findAllOrganisms REST endpoint

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findAllOrganisms REST endpoint

Michael Paulini
Hia,


could it be that the findAllOrganisms REST endpoint ignores the
organisms parameter? A quick look  into the python library also shows
some hacks around that.

But to be fair, I don't know if the documentation
http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M





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Re: findAllOrganisms REST endpoint

Michael Paulini
"organism" parameter

On 25/07/17 15:38, Michael Paulini wrote:
Hia,


could it be that the findAllOrganisms REST endpoint ignores the organisms parameter? A quick look  into the python library also shows some hacks around that.

But to be fair, I don't know if the documentation http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M





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Re: findAllOrganisms REST endpoint

nathandunn

Michael,

Thanks for the feedback.

That’s an optional parameter that can be the commonName or organism ID.    I think I described in the method description, but not in the parameters. 

If supplied, it only looks up the single organism and verifies that the user has permission for it. 

I’ve updated the webservice docs on master to reflect this.  

Nathan

On Jul 25, 2017, at 7:39 AM, Michael Paulini <[hidden email]> wrote:

"organism" parameter

On 25/07/17 15:38, Michael Paulini wrote:
Hia,


could it be that the findAllOrganisms REST endpoint ignores the organisms parameter? A quick look  into the python library also shows some hacks around that.

But to be fair, I don't know if the documentation http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M




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Re: findAllOrganisms REST endpoint

Michael Paulini
Hi Nathan,

are you sure it actually works?
Because when I provided a name it didn't return anything and also
https://github.com/galaxy-genome-annotation/python-apollo/blob/7f1c533d82504e295deccb73a16229d5074915c3/apollo/organisms/__init__.py

has that comment:
def show_organism(self, organism_id):
      
        Get information about a specific organism. Due to the lack of an API,
        this call requires fetching the entire list of organisms and iterating
        through. If you find this painfully slow, please submit a bug report
        upstream.

the get_organisms() has also a funky dictionary match loop

M


On 25/07/17 17:01, Nathan Dunn wrote:

Michael,

Thanks for the feedback.

That’s an optional parameter that can be the commonName or organism ID.    I think I described in the method description, but not in the parameters. 

If supplied, it only looks up the single organism and verifies that the user has permission for it. 

I’ve updated the webservice docs on master to reflect this.  

Nathan

On Jul 25, 2017, at 7:39 AM, Michael Paulini <[hidden email]> wrote:

"organism" parameter

On 25/07/17 15:38, Michael Paulini wrote:
Hia,


could it be that the findAllOrganisms REST endpoint ignores the organisms parameter? A quick look  into the python library also shows some hacks around that.

But to be fair, I don't know if the documentation http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
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Re: findAllOrganisms REST endpoint

Michael Paulini
Sorry, had a typo. It does work.

M

On 25/07/17 17:06, Michael Paulini wrote:
Hi Nathan,

are you sure it actually works?
Because when I provided a name it didn't return anything and also
https://github.com/galaxy-genome-annotation/python-apollo/blob/7f1c533d82504e295deccb73a16229d5074915c3/apollo/organisms/__init__.py

has that comment:
def show_organism(self, organism_id):
      
        Get information about a specific organism. Due to the lack of an API,
        this call requires fetching the entire list of organisms and iterating
        through. If you find this painfully slow, please submit a bug report
        upstream.

the get_organisms() has also a funky dictionary match loop

M


On 25/07/17 17:01, Nathan Dunn wrote:

Michael,

Thanks for the feedback.

That’s an optional parameter that can be the commonName or organism ID.    I think I described in the method description, but not in the parameters. 

If supplied, it only looks up the single organism and verifies that the user has permission for it. 

I’ve updated the webservice docs on master to reflect this.  

Nathan

On Jul 25, 2017, at 7:39 AM, Michael Paulini <[hidden email]> wrote:

"organism" parameter

On 25/07/17 15:38, Michael Paulini wrote:
Hia,


could it be that the findAllOrganisms REST endpoint ignores the organisms parameter? A quick look  into the python library also shows some hacks around that.

But to be fair, I don't know if the documentation http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M



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Re: findAllOrganisms REST endpoint

nathandunn

No worries. 

Nathan


On Jul 25, 2017, at 9:18 AM, Michael Paulini <[hidden email]> wrote:

Sorry, had a typo. It does work.

M

On 25/07/17 17:06, Michael Paulini wrote:
Hi Nathan,

are you sure it actually works?
Because when I provided a name it didn't return anything and also
https://github.com/galaxy-genome-annotation/python-apollo/blob/7f1c533d82504e295deccb73a16229d5074915c3/apollo/organisms/__init__.py

has that comment:
def show_organism(self, organism_id):
      
        Get information about a specific organism. Due to the lack of an API,
        this call requires fetching the entire list of organisms and iterating
        through. If you find this painfully slow, please submit a bug report
        upstream.

the get_organisms() has also a funky dictionary match loop

M


On 25/07/17 17:01, Nathan Dunn wrote:

Michael,

Thanks for the feedback.

That’s an optional parameter that can be the commonName or organism ID.    I think I described in the method description, but not in the parameters. 

If supplied, it only looks up the single organism and verifies that the user has permission for it. 

I’ve updated the webservice docs on master to reflect this.  

Nathan

On Jul 25, 2017, at 7:39 AM, Michael Paulini <[hidden email]> wrote:

"organism" parameter

On 25/07/17 15:38, Michael Paulini wrote:
Hia,


could it be that the findAllOrganisms REST endpoint ignores the organisms parameter? A quick look  into the python library also shows some hacks around that.

But to be fair, I don't know if the documentation http://icebox.lbl.gov/Apollo2/jbrowse/web_services/api is up to date.


M



This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. 





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