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Topic/getmicrobedata quick fix #5258

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bernt-matthias commented Jan 3, 2018

There seems to be no UnvalidatedValue class anymore. So I removed these checks which seems to make the tool functional again.

Note that there is one more instance of such a check in the Galaxy sources (in tools/parameters/basic.py). I guess this can also be removed?

Could someone explain me why I see all my merge commits here? Is this normal or are my git workflows somehow wrong?

@galaxybot galaxybot added the triage label Jan 3, 2018

@galaxybot galaxybot added this to the 18.01 milestone Jan 3, 2018

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bernt-matthias commented Jan 3, 2018

See also #4691

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bernt-matthias commented Jan 3, 2018

I would also like to start a discussion on improving/removing/replacing the tool. For me it lacks the following functionality:

  • selection of multiple species or taxa should let the tool download all data for the taxa, this should be based on the NCBI taxonomy
  • optionally get all data in one data set (i.e. all beds in one data, all cds in another,...)
  • there should be a data_manager that could download the index of available data or the complete data ... given the bimonthly updates I would prefer the former.

Since I was just researching a bit I found this useful document ftp://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_Downloading_Genomic_Data.pdf

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bgruening commented Jan 3, 2018

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bernt-matthias commented Jan 3, 2018

Thanks for the tip. I will give it a try.

What would also be useful if the scripts that were used to generate the loc file and data that can be synced from usegalaxy (https://galaxyproject.org/admin/use-galaxy-rsync/) would be available. File paths in some of the text files it seems that a Dan produced the data. See also
#4691

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bgruening commented Jan 3, 2018

Imho the entire depot should be more open for community contributions. For example to populate the CVMFS by community members. This will be one of my aims for 2018. I envision a similar approach to our singularity containers but more discussions needs to happen here.

@martenson martenson added the kind/bug label Jan 17, 2018

@martenson martenson requested a review from guerler Jan 17, 2018

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nsoranzo commented Jan 17, 2018

The UnvalidatedValue class was removed in PR #1572 .

fix for microbial import tool
There seems to be no UnvalidatedValue class anymore. So I removed these
checks which seems to make the tool functional again.

Note that there is one more instance of such a check in the Galaxy
sources (in tools/parameters/basic.py). I guess this can also be
removed?

@nsoranzo nsoranzo force-pushed the bernt-matthias:topic/getmicrobedata-quick-fix branch from 2b41e21 to 4b2bf12 Jan 17, 2018

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nsoranzo commented Jan 17, 2018

Failed API test is unrelated.

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martenson commented Jan 17, 2018

@bernt-matthias thanks for the contribution!

as of the suggested improvements please open a new issue since once merged this place will be far less visible.

@martenson martenson merged commit d2530f4 into galaxyproject:dev Jan 17, 2018

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