def create_project(request):
manager = Manager()
if request.is_ajax():
projectName = request.GET.get('projectName')
manager.createProject(projectName)
return HttpResponse(mimetype='application/javascript')
def create_project(request):
manager = Manager()
if request.is_ajax():
projectName = request.GET.get('projectName')
manager.createProject(projectName)
return HttpResponse(mimetype='application/javascript')
def create_project(request):
manager = Manager()
if request.is_ajax():
projectName = getVarFromRequest(request, PROJECT_NAME)
workflow = getVarFromRequest(request, WORKFLOW)
manager.createProject(projectName, chdir=False, workflow=workflow)
return HttpResponse(content_type='application/javascript')
def test_createNoChdir(self):
"""Test the list with several Complex"""
cwd = os.getcwd()
manager = Manager()
projectName = "TestProjectCreate"
project = manager.createProject(projectName, chdir=False)
dataset = DataSet.getDataSet('emx')
prot1 = project.newProtocol(
em.ProtImportParticles,
objLabel='from emx (coordinatesT1)',
importFrom=em.ProtImportParticles.IMPORT_FROM_EMX,
emxFile=dataset.getFile('coordinatesT1'),
alignType=3,
voltage=100,
magnification=10000,
samplingRate=2.46)
project.launchProtocol(prot1, wait=True)
# Execute a copy of prot1
prot2 = project.copyProtocol(prot1)
project.launchProtocol(prot2, wait=True)
# Now restart prot2
prot2.runMode.set(MODE_RESTART)
project.launchProtocol(prot2, wait=True)
#self.assertEqual(cwd, project.getPath())
self.assertEqual(cwd, os.getcwd())
def test_create(self):
"""Test the list with several Complex"""
cwd = os.getcwd()
manager = Manager()
projectName = "TestProjectCreate"
project = manager.createProject(projectName)
self.assertNotEqual(cwd, os.getcwd())
self.assertEqual(project.getPath(), os.getcwd())
os.chdir(cwd)
manager.deleteProject(projectName)
def __init__(self):
projName = self.__class__.__name__
manager = Manager()
if manager.hasProject(projName):
self.project = manager.loadProject(projName)
else:
self.project = manager.createProject(projName)
# Use graph view as default
settings = self.project.getSettings()
settings.setRunsView(1) # graph view
settings.write()
self.loadWorkflow()
n = len(sys.argv)
if n < 2 or n > 5:
usage("Incorrect number of input parameters")
fromLocation = sys.argv[1]
projName = fromLocation.rsplit('/', 1)[-1] if n < 3 else sys.argv[2]
jsonFile = None if n < 4 else os.path.abspath(sys.argv[3])
location = None if n < 5 else sys.argv[4]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'gui',
'no-tkinter')
sys.path.insert(1, path)
# Create a new project
manager = Manager()
# if manager.hasProject(projName):
# usage("There is already a project with this name: %s"
# % pwutils.red(projName))
project = manager.createProject(projName, location=location)
# copy sqlite and make links of runs
pwutils.copyFile(os.path.join(fromLocation, PROJECT_DBNAME), project.path)
fromRuns = os.path.join(fromLocation, PROJECT_RUNS)
for r in os.listdir(fromRuns):
print " %s,%s" % (os.path.join(fromRuns,
r), os.path.join(project.runsPath, r))
pwutils.createAbsLink(os.path.join(fromRuns, r),
os.path.join(project.runsPath, r))
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(os.environ['SCIPION_USER_DATA'],
'tmp', tempSpace)
pwutils.makePath(os.path.join(customUserData, 'projects'))
print "Loading projects from:\n", customUserData
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
projName = os.path.basename(jsonFn)
proj = manager.createProject(projName)
projPath = manager.getProjectPath(projName)
proj.loadProtocols(jsonFn)
class EditorProjectWindow(ProjectWindow):
def close(self, e=None):
try:
print "Writing protocols to: ", jsonFn
proj.getRunsGraph() # Build project runs graph
proj.exportProtocols(proj.getRuns(), jsonFn)
print "Deleting temporary folder: ", customUserData
pwutils.cleanPath(customUserData)
except Exception, ex:
print "Error saving the workflow: ", ex
ProjectWindow.close(self, e)
def _createScipionProject(self, projName, projPath, scipionProjPath):
manager = Manager()
project = manager.createProject(projName, location=scipionProjPath)
self.lastProt = None
pattern = self._getConfValue(PATTERN)
smtpServer = self._getConfValue(SMTP_SERVER, '')
smtpFrom = self._getConfValue(SMTP_FROM, '')
smtpTo = self._getConfValue(SMTP_TO, '')
doMail = self._getValue(EMAIL_NOTIFICATION)
doPublish = self._getValue(HTML_REPORT)
protImport = project.newProtocol(em.ProtImportMovies,
objLabel='Import movies',
filesPath=projPath,
filesPattern=pattern,
sphericalAberration=self._getConfValue(CS),
dataStreaming=True)
