def testExportSteps(self):
manager = Manager()
stepsStats = dict()
for project in manager.listProjects():
projectFolder = manager.getProjectPath(project.projName)
project = Project(pyworkflow.Config.getDomain(), projectFolder)
project.load()
for prot in project.getRuns():
protName = prot.getClassName()
for step in prot.loadSteps():
stepName = "-".join([
prot.getClassPackageName(), protName,
step.funcName.get()
])
stepSeconds = step.getElapsedTime().total_seconds()
if stepName not in stepsStats:
stepsStats[stepName] = []
stepsStats[stepName].append(stepSeconds)
# average steps
for name in stepsStats:
plugin, protClass, step = name.split("-")
stepStats = stepsStats[name]
mean = sum(stepStats) / len(stepStats)
# DO not send mean values if higher than a threshold to keep chart in a decent visualization range
# We are loosing long duration steps, probably due to large
if mean < 30:
bm = Benchmark(time=mean, name="-".join([protClass, step]))
codespeed.sendData(bm)
def openProject(projectName):
""" Opens a scipion project:
:param projectName: Name of a existing project to open,
or "here" to create a project in the current working dir,
or "last" to open the most recent project
"""
manager = Manager()
projName = os.path.basename(projectName)
# Handle special name 'here' to create a project
# from the current directory
if projName == 'here':
cwd = Config.SCIPION_CWD
if " " in cwd:
print("Projects can't have spaces in the name: %s" % cwd)
sys.exit(1)
print("\nYou are trying to create a project here:", pwutils.cyan(cwd))
if os.listdir(cwd):
print(pwutils.red('\nWARNING: this folder is not empty!!!'))
key = input("\nDo you want to create a project here? [y/N]?")
if key.lower().strip() != 'y':
print("\nAborting...")
sys.exit(0)
else:
print("\nCreating project....")
projName = os.path.basename(cwd)
projDir = os.path.dirname(cwd)
manager.createProject(projName, location=projDir)
elif projName == 'last': # Get last project
projects = manager.listProjects()
if not projects:
sys.exit("No projects yet, cannot open the last one.")
projName = projects[0].projName
projPath = manager.getProjectPath(projName)
projWindow = ProjectWindow(projPath)
projWindow.show()
# This fails, since it is triggering matplotlib.pyplot and then import error happens:
# ... pyworkflow/gui/no-tkinter/_tkinter.py: invalid ELF header. If we want this back we might need to
# invest some time "faking" tkinter again for python3.
# path = pw.join('gui', 'no-tkinter')
# sys.path.insert(1, path)
# Create a new project
manager = Manager()
if not manager.hasProject(projName):
usage("There is no project with this name: %s"
% pwutils.red(projName))
# the project may be a soft link which may be unavailable to the cluster so get the real path
try:
projectPath = os.readlink(manager.getProjectPath(projName))
except:
projectPath = manager.getProjectPath(projName)
project = Project(pw.Config.getDomain(), projectPath)
project.load()
runs = project.getRuns()
# Now assuming that there is no dependencies between runs
# and the graph is lineal
for prot in runs:
protClassName = prot.getClassName()
protLabelName = prot.getObjLabel()
if (protClassName not in sys.argv[3:] and
protLabelName not in sys.argv[3:]):
"""
Launch main project window
"""
import pickle
import sys
import os
from pyworkflow.project import Manager, Label
from pyworkflow.gui.project import ProjectWindow
if __name__ == '__main__':
manager = Manager()
projName = os.path.basename(sys.argv[1])
projPath = manager.getProjectPath(projName)
projWindow = ProjectWindow(projPath)
proj = projWindow.project
sett = proj.getSettings()
sett.setColorMode(sett.COLOR_MODE_LABELS)
with open(proj.getPath('labels.pkl'), 'r') as f:
labelsDict, colorsDict = pickle.load(f)
for labelName, prots in labelsDict.iteritems():
label = Label(name=labelName, color=colorsDict[labelName])
sett.getLabels().addLabel(label)
for protId in prots:
node = sett.getNodeById(protId)
jsonFn = os.path.abspath(sys.argv[1])
now = datetime.now()
tempSpace = "editor-%s" % now.strftime('%Y%m%d-%H%M%S')
customUserData = os.path.join(pw.Config.SCIPION_USER_DATA, 'tmp', tempSpace)
pwutils.makePath(os.path.join(customUserData, 'projects'))
print("Loading projects from:\n", customUserData)
# Create a new project
manager = Manager(workspace=customUserData)
projName = os.path.basename(jsonFn)
proj = manager.createProject(projName)
projPath = manager.getProjectPath(proj.getShortName())
proj.loadProtocols(jsonFn)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print("Writing protocols to: ", jsonFn)
proj.getRunsGraph(refresh=True) # Build project runs graph
proj.exportProtocols(proj.getRuns(), jsonFn)
print("Deleting temporary folder: ", customUserData)
pwutils.cleanPath(customUserData)
except Exception as ex:
print("Error saving the workflow: ", ex)
ProjectWindow.close(self, e)
