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committing delete query throws UNKNOWN #4447

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sorsaffari opened this Issue Oct 9, 2018 · 5 comments

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@sorsaffari
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sorsaffari commented Oct 9, 2018

Grakn version: 1.5.0-SNAPSHOT

Expected output:

>>> match $pr isa protein has name "ORM1-like protein 3"; $sourcing ($pr) isa sourcing-of-information; delete $sourcing;
{V1032224, V73928}
>>> commit
>>>

Actual output

>>> match $pr isa protein has name "ORM1-like protein 3"; $sourcing ($pr) isa sourcing-of-information; delete $sourcing;
{V1032224, V73928}
>>> commit
UNKNOWN: Vertex with id 1032224 was removed.. Please check server logs for the stack trace.
>>>

Reproducing

git clone git@github.com:sorsaffari/biograkn.git
cd biograkn/blast
git checkout --track origin/blast-example
path/to/grakn-core-1.5.0-SNAPSHOT/graql console -k proteins -f schema.gql
pip3 install grakn
pip3 install biopython
python3 migrate.py
python3 blast.py
wait for blast output to be imported
enter 0 for all questions (cleaning data) > this is actually where the bug was identified. selecting a protein number from the list, throws the error in question.
path/to/grakn-core-1.5.0-SNAPSHOT/graql console -k proteins
>>> match $pr isa protein has name "ORM1-like protein 3"; $sourcing ($pr) isa sourcing-of-information; delete $sourcing;
{V1032224, V73928}
>>> commit
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sorsaffari commented Oct 10, 2018

@lolski just to give you some context on how the BLAST example(and its timeline) is associated with this bug: the part of the BLAST code that is blocked by this, is not the main part of the code and can be left out till this bug is fixed.

We're planning to:

  • publish the blog post and the example code on Friday (12th October).
  • present the work on BLAST <> Grakn in a meetup on (18th October).

If you've too much on your hand, it's completely fine. we don't have to have that part of the BLAST example for these 2 milestones.

@BFergerson

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BFergerson commented Nov 12, 2018

Just ran into this exact issue. Is there a workaround for this or do deletes just not work in Grakn 1.4.2?

@lolski

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lolski commented Nov 13, 2018

Can you post the reproducible step using your data and query, @BFergerson ? Is it deterministic or non-deterministic?

It's always good to have more data.

@BFergerson

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BFergerson commented Nov 13, 2018

@lolski, sure thing. Please check out this branch: https://github.com/bfergerson/grakn-calendar-test/tree/delete-test

Running it causes:

Ontology setup
Most recent thing inserted: [[$d/V16480][$m/V36880][$t/V28712]]
Most recent thing inserted: [[$d/V16480][$m/V20600][$t/V24688]]
Inserted things
Exception in thread "main" java.lang.RuntimeException: UNKNOWN: Vertex with id 36880 was removed.. Please check server logs for the stack trace.
	at ai.grakn.client.Grakn$Transaction.responseOrThrow(Grakn.java:218)
	at ai.grakn.client.Grakn$Transaction.commit(Grakn.java:228)
	at ai.grakn.GraknTx$commit$0.call(Unknown Source)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:45)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:108)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:112)
	at GraknCalendarTest.main(GraknCalendarTest.groovy:41)

Process finished with exit code 1
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lolski commented Nov 15, 2018

@BFergerson thanks, we will have a look at it.

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