# VisTrails does funny stuff with unittest/unittest2, be sure to load that
# after vistrails
import unittest
# reinitializing arguments and options so VisTrails does not try parsing them
sys.argv = sys.argv[:1]
vistrails.gui.application.VistrailsApplicationSingleton.use_event_filter = \
False
root_directory = os.path.realpath(vistrails_root_directory())
###############################################################################
# Testing Examples
EXAMPLES_PATH = vistrails_examples_directory()
#dictionary of examples that will be run with the workflows that will be ignored
VT_EXAMPLES = {
'EMBOSS_webservices.vt': ["ProphetOutput"],
'KEGGPathway.vt': [],
'KEGG_SearchEntities_webservice.vt': [],
'KEGG_webservices.vt': [],
'brain_vistrail.vt': [],
'chebi_webservice.vt': [],
'head.vt': [],
'infovis.vt': [],
'noaa_webservices.vt': [],
'offscreen.vt': [],
'plot.vt': [],
'spx.vt': [],
'structure_or_id_webservice.vt': [],
# VisTrails does funny stuff with unittest/unittest2, be sure to load that
# after vistrails
import unittest
# reinitializing arguments and options so VisTrails does not try parsing them
sys.argv = sys.argv[:1]
vistrails.gui.application.VistrailsApplicationSingleton.use_event_filter = \
False
root_directory = os.path.realpath(vistrails_root_directory())
###############################################################################
# Testing Examples
EXAMPLES_PATH = vistrails_examples_directory()
#dictionary of examples that will be run with the workflows that will be ignored
VT_EXAMPLES = { 'EMBOSS_webservices.vt': ["ProphetOutput"],
'KEGGPathway.vt': [],
'KEGG_SearchEntities_webservice.vt': [],
'KEGG_webservices.vt': [],
'brain_vistrail.vt': [],
'chebi_webservice.vt': [],
'head.vt': [],
'infovis.vt': [],
'noaa_webservices.vt': [],
'offscreen.vt': [],
'plot.vt': [],
'spx.vt': [],
'structure_or_id_webservice.vt': [],
'terminator.vt': ["Isosurface Script"],
def from_link_file(filename):
"""from_link_file(filename: str) -> DBLocator
This will parse a '.vtl' file and will create a DBLocator. .vtl files
are vistrail link files and they are used to point vistrails to open
vistrails from the database on the web. """
def convert_from_str(value, type):
def bool_conv(x):
s = str(x).upper()
if s == 'TRUE':
return True
if s == 'FALSE':
return False
if value is not None:
if type == 'str':
return str(value)
elif value.strip() != '':
if type == 'long':
return long(value)
elif type == 'float':
return float(value)
elif type == 'int':
return int(value)
elif type == 'bool':
return bool_conv(value)
elif type == 'base64':
return base64.b64decode(value)
return None
def guess_extension_from_contents(contents):
if contents.startswith("<vistrail"):
return ".xml"
else:
return ".vt"
tree = ElementTree.parse(filename)
node = tree.getroot()
if node.tag != 'vtlink':
return None
#read attributes
data = node.get('host', None)
host = convert_from_str(data, 'str')
data = node.get('port', None)
port = convert_from_str(data, 'int')
data = node.get('database', None)
database = convert_from_str(data, 'str')
data = node.get('vtid')
vt_id = convert_from_str(data, 'int')
data = node.get('version')
version = convert_from_str(data, 'str')
data = node.get('tag')
tag = convert_from_str(data, 'str')
data = node.get('execute')
execute = convert_from_str(data, 'bool')
data = node.get('showSpreadsheetOnly')
showSpreadsheetOnly = convert_from_str(data, 'bool')
data = node.get('url', None)
url = convert_from_str(data, 'str')
data = node.get('vtcontent', None)
vtcontent = convert_from_str(data, 'base64')
data = node.get('filename', None)
vtname = convert_from_str(data, 'str')
data = node.get('forceDB', None)
forceDB = convert_from_str(data, 'bool')
data = node.get('mashuptrail', None)
mashuptrail = convert_from_str(data, 'str')
data = node.get('mashupVersion', None)
mashupVersion = convert_from_str(data, 'int')
data = node.get('parameterExploration', None)
parameterExploration = convert_from_str(data, 'int')
#if execute is False, we will show the builder too
if showSpreadsheetOnly and not execute:
showSpreadsheetOnly = False
try:
version = int(version)
except (ValueError, TypeError):
pass
if tag is None:
tag = ''
