scipion-pyworkflow 3.3.1__tar.gz → 3.5.0__tar.gz

{scipion-pyworkflow-3.3.1/scipion_pyworkflow.egg-info → scipion-pyworkflow-3.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipion-pyworkflow
-Version: 3.3.1
+Version: 3.5.0
 Summary: Simple workflow platform used in scientific applications, initially developed within the Scipion framework for image processing in Electron Microscopy.
 Home-page: https://github.com/scipion-em/scipion-pyworkflow
 Author: J.M. De la Rosa Trevin, Roberto Marabini, Grigory Sharov, Josue Gomez Blanco, Pablo Conesa, Yunior Fonseca Reyna

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/apps/pw_project.py

@@ -36,19 +36,14 @@ from pyworkflow.project import Manager
 from pyworkflow.gui.project import ProjectWindow
 import pyworkflow.utils as pwutils
 
-import logging
-
 HERE = 'here'
-
 LAST = 'last'
-
 LIST = 'list'
-logger = logging.getLogger(__name__)
 
 def openProject(projectName):
     """ Opens a scipion project:
 
-    :param projectName: Name of a existing project to open,
+    :param projectName: Name of an existing project to open,
             or "here" to create a project in the current working dir,
             or "last" to open the most recent project
 
@@ -97,7 +92,7 @@ def openProject(projectName):
         projWindow = ProjectWindow(projPath)
         projWindow.show()
     else:
-        logger.error("Can't open project %s. It does not exist" % projPath)
+        print("Can't open project %s. It does not exist" % projPath)
 
         #Show the list of projects
         showProjectList(manager)
@@ -115,4 +110,4 @@ if __name__ == '__main__':
     if len(sys.argv) > 1:
         openProject(sys.argv[1])
     else:
-        logger.info("usage: pw_project.py PROJECT_NAME or %s or %s or %s" % (HERE, LAST, LIST))
+        print("usage: pw_project.py PROJECT_NAME or %s or %s or %s" % (HERE, LAST, LIST))

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/config.py

@@ -1,4 +1,4 @@
-
+import enum
 import logging
 logger = logging.getLogger(__file__)
 import ast
@@ -20,12 +20,15 @@ def join(*paths):
     return os.path.join(HOME, *paths)
 
 
-__resourcesPath = [join('resources')]
+__resourcesPath = join('resources')
+
+def getResourcesPath(file=None):
 
+    return __resourcesPath if file is None else os.path.join(__resourcesPath, file)
 
 def findResource(filename):
     from .utils.path import findFile
-    return findFile(filename, *__resourcesPath)
+    return findFile(filename, *[__resourcesPath])
 
 
 def genNotesHeading():
@@ -62,6 +65,49 @@ def getModuleFolder(moduleName):
     spec = importlib.util.find_spec(moduleName)
     return os.path.dirname(spec.origin)
 
+class VarTypes(enum.Enum):
+    STRING = 1
+    INTEGER = 2
+    BOOLEAN = 3
+    PATH = 4
+
+class Variable(object):
+    """ Class for variables of the Config class."""
+    def __init__(self, value, varType:VarTypes=VarTypes.STRING):
+        """
+        :param value: Value of the variable
+        :param type: Type of the variable"""
+        super().__init__()
+        self.value = value
+        self.varType = varType
+    def __bool__(self):
+        return bool(self.value)
+
+    def __int__(self):
+        return int(self.value)
+    def __str__(self):
+        return str(self.value)
+
+    def __eq__(self, other):
+        return other == self.value
+
+    def __repr__(self):
+        return self.__str__()
+
+    def __fspath__(self):
+        return self.__str__()
+
+    " We migth need to imlement more like this--> https://docs.python.org/3.3/reference/datamodel.html#object.__truediv__"
+    def __truediv__(self, other):
+        return float(self.value)/other
+
+    def __rtruediv__(self, other):
+        return  other / float(self.value)
+
+    def __add__(self, other):
+        return self.value+other
+    def __radd__(self, other):
+        return other+self.value
 
 class Config:
     """ Main Config for pyworkflow. It contains the main Scipion configuration variables
@@ -104,7 +150,7 @@ class Config:
     SCIPION_HOME_DEFINED = _get(SCIPION_HOME_VAR, False)
     "False if SCIPION_HOME is not found in the environment"
 
-    _root = Root(SCIPION_HOME)
+    _root = Root(str(SCIPION_HOME))
     _join = _root.join
 
     # Internal cached variables, use __ so they are not returned in getVars
@@ -157,8 +203,6 @@ class Config:
 
     SCIPION_SUPPORT_EMAIL = _get('SCIPION_SUPPORT_EMAIL', 'scipion@cnb.csic.es')
 
-    SCIPION_LOGO = _get('SCIPION_LOGO', 'scipion_logo.gif')
-
     # Config variables
     SCIPION_CONFIG = _get('SCIPION_CONFIG', 'scipion.conf')
     "Path to the scipion configuration file where all this variables could be defined."
@@ -209,6 +253,15 @@ class Config:
     WIZARD_MASK_COLOR = _get('WIZARD_MASK_COLOR', '[0.125, 0.909, 0.972]')
     "Color to use in some wizards."
 
