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monarch-initiative / dipper

Data Ingestion Pipeline for Monarch
https://dipper.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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Unable to access HPO data repository #868

Closed Prakash2403 closed 4 years ago

Prakash2403 commented 4 years ago

Unable to run for hpoa source. Tries to clone a private repo. How to fix this issue? @cmungall @justaddcoffee @balhoff

justaddcoffee commented 4 years ago

Hi Prakash - could you please run: git show and ./dipper-etl.py -s hpoa and copy/paste the output?

kshefchek commented 4 years ago

we previously ingested text mined common disease to phenotype associations from a private repo, since we no longer use this we should remove it from the ingest

kshefchek commented 4 years ago

looking a little closer at this, the hpoa file is returning a 404: http://compbio.charite.de/jenkins/job/hpo.annotations.2018/lastSuccessfulBuild/artifact/misc_2018/phenotype.hpoa

@pnrobinson @drseb has this file been rehomed or renamed?

pnrobinson commented 4 years ago

Sorry, yes the new address is http://compbio.charite.de/jenkins/job/hpo.annotations.current/lastSuccessfulBuild/artifact/misc_2018/phenotype.hpoa

I also have asked @drseb to change this to

http://compbio.charite.de/jenkins/job/hpo.annotations.current/lastSuccessfulBuild/artifact/current/phenotype.hpoa

or even http://compbio.charite.de/jenkins/job/hpo.annotations.current/lastSuccessfulBuild/artifact/phenotype.hpoa

but I do not think he has had time yet/

kshefchek commented 4 years ago

looks like this was updated already and I was just running an old version of dipper, sorry for the false alarm!

@Prakash2403 I'm not able to replicate the issue, unless you are modifying the code slightly to fetch the common disease annotations.

Prakash2403 commented 4 years ago

@kshefchek @justaddcoffee Just figured out the issue. Was installing dipper using pip install dipper which installs version 0.2.32( ~ 2 years older version). Installing from source fixed it.

Thanks for all the help :)

kshefchek commented 4 years ago

sorry about this! we'll update the package on pypi