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opencobra / COBRA.jl

High-level, high-performance, constraint-based reconstruction and analysis in Julia
https://git.io/COBRA.jl
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New .mat file in test script is causing script to fail #82

Open jdesbonnet opened 4 years ago

jdesbonnet commented 4 years ago

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 commented 4 years ago

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

<!DOCTYPE html>

jdesbonnet commented 4 years ago

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 commented 4 years ago

Yes, definitely. I just wanted to point out that the test framework needs to be updated. Bill

From: Joe Desbonnet notifications@github.com Reply-To: "opencobra/COBRA.jl" reply@reply.github.com Date: Wednesday, September 23, 2020 at 1:03 PM To: "opencobra/COBRA.jl" COBRA.jl@noreply.github.com Cc: "Cannon, William R" William.Cannon@pnnl.gov, Comment comment@noreply.github.com 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 GitHubhttps://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 unsubscribehttps://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 commented 4 years ago

@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 commented 4 years ago

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

On Thu, 24 Sep 2020 at 15:38, Joe Desbonnet notifications@github.com 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.

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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.

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