patch for workflow api
Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below. #### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, 'step_output': conn.output_name} item['steps'] = steps return item Could someone add this simple fix? I'd really appreciate it. Please let me know if I should be submtting a patch or pull request somewhere else. thanks, Richard
Hey Richard, If you could, submit a pull request to galaxy-central through bitbucket. Even for changes this small, it really helps keep things organized and preserves the change history. Thanks! Dannon On Jan 30, 2013, at 2:54 PM, Richard Park <rpark@bu.edu> wrote:
Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below.
#### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, 'step_output': conn.output_name} item['steps'] = steps return item
Could someone add this simple fix? I'd really appreciate it. Please let me know if I should be submtting a patch or pull request somewhere else. thanks, Richard ___________________________________________________________ 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:
Hi Dannon, Thanks for the help again, I just forked galaxy-central, committed the patch, and submitted the pull request. https://bitbucket.org/galaxy/galaxy-central/pull-request/114/fixed-error-whe... Let me know if you need anything else, thanks, Richard On Wed, Jan 30, 2013 at 2:59 PM, Dannon Baker <dannonbaker@me.com> wrote:
Hey Richard,
If you could, submit a pull request to galaxy-central through bitbucket. Even for changes this small, it really helps keep things organized and preserves the change history.
Thanks!
Dannon
On Jan 30, 2013, at 2:54 PM, Richard Park <rpark@bu.edu> wrote:
Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below.
#### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id,
'step_output': conn.output_name}
item['steps'] = steps return item
Could someone add this simple fix? I'd really appreciate it. Please let
me know if I should be submtting a patch or pull request somewhere else.
thanks, Richard ___________________________________________________________ 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:
Perfect, thanks! I've merged the changes. -Dannon On Jan 30, 2013, at 3:55 PM, Richard Park <rpark@bu.edu> wrote:
Hi Dannon,
Thanks for the help again, I just forked galaxy-central, committed the patch, and submitted the pull request.
https://bitbucket.org/galaxy/galaxy-central/pull-request/114/fixed-error-whe...
Let me know if you need anything else, thanks, Richard
On Wed, Jan 30, 2013 at 2:59 PM, Dannon Baker <dannonbaker@me.com> wrote: Hey Richard,
If you could, submit a pull request to galaxy-central through bitbucket. Even for changes this small, it really helps keep things organized and preserves the change history.
Thanks!
Dannon
On Jan 30, 2013, at 2:54 PM, Richard Park <rpark@bu.edu> wrote:
Hi Guys, I've just updated to the latest galaxy-central and notice a problem when trying to export workflows via the api. In galaxy-central/lib/webapps/galaxy/api/workflows.py, I just need to add in an extra tab in lines 88 and 89, the patch is below.
#### PATCH #### using hg diff diff -r 43fa4cb72e0f lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 13:49:43 2013 -0500 +++ b/lib/galaxy/webapps/galaxy/api/workflows.py Wed Jan 30 14:43:46 2013 -0500 @@ -85,8 +85,8 @@ 'type': step.type, 'tool_id': step.tool_id, 'input_steps': {}} - for conn in step.input_connections: - steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, + for conn in step.input_connections: + steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id, 'step_output': conn.output_name} item['steps'] = steps return item
Could someone add this simple fix? I'd really appreciate it. Please let me know if I should be submtting a patch or pull request somewhere else. thanks, Richard ___________________________________________________________ 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:
participants (2)
-
Dannon Baker -
Richard Park