# Should I publish html report?
if doPublish == 1:
publish = self._getConfValue('HTML_PUBLISH')
print("\n\nReport available at URL: %s/%s\n\n"
%('http://scipion.cnb.csic.es/scipionbox',projName))
else:
publish = ''
protMonitor = project.newProtocol(em.ProtMonitorSummary,
objLabel='Summary Monitor',
doMail=doMail,
emailFrom=smtpFrom,
emailTo=smtpTo,
smtp=smtpServer,
publishCmd=publish)
def _saveProtocol(prot, movies=True, monitor=True):
if movies:
prot.inputMovies.set(self.lastProt)
prot.inputMovies.setExtended('outputMovies')
project.saveProtocol(prot)
self.lastProt = prot
if monitor:
protMonitor.inputProtocols.append(prot)
_saveProtocol(protImport, movies=False)
useMC2 = self._getValue(MOTIONCOR2)
useMC = self._getValue(MOTIONCORR) or useMC2
useOF = self._getValue(OPTICAL_FLOW)
useSM = self._getValue(SUMMOVIE)
useCTF = self._getValue(CTFFIND4)
useGCTF = self._getValue(GCTF)
kwargs = {}
frames = self._getValue(FRAMES_RANGE).split()
if frames:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = frames[0]
kwargs['alignFrameN'] = kwargs['sumFrameN'] = frames[1]
if useMC:
# Create motioncorr
from pyworkflow.em.packages.motioncorr import ProtMotionCorr
protMC = project.newProtocol(ProtMotionCorr,
objLabel='Motioncorr',
useMotioncor2=useMC2,
**kwargs)
_saveProtocol(protMC)
if useOF:
# Create Optical Flow protocol
from pyworkflow.em.packages.xmipp3 import XmippProtOFAlignment
protOF = project.newProtocol(XmippProtOFAlignment,
objLabel='Optical Flow',
doSaveMovie=useSM,
**kwargs)
_saveProtocol(protOF)
if useSM:
# If OF write the movie, then we need to reset frames count
if frames and useOF:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = 1
kwargs['alignFrameN'] = kwargs['sumFrameN'] = 0
from pyworkflow.em.packages.grigoriefflab import ProtSummovie
protSM = project.newProtocol(ProtSummovie,
objLabel='Summovie',
cleanInputMovies=useOF,
numberOfThreads=1,
**kwargs)
_saveProtocol(protSM)
lastBeforeCTF = self.lastProt
if useCTF:
from pyworkflow.em.packages.grigoriefflab import ProtCTFFind
protCTF = project.newProtocol(ProtCTFFind,
objLabel='Ctffind',
numberOfThreads=1)
protCTF.inputMicrographs.set(lastBeforeCTF)
protCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protCTF, movies=False)
if useGCTF:
from pyworkflow.em.packages.gctf import ProtGctf
protGCTF = project.newProtocol(ProtGctf,
objLabel='Gctf')
protGCTF.inputMicrographs.set(lastBeforeCTF)
protGCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protGCTF, movies=False)
project.saveProtocol(protMonitor)
os.system('%s project %s &' % (pw.getScipionScript(), projName))
self.windows.close()
def _createScipionProject(self, projName, projPath, scipionProjPath):
manager = Manager()
project = manager.createProject(projName, location=scipionProjPath)
self.lastProt = None
pattern = self._getConfValue(PATTERN)
smtpServer = self._getConfValue(SMTP_SERVER, '')
smtpFrom = self._getConfValue(SMTP_FROM, '')
smtpTo = self._getConfValue(SMTP_TO, '')
doMail = self._getValue(EMAIL_NOTIFICATION)
doPublish = self._getValue(HTML_REPORT)
protImport = project.newProtocol(
em.ProtImportMovies,
objLabel='Import movies',
filesPath=projPath,
filesPattern=pattern,
sphericalAberration=self._getConfValue(CS),
dataStreaming=True)
