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Boris Pelakh sa-bpelakh @semanticarts Florida

semanticarts/gist 66

gist upper enterprise ontology

semanticarts/ontology-toolkit 15

Tools to update and export ontology RDF.

RDFLib/pyTARQL 9

Python implementation of TARQL

semanticarts/shacl-validator 2

Node.js SHACL Valdiator

sa-bpelakh/incubator-rya 1

Mirror of Apache Rya (Incubating)

semanticarts/pytarql 1

Python implementation of TARQL

sa-bpelakh/pySHACL 0

A Python validator for SHACL

sa-bpelakh/rdflib 0

RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.

sa-bpelakh/sparql-endpoint-fixture 0

RDFLIB-based SPARQL Endpoint Fixture for pytest

issue openedsemanticarts/ontology-toolkit

Potential defect in data graph

@uscholdm observed the following when trying to generate a data graph:

onto_tool graphic --data -e https://user:password@agraph.semanticarts.com/catalogs/ibb/repositories/2021-06-10_Test -o ibbTriples --exclude-pattern [Via]

I get these errors:

Processing predicates: |XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX| 100.0% Complete
Traceback (most recent call last):
  File "c:\users\michael\appdata\local\programs\python\python37\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "c:\users\michael\appdata\local\programs\python\python37\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "C:\Users\Michael\AppData\Local\Programs\Python\Python37\Scripts\onto_tool.exe\__main__.py", line 7, in <module>
  File "c:\users\michael\appdata\local\programs\python\python37\lib\site-packages\onto_tool\onto_tool.py", line 1142, in run_tool
    main(sys.argv[1:] if len(sys.argv) > 1 else ['-h'])
  File "c:\users\michael\appdata\local\programs\python\python37\lib\site-packages\onto_tool\onto_tool.py", line 1129, in main
    show_shacl=args.show_shacl)
  File "c:\users\michael\appdata\local\programs\python\python37\lib\site-packages\onto_tool\onto_tool.py", line 321, in generate_graphic
    og.create_instance_graf()
  File "c:\users\michael\appdata\local\programs\python\python37\lib\site-packages\onto_tool\ontograph.py", line 549, in create_instance_graf
    max_common = max(occurs for class_data in data_dict.values() for occurs in class_data['links'].values())
ValueError: max() arg is an empty sequence

Need to look at how that sequence can end up empty - perhaps due to limit config?

created time in 3 days

issue commentsemanticarts/ontology-toolkit

Add option to run serializer on migration output

That should just be another step in the migration bundle file. No additional functionality required.

rjyounes

comment created time in 3 days

issue commentsemanticarts/ontology-toolkit

Write report even on successful completion of migration

I think the primary point is that migration is not a built-in functionality in onto-tool - it's just a specific utilization of its ability to perform queries and transform RDF.

rjyounes

comment created time in 3 days

issue commentsemanticarts/ontology-toolkit

Write report even on successful completion of migration

What would that entail, exactly? You can attach message fields to your build file, so that onto-tool reports the steps as they are executed (eg https://github.com/semanticarts/gist/blob/develop/migration/v10.0/migrate_local.yaml#L16), and if you are really curious, you can smack a --debug on the command line and really dive into it.

But if you are looking for something like 'Updated 32 triples' - we don't have a good way of doing that, especially when the changes are performed on a remote endpoint as opposed to local content. Technically you could write two sets of queries - a SELECT query which reports how many entities it's going to update, followed by the actual UPDATE query that does the job.

rjyounes

comment created time in 3 days

pull request commentsemanticarts/gist

Dylan + Jess attempt at renaming instances and adding the gistx namespace. Fixes #556.

I was talking about automatic URI minting, e.g.

BIND(tarql:expandPrefixedName(CONCAT('gistx:_BaseUnit_', ?unitFromCSV)) as ?unitRef)

though the mapping is rarely that simple.

JessSing

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pull request commentsemanticarts/gist

Dylan + Jess attempt at renaming instances and adding the gistx namespace.

@rjyounes I like the idea of using the more specific infix, but I am concerned of how it may get in the way of ETL where unit references are automatically generated.

