def generate_vtl(locator,
version,
pipeline,
execute=False,
forceDB=False,
showSpreadsheetOnly=False,
embedWorkflow=False):
"""generate_vtl(locator:DBLocator or XMLLocator,
version: str, pipeline:Pipeline, execute:boolean,
forceDB:boolean, showspreadsheetOnly:boolean,
embedWorkflow: boolean) -> str
It generates the contents of a .vtl file with the information
given.
"""
node = ElementTree.Element('vtlink')
if isinstance(locator, DBLocator):
node.set('host', str(locator.host))
node.set('port', str(locator.port))
node.set('database', str(locator.db))
node.set('vtid', str(locator.obj_id))
elif locator is not None:
node.set('filename', str(locator.name))
node.set('version', str(version))
node.set('execute', str(execute))
node.set('forceDB', str(forceDB))
node.set('showSpreadsheetOnly', str(showSpreadsheetOnly))
if embedWorkflow == True:
vistrail = Vistrail()
action_list = []
for module in pipeline.module_list:
action_list.append(('add', module))
for connection in pipeline.connection_list:
action_list.append(('add', connection))
action = core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.addTag("Imported workflow", action.id)
if not forceDB:
node.set('version', str(action.id))
if not vistrail.db_version:
vistrail.db_version = currentVersion
pipxmlstr = io.serialize(vistrail)
vtcontent = base64.b64encode(pipxmlstr)
node.set('vtcontent', vtcontent)
return ElementTree.tostring(node)
def load_vistrail(locator, is_abstraction=False):
from core.vistrail.vistrail import Vistrail
abstraction_files = []
thumbnail_files = []
mashups = []
vistrail = None
if locator is None:
vistrail = Vistrail()
else:
res = locator.load()
if type(res) == type(SaveBundle(None)):
vistrail = res.vistrail
abstraction_files.extend(res.abstractions)
thumbnail_files.extend(res.thumbnails)
mashups.extend(res.mashups)
else:
vistrail = res
vistrail.is_abstraction = is_abstraction
return (vistrail, abstraction_files, thumbnail_files, mashups)
def open_workflow(self, locator, version=None):
self.close_first_vistrail_if_necessary()
if self.single_document_mode and self.currentView():
self.closeVistrail()
vistrail = Vistrail()
try:
if locator is not None:
workflow = locator.load(Pipeline)
action_list = []
for module in workflow.module_list:
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
vistrail.addTag("Imported workflow", action.id)
# FIXME might need different locator?
except ModuleRegistryException, e:
msg = ('Cannot find module "%s" in package "%s". '
'Make sure package is '
'enabled in the Preferences dialog.' % \
(e._name, e._identifier))
debug.critical(msg)
def __init__(self, parent=None):
""" QQueryTab(parent: QWidget) -> QQueryTab
Create an empty vistrail controller for this query tab
"""
QPipelineTab.__init__(self, parent)
self.pipelineView.setBackgroundBrush(
CurrentTheme.QUERY_BACKGROUND_BRUSH)
self.moduleMethods.vWidget.formType = QFunctionQueryForm
controller = QueryVistrailController(auto_save=False)
controller.set_vistrail(Vistrail(), None)
self.setController(controller)
controller.change_selected_version(0)
self.connect(controller, QtCore.SIGNAL('vistrailChanged()'),
self.vistrailChanged)
def build_widget(self):
layout = QtGui.QVBoxLayout()
layout.setMargin(0)
layout.setSpacing(0)
self.query_controller = QueryController(self)
self.vt_controller = VistrailController(auto_save=False)
self.p_controller = VistrailController(Vistrail(), auto_save=False)
self.connect(self.p_controller,
QtCore.SIGNAL('vistrailChanged()'),
self.vistrailChanged)
self.query_box = QQueryBox()
self.query_box.set_controller(self.query_controller)
layout.addWidget(self.query_box)
self.stacked_widget = QtGui.QStackedWidget()
self.pipeline_view = QQueryPipelineView()
self.p_controller.current_pipeline_view = self.pipeline_view.scene()
self.pipeline_view.set_controller(self.p_controller)
self.pipeline_view.set_query_controller(self.query_controller)
QQueryView.VISUAL_SEARCH_VIEW = \
self.stacked_widget.addWidget(self.pipeline_view)
self.global_result_view = QQueryResultGlobalView()
QQueryView.GLOBAL_RESULT_VIEW = \
self.stacked_widget.addWidget(self.global_result_view)
self.version_result_view = QQueryResultVersionView()
self.connect(self.version_result_view.scene(),
QtCore.SIGNAL('versionSelected(int,bool,bool,bool,bool)'),
self.result_version_selected)
# self.version_result_view.set_controller(self.vt_controller)
QQueryView.VERSION_RESULT_VIEW = \
self.stacked_widget.addWidget(self.version_result_view)
self.workflow_result_view = QQueryResultWorkflowView()
# self.workflow_result_view.set_controller(self.vt_controller)
QQueryView.WORKFLOW_RESULT_VIEW = \
self.stacked_widget.addWidget(self.workflow_result_view)
self.stacked_widget.setCurrentWidget(self.pipeline_view)
layout.addWidget(self.stacked_widget)
self.setLayout(layout)
self.current_display = QQueryView.VISUAL_SEARCH_VIEW
self.current_result_view = QQueryView.VERSION_RESULT_VIEW
def generate_vtl(locator,version,pipeline,execute=False,forceDB=False,
showSpreadsheetOnly=False,embedWorkflow=False):
"""generate_vtl(locator:DBLocator or XMLLocator,
version: str, pipeline:Pipeline, execute:boolean,
forceDB:boolean, showspreadsheetOnly:boolean,
embedWorkflow: boolean) -> str
It generates the contents of a .vtl file with the information
given.
"""
node = ElementTree.Element('vtlink')
if isinstance(locator, DBLocator):
node.set('host', str(locator.host))
node.set('port', str(locator.port))
node.set('database', str(locator.db))
node.set('vtid', str(locator.obj_id))
elif locator is not None:
node.set('filename', str(locator.name))
node.set('version', str(version))
node.set('execute', str(execute))
node.set('forceDB', str(forceDB))
node.set('showSpreadsheetOnly', str(showSpreadsheetOnly))
if embedWorkflow == True:
vistrail = Vistrail()
action_list = []
for module in pipeline.module_list:
action_list.append(('add', module))
for connection in pipeline.connection_list:
action_list.append(('add', connection))
action = core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.addTag("Imported workflow", action.id)
if not forceDB:
node.set('version', str(action.id))
if not vistrail.db_version:
vistrail.db_version = currentVersion
pipxmlstr = io.serialize(vistrail)
vtcontent = base64.b64encode(pipxmlstr)
node.set('vtcontent',vtcontent)
return ElementTree.tostring(node)
def processWorkFlow(self, xmlFile):
global _outputFilePath
# there should probably be a call in the api for this block of code
vistrail = Vistrail()
locator = FileLocator(xmlFile)
workflow = locator.load(Pipeline)
action_list = []
for module in workflow.module_list:
if module.name == 'FileSink':
_outputFilePath = _tmpDir + '/cp_tmp_' + uuid.uuid4().hex + '.png'
for i in xrange(module.getNumFunctions()):
if 'outputPath' == module.functions[i].name:
module.functions[i].params[0].strValue = _outputFilePath;
action_list.append(('add', module))
for connection in workflow.connection_list:
action_list.append(('add', connection))
action = core.db.action.create_action(action_list)
vistrail.add_action(action, 0L)
vistrail.update_id_scope()
vistrail.addTag("Imported workflow", action.id)
vt = get_api()
# there should probably be a call in the api for this next line
vt._controller.set_vistrail(vistrail, locator)
vt.select_version(action.id)
# Assuming that this call is synchronou
vt.execute()
# Close and exit
vt.close_vistrail()
def exportMashup(filename, vtcontroller, mashuptrail, mashupversion,
etype):
"""exportMashup(filename: str, vtcontroller: VistrailController,
mashuptrail: Mashuptrail, type: int) -> bool
where etype is
0: include full tree
1: include only workflow and mashup identified by version
2: as a link, it will point to a local file.
"""
result = False
if vtcontroller is not None and mashuptrail is not None:
locator = vtcontroller.locator
version = mashuptrail.vtVersion
node = ElementTree.Element('vtlink')
if isinstance(locator, DBLocator):
node.set('host', str(locator.host))
node.set('port', str(locator.port))
node.set('database', str(locator.db))
node.set('vtid', str(locator.obj_id))
else:
node.set('filename', str(locator.name))
node.set('version', str(version))
node.set('execute', "True")
node.set('forceDB', "False")
node.set('showSpreadsheetOnly', "True")
node.set('mashuptrail', str(mashuptrail.id))
node.set('mashupVersion', str(mashupversion))
if etype in [0, 1]:
if etype == 1: #minimal
pip = vtcontroller.vistrail.getPipeline(version)
vistrail = Vistrail()
id_remap = {}
action = core.db.action.create_paste_action(
pip, vistrail.idScope, id_remap)
vistrail.add_action(action, 0L, 0)
tag = vtcontroller.vistrail.get_tag(version)
if tag is None:
tag = "Imported workflow"
vistrail.addTag(tag, action.id)
node.set('version', str(action.id))
id_scope = IdScope(1L)
newmashuptrail = Mashuptrail(
MashupsManager.getNewMashuptrailId(), action.id,
id_scope)
maction = mashuptrail.actionMap[mashupversion]
mtag = mashuptrail.getTagForActionId(mashupversion)
newmashup = copy.copy(maction.mashup)
newmashup.remapPipelineObjects(id_remap)
currVersion = newmashuptrail.addVersion(
newmashuptrail.getLatestVersion(), newmashup,
maction.user, maction.date)
newmashuptrail.currentVersion = currVersion
newmashuptrail.changeTag(currVersion, mtag, maction.user,
maction.date)
newvtcontroller = BaseVistrailController()
newvtcontroller.set_vistrail(vistrail, None)
MashupsManager.addMashuptrailtoVistrailController(
newvtcontroller, newmashuptrail)
node.set('mashuptrail', str(newmashuptrail.id))
node.set('mashupVersion',
str(newmashuptrail.currentVersion))
else:
vistrail = vtcontroller.vistrail
newvtcontroller = MashupsManager.copyBaseVistrailController(
vtcontroller)
#create temporary file
(fd, name) = tempfile.mkstemp(prefix='vt_tmp', suffix='.vt')
os.close(fd)
fileLocator = FileLocator(name)
newvtcontroller.write_vistrail(fileLocator)
contents = open(name).read()
vtcontent = base64.b64encode(contents)
os.unlink(name)
#if not vistrail.db_version:
# vistrail.db_version = currentVersion
node.set('vtcontent', vtcontent)
xmlstring = ElementTree.tostring(node)
file_ = open(filename, 'w')
file_.write(xmlstring)
file_.close()
result = True
return result
def exportMashup(filename, vtcontroller, mashuptrail, mashupversion, etype):
"""exportMashup(filename: str, vtcontroller: VistrailController,
mashuptrail: Mashuptrail, type: int) -> bool
where etype is
0: include full tree
1: include only workflow and mashup identified by version
2: as a link, it will point to a local file.
"""
result = False
if vtcontroller is not None and mashuptrail is not None:
locator = vtcontroller.locator
version = mashuptrail.vtVersion
node = ElementTree.Element("vtlink")
if isinstance(locator, DBLocator):
node.set("host", str(locator.host))
node.set("port", str(locator.port))
node.set("database", str(locator.db))
node.set("vtid", str(locator.obj_id))
else:
node.set("filename", str(locator.name))
node.set("version", str(version))
node.set("execute", "True")
node.set("forceDB", "False")
node.set("showSpreadsheetOnly", "True")
node.set("mashuptrail", str(mashuptrail.id))
node.set("mashupVersion", str(mashupversion))
if etype in [0, 1]:
if etype == 1: # minimal
pip = vtcontroller.vistrail.getPipeline(version)
vistrail = Vistrail()
id_remap = {}
action = core.db.action.create_paste_action(pip, vistrail.idScope, id_remap)
vistrail.add_action(action, 0L, 0)
tag = vtcontroller.vistrail.get_tag(version)
if tag is None:
tag = "Imported workflow"
vistrail.addTag(tag, action.id)
node.set("version", str(action.id))
id_scope = IdScope(1L)
newmashuptrail = Mashuptrail(MashupsManager.getNewMashuptrailId(), action.id, id_scope)
maction = mashuptrail.actionMap[mashupversion]
mtag = mashuptrail.getTagForActionId(mashupversion)
newmashup = copy.copy(maction.mashup)
newmashup.remapPipelineObjects(id_remap)
currVersion = newmashuptrail.addVersion(
newmashuptrail.getLatestVersion(), newmashup, maction.user, maction.date
)
newmashuptrail.currentVersion = currVersion
newmashuptrail.changeTag(currVersion, mtag, maction.user, maction.date)
newvtcontroller = BaseVistrailController()
newvtcontroller.set_vistrail(vistrail, None)
MashupsManager.addMashuptrailtoVistrailController(newvtcontroller, newmashuptrail)
node.set("mashuptrail", str(newmashuptrail.id))
node.set("mashupVersion", str(newmashuptrail.currentVersion))
else:
vistrail = vtcontroller.vistrail
newvtcontroller = MashupsManager.copyBaseVistrailController(vtcontroller)
# create temporary file
(fd, name) = tempfile.mkstemp(prefix="vt_tmp", suffix=".vt")
os.close(fd)
fileLocator = FileLocator(name)
newvtcontroller.write_vistrail(fileLocator)
contents = open(name).read()
vtcontent = base64.b64encode(contents)
os.unlink(name)
# if not vistrail.db_version:
# vistrail.db_version = currentVersion
node.set("vtcontent", vtcontent)
xmlstring = ElementTree.tostring(node)
file_ = open(filename, "w")
file_.write(xmlstring)
file_.close()
result = True
return result
def get_vistrail(self):
if self._vistrail is None:
self._vistrail = Vistrail()
return self._vistrail
def read_vistrail(vt_fname):
import db.services.io
from core.vistrail.vistrail import Vistrail
vistrail = db.services.io.open_vistrail_from_xml(vt_fname)
Vistrail.convert(vistrail)
return vistrail
def read_vistrail(vt_fname):
import db.services.io
from core.vistrail.vistrail import Vistrail
vistrail = db.services.io.open_vistrail_from_xml(vt_fname)
Vistrail.convert(vistrail)
return vistrail
