WIP: ShEx validation method

.gitignore

@@ -2,3 +2,9 @@ _site/
 .sass-cache/
 .jekyll-cache/
 .jekyll-metadata
+__pycache__
+build
+*egg-info
+.coverage
+coverage.xml
+dist

MANIFEST.in

@@ -1,6 +1,7 @@
 graft docs
 graft src
 
+include *.shex
 include *.rst
 include LICENSE
 include requirements.txt

setup.cfg

@@ -36,7 +36,13 @@ install_requires=
     cwlprov==0.1.1
     networkx==2.8
     prov>=1.5.1
-    rocrate~=0.7
+    rocrate~=0.7    
+    rdflib~=6.2
+    PyShEx~=0.8.1
+    arcp~=0.2.1
+    rdflib_shim>=1.0.3
+    rocrateValidator @ git+https://github.com/ResearchObject/ro-crate-validator-py.git@v0.2.16-RC4
+    importlib_resources~=5.12
 
 [options.entry_points]
 console_scripts=

src/runcrate/cli.py

@@ -14,10 +14,10 @@
 
 import sys
 from pathlib import Path
-
 import click
 
 from . import __version__
+from .validator import CrateValidator
 from .convert import ProvCrateBuilder
 from .report import dump_crate_actions
 
@@ -56,8 +56,7 @@ def cli():
     help="path to a README file (should be README.md in Markdown format)",
 )
 def convert(root, output, license, workflow_name, readme):
-    """\
-    Convert a CWLProv RO bundle into a Workflow Run RO-Crate.
+    """Convert a CWLProv RO bundle into a Workflow Run RO-Crate.
 
     RO_DIR: top-level directory of the CWLProv RO
     """
@@ -72,6 +71,64 @@ def convert(root, output, license, workflow_name, readme):
 
 
 @cli.command()
+@click.option("-s", "--skip-ro-crate-check", is_flag=True, help="Skip general RO-Crate validation")
+@click.option("-p", "--process-run", is_flag=True, help="Validate against the Process Run Crate profile")
+@click.option("-w", "--workflow-run", is_flag=True, help="Validate against the Workflow Run Crate profile")
+@click.option("-P", "--provenance-run", is_flag=True, help="Validate against the Provenance Run Crate profile")
+@click.option("-W", "--workflow", is_flag=True, help="Validate against the Workflow RO-Crate profile")
+@click.option("-b", "--bioschemas", is_flag=True, help="Validate against Bioschemas profiles (ComputationalWorkflow FormalParameter)")
+@click.option("-d", "--debug", is_flag=True, help="Enable debug output")
+
+@click.argument(
+    "crate",
+    metavar="CRATE",
+    type=click.Path(exists=True, file_okay=False, readable=True, path_type=Path),
+)
+
+def validate(crate, skip_ro_crate_check, workflow, process_run, workflow_run, provenance_run, bioschemas, debug):
+    """Validate a Process/Workflow/Provenance Run Crate (experimental)
+
+    CRATE: RO-Crate Root directory
+
+    Unless forced (e.g. --workflow-run), the validation will use
+    the crate's profile(s) as indicated with conformsTo.
+    """
+    validator = CrateValidator(crate)
+    if debug:
+        validator.debug = True
+    if not skip_ro_crate_check:
+        validator.ro_crate_check()
+        # TODO: Check output
+
+    # Make sure Metadata File is readable and described
+    if not validator.metadata_file_check():
+        return -2
+
+    guess_profile = not workflow and not process_run and not workflow_run and not process_run and not bioschemas
+    if guess_profile:
+        # Detect profile from conformsTo
+        (workflow,process_run,workflow_run,provenance_run,bioschemas) = validator._detect_profiles()
+
+    if not workflow and not process_run and not workflow_run and not process_run:
+        print("Could not detect profile, check \"conformsTo\" or force profile check (e.g. --workflow-run)", file=sys.stderr)
+        return -1
+
+    if workflow:
+        print("Validating against Workflow profile")
+        validator.workflow_check()
+    if bioschemas:
+        print("Validating against Bioschemas ComputationalWorkflow profile")
+        validator.computationalworkflow_check()
+    if process_run:
+        print("Validating against Process Run profile")
+        validator.process_run_check()
+    if workflow_run:
+        print("Validating against Workflow Run profile")
+        validator.workflow_run_check()
+    if provenance_run:
+        print("Validating against Provenance Run profile")
+        validator.provenance_run_check()
+        return
 @click.argument(
     "crate",
     metavar="RO_CRATE",

