Re: [galaxy-dev] Visualise Galaxy workflows using graphviz
please find attached a small patch that add the gen_image() functionality to the export-workflow UI. Thanks for the contribution. I committed a modified version of it: https://bitbucket.org/galaxy/galaxy-central/commits/0e064a23864c846483b35f893cf0a769dedf24f1 Specifically, I (a) used gen_image directly rather than a wrapper method and (b) added the code to workflow's export template rather than the base template. I was not able to figure out how to add a patch to the trello card. But at least i created one ;). This isn't possible as best I know. Pull requests are the (highly) preferred way to contribute code to the project. Best, J.___ 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] Visualise Galaxy workflows using graphviz
Hi,
please find attached a small patch that add the gen_image()
functionality to the export-workflow UI.
I was not able to figure out how to add a patch to the trello card. But
at least i created one ;).
https://trello.com/c/PGz7JNzO
Ciao,
Bjoern
Thanks for sharing Peter.
FWIW, there is already code in Galaxy to generate SVG from a workflow. See
the gen_image function in web/controllers/workflow.py I think this code is
used when workflows are included in the tool shed as well.
If your code is better in some way(s), please consider a pull request. It
should be fairly straightforward to add an option to a workflow's menu to
generate SVG for it.
Best,
J.
On May 23, 2012, at 4:44 PM, Peter van Heusden wrote:
Hi there
Because my Galaxy workflows tend to sprawl outside the viewable space in
my browser, I've written a script that, when given a workflow JSON file
as input, writes out a graphviz dot format graph of the workflow. By
default the graph treats datasets as nodes and analyses as edges (unlike
the Galaxy workflow editor, but quite like the way the history is
presented), but you can choose to have analyses as nodes (and thus
datasets as edges) too.
In case anyone else finds this useful, the code can be downloaded from
my bitbucket:
https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_dot.py
Usage is something like:
./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg workflow.svg
and then you can view your workflow.svg with eog or another viewer.
Peter
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diff -r 34404f848979 lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py Sat Jan 19 17:54:48 2013 -0500
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py Sun Jan 20 16:32:39 2013 +0100
@@ -993,6 +993,14 @@
stored = self.get_stored_workflow( trans, id, check_ownership=False, check_accessible=True )
return self._workflow_to_dict( trans, stored )
+@web.expose
+def export_to_image( self, trans, id ):
+
+Get the latest Workflow for the StoredWorkflow identified by `id` and plot it to a canvas XML object.
+
+
+return self.gen_image(trans, id)
+
@web.json_pretty
def export_to_file( self, trans, id ):
diff -r 34404f848979 templates/export_base.mako
--- a/templates/export_base.mako Sat Jan 19 17:54:48 2013 -0500
+++ b/templates/export_base.mako Sun Jan 20 16:32:39 2013 +0100
@@ -92,6 +92,13 @@
Download ${get_class_display_name( item.__class__ ).lower()} to file so that it can be saved or imported into another Galaxy server./a
/%def
+%def name=render_workflow_to_image(item)
+h3Download as Image/h3
+
+a href=${h.url_for( action='export_to_image', id=trans.security.encode_id( item.id ) )}
+Create ${get_class_display_name( item.__class__ ).lower()} image and download it as vector image./a
+/%def
+
%def name=render_more(item)
## Override.
/%def
@@ -109,9 +116,11 @@
${self.render_download_to_file(item)}
+${self.render_workflow_to_image(item)}
+
${self.render_url_for_importing(item)}
${self.render_more(item)}
${self.render_footer()}
-/%def
\ No newline at end of file
+/%def
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[galaxy-dev] Visualise Galaxy workflows using graphviz
Hi there Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too. In case anyone else finds this useful, the code can be downloaded from my bitbucket: https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_dot.py Usage is something like: ./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg workflow.svg and then you can view your workflow.svg with eog or another viewer. Peter ___ 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] Visualise Galaxy workflows using graphviz
Thanks for sharing Peter. FWIW, there is already code in Galaxy to generate SVG from a workflow. See the gen_image function in web/controllers/workflow.py I think this code is used when workflows are included in the tool shed as well. If your code is better in some way(s), please consider a pull request. It should be fairly straightforward to add an option to a workflow's menu to generate SVG for it. Best, J. On May 23, 2012, at 4:44 PM, Peter van Heusden wrote: Hi there Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too. In case anyone else finds this useful, the code can be downloaded from my bitbucket: https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_dot.py Usage is something like: ./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg workflow.svg and then you can view your workflow.svg with eog or another viewer. Peter ___ 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 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/
