Problem with HMDB MS search

Workflow4Metabolomics
1

Hello,

HMDB MS search seems to run correctly, the standard output being: Testing HMDB server connexion (1 time(s) )... Status: 200 The HMDB server returns that your request (connexion test) was fulfilled.

The output however, is empty. The tool standard error is:
Error GETing https://hmdb.ca/spectra/ms/generate_csv.csv?results[action]=search&results[adduct_type .... : Bad Gateway at /shared/ifbstor1/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/29195cb5d378/hmdb_ms_search/lib/hmdb.pm line 660.

I have tried to run the tool multiple times on different days but always run into the same error. Do you have any advice on how to proceed?

Have a nice day,
Rina

2

Hi @rmekuli

The tool has been updated and is functionnal (at least on y side).
Can you check that you are using the 1.7.6 version of the HMDB MS search tool? see image below

image
image914×473 42 KB

Best

3

Hello @rmekuli

The problem was on HMDB server side. All is back to normal now

You can try
Best

4

Hello,

Apologies for the late reply, I had not realized you replied here. I am afraid I still get an error:

Error GETing https://hmdb.ca/spectra/ms/generate_csv.csv?results[action]=search&results[adduct_type][]=M%2BH&results[ccs_predictors]=&results[ccs_tolerance]=&results[commit]=Search&results[controller]=specdb%2Fms&results[ms_search_ion_mode]=positive&results[query_masses]=85.0636923013236 359.231683328131 158.05164939882 140.023007863576 185.10170361321 &results[tolerance]=0.05&results[tolerance_units]=Da&results[utf8]=✓: Bad Gateway at /shared/ifbstor1/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/fgiacomoni/hmdb_ms_search/29195cb5d378/hmdb_ms_search/lib/hmdb.pm line 660.