Bug: no goal for reports/doid.subclass.direct-in-mondo-only.tsv

[joeflack4]

Overview

Nico is running build-mondo-ingest, but it errored out on sync (original comment).

Investigation

I don't know why this is happening.

(1) There is a goal
It's entry number 3 in this multi-output goal: $(REPORTDIR)/%.subclass.added.robot.tsv $(REPORTDIR)/%.subclass.confirmed.robot.tsv $(REPORTDIR)/%.subclass.direct-in-mondo-only.tsv $(REPORTDIR)/%.subclass.added-obsolete.robot.tsv: tmp/mondo-ingest.db tmp/mondo.db tmp/mondo.sssom.tsv

(2) make reports/doid.subclass.direct-in-mondo-only.tsv works for me

Details

sh run.sh make reports/doid.subclass.direct-in-mondo-only.tsv
Running  with -Xmx20G of memory for ROBOT and Java-based pipeline steps.
...
RUST_BACKTRACE=full semsql make tmp/mondo.db -P config/prefixes.csv
make[1]: Entering directory '/work/src/ontology'
robot \
...

(3) Even just running make sync works for me

Sub-tasks

• Open a PR to reinstate the sync pipeline: try a fresh checkout of the repo (different folder) and see if can replicate the problem
• When done: resolve this comment

[joeflack4]

@matentzn Apologies for assigning this to you as well but I can't replicate.

Maybe it has something to do with how it's being run? This happened during build-mondo-ingest?

[matentzn]

If you delete the sync folder/files first (this is my state) - can you try and replicate?

[joeflack4]

I'll try that tomorrow!

[matentzn]

This has been fixed by #403