'mtsv report' cannot be executed on an air-gapped system

[lovettse]

mtsv report attempts to contact the internet and crashes when run on an air-gapped system. Is this fixable?

[tfursten]

I am looking into this but it seems like an issue with Snakemake. In order to ensure that viewing the report itself does not require an internet connection, Snakemake includes all of the external CSS and JavaScript files as text in the final HTML for the report. Unfortunately, instead of including this text in the Jinja2 template, they download it during report creation which requires an internet connection. This can be postponed until the report is opened in the browser by editing the jinja2 template at ~/.conda/envs/<ENVNAME>/lib/python3.6/site-packages/snakemake/report/report.html and ~/.conda/envs/<ENVNAME>/lib/python3.6/site-packages/snakemake/report/table.html to remove all of the places where get_resource_as_string is called.

Changing for example:

<style>{{ "https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/css/bootstrap.min.css"|get_resource_as_string }}</style>

to

<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.1/css/bootstrap.min.css">

and change

<script>{{ "https://cdnjs.cloudflare.com/ajax/libs/vega/5.6.0/vega.min.js"|get_resource_as_string }}</script>

to

<script src="https://cdnjs.cloudflare.com/ajax/libs/vega/5.6.0/vega.min.js"></script>

I will test this out and see if it solves the problem.

[tfursten]

It looks like there is an open enhancement request for an offline report in the Snakemake Repo but no updates yet.

[tfursten]

Update: This does seem to work if you are ok with editing your local Snakemake report.html template. This should allow you to generate the report offline and then open the report on different machine with internet access. There was one caveat, Filesaver.js will not download properly with the raw.githubusercontent url provided. You can change the url to https://cdn.jsdelivr.net/gh/eligrey/FileSaver.js/src/FileSaver.js to pull it instead from jsdelivr or you can save a copy of https://raw.githubusercontent.com/eligrey/FileSaver.js/2.0.0/src/FileSaver.js and point to your local copy within the script tag. Please let us know if you run into any issues with this approach.