def setupTestProject(cls):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(
projName) # Now it will be loaded if exists
cls.outputPath = proj.path
cls.projName = projName
cls.proj = proj
def setupTestProject(cls):
""" Create and setup a Project for a give Test class. """
projName = cls.__name__
if os.environ.get('SCIPION_TEST_CONTINUE', None) == '1':
proj = Manager().loadProject(projName)
else:
proj = Manager().createProject(projName) # Now it will be loaded if exists
cls.outputPath = proj.path
# Create project does not change the working directory anymore
os.chdir(cls.outputPath)
cls.projName = projName
cls.proj = proj
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 run_scipion_qc(movie_file):
manager = Manager()
project = manager.loadProject(PROJECT)
path, pattern = os.path.split(movie_file)
add_movies = project.newProtocol(
ProtImportMovies,
filesPath=path,
filesPattern=pattern,
voltage=VOLTAGE,
samplingRate=SAMPLING_RATE,
)
project.launchProtocol(add_movies, wait=True)
align_movies = project.newProtocol(
ProtMovieAlignment,
inputMovies=add_movies.outputMovies,
)
project.launchProtocol(align_movies, wait=True)
find_ctf = project.newProtocol(
ProtCTFFind,
inputMicrographs=align_movies.outputMicrographs,
)
project.launchProtocol(find_ctf, wait=False)
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 delete_project(request):
manager = Manager()
if request.is_ajax():
projectName = request.GET.get('projectName')
manager.deleteProject(projectName)
return HttpResponse(mimetype='application/javascript')
def delete_project(request):
manager = Manager()
if request.is_ajax():
projectName = getVarFromRequest(request, PROJECT_NAME)
manager.deleteProject(projectName)
return HttpResponse(content_type='application/javascript')
def project_content(request):
projectName = request.GET.get('projectName', None)
if projectName is None:
projectName = request.POST.get('projectName', None)
project = Manager().loadProject(projectName)
context = contentContext(request, project)
context.update({'mode': None, 'formUrl': 'form'})
return render_to_response('project_content/project_content.html', context)
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 project_content(request):
projectName = getVarFromRequest(request, PROJECT_NAME)
mode = getVarFromRequest(request, MODE)
project = Manager().loadProject(projectName, chdir=False)
context = contentContext(request, project)
context.update({'mode': mode, 'formUrl': 'form'})
if mode == MODE_WORKFLOW:
context.update({'nowest': True})
return render_to_response('project_content/project_content.html', context)
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()
def __init__(self, config, **kwargs):
try:
title = '%s (%s on %s)' % (Message.LABEL_PROJECTS,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
title = Message.LABEL_PROJECTS
settings = ProjectSettings()
self.generalCfg = settings.getConfig()
self.config = config
ProjectBaseWindow.__init__(self, title, minsize=(400, 550), **kwargs)
self.viewFuncs = {VIEW_WIZARD: BoxWizardView}
self.manager = Manager()
self.switchView(VIEW_WIZARD)
def _select(self):
projName = self.projName.get().strip()
projLocation = self.projLocation.get().strip()
copyFiles = self.tkCheckVar.get() != 0
searchLocation = self.searchLocation.get().strip()
manager = Manager()
# If project name is empty we will use the same name as the source
if not projName:
projName = os.path.basename(projLocation)
errorMessage = ''
# Validate that project location is not empty
if not projLocation:
errorMessage = "Project location is empty\n"
# Validate that project location exists
elif not os.path.exists(projLocation):
errorMessage += "Project location does not exist\n"
# Validate that project location is a directory
elif not os.path.isdir(projLocation):
errorMessage += "Project location is not a directory\n"
# Validate that the project location is a scipion project folder
elif not os.path.exists(os.path.join(projLocation, PROJECT_DBNAME)):
errorMessage += "Project location doesn't look like a scipion folder\n"
# Validate that there isn't already a project with the same name
if manager.hasProject(projName):
errorMessage += "Project [%s] already exists\n" % projName
# Validate that search location exists
if searchLocation:
if not os.path.exists(searchLocation):
errorMessage += "Raw files location does not exist\n"
# Validate that search location is a directory
elif not os.path.isdir(searchLocation):
errorMessage += "Raw files location is not a directory\n"
if errorMessage:
showError("Validation error", errorMessage, self.root)
