:SoftwareSourceCode } UNION
+                { ?this a bioschemas:ComputationalWorkflow } .
+                ?workflow schema:hasPart ?this .
+                ?workflow a bioschemas:ComputationalWorkflow .
+            }
+        """
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "tool input" ;
+        sh:description "A tool MAY have an input" ;
+        sh:path bioschemas-cw:input ;
+        sh:minCount 1 ;
+        sh:message "A tool MAY have an input" ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "tool output" ;
+        sh:description "A tool MAY have an output" ;
+        sh:path bioschemas-cw:output ;
+        sh:minCount 1 ;
+        sh:message "A tool MAY have an output" ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "tool environment" ;
+        sh:description "A tool MAY have an environment" ;
+        sh:path wfrun:environment ;
+        sh:minCount 1 ;
+        sh:message "A tool MAY have an environment" ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "tool softwareRequirements" ;
+        sh:description "The tool MAY have a softwareRequirements that points to a SoftwareApplication" ;
+        sh:message "The tool MAY have a softwareRequirements that points to a SoftwareApplication" ;
+        sh:path schema:softwareRequirements ;
+        sh:class schema:SoftwareApplication ;
+        sh:minCount 1 ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "tool mainEntity" ;
+        sh:description "The tool MAY have a mainEntity that points to a SoftwareApplication" ;
+        sh:message "The tool MAY have a mainEntity that points to a SoftwareApplication" ;
+        sh:path schema:mainEntity ;
+        sh:class schema:SoftwareApplication ;
+        sh:minCount 1 ;
+    ] .
diff --git a/rocrate_validator/profiles/provenance-run-crate/may/1_howtostep.ttl b/rocrate_validator/profiles/provenance-run-crate/may/1_howtostep.ttl
@@ -0,0 +1,54 @@
+# Copyright (c) 2024 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
+@prefix codemeta: <https://codemeta.github.io/terms/> .
+
+provenance-run-crate:ProvRCHowToStepOptional a sh:NodeShape ;
+    sh:name "ProvRC HowToStep MAY" ;
+    sh:description "Optional properties of a Provenance Run Crate HowToStep" ;
+    sh:targetClass schema:HowToStep ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "HowToStep position" ;
+        sh:description "A HowToStep may indicate its position in the execution order via position" ;
+        sh:path schema:position ;
+        sh:minCount 1 ;
+        sh:message "A HowToStep may indicate its position in the execution order via position" ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "HowToStep connection" ;
+        sh:description "HowToStep may have a connection property" ;
+        sh:path wfrun:connection ;
+        sh:minCount 1 ;
+        sh:message "HowToStep may have a connection property" ;
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "HowToStep buildInstructions" ;
+        sh:description "A HowToStep MAY have a buildInstructions pointing to a File" ;
+        sh:path codemeta:buildInstructions ;
+        sh:class schema:MediaObject ;
+        sh:minCount 1 ;
+        sh:message "A HowToStep MAY have a buildInstructions pointing to a File" ;
+    ] .
diff --git a/rocrate_validator/profiles/provenance-run-crate/may/1_tool_action.ttl b/rocrate_validator/profiles/provenance-run-crate/may/1_tool_action.ttl
@@ -0,0 +1,51 @@
+# Copyright (c) 2024 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
+@prefix schema: <http://schema.org/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
+
+provenance-run-crate:ProvRCToolActionOptional a sh:NodeShape ;
+    sh:name "Provenance Run Crate tool action MAY" ;
+    sh:description "Optional properties of a Provenance Run Crate action that represents a tool execution" ;
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:prefixes ro-crate:sparqlPrefixes ;
+        sh:select """
+            SELECT ?this
+            WHERE {
+                { ?this a schema:CreateAction } UNION
+                { ?this a schema:ActivateAction } UNION
+                { ?this a schema:UpdateAction } .
+                ?this schema:instrument ?tool .
+                { ?tool a schema:SoftwareApplication } UNION
+                { ?tool a schema:SoftwareSourceCode } UNION
+                { ?tool a bioschemas:ComputationalWorkflow } .
+                ?workflow schema:hasPart ?tool .
+                ?workflow a bioschemas:ComputationalWorkflow .
+            }
+        """
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "Tool action resourceUsage" ;
+        sh:description "A tool action MAY have a resourceUsage" ;
+        sh:path wfrun:resourceUsage ;
+        sh:minCount 1 ;
+        sh:message "A tool action MAY have a resourceUsage" ;
+    ] .
diff --git a/rocrate_validator/profiles/provenance-run-crate/may/3_controlaction_organizeaction.ttl b/rocrate_validator/profiles/provenance-run-crate/may/3_controlaction_organizeaction.ttl
@@ -0,0 +1,60 @@
+# Copyright (c) 2024 CRS4
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+@prefix ro: <./> .
+@prefix ro-crate: <https://github.com/crs4/rocrate-validator/profiles/ro-crate/> .
+@prefix provenance-run-crate: <https://github.com/crs4/rocrate-validator/profiles/provenance-run-crate/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix schema: <http://schema.org/> .
+@prefix bioschemas: <https://bioschemas.org/> .
+@prefix bioschemas-cw: <https://bioschemas.org/ComputationalWorkflow#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix wfrun: <https://w3id.org/ro/terms/workflow-run#> .
+
+provenance-run-crate:ProvRCControlOrganizeActionOptional a sh:NodeShape ;
+    sh:name "ProvRC ControlAction and OrganizeAction MAY" ;
+    sh:description "Optional properties of a Provenance Run Crate ControlAction and OrganizeAction" ;
+    sh:targetClass schema:ControlAction ,
+                   schema:OrganizeAction ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:name "ControlAction and OrganizeAction actionStatus" ;
+        sh:description "The action MAY have an actionStatus" ;
+        sh:path schema:actionStatus ;
+        sh:minCount 1 ;
+        sh:message "The Action MAY have an actionStatus" ;
+    ] .
+
+provenance-run-crate:ProvRCControlOrganizeActionErrorOptional a sh:NodeShape ;
+    sh:name "ProvRC ControlAction and OrganizeAction error" ;
+    sh:description "error MAY be specified if actionStatus is set to FailedActionStatus" ;
+    sh:target [
+        a sh:SPARQLTarget ;
+        sh:prefixes ro-crate:sparqlPrefixes ;
+        sh:select """
+            SELECT ?this
+            WHERE {
+                { ?this a schema:ControlAction } UNION
+                { ?this a schema:OrganizeAction } .
+                ?this schema:actionStatus ?status .
+                FILTER(?status = "http://schema.org/FailedActionStatus") .
+            }
+        """
+    ] ;
+    sh:property [
+        a sh:PropertyShape ;
+        sh:path schema:error ;
+        sh:minCount 1 ;
+        sh:message "error MAY be specified if actionStatus is set to FailedActionStatus" ;
+    ] .