Current history via the REST API (or blend4j)
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#m... ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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 <suderman@cs.vassar.edu> 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#m...
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>> 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/ <http://jmchilton.github.io/blend4j/apidocs/> 2. https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#m... <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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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 <suderman@cs.vassar.edu> wrote:
On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu> 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#m...
------------------------------ 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
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 <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu> wrote:
On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu> 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#m...
------------------------------ 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
On May 24, 2016, at 11:14 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <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 <carlfeberhard@gmail.com <mailto:carlfeberhard@gmail.com>> 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 <suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>> wrote:
On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberhard@gmail.com <mailto:carlfeberhard@gmail.com>> 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 <suderman@cs.vassar.edu <mailto:suderman@cs.vassar.edu>> 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/ <http://jmchilton.github.io/blend4j/apidocs/> 2. https://galaxy.readthedocs.io/en/master/lib/galaxy.webapps.galaxy.api.html#m... <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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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 <suderman@cs.vassar.edu> wrote:
On May 24, 2016, at 11:14 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu> wrote:
On May 23, 2016, at 3:34 PM, Carl Eberhard <carlfeberhard@gmail.com> 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 <suderman@cs.vassar.edu> 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#m...
------------------------------ 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
------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
participants (2)
-
Carl Eberhard -
Suderman Keith