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 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
def push_vistrail_to_repository(self, branching=False):
""" uploads current VisTrail to web repository """
self._repository_status['details'] = "Pushing to repository..."
self._push_button.setEnabled(False)
self._branch_button.setEnabled(False)
self.update_push_information()
try:
# create temp file
self.directory = tempfile.mkdtemp(prefix='vt_tmp')
(fd, filename) = tempfile.mkstemp(suffix='.vt',
prefix='vt_tmp',
dir=self.directory)
os.close(fd)
# writing tmp vt and switching back to orginal vt
locator = ZIPFileLocator(filename)
controller = api.get_current_controller()
tmp_controller = VistrailController()
tmp_controller.set_vistrail(controller.vistrail.do_copy(), locator)
tmp_controller.changed = True
tmp_controller.write_vistrail(locator)
# check if this vt is from the repository
if controller.vistrail.get_annotation('repository_vt_id'):
repository_vt_id = controller.vistrail.get_annotation(
'repository_vt_id').value
else:
repository_vt_id = -1
# upload vistrail temp file to repository
register_openers(cookiejar=self.dialog.cookiejar)
project = self.serverCombo.itemData(
self.serverCombo.currentIndex()).toList()[0].toString()
if project == "Default": project = ""
params = {'vistrail_file': open(filename, 'rb'),
'action': 'upload',
'name': controller.locator.short_name,
'repository_vt_id': repository_vt_id if not branching else -1,
'is_runnable': not bool(len(self.unsupported_packages)+ \
len(self.local_data_modules)),
'vt_id': 0,
'branched_from': "" if not branching else repository_vt_id,
'project': project,
'everyone_can_view': self.perm_view.checkState(),
'everyone_can_edit': self.perm_edit.checkState(),
'everyone_can_download': self.perm_download.checkState()
}
upload_url = "%s/vistrails/remote_upload/" % \
self.config.webRepositoryURL
datagen, headers = multipart_encode(params)
request = urllib2.Request(upload_url, datagen, headers)
result = urllib2.urlopen(request)
updated_response = result.read()
os.unlink(filename)
if updated_response[:6] == "upload":
# No update, just upload
if result.code != 200:
self._repository_status['details'] = \
"Push to repository failed"
else:
repository_vt_id = int(updated_response[8:])
controller.vistrail.set_annotation('repository_vt_id',
repository_vt_id)
controller.vistrail.set_annotation(
'repository_creator', self.dialog.loginUser.text())
# ensure that the annotations get saved
controller.set_changed(True)
self._repository_status['details'] = \
"Push to repository was successful"
else:
# update, load updated vistrail
if result.code != 200:
self._repository_status['details'] = "Update Failed"
else:
debug.log("getting version from web")
# request file to download
download_url = "%s/vistrails/download/%s/" % \
(self.config.webRepositoryURL, updated_response)
request = urllib2.Request(download_url)
result = urllib2.urlopen(request)
updated_file = result.read()
# create temp file of updated vistrail
self.directory = tempfile.mkdtemp(prefix='vt_tmp')
(fd,
updated_filename) = tempfile.mkstemp(suffix='.vtl',
prefix='vtl_tmp',
dir=self.directory)
os.close(fd)
updated_vt = open(updated_filename, 'w')
updated_vt.write(updated_file)
updated_vt.close()
# switch vistrails to updated one
controller = api.get_current_controller()
updated_locator = FileLocator(updated_filename)
(up_vistrail, abstractions, thumbnails, mashups) = \
load_vistrail(updated_locator)
controller.set_vistrail(up_vistrail,
controller.vistrail.locator,
abstractions, thumbnails, mashups)
# update version tree drawing
controller.recompute_terse_graph()
controller.invalidate_version_tree()
os.remove(updated_filename)
os.remove(updated_filename[:-1])
os.rmdir(self.directory)
self._repository_status['details'] = \
"Update to repository was successful"
except Exception, e:
debug.critical(str(e))
self._repository_status['details'] = "An error occurred"
def push_vistrail_to_repository(self, branching=False):
""" uploads current VisTrail to web repository """
self._repository_status['details'] = "Pushing to repository..."
self._push_button.setEnabled(False)
self._branch_button.setEnabled(False)
self.update_push_information()
try:
# create temp file
self.directory = tempfile.mkdtemp(prefix='vt_tmp')
(fd, filename) = tempfile.mkstemp(suffix='.vt', prefix='vt_tmp',
dir=self.directory)
os.close(fd)
# writing tmp vt and switching back to orginal vt
locator = ZIPFileLocator(filename)
controller = api.get_current_controller()
tmp_controller = VistrailController()
tmp_controller.set_vistrail(controller.vistrail.do_copy(), locator)
tmp_controller.changed = True
tmp_controller.write_vistrail(locator)
# check if this vt is from the repository
if controller.vistrail.get_annotation('repository_vt_id'):
repository_vt_id = controller.vistrail.get_annotation('repository_vt_id').value
else:
repository_vt_id = -1
# upload vistrail temp file to repository
register_openers(cookiejar=self.dialog.cookiejar)
project = self.serverCombo.itemData(self.serverCombo.currentIndex()).toList()[0].toString()
if project == "Default": project = ""
params = {'vistrail_file': open(filename, 'rb'),
'action': 'upload',
'name': controller.locator.short_name,
'repository_vt_id': repository_vt_id if not branching else -1,
'is_runnable': not bool(len(self.unsupported_packages)+ \
len(self.local_data_modules)),
'vt_id': 0,
'branched_from': "" if not branching else repository_vt_id,
'project': project,
'everyone_can_view': self.perm_view.checkState(),
'everyone_can_edit': self.perm_edit.checkState(),
'everyone_can_download': self.perm_download.checkState()
}
upload_url = "%s/vistrails/remote_upload/" % \
self.config.webRepositoryURL
datagen, headers = multipart_encode(params)
request = urllib2.Request(upload_url, datagen, headers)
result = urllib2.urlopen(request)
updated_response = result.read()
os.unlink(filename)
if updated_response[:6] == "upload":
# No update, just upload
if result.code != 200:
self._repository_status['details'] = \
"Push to repository failed"
else:
repository_vt_id = int(updated_response[8:])
controller.vistrail.set_annotation('repository_vt_id',
repository_vt_id)
controller.vistrail.set_annotation('repository_creator',
self.dialog.loginUser.text())
# ensure that the annotations get saved
controller.set_changed(True)
self._repository_status['details'] = \
"Push to repository was successful"
else:
# update, load updated vistrail
if result.code != 200:
self._repository_status['details'] = "Update Failed"
else:
debug.log("getting version from web")
# request file to download
download_url = "%s/vistrails/download/%s/" % \
(self.config.webRepositoryURL, updated_response)
request = urllib2.Request(download_url)
result = urllib2.urlopen(request)
updated_file = result.read()
# create temp file of updated vistrail
self.directory = tempfile.mkdtemp(prefix='vt_tmp')
(fd, updated_filename) = tempfile.mkstemp(suffix='.vtl',
prefix='vtl_tmp',
dir=self.directory)
os.close(fd)
updated_vt = open(updated_filename, 'w')
updated_vt.write(updated_file)
updated_vt.close()
# switch vistrails to updated one
controller = api.get_current_controller()
updated_locator = FileLocator(updated_filename)
(up_vistrail, abstractions, thumbnails, mashups) = \
load_vistrail(updated_locator)
controller.set_vistrail(up_vistrail,
controller.vistrail.locator,
abstractions, thumbnails, mashups)
# update version tree drawing
controller.recompute_terse_graph()
controller.invalidate_version_tree()
os.remove(updated_filename)
os.remove(updated_filename[:-1])
os.rmdir(self.directory)
self._repository_status['details'] = \
"Update to repository was successful"
except Exception, e:
debug.critical(str(e))
self._repository_status['details'] = "An error occurred"
