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MassBank / MassBank-data

Official repository of open data MassBank records
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Gulde et al. oxidation transformation products #166

Closed lauperbe closed 3 years ago

lauperbe commented 3 years ago

Here is a batch of identified oxidation transformation products from Gulde et al. Due to the measurment type we unfortunately only have 1 collision energy per compound and ionisation mode but they can still be informative.

Cheers Benedikt

tsufz commented 3 years ago

Hi @lauperbe, Your branch has the wrong version tag. Please merge the upstream dev branch into your local branch before running pull requests. Keep the pull-request open and do the following:

Add the remote upstream repository to your local repository (on your computer, not on GitHub):

git remote add upstream https://github.com/MassBank/MassBank-data
git remote -v
git fetch upstream

Set the focus to your local dev branch: git checkout Gulde

Merge the upstream branch in your local branch: git pull upstream dev

Push the merged stream to your fork on GitHub git push origin Gulde

The open Pull-Request will handle the new situation and the merge should be possible.

If you work on GitHub only, you need to run a pull-request MassBank/MassBank-data:dev -> lauperbe:Gulde.

Best wishes, Tobias

lauperbe commented 3 years ago

Thanks for the advice. I followed it and have fixed it as well as some ACESSIONs that did not match the filename (error on my side). The automated check now gives the error found below. It says that PK$SPLASH are expected but they have the splash in the records, same as the other compounds that do not result in an Error. Do you know what the Error is in this case? Thanks in advance

Benedikt

ERROR message: $ git clone --depth 1 -q https://github.com/MassBank/MassBank-web.git .scripts/MassBank-web install.2 13.51s$ mvn -q -f .scripts/MassBank-web/MassBank-Project/MassBank-lib/pom.xml package 185.75s$ .scripts/MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib/MassBank-lib/bin/Validator ./ Validator version: 2.1.8 12:37:30.201 ERROR massbank.cli.Validator - PK$SPLASH expected 12:37:30.207 ERROR massbank.cli.Validator - MS$FOCUSED_ION: PRECURSOR_TYPE [M+HCOO-]- 12:37:30.207 ERROR massbank.cli.Validator - ^ 12:37:30.208 ERROR massbank.cli.Validator - Error in './Eawag_Additional_Specs/ET406267.txt'. 12:37:30.540 ERROR massbank.cli.Validator - PK$SPLASH expected 12:37:30.540 ERROR massbank.cli.Validator - MS$FOCUSED_ION: PRECURSOR_TYPE [M+HCOO-]- 12:37:30.541 ERROR massbank.cli.Validator - ^ 12:37:30.542 ERROR massbank.cli.Validator - Error in './Eawag_Additional_Specs/ET408367.txt'. The command ".scripts/MassBank-web/MassBank-Project/MassBank-lib/target/MassBank-lib/MassBank-lib/bin/Validator ./" exited with 1. cache.2 store build cache

lauperbe commented 3 years ago

The error was in the naming of the FA addukt. in the documentation (https://github.com/MassBank/MassBank-web/blob/main/Documentation/MassBankRecordFormat.md#2.6.1) it is written as [M+HCOO-]- but that gave the parser error. When I changed it to [M+HCOO]- it worked. Might be worth to adapt the documentation.

Benedikt