Bluegenes

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Bluegenes

Paulo Nuin
Hello

I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.

lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.

Any help appreciated

Thanks

Paulo
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Re: Bluegenes

Yo Yehudi-2
Hey Paulo!

What commands are you using to deploy things, and/or is there a public URL we can preview? (Also feel free to DM on discord if you'd prefer to keep it private)

Yo

On Tue, 4 Feb 2020 at 14:13, Paulo Nuin <[hidden email]> wrote:
Hello

I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.

lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.

Any help appreciated

Thanks

Paulo
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

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Re: Bluegenes

K.H. Reierskog
In reply to this post by Paulo Nuin
Hi Paulo,

What do you mean when you say "copy the configuration for FlyMine"?

BlueGenes should read the parameters from your mine's property file in
`~/.intermine/`
(https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment)
when you use Gradle to start it
(https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes).
So there shouldn't be any configuration required, unless you're running
your mine and BlueGenes on different servers.

Kind regards,

Kevin


On 2/4/20 2:12 PM, Paulo Nuin wrote:

> Hello
>
> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>
> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>
> Any help appreciated
>
> Thanks
>
> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
_______________________________________________
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[hidden email]
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Re: Bluegenes

Paulo Nuin
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
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[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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Re: Bluegenes

Yo Yehudi-2
whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

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Re: Bluegenes

Paulo Nuin
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo



On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev

bluegenes_gradle (20K) Download Attachment
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Re: Bluegenes

Yo Yehudi-2
hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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Re: Bluegenes

Paulo Nuin
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs


_______________________________________________
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Re: Bluegenes

Paulo Nuin
Hi

Just another note. It might be interesting to check a deployment with a bare bones interface too. At the AGR, we might need to have a centralized interface to connect to the MOD mines each on its own server, so I guess the only way to serve would be with kind of deployment with lein or another server type.

Cheers

Paulo



On Feb 4, 2020, at 10:09 AM, Paulo Nuin <[hidden email]> wrote:

Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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Re: Bluegenes

K.H. Reierskog
In reply to this post by Paulo Nuin

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs


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Re: Bluegenes

K.H. Reierskog
In reply to this post by Paulo Nuin

Not sure if I understood you correctly, but if you're talking about having a single centralized Bluegenes instance for multiple MOD mines, instead of one for each mine, it's something we plan to support.

Right now, Bluegenes only supports having a single default (as configured) mine but will still allow you to switch to mines present in the InterMine registry (that are of sufficiently new versions). We have discussed adding support for configuring Bluegenes to connect to a chosen subset of mines, either manually specified in the EDN config file, or by reading some parameter set in the InterMine registry (for instance `neighbours` which groups mines into plants, microbes, animals, etc). You would still only be able to query one mine at a time, but would be able to quickly switch between them.

Kind regards,

Kevin


On 2/5/20 4:50 AM, Paulo Nuin wrote:
Hi

Just another note. It might be interesting to check a deployment with a bare bones interface too. At the AGR, we might need to have a centralized interface to connect to the MOD mines each on its own server, so I guess the only way to serve would be with kind of deployment with lein or another server type.

Cheers

Paulo



On Feb 4, 2020, at 10:09 AM, Paulo Nuin <[hidden email]> wrote:

Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



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Re: Bluegenes

Gos Micklem-3

> Not sure if I understood you correctly, but if you're talking about having a
> single centralized Bluegenes instance for multiple MOD mines, instead of one
> for each mine, it's something we plan to support.
>
> Right now, Bluegenes only supports having a single default (as configured)
> mine but will still allow you to switch to mines present in the InterMine
> registry (that are of sufficiently new versions). We have discussed adding
> support for configuring Bluegenes to connect to a chosen subset of mines,
> either manually specified in the EDN config file, or by reading some
> parameter set in the InterMine registry (for instance `neighbours` which
> groups mines into plants, microbes, animals, etc). You would still only be
> able to query one mine at a time, but would be able to quickly switch
> between them.

