def get_vt_graph(vt_list, tree_info, pdf=False):
"""get_vt_graph(vt_list: list of locator, tree_info:str)
Load all vistrails in vt_list and dump their tree to tree_info.
"""
result = []
if is_running_gui():
from gui.vistrail_controller import VistrailController as \
GUIVistrailController
for locator in vt_list:
try:
(v, abstractions, thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController()
if tree_info is not None:
from gui.version_view import QVersionTreeView
version_view = QVersionTreeView()
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
controller.current_pipeline_view = pipeline_view.scene()
controller.set_vistrail(v, locator, abstractions,
thumbnails, mashups)
version_view.scene().setupScene(controller)
if pdf:
base_fname = "graph_%s.pdf" % locator.short_name
filename = os.path.join(tree_info, base_fname)
version_view.scene().saveToPDF(filename)
else:
base_fname = "graph_%s.png" % locator.short_name
filename = os.path.join(tree_info, base_fname)
version_view.scene().saveToPNG(filename)
del version_view
result.append((True, ""))
except Exception, e:
result.append((False, str(e)))
def get_vt_graph(vt_list, tree_info, pdf=False):
"""get_vt_graph(vt_list: list of locator, tree_info:str)
Load all vistrails in vt_list and dump their tree to tree_info.
"""
result = []
if is_running_gui():
from gui.vistrail_controller import VistrailController as \
GUIVistrailController
for locator in vt_list:
try:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController()
if tree_info is not None:
from gui.version_view import QVersionTreeView
version_view = QVersionTreeView()
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
controller.current_pipeline_view = pipeline_view.scene()
controller.set_vistrail(v, locator, abstractions, thumbnails,
mashups)
version_view.scene().setupScene(controller)
if pdf:
base_fname = "graph_%s.pdf" % locator.short_name
filename = os.path.join(tree_info, base_fname)
version_view.scene().saveToPDF(filename)
else:
base_fname = "graph_%s.png" % locator.short_name
filename = os.path.join(tree_info, base_fname)
version_view.scene().saveToPNG(filename)
del version_view
result.append((True, ""))
except Exception, e:
result.append((False, str(e)))
def extract_text(escaped_html_str):
notes = xml.sax.saxutils.unescape(escaped_html_str)
if is_running_gui():
from PyQt4 import QtGui
from PyQt4.QtCore import QString
fragment = QtGui.QTextDocumentFragment.fromHtml(QString(notes))
return str(fragment.toPlainText())
else:
return str(notes)
def extract_text(escaped_html_str):
notes = xml.sax.saxutils.unescape(escaped_html_str)
if is_running_gui():
from PyQt4 import QtGui
from PyQt4.QtCore import QString
fragment = QtGui.QTextDocumentFragment.fromHtml(QString(notes))
return str(fragment.toPlainText())
else:
return str(notes)
def get_wf_graph(w_list, workflow_info=None, pdf=False):
"""run_and_get_results(w_list: list of (locator, version),
workflow_info:str, pdf:bool)
Load all workflows in wf_list and dump their graph to workflow_info.
"""
result = []
if is_running_gui():
from gui.vistrail_controller import VistrailController as \
GUIVistrailController
for locator, workflow in w_list:
try:
(v, abstractions, thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController()
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
if (workflow_info is not None
and controller.current_pipeline is not None):
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
controller.current_pipeline_view = pipeline_view.scene()
controller.set_vistrail(v, locator, abstractions,
thumbnails, mashups)
pipeline_view.scene().setupScene(
controller.current_pipeline)
if pdf:
base_fname = "%s_%s_pipeline.pdf" % (
locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
else:
base_fname = "%s_%s_pipeline.png" % (
locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPNG(filename)
del pipeline_view
result.append((True, ""))
except Exception, e:
result.append((False, str(e)))
def get_wf_graph(w_list, workflow_info=None, pdf=False):
"""run_and_get_results(w_list: list of (locator, version),
workflow_info:str, pdf:bool)
Load all workflows in wf_list and dump their graph to workflow_info.
"""
result = []
if is_running_gui():
from gui.vistrail_controller import VistrailController as \
GUIVistrailController
for locator, workflow in w_list:
try:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
controller = GUIVistrailController()
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [ type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
if (workflow_info is not None and
controller.current_pipeline is not None):
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
controller.current_pipeline_view = pipeline_view.scene()
controller.set_vistrail(v, locator, abstractions, thumbnails,
mashups)
pipeline_view.scene().setupScene(controller.current_pipeline)
if pdf:
base_fname = "%s_%s_pipeline.pdf" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
else:
base_fname = "%s_%s_pipeline.png" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPNG(filename)
del pipeline_view
result.append((True, ""))
except Exception, e:
result.append((False, str(e)))
def run_and_get_results(w_list,
parameters='',
workflow_info=None,
update_vistrail=True,
extra_info=None,
reason='Console Mode Execution'):
"""run_and_get_results(w_list: list of (locator, version), parameters: str,
workflow_info:str, update_vistrail: boolean,
extra_info:dict)
Run all workflows in w_list, and returns an interpreter result object.
version can be a tag name or a version id.
