Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Any more thought on how to accomplish this without my current hack? Ideally it would be great if this feature could become part of galaxy-central. This is a feature that we would really like to implement so that our reports can link to the output files. Thanks, Ilya -Original Message- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Friday, October 21, 2011 9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper? Excerpts from Chorny, Ilya's message of 2011-10-21 01:51:03 +: > I get the following error from routes > > AttributeError: 'thread._local' object has no attribute 'mapper' Okay, what I suspected. This is a product of the fact that job running is decoupled from the web frontend. The job runner doesn't necessarily live in the same process or even on the same machine as the web interface. You could have multiple web interfaces serving different base urls feeding one job runner. I don't have any simple answer to this. You could try to initialize route's mapper in the job runner, but I think this would be a big mistake. Instead you probably want to capture the URL somehow when the job is created. I need to think about it some more. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Excerpts from Chorny, Ilya's message of 2011-10-21 15:43:35 +: > Also, I do not have access to trans in the Tools class in > lib/galaxy/tools/__init__.py. 'trans' is the state of a web transaction (a single request response cycle). It is this only accessible for code that occurs within that scope. For tools/__init__.py there are some methods that have access and some that don't, it depends on how they are called (all the user interface generation related code has access to trans for example). -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Excerpts from Chorny, Ilya's message of 2011-10-21 01:51:03 +: > I get the following error from routes > > AttributeError: 'thread._local' object has no attribute 'mapper' Okay, what I suspected. This is a product of the fact that job running is decoupled from the web frontend. The job runner doesn't necessarily live in the same process or even on the same machine as the web interface. You could have multiple web interfaces serving different base urls feeding one job runner. I don't have any simple answer to this. You could try to initialize route's mapper in the job runner, but I think this would be a big mistake. Instead you probably want to capture the URL somehow when the job is created. I need to think about it some more. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Ilya,
Tools are not tightly coupled to the Galaxy web framework ( they can be
executed on the command line outside of Galaxy ) so, as you've commented, you
don't have access to the web framework from there. It's unclear to me what you
are trying to do. Can you clarify a bit more?
Greg Von Kuster
On Oct 21, 2011, at 11:43 AM, Chorny, Ilya wrote:
> Also, I do not have access to trans in the Tools class in
> lib/galaxy/tools/__init__.py.
>
> Thanks,
>
> Ilya
>
>
> -Original Message-
> From: galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
> Sent: Friday, October 21, 2011 8:40 AM
> To: Greg Von Kuster
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
> files to my tool wrapper?
>
> I need the base_url and the proxy. That is why I am using cookie_path. Any
> thoughts on how to get both.
>
> Thanks,
>
> Ilya
>
>
> -Original Message-
> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Sent: Friday, October 21, 2011 6:11 AM
> To: Chorny, Ilya
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
> files to my tool wrapper?
>
> Ilya, you can use trans.request.host to get the base url.
>
>
> On Oct 20, 2011, at 11:52 AM, Chorny, Ilya wrote:
>
>> I thought I would add this to the list in case anyone in the galaxy :) knew
>> the answer. I get a mapping error every time I invoke url_for. What
>> variable stores the base url for the galaxy instance?
>>
>> Thanks,
>>
>> Ilya
>>
>> -Original Message-
>> From: Chorny, Ilya
>> Sent: Wednesday, October 19, 2011 4:21 PM
>> To: 'James Taylor'
>> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> Hi James,
>>
>> I got the code working but I can't figure out how to set the URL. I have a
>> hack right now (i.e. url = 'http://' + socket.getfqdn() +
>> config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) +
>> '/display/?preview=True' ). I tried using url_for() but was unable to get
>> that to work. Attached are the diff's for the files I made changes to.
>>
>> If you have any suggestions on how to properly set the url please let me
>> know.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> -Original Message-
>> From: James Taylor [mailto:ja...@jamestaylor.org]
>> Sent: Tuesday, October 18, 2011 11:38 AM
>> To: Chorny, Ilya
>> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> Hi Ilya, I think any case where $__app__ is used should raise red flags, it
>> is definitely breaking abstraction. In this case, you're passing a very
>> specific implementation detail of the web layer all the way down to your
>> tool.
>>
>> I think the right way to do what you want is to add a 'web_display_url'
>> attribute to the class DatasetFilenameWrapper in tools/__init__.py.
>> Every dataset gets wrapped by this when put into the namespace for building
>> command lines. If you added an attribute it would them be available as
>> ${input.web_display_url} in the command line template.
>>
>> Historically tool wrappers were designed so that they have no knowledge of
>> the UI, allowing non-web UIs to be added on top. At this point it seems
>> unlikely that this will ever happen, but it is still a good idea to avoid
>> this kind of coupling. Otherwise we can't change how the web interface does
>> security without changing individual tools.
