New .mat file in test script is causing script to fail

[jdesbonnet]

Ref pull request #80 merged to master branch in around 2020-09-07

The new ecoli model at
http://bigg.ucsd.edu/static/models/e_coli_core.mat (size 114736) is causing test script to fail.

The older URL
https://github.com/opencobra/COBRA.models/raw/master/mat/ecoli_core_model.mat does work but is a considerably smaller file of 8818 bytes)

URL is specified in file test/getTestModel.jl

To replicate error from command line on king.nuigalway.ie, create an empty directory and 'cd' into it. Then:

git clone https://github.com/opencobra/COBRA.jl 
cd COBRA.jl
/home/vmhadmin/julia-1.2.0/bin/julia --color=yes -e 'import Pkg; Pkg.clone(pwd()); Pkg.test("COBRA", coverage=true); Pkg.rm("COBRA");'

Error text:

Running s_all.jl ...

[ Info: The ecoli_core model already exists.
ERROR: LoadError: LoadError: The variable named `model` does not exist. Please set `model` to a known variable in the `.mat` file.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] loadModel(::String, ::String, ::Int64) at /home/vmhadmin/tmp/t/COBRA.jl/src/load.jl:220
 [3] loadModel at /home/vmhadmin/tmp/t/COBRA.jl/src/load.jl:226 [inlined] (repeats 3 times)
 [4] top-level scope at /home/vmhadmin/tmp/t/COBRA.jl/test/s_all.jl:48
 [5] include at ./boot.jl:328 [inlined]
 [6] include_relative(::Module, ::String) at ./loading.jl:1094
 [7] include(::Module, ::String) at ./Base.jl:31
 [8] include(::String) at ./client.jl:431
 [9] top-level scope at /home/vmhadmin/tmp/t/COBRA.jl/test/runtests.jl:133
 [10] include at ./boot.jl:328 [inlined]
 [11] include_relative(::Module, ::String) at ./loading.jl:1094
 [12] include(::Module, ::String) at ./Base.jl:31
 [13] include(::String) at ./client.jl:431
 [14] top-level scope at none:5
in expression starting at /home/vmhadmin/tmp/t/COBRA.jl/test/s_all.jl:48
in expression starting at /home/vmhadmin/tmp/t/COBRA.jl/test/runtests.jl:118
ERROR: Package COBRA errored during testing
Stacktrace:
 [1] pkgerror(::String, ::Vararg{String,N} where N) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Types.jl:112
 [2] #test#119(::Bool, ::Nothing, ::typeof(Pkg.Operations.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/Operations.jl:1288
 [3] #test at ./none:0 [inlined]
 [4] #test#62(::Bool, ::Nothing, ::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::typeof(Pkg.API.test), ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:245
 [5] #test at ./none:0 [inlined]
 [6] #test#61 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:230 [inlined]
 [7] #test at ./none:0 [inlined]
 [8] #test#60 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:229 [inlined]
 [9] #test at ./none:0 [inlined]
 [10] #test#59(::Base.Iterators.Pairs{Symbol,Bool,Tuple{Symbol},NamedTuple{(:coverage,),Tuple{Bool}}}, ::typeof(Pkg.API.test), ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.2/Pkg/src/API.jl:228
 [11] (::getfield(Pkg.API, Symbol("#kw##test")))(::NamedTuple{(:coverage,),Tuple{Bool}}, ::typeof(Pkg.API.test), ::String) at ./none:0
 [12] top-level scope at none:1

[wrcannon]

I have a similar problem after downloading COBRA via Pkg.add("COBRA"):