We have built demonstration interfaces that collate the results from queries to multiple
InterMine instances and we intend to develop this functionality.

Best wishes,

Gos


> On 2/5/20 4:50 AM, Paulo Nuin wrote:
> > Hi
> >
> > Just another note. It might be interesting to check a deployment with a
> > bare bones interface too. At the AGR, we might need to have a
> > centralized interface to connect to the MOD mines each on its own
> > server, so I guess the only way to serve would be with kind of
> > deployment with lein or another server type.
> >
> > Cheers
> >
> > Paulo
> >
> >
> >
> > > On Feb 4, 2020, at 10:09 AM, Paulo Nuin <[hidden email]
> > > <mailto:[hidden email]>> wrote:
> > >
> > > Hi
> > >
> > > I was able to find these
> > >
> > > /home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
> > > /home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
> > > /home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
> > > /home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes
> > >
> > > Don’t know if what are you looking for. Our build is on 4.1.1.
> > >
> > > Cheers
> > >
> > > Paulo
> > >
> > >
> > >
> > > > On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]
> > > > <mailto:[hidden email]>> wrote:
> > > >
> > > > hmmm, this line (282) might be the culprit:
> > > >
> > > > java.lang.ClassNotFoundException: clojure.core.async.Mutex
> > > >
> > > > I feel like I've seen this error somewhere before, but I'm not sure.
> > > >
> > > > What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134
> > > > )
> > > >
> > > >
> > > >
> > > > On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]
> > > > <mailto:[hidden email]>> wrote:
> > > >
> > > >     Hi
> > > >
> > > >     The gradle output (stdout and stderr) is attached.
> > > >
> > > >     Cheers
> > > >
> > > >     Paulo
> > > >
> > > >
> > > > >     On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]
> > > > >     <mailto:[hidden email]>> wrote:
> > > > >
> > > > >     whoops, sorry about Discord - fixed now!
> > > > >
> > > > >     IT would be good to fix the gradle task - can you share the
> > > > >     full stack trace?
> > > > >
> > > > >     Yo
> > > > >
> > > > >     On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]
> > > > >     <mailto:[hidden email]>> wrote:
> > > > >
> > > > >         Hi
> > > > >
> > > > >         @Yo your handle on Discord is on not disturb …
> > > > >
> > > > >         I tried deploying with gradle and got this error:
> > > > >
> > > > >         org.gradle.api.tasks.TaskExecutionException: Execution
> > > > >         failed for task ':webapp:blueGenesStart’.
> > > > >         ...
> > > > >         Caused by: org.gradle.process.internal.ExecException:
> > > > >         Process 'command
> > > > >         '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java''
> > > > >         finished with non-zero exit value 1
> > > > >         …
> > > > >
> > > > >         That’s why I am trying with a
> > > > >
> > > > >         lein dev/prod
> > > > >
> > > > >         now, with some configuration changes on edn files.
> > > > >
> > > > >         Cheers
> > > > >
> > > > >         Paulo
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >         > On Feb 4, 2020, at 7:25 AM, K.H. Reierskog
> > > > >         <[hidden email] <mailto:[hidden email]>> wrote:
> > > > >         >
> > > > >         > Hi Paulo,
> > > > >         >
> > > > >         > What do you mean when you say "copy the configuration for
> > > > >         FlyMine"?
> > > > >         >
> > > > >         > BlueGenes should read the parameters from your mine's
> > > > >         property file in `~/.intermine/`
> > > > >         (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment)
> > > > >         when you use Gradle to start it
> > > > >         (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes).
> > > > >         So there shouldn't be any configuration required, unless
> > > > >         you're running your mine and BlueGenes on different servers.
> > > > >         >
> > > > >         > Kind regards,
> > > > >         >
> > > > >         > Kevin
> > > > >         >
> > > > >         >
> > > > >         > On 2/4/20 2:12 PM, Paulo Nuin wrote:
> > > > >         >> Hello
> > > > >         >>
> > > > >         >> I am trying to deploy a Bluegenes test instance in order
> > > > >         to start playing with it a bit and understand it, but I am
> > > > >         having a lot of problems with configuration. I am having
> > > > >         lots of CORS like errors when I try to copy the
> > > > >         configuration for FlyMine. Things seem to work fine with
> > > > >         default configuration, but when I try to connect to our
> > > > >         database, nothing works.
> > > > >         >>
> > > > >         >> lein and the DB are in the same machine. All nodejs
> > > > >         modules were installed properly and the server works fine.
> > > > >         >>
> > > > >         >> Any help appreciated
> > > > >         >>
> > > > >         >> Thanks
> > > > >         >>
> > > > >         >> Paulo
> > > > >         >> _______________________________________________
> > > > >         >> dev mailing list
> > > > >         >> [hidden email] <mailto:[hidden email]>
> > > > >         >> https://lists.intermine.org/mailman/listinfo/dev
> > > > >
> > > > >         _______________________________________________
> > > > >         dev mailing list
> > > > >         [hidden email] <mailto:[hidden email]>
> > > > >         https://lists.intermine.org/mailman/listinfo/dev
> > > > >
> > > > >
> > > > >
> > > > >     --     /Please note I am ‘working to contract’ as part
> > > > > of the UCU
> > > > >     industrial action to defend our pensions and fight for fair pay
> > > > >     and equality. This may mean it takes longer for me to respond
> > > > >     to emails. You can find out more about the dispute at:
> > > > >     www.ucu.cam.ac.uk/faqs <http://www.ucu.cam.ac.uk/faqs>/
> > > >
> > > >
> > > >
> > > > --
> > > > /Please note I am ‘working to contract’ as part of the UCU
> > > > industrial action to defend our pensions and fight for fair pay
> > > > and equality. This may mean it takes longer for me to respond to
> > > > emails. You can find out more about the dispute at:
> > > > www.ucu.cam.ac.uk/faqs <http://www.ucu.cam.ac.uk/faqs>/
> > >
> >

> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Bluegenes

Paulo Nuin
In reply to this post by K.H. Reierskog
Hi Kevin

This is the exactly functionality we are looking at, switching between mines quickly if required. At first we would like to connect to most MOD mines (or at least the ones that are Bluegenes capable). 

Cheers

Paulo


On Feb 5, 2020, at 2:43 AM, K.H. Reierskog <[hidden email]> wrote:

Not sure if I understood you correctly, but if you're talking about having a single centralized Bluegenes instance for multiple MOD mines, instead of one for each mine, it's something we plan to support.

Right now, Bluegenes only supports having a single default (as configured) mine but will still allow you to switch to mines present in the InterMine registry (that are of sufficiently new versions). We have discussed adding support for configuring Bluegenes to connect to a chosen subset of mines, either manually specified in the EDN config file, or by reading some parameter set in the InterMine registry (for instance `neighbours` which groups mines into plants, microbes, animals, etc). You would still only be able to query one mine at a time, but would be able to quickly switch between them.

Kind regards,

Kevin


On 2/5/20 4:50 AM, Paulo Nuin wrote:
Hi

Just another note. It might be interesting to check a deployment with a bare bones interface too. At the AGR, we might need to have a centralized interface to connect to the MOD mines each on its own server, so I guess the only way to serve would be with kind of deployment with lein or another server type.

Cheers

Paulo



On Feb 4, 2020, at 10:09 AM, Paulo Nuin <[hidden email]> wrote:

Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs




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Re: Bluegenes

Paulo Nuin
In reply to this post by K.H. Reierskog
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



_______________________________________________
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Re: Bluegenes

K.H. Reierskog

Hello

You can set a different port by specifying the PORT envvar.

    PORT=3001 ./gradlew bluegenesstart

It shouldn't need any more configuration. To fix the origin error, I think you need to change Tomcat's `Access-Control-Allow-Origin` to include the address you're hosting Bluegenes from, which seems to be `http://im-dev1.wormbase.org` (you might have to include the port number you choose to use). You can search for guides to do this for the version of Tomcat you're running.


