error running make ott after refreshing amendments

[kcranston]

**Update - I think this has to do with pointing foo-HEAD too foo-NEW too early in the pipeline (or alternately, looking in foo-HEAD rather than creating foo-PREVIOUS and looking there) **

Following the instructions for building ott3.1 and having problems with a subsequent invocation of make ott after refresh. Pinging @jar398 in case he has some insight. Steps to reproduce (all taken directly from docs, linked above):

From fresh clone, build ott3.1 (works great):

    bin/configure ott3.1 ott3.0
    bin/unpack-archive ott-HEAD   #get previous OTT
    bin/set-previous idlist idlist-2.10
    make refresh/idlist    #make 3.0 idlist from idlist-2.10 and ott3.0
    bin/use-version genbank-20161216
    bin/use-version irmng-20140131
    bin/use-version worms-20170604
    bin/fetch-archive amendments bcafdea7f2e9231274cae2df2beed7d732ca46c5
    bin/use-version amendments-bcafdea7f2e9231274cae2df2beed7d732ca46c5
    make r/amendments-HEAD/resource/.made
    make ott

(Running make ott again immediately runs fine, but does rebuild the whole thing, with the only difference in output being a bump in the draft number)

Then run:

   make refresh/amendments
   make refresh/ncbi
   make ott

which fails with error:

SET THE VERSION.
bin/put ott-NEW draft $((1 + `bin/get ott-NEW draft 0`))
Writing transcript to r/ott-NEW/source/debug/transcript.out
rm -f /tmp/make-ott-completed
(time bin/jython make-ott.py ott-NEW 2>&1 \
  && touch /tmp/make-ott-completed) \
  | tee r/ott-NEW/source/transcript.out.new
# cannot find r/amendments-HEAD/resource/amendments-1

real	0m2.297s
user	0m6.925s
sys	0m0.213s
[ -e /tmp/make-ott-completed ]
make: *** [Makefile:87: r/ott-NEW/source/debug/transcript.out] Error 1

[kcranston]

So, after any refresh/foo action, e.g. make refresh/amendments, the foo-HEAD and foo-NEW links both point to the dir containing the new version of the resource (which does not contain a resource link). The previously-used amendments-version dir does still contain a resource link. Some confusion about whether foo-HEAD should point to foo-NEW or to the last version used at this point, or maybe we should be creating foo-PREVIOUS and looking there instead?

[jar398]

I am traveling now but can look at this over the weekend. Sent from a phone

…

On Sep 11, 2019, at 08:32, Karen Cranston ***@***.***> wrote: So, after any refresh/foo action, e.g. make refresh/amendments, the foo-HEAD and foo-NEW links both point to the dir containing the new version of the resource (which does not contain a resource link). The previously-used amendments-version dir does still contain a resource link. Some confusion about whether foo-HEAD should point to foo-NEW or to the last version used at this point, or maybe we should be creating foo-PREVIOUS and looking there instead? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[kcranston]

I think this issue might be that make refresh/amendments does not run the r/amendments-HEAD/resource/.made target. If I run that manually after refreshing, I get past the 'cannot find' error.

[kcranston]

I suppose my only question left at this point is whether we should add make r/amendments-HEAD/resource/.made as an explicit step in the docs, or change the Makefile so that this gets built automatically as part of make refresh/amendments.