Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

Yes, that's correct. I had a PR to bump update times when a user switched
to a history, but it did not make it in.

re: history/current: there has been a push to make the API more stateless
and remove references to any 'current' history. Overall I still agree with
that but maybe, for such a practical case, it can be re-added for a while.

Agreed on the error, but I'd rather prioritize removing that endpoint
altogether and replace it with something better.

On Wed, May 25, 2016 at 6:14 AM, Suderman Keith 
wrote:

>
> On May 24, 2016, at 11:14 PM, Carl Eberhard 
> wrote:
>
> most_recently_used *was* broken - thanks for finding that.
>
>
> Glad I could be of assistance!  Just to clarify, the user has to actually
> *do* something with a history (i.e. add something to the history) for it to
> be considered the MRU; simply selecting switching to a history (without
> using/adding to it) is not sufficient to make it the MRU history. Correct?
>
> A planning issue for a session API is here:
> https://github.com/galaxyproject/galaxy/issues/2404
>
>
> I will let you folks decide if a session API is appropriate, however I was
> surprised that something like /api/histories/current wasn’t an available
> endpoint. For my purposes I think this would be sufficient and this way I
> wouldn’t have to keep track of the user’s API key as well as an additional
> session cookie.
>
> Also, I should likely open an issue for this, but trying to access
> http://my.galaxy.instance/history/current_history_json?key=myapikey
> results in a "HTTP 500 Server Error” response.  I realize (now) that this
> shouldn’t work, but it likely should result in a server error either.
>
> Cheers,
> Keith
>
>
> On Tue, May 24, 2016 at 4:16 PM, Carl Eberhard 
> wrote:
>
>> Yeah - I understand what you're trying to do now and you're right. In an
>> effort to make the API stateless I think we've introduced a gap in
>> functionality for a good, practical use case.
>>
>> I've been wanting to replace the history/current_history* endpoints for a
>> while now with a session API (that would include a 'current' history) so
>> I'll bump that up in priority.
>>
>> The most_recently_used may be broken - I'll check that now. Note, though,
>> that changing the current history doesn't change the update time for a
>> given history. You have to alter/change it for the time to change - then it
>> will become the 'most recently used'. It's confusing and doesn't really
>> match user expectations. I'll see what I can do about that and possibly
>> make it an alias to the above API when/if that makes it to a release. In
>> any event, again, I'll double check that it's at least doing that.
>>
>> I'll also take a look and see if there's some other option for something
>> like this if most_recently_used won't fit the use case.
>>
>>
>>
>> On Tue, May 24, 2016 at 2:16 AM, Suderman Keith 
>> wrote:
>>
>>>
>>> On May 23, 2016, at 3:34 PM, Carl Eberhard 
>>> wrote:
>>>
>>> There's a way to get the current history data through a non-api url:
>>> /history/current_history_json
>>>
>>>
>>> That works, but to get the current history for a user I need to set the
>>> galaxysession cookie. So it is not really a good solution unless I can find
>>> an api to determine the session cookie for the user.  I’ve also noticed
>>> that /api/histories/most_recently_used is not returning the most recently
>>> used history!  A bug maybe?
>>>
>>> Keith
>>>
>>>
>>> ...but, I don't believe those are accessible through any of the
>>> bio/blend libraries.
>>>
>>> Failing the above, is there some way to get the history ID from the UI?
>>>
>>>
>>> You can click the information button ('i' with a circle around it) for
>>> any dataset in a history. The encoded history API id will be listed under:
>>> history api id.
>>>
>>> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith 
>>> wrote:
>>>
 I have been looking at the JavaDoc for Blend4J [1] and the REST API
 [2], but I don’t see any way to obtain the “current” history as selected by
 the user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but
 it seems that simply selecting a history as the current history in the UI
 does not make it the “most recently used” (MRU) history; I guess the user
 has to actually _do_ something with before it becomes the MRU history.  Am
 I missing something?

 Failing the above, is there some way to get the history ID from the UI?