Kind regards,

Kevin

On 2/6/20 4:49 AM, Paulo Nuin wrote:
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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|

Re: Bluegenes

Paulo Nuin
Hi

I was able to make the interface appear but I still see the CORS errors and the missing token now


I added a filter to web.xml

     <filter>
       <filter-name>CorsFilter</filter-name>
       <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
     </filter>
     <filter-mapping>
       <filter-name>CorsFilter</filter-name>
       <url-pattern>/*</url-pattern>
     </filter-mapping>

But the errors still appear. Screencap of the message attached.

Thanks

Paulo


On Feb 6, 2020, at 3:26 AM, K.H. Reierskog <[hidden email]> wrote:

Hello

You can set a different port by specifying the PORT envvar.

    PORT=3001 ./gradlew bluegenesstart

It shouldn't need any more configuration. To fix the origin error, I think you need to change Tomcat's `Access-Control-Allow-Origin` to include the address you're hosting Bluegenes from, which seems to be `http://im-dev1.wormbase.org` (you might have to include the port number you choose to use). You can search for guides to do this for the version of Tomcat you're running.


Kind regards,

Kevin

On 2/6/20 4:49 AM, Paulo Nuin wrote:
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs




_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
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Open this post in threaded view
|

Re: Bluegenes

K.H. Reierskog

I'm not sure if this configuration is enough to allow origins. The documentation at http://tomcat.apache.org/tomcat-7.0-doc/config/filter.html#CORS_Filter reads  "The above configuration enables the filter but does not relax the cross-origin policy. As a minimum, you will need to add a cors.allowed.origins initialisation parameter as described below to enable cross-origin requests." Try using the following filter instead.

<filter>
  <filter-name>CorsFilter</filter-name>
  <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
  <init-param>
    <param-name>cors.allowed.origins</param-name>
    <param-value>*</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.methods</param-name>
    <param-value>DELETE,POST,GET,OPTIONS,PUT</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.headers</param-name>
    <param-value>Origin,X-Requested-With,Content-Type,Accept,Range,Authorization,Content-Length,Content-Range</param-value>
  </init-param>
  <init-param>
    <param-name>cors.exposed.headers</param-name>
    <param-value>Content-Encoding,Content-Type,Content-Length,Content-Range</param-value>
  </init-param>
</filter>
<filter-mapping>
  <filter-name>CorsFilter</filter-name>
  <url-pattern>/*</url-pattern>
</filter-mapping>

If you're still having problems, I'd appreciate it if you opened your browser's network panel and copied the response headers for a request.

Kind regards,

Kevin


On 2/7/20 4:52 AM, Paulo Nuin wrote:
Hi

I was able to make the interface appear but I still see the CORS errors and the missing token now


I added a filter to web.xml

     <filter>
       <filter-name>CorsFilter</filter-name>
       <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
     </filter>
     <filter-mapping>
       <filter-name>CorsFilter</filter-name>
       <url-pattern>/*</url-pattern>
     </filter-mapping>

But the errors still appear. Screencap of the message attached.

Thanks

Paulo


On Feb 6, 2020, at 3:26 AM, K.H. Reierskog <[hidden email]> wrote:

Hello

You can set a different port by specifying the PORT envvar.

    PORT=3001 ./gradlew bluegenesstart

It shouldn't need any more configuration. To fix the origin error, I think you need to change Tomcat's `Access-Control-Allow-Origin` to include the address you're hosting Bluegenes from, which seems to be `http://im-dev1.wormbase.org` (you might have to include the port number you choose to use). You can search for guides to do this for the version of Tomcat you're running.


Kind regards,

Kevin

On 2/6/20 4:49 AM, Paulo Nuin wrote:
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs




_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Bluegenes

K.H. Reierskog

Hello

I didn't know you were using Apache as a proxy for Tomcat. The HTTP requests from Bluegenes are getting this reponse:

Service Temporarily Unavailable
The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later.
Apache/2.2.34 (Amazon) Server at im-dev1.wormbase.org Port 80

If the JSP (current InterMine webap) is working fine, this might be caused by `Access-Control-Allow-Origin` not being configured correctly on Apache. Sorry for asking you to configure this on Tomcat first.