>>
>> Excerpts from Chorny, Ilya's message of 2011-10-17 22:56:40 +:
>>> So we came up with a work around and I wouldn't mind getting your opinion
>>> on it. Specifically with respect to passing cookie_path. I could not figure
>>> out how to get the proxy prefix from the universe_wsgi.ini file via the
>>> $__app__ call. Also you mention in the wiki the the $__app__ may get
>>> deprecated.
>>>
>>> Thanks,
>>>
>>> Ilya
>>>
>>>
>>> We copied the encryption code (i.e)
>>>
>>> def encode_id(dataset_id,id_secret):
>>> id_cipher = Blowfish.new(id_secret)
>>> s = dataset_id
>>> s = ( "!" * ( 8 - len(s) % 8 ) ) + s
>>> encrypted_id = id_cipher.encrypt( s ).encode( 'hex' )
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Also, I do not have access to trans in the Tools class in
lib/galaxy/tools/__init__.py.
Thanks,
Ilya
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
Sent: Friday, October 21, 2011 8:40 AM
To: Greg Von Kuster
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
files to my tool wrapper?
I need the base_url and the proxy. That is why I am using cookie_path. Any
thoughts on how to get both.
Thanks,
Ilya
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, October 21, 2011 6:11 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
files to my tool wrapper?
Ilya, you can use trans.request.host to get the base url.
On Oct 20, 2011, at 11:52 AM, Chorny, Ilya wrote:
> I thought I would add this to the list in case anyone in the galaxy :) knew
> the answer. I get a mapping error every time I invoke url_for. What variable
> stores the base url for the galaxy instance?
>
> Thanks,
>
> Ilya
>
> -Original Message-
> From: Chorny, Ilya
> Sent: Wednesday, October 19, 2011 4:21 PM
> To: 'James Taylor'
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi James,
>
> I got the code working but I can't figure out how to set the URL. I have a
> hack right now (i.e. url = 'http://' + socket.getfqdn() +
> config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) +
> '/display/?preview=True' ). I tried using url_for() but was unable to get
> that to work. Attached are the diff's for the files I made changes to.
>
> If you have any suggestions on how to properly set the url please let me know.
>
> Thanks,
>
> Ilya
>
>
> -Original Message-
> From: James Taylor [mailto:ja...@jamestaylor.org]
> Sent: Tuesday, October 18, 2011 11:38 AM
> To: Chorny, Ilya
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi Ilya, I think any case where $__app__ is used should raise red flags, it
> is definitely breaking abstraction. In this case, you're passing a very
> specific implementation detail of the web layer all the way down to your tool.
>
> I think the right way to do what you want is to add a 'web_display_url'
> attribute to the class DatasetFilenameWrapper in tools/__init__.py.
> Every dataset gets wrapped by this when put into the namespace for building
> command lines. If you added an attribute it would them be available as
> ${input.web_display_url} in the command line template.
>
> Historically tool wrappers were designed so that they have no knowledge of
> the UI, allowing non-web UIs to be added on top. At this point it seems
> unlikely that this will ever happen, but it is still a good idea to avoid
> this kind of coupling. Otherwise we can't change how the web interface does
> security without changing individual tools.
>
> Excerpts from Chorny, Ilya's message of 2011-10-17 22:56:40 +:
>> So we came up with a work around and I wouldn't mind getting your opinion on
>> it. Specifically with respect to passing cookie_path. I could not figure out
>> how to get the proxy prefix from the universe_wsgi.ini file via the $__app__
>> call. Also you mention in the wiki the the $__app__ may get deprecated.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> We copied the encryption code (i.e)
>>
>> def encode_id(dataset_id,id_secret):
>>id_cipher = Blowfish.new(id_secret)
>>s = dataset_id
>>s = ( "!" * ( 8 - len(s) % 8 ) ) + s
>>encrypted_id = id_cipher.encrypt( s ).encode( 'hex' )
>>return encrypted_id
>>
>> and we passed to the too wrapperl:
>>
>> -i input -i $input.dataset.id
>>
>> as well as
>>
>> --id_secret=$__app__.config.id_secret
>> --cookie_path=$__app__.config.cookie_path
>>
>> -Original Message-
>> From: Chorny, Ilya
>> Sent: Monday, October 17, 2011 11:10 AM
>> To: Chorny, Ilya; James Taylor
>> Cc: galaxy-dev
>> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> Would it be difficult to add the url as an attribute of the input and output
>> parameters ($param.url)? If you point me to where these values are set, I
>> can try to make the changes to the code.
>>
>> Thanks,
>>
>> Ilya
>
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
I need the base_url and the proxy. That is why I am using cookie_path. Any
thoughts on how to get both.