 Thanks,
 Keith

 REFERENCES

 1.http://jmchilton.github.io/blend4j/apidocs/
 2.
 https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories

 --
 Research Associate
 Department of Computer Science
 Vassar College
 Poughkeepsie, NY


 ___
 Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Suderman Keith]

> On May 24, 2016, at 11:14 PM, Carl Eberhard  wrote:
> 
> most_recently_used *was* broken - thanks for finding that.

Glad I could be of assistance!  Just to clarify, the user has to actually *do* 
something with a history (i.e. add something to the history) for it to be 
considered the MRU; simply selecting switching to a history (without 
using/adding to it) is not sufficient to make it the MRU history. Correct?

> A planning issue for a session API is here: 
> https://github.com/galaxyproject/galaxy/issues/2404 
> 
I will let you folks decide if a session API is appropriate, however I was 
surprised that something like /api/histories/current wasn’t an available 
endpoint. For my purposes I think this would be sufficient and this way I 
wouldn’t have to keep track of the user’s API key as well as an additional 
session cookie.

Also, I should likely open an issue for this, but trying to access 
http://my.galaxy.instance/history/current_history_json?key=myapikey results in 
a "HTTP 500 Server Error” response.  I realize (now) that this shouldn’t work, 
but it likely should result in a server error either.

Cheers,
Keith

> 
> On Tue, May 24, 2016 at 4:16 PM, Carl Eberhard  > wrote:
> Yeah - I understand what you're trying to do now and you're right. In an 
> effort to make the API stateless I think we've introduced a gap in 
> functionality for a good, practical use case.
> 
> I've been wanting to replace the history/current_history* endpoints for a 
> while now with a session API (that would include a 'current' history) so I'll 
> bump that up in priority.
> 
> The most_recently_used may be broken - I'll check that now. Note, though, 
> that changing the current history doesn't change the update time for a given 
> history. You have to alter/change it for the time to change - then it will 
> become the 'most recently used'. It's confusing and doesn't really match user 
> expectations. I'll see what I can do about that and possibly make it an alias 
> to the above API when/if that makes it to a release. In any event, again, 
> I'll double check that it's at least doing that.
> 
> I'll also take a look and see if there's some other option for something like 
> this if most_recently_used won't fit the use case.
> 
> 
> 
> On Tue, May 24, 2016 at 2:16 AM, Suderman Keith  > wrote:
> 
>> On May 23, 2016, at 3:34 PM, Carl Eberhard > > wrote:
>> 
>> There's a way to get the current history data through a non-api url:
>> /history/current_history_json
> 
> That works, but to get the current history for a user I need to set the 
> galaxysession cookie. So it is not really a good solution unless I can find 
> an api to determine the session cookie for the user.  I’ve also noticed that 
> /api/histories/most_recently_used is not returning the most recently used 
> history!  A bug maybe?
> 
> Keith
> 
>> 
>> ...but, I don't believe those are accessible through any of the bio/blend 
>> libraries.
>> 
>> Failing the above, is there some way to get the history ID from the UI?
>> 
>> You can click the information button ('i' with a circle around it) for any 
>> dataset in a history. The encoded history API id will be listed under: 
>> history api id.
>> 
>> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith > > wrote:
>> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2], but 
>> I don’t see any way to obtain the “current” history as selected by the user 
>> in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it seems 
>> that simply selecting a history as the current history in the UI does not 
>> make it the “most recently used” (MRU) history; I guess the user has to 
>> actually _do_ something with before it becomes the MRU history.  Am I 
>> missing something?
>> 
>> Failing the above, is there some way to get the history ID from the UI?
>> 
>> Thanks,
>> Keith
>> 
>> REFERENCES
>> 
>> 1.http://jmchilton.github.io/blend4j/apidocs/ 
>> 
>> 2. 
>> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>>  
>> 
>> 
>> --
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>> 
>> 
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/ 
>> 
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/ 
>> 

Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

most_recently_used *was* broken - thanks for finding that. A pull request
going back to the 16.01 release is here:
https://github.com/galaxyproject/galaxy/pull/2407

A planning issue for a session API is here:
https://github.com/galaxyproject/galaxy/issues/2404

On Tue, May 24, 2016 at 4:16 PM, Carl Eberhard 
wrote:

