SQLite console opens (0.1.7)

[joeflack4]

Overview

When using semsql, the SQLite console opens. I need to exit it manually in order for the command to continue. Since this is running in a pipeline that is meant to be automated, I shouldn't use semsql until I can fix this.

Log

Problem beings at sqlite>:

sh [run.sh](http://run.sh/) semsql make mirror/doid.db; beep
cat /usr/local/lib/python3.10/dist-packages/semsql/builder//sql_schema/semsql.sql | sqlite3 .template.db.tmp && \
sqlite3 -echo .template.db.tmp -cmd ".mode csv" -cmd ".import /usr/local/lib/python3.10/dist-packages/semsql/builder//prefixes/prefixes.csv prefix" -cmd ".exit" && \
mv .template.db.tmp .template.db
SQLite version 3.37.2 2022-01-06 13:25:41
Enter ".help" for usage hints.
sqlite>

relation-graph --disable-owl-nothing true \
                       --ontology-file mirror/doid.owl\
                       --output-file mirror/doid-relation-graph.tsv.ttl.tmp \
                       --equivalence-as-subclass true \
               --output-subclasses true \
                       --reflexive-subclasses true && \
riot --out RDFXML mirror/doid-relation-graph.tsv.ttl.tmp > mirror/doid-relation-graph.tsv.owl.tmp && \
sqlite3 mirror/doid-relation-graph.tsv.db.tmp -cmd ".mode csv" ".import /usr/local/lib/python3.10/dist-packages/semsql/builder//prefixes/prefixes.csv prefix" && \
rdftab mirror/doid-relation-graph.tsv.db.tmp < mirror/doid-relation-graph.tsv.owl.tmp && \
sqlite3 mirror/doid-relation-graph.tsv.db.tmp -cmd '.separator "\t"' -cmd '.header on' "SELECT subject,predicate,object FROM statements " > mirror/doid-relation-graph.tsv.tmp && \
mv mirror/doid-relation-graph.tsv.tmp mirror/doid-relation-graph.tsv && \
rm mirror/doid-relation-graph.tsv.*.tmp
ls
2022.08.10 14:30:55:858 zio-default-async-1 INFO org.renci.relationgraph.Main.program:57
    Running reasoner
2022.08.10 14:31:01:715 zio-default-async-1 INFO org.renci.relationgraph.Main.program:60
    Done running reasoner
2022.08.10 14:31:27:450 zio-default-async-4 INFO org.renci.relationgraph.Main.program:70
    Computed relations in 25.638s
beep
cp .template.db mirror/doid.db.tmp && \
rdftab mirror/doid.db.tmp < mirror/doid.owl && \
sqlite3 mirror/doid.db.tmp -cmd '.separator "\t"' ".import mirror/doid-relation-graph.tsv entailed_edge" && \
gzip mirror/doid-relation-graph.tsv && \
cat /usr/local/lib/python3.10/dist-packages/semsql/builder//indexes/*.sql | sqlite3 mirror/doid.db.tmp && \
mv mirror/doid.db.tmp mirror/doid.db

Additional information

Version: 0.1.7: Using this version because I'm not currently able to use the next highest version, 0.2.0.

I have to exit using Ctrl+D. @hrshdhgd Do you happen to have this issue? Do you know of any other way to exit the SQLite console? Also, this causes a bug if I have a chained command, where my terminal window freezes and I have to close it. For example, I'm doing semsql make mirror/doid.db; beep. The ; beep part makes a sound after running so I know it's done. But if there is a ; or an && and I use Ctrl+D to exit the console, instead of it continuing, my terminal freezes at this point.

[joeflack4]

@matentzn FYI just wanting to let you know where I'm at.

[hrshdhgd]

To be honest, I haven't directly used semsql as a user. We could get together and figure it out if you have time. In terms of not being able to use the latest version. I think it requires an installation of relation-graph which is a project under Chris' org. I have no idea if it is ready for prime time.

[joeflack4]

@hrshdhgd Yeah, I figured that would be the case for relation-graph. That's a little too involved to install that with the pipeline we have. I think I'll wait until that is automatically installed along with semsql. For now, I'll probably just use ProntoImplementation, since I'm not having any issues with it, rather thanSqlImplementation.

I would meet with you to try to solve this if I could, but I don't have the bandwidth at the moment. Thanks for asking though; maybe in the future.

[matentzn]

@hrshdhgd it seems you are using it in mondo-ingest as a prerequisite to oak matching!