ERROR: LoadError: HTTP.ExceptionRequest.StatusError(404, "GET", "/LCSB-BioCore/COBRA.models/raw/master/mat/ecoli_core_model.mat", HTTP.Messages.Response:
"""
HTTP/1.1 404 Not Found
date: Wed, 23 Sep 2020 15:30:25 GMT
content-type: text/html; charset=utf-8
server: GitHub.com
status: 404 Not Found
vary: X-PJAX, Accept-Encoding, Accept, X-Requested-With
link: https://github.githubassets.com/_error.js; rel=preload; as=script; nopush
cache-control: no-cache
strict-transport-security: max-age=31536000; includeSubdomains; preload
x-frame-options: deny
x-content-type-options: nosniff
x-xss-protection: 1; mode=block
referrer-policy: origin-when-cross-origin, strict-origin-when-cross-origin
expect-ct: max-age=2592000, report-uri="https://api.github.com/_private/browser/errors"
content-security-policy: default-src 'none'; base-uri 'self'; block-all-mixed-content; connect-src 'self' uploads.github.com www.githubstatus.com collector.githubapp.com api.github.com www.google-analytics.com github-cloud.s3.amazonaws.com github-production-repository-file-5c1aeb.s3.amazonaws.com github-production-upload-manifest-file-7fdce7.s3.amazonaws.com github-production-user-asset-6210df.s3.amazonaws.com cdn.optimizely.com logx.optimizely.com/v1/events wss://alive.github.com; font-src github.githubassets.com; form-action 'self' github.com gist.github.com; frame-ancestors 'none'; frame-src render.githubusercontent.com; img-src 'self' data: github.githubassets.com identicons.github.com collector.githubapp.com github-cloud.s3.amazonaws.com *.githubusercontent.com; manifest-src 'self'; media-src 'none'; script-src github.githubassets.com; style-src 'unsafe-inline' github.githubassets.com; worker-src github.com/socket-worker.js gist.github.com/socket-worker.js
Content-Length: 176100
X-GitHub-Request-Id: DFDB:91E1:6BFCC:9AA73:5F6B6A33

[jdesbonnet]

Replacing "LCSB-BioCore" with "opencobra" in the URL should cause that test to succeed (the repositories moved from LCSB-BioCore to opencobra on github.com earlier this year.

[wrcannon]

Yes, definitely. I just wanted to point out that the test framework needs to be updated. Bill From: Joe Desbonnet <[email protected]> Reply-To: "opencobra/COBRA.jl" <[email protected]> Date: Wednesday, September 23, 2020 at 1:03 PM To: "opencobra/COBRA.jl" <[email protected]> Cc: "Cannon, William R" <[email protected]>, Comment <[email protected]> Subject: Re: [opencobra/COBRA.jl] New .mat file in test script is causing script to fail (#82) Replacing "LCSB-BioCore" with "opencobra" in the URL should cause that test to succeed (the repositories moved from LCSB-BioCore to opencobra on github.com earlier this year. — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://protect2.fireeye.com/v1/url?k=f5ce72c7-a97b4d7e-f5ce58d2-0cc47adc5fce-52a33634a105b2d6&q=1&e=9888b384-f4ae-4b65-ab3a-b539b431baa2&u=https%3A%2F%2Fgithub.com%2Fopencobra%2FCOBRA.jl%2Fissues%2F82%23issuecomment-697941783>, or unsubscribe<https://protect2.fireeye.com/v1/url?k=465bdec7-1aeee17e-465bf4d2-0cc47adc5fce-27de50d70255b0c1&q=1&e=9888b384-f4ae-4b65-ab3a-b539b431baa2&u=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FADTGAVBD44BTYCNC2TIPAVTSHJH37ANCNFSM4RSB7VOA>.

[jdesbonnet]

@rmtfleming Hi Ronan, what's the best .mat file to use here? The original one when corrected for the github move completes the test sucessfully. But the new one introduced about 2 weeks ago ( http://bigg.ucsd.edu/static/models/e_coli_core.mat ) currently fails the test.

[rmtfleming]

https://github.com/opencobra/COBRA.models/raw/master/mat/ecoli_core_model.mat

…

On Thu, 24 Sep 2020 at 15:38, Joe Desbonnet ***@***.***> wrote: @rmtfleming Hi Ronan, what's the best .mat file to use here? The original one when corrected for the github move completes the test sucessfully. But the new one introduced about 2 weeks ago ( http://bigg.ucsd.edu/static/models/e_coli_core.mat ) currently fails the test. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

-- -- Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D. ---------------------------------------------------------------------------- Assistant Professor, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Faculty of Science, Leiden University. https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming & H2020 Project Coordinator, Systems Medicine of Mitochondrial Parkinson’s Disease, http://sysmedpd.eu & Adjunct Lecturer, School of Medicine, National University of Ireland, Galway. ---------------------------------------------------------------------------- Peer-reviewed publications: https://goo.gl/FZPG23 Mobile: +353 852 109 806 Skype: ronan.fleming ---------------------------------------------------------------------------- (This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.)