Add cli option to allow running checks against a graphstore journal.

[balhoff]

New CLI option --check-graph-type. Fixes #541.

[kltm]

Adds a default "off" flag that will bypass certain problematic models--from the POV of QC; if "on", it will skip anything that doesn't have the appropriate data.

I just want to confirm that the -> operator is Java 8?

                    if (gocam.getAnnotations().stream().noneMatch(annotation ->
                            annotation.getProperty().getIRI().equals(graphType)

[kltm]

Noticing that tests did not pass?

[balhoff]

I will look at the tests—they are unfortunately sensitive to changing external data.

[balhoff]

Adds a default "off" flag that will bypass certain problematic models--from the POV of QC; if "on", it will skip anything that doesn't have the appropriate data.

I just want to confirm that the -> operator is Java 8?

                    if (gocam.getAnnotations().stream().noneMatch(annotation ->
                            annotation.getProperty().getIRI().equals(graphType)

Java 8!

[balhoff]

Test failure relates to website problems at biopax.org. Fix at #543.

[balhoff]

Adds a default "off" flag that will bypass certain problematic models--from the POV of QC; if "on", it will skip anything that doesn't have the appropriate data.

@kltm one thing to note—don't use this flag if testing the actual Minerva database. The models there don't have this annotation, which is inserted by the graphstore build.

[kltm]

Adds a default "off" flag that will bypass certain problematic models--from the POV of QC; if "on", it will skip anything that doesn't have the appropriate data.

@kltm one thing to note—don't use this flag if testing the actual Minerva database. The models there don't have this annotation, which is inserted by the graphstore build.

@balhoff Not that I was planning on changing the flags for our production Noctua stuff, but wouldn't that check be safe when looking at just a "TTL models only" store?

[balhoff]

@kltm in a TTL models only store, all of them would get skipped if you use that flag. They won't contain the triple ?ont :graphType :noctuaCam.

[kltm]

@balhoff Ah, I think I understand: the trick is that they are marked in the "extended" store, but not so in the "noctua" one, and you're using that as the criteria?

[balhoff]

Yes.