## execute and showSpreadsheetOnly should be written to the current
## configuration
config = get_vistrails_configuration()
config.execute = execute
config.showWindow = not showSpreadsheetOnly
if not forceDB:
if vtcontent is not None:
if url is not None:
basename = url.split('/')[-1]
base, ext = os.path.splitext(basename)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname, basename)
else:
basename = os.path.basename(filename)
base, ext = os.path.splitext(basename)
ext = guess_extension_from_contents(vtcontent)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname, "%s%s" % (base, ext))
create_file = True
if os.path.exists(fname): #file was extracted before
create_file = False
oldf = open(fname)
oldcontents = oldf.read()
if oldcontents != vtcontent:
import vistrails.gui.extras.core.db.locator as db_gui
(overwrite, newname) = \
db_gui.ask_to_overwrite_file(None, 'vistrail')
create_file = True
if newname:
fname = newname
elif overwrite == False:
i = 1
while os.path.exists(fname):
newbase = "%s_%s%s" % (base, i, ext)
fname = os.path.join(dirname, newbase)
i += 1
if create_file:
f = open(fname, 'wb')
f.write(vtcontent)
f.close()
return FileLocator(fname,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
if host is not None:
user = ""
passwd = ""
return DBLocator(host,
port,
database,
user,
passwd,
None,
obj_id=vt_id,
obj_type='vistrail',
connection_id=None,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
elif vtname is not None:
if os.path.dirname(vtname) == '':
#check if file exists in the same directory as the .vtl file
dirname = os.path.dirname(filename)
newvtname = os.path.join(dirname, vtname)
if os.path.exists(newvtname):
vtname = newvtname
#check for magic strings
if "@examples" in vtname:
vtname = vtname.replace("@examples",
vistrails_examples_directory())
return FileLocator(vtname,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
def from_link_file(filename):
"""from_link_file(filename: str) -> DBLocator
This will parse a '.vtl' file and will create a DBLocator. .vtl files
are vistrail link files and they are used to point vistrails to open
vistrails from the database on the web. """
def convert_from_str(value,type):
def bool_conv(x):
s = str(x).upper()
if s == 'TRUE':
return True
if s == 'FALSE':
return False
if value is not None:
if type == 'str':
return str(value)
elif value.strip() != '':
if type == 'long':
return long(value)
elif type == 'float':
return float(value)
elif type == 'int':
return int(value)
elif type == 'bool':
return bool_conv(value)
elif type == 'base64':
return base64.b64decode(value)
return None
def guess_extension_from_contents(contents):
if contents.startswith("<vistrail"):
return ".xml"
else:
return ".vt"
tree = ElementTree.parse(filename)
node = tree.getroot()
if node.tag != 'vtlink':
return None
#read attributes
data = node.get('host', None)
host = convert_from_str(data, 'str')
data = node.get('port', None)
port = convert_from_str(data,'int')
data = node.get('database', None)
database = convert_from_str(data,'str')
data = node.get('vtid')
vt_id = convert_from_str(data, 'int')
data = node.get('version')
version = convert_from_str(data, 'str')
data = node.get('tag')
tag = convert_from_str(data, 'str')
data = node.get('execute')
execute = convert_from_str(data, 'bool')
data = node.get('showSpreadsheetOnly')
showSpreadsheetOnly = convert_from_str(data, 'bool')
data = node.get('url', None)
url = convert_from_str(data,'str')
data = node.get('vtcontent', None)
vtcontent = convert_from_str(data,'base64')
data = node.get('filename', None)
vtname = convert_from_str(data, 'str')
data = node.get('forceDB',None)
forceDB = convert_from_str(data,'bool')
data = node.get('mashuptrail', None)
mashuptrail = convert_from_str(data, 'str')
data = node.get('mashupVersion', None)
mashupVersion = convert_from_str(data, 'int')
data = node.get('parameterExploration', None)
parameterExploration = convert_from_str(data, 'int')
#if execute is False, we will show the builder too
if showSpreadsheetOnly and not execute:
showSpreadsheetOnly = False
try:
version = int(version)
except (ValueError, TypeError):
pass
if tag is None:
tag = ''
## execute and showSpreadsheetOnly should be written to the current
## configuration
config = get_vistrails_configuration()