> Yeah - I understand what you're trying to do now and you're right. In an
> effort to make the API stateless I think we've introduced a gap in
> functionality for a good, practical use case.
>
> I've been wanting to replace the history/current_history* endpoints for a
> while now with a session API (that would include a 'current' history) so
> I'll bump that up in priority.
>
> The most_recently_used may be broken - I'll check that now. Note, though,
> that changing the current history doesn't change the update time for a
> given history. You have to alter/change it for the time to change - then it
> will become the 'most recently used'. It's confusing and doesn't really
> match user expectations. I'll see what I can do about that and possibly
> make it an alias to the above API when/if that makes it to a release. In
> any event, again, I'll double check that it's at least doing that.
>
> I'll also take a look and see if there's some other option for something
> like this if most_recently_used won't fit the use case.
>
>
>
> On Tue, May 24, 2016 at 2:16 AM, Suderman Keith 
> wrote:
>
>>
>> On May 23, 2016, at 3:34 PM, Carl Eberhard 
>> wrote:
>>
>> There's a way to get the current history data through a non-api url:
>> /history/current_history_json
>>
>>
>> That works, but to get the current history for a user I need to set the
>> galaxysession cookie. So it is not really a good solution unless I can find
>> an api to determine the session cookie for the user.  I’ve also noticed
>> that /api/histories/most_recently_used is not returning the most recently
>> used history!  A bug maybe?
>>
>> Keith
>>
>>
>> ...but, I don't believe those are accessible through any of the bio/blend
>> libraries.
>>
>> Failing the above, is there some way to get the history ID from the UI?
>>
>>
>> You can click the information button ('i' with a circle around it) for
>> any dataset in a history. The encoded history API id will be listed under:
>> history api id.
>>
>> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith 
>> wrote:
>>
>>> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2],
>>> but I don’t see any way to obtain the “current” history as selected by the
>>> user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it
>>> seems that simply selecting a history as the current history in the UI does
>>> not make it the “most recently used” (MRU) history; I guess the user has to
>>> actually _do_ something with before it becomes the MRU history.  Am I
>>> missing something?
>>>
>>> Failing the above, is there some way to get the history ID from the UI?
>>>
>>> Thanks,
>>> Keith
>>>
>>> REFERENCES
>>>
>>> 1.http://jmchilton.github.io/blend4j/apidocs/
>>> 2.
>>> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>>>
>>> --
>>> Research Associate
>>> Department of Computer Science
>>> Vassar College
>>> Poughkeepsie, NY
>>>
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>> --
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>>
>>
>
___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

Yeah - I understand what you're trying to do now and you're right. In an
effort to make the API stateless I think we've introduced a gap in
functionality for a good, practical use case.

I've been wanting to replace the history/current_history* endpoints for a
while now with a session API (that would include a 'current' history) so
I'll bump that up in priority.

The most_recently_used may be broken - I'll check that now. Note, though,
that changing the current history doesn't change the update time for a
given history. You have to alter/change it for the time to change - then it
will become the 'most recently used'. It's confusing and doesn't really
match user expectations. I'll see what I can do about that and possibly
make it an alias to the above API when/if that makes it to a release. In
any event, again, I'll double check that it's at least doing that.

I'll also take a look and see if there's some other option for something
like this if most_recently_used won't fit the use case.



On Tue, May 24, 2016 at 2:16 AM, Suderman Keith 
wrote:

>
> On May 23, 2016, at 3:34 PM, Carl Eberhard 
> wrote:
>
> There's a way to get the current history data through a non-api url:
> /history/current_history_json
>
>
> That works, but to get the current history for a user I need to set the
> galaxysession cookie. So it is not really a good solution unless I can find
> an api to determine the session cookie for the user.  I’ve also noticed
> that /api/histories/most_recently_used is not returning the most recently
> used history!  A bug maybe?
>
> Keith
>
>
> ...but, I don't believe those are accessible through any of the bio/blend
> libraries.
>
> Failing the above, is there some way to get the history ID from the UI?
>
>
> You can click the information button ('i' with a circle around it) for any
> dataset in a history. The encoded history API id will be listed under:
> history api id.
>
> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith 
> wrote:
>
>> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2],
>> but I don’t see any way to obtain the “current” history as selected by the
>> user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it
>> seems that simply selecting a history as the current history in the UI does
>> not make it the “most recently used” (MRU) history; I guess the user has to
>> actually _do_ something with before it becomes the MRU history.  Am I
>> missing something?
>>
>> Failing the above, is there some way to get the history ID from the UI?
>>
>> Thanks,
>> Keith
>>
>> REFERENCES
>>
>> 1.http://jmchilton.github.io/blend4j/apidocs/
>> 2.
>> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>>
>> --
>> Research Associate
>> Department of Computer Science
>> Vassar College
>> Poughkeepsie, NY
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Suderman Keith]

