Configure planteome instance of biolink

[planteome]

Configure planteome instance of biolink

[cmungall]

OK, everything should now work out the box.

Examples:

http://localhost:8888/api/bioentity/gene/GR_gene%3AGR%3A0060769/phenotypes/?fetch_objects=true&rows=20

http://localhost:8888/api/bioentity/gene/TAIR%3Alocus%3A2155869/function/?fetch_objects=true&rows=20

http://localhost:8888/api/bioentity/gene/TAIR%3Alocus%3A2155869/expressed/?fetch_objects=true&rows=20

[cmungall]

Hi @elserj we want to use this for an upcoming meeting at the end of the month - can we get this service up?

[elserj]

Might have a couple of issues. I cloned it to our server and tried running it. Looks like gunicorn is missing. Problem is that this is a service and I will have to get approval from sysadmin on this. Probably will, but it could take some time. I'm also going on vacation next week, but can get back to it after.

[nathandunn]

I’ll be presenting it and the end of June. I’ve started work with getting the same stuff to work with Monarch, so hopefully it translates fairly readily, but it would be good to have a little bit of lead time on this. Nathan

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On Jun 9, 2017, at 4:12 PM, elserj ***@***.***> wrote: Might have a couple of issues. I cloned it to our server and tried running it. Looks like gunicorn is missing. Problem is that this is a service and I will have to get approval from sysadmin on this. Probably will, but it could take some time. I'm also going on vacation next week, but can get back to it after. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qvq_LTAgcc9TqDuuWImDoorNGMPhks5sCdF2gaJpZM4NkaT_>.

[cmungall]

Sorry about that, this fixes it e77a20e

you had gunicorn, it just wasn't in your path (we're using pyvenv, which places everything you need in a venv folder)

[elserj]

That didn't actually fix my issue, but looking a bit closer at it, it was failing on installing scipy in pyvenv. Had to do
sudo yum install lapack-devel blas-devel
as they weren't installed. The non-devel packages were, but I guess it needed the devel to build. Once I did that I ran start-server.sh and it took about 15 minutes or so, but it did then start. I get responses from your examples above.

I'm waiting for the sysadmin to create the CName for biolink.planteome.org as I don't have permissions to do that. I already got permission to start the systemd service, so should be good there. Once the CName is done, I will let you know.

[nathandunn]

This is great news. Thanks.

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On Jun 9, 2017, at 5:17 PM, Chris Mungall ***@***.***> wrote: Sorry about that, this fixes it e77a20e you had gunicorn, it just wasn't in your path (we're using pyvenv, which places everything you need in a venv folder) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[elserj]

I think everything is working now:
http://biolink.planteome.org/api/bioentity/gene/GR_gene%3AGR%3A0060769/phenotypes/?fetch_objects=true&rows=20

Let me know if you find any issues.

[nathandunn]

@elserj It is close. I think that their might be CORS issues. When I go to this:

http://biolink.planteome.org/api/

Can't read from server. It may not have the appropriate access-control-origin settings.

There is an errored out connection when it tries to retrieve this file:

http://localhost:8888/api/swagger.json

When you do the same thing with Monarch you get:

https://api.monarchinitiative.org/api/swagger.json

[nathandunn]

But the initial link you sent worked.

[nathandunn]

@kltm / @cmungall / @kshefchek Was there a trick to getting swagger installed and made public?

Looks like the underlying service is working great.

[elserj]

Sorry for the delay, took quite some time figure out how to fix this. Probably longer than it should have, but it seems to be fine now.

Enabling CORS alone didn't seem to fix it. Finally started working once I added:
ProxyPreserveHost on
to the Apache vhost config.

Let me know if you find any more issues.

[nathandunn]

@elserj This is great.

Question (for @cmungall as well).

Should I expect the same set of implementation as with monarch?

Also, for now do we not handle trait, QTL, etc. or are they mapped to something else?

Thanks!

[nathandunn]

It looks like most of these are conserved. I'll try to finish this off shortly and let you know what the mappings are or if I run into any troubles.