else:
self.parent.importProject(projLocation, copyFiles, projName,
searchLocation)
self.close()
def getServiceManager(serviceName):
print "getServiceManager"
print "serviceName: ", serviceName
scipionUserData = os.path.join(os.environ['SCIPION_USER_DATA'],
serviceName)
manager = Manager(SCIPION_USER_DATA=scipionUserData)
serviceConf = os.path.join(os.environ['HOME'], '.config', 'scipion',
serviceName)
manager.config = os.path.join(serviceConf, 'scipion.conf')
manager.protocols = os.path.join(serviceConf, 'protocols.conf')
manager.hosts = os.path.join(serviceConf, 'hosts.conf')
print "config: ", manager.config
print "protocols: ", manager.protocols
print "hosts: ", manager.hosts
return manager
def check_project_id(request):
result = 0
projectName = request.GET.get('code', None)
serviceName = request.GET.get('serviceName', None)
try:
if serviceName is None:
project = Manager().loadProject(projectName)
else:
manager = getServiceManager(serviceName)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
result = 1
except Exception:
pass
return HttpResponse(result, mimetype='application/javascript')
def projects(request):
from pyworkflow.utils.utils import prettyDate
manager = Manager()
projects = manager.listProjects()
for p in projects:
p.pTime = prettyDate(p.mTime)
if 'projectName' in request.session: request.session['projectName'] = ""
if 'projectPath' in request.session: request.session['projectPath'] = ""
context = {
'projects': projects,
'projects_css': getResourceCss('projects'),
'project_utils_js': getResourceJs('project_utils'),
}
context = base_grid(request, context)
return render_to_response('projects.html', context)
def _writeSubset(self, subset):
""" Generated the output of this subset. """
newSubsetName = 'outputParticles_%03d' % self._counter
self.info("Creating new subset: %s" % newSubsetName)
subset.write()
self._defineOutputs(**{newSubsetName: subset})
self._defineTransformRelation(self.inputParticles, subset)
# The following is required to commit the changes to the database
self._store(subset)
subset.close()
from pyworkflow.manager import Manager
manager = Manager()
project = manager.loadProject(self.getProject().getName())
input2D = self.input2dProtocol.get()
copyProt = project.copyProtocol(project.getProtocol(input2D.getObjId()))
copyProt.inputParticles.set(project.getProtocol(self.getObjId()))
copyProt.inputParticles.setExtended(newSubsetName)
project.scheduleProtocol(copyProt, self._runPrerequisites)
# Next schedule will be after this one
self._runPrerequisites.append(copyProt.getObjId())
def getServiceManager(serviceName):
global SERVICE_MANAGERS
manager = SERVICE_MANAGERS.get(serviceName, None)
if manager is None:
print "...Creating new cached Manager"
scipionUserData = os.environ['SCIPION_USER_DATA']
servicePath = '' if serviceName is None else serviceName
scipionUserData = os.path.join(scipionUserData, servicePath)
manager = Manager(SCIPION_USER_DATA=scipionUserData)
serviceConf = os.path.join(os.environ['HOME'], '.config', 'scipion',
servicePath)
manager.config = os.path.join(serviceConf, 'scipion.conf')
manager.protocols = os.path.join(serviceConf, 'protocols.conf')
manager.hosts = os.path.join(serviceConf, 'hosts.conf')
SERVICE_MANAGERS[serviceName] = manager
return manager
def data_content(request):
projectName = request.GET.get('projectName', None)
manager = Manager()
request.session['projectPath'] = manager.getProjectPath(projectName)
project = loadProject(request)
context = {'projectName': projectName,
'editTool': getResourceIcon('edit_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'data_content_utils': getResourceJs('data_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css':getResourceCss('project_content'),
'view':'data'
}
context = base_flex(request, context)
return render_to_response('data_content/data_content.html', context)
def data_content(request):
projectName = getVarFromRequest(request, PROJECT_NAME)
manager = Manager()
request.session[CTX_PROJECT_PATH] = manager.getProjectPath(projectName)
# project = loadProject(request)
context = {CTX_PROJECT_NAME: projectName,
'editTool': getResourceIcon('edit_toolbar'),
'graph_utils': getResourceJs('graph_utils'),
'project_content_utils': getResourceJs('project_content_utils'),
'data_content_utils': getResourceJs('data_content_utils'),
'jquery_cookie': getResourceJs('jquery_cookie'),
'jquery_treeview': getResourceJs('jquery_treeview'),
'project_content_css': getResourceCss('project_content'),
'view': 'data'
}
context = base_flex(request, context)