config.execute = execute
config.showWindow = not showSpreadsheetOnly
if not forceDB:
if vtcontent is not None:
if url is not None:
basename = url.split('/')[-1]
base,ext = os.path.splitext(basename)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname,basename)
else:
basename = os.path.basename(filename)
base,ext = os.path.splitext(basename)
ext = guess_extension_from_contents(vtcontent)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname,"%s%s"%(base,ext))
create_file = True
if os.path.exists(fname): #file was extracted before
create_file = False
oldf = open(fname)
oldcontents = oldf.read()
if oldcontents != vtcontent:
import vistrails.gui.extras.core.db.locator as db_gui
(overwrite, newname) = \
db_gui.ask_to_overwrite_file(None, 'vistrail')
create_file = True
if newname:
fname = newname
elif overwrite == False:
i=1
while os.path.exists(fname):
newbase = "%s_%s%s" % (base, i, ext)
fname = os.path.join(dirname,newbase)
i+=1
if create_file:
f = open(fname,'wb')
f.write(vtcontent)
f.close()
return FileLocator(fname, version_node=version, version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
if host is not None:
user = ""
passwd = ""
return DBLocator(host, port, database,
user, passwd, None, obj_id=vt_id,
obj_type='vistrail',connection_id=None,
version_node=version, version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
elif vtname is not None:
if os.path.dirname(vtname) == '':
#check if file exists in the same directory as the .vtl file
dirname = os.path.dirname(filename)
newvtname = os.path.join(dirname,vtname)
if os.path.exists(newvtname):
vtname = newvtname
#check for magic strings
if "@examples" in vtname:
vtname=vtname.replace("@examples", vistrails_examples_directory())
return FileLocator(vtname, version_node=version, version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration)
def from_link_file(filename):
"""from_link_file(filename: str) -> DBLocator
This will parse a '.vtl' file and will create a DBLocator. .vtl files
are vistrail link files and they are used to point vistrails to open
vistrails from the database on the web. """
def convert_from_str(value, type):
def bool_conv(x):
s = str(x).upper()
if s == "TRUE":
return True
if s == "FALSE":
return False
if value is not None:
if type == "str":
return str(value)
elif value.strip() != "":
if type == "long":
return long(value)
elif type == "float":
return float(value)
elif type == "int":
return int(value)
elif type == "bool":
return bool_conv(value)
elif type == "base64":
return base64.b64decode(value)
return None
def guess_extension_from_contents(contents):
if contents.startswith("<vistrail"):
return ".xml"
else:
return ".vt"
tree = ElementTree.parse(filename)
node = tree.getroot()
if node.tag != "vtlink":
return None
# read attributes
data = node.get("host", None)
host = convert_from_str(data, "str")
data = node.get("port", None)
port = convert_from_str(data, "int")
data = node.get("database", None)
database = convert_from_str(data, "str")
data = node.get("vtid")
vt_id = convert_from_str(data, "int")
data = node.get("version")
version = convert_from_str(data, "str")
data = node.get("tag")
tag = convert_from_str(data, "str")
data = node.get("execute")
execute = convert_from_str(data, "bool")
data = node.get("showSpreadsheetOnly")
showSpreadsheetOnly = convert_from_str(data, "bool")
data = node.get("url", None)
url = convert_from_str(data, "str")
data = node.get("vtcontent", None)
vtcontent = convert_from_str(data, "base64")
data = node.get("filename", None)
vtname = convert_from_str(data, "str")
data = node.get("forceDB", None)
forceDB = convert_from_str(data, "bool")
data = node.get("mashuptrail", None)
mashuptrail = convert_from_str(data, "str")
data = node.get("mashupVersion", None)
mashupVersion = convert_from_str(data, "int")
data = node.get("parameterExploration", None)
parameterExploration = convert_from_str(data, "int")
# if execute is False, we will show the builder too
if showSpreadsheetOnly and not execute:
showSpreadsheetOnly = False
try:
version = int(version)
except:
pass
if tag is None:
tag = ""
## execute and showSpreadsheetOnly should be written to the current
## configuration
config = get_vistrails_configuration()