"""
elements = parameters.split("$&$")
aliases = {}
result = []
for locator, workflow in w_list:
(v, abstractions, thumbnails, mashups) = load_vistrail(locator)
controller = VistrailController(auto_save=update_vistrail)
controller.set_vistrail(v, locator, abstractions, thumbnails, mashups)
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
for e in elements:
pos = e.find("=")
if pos != -1:
key = e[:pos].strip()
value = e[pos + 1:].strip()
if controller.current_pipeline.has_alias(key):
aliases[key] = value
if workflow_info is not None and controller.current_pipeline is not None:
if is_running_gui():
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
pipeline_view.scene().setupScene(controller.current_pipeline)
base_fname = "%s_%s_pipeline.pdf" % (locator.short_name,
version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
del pipeline_view
else:
debug.critical("Cannot save pipeline figure when not "
"running in gui mode")
base_fname = "%s_%s_pipeline.xml" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
core.db.io.save_workflow(controller.current_pipeline, filename)
if not update_vistrail:
conf = get_vistrails_configuration()
if conf.has('thumbs'):
conf.thumbs.autoSave = False
(results, _) = \
controller.execute_current_workflow(custom_aliases=aliases,
extra_info=extra_info,
reason=reason)
new_version = controller.current_version
if new_version != version:
debug.warning("Version '%s' (%s) was upgraded. The actual "
"version executed was %s" % \
(workflow, version, new_version))
run = results[0]
run.workflow_info = (locator.name, new_version)
run.pipeline = controller.current_pipeline
if update_vistrail:
controller.write_vistrail(locator)
result.append(run)
return result
def run_and_get_results(w_list, parameters='', workflow_info=None,
update_vistrail=True, extra_info=None,
reason='Console Mode Execution'):
"""run_and_get_results(w_list: list of (locator, version), parameters: str,
workflow_info:str, update_vistrail: boolean,
extra_info:dict)
Run all workflows in w_list, and returns an interpreter result object.
version can be a tag name or a version id.
"""
elements = parameters.split("$&$")
aliases = {}
result = []
for locator, workflow in w_list:
(v, abstractions , thumbnails, mashups) = load_vistrail(locator)
controller = VistrailController(auto_save=update_vistrail)
controller.set_vistrail(v, locator, abstractions, thumbnails, mashups)
if type(workflow) == type("str"):
version = v.get_version_number(workflow)
elif type(workflow) in [ type(1), long]:
version = workflow
elif workflow is None:
version = controller.get_latest_version_in_graph()
else:
msg = "Invalid version tag or number: %s" % workflow
raise VistrailsInternalError(msg)
controller.change_selected_version(version)
for e in elements:
pos = e.find("=")
if pos != -1:
key = e[:pos].strip()
value = e[pos+1:].strip()
if controller.current_pipeline.has_alias(key):
aliases[key] = value
if workflow_info is not None and controller.current_pipeline is not None:
if is_running_gui():
from gui.pipeline_view import QPipelineView
pipeline_view = QPipelineView()
pipeline_view.scene().setupScene(controller.current_pipeline)
base_fname = "%s_%s_pipeline.pdf" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
pipeline_view.scene().saveToPDF(filename)
del pipeline_view
else:
debug.critical("Cannot save pipeline figure when not "
"running in gui mode")
base_fname = "%s_%s_pipeline.xml" % (locator.short_name, version)
filename = os.path.join(workflow_info, base_fname)
core.db.io.save_workflow(controller.current_pipeline, filename)
if not update_vistrail:
conf = get_vistrails_configuration()
if conf.has('thumbs'):
conf.thumbs.autoSave = False
(results, _) = \
controller.execute_current_workflow(custom_aliases=aliases,
extra_info=extra_info,
reason=reason)
new_version = controller.current_version
if new_version != version:
debug.warning("Version '%s' (%s) was upgraded. The actual "
"version executed was %s" % \
(workflow, version, new_version))
run = results[0]
run.workflow_info = (locator.name, new_version)
run.pipeline = controller.current_pipeline
if update_vistrail:
controller.write_vistrail(locator)
result.append(run)
return result