[nathandunn]

BTW, @elserj / @cmungall I'm updating the examples (I need to to build tests). You may want to do the same thing in your own swagger:

https://github.com/nathandunn/biolink-planteome

[nathandunn]

These are the ones not working so far. Of course it is possible we don't have the data or they just simply don't make sense:

• all (working) examples need to be updated to include plant-specific examples
• 500 error: http://biolink.planteome.org/api/#!/bioentity/get_gene_homolog_associations
• 500 error: http://biolink.planteome.org/api/#!/bioentity/get_gene_interactions
• Gene / disease associations seems to return go terms from biological process. Maybe these are correct?
• Phenotype to gene returns only null fields
• Genotype mapped to gene.
• Phenotypes seem to have empty mappings. I would expect them to be mapped to the trait ontology, but maybe there is a better solution.
• no hits coming out of "search" operation
• "substance" relies on CHEBI, which we don't have loaded. That is fine. Just need to know if it is mapped to something else.
• are variants mapped to anything? I tried QTL's, but maybe there is another designation?
• there seems to be a load problem with bioentity-association and bulk-operations (http://biolink.planteome.org/api/bioentity/EnsemblPlants:GRMZM2G061969_T01/associations/?rows=20&fetch_objects=true) . When I run it individually it is fine, but as part of a test suite, it chokes with this error:

+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
+<html><head>
+<title>502 Proxy Error</title>
+</head><body>
+<h1>Proxy Error</h1>
+<p>The proxy server received an invalid
+response from an upstream server.<br />
+The proxy server could not handle the request <em><a href="/api/bioentity/EnsemblPlants:GRMZM2G061969_T01/associations/">GET&nbsp;/api/bioentity/EnsemblPlants:GRMZM2G061969_T01/associations/</a></em>.<p>
+Reason: <strong>Error reading from remote server</strong></p></p>
+</body></html>

[nathandunn]

What is the equivalent genotype? My guess is that they may not be represented, which is fine.

[nathandunn]

Looks like genotype maps to gene. I'll note above.

[nathandunn]

So, overall (I gave a few instances) the server is pretty fragile. If I run the same set of test suites over it, I get different 502 errors each time (though they are always fine if I run them individually).

Anyway, not sure if that is something that could be solved this week, but its definitely worth doing.

[cmungall]

Yes, we need to switch off endpoints that planteome-solr cannot answer.

We should have at least gene-function(GO), gene-anatomy(expr), germplasm-trait (should be mapped to genotype)

When I run it individually it is fine, but as part of a test suite, it chokes with this error

weird

thanks for the testing

[nathandunn]

FYI you can reproduce the choking pretty easily by just running a bunch of large queries at once. For the mapping .. is there a file that exists for this (and monarch for that matter)? Nathan

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On Jun 28, 2017, at 12:28 AM, elserj ***@***.***> wrote: Sorry for the delay, took quite some time figure out how to fix this. Probably longer than it should have, but it seems to be fine now. Enabling CORS alone didn't seem to fix it. Finally started working once I added: ProxyPreserveHost on to the Apache vhost config. Let me know if you find any more issues. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[cmungall]

mapping: https://github.com/Planteome/biolink-api/blob/master/conf/config.yaml#L22-L28

[nathandunn]

Thanks. That is exactly what I needed.

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On Jun 29, 2017, at 12:36 AM, Chris Mungall ***@***.***> wrote: mapping: https://github.com/Planteome/biolink-api/blob/master/conf/config.yaml#L22-L28 <https://github.com/Planteome/biolink-api/blob/master/conf/config.yaml#L22-L28> — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAt2qgqQavjJrsJ0eIRaWN-jC_cmw08Rks5sItVrgaJpZM4NkaT_>.

[nathandunn]

1. Almost all "fetch X for ID" return 500 errors. Gene, phenotye, anatomy, etc.

2. Anatomy subclasses return null property value results including for sub-classes that we have confirmed gene (or phenotype) associations: http://biolink.planteome.org/api/bioentity/anatomy/PO%3A0025131/genes/?rows=20&fetch_objects=true (returns null property results)

Same for phenotypes and environment.