Hey,
I've just realised I never got back to this thread and elaborated on this
issue... Here goes:
To begin with, our reference code will be downloadNLMSA_megatest.py from
the current master.
Secondly, what happens is an error, not a warning.
Thirdly, here is what exactly happens:
- good case, i.e. with WORLDBASEPATH pointing at the UCLA XML-RPC
server
[...]
INFO downloader.download_unpickler: Download done.
INFO downloader.uncompress_file: gunzipping
/var/tmp/megatestSNZtX8/dm2_multiz9way.txt.gz...
INFO nlmsa_utils.nlmsa_textdump_unpickler: Saving NLMSA indexes from
textdump: /var/tmp/megatestSNZtX8/dm2_multiz9way.txt
/result/mareks/pygr/pygr/sqlgraph.py:1111: DeprecationWarning: The cursor
argument is deprecated. Use serverInfo instead!
SQLTableBase.__init__(self, *args, **kwargs)
INFO nlmsa_utils.nlmsa_textdump_unpickler: Saving NLMSA binary index: 0
NLMSA_LPO_Internal0 165964729
...
INFO nlmsa_utils.nlmsa_textdump_unpickler: Saving NLMSA binary index: 1
NLMSA_UNION_Internal 1 1847310997
...
ok
- bad case, i.e. after setting WORLDBASEPATH so that worldbase can't find
any resources - 'export WORLDBASEPATH=/nonexistent', for instance)
[...]
INFO downloader.download_unpickler: Download done.
INFO downloader.uncompress_file: gunzipping
/var/tmp/megatestJLHQ9l/dm2_multiz9way.txt.gz...
INFO nlmsa_utils.nlmsa_textdump_unpickler: Saving NLMSA indexes from
textdump: /var/tmp/megatestJLHQ9l/dm2_multiz9way.txt
ERROR
======================================================================
ERROR: Test downloading NLMSA data
----------------------------------------------------------------------
Traceback (most recent call last):
File "downloadNLMSA_megatest.py", line 69, in test_download
msa_dl = self.mdb_dl(self.resource_name) # download and build it!
File "/result/mareks/pygr/pygr/metabase.py", line 777, in __call__
for objdata, docstr in self.find_resource(resID, download):
File "/result/mareks/pygr/pygr/metabase.py", line 1047, in find_resource
% resID)
WorldbaseNotFoundError: 'unable to find Test.NLMSA in WORLDBASEPATH'
----------------------------------------------------------------------
Finally, the issues I have got here are as follows:
- despite using an individual metabase, one still uses $WORLDBASEDOWNLOAD
and $WORLDBASEBUILDDIR to control the destination of alignment files. This
may be somewhat confusing, not to mention it is impossible to set these
individually for different metabases. Possible solution - make these
metabase-specific options which only fall back to the environment if the
local option is not set?
- the error message given in the bad case is very confusing. Test.NLMSA
is not in WORLDBASEPATH because it's not supposed to be in it, which
brings us to an important question - why has Pygr begun looking in the
worldbase even though the resource has been requested specifically from
a dedicated metabase. Possible solution: none right now, we should
however discuss whether we want metabase isolation or not, how to control
it and so on;
- another question posed by the above is what exactly happened that has
caused the downloaded Test.NLMSA not to be accessed correctly. My guess is
that with no worldbase resources available, Pygr has failed to locate the
necessary sequence data, quietly aborted the build and went on to look
for Test.NLMSA elsewhere. The problem here is the "quietly aborted" bit -
given how talkative NLMSA building normally is, at least at high verbosity
levels, it really should report such problems, even when not invoked
diretly. Possible solution: make sure errors from NLMSA building are
not suppressed by code invoking in and explain what specifically has been
wrong.
Let me know what you think, guys.
Cheers,
--
MS
--
You received this message because you are subscribed to the Google Groups
"pygr-dev" group.
To post to this group, send email to pygr-...@googlegroups.com.
To unsubscribe from this group, send email to
pygr-dev+unsubscr...@googlegroups.com.
For more options, visit this group at
http://groups.google.com/group/pygr-dev?hl=en.