config.executeWorkflows = execute
config.showSpreadsheetOnly = showSpreadsheetOnly
if not forceDB:
if vtcontent is not None:
if url is not None:
basename = url.split("/")[-1]
base, ext = os.path.splitext(basename)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname, basename)
else:
basename = os.path.basename(filename)
base, ext = os.path.splitext(basename)
ext = guess_extension_from_contents(vtcontent)
dirname = os.path.dirname(filename)
fname = os.path.join(dirname, "%s%s" % (base, ext))
create_file = True
if os.path.exists(fname): # file was extracted before
create_file = False
oldf = open(fname)
oldcontents = oldf.read()
if oldcontents != vtcontent:
import vistrails.gui.extras.core.db.locator as db_gui
(overwrite, newname) = db_gui.ask_to_overwrite_file(None, "vistrail")
create_file = True
if newname:
fname = newname
elif overwrite == False:
i = 1
while os.path.exists(fname):
newbase = "%s_%s%s" % (base, i, ext)
fname = os.path.join(dirname, newbase)
i += 1
if create_file:
f = open(fname, "wb")
f.write(vtcontent)
f.close()
return FileLocator(
fname,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration,
)
if host is not None:
user = ""
passwd = ""
return DBLocator(
host,
port,
database,
user,
passwd,
None,
obj_id=vt_id,
obj_type="vistrail",
connection_id=None,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration,
)
elif vtname is not None:
if os.path.dirname(vtname) == "":
# check if file exists in the same directory as the .vtl file
dirname = os.path.dirname(filename)
newvtname = os.path.join(dirname, vtname)
if os.path.exists(newvtname):
vtname = newvtname
# check for magic strings
if "@examples" in vtname:
vtname = vtname.replace("@examples", vistrails_examples_directory())
return FileLocator(
vtname,
version_node=version,
version_tag=tag,
mashuptrail=mashuptrail,
mashupVersion=mashupVersion,
parameterExploration=parameterExploration,
)
def record_vistrail(what, vistrail):
"""Record info about a vistrail we used.
"""
if not usage_report.recording:
return
from vistrails.core.vistrail.controller import VistrailController
from vistrails.core.vistrail.pipeline import Pipeline
from vistrails.core.vistrail.vistrail import Vistrail
from vistrails.db.services.locator import XMLFileLocator
if isinstance(vistrail, VistrailController):
vistrail = vistrail.vistrail
if what == 'save':
# Don't report now, but mark it for reporting when it gets closed
saved_vistrails[id(vistrail)] = vistrail
return
elif what == 'close':
i = id(vistrail)
if i in saved_vistrails:
del saved_vistrails[i]
what = 'saved_close'
else:
return
if isinstance(vistrail, Vistrail):
upgrade_from = set()
upgrade_to = set()
nb_notes = 0
nb_paramexplorations = 0
for annotation in vistrail.action_annotations:
if annotation.key == Vistrail.UPGRADE_ANNOTATION:
upgrade_from.add(annotation.action_id)
upgrade_to.add(int(annotation.value))
elif annotation.key == Vistrail.NOTES_ANNOTATION:
nb_notes += 1
elif annotation.key == Vistrail.PARAMEXP_ANNOTATION:
nb_paramexplorations += 1
nb_upgrades = len(upgrade_from - upgrade_to)
if isinstance(vistrail.locator, XMLFileLocator):
usage_report.note({'in_examples_dir':
os.path.realpath(vistrail.locator._name).startswith(
os.path.realpath(vistrails_examples_directory()))})
nb_modules = 0
nb_groups = 0
nb_abstractions = 0
for action in vistrail.actions:
if action.id in upgrade_to or action.description == "Upgrade":
continue
for operation in action.operations:
if operation.vtType == 'add' or operation.vtType == 'change':
if operation.what == 'module':
nb_modules += 1
if operation.data.is_group():
nb_groups += 1
elif operation.data.is_abstraction():
nb_abstractions += 1
usage_report.note(dict(use_vistrail=what,
nb_versions=len(vistrail.actionMap),
nb_tags=len(vistrail.get_tagMap()),
nb_notes=nb_notes,
nb_paramexplorations=nb_paramexplorations,
nb_upgrades=nb_upgrades,
nb_variables=len(vistrail.vistrail_variables),
nb_modules=nb_modules,
nb_groups=nb_groups,
nb_abstractions=nb_abstractions))
for feature in features_for_vistrails.pop(id(vistrail), ()):
usage_report.note({'feature_for_vistrail': feature})
elif isinstance(vistrail, Pipeline):
usage_report.note(dict(use_workflow=what,
nb_modules=len(vistrail.module_list)))
else:
raise TypeError