Thanks,
Ilya
-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Friday, October 21, 2011 6:11 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output
files to my tool wrapper?
Ilya, you can use trans.request.host to get the base url.
On Oct 20, 2011, at 11:52 AM, Chorny, Ilya wrote:
> I thought I would add this to the list in case anyone in the galaxy :) knew
> the answer. I get a mapping error every time I invoke url_for. What variable
> stores the base url for the galaxy instance?
>
> Thanks,
>
> Ilya
>
> -Original Message-
> From: Chorny, Ilya
> Sent: Wednesday, October 19, 2011 4:21 PM
> To: 'James Taylor'
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi James,
>
> I got the code working but I can't figure out how to set the URL. I have a
> hack right now (i.e. url = 'http://' + socket.getfqdn() +
> config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) +
> '/display/?preview=True' ). I tried using url_for() but was unable to get
> that to work. Attached are the diff's for the files I made changes to.
>
> If you have any suggestions on how to properly set the url please let me know.
>
> Thanks,
>
> Ilya
>
>
> -Original Message-
> From: James Taylor [mailto:ja...@jamestaylor.org]
> Sent: Tuesday, October 18, 2011 11:38 AM
> To: Chorny, Ilya
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi Ilya, I think any case where $__app__ is used should raise red flags, it
> is definitely breaking abstraction. In this case, you're passing a very
> specific implementation detail of the web layer all the way down to your tool.
>
> I think the right way to do what you want is to add a 'web_display_url'
> attribute to the class DatasetFilenameWrapper in tools/__init__.py.
> Every dataset gets wrapped by this when put into the namespace for building
> command lines. If you added an attribute it would them be available as
> ${input.web_display_url} in the command line template.
>
> Historically tool wrappers were designed so that they have no knowledge of
> the UI, allowing non-web UIs to be added on top. At this point it seems
> unlikely that this will ever happen, but it is still a good idea to avoid
> this kind of coupling. Otherwise we can't change how the web interface does
> security without changing individual tools.
>
> Excerpts from Chorny, Ilya's message of 2011-10-17 22:56:40 +:
>> So we came up with a work around and I wouldn't mind getting your opinion on
>> it. Specifically with respect to passing cookie_path. I could not figure out
>> how to get the proxy prefix from the universe_wsgi.ini file via the $__app__
>> call. Also you mention in the wiki the the $__app__ may get deprecated.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> We copied the encryption code (i.e)
>>
>> def encode_id(dataset_id,id_secret):
>>id_cipher = Blowfish.new(id_secret)
>>s = dataset_id
>>s = ( "!" * ( 8 - len(s) % 8 ) ) + s
>>encrypted_id = id_cipher.encrypt( s ).encode( 'hex' )
>>return encrypted_id
>>
>> and we passed to the too wrapperl:
>>
>> -i input -i $input.dataset.id
>>
>> as well as
>>
>> --id_secret=$__app__.config.id_secret
>> --cookie_path=$__app__.config.cookie_path
>>
>> -Original Message-
>> From: Chorny, Ilya
>> Sent: Monday, October 17, 2011 11:10 AM
>> To: Chorny, Ilya; James Taylor
>> Cc: galaxy-dev
>> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> Would it be difficult to add the url as an attribute of the input and output
>> parameters ($param.url)? If you point me to where these values are set, I
>> can try to make the changes to the code.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> -Original Message-
>> From: galaxy-dev-boun...@lists.bx.psu.edu
>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny,
>> Ilya
>> Sent: Sunday, October 16, 2011 7:36 AM
>> To: James Taylor
>> Cc: galaxy-dev
>> Subject: Re: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> PDF report.
>&
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Ilya, you can use trans.request.host to get the base url.
On Oct 20, 2011, at 11:52 AM, Chorny, Ilya wrote:
> I thought I would add this to the list in case anyone in the galaxy :) knew
> the answer. I get a mapping error every time I invoke url_for. What variable
> stores the base url for the galaxy instance?
>
> Thanks,
>
> Ilya
>
> -Original Message-
> From: Chorny, Ilya
> Sent: Wednesday, October 19, 2011 4:21 PM
> To: 'James Taylor'
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi James,
>
> I got the code working but I can't figure out how to set the URL. I have a
> hack right now (i.e. url = 'http://' + socket.getfqdn() +
> config_info.cookie_path + '/datasets/' + sec.encode_id(dataset.id) +
> '/display/?preview=True' ). I tried using url_for() but was unable to get
> that to work. Attached are the diff's for the files I made changes to.
>
> If you have any suggestions on how to properly set the url please let me know.
