Many "Replacing opener..." warnings for SEQROW

[Tom Goddard]

I bug report #3855 there apparently more than 30 warnings at startup about replacing SEQROW opener with one from SEQROW. Not sure if this is a SEQROW problem, a toolshed problem, or an open command problem.

The following bug report has been submitted:
Platform: macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202010200604 (2020-10-20 06:04:27 UTC)
Description
ModuleNotFoundError: No module named 'chimerax.surface.squaremesh'

after showing a molecular surface and using command "surface squaremesh"

Log:
Startup Messages
---
warnings | Replacing opener for 'Gaussian input file' from SEQCROW bundle with
that from SEQCROW bundle
Replacing opener for 'Gaussian output file' from SEQCROW bundle with that from
SEQCROW bundle
Replacing opener for 'ORCA output file' from SEQCROW bundle with that from
SEQCROW bundle
Replacing opener for 'Psi4 output file' from SEQCROW bundle with that from
SEQCROW bundle
Replacing opener for 'XYZ file' from SEQCROW bundle with that from SEQCROW
bundle
29 messages similar to the above omitted
notes | Replacing data format 'Gaussian input file' as defined by SEQCROW
bundle with definition from SEQCROW bundle
Replacing data format 'Gaussian output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle
Replacing data format 'ORCA output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle
Replacing data format 'Psi4 output file' as defined by SEQCROW bundle with
definition from SEQCROW bundle
Replacing data format 'XYZ file' as defined by SEQCROW bundle with definition
from SEQCROW bundle
27 messages similar to the above omitted

open /Users/meng/Desktop/startup.cxc

alias reset view orient; view initial

alias start tool show $1

alias whereprefs info path user unversioned config

alias captut open help:user/tutorials/binding-sites.html#cap-example

alias previewts toolshed url ​https://cxtoolshed-
preview.rbvi.ucsf.edu;toolshed reload available

alias normalts toolshed url ​https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
available

executed startup.cxc
UCSF ChimeraX version: 1.2.dev202010200604 (2020-10-20)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX

open 1mcy format mmcif fromDatabase pdb

[pett]

Probably a toolshed problem from the recent change that enabled manager/provider info for uninstalled bundles. Will investigate.

[pett]

There's some kind of heinous bug with the new code that provides info about bundles available from the toolshed. My 'available.json' file (available bundle cache) lists the ChimeraX_RMF bundle (for example) 27 times!

Once _that_ is fixed so that the bundle only shows up once, then there might be a residual bug where the provider call happens twice -- once for the available bundles and once for the installed bundles. So once the available bundle bug is fixed, you can reassign this to me to clear up that remaining problem.

[Greg Couch]

That is not a bug. According to the RMF metadata, any one of those versions could be installed.

[pett]

Seems like TMI :-) but okay,

Anyway, I have fixed the issue by only issuing the "Replacing" warning when both bundles are installed (and only replacing if the incoming bundle is installed).

[pett]

Isn't 27 (9 versions [0.1-0.9] x 3 platforms) wrong? Shouldn't it be 9 (9 versions x the one platform that the installation is on)? Otherwise Windows installations will think they can install/do things that are Linux-only, etc.

[Greg Couch]

It's not efficient, but not necessarily wrong. There is platform filtering, but I'll need to investigate where it is being done. The filtering is not perfect, for example, a MacOS 10.14 binary package will still show up on 10.13 systems. Will investigate.

[Greg Couch]

The query to the toolshed from ChimeraX for the available packages does not include the platform. I'll change that.

[pett]

Sounds good.

[Greg Couch]

Found the ticket. Modified ChimeraX to set the user agent when querying for bundles so toolshed can know what platform the query is for. Modified the toolshed to limit its responses to bundles that match the platform and ChimeraX core requirements.