return render_to_response('data_content/data_content.html', context)
def __init__(self, **kwargs):
# Load global configuration
settings = ProjectSettings()
# TODO: put the menu part more nicely. From here:
menu = MenuConfig()
fileMenu = menu.addSubMenu('File')
fileMenu.addSubMenu('Browse files',
'browse',
icon='fa-folder-open.png')
fileMenu.addSubMenu('Exit', 'exit', icon='fa-sign-out.png')
confMenu = menu.addSubMenu('Configuration')
confMenu.addSubMenu('General', 'general')
confMenu.addSubMenu('Hosts', 'hosts')
confMenu.addSubMenu('Protocols', 'protocols')
confMenu.addSubMenu('User', 'user')
helpMenu = menu.addSubMenu('Help')
helpMenu.addSubMenu('Online help',
'online_help',
icon='fa-external-link.png')
helpMenu.addSubMenu('About', 'about', icon='fa-question-circle.png')
self.menuCfg = menu
self.generalCfg = settings.getConfig()
try:
title = '%s (%s on %s)' % (Message.LABEL_PROJECTS,
pwutils.getLocalUserName(),
pwutils.getLocalHostName())
except Exception:
title = Message.LABEL_PROJECTS
ProjectBaseWindow.__init__(self, title, minsize=(750, 500), **kwargs)
self.manager = Manager()
self.switchView(VIEW_PROJECTS)
def projects(request):
from pyworkflow.utils.utils import prettyDate
manager = Manager()
projectsList = manager.listProjects()
for p in projectsList:
p.pTime = prettyDate(p.mTime)
if CTX_PROJECT_NAME in request.session:
request.session[CTX_PROJECT_NAME] = ""
if CTX_PROJECT_PATH in request.session:
request.session[CTX_PROJECT_PATH] = ""
context = {
'projects': projectsList,
'projects_css': getResourceCss('projects'),
'project_utils_js': getResourceJs('project_utils'),
'workflows': json.dumps(getWorkflowsList())
}
context = base_grid(request, context)
return render_to_response('projects.html', context)
n = len(sys.argv)
if n > 3:
usage("Incorrect number of input parameters")
delete = '--delete' in sys.argv
arg1 = sys.argv[1]
if n > 1 and arg1 != '--delete':
customUserData = arg1
else:
customUserData = os.environ['SCIPION_USER_DATA']
print "Loading projects from:\n", customUserData
# Create a new project
manager = Manager(SCIPION_USER_DATA=customUserData)
for projInfo in manager.listProjects():
projName = projInfo.getName()
proj = manager.loadProject(projName)
settings = proj.getSettings()
leftTime = proj.getLeftTime()
if (leftTime is not None and leftTime.days < 0):
if delete:
print "Deleting: %s (%s) " % (projName, leftTime)
manager.deleteProject(projName)
else:
print "Should delete: %s (%s)" % (projName, leftTime)
def __init__(self, parent, windows, **kwargs):
tk.Frame.__init__(self, parent, bg='white', **kwargs)
self.windows = windows
self.manager = windows.manager
self.root = windows.root
self.vars = {}
self.checkvars = []
self.microscope = None
# Regular expression to validate username and sample name
self.re = re.compile('\A[a-zA-Z][a-zA-Z0-9_-]+\Z')
# tkFont.Font(size=12, family='verdana', weight='bold')
bigSize = pwgui.cfgFontSize + 2
smallSize = pwgui.cfgFontSize - 2
fontName = pwgui.cfgFontName
self.bigFont = tkFont.Font(size=bigSize, family=fontName)
self.bigFontBold = 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()
# Header section
headerFrame = tk.Frame(self, bg='white')
headerFrame.grid(row=0, column=0, sticky='new')
headerText = "Create New Session"
headerText += " %s" % pwutils.prettyTime(dateFormat='%Y-%m-%d')
label = tk.Label(headerFrame,
text=headerText,
font=self.bigFontBold,
borderwidth=0,
anchor='nw',
bg='white',
fg=pwgui.Color.DARK_GREY_COLOR)
label.grid(row=0, column=0, sticky='nw', padx=(20, 5), pady=10)
# Body section
bodyFrame = tk.Frame(self, bg='white')
bodyFrame.grid(row=1, column=0, sticky='news')
self._fillContent(bodyFrame)
# Add the create project button
btnFrame = tk.Frame(self, bg='white')
btn = HotButton(btnFrame,
text="Create New Session",
font=self.bigFontBold,
command=self._onAction)
btn.grid(row=0, column=1, sticky='ne', padx=10, pady=10)
# Add the Import project button
btn = Button(btnFrame,
Message.LABEL_BUTTON_CANCEL,
Icon.ACTION_CLOSE,
font=self.bigFontBold,
command=self.windows.close)
btn.grid(row=0, column=0, sticky='ne', padx=10, pady=10)
btnFrame.grid(row=2, column=0, sticky='sew')
btnFrame.columnconfigure(0, weight=1)
self.columnconfigure(0, weight=1)
self.rowconfigure(1, weight=1)
sys.exit(1)
n = len(sys.argv)
if n <> 2:
usage("This script accepts 1 parameter: the project name.")
projName = sys.argv[1]
path = os.path.join(os.environ['SCIPION_HOME'], 'pyworkflow', '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(projectPath)
project.load()
runs = project.getRuns()
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()