Kind regards,

Kevin

On 2/10/20 3:13 AM, Paulo Nuin wrote:
Hi

Tried adding the filter you sent me, still the same error. 

You can access the site on


Files and resources that are failing are on the screencap.


Cheers

Paulo




On Feb 7, 2020, at 3:24 AM, K.H. Reierskog <[hidden email]> wrote:

I'm not sure if this configuration is enough to allow origins. The documentation at http://tomcat.apache.org/tomcat-7.0-doc/config/filter.html#CORS_Filter reads  "The above configuration enables the filter but does not relax the cross-origin policy. As a minimum, you will need to add a cors.allowed.origins initialisation parameter as described below to enable cross-origin requests." Try using the following filter instead.

<filter>
  <filter-name>CorsFilter</filter-name>
  <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
  <init-param>
    <param-name>cors.allowed.origins</param-name>
    <param-value>*</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.methods</param-name>
    <param-value>DELETE,POST,GET,OPTIONS,PUT</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.headers</param-name>
    <param-value>Origin,X-Requested-With,Content-Type,Accept,Range,Authorization,Content-Length,Content-Range</param-value>
  </init-param>
  <init-param>
    <param-name>cors.exposed.headers</param-name>
    <param-value>Content-Encoding,Content-Type,Content-Length,Content-Range</param-value>
  </init-param>
</filter>
<filter-mapping>
  <filter-name>CorsFilter</filter-name>
  <url-pattern>/*</url-pattern>
</filter-mapping>

If you're still having problems, I'd appreciate it if you opened your browser's network panel and copied the response headers for a request.

Kind regards,

Kevin


On 2/7/20 4:52 AM, Paulo Nuin wrote:
Hi

I was able to make the interface appear but I still see the CORS errors and the missing token now


I added a filter to web.xml

     <filter>
       <filter-name>CorsFilter</filter-name>
       <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
     </filter>
     <filter-mapping>
       <filter-name>CorsFilter</filter-name>
       <url-pattern>/*</url-pattern>
     </filter-mapping>

But the errors still appear. Screencap of the message attached.

Thanks

Paulo


On Feb 6, 2020, at 3:26 AM, K.H. Reierskog <[hidden email]> wrote:

Hello

You can set a different port by specifying the PORT envvar.

<Screenshot 2020-02-06 21.50.15.png>    PORT=3001 ./gradlew bluegenesstart

It shouldn't need any more configuration. To fix the origin error, I think you need to change Tomcat's `Access-Control-Allow-Origin` to include the address you're hosting Bluegenes from, which seems to be `http://im-dev1.wormbase.org` (you might have to include the port number you choose to use). You can search for guides to do this for the version of Tomcat you're running.


Kind regards,

Kevin

On 2/6/20 4:49 AM, Paulo Nuin wrote:
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs





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Re: Bluegenes

K.H. Reierskog

Hello

Glad to hear!

Do you have a Solr server running together with the mine? That is a requirement for keyword search.
Try doing a keyword search in the JSP for your mine. If there's an error, you know your Solr isn't correctly configured.


Sure, we can continue the discussion of using BlueGenes with multiple AGR mines.
I think adding all your mine's webservice URLs to Bluegenes' EDN config would be sufficient for your use case. When Bluegenes is started with this configuration, it will only display the configured mines in the mine switcher (button with the cog icon in the nav bar).

When do you want this feature? It shouldn't be too much work to implement, so I might get it done for the next Alpha release (0.10.0, hopefully within a month).

Kind regards,

Kevin

On 2/11/20 4:31 AM, Paulo Nuin wrote:
Hi

I added CORS to Apache and it seems fine now, with the exception of the search that goes nowhere.

Is there a way to debug it?


