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Wang-Bioinformatics-Lab / GNPS2_Workflows

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Agilent file sequential scan conversion #10

Closed warkdave closed 10 months ago

warkdave commented 10 months ago

This function was in https://gnps-quickstart.ucsd.edu/conversion. It's essential for making our Agilent QTOF MS/MS files usable in Library search workflows.

mwang87 commented 10 months ago

Thanks Dave, we'll have to refactor it and deploy it on the GNPS2 infrasturcture. I think likely v1 we'll include only conversion and none of the other quickstart features.

mwang87 commented 10 months ago

Give this a try!

https://quickstart.gnps2.org/conversion

warkdave commented 10 months ago

I tested on Chrome and Edge and neither completed the process, just hung on the "Converting please wait" portion. I attached a screencap of the error if that's helpful. image

mwang87 commented 10 months ago

Can you describe the problem and what you tried to do and share the input data?

Ming

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warkdave commented 10 months ago

What I did:

  1. Dragged a file (75MB MZXML) into the window, it completed uploading indicated by the "checkmark" popup.
  2. Clicked Convert Uploaded Agilent Files. Converting Please Wait popup appears with spinning circle.
  3. Nothing else happened. I waited about 5 minutes and opened the console to see if there was any indication of HTTP response or error code.

Here is the data file: https://drive.google.com/file/d/1PF91IJ_pbVvB8qoPjOOtpYu4vxi20xNs/view?usp=drive_link It's an Agilent .d file, QTOF ESI- MS2, that was converted using MSConvert through the process that was in the GNPS documentation.

mwang87 commented 10 months ago

Verified and fixed.

warkdave commented 9 months ago

The problem has returned (500 error on processagilentconvert, hangs on "Converting files please wait"). I had trouble connecting to the server earlier so I'm assuming there's some maintenance going on - I'll try again tomorrow.