+    SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', _join(getResourcesPath(),'sprites.png'))
+    "File (png) with the icons in a collage. Default is found at pyworkflow/resources/sprites.png. And a GIMP file could be found at the same folder in the github repo."
+
+    SCIPION_SHOW_TEXT_IN_TOOLBAR = _get('SCIPION_SHOW_TEXT_IN_TOOLBAR', TRUE_STR) == TRUE_STR
+    "Define it to anything else except False to show the label of the icons. It will take more space."
+
+    SCIPION_ICON_ZOOM = int(_get('SCIPION_ICON_ZOOM', 50))
+    "Define it to anything else except False to show the label of the icons. It will take more space."
+
     # Notification
     SCIPION_NOTIFY = _get('SCIPION_NOTIFY', TRUE_STR) == TRUE_STR
     "If set to False, Scipion developers will know almost nothing about Scipion usage and will have less information to improve it."
@@ -249,6 +302,12 @@ class Config:
     SCIPION_USE_QUEUE = _get("SCIPION_USE_QUEUE", FALSE_STR) != FALSE_STR
     "Default value for using the queue. By default is False. ANY value will be True except and empty value. \"False\" or \"0\" will be True too."
 
+    SCIPION_DEFAULT_EXECUTION_ACTION = int(_get('SCIPION_DEFAULT_EXECUTION_ACTION', DEFAULT_EXECUTION_ACTION_ASK))
+    """Ask if you want to launch a single protocol or a sub-workflow. The default value is 1
+       1: Scipion always ask
+       2: Run a single protocol
+       3: Run a sub-workflow """
+
     try:
         VIEWERS = ast.literal_eval(_get('VIEWERS', "{}"))
     except Exception as e:
@@ -300,7 +359,7 @@ class Config:
             for name, value in vars(baseCls).items():
                 # Skip methods and internal attributes starting with __
                 # (e.g __doc__, __module__, etc)
-                if (isinstance(value, str) or isinstance(value, int)) and not name.startswith('__'):
+                if isinstance(value, (str, int, Variable)) and not name.startswith('__'):
                     configVars[name] = str(value)
         return configVars
 
@@ -354,7 +413,8 @@ class Config:
 
     @staticmethod
     def debugSQLOn():
-        return Config.debugOn()
+        from .utils import envVarOn
+        return bool(envVarOn(SCIPION_DEBUG_SQLITE))
 
     @staticmethod
     def toggleDebugSQL():

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/constants.py

@@ -42,7 +42,7 @@ VERSION_1 = '1.0.0'
 VERSION_1_1 = '1.1.0'
 VERSION_1_2 = '1.2.0'
 VERSION_2_0 = '2.0.0'
-VERSION_3_0 = '3.3.1'
+VERSION_3_0 = '3.5.0'
 
 # For a new release, define a new constant and assign it to LAST_VERSION
 # The existing one has to be added to OLD_VERSIONS list.
@@ -198,3 +198,12 @@ class TK:
     LEFT_DOUBLE_CLICK = '<Double-1>'
     TREEVIEW_OPEN = '<<TreeviewOpen>>'
     TREEVIEW_CLOSE = '<<TreeviewClose>>'
+
+
+HELP_DURATION_FORMAT = "Duration format example: 1d 20h 30m 30s --> 1 day 20 hours 30 minutes and 30 seconds"
+
+# Run protocol modes
+DEFAULT_EXECUTION_ACTION_ASK = 1
+DEFAULT_EXECUTION_ACTION_SINGLE = 2
+DEFAULT_EXECUTION_ACTION_ALL = 3
+

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/gui/browser.py

@@ -34,6 +34,7 @@ import stat
 import tkinter as tk
 import time
 import logging
+
 logger = logging.getLogger(__name__)
 
 import pyworkflow.utils as pwutils
@@ -124,7 +125,7 @@ class ObjectBrowser(tk.Frame):
         img, desc = self.treeProvider.getObjectPreview(obj)
         # Update image preview
         if self.showPreviewTop:
-            if isinstance(img, str):
+            if isinstance(img, (str, pwutils.SpriteImage)):
                 img = self.getImage(img)
             if img is None:
                 img = self.noImage
@@ -716,13 +717,4 @@ class FileBrowserWindow(BrowserWindow):
                  '.txt', '.log', '.out', '.err', '.stdout', '.stderr', '.emx',
                  '.json', '.xml', '.pam')
         register(TextFileHandler(pwutils.Icon.PYTHON_FILE), '.py')
-        register(TextFileHandler(pwutils.Icon.JAVA_FILE), '.java')
-        register(SqlFileHandler(), '.sqlite', '.db')
-        # register(MdFileHandler(), '.xmd', '.star', '.pos', '.ctfparam', '.doc')
-        # register(ParticleFileHandler(),
-        #          '.xmp', '.tif', '.tiff', '.spi', '.mrc', '.map', '.raw',
-        #          '.inf', '.dm3', '.em', '.pif', '.psd', '.spe', '.ser', '.img',
-        #          '.hed', *STANDARD_IMAGE_EXTENSIONS)
-        # register(VolFileHandler(), '.vol')
-        # register(StackHandler(), '.stk', '.mrcs', '.st', '.pif', '.dm4')
-        # register(ChimeraHandler(), '.bild')
+        register(SqlFileHandler(), '.sqlite', '.db')

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/gui/canvas.py

@@ -134,7 +134,7 @@ class Canvas(tk.Canvas, Scrollable):
         return self._runsFont
 
     def getImage(self, img):
-        return gui.getImage(img, self._images)
+        return gui.getImage(img)
 
     def _unpostMenu(self, e=None):
         self._menu.unpost()

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/gui/dialog.py

@@ -34,7 +34,7 @@ from tkcolorpicker import askcolor as _askColor
 from pyworkflow import Config
 from pyworkflow.exceptions import PyworkflowException
 from pyworkflow.utils import Message, Icon, Color
-from . import gui, Window, widgets, configureWeigths, LIST_TREEVIEW, defineStyle
+from . import gui, Window, widgets, configureWeigths, LIST_TREEVIEW, defineStyle, ToolTip
 from .tree import BoundTree, Tree
 from .text import Text, TaggedText
 
@@ -58,7 +58,7 @@ class Dialog(tk.Toplevel):
     An image name can be passed to display left to the message.
     """
 
-    def __init__(self, parent, title, **kwargs):
+    def __init__(self, parent, title, lockGui=True, **kwargs):
         """Initialize a dialog.
         Arguments:
             parent -- a parent window (the application window)
@@ -82,7 +82,7 @@ class Dialog(tk.Toplevel):
         # If the master is not viewable, don't
         # make the child transient, or else it
         # would be opened withdrawn
-        if parent.winfo_viewable():
+        if parent.winfo_viewable() and lockGui:
             self.transient(parent)
 
         if title:
@@ -102,7 +102,7 @@ class Dialog(tk.Toplevel):
         # Frame for the info/message label
         infoFrame = tk.Frame(self)
         infoFrame.grid(row=1, column=0, sticky='sew',
-                      padx=5, pady=(0, 5))
+                       padx=5, pady=(0, 5))
         self.floatingMessage = tk.Label(infoFrame, text="", fg=Config.SCIPION_MAIN_COLOR)
         self.floatingMessage.grid(row=0, column=0, sticky='news')
 
@@ -141,7 +141,8 @@ class Dialog(tk.Toplevel):
         # window ".139897767953072.139897384058440" was deleted before its visibility changed
         # wait for window to appear on screen before calling grab_set
         self.wait_visibility()
-        self.grab_set()
+        if lockGui:
+            self.grab_set()
         self.wait_window(self)
 
     def destroy(self):
@@ -191,7 +192,8 @@ class Dialog(tk.Toplevel):
         self.result = resultValue
         noCancel = self.result != RESULT_CANCEL and self.result != RESULT_CLOSE
 
-        if noCancel and not self.validate():
+        callBack = self.validate if noCancel else self.validateClose
+        if not callBack():
             self.initial_focus.focus_set()  # put focus back
             return
 
@@ -227,6 +229,9 @@ class Dialog(tk.Toplevel):
         """
         return 1  # override
 
+    def validateClose(self):
+        return True
+
     def apply(self):
         """process the data
         This method is called automatically to process the data, *after*
@@ -236,7 +241,7 @@ class Dialog(tk.Toplevel):
 
     def getImage(self, imgName):
         """A shortcut to get an image from its name"""
-        return gui.getImage(imgName, self._images)
+        return gui.getImage(imgName)
 
     def getResult(self):
         return self.result
@@ -328,7 +333,7 @@ class ExceptionDialog(MessageDialog):
             detailsText = TaggedText(bodyFrame, bg=Config.SCIPION_BG_COLOR, bd=0, highlightthickness=0)
             traceStr = traceback.format_exc()
             fillMessageText(detailsText, traceStr)
-            detailsText.frame.grid(row=row+1, column=0, columnspan=2, sticky='news', padx=5, pady=5)
+            detailsText.frame.grid(row=row + 1, column=0, columnspan=2, sticky='news', padx=5, pady=5)
             event.widget.grid_forget()
 
         row = 1
@@ -337,7 +342,7 @@ class ExceptionDialog(MessageDialog):
             if isinstance(self._exception, PyworkflowException):
                 helpUrl = self._exception.getUrl()
                 labelUrl = TaggedText(bodyFrame, bg=Config.SCIPION_BG_COLOR, bd=0, highlightthickness=0)
-                fillMessageText(labelUrl,"Please go here for more details: %s" % helpUrl)
+                fillMessageText(labelUrl, "Please go here for more details: %s" % helpUrl)
                 labelUrl.grid(row=row, column=0, columnspan=2, sticky='news')
                 row += 1
 
@@ -621,7 +626,7 @@ class ListDialog(Dialog):
 
     def _createPreviewPanel(self, parent):
         self.previewFrame = tk.Frame(parent)
-        self.previewFrame.grid(row=1,column=1)
+        self.previewFrame.grid(row=1, column=1)
 
     def _createFilterBox(self, content):
         """ Create the Frame with Filter widgets """
@@ -696,11 +701,12 @@ class ToolbarButton:
     Store information about the buttons that will be added to the toolbar.
     """
 
-    def __init__(self, text, command, icon=None, tooltip=None):
+    def __init__(self, text, command, icon=None, tooltip=None, shortcut=None):
         self.text = text
         self.command = command
         self.icon = icon
         self.tooltip = tooltip
+        self.shortcut = shortcut
 
 
 class ToolbarListDialog(ListDialog):
@@ -725,29 +731,36 @@ class ToolbarListDialog(ListDialog):
         ListDialog.__init__(self, parent, title, provider, message, **kwargs)
 
     def body(self, bodyFrame):
-        bodyFrame.config(bg=Config.SCIPION_BG_COLOR)
         gui.configureWeigths(bodyFrame, 1, 0)
 
         # Add an extra frame to insert the Toolbar
         # and another one for the ListDialog's body
-        self.toolbarFrame = tk.Frame(bodyFrame, bg=Config.SCIPION_BG_COLOR)
+        self.toolbarFrame = tk.Frame(bodyFrame)
         self.toolbarFrame.grid(row=0, column=0, sticky='new')
-        if self.toolbarButtons:
-            for i, b in enumerate(self.toolbarButtons):
-                self._addButton(b, i)
 
         subBody = tk.Frame(bodyFrame)
         subBody.grid(row=1, column=0, sticky='news', padx=5, pady=5)
         ListDialog.body(self, subBody)
+
+        if self.toolbarButtons:
+            for i, b in enumerate(self.toolbarButtons):
+                self._addButton(b, i)
+
         if self._itemDoubleClick:
             self.tree.itemDoubleClick = self._itemDoubleClick
 
     def _addButton(self, button, col):
         btn = tk.Label(self.toolbarFrame, text=button.text,
                        image=self.getImage(button.icon),
-                       compound=tk.LEFT, cursor='hand2', bg=Config.SCIPION_BG_COLOR)
+                       compound=tk.LEFT, cursor='hand2')
         btn.grid(row=0, column=col, sticky='nw', padx=(5, 0), pady=(5, 0))
         btn.bind('<Button-1>', button.command)
+        if button.tooltip:
+            tooltip = button.tooltip + ' (%s)' % button.shortcut if button.shortcut else button.tooltip
+            self.bind(button.shortcut, button.command)
+            ToolTip(btn, tooltip, delay=150)
+        if button.shortcut:
+            self.bind(button.shortcut, button.command)
 
 
 class FlashMessage:
@@ -781,10 +794,9 @@ class FlashMessage:
 class FloatingMessage:
     def __init__(self, master, msg, xPos=None, yPos=None, textWidth=280,
                  font='Helvetica', size=12, bd=1, bg=Config.SCIPION_MAIN_COLOR, fg='white'):
-
         if xPos is None:
-            xPos = (master.winfo_width()-textWidth)/2
-            yPos = master.winfo_height()/2
+            xPos = (master.winfo_width() - textWidth) / 2
+            yPos = master.winfo_height() / 2
 
         self.floatingMessage = tk.Label(master, text="   %s   " % msg,
                                         bd=bd, bg=bg, fg=fg)
@@ -839,9 +851,6 @@ class FileBrowseDialog(Dialog):
         return True
 
 
-
-
-
 class SearchBaseWindow(Window):
     """ Base window