Also, as I mentioned before, it would be interesting to discuss possibilities to install BlueGenes in the Alliance of Genomic Resources with the possibility of switching mines easily (not cross query yet).

Thanks a lot

Paulo



On Feb 10, 2020, at 4:09 AM, K.H. Reierskog <[hidden email]> wrote:

Hello

I didn't know you were using Apache as a proxy for Tomcat. The HTTP requests from Bluegenes are getting this reponse:

Service Temporarily Unavailable
The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later.
Apache/2.2.34 (Amazon) Server at im-dev1.wormbase.org Port 80

If the JSP (current InterMine webap) is working fine, this might be caused by `Access-Control-Allow-Origin` not being configured correctly on Apache. Sorry for asking you to configure this on Tomcat first.


Kind regards,

Kevin

On 2/10/20 3:13 AM, Paulo Nuin wrote:
Hi

Tried adding the filter you sent me, still the same error. 

You can access the site on


Files and resources that are failing are on the screencap.


Cheers

Paulo



<Image 2020-02-09 at 8.12 PM.jpg>
On Feb 7, 2020, at 3:24 AM, K.H. Reierskog <[hidden email]> wrote:

I'm not sure if this configuration is enough to allow origins. The documentation at http://tomcat.apache.org/tomcat-7.0-doc/config/filter.html#CORS_Filter reads  "The above configuration enables the filter but does not relax the cross-origin policy. As a minimum, you will need to add a cors.allowed.origins initialisation parameter as described below to enable cross-origin requests." Try using the following filter instead.

<filter>
  <filter-name>CorsFilter</filter-name>
  <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
  <init-param>
    <param-name>cors.allowed.origins</param-name>
    <param-value>*</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.methods</param-name>
    <param-value>DELETE,POST,GET,OPTIONS,PUT</param-value>
  </init-param>
  <init-param>
    <param-name>cors.allowed.headers</param-name>
    <param-value>Origin,X-Requested-With,Content-Type,Accept,Range,Authorization,Content-Length,Content-Range</param-value>
  </init-param>
  <init-param>
    <param-name>cors.exposed.headers</param-name>
    <param-value>Content-Encoding,Content-Type,Content-Length,Content-Range</param-value>
  </init-param>
</filter>
<filter-mapping>
  <filter-name>CorsFilter</filter-name>
  <url-pattern>/*</url-pattern>
</filter-mapping>

If you're still having problems, I'd appreciate it if you opened your browser's network panel and copied the response headers for a request.

Kind regards,

Kevin


On 2/7/20 4:52 AM, Paulo Nuin wrote:
Hi

I was able to make the interface appear but I still see the CORS errors and the missing token now


I added a filter to web.xml

     <filter>
       <filter-name>CorsFilter</filter-name>
       <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
     </filter>
     <filter-mapping>
       <filter-name>CorsFilter</filter-name>
       <url-pattern>/*</url-pattern>
     </filter-mapping>

But the errors still appear. Screencap of the message attached.

Thanks

Paulo


On Feb 6, 2020, at 3:26 AM, K.H. Reierskog <[hidden email]> wrote:

Hello

You can set a different port by specifying the PORT envvar.

<Screenshot 2020-02-06 21.50.15.png>    PORT=3001 ./gradlew bluegenesstart

It shouldn't need any more configuration. To fix the origin error, I think you need to change Tomcat's `Access-Control-Allow-Origin` to include the address you're hosting Bluegenes from, which seems to be `http://im-dev1.wormbase.org` (you might have to include the port number you choose to use). You can search for guides to do this for the version of Tomcat you're running.


Kind regards,

Kevin

On 2/6/20 4:49 AM, Paulo Nuin wrote:
Hi

I did remove all my .gradle dir and add the line and the server starts fine on 5000. Now, does it need more ports open? Any other configuration?

