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Python-based RO-Crate validator (alpha)

License: Apache License 2.0

Python 40.61% HTML 22.02% Jupyter Notebook 37.37%

ro-crate validation json json-ld schema-org

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ro-crate-validator-py's Issues

Licence is incorrectly rejected

I have trouble validating my crate due to the second term at

ro-crate-validator-py/src/rocrateValidator/semanticCheck.py

Line 581 in c3c5c18

    
           if utils.is_url(license[0]) and utils.get_norm_value(entity, "@id")[0] != "./" and utils.get_norm_value(entity, "@id")[0] != "ro-crate-metadata.json":

It excludes the root data entity but shouldn’t only ro-crate-metadata.json be excluded?

Support for zip files?

Am I correct in interpreting this commented out bit of code to mean that it doesn't currently support zip archives? https://github.com/ResearchObject/ro-crate-validator-py/blob/a5ff613e6e5d871f94d6e8722a5f18bb129b45d7/src/rocrateValidator/syntaxCheck.py#L42C1-L45C34

pytest needed as extra dependency when using ro-crate-validator-py

From the WIP PR: https://github.com/ResearchObject/runcrate/pull/17/files#diff-fa602a8a75dc9dcc92261bac5f533c2a85e34fcceaff63b3a3a81d9acde2fc52R45

Probably because of a loose import in this module (there could be others): https://github.com/ResearchObject/ro-crate-validator-py/blob/main/src/rocrateValidator/semanticCheck.py#L11

suggestion for README

As rocrate is a dependency, you could add this to the README.md

Is a workflow necessary?

You seem to be able to leave the function

ro-crate-validator-py/src/rocrateValidator/semanticCheck.py

Lines 769 to 816 in c3c5c18

    
           def scripts_and_workflow_check(tar_file, extension): 
        
               """ 
        
               For workflow RO-Crate, if there is an unrecognised workflow file, the function will return an warning message. 
        
               Please check more details at RO-Crate website: 
        
               <https://www.researchobject.org/ro-crate/1.1/workflow-and-scripts.html> 
        
               """ 
        
               NAME = "Scripts and workflow check" 
        
               # wkfext_path = '/Users/xuanqili/Desktop/ro-crate-validator-py/src/workflow_extension.txt' 
        
               error_message = { 
        
                   "WorkflowError":"Semantic Error: Scripts and Workflow is Wrong", 
        
                   "TypeError": "Semantic Error: Invalid @type value for workflow file {}. It must have File, SoftwareSourceCode and ComputationalWorkflow as value." 
        
               } 
        
               warning_message = { 
        
                   "UnrecognizedWkf" : "WARNING: {} is not a recognised workflow extension. Please raise an issue at GitHub: <https://github.com/ResearchObject/ro-crate-validator-py/issues>." 
        
               } 
        
               ### dictionary to store checking result 
        
               workflow_result = {} 
        
               context, metadata = rocrate.read_metadata(os.path.join(tar_file, "ro-crate-metadata.json")) 
        
               ### check if recognised workflow file meets the requirments 
        
               for entity in metadata.values(): 
        
                   id_ = utils.get_norm_value(entity, "@id")[0] 
        
                   extension_set = list(we.get_workflow_extension()) 
        
                   # with open (wkfext_path, "r") as file: 
        
                   #     extension_set = file.read().splitlines() 
        
                   recognisedWkf_upd(extension_set, entity, workflow_result, id_, error_message) 
        
               ### check unrecognised workflow file with ComputaionalWorkflow in its @type 
        
               for entity in metadata.values(): 
        
                   type = utils.get_norm_value(entity, "@type") 
        
                   if "ComputationalWorkflow" in type: 
        
                       unrecognisedWfk_upd(type, extension_set, entity, workflow_result, warning_message, error_message) 
        
               ### fucntion will return True only when the all of the recognised workflow file are correct       
        
               for values in workflow_result.values(): 
        
                   if isinstance(values, list): 
        
                       return Result(NAME, code = -1, message = values[1]) 
        
                   elif isinstance(values, str): 
        
                       return Result(NAME, code = 1, message = values) 
        
                   else: 
        
                       return Result(NAME) 
        
               return Result(NAME, code = -1, message = error_message["WorkflowError"])

only if you have at least one workflow. But is such a thing mandatory in an RO-Crate?

undeclared dependency on pytest, new release requested

Hey y'all, just installed the package via pip and saw an error due to pytest, I'd written a long issue about it before discovering e95b1ab so it's already been fixed, yay! Could a new release be made at some point in the future (no rush from my side.)

feature request: cli

Even something as simple as

import sys                                          
                                                    
from rocrateValidator import validate as validate   
v = validate.validate(sys.argv[1])                  
v.validator()

would be a great help! Additionally to return the message on validator() rather than invoking print could be nice for consumers to decide how they want to handle the output.

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	def scripts_and_workflow_check(tar_file, extension):

	"""
	For workflow RO-Crate, if there is an unrecognised workflow file, the function will return an warning message.
	Please check more details at RO-Crate website:
	<https://www.researchobject.org/ro-crate/1.1/workflow-and-scripts.html>
	"""

	NAME = "Scripts and workflow check"
	# wkfext_path = '/Users/xuanqili/Desktop/ro-crate-validator-py/src/workflow_extension.txt'

	error_message = {
	"WorkflowError":"Semantic Error: Scripts and Workflow is Wrong",
	"TypeError": "Semantic Error: Invalid @type value for workflow file {}. It must have File, SoftwareSourceCode and ComputationalWorkflow as value."
	}
	warning_message = {
	"UnrecognizedWkf" : "WARNING: {} is not a recognised workflow extension. Please raise an issue at GitHub: <https://github.com/ResearchObject/ro-crate-validator-py/issues>."
	}

	### dictionary to store checking result
	workflow_result = {}

	context, metadata = rocrate.read_metadata(os.path.join(tar_file, "ro-crate-metadata.json"))

	### check if recognised workflow file meets the requirments
	for entity in metadata.values():
	id_ = utils.get_norm_value(entity, "@id")[0]
	extension_set = list(we.get_workflow_extension())
	# with open (wkfext_path, "r") as file:
	# extension_set = file.read().splitlines()
	recognisedWkf_upd(extension_set, entity, workflow_result, id_, error_message)

	### check unrecognised workflow file with ComputaionalWorkflow in its @type
	for entity in metadata.values():
	type = utils.get_norm_value(entity, "@type")
	if "ComputationalWorkflow" in type:
	unrecognisedWfk_upd(type, extension_set, entity, workflow_result, warning_message, error_message)

	### fucntion will return True only when the all of the recognised workflow file are correct
	for values in workflow_result.values():
	if isinstance(values, list):
	return Result(NAME, code = -1, message = values[1])
	elif isinstance(values, str):
	return Result(NAME, code = 1, message = values)
	else:
	return Result(NAME)

	return Result(NAME, code = -1, message = error_message["WorkflowError"])