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.

5

It seems like you're encountering a "Bad Gateway" error when trying to run the HMDB MS search tool, which typically indicates a server-side issue or a problem with the way the tool is attempting to retrieve data from the HMDB server. The error message specifically points to an issue at line 660 in the hmdb.pm script, which might be related to how the tool is generating or processing the CSV results. A few things to check include:

  1. HMDB Server Status: While you received a status 200 (which means the server connection is successful), it's possible the HMDB server is temporarily down or experiencing issues. You can check the HMDB website or contact their support to verify if the server is functioning properly.

  2. Request Format: There might be an issue with the URL request being sent to the server, such as malformed parameters or query strings. Verify that the parameters being passed to the HMDB server are correctly formatted, and try testing with simpler queries to rule out overly complex requests causing issues.

  3. Tool Configuration: Ensure that the tool and its dependencies are up-to-date. It’s also worth checking whether any recent updates to the tool or Galaxy platform might have changed how requests are handled.

  4. Proxy or Network Issues: If the tool is running in a shared environment or behind a proxy, it's possible that network restrictions are interfering with the request. You may want to try running the tool in a different network environment or reach out to your IT team to ensure that there aren’t any network or firewall-related issues causing the "Bad Gateway" error.

  5. Error Logs and Debugging: If you have access to additional logs or the ability to debug the script, check for more detailed error messages or stack traces. This might provide further insight into what is going wrong at line 660 in the hmdb.pm file.

If the issue persists after verifying these points, it could be helpful to reach out to the tool’s maintainers or the Galaxy tool shed repository where the tool is hosted to report the issue and see if they are aware of any ongoing server-side problems.