# Should I publish html report?
if doPublish == 1:
publish = self._getConfValue('HTML_PUBLISH')
print("\n\nReport available at URL: %s/%s\n\n" %
('http://scipion.cnb.csic.es/scipionbox', projName))
else:
publish = ''
protMonitor = project.newProtocol(em.ProtMonitorSummary,
objLabel='Summary Monitor',
doMail=doMail,
emailFrom=smtpFrom,
emailTo=smtpTo,
smtp=smtpServer,
publishCmd=publish)
def _saveProtocol(prot, movies=True, monitor=True):
if movies:
prot.inputMovies.set(self.lastProt)
prot.inputMovies.setExtended('outputMovies')
project.saveProtocol(prot)
self.lastProt = prot
if monitor:
protMonitor.inputProtocols.append(prot)
_saveProtocol(protImport, movies=False)
useMC2 = self._getValue(MOTIONCOR2)
useMC = self._getValue(MOTIONCORR) or useMC2
useOF = self._getValue(OPTICAL_FLOW)
useSM = self._getValue(SUMMOVIE)
useCTF = self._getValue(CTFFIND4)
useGCTF = self._getValue(GCTF)
kwargs = {}
frames = self._getValue(FRAMES_RANGE).split()
if frames:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = frames[0]
kwargs['alignFrameN'] = kwargs['sumFrameN'] = frames[1]
if useMC:
# Create motioncorr
from pyworkflow.em.packages.motioncorr import ProtMotionCorr
protMC = project.newProtocol(ProtMotionCorr,
objLabel='Motioncorr',
useMotioncor2=useMC2,
**kwargs)
_saveProtocol(protMC)
if useOF:
# Create Optical Flow protocol
from pyworkflow.em.packages.xmipp3 import XmippProtOFAlignment
protOF = project.newProtocol(XmippProtOFAlignment,
objLabel='Optical Flow',
doSaveMovie=useSM,
**kwargs)
_saveProtocol(protOF)
if useSM:
# If OF write the movie, then we need to reset frames count
if frames and useOF:
kwargs['alignFrame0'] = kwargs['sumFrame0'] = 1
kwargs['alignFrameN'] = kwargs['sumFrameN'] = 0
from pyworkflow.em.packages.grigoriefflab import ProtSummovie
protSM = project.newProtocol(ProtSummovie,
objLabel='Summovie',
cleanInputMovies=useOF,
numberOfThreads=1,
**kwargs)
_saveProtocol(protSM)
lastBeforeCTF = self.lastProt
if useCTF:
from pyworkflow.em.packages.grigoriefflab import ProtCTFFind
protCTF = project.newProtocol(ProtCTFFind,
objLabel='Ctffind',
numberOfThreads=1)
protCTF.inputMicrographs.set(lastBeforeCTF)
protCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protCTF, movies=False)
if useGCTF:
from pyworkflow.em.packages.gctf import ProtGctf
protGCTF = project.newProtocol(ProtGctf, objLabel='Gctf')
protGCTF.inputMicrographs.set(lastBeforeCTF)
protGCTF.inputMicrographs.setExtended('outputMicrographs')
_saveProtocol(protGCTF, movies=False)
project.saveProtocol(protMonitor)
os.system('%s project %s &' % (pw.getScipionScript(), projName))
self.windows.close()
class ProjectsView(tk.Frame):
def __init__(self, parent, windows, **args):
tk.Frame.__init__(self, parent, bg='white', **args)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
#tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.projNameFont = tkFont.Font(size=bigSize, family=fontName, weight='bold')
self.projDateFont = tkFont.Font(size=smallSize, family=fontName)
self.projDelFont = tkFont.Font(size=smallSize, family=fontName, weight='bold')
self.manager = Manager()
btn = HotButton(self, text=Message.LABEL_CREATE_PROJECT, font=self.projNameFont,
command=self._onCreateProject)
btn.grid(row=0, column=0, sticky='nw', padx=10, pady=10)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
text = TaggedText(self, width=40, height=15, bd=0, bg='white')
text.grid(row=1, column=0, sticky='news')
self.createProjectList(text)
text.setReadOnly(True)
self.text = text
def createProjectList(self, text):
"""Load the list of projects"""
r = 0
text.setReadOnly(False)
text.clear()
parent = tk.Frame(text, bg='white')
parent.columnconfigure(0, weight=1)
colors = ['white', '#EAEBFF']
for i, p in enumerate(self.manager.listProjects()):
project = self.manager.loadProject(p.getName(), chdir=False)
# Add creation time to project info
p.cTime = project.getCreationTime()
frame = self.createProjectLabel(parent, p, color=colors[i%2])
frame.grid(row=r, column=0, padx=10, pady=5, sticky='new')
r += 1
text.window_create(tk.INSERT, window=parent)
text.bindWidget(parent)
text.setReadOnly(True)
def createProjectLabel(self, parent, projInfo, color):
frame = tk.Frame(parent, bg=color)
label = tk.Label(frame, text=projInfo.projName, anchor='nw', bg=color,
justify=tk.LEFT, font=self.projNameFont, cursor='hand1', width=50)
label.grid(row=0, column=0, padx=2, pady=2, sticky='nw')