JessSing

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PullRequestReviewEvent
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Pull request review commentsemanticarts/gist

Dylan + Jess attempt at renaming instances and adding the gistx namespace.

 gist:GreenwichInstant 			[ 				a owl:Restriction ; 				owl:onProperty gist:usesTimeZoneStandard ;-				owl:hasValue gist:_greenwichTimeZone ;+				owl:hasValue gistx:_TimeZoneStandard_greenwich_Time_Zone ; 			]

👍 to gistx:_TimeZoneStandard_greenwich to reduce redundancy. One possible consideration - use the standard abbreviations for brevity and consistency, e.g. gistx:_TimeZoneStandard_gmt

JessSing

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Pull request review commentsemanticarts/gist

Dylan + Jess attempt at renaming instances and adding the gistx namespace.

 gist:VolumeUnit 	skos:prefLabel "Volume Unit"^^xsd:string ; 	. -gist:_USDollar+gistx:_BaseUnit_US_Dollar 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_USDollar ;+	gist:hasBaseUnit gistx:_BaseUnit_US_Dollar ; 	. -gist:_ampere+gistx:_BaseUnit_ampere 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_ampere ;+	gist:hasBaseUnit gistx:_BaseUnit_ampere ; 	. -gist:_bit+gistx:_BaseUnit_bit  	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	skos:definition "A bit (short for binary digit) is the smallest unit of data in a computer. A bit has a single binary value, either 0 or 1."^^xsd:string ; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_bit ;+	gist:hasBaseUnit gistx:_BaseUnit_bit ; 	. -gist:_candela+gistx:_BaseUnit_candela 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_candela ;+	gist:hasBaseUnit gistx:_BaseUnit_candela ; 	. -gist:_day+gistx:_DurationUnit_day 	a 		owl:NamedIndividual , 		gist:DurationUnit 		; 	gist:baseConversionFactor "86400.0"^^xsd:double ;-	gist:hasBaseUnit gist:_second ;+	gist:hasBaseUnit gistx:_BaseUnit_second ; 	. -gist:_each+gistx:_BaseUnit_each 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_each ;+	gist:hasBaseUnit gistx:_BaseUnit_each ; 	. -gist:_greenwichTimeZone+gistx:_TimeZoneStandard_greenwich_Time_Zone 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:TimeZoneStandard 		; 	. -gist:_kelvin+gistx:_BaseUnit_kelvin 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ; 	gist:conversionOffset "0.0"^^xsd:double ;-	gist:hasBaseUnit gist:_kelvin ;+	gist:hasBaseUnit gistx:_BaseUnit_kelvin ; 	. -gist:_kilogram+gistx:_BaseUnit_kilogram 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_kilogram ;+	gist:hasBaseUnit gistx:_BaseUnit_kilogram ; 	. -gist:_meter+gistx:_BaseUnit_meter 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_meter ;+	gist:hasBaseUnit gistx:_BaseUnit_meter ; 	. -gist:_millisecond+gistx:_DurationUnit_millisecond 	a 		owl:NamedIndividual , 		gist:DurationUnit 		; 	gist:baseConversionFactor "0.001"^^xsd:double ;-	gist:hasBaseUnit gist:_second ;+	gist:hasBaseUnit gistx:_BaseUnit_second ; 	. -gist:_minute+gistx:_DurationUnit_minute 	a 		owl:NamedIndividual , 		gist:DurationUnit 		; 	gist:baseConversionFactor "60.0"^^xsd:double ;-	gist:hasBaseUnit gist:_second ;+	gist:hasBaseUnit gistx:_BaseUnit_second ; 	. -gist:_mole+gistx:_BaseUnit_mole 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:BaseUnit 		; 	gist:baseConversionFactor "1.0"^^xsd:double ;-	gist:hasBaseUnit gist:_mole ;+	gist:hasBaseUnit gistx:_BaseUnit_mole ; 	. -gist:_one_day+gistx:_Duration_one_day 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:Duration 		;-	gist:hasUnitOfMeasure gist:_day ;+	gist:hasUnitOfMeasure gistx:_DurationUnit_day ; 	gist:numericValue "1.0"^^xsd:double ; 	. -gist:_one_millisecond+gistx:_Duration_one_millisecond 	a 		owl:NamedIndividual , 		owl:Thing , 		gist:Duration 		;-	gist:hasUnitOfMeasure gist:_millisecond ;+	gist:hasUnitOfMeasure gistx:_DurationUnit_millisecond ; 	gist:numericValue "1.0"^^xsd:double ; 	. -gist:_one_minute+gistx:_Duration_one_minute

It seems redundant that gistx:_Duration_one_day, gistx:_Duration_one_millisecond and gistx:_Duration_one_minute include the one in the URI.

