KNIME and ops

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KNIME and ops

Brian Northan
Hi

I have a question for the KNIME folks. 

My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??

How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??

Thanks

Brian

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Re: KNIME and ops

Christian Dietz
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:

>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Curtis Rueden
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Christian Dietz

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Brian Northan
Thanks Christian

I'll ping you next week for more instructions. 

Brian

On Wed, Aug 19, 2015 at 3:19 PM, Christian Dietz <[hidden email]> wrote:

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Jay Warrick
In reply to this post by Christian Dietz
I'd be interested in keeping up with this conversation. We do the same thing in JEX to expose ImageJ commands (that are headless and have a menu path) as functions. Exposing some Ops would be great too. Will you be at the imagej conference that I could pick your brain on related questions?

Cheers,

Jay

On Aug 19, 2015, at 2:19 PM, Christian Dietz <[hidden email]> wrote:

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Curtis Rueden

Hi Jay,

Christian will not be at the IJ conference (conflict with another conference), but will be at the hackathon afterward.

Regards,
Curtis

On Aug 20, 2015 9:42 AM, "JAY W WARRICK" <[hidden email]> wrote:
I'd be interested in keeping up with this conversation. We do the same thing in JEX to expose ImageJ commands (that are headless and have a menu path) as functions. Exposing some Ops would be great too. Will you be at the imagej conference that I could pick your brain on related questions?

Cheers,

Jay

On Aug 19, 2015, at 2:19 PM, Christian Dietz <[hidden email]> wrote:

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Jay Warrick
It happens that I just put that in my calendar to try and attend (at least what I can fit in). Cool.

J

On Aug 20, 2015, at 9:47 AM, Curtis Rueden <[hidden email]> wrote:

Hi Jay,

Christian will not be at the IJ conference (conflict with another conference), but will be at the hackathon afterward.

Regards,
Curtis

On Aug 20, 2015 9:42 AM, "JAY W WARRICK" <[hidden email]> wrote:
I'd be interested in keeping up with this conversation. We do the same thing in JEX to expose ImageJ commands (that are headless and have a menu path) as functions. Exposing some Ops would be great too. Will you be at the imagej conference that I could pick your brain on related questions?

Cheers,

Jay

On Aug 19, 2015, at 2:19 PM, Christian Dietz <[hidden email]> wrote:

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Brian Northan
Hi Christian

I hope you had a nice holiday.  Are you back now??

I found some example KNIME workflows for imagej/imagej2 integration here https://tech.knime.org/community/imagej
.
The problem is that I cannot find the 'ImageJ Macro' or the 'Image2 integration' nodes.  I searched for 'imagej' in the node repository and explored the community nodes.  I also looked for them using "Install KNIME extensions...", but couldn't find anything imagej related.

Any suggestions??

Thanks

Brian

On Thu, Aug 20, 2015 at 10:50 AM, JAY W WARRICK <[hidden email]> wrote:
It happens that I just put that in my calendar to try and attend (at least what I can fit in). Cool.

J

On Aug 20, 2015, at 9:47 AM, Curtis Rueden <[hidden email]> wrote:

Hi Jay,

Christian will not be at the IJ conference (conflict with another conference), but will be at the hackathon afterward.

Regards,
Curtis

On Aug 20, 2015 9:42 AM, "JAY W WARRICK" <[hidden email]> wrote:
I'd be interested in keeping up with this conversation. We do the same thing in JEX to expose ImageJ commands (that are headless and have a menu path) as functions. Exposing some Ops would be great too. Will you be at the imagej conference that I could pick your brain on related questions?

Cheers,

Jay

On Aug 19, 2015, at 2:19 PM, Christian Dietz <[hidden email]> wrote:

Sorry, I was not really precise: all Commands which are declared as headless and have a menu path.

And yes: like this we could select the ops which are exposed as nodes.

Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden <[hidden email]>:
Hi Christian,

> currently, we can automatically create nodes from Commands and not
> from ops.