I am getting this error (with some small variations) on Safari

[Error] Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin.
[Error] XMLHttpRequest cannot load http://im-dev1.wormbase.org/tools/wormmine/service/session?format=json due to access control checks.
[Error] Failed to load resource: Origin http://im-dev1.wormbase.org:5000 is not allowed by Access-Control-Allow-Origin. (session, line 0)

And BTW, how do I change the server port?

Thanks

Paulo




On Feb 5, 2020, at 2:27 AM, K.H. Reierskog <[hidden email]> wrote:

Could you edit the `gradle.properties` file where you're running the gradle script to use

systemProp.blueGenesVersion=0.9.12

then try running the blueGenesStart gradle task again.

That is the latest version of bluegenes: https://clojars.org/org.intermine/bluegenes/


Kind regards,

Kevin


On 2/4/20 5:09 PM, Paulo Nuin wrote:
Hi

I was able to find these

/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/f099492217c6669cbc93563e749640d7b516bb62/bluegenes-0.9.4-SNAPSHOT.jar
/home/nuin/.gradle/caches/modules-2/files-2.1/org.intermine/bluegenes/0.9.4-SNAPSHOT/35a34906cf1490af13a7cbb291cd12153a080d47/bluegenes-0.9.4-SNAPSHOT.pom
/home/nuin/.gradle/caches/modules-2/metadata-2.58/descriptors/org.intermine/bluegenes

Don’t know if what are you looking for. Our build is on 4.1.1.

Cheers

Paulo



On Feb 4, 2020, at 9:47 AM, Yo Yehudi <[hidden email]> wrote:

hmmm, this line (282) might be the culprit:

java.lang.ClassNotFoundException: clojure.core.async.Mutex

I feel like I've seen this error somewhere before, but I'm not sure.

What version of the bluegenes jar do you have set? (example: https://github.com/intermine/humanmine/blob/master/webapp/build.gradle#L134



On Tue, 4 Feb 2020 at 16:31, Paulo Nuin <[hidden email]> wrote:
Hi

The gradle output (stdout and stderr) is attached.

Cheers

Paulo


On Feb 4, 2020, at 9:12 AM, Yo Yehudi <[hidden email]> wrote:

whoops, sorry about Discord - fixed now!

IT would be good to fix the gradle task - can you share the full stack trace?

Yo

On Tue, 4 Feb 2020 at 15:28, Paulo Nuin <[hidden email]> wrote:
Hi

@Yo your handle on Discord is on not disturb …

I tried deploying with gradle and got this error:

org.gradle.api.tasks.TaskExecutionException: Execution failed for task ':webapp:blueGenesStart’.
...
Caused by: org.gradle.process.internal.ExecException: Process 'command '/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.222.b10-0.47.amzn1.x86_64/bin/java'' finished with non-zero exit value 1


That’s why I am trying with a

lein dev/prod

now, with some configuration changes on edn files.

Cheers

Paulo




> On Feb 4, 2020, at 7:25 AM, K.H. Reierskog <[hidden email]> wrote:
>
> Hi Paulo,
>
> What do you mean when you say "copy the configuration for FlyMine"?
>
> BlueGenes should read the parameters from your mine's property file in `~/.intermine/` (https://intermine.readthedocs.io/en/latest/webapp/blue-genes/?highlight=bluegenes#environment) when you use Gradle to start it (https://intermine.readthedocs.io/en/latest/system-requirements/software/gradle/?highlight=bluegenes#deploy-blue-genes). So there shouldn't be any configuration required, unless you're running your mine and BlueGenes on different servers.
>
> Kind regards,
>
> Kevin
>
>
> On 2/4/20 2:12 PM, Paulo Nuin wrote:
>> Hello
>>
>> I am trying to deploy a Bluegenes test instance in order to start playing with it a bit and understand it, but I am having a lot of problems with configuration. I am having lots of CORS like errors when I try to copy the configuration for FlyMine. Things seem to work fine with default configuration, but when I try to connect to our database, nothing works.
>>
>> lein and the DB are in the same machine. All nodejs modules were installed properly and the server works fine.
>>
>> Any help appreciated
>>
>> Thanks
>>
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs



--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs






_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev