FAQ - Revision history

Remi: /* How do I open and execute workflows in a standard python shell? */

2017-05-26T13:59:01Z

How do I open and execute workflows in a standard python shell?

← Older revision		Revision as of 13:59, 26 May 2017
Line 198:		Line 198:
	>>> result.output_port('out_plus')		>>> result.output_port('out_plus')
	6.0		6.0

			A more complete example is available in the VisTrails distribution as [https://github.com/VisTrails/VisTrails/blob/v2.2/examples/api/ipython-notebook.ipynb examples/api/ipython-notebook.ipynb]

	== Control Flow ==		== Control Flow ==

Remi: Update API docs

2017-05-26T13:57:54Z

Update API docs

← Older revision		Revision as of 13:57, 26 May 2017
Line 185:		Line 185:
	=== Can I use VisTrails as a Python module without installing PyQt? ===		=== Can I use VisTrails as a Python module without installing PyQt? ===

	We ~~are working on improving~~ the ability to use VisTrails from other software, and have eliminated most GUI (PyQt) dependencies in the core part of the code. Thus, you can now work with workflow versions and provenance information in a standard python shell. Note that ~~workflows that take advantage of graphical output~~ like ~~that of~~ the VisTrails Spreadsheet will still require PyQt to be installed.		Yes! We have improved the ability to use VisTrails from other software, and have eliminated most GUI (PyQt) dependencies in the core part of the code. Thus, you can now work with workflow versions and provenance information in a standard python shell. Note packages that directly rely on the GUI like the VisTrails Spreadsheet will still require PyQt to be installed.

	=== How do I ~~create~~ and execute workflows in a standard python shell? ===		=== How do I open and execute workflows in a standard python shell? ===

	~~'''Note: this example requires the latest 2.0 alpha source.'''~~ Here is a simple example that shows how you can ~~build, tag,~~ and execute ~~workflows with~~ a ~~python~~ script:		Here is a simple example that shows how you can open and execute a workflow from a Python script:

	import ~~sys~~		>>> import vistrails as vt
	~~sys.path.append("/path/to/vistrails_src")~~		>>>
			>>> vistrail = vt.load_vistrail('simplemath.vt')
	~~import core.application~~ as ~~vt_app~~		>>> vistrail.select_latest_version()
	~~vt_app.init()~~		>>> result = vistrail.execute(in_a=2, in_b=4)
			>>> result.output_port('out_plus')
	~~import core.api~~		6.0
	~~vt = core.api.get_api()~~
	~~basic~~ = vt.~~get_package~~(~~"edu~~.~~utah.sci.vistrails.basic"~~)
	~~m1 = basic~~.~~String~~(~~value="Hello "~~)
	m2 = ~~basic~~.~~String~~(~~value~~=~~"World!")~~
	m3 = ~~basic.ConcatenateString(~~)
	m3.~~str1 = m1.value~~
	~~m3.str2 = m2.value~~
	~~m4 = basic.StandardOutput~~(~~value=m3.value~~)
	~~vt.tag_version("Hello World")~~
	~~vt.execute()~~
	vt.~~save_vistrail("/tmp/helloworld.vt")~~

	== Control Flow ==		== Control Flow ==
Line 488:		Line 477:
	=== Where should I go to find out what I can call from the console and how to import it? ===		=== Where should I go to find out what I can call from the console and how to import it? ===

	We have tried to make some methods more accessible in the console via an api. You can import the api via <code>import api</code> in the console and see the available methods with <code>dir(api)</code>. To open a vistrail:		We have tried to make some methods more accessible in the console via an api. You can import the api via <code>from vistrails import api</code> in the console and see the available methods with <code>dir(api)</code>. To open a vistrail:

	import api		from vistrails import api
	api.open_vistrail_from_file('/Applications/VisTrails/examples/terminator.vt')		api.open_vistrail_from_file('/Applications/VisTrails/examples/terminator.vt')

Line 533:		Line 522:
	Here's an example:		Here's an example:

	import api		import api

	vtvtk = 'edu.utah.sci.vistrails.vtk'		vtvtk = 'edu.utah.sci.vistrails.vtk'

	module = api.add_module(0, 0, vtvtk, 'vtkContourFilter', '')		module = api.add_module(0, 0, vtvtk, 'vtkContourFilter', '')

Tommy: /* Running workflows */

2015-07-10T13:28:01Z

Running workflows

← Older revision		Revision as of 13:28, 10 July 2015
Line 104:		Line 104:
	return platform.linux_distribution()[0]=='Ubuntu' or \		return platform.linux_distribution()[0]=='Ubuntu' or \
	platform.linux_distribution()[0]=='YourSystemName'		platform.linux_distribution()[0]=='YourSystemName'

			=== Cannot update subworkflows after upgrading packages or vistrails version ===

			When packages used by a subworkflow is upgraded, any subworkflows that use it will be automatically upgraded. It may then lose the ability to be updated to a newer local subworkflow. In this case the subworkflow needs to be updated by hand by removing it from the pipeline and be dragged in again from the module palette. This may get fixed in a future release.

	== Building workflows ==		== Building workflows ==

Remi: Fixes broken links

2014-04-28T18:18:31Z

Fixes broken links

Remi: Use v2.1 doc links

2014-04-28T18:12:28Z

Use v2.1 doc links

Show changes

Dakoop: /* Integrating your software into VisTrails */

2014-01-06T20:09:53Z

Integrating your software into VisTrails

← Older revision		Revision as of 20:09, 6 January 2014
Line 474:		Line 474:

	See [[Module Configuration Example]] for a full example and notes about doing this.		See [[Module Configuration Example]] for a full example and notes about doing this.

			=== Can I make a PythonSource module cacheable? ===

			Yes. If you have a module that you are planning to re-use in a workflow, we recommend making a packaged module (which are by default cacheable). However, you can make a PythonSource (which are by default not cacheable) cacheable using the line

			self.is_cacheable = lambda args, *kwargs: True

			in the source of the PythonSource module.

	== The Console ==		== The Console ==

Tommy: /* AVG Antivirus falsely report a virus in VisTrails 2.0.2 32-bit Windows installer */

2013-10-24T16:04:39Z

AVG Antivirus falsely report a virus in VisTrails 2.0.2 32-bit Windows installer

← Older revision		Revision as of 16:04, 24 October 2013
Line 614:		Line 614:
	Problematic file is vistrails/Python27/Lib/site-packages/_mysql.pyd:		Problematic file is vistrails/Python27/Lib/site-packages/_mysql.pyd:
	https://www.virustotal.com/en/file/d8aabd921b5eba8aabcce936ce3b92e3d1de43eb44c43d921ca1b9ab91d7fd81/analysis/1366640335/. This is most likely a false positive and can be ignored.		https://www.virustotal.com/en/file/d8aabd921b5eba8aabcce936ce3b92e3d1de43eb44c43d921ca1b9ab91d7fd81/analysis/1366640335/. This is most likely a false positive and can be ignored.

			=== VisTrails fails after upgrading to OSX 10.9 ===

			Reinstalling [http://xquartz.macosforge.org/ XQuartz] should solve the problem.

Dakoop: /* Integrating your software into VisTrails */

2013-10-02T00:24:26Z

Integrating your software into VisTrails

← Older revision		Revision as of 00:24, 2 October 2013
Line 469:		Line 469:
	class MplFigureManagerSubclass(MplFigureManager):		class MplFigureManagerSubclass(MplFigureManager):
	pass		pass


			=== How do I create a custom module configuration widget? ===

			See [[Module Configuration Example]] for a full example and notes about doing this.

	== The Console ==		== The Console ==

Tommy: /* VisTrails Binaries */

2013-04-22T17:07:16Z

VisTrails Binaries

← Older revision		Revision as of 17:07, 22 April 2013
Line 604:		Line 604:
	cp -r /vistrails1.7/extensions /Applications/VisTrails1.7/		cp -r /vistrails1.7/extensions /Applications/VisTrails1.7/
	cp -r /vistrails1.7/scripts /Applications/VisTrails1.7/		cp -r /vistrails1.7/scripts /Applications/VisTrails1.7/

			=== AVG Antivirus falsely report a virus in VisTrails 2.0.2 32-bit Windows installer ===

			Problematic file is vistrails/Python27/Lib/site-packages/_mysql.pyd:
			https://www.virustotal.com/en/file/d8aabd921b5eba8aabcce936ce3b92e3d1de43eb44c43d921ca1b9ab91d7fd81/analysis/1366640335/. This is most likely a false positive and can be ignored.

Tommy: /* rpy */

2013-03-20T14:36:06Z

rpy

← Older revision		Revision as of 14:36, 20 March 2013
Line 544:		Line 544:
	The rpy package needs to be updated to support a newer rpy version. In "packages/rpy/init.py", replace all instances of "objects.RVector" with "objects.Vector", or use [https://raw.github.com/VisTrails/VisTrails/d0711a8d5ba8992662f69ed7924c625a3658b6a7/vistrails/packages/rpy/init.py this] file.		The rpy package needs to be updated to support a newer rpy version. In "packages/rpy/init.py", replace all instances of "objects.RVector" with "objects.Vector", or use [https://raw.github.com/VisTrails/VisTrails/d0711a8d5ba8992662f69ed7924c625a3658b6a7/vistrails/packages/rpy/init.py this] file.

	==~~= How do I use the~~ JobSubmission ~~package? =~~==		== JobSubmission ==

	The JobSubmission package depends on the stable version of BatchQ. Download https://github.com/troelsfr/BatchQ/archive/stable.zip, copy the "BatchQ-stable/batchq" directory to your local site-packages folder. Copying it to the "vistrails/packages/JobSubmission" folder should also work. See batchq/contrib/vistrails for examples.		The JobSubmission package depends on the stable version of BatchQ. Download https://github.com/troelsfr/BatchQ/archive/stable.zip, copy the "BatchQ-stable/batchq" directory to your local site-packages folder. Copying it to the "vistrails/packages/JobSubmission" folder should also work. See batchq/contrib/vistrails for examples.

← Older revision		Revision as of 18:18, 28 April 2014
Line 109:		Line 109:
	=== Is there a way to give each widget a "display name" in addition to the module name at the center of the widget? ===		=== Is there a way to give each widget a "display name" in addition to the module name at the center of the widget? ===

	Yes, a "display name" can be assigned to a module by selecting the triangle in its top right corner to open a popup menu and selecting the Set Module Label... menu item. You will then be prompted to enter the "display name". [http://www.vistrails.org/usersguide/v2.1/html/creating.html#~~changing~~-module-labels Changing Module Labels]		Yes, a "display name" can be assigned to a module by selecting the triangle in its top right corner to open a popup menu and selecting the Set Module Label... menu item. You will then be prompted to enter the "display name". [http://www.vistrails.org/usersguide/v2.1/html/creating.html#configuring-module-labels Changing Module Labels]

	=== Is there a way to re-center the picture-in-picture (PiP) view? ===		=== Is there a way to re-center the picture-in-picture (PiP) view? ===
Line 131:		Line 131:
	=== What is the VisTrails server-mode? ===		=== What is the VisTrails server-mode? ===

	Using the VisTrails server mode, it is possible to ''execute workflows and control VisTrails through another application''. For example, the CrowdLabs Web portal (http://www.crowdlabs.org) accesses a VisTrails sever to execute workflows, retrieve and display vistrail trees and workflows. [http://www.vistrails.org/usersguide~~/html~~/v2.1/html/batch.html#using-vistrails-as-a-server Using VisTrails as a Server]		Using the VisTrails server mode, it is possible to ''execute workflows and control VisTrails through another application''. For example, the CrowdLabs Web portal (http://www.crowdlabs.org) accesses a VisTrails sever to execute workflows, retrieve and display vistrail trees and workflows. [http://www.vistrails.org/usersguide/v2.1/html/batch.html#using-vistrails-as-a-server Using VisTrails as a Server]

	=== How do I execute workflows and control VisTrails through another application? ===		=== How do I execute workflows and control VisTrails through another application? ===
Line 144:		Line 144:
	http://www.crowdlabs.org/site_media/static/dev_docs/vistrails_database_setup.html		http://www.crowdlabs.org/site_media/static/dev_docs/vistrails_database_setup.html