But all Ops are Commands...?

> From a technical point of view it would be easy to adapt this
> mechanism to Ops, but I am not sure if we want that (as you dont want
> to create a node for each and every atomar op). I hope we will
> find a nice strategy when to expose an Op as a KNIME node.

Possible solutions:
* Expose all Commands (including Ops) that declare a menu path.
* Expose Commands which have (or do not have) a particular attribute key. We use this for ImageJ1, adding a "no-legacy" attribute for commands which should not be exposed from the legacy ImageJ1 user interface.

Regards,
Curtis

On Wed, Aug 19, 2015 at 12:36 PM, Christian Dietz <[hidden email]> wrote:
Hi Brian,

currently, we can automatically create nodes from Commands and not from ops. From a technical point of view it would be easy to adapt this mechanism to Ops, but I am not sure if we want that (as you dont want to create a node for each and every atomar op). I hope we will find a nice strategy when to expose an Op as a KNIME node.

Anyway, Commands can be installed if the imagej2 extension is also installed within KNIME. I can send you more details next Monday, when I'm back from vacation.

Hope this helps,

Christian

Am 19.08.2015 5:58 nachm. schrieb Brian Northan <[hidden email]>:
>
> Hi
>
> I have a question for the KNIME folks. 
>
> My understanding is that KNIME can auto-generate a node for every class that implements an op.  Is this correct??  And if so does the current release of KNIME recognize ops??  Or do I need a development version??
>
> How does one install an op to KNIME??  Do you just place the .jar file in a certain directory??  Or do you have to go through the 'install KNIME extensions' option??  Or something else??
>
> Thanks
>
> Brian
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Re: KNIME and ops

Christian Dietz
Hi Brian,

The ImageJ2 Extension of KNIME is not part of the "Trusted Community
Nodes", and therefore not visible directly in the "Trusted Community
Contributions" Update-Site, as some testing workflows are missing and
there will be some refactoring before it's considered as "trusted".
However, you can install it via the "Stable" or "Nightly" update-sites
of the KNIME Community Contributions (see "Step 2.2" in
https://tech.knime.org/wiki/install-knime-image-processing and
https://tech.knime.org/wiki/knime-image-processing-nightly-build ).

Let me know if you need further help.

Christian




On Mo, 2015-08-24 at 17:04 -0400, Brian Northan wrote:

> Hi Christian
>
>
> I hope you had a nice holiday.  Are you back now??
>
>
> I found some example KNIME workflows for imagej/imagej2 integration
> here https://tech.knime.org/community/imagej
> .
>
> The problem is that I cannot find the 'ImageJ Macro' or the 'Image2
> integration' nodes.  I searched for 'imagej' in the node repository
> and explored the community nodes.  I also looked for them using
> "Install KNIME extensions...", but couldn't find anything imagej
> related.
>
>
> Any suggestions??
>
>
> Thanks
>
>
> Brian
>
>
> On Thu, Aug 20, 2015 at 10:50 AM, JAY W WARRICK <[hidden email]>
> wrote:
>         It happens that I just put that in my calendar to try and
>         attend (at least what I can fit in). Cool.
>        
>         J
>        
>         On Aug 20, 2015, at 9:47 AM, Curtis Rueden <[hidden email]>
>         wrote:
>        
>        
>         > Hi Jay,
>         >
>         > Christian will not be at the IJ conference (conflict with
>         > another conference), but will be at the hackathon afterward.
>         >
>         > Regards,
>         > Curtis
>         >
>         > On Aug 20, 2015 9:42 AM, "JAY W WARRICK" <[hidden email]>
>         > wrote:
>         >         I'd be interested in keeping up with this
>         >         conversation. We do the same thing in JEX to expose
>         >         ImageJ commands (that are headless and have a menu
>         >         path) as functions. Exposing some Ops would be great
>         >         too. Will you be at the imagej conference that I
>         >         could pick your brain on related questions?
>         >        
>         >        
>         >         Cheers,
>         >        
>         >        
>         >         Jay
>         >        
>         >         > On Aug 19, 2015, at 2:19 PM, Christian Dietz
>         >         > <[hidden email]> wrote:
>         >         >
>         >         > Sorry, I was not really precise: all Commands
>         >         > which are declared as headless and have a menu
>         >         > path.
>         >         >
>         >         > And yes: like this we could select the ops which
>         >         > are exposed as nodes.
>         >         >
>         >         > Am 19.08.2015 8:00 nachm. schrieb Curtis Rueden
>         >         > <[hidden email]>:
>         >         >         Hi Christian,
>         >         >        
>         >         >        
>         >         >         > currently, we can automatically create
>         >         >         nodes from Commands and not
>         >         >         > from ops.
>         >         >        
>         >         >        
>         >         >         But all Ops are Commands...?
>         >         >        
>         >         >        
>         >         >         > From a technical point of view it would
>         >         >         be easy to adapt this
>         >         >         > mechanism to Ops, but I am not sure if
>         >         >         we want that (as you dont want
>         >         >         > to create a node for each and every
>         >         >         atomar op). I hope we will
>         >         >         > find a nice strategy when to expose an
>         >         >         Op as a KNIME node.
>         >         >        
>         >         >        
>         >         >         Possible solutions:
>         >         >         * Expose all Commands (including Ops) that
>         >         >         declare a menu path.
>         >         >         * Expose Commands which have (or do not
>         >         >         have) a particular attribute key. We use
>         >         >         this for ImageJ1, adding a "no-legacy"
>         >         >         attribute for commands which should not be
>         >         >         exposed from the legacy ImageJ1 user
>         >         >         interface.
>         >         >        
>         >         >        
>         >         >         Regards,
>         >         >         Curtis
>         >         >        
>         >         >         On Wed, Aug 19, 2015 at 12:36 PM,
>         >         >         Christian Dietz
>         >         >         <[hidden email]> wrote:
>         >         >                 Hi Brian,
>         >         >                
>         >         >                 currently, we can automatically
>         >         >                 create nodes from Commands and not
>         >         >                 from ops. From a technical point
>         >         >                 of view it would be easy to adapt
>         >         >                 this mechanism to Ops, but I am
>         >         >                 not sure if we want that (as you
>         >         >                 dont want to create a node for
>         >         >                 each and every atomar op). I hope
>         >         >                 we will find a nice strategy when
>         >         >                 to expose an Op as a KNIME node.
>         >         >                
>         >         >                 Anyway, Commands can be installed
>         >         >                 if the imagej2 extension is also
>         >         >                 installed within KNIME. I can send
>         >         >                 you more details next Monday, when
>         >         >                 I'm back from vacation.
>         >         >                
>         >         >                 Hope this helps,
>         >         >                
>         >         >                 Christian
>         >         >                
>         >         >                 Am 19.08.2015 5:58 nachm. schrieb
>         >         >                 Brian Northan
>         >         >                 <[hidden email]>:
>         >         >                 >
>         >         >                 > Hi
>         >         >                 >
>         >         >                 > I have a question for the KNIME
>         >         >                 folks.
>         >         >                 >
>         >         >                 > My understanding is that KNIME
>         >         >                 can auto-generate a node for every
>         >         >                 class that implements an op.  Is
>         >         >                 this correct??  And if so does the
>         >         >                 current release of KNIME recognize
>         >         >                 ops??  Or do I need a development
>         >         >                 version??
>         >         >                 >
>         >         >                 > How does one install an op to
>         >         >                 KNIME??  Do you just place
>         >         >                 the .jar file in a certain
>         >         >                 directory??  Or do you have to go
>         >         >                 through the 'install KNIME
>         >         >                 extensions' option??  Or something
>         >         >                 else??
>         >         >                 >
>         >         >                 > Thanks
>         >         >                 >
>         >         >                 > Brian
>         >         >                
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