fix-add a error report in the import/export cycle

[feiranl]

Main improvements in this PR:

This PR is to fix only the bug found in Yaml file, as reported in #628. In the meantime, another PR #635 is to fix error of GH workflow test

[feiranl]

@haowang-bioinfo Could you help to fix this? I add an error catch, but the task still succeed.

[haowang-bioinfo]

I propose a error message to fix the bug.

looks good - the actual cause is now fixed in 182010d

Regarding the pass of yamlConversion task, it is presumably due to using previously cached model by the GitHub action cloud server. So a probable solution might be "forcing" GH action to use freshly loaded Yaml model every time. What do you think @mihai-sysbio?

One practical solution (that I used sometimes) could be locally running testYamlConversion function to make sure everything is ok

[mihai-sysbio]

I'm confused - the test is now successful. Is that right?

My idea was to start by fixing the test first, so that we can confirm that the test will trigger a failure of the GH workflow. Only after that the yaml problem would be fixed, and the re-run of the workflow would then pass.

[mihai-sysbio]

I renamed the branch to fix/importExportCycle, which then triggered a closure of the PR and deletion of the branch.

[feiranl]

It is not ready for closing. There is another bug I identified in importYaml.

the import and export cycle changes the yml file.

[mihai-sysbio]

It is not ready for closing

Absolutely! It was not the intention to close the PR, sorry about that. Normally branch renaming is seamless, but apparently when a PR is already open, GitHub will close it. Let's continue in #635.

[haowang-bioinfo]

There is another bug I identified in importYaml.
the import and export cycle changes the yml file.

yes indeed, working on this now

[haowang-bioinfo]

There is another bug I identified in importYaml.
the import and export cycle changes the yml file.

yes indeed, working on this now

this bug is located from Yaml file line 307295: - metabolties: !!omap, where there is typo that supposed to be - metabolites: !!omap. This particular bug was introduced by #606. This type of bug probably can be detected by Yaml lint checker by providing a finite set of keys, from which any unknown keys could thus be reported.

another bug introduced from #606 was the met id MAM1261m in the line 307296 - the middle 0 is missing and correct value should be MAM01261m

[haowang-bioinfo]

this PR is reopened for fixing yaml import/export cycle only, while the issue of GH workflow test will be fixed in #635

[feiranl]

LGTM! The import and export cycle works fine now