>
> Thanks,
>
> Ilya
>
>
> -Original Message-
> From: James Taylor [mailto:ja...@jamestaylor.org]
> Sent: Tuesday, October 18, 2011 11:38 AM
> To: Chorny, Ilya
> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output files
> to my tool wrapper?
>
> Hi Ilya, I think any case where $__app__ is used should raise red flags, it
> is definitely breaking abstraction. In this case, you're passing a very
> specific implementation detail of the web layer all the way down to your tool.
>
> I think the right way to do what you want is to add a 'web_display_url'
> attribute to the class DatasetFilenameWrapper in tools/__init__.py.
> Every dataset gets wrapped by this when put into the namespace for building
> command lines. If you added an attribute it would them be available as
> ${input.web_display_url} in the command line template.
>
> Historically tool wrappers were designed so that they have no knowledge of
> the UI, allowing non-web UIs to be added on top. At this point it seems
> unlikely that this will ever happen, but it is still a good idea to avoid
> this kind of coupling. Otherwise we can't change how the web interface does
> security without changing individual tools.
>
> Excerpts from Chorny, Ilya's message of 2011-10-17 22:56:40 +:
>> So we came up with a work around and I wouldn't mind getting your opinion on
>> it. Specifically with respect to passing cookie_path. I could not figure out
>> how to get the proxy prefix from the universe_wsgi.ini file via the $__app__
>> call. Also you mention in the wiki the the $__app__ may get deprecated.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> We copied the encryption code (i.e)
>>
>> def encode_id(dataset_id,id_secret):
>>id_cipher = Blowfish.new(id_secret)
>>s = dataset_id
>>s = ( "!" * ( 8 - len(s) % 8 ) ) + s
>>encrypted_id = id_cipher.encrypt( s ).encode( 'hex' )
>>return encrypted_id
>>
>> and we passed to the too wrapperl:
>>
>> -i input -i $input.dataset.id
>>
>> as well as
>>
>> --id_secret=$__app__.config.id_secret
>> --cookie_path=$__app__.config.cookie_path
>>
>> -Original Message-
>> From: Chorny, Ilya
>> Sent: Monday, October 17, 2011 11:10 AM
>> To: Chorny, Ilya; James Taylor
>> Cc: galaxy-dev
>> Subject: RE: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> Would it be difficult to add the url as an attribute of the input and output
>> parameters ($param.url)? If you point me to where these values are set, I
>> can try to make the changes to the code.
>>
>> Thanks,
>>
>> Ilya
>>
>>
>> -Original Message-
>> From: galaxy-dev-boun...@lists.bx.psu.edu
>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Chorny, Ilya
>> Sent: Sunday, October 16, 2011 7:36 AM
>> To: James Taylor
>> Cc: galaxy-dev
>> Subject: Re: [galaxy-dev] how do I pass the URL of the input and output
>> files to my tool wrapper?
>>
>> PDF report.
>>
>> Sent from my iPhone
>>
>> On Oct 15, 2011, at 7:36 PM, "James Taylor" wrote:
>>
>>> Excerpts from Chorny, Ilya's message of 2011-10-14 23:46:25 +:
Anyone know if it possible to pass the url (shown in the eye ball) to a
tool wrapper?
>>>
>>> Ilya, this isn't currently supported because it breaks the
>>> abstraction between the web interface and tools (tools shouldn't
>>> know they are being invoked by a web application). What are you trying to
>>> achieve with this?
>>> Is this for a tool generating an HTML report?
>>> --
>>> James Taylor, Assistant Professor, Biology / Computer Science, Emory
>>> University
>>> ___
>>> 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:
>>>
>>> http://lists.bx.psu.edu/
>>
>> ___
>> Please k
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
I get the following error from routes AttributeError: 'thread._local' object has no attribute 'mapper' -Original Message- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Thursday, October 20, 2011 5:46 PM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper? Excerpts from Chorny, Ilya's message of 2011-10-20 15:52:03 +: > I thought I would add this to the list in case anyone in the galaxy :) > knew the answer. I get a mapping error every time I invoke url_for. > What variable stores the base url for the galaxy instance? Can you provide the specific error you get from url_for? There is no single variable that stores the app url, it is constructed from the routing system which url_for is connected to. If you look in form_builder.py for example you can see the use of url_for from non template code. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Excerpts from Chorny, Ilya's message of 2011-10-20 15:52:03 +: > I thought I would add this to the list in case anyone in the galaxy :) > knew the answer. I get a mapping error every time I invoke url_for. > What variable stores the base url for the galaxy instance? Can you provide the specific error you get from url_for? There is no single variable that stores the app url, it is constructed from the routing system which url_for is connected to. If you look in form_builder.py for example you can see the use of url_for from non template code. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ 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: http://lists.bx.psu.edu/
