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bridgedb / BridgeDb

The BridgeDb Library source code
https://bridgedb.org/
Apache License 2.0
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Webservice not working. #49

Closed KeironO closed 7 years ago

KeironO commented 7 years ago

Hey there,

I'm experiencing connection issues with the BridgeDb web service.

Example:

http://webservice.bridgedb.org/Human/xrefs/Ik/HAFLLMSZAQXSPB-LDLOPFEMSA-N

Returns:

java.sql.SQLNonTransientConnectionException: No current connection.

Would it be possible to have this fixed?

Thanks,

Keiron.

KeironO commented 7 years ago

Now back online, thank you :+1:

JonathanMELIUS commented 7 years ago

@KeironO @egonw

The web service is back to normal now.

But about your query, are you sure that your InChI id is valid ? The id is not present in your databases and in our sources.

KeironO commented 7 years ago

@JonathanMELIUS I am aware that the InChI is invalid in your db, it was just a working example(!)

egonw commented 7 years ago

@JonathanMELIUS, it's not an InChI, but an InChIKey, and it's valid. Here's the compound in ChemSpider:

http://www.chemspider.com/Chemical-Structure.59693137.html

@DeniseSl22, can you please add the compound to Wikidata? Then it will be in our database in the next ID mapping round.

DeniseSl22 commented 7 years ago

HI guys, I will add it all... However, when I use molview; I find a completely different compound (https://www.wikidata.org/wiki/Q3665764 ).

DeniseSl22 commented 7 years ago

Done: https://www.wikidata.org/wiki/Q33634164

egonw commented 7 years ago

@KeironO, if you find (or know) additional identifiers, feel free to add those to Wikidata too :)

KeironO commented 7 years ago

I'm afraid its down again(!)

JonathanMELIUS commented 7 years ago

@KeironO It's back to live.

Same error again. We will investigate on the cause to fix it.

nunogit commented 7 years ago

@KeironO do you know when (at what time) you did the querys? That way I will be able to look into server load. @JonathanMELIUS That seems like a JDBC problem (connection to the database). It might be either load, or some bug.

egonw commented 7 years ago

Observation just now:

java.sql.SQLNonTransientConnectionException: No current connection.
JonathanMELIUS commented 7 years ago

It's back. I also increased the memory allocated to the web service.

KeironO commented 7 years ago

Thank you :)

On 21 August 2017 at 16:00, JonathanMELIUS notifications@github.com wrote:

It's back. I also increased the memory allocated to the web service.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bridgedb/BridgeDb/issues/49#issuecomment-323766774, or mute the thread https://github.com/notifications/unsubscribe-auth/AELu0_pkfrNtrCtvOeM7RkxNkGZQJCFfks5saZudgaJpZM4Ombln .

-- Keiron O'Shea 毛毛

Aberystwyth University PhD Postgraduate Researcher, Institute of Biological, Rural and Earth Sciences keo7@aber.ac.uk | http://users.aber.ac.uk/keo7

egonw commented 7 years ago

OK, that seems to have helped... the following works: http://webservice.bridgedb.org/Human/xrefs/Ik/QTBSBXVTEAMEQO-UHFFFAOYSA-N