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[bioontology-support] EDAM update - same problem again - please help

John Graybeal jgraybeal at stanford.edu
Wed Jan 17 11:02:23 PST 2018


Hi Matus,

I am also replying in more detail separately, to understand the exact needs to address this request:

This looks like quite a mess. Could you guys please somehow prioritize fixing these issues? It's causing us and our users some serious trouble.

But I mainly wanted to note that I think there may be a way to download CSVs before the link is available. I haven't tested this, but I see the CSV link looks like this:
  http://data.bioontology.org/ontologies/EDAM-BIOIMAGING/download?apikey=<YOUR_KEY_HERE>&download_format=csv

Unless I am mistaken, this will always download the most recent CSV which has been created. So as soon as we've created a CSV, even if your UI is not showing it is available yet, this call may work just fine.

John


On Jan 16, 2018, at 12:38 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Matus,

It would be helpful if you could send your comments to the support list so that my colleagues are able to remain in the loop on correspondences regarding BioPortal issues.


On Jan 15, 2018, at 3:15 PM, Matus Kalas <Matus.Kalas at uib.no<mailto:Matus.Kalas at uib.no>> wrote:

When I open http://bioportal.bioontology.org/ontologies/EDAM/?p=classes without being loggen in, in a private browser window, it works fine.

When I'm logged in, http://bioportal.bioontology.org/ontologies/EDAM/?p=classes shows "We're sorry but something has gone wrong. We have been notified of this error.", and clicking "Classes" at http://bioportal.bioontology.org/ontologies/EDAM shows "Problem retrieving classes”.


Are you still seeing a 500 error for EDAM classes page? I’m logged in and can’t reproduce this at the moment.



Another instance of the same kind of problem:

I uploaded a new version of http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING about an hour ago, and it still shows it as not parsed at the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING, whether I'm looged in, or not logged in a private browser window.


I was able to reproduce this behavior here (I’ve cleared BioPortal’s caches, so your ontology is accessible now). BioPortal has 3 distinct caching layers in the stack. Based on the information provided in your last two messages, we think we’ve narrowed the problem to the client side in-memory cache.



One more question, or rather two:

Is the CSV version for download generated by some internal BioPortal machinery, or is it using some available libraries?


The CSV is generated internally, using Ruby’s standard CSV library:

https://github.com/ncbo/ontologies_linked_data/blob/master/lib/ontologies_linked_data/utils/ontology_csv_writer.rb



Related to that, if the summary page at http://bioportal.bioontology.org/ontologies/EDAM-BIOIMAGING doesn't show the new version as parsed, and thus doesn't provide it CSV, is there another URL I could use to download the newly generated CSV?


No, not that I’m aware of.



This looks like quite a mess. Could you guys please somehow prioritize fixing these issues? It's causing us and our users some serious trouble.


We take all problem reports seriously and care a great deal about providing end users with the best experience possible. Having said that, we’re a very small team supporting a relatively large user community. We’re doing the best we can with the resources we have and will continue to look into / address this issue as time permits.

Kind regards,
Jennifer

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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