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INCATools / semantic-sql

SQL and SQLite builds of OWL ontologies
https://incatools.github.io/semantic-sql/
BSD 3-Clause "New" or "Revised" License
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Empty `.db` file created #56

Closed joeflack4 closed 1 year ago

joeflack4 commented 1 year ago

Overview

When I'm using OAK SqlImplementation, I sometimes get empty .db files.

Related issues

https://github.com/INCATools/ontology-access-kit/issues/293

joeflack4 commented 1 year ago

Seems like issue is on the OAK side. Closing.

semsql make doid.db result: valid db

semsql make doid.db
cat /Users/joeflack4/virtualenvs/mondo-ingest/lib/python3.9/site-packages/semsql/builder//sql_schema/semsql.sql | sqlite3 .template.db.tmp && \
    echo .exit | sqlite3 -echo .template.db.tmp -cmd ".mode csv" -cmd ".import /Users/joeflack4/virtualenvs/mondo-ingest/lib/python3.9/site-packages/semsql/builder//prefixes/prefixes.csv prefix" && \
    mv .template.db.tmp .template.db
.exit
robot remove -i doid.owl --axioms "equivalent disjoint annotation" -o doid-min.owl
beep
relation-graph --disable-owl-nothing true \
                       --ontology-file doid-min.owl\
                       --output-file doid-relation-graph.tsv.ttl.tmp \
                       --equivalence-as-subclass true \
                   --output-subclasses true \
                       --reflexive-subclasses true && \
    riot --out RDFXML doid-relation-graph.tsv.ttl.tmp > doid-relation-graph.tsv.owl.tmp && \
    sqlite3 doid-relation-graph.tsv.db.tmp -cmd ".mode csv" ".import /Users/joeflack4/virtualenvs/mondo-ingest/lib/python3.9/site-packages/semsql/builder//prefixes/prefixes.csv prefix" && \
    rdftab doid-relation-graph.tsv.db.tmp < doid-relation-graph.tsv.owl.tmp && \
    sqlite3 doid-relation-graph.tsv.db.tmp -cmd '.separator "\t"' -cmd '.header on' "SELECT subject,predicate,object FROM statements " > doid-relation-graph.tsv.tmp && \
    mv doid-relation-graph.tsv.tmp doid-relation-graph.tsv && \
    rm doid-relation-graph.tsv.*.tmp
2022.09.23 16:00:10:454 zio-default-blocking-2 INFO org.renci.relationgraph.RelationGraph$
    Running reasoner
    Done running reasoner
2022.09.23 16:00:13:943 ZScheduler-Worker-4 INFO org.renci.relationgraph.Main.program:39
    Done computing relations
cp .template.db doid.db.tmp && \
    rdftab doid.db.tmp < doid.owl && \
    sqlite3 doid.db.tmp -cmd '.separator "\t"' ".import doid-relation-graph.tsv entailed_edge" && \
    gzip -f doid-relation-graph.tsv && \
    cat /Users/joeflack4/virtualenvs/mondo-ingest/lib/python3.9/site-packages/semsql/builder//indexes/*.sql | sqlite3 doid.db.tmp && \
    mv doid.db.tmp doid.db
rm doid-min.owl
beep
file doid.db
doid.db: SQLite 3.x database, last written using SQLite version 3028000