label.bind('<Button-1>', lambda e: self.openProject(projInfo.projName))
dateMsg = '%s%s %s%s' % (Message.LABEL_MODIFIED, prettyDate(projInfo.mTime),
Message.LABEL_CREATED, prettyTime(projInfo.cTime, time=False))
dateLabel = tk.Label(frame, text=dateMsg, font=self.projDateFont, bg=color)
dateLabel.grid(row=1, column=0, sticky='nw')
delLabel = tk.Label(frame, text=Message.LABEL_DELETE_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
delLabel.grid(row=1, column=1, padx=10)
delLabel.bind('<Button-1>', lambda e: self.deleteProject(projInfo.projName))
mvLabel = tk.Label(frame, text=Message.LABEL_RENAME_PROJECT, font=self.projDelFont, bg=color, cursor='hand1')
mvLabel.grid(row=1, column=2)
mvLabel.bind('<Button-1>', lambda e: self.renameProject(projInfo.projName))
return frame
def createNewProject(self, projName, projLocation):
self.manager.createProject(projName, location=projLocation)
self.createProjectList(self.text)
self.openProject(projName)
def _onCreateProject(self, e=None):
projWindow = ProjectCreateWindow("Create project", self)
projWindow.show()
def openProject(self, projName):
from subprocess import Popen
script = pw.join('apps', 'pw_project.py')
Popen([os.environ['SCIPION_PYTHON'], script, projName])
def deleteProject(self, projName):
if askYesNo(Message.TITLE_DELETE_PROJECT,
"Project *%s*. " % projName + Message.MESSAGE_DELETE_PROJECT, self.root):
self.manager.deleteProject(projName)
self.createProjectList(self.text)
def renameProject(self, projName):
newName = askString("Rename project %s" % projName, "Enter new name:", self.root)
if not newName or newName == projName:
return
if self.manager.hasProject(newName):
showError("Rename cancelled",
"Project name already exists: %s" % newName, self.root)
return
self.manager.renameProject(projName, newName)
self.createProjectList(self.text)
if projName == 'here':
cwd = os.environ['SCIPION_CWD']
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 = raw_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)
proj = 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)
try:
projWindow = ProjectWindow(projPath)
except Exception as e:
# Print any exception
print("ERROR: At pw_project.py loading Project %s.\n"
" Message: %s\n" % (projPath, e))
""" % error
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 4:
usage("Incorrect number of input parameters")
projName = sys.argv[1]
jsonFile = None if n < 3 else os.path.abspath(sys.argv[2])
location = None if n < 4 else sys.argv[3]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', 'gui', 'no-tkinter')
sys.path.insert(1, path)
# Create a new project
manager = Manager()
if manager.hasProject(projName):
usage("There is already a project with this name: %s"
% pwutils.red(projName))
if jsonFile is not None and not os.path.exists(jsonFile):
usage("Unexistent json file: %s" % pwutils.red(jsonFile))
project = manager.createProject(projName, location=location)
if jsonFile is not None:
protDict = project.loadProtocols(jsonFile)
ERROR: %s
Usage: scipion python new-session-aarhus.py workflow.json PROJECT_FOLDER
""" % error)
sys.exit(1)
n = len(sys.argv)
if n < 2 or n > 3:
usage("Incorrect number of input parameters")
scipionProjPath = sys.argv[2] if n == 3 else None
jsonFn = os.path.abspath(sys.argv[1])
now = datetime.now()
projName = "scipion-%s" % now.strftime('%Y%m%d-%H%M%S')
print("Creating project: ", projName)
# Create a new project
manager = Manager()
proj = manager.createProject(projName, location=scipionProjPath)
projPath = manager.getProjectPath(projName)
proj.loadProtocols(jsonFn)
projWindow = ProjectWindow(projPath)
projWindow.show()
parser.add_argument('directory', type=str, help='Directory to monitor')
args = parser.parse_args()
PROJECT = args.project
VOLTAGE = args.voltage
SAMPLING_RATE = args.sampling_rate
PROCESSES = args.processes
POOL = Pool(processes=PROCESSES)
# Create or load project
manager = Manager()
if manager.hasProject(PROJECT):
project = manager.loadProject(PROJECT)
else:
project = manager.createProject(PROJECT)
# First, start up watchdog
event_handler = MyEventHandler()
observer = Observer()
observer.schedule(event_handler, path=args.directory, recursive=False)
observer.start()
print('Watchdog started; to exit, press Control-C')
# Second, run all existing files
for f in os.listdir(args.directory):
try:
ext = os.path.splitext(f)[1].split('.')[1]
if ext in ACCEPTED_EXTENSIONS:
full_path = os.path.join(args.directory,
os.listdir(args.directory)[0])