src/runcrate/shex/bioschemas-computationalworkflow-1.0.shex

@@ -0,0 +1,197 @@
+# Copyright 2023 The University of Manchester
+#
+# 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.
+
+## ShEX shape for https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE and
+# https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE
+# following MUST requirements ("marginality: minimum"), with
+# all SHOULD/COULD (recommended/optional) marked as optional (*/?)
+# 
+# NOTE: As this shape is meant to be used with a workflow-crate,  it assumes the
+# workflow is mainEntity of an RO-Crate root, which is the start focus. That also
+# means some contextual entities are assumed to be explicit with a @type and s:name
+# rather than just a IRI.
+
+## FIXME: Update namespace
+PREFIX p: <https://bioschemas.example.org/profiles/ComputationalWorkflow/1.0-RELEASE#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX s: <http://schema.org/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX bioschemas: <https://bioschemas.org/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX sh: <http://www.w3.org/ns/shacl#>
+
+start = @p:Root
+
+p:Root {  
+  s:mainEntity IRI @p:MainWorkflow;
+}
+p:MainWorkflow extra rdf:type { 
+  ## Marginality: Minimum
+
+  a [bioschemas:ComputationalWorkflow];
+  dct:conformsTo [<https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE>];
+  s:creator @p:PersonOrOrg+;
+  # NOTE: We won't be picky about xsd type even if profile insists Date or DateTime
+  s:dateCreated LITERAL;
+
+  # NOTE: interpret profile liberally,  in/out can be 0 if no input/output, otherwise required
+  s:input @p:FormalParameter*;
+  s:output @p:FormalParameter*;
+
+  ( s:licence LITERAL |
+    s:licence {
+      # Require contextual entity in RO-Crate
+      a [s:Creativework];
+      s:name LITERAL;
+    }
+  )+;
+  s:name LITERAL;
+
+  ( s:programmingLanguage LITERAL | 
+    s:programmingLanguage {
+      # Require contextual entity in RO-Crate
+      a [s:ComputerLanguage];
+      s:name LITERAL;
+    }
+  );
+
+  s:sdPublisher @p:PersonOrOrg;
+  ( # Depends on context
+    s:url IRI|
+    s:url xsd:string;
+  );
+
+  s:version LITERAL;
+
+  ## Marginality: Recommended
+
+  ( s:citation LITERAL | 
+    s:citation { 
+      # FIXME: Won't detect subtypes like s:ScholarlyArticle without rdfs inferencing
+      a [s:CreativeWork];
+#      s:name xsd:string
+    };
+  )? // sh:severity sh:Info // sh:message "It is RECOMMENDED to include a citation";
+
+  s:contributor @p:PersonOrOrg*;
+
+  ( s:creativeWorkStatus LITERAL | 
+    s:creativeWorkStatus IRI;
+  )?;
+
+  ( s:documentation {
+      a [s:CreativeWork];      
+   } |
+    s:documentation IRI;
+  );
+
+  s:funding {
+    a [s:Grant];
+  }*;
+
+  s:hasPart {
+    # Extended types to include tools
+    ( a [s:CreativeWork] | 
+      a [s:SoftwareApplication] | 
+      a [s:SoftwareSourceCode]
+    ) ;
+  }*; 
+
+  ( 
+    s:isBasedOn { a [s:CreativeWork] } | 
+    s:isBasedOn { a [s:Product] } | 
+    s:isBasedOn IRI 
+  )?;
+
+  s:keywords LITERAL?;
+
+  s:maintainer @p:PersonOrOrg*;
+
+  s:producer @p:PersonOrOrg*;
+
+  s:publisher @p:PersonOrOrg*;
+
+  s:runtimePlatform LITERAL?;
+  ( 
+    s:softwareRequirements LITERAL | 
+    s:softwareRequirements IRI
+  )*;
+
+  s:targetProduct { 
+    a [s:SoftwareApplication];
+  }*;
+
+  ## Marginality: Optional
+
+  s:alternateName Literal*;
+  s:conditionsOfAccess Literal?;
+  # FIXME: ISO8601 regex pattern without forcing xsd:dateTime/xsd:date/xsd:timestamp etc. declaration
+  s:dateModified LITERAL?;
+  s:datePublished LITERAL?;
+
+  (
+    s:encodingFormat LITERAL | 
+    s:encodingFormat IRI
+  )?;
+
+  $p:identifier (
+    s:identifier {
+      a [s:PropertyValue];
+    } | 
+    s:identifier xsd:string;
+    s:identifier IRI;
+  )*;
+
+  ( 
+    s:image { 
+      a [s:ImageObject];
+    } | 
+    s:image IRI;
+  )?;
+}
+
+p:PersonOrOrg extra rdf:type {
+    # As we're in RO-Crate, the contextual entity is required
+    (a [s:Person] | 
+     a [s:Organization]
+    );
+    s:name LITERAL;
+  }
+
+p:FormalParameter { 
+  a [bioschemas:FormalParameter];
+  dct:conformsTo [<https://bioschemas.org/profiles/FormalParameter/1.0-RELEASE>];
+  s:name LITERAL;
+  s:additionalType IRI*;
+  s:description LITERAL?;
+  (
+    s:encodingFormat LITERAL |
+    s:encodingFormat IRI;
+  )?;
+  ( 
+    s:defaultValue Literal |
+    s:defaultValue IRI;
+  )?;
+  #&identifier*;
+  (
+    s:identifier {
+      a [s:PropertyValue];
+    } | 
+    s:identifier xsd:string;
+    s:identifier IRI;
+  )*;
+  s:valueRequired xsd:boolean?;
+}
+