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Boris Pelakh

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Correct definition of OrderedMember.

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rjyounes

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Remove an unnecessary restriction

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Boris Pelakh

commit sha fd8a4c15cdb7ea97562e44f5795fb2a8e762d115

Merge pull request #569 from semanticarts/patch/issue-540 Correct definition of OrderedMember. Fixes #540

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Boris Pelakh

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OrderedCollection fix for Issue 540

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Correct definition of OrderedMember.

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Remove an unnecessary restriction

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Boris Pelakh

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Merge pull request #569 from semanticarts/patch/issue-540 Correct definition of OrderedMember. Fixes #540

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issue closedsemanticarts/gist

Remove predicate hasOrderedMember

I don't think we need the predicate hasOrderedMember to support the new OrderedCollection model. We can use the existing hasMember and isMemberOf with a restriction on OrderedCollection:

gist:OrderedCollection
	a owl:Class ;
	owl:equivalentClass [
		owl:intersectionOf (
			gist:Collection
			[
				a owl:Restriction ;
				owl:onProperty gist:hasMember ;
				owl:allValuesFrom gist:OrderedMember ;
			]
		) ;
	] ;
        etc.

And an additional allValuesFrom restriction on OrderedMember on property isMemberOf. Further restrictions achieve the same thing as defininghasOrderedMember as an InverseFunctionalProperty:

gist:OrderedMember
	a owl:Class ;
	owl:equivalentClass [
		owl:intersectionOf (
			[
				a owl:Restriction ;
				owl:onProperty gist:isMemberOf ;
				owl:cardinality "1"^^xsd:nonNegativeInteger ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:isMemberOf ;
				owl:allValuesFrom gist:OrderedCollection ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:followsDirectly ;
				owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:followsDirectly ;
				owl:allValuesFrom gist:OrderedMember ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:precedesDirectly ;
				owl:maxCardinality "1"^^xsd:nonNegativeInteger ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:precedesDirectly ;
				owl:allValuesFrom gist:OrderedMember ;
			]
			[
				a owl:Restriction ;
				owl:onProperty gist:sequence ;
				owl:cardinality "1"^^xsd:integer ;
			]
		) ;
	] ;
       etc.

(Note that there always is an index even if it's not asserted.)

This follows our principle of generalizing predicates rather than defining new predicates with specialized domains and ranges.

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rjyounes

PR opened semanticarts/gist

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Correct definition of OrderedMember. Fixes #540
+5 -5

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Boris Pelakh

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Rename on format then rename back to avoid serialization issue.

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Boris Pelakh

commit sha 8a4f9b11161f63a27b41b5bfef8559eb9352f524

Merge pull request #568 from semanticarts/patch/rename-to-format Rename on format then rename back to avoid serialization issue.

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Boris Pelakh

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Fix to build script from develop

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Boris Pelakh

commit sha 100ad0c9597e50bc562657bf80b0c1ab43e89a2e

Rename on format then rename back to avoid serialization issue.

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Boris Pelakh

commit sha 8a4f9b11161f63a27b41b5bfef8559eb9352f524

Merge pull request #568 from semanticarts/patch/rename-to-format Rename on format then rename back to avoid serialization issue.

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PR merged semanticarts/gist

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Rename on format then rename back to avoid serialization issue.

The issue introduced by the Java11-based rdf-toolkit is the inability to serialize in place - the input and output files have to be different. For some reason I did not catch this when testing, and we have no automated sanity test in place to make sure the formatted output is similar to the input - that's a deficiency to consider.

Regardless, I modified the build to rename the Turtle files during formatting, then move them back. No need to do for any of the others, since they have different extensions, so they are not overwritten.

+11 -0

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sa-bpelakh

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PR opened semanticarts/gist

Reviewers
Rename on format then rename back to avoid serialization issue.

The issue introduced by the Java11-based rdf-toolkit is the inability to serialize in place - the input and output files have to be different. For some reason I did not catch this when testing, and we have no automated sanity test in place to make sure the formatted output is similar to the input - that's a deficiency to consider.

Regardless, I modified the build to rename the Turtle files during formatting, then move them back. No need to do for any of the others, since they have different extensions, so they are not overwritten.

+11 -0

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Boris Pelakh

commit sha 9630a83a6d234a987dae80e092940b9add366d90

Rename MimeType to MediaType, create ontology to declare instances.

