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Example workflows for refine.bio data
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Ortholog mapping notebook (temporarily?) won't render because of problem with HCOP data download #439

Closed jaclyn-taroni closed 3 years ago

jaclyn-taroni commented 3 years ago

Background

The rendering upon merge step is failing with the following on the 03-rnaseq/ortholog-mapping_rnaseq_01_ensembl.Rmd notebook:

trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hcop/human_mouse_hcop_fifteen_column.txt.gz'
Quitting from lines 223-232 (ortholog-mapping_rnaseq_01_ensembl-tmp-torender.Rmd) 
Error in download.file(paste0("ftp://ftp.ebi.ac.uk/pub/databases/genenames/hcop/",  : 
  cannot open URL 'ftp://ftp.ebi.ac.uk/pub/databases/genenames/hcop/human_mouse_hcop_fifteen_column.txt.gz'
Calls: <Anonymous> ... withCallingHandlers -> withVisible -> eval -> eval -> download.file

Problem

I believe this may only be temporary because the FTP server isn't available. You can't access the files using this page either: https://www.genenames.org/tools/hcop/

However, I'll note that the download is now called 16 columns instead of 15 columns.

What are the recommended next steps?

For now, my recommendation is to wait a day or so and try again. If the issue isn't temporary, we should find another source of data (or means/package) for ortholog mapping. If that proves to be too much work in a short time frame, we might consider temporarily removing this example from GH pages.

Is there a particular timeframe for this issue?

We want to make sure some solution is in place this week since it prevents this notebook from rendering.

jashapiro commented 3 years ago

However, I'll note that the download is now called 16 columns instead of 15 columns.

On the website it still looks like 15 columns to me? The 16 column table is the all human orthologs, with the extra column presumably species?

I just confirmed that http://ftp.ebi.ac.uk/pub/databases/genenames/hcop/human_mouse_hcop_fifteen_column.txt.gz works in the browser, so perhaps the solution could be as easy as substituting http for ftp.

jaclyn-taroni commented 3 years ago

You're right, I was looking at the wrong file based on how we used to use the hcop package. We can probably make the ftp -> http change on #436.

jashapiro commented 3 years ago

Updated in https://github.com/AlexsLemonade/refinebio-examples/pull/436/commits/4617b73a69dfc155a3da4604d8ab9b4c601576d5 (Part of #436)

jaclyn-taroni commented 3 years ago

This has been resolved (for now 😱 ).