> On May 23, 2016, at 3:34 PM, Carl Eberhard  wrote:
> 
> There's a way to get the current history data through a non-api url:
> /history/current_history_json

That works, but to get the current history for a user I need to set the 
galaxysession cookie. So it is not really a good solution unless I can find an 
api to determine the session cookie for the user.  I’ve also noticed that 
/api/histories/most_recently_used is not returning the most recently used 
history!  A bug maybe?

Keith

> 
> ...but, I don't believe those are accessible through any of the bio/blend 
> libraries.
> 
> Failing the above, is there some way to get the history ID from the UI?
> 
> You can click the information button ('i' with a circle around it) for any 
> dataset in a history. The encoded history API id will be listed under: 
> history api id.
> 
> On Sat, May 21, 2016 at 7:03 PM, Suderman Keith  > wrote:
> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2], but 
> I don’t see any way to obtain the “current” history as selected by the user 
> in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it seems 
> that simply selecting a history as the current history in the UI does not 
> make it the “most recently used” (MRU) history; I guess the user has to 
> actually _do_ something with before it becomes the MRU history.  Am I missing 
> something?
> 
> Failing the above, is there some way to get the history ID from the UI?
> 
> Thanks,
> Keith
> 
> REFERENCES
> 
> 1.http://jmchilton.github.io/blend4j/apidocs/ 
> 
> 2. 
> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>  
> 
> 
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/ 
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/ 
> 
> 

--
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY



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Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Current history via the REST API (or blend4j)

[Carl Eberhard]

There's a way to get the current history data through a non-api url:
/history/current_history_json

...but, I don't believe those are accessible through any of the bio/blend
libraries.

Failing the above, is there some way to get the history ID from the UI?


You can click the information button ('i' with a circle around it) for any
dataset in a history. The encoded history API id will be listed under:
history api id.

On Sat, May 21, 2016 at 7:03 PM, Suderman Keith 
wrote:

> I have been looking at the JavaDoc for Blend4J [1] and the REST API [2],
> but I don’t see any way to obtain the “current” history as selected by the
> user in the Galaxy UI.  I see `/api/histories/most_recently_used`, but it
> seems that simply selecting a history as the current history in the UI does
> not make it the “most recently used” (MRU) history; I guess the user has to
> actually _do_ something with before it becomes the MRU history.  Am I
> missing something?
>
> Failing the above, is there some way to get the history ID from the UI?
>
> Thanks,
> Keith
>
> REFERENCES
>
> 1.http://jmchilton.github.io/blend4j/apidocs/
> 2.
> https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories
>
> --
> Research Associate
> Department of Computer Science
> Vassar College
> Poughkeepsie, NY
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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To search Galaxy mailing lists use the unified search at:
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[galaxy-dev] Current history via the REST API (or blend4j)

[Suderman Keith]

I have been looking at the JavaDoc for Blend4J [1] and the REST API [2], but I 
don’t see any way to obtain the “current” history as selected by the user in 
the Galaxy UI.  I see `/api/histories/most_recently_used`, but it seems that 
simply selecting a history as the current history in the UI does not make it 
the “most recently used” (MRU) history; I guess the user has to actually _do_ 
something with before it becomes the MRU history.  Am I missing something?

Failing the above, is there some way to get the history ID from the UI?

Thanks,
Keith

REFERENCES

1.http://jmchilton.github.io/blend4j/apidocs/
2. 
https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.histories

--
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY



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___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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To search Galaxy mailing lists use the unified search at:
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