ConnectionTimeout when downloading gene templates from IMGT

[GabevandenHoeven]

Hi,
I tried to install IGoR first but found that after some complications on the commandline it was probably easier to use this package. Anyway to be able to do anything I need the gene templates from IMGT, but I ran into a connection timeout when using the method described in the documentation for building a new model.
I tried
pygor imgt-get-genomes -t VDJ --imgt-species Homo+sapiens --imgt-chain TRB
I also tried to use the get_IgorRefGenome_VDJ_from_IMGT('Homo+sapiens', 'TRB') function but both gave me the same connection timeout:
requests.exceptions.ConnectTimeout: HTTPConnectionPool(host='www.imgt.org', port=80): Max retries exceeded with url: /download/GENE-DB/IMGTGENEDB-GeneList (Caused by ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x000002658930A050>, 'Connection to www.imgt.org timed out. (connect timeout=None)'))

I realise that this is probably not really an error in Pygor but since these retrieve files automatically and put them in a specific directory structure, idk how I'd have to go about it if I had to do this manually. Is there a fix for this problem? What would you suggest I'd do?

Kind regards,
Gabe van den Hoeven

[GabevandenHoeven]

I found the issue although to make it work for me I had to make changes to the Python source code. The first issue was that I'm assuming IMGT changed their URL protocol's from http to https for the added security. Other's I ran into as I continued debugging until it worked.

List of changes I made in pygor3 python package source code to make it work:

imgt.py:

• changed the url's in the global dictionary imgt_params from http to https
• changed the path directory seperator in download_gene_template from '/' to '\' since I'm working in Pycharm on Windows (Think of making it more cross-platform compatible, these things should really not be an issue in my opinion)
• copied the mkdir command from line 143 to after line 139 (if the ref_genes_path does not exist then you should still create it)

[GabevandenHoeven]

I'll leave this here as an 'Open issue' for others running into the same issues, since when I closed it the issue disappeared