fix: make omicsintegrator2 work offline #226
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[I mainly used this issue as an excuse to experiment with a git patch workflow over the forking method that seems to be present in SPRAS] Forces OI2 to work offline by disabling the unused networkx graph as interactive HTML feature (we already have workflows in SPRAS that enable this). The network error was coming from `output_networkx_graph_as_interactive_html` dynamically fetching jQuery to insert it as an inline script. This could have also been fixed by providing a `local` folder with all of the scripts, but putting the several hundred-kilobyte scripts on this repository did not seem worth it for an unused feature.
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needed for benchmarking
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Now that OI2 is patched, what is the goal of network_disabled? Is it for SPRAS developers to test algorithms to see if they fail without a network?
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Yes. |
That helps. So it is in fact a decision made by the SPRAS contributor who is wrapping the algorithm. |
Documentation build overview
Show files changed (7 files in total): 📝 5 modified | ➕ 1 added | ➖ 1 deleted
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tristan-f-r
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P-medium
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The patching documentation looks good. The OI2 test cases are failing, and I didn't dig in yet to see why. |
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The error was because of |
ntalluri
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needed for benchmarking
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I suggest we merge this before the larger #314. That means sticking with the existing versioning updates, readme update, etc. and manual DockerHub image push. |
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[I don't have permission to push to Reed-CompBio's DockerHub, so someone else will have to do it / reconfigure my permissions] |
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Tests pass, and I ran it locally.
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Forces OI2 to work offline by disabling the unused networkx graph as interactive HTML feature (we already have workflows in SPRAS that enable this).
The network error was coming from
output_networkx_graph_as_interactive_htmldynamically fetching jQuery to insert it as an inline script. This could have also been fixed by providing alocalfolder with all of the scripts, but putting the several hundred-kilobyte scripts on this repository did not seem worth it for an unused feature.This is tested - this also introduces a (docker-only)
network_disabledparameter for running containers with a detached network.Closes #78.
This is set as
P-mediumas this PR sets the precedent for patch files for both any regular patching, and (more importantly) seeding algorithms.