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Boris Pelakh

commit sha 1a87712afbc0e7887a40b52b06941914e7289aa9

Clean up labels and namespaces.

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Boris Pelakh

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Fix class names and add validation for instances.

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uscholdm

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Addressing issue: https://github.com/semanticarts/gist/issues/389 - added two annotation properties: domainIncludes and rangeIncludes

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uscholdm

commit sha 0e4f3114259cd4289508d5701e14d09114ad6b70

Addressing issue: https://github.com/semanticarts/gist/issues/389 - updated release notes

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uscholdm

commit sha b4ee45c3af50ea3e160065b588b530de343c34ee

Addressing issue: https://github.com/semanticarts/gist/issues/389 - added specific uses of domainIncludes and rangeIncludes

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uscholdm

commit sha 2616544797cb68d1161667862fc133142586c617

Addressing issue: https://github.com/semanticarts/gist/issues/389 - updated release notes

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uscholdm

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Addressing issue: https://github.com/semanticarts/gist/issues/389 - updated release notes (again)

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uscholdm

commit sha ad7d4521c7b2861e90d4aa8894b12912d12bc7c0

Addressing https://github.com/semanticarts/gist/issues/139 - updated annotations for basedOn and basisFor

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uscholdm

commit sha df7df81c5c24d7ab7f1cbd11d95a8fb3e1141b9f

Merge branch 'domain-range-includes' into basisFor-issue139

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uscholdm

commit sha fb349e85c0f82228e558953b6ca2755aaca4f950

Addressing https://github.com/semanticarts/gist/issues/139 - updated release notes

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uscholdm

commit sha a20dfcda62d5ee1554b80cc3256df2c3217fd657

Addressing https://github.com/semanticarts/gist/issues/139 - updated release notes

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uscholdm

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Addressing https://github.com/semanticarts/gist/issues/139 - additional changes to annotations for basedOn and basisFor

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uscholdm

commit sha ba19d244b41694cf86bd4606469513616ac68f00

Addressing issue: https://github.com/semanticarts/gist/issues/389 - made a few tweaks to tidy things up a bit - updated release notes (again)

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uscholdm

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Addressing issue: https://github.com/semanticarts/gist/issues/389 - Fixed punctuation and spelling in annotations.

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rjyounes

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Added punctuation and capitalized Schema.org

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rjyounes

commit sha 623d73bc0ca5c947c84e0eedced8b12da2729f0f

Copied scopeNote of rangeIncludes to domainIncludes

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Boris Pelakh

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Address review comments - primarily labels.

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uscholdm

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- Updated release notes to be minor change Addressing issue: https://github.com/semanticarts/gist/issues/389

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uscholdm

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Importing changes the Rebecca made separately.

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Boris Pelakh

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Local and endpoint migration for renamed and removed entities.

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Boris Pelakh

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Cleanup per review.

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Boris Pelakh

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Review update, documentation of migration.

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Merge branch 'release-10.0.0' into basic-migration

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Jamie-SA

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Validation query for hasCommunicationAddress

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Boris Pelakh

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Adjusted documentation as per review.

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Rename files so they will auto run

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Update w/BP suggestions

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Fix typo

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rjyounes

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Fix table lines in style guide

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Rebecca Younes

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Merge pull request #563 from semanticarts/doc/fix_table_lines Fix table lines in style guide

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Boris Pelakh

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Merge pull request #561 from semanticarts/migration_hasCommunicationAddress Validation query for hasCommunicationAddress

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Boris Pelakh

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Explicitly reference detect queries.

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Boris Pelakh

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Merge pull request #554 from semanticarts/basic-migration Local and endpoint migration for renamed and removed entities.

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Boris Pelakh

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Include migration scripts and instructions in release package.

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Borislav Iordanov

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Merge pull request #564 from semanticarts/update-build-for-migration Include migration scripts and instructions in release package.

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Boris Pelakh

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Merge remote-tracking branch 'origin/release-10.0.0' into develop

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PR merged semanticarts/gist

Release 10.0.0
+548 -3

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bolerio

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PR merged semanticarts/gist

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Release 10.0.0
+1719 -1039

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bolerio

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PR opened semanticarts/gist

Reviewers
Include migration scripts and instructions in release package.

Just realized that the migration scripts and instructions were not being included in the release package. Which, of course, let me to discover that onto-tool did not properly handle copying directories. It has been patched (v1.4.2), so you will need to re-install (pip install -U) before rerunning the bundle. Sorry.

+16 -2

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