Simon add belstrom 2017

[simonleandergrimm]

Hi Jeff, this is the pull request for adding "Metagenomic and metatranscriptomic analysis of saliva reveals disease-associated microbiota in patients with periodontitis and dental caries" to the dashboard.

Additionally this PR:

• comments out the entry for "Cebria-Mendoza 2021" in sample_metadata_classifier.py. The presence of this entry breaks the pipeline: The dictionary that gets read out by the script contains no entry for "Cebria-Mendoza 2021" because the relevant BioProject is currently skipped within prepare-dashboard-data.py (link).
• Fixes the structure of import-accession.sh to account for the new $SRA_FILES structure (see your dm here)

After running prepare-dashboard-data.py the script returns:

Now check in data.js and the json files and check out on prod
Then run copy-down-hvreads.sh and send the result to prod out of band

Is the latter part something you do, or something I should do?

[simonleandergrimm]

Note to self, do the following once PR is done:

After review is complete and the changes are merged, you'll need to ssh into data.securebio.org and run: cd mgs-pipeline/ git pull To update the dashboard.

[simonleandergrimm]

In general it's much better to do a larger number of smaller PRs. For example, cbc9d53 could have been its own PR. This makes reviewing easier and makes it less likely people overlook bugs.

I also see lots of removals from unrelated papers. Can you try deleting dashboard/top_species_counts and dashboard/top_species_scratch and rerunning prepare dashboard data.

I removed those folders and reran prepare-dashboard-data.sh. I'm not entirely sure what you mean by removals from unrelated papers, though I do see that comparison_sample_counts files for other BioProjects have added content (and I do not know if this is to be expected."

[simonleandergrimm]

Ok that makes sense, thanks!