	If what you want is just to execute a series of workflows in batch mode, a simpler solution would be to ''use the VisTrails client in batch mode''. Chapter 12 of the user's guide contains detailed information and examples on that. [http://www.vistrails.org/usersguide~~/html~~/v2.1/html/batch.html#sec-cli-batch Running VisTrails in Batch Mode]		If what you want is just to execute a series of workflows in batch mode, a simpler solution would be to ''use the VisTrails client in batch mode''. Chapter 12 of the user's guide contains detailed information and examples on that. [http://www.vistrails.org/usersguide/v2.1/html/batch.html#sec-cli-batch Running VisTrails in Batch Mode]

	=== VisTrails server executes a workflow but generates a blank image and generates the error message ''cannot get access to X server'' ===		=== VisTrails server executes a workflow but generates a blank image and generates the error message ''cannot get access to X server'' ===
Line 270:		Line 270:
	(2) The spreadsheet is extensible so you can write a custom spreadsheet cell widget that has a button or label with the desired link (a QLabel with openExternalLinks set to True, for example).		(2) The spreadsheet is extensible so you can write a custom spreadsheet cell widget that has a button or label with the desired link (a QLabel with openExternalLinks set to True, for example).

	(3) You can tweak the existing RichTextCell be adding the line "self.browser.setOpenExternalLinks(True)" at line 63 of the source file "vistrails/packages/spreadsheet/widgets/richtext/richtext.py". Then, if your workflow creates a file with html markup text like "<a href="http://www.vistrails.org">VisTrails</a>" connected to a RichTextCell, clicking on the rendered link in the cell will open it in a web browser. You need to add the aforementioned line to the source to let Qt know that you want the link opened externally; by default, it will just issue an event that isn't processed. [http://www.vistrails.org/usersguide/v2.1/html/spreadsheet.html#launching-a-web-browser Launching a Web Browser]		(3) You can tweak the existing RichTextCell be adding the line "self.browser.setOpenExternalLinks(True)" at line 63 of the source file "vistrails/packages/spreadsheet/widgets/richtext/richtext.py". Then, if your workflow creates a file with html markup text like "<a href="http://www.vistrails.org/">VisTrails</a>" connected to a RichTextCell, clicking on the rendered link in the cell will open it in a web browser. You need to add the aforementioned line to the source to let Qt know that you want the link opened externally; by default, it will just issue an event that isn't processed. [http://www.vistrails.org/usersguide/v2.1/html/spreadsheet.html#launching-a-web-browser Launching a Web Browser]

	== Integrating your software into VisTrails ==		== Integrating your software into VisTrails ==
Line 418:		Line 418:
	# ...		# ...

	With the _modules dictionary shortcut (for more details, see [http://www.vistrails.org/index.php/FAQ#~~Are_there_shortucts_for_registry_initialization~~.3F the FAQ section on this]), you include it in a kwargs dict as part of a module tuple:		With the _modules dictionary shortcut (for more details, see [http://www.vistrails.org/index.php/FAQ#Are_there_shortcuts_for_registry_initialization.3F the FAQ section on this]), you include it in a kwargs dict as part of a module tuple:

	_modules = [AnotherModule, (InvisibleModule, {'abstract': True})]		_modules = [AnotherModule, (InvisibleModule, {'abstract': True})]
Line 562:		Line 562:
	=== I would like to build VisTrails from source. Are there instructions on how to do this? ===		=== I would like to build VisTrails from source. Are there instructions on how to do this? ===

	Yes! Take a look at ~~http://www.vistrails.org/index.php/Mac_Intel_Instructions~~		Yes! Take a look at [http://www.vistrails.org/usersguide/v2.1/html/getting_started.html#installing-vistrails-from-source Installing VisTrails from source]
	[http://www.vistrails.org/usersguide/v2.1/html/getting_started.html#installing-vistrails-from-source Installing VisTrails from source]

	== Accessing Provenance Information ==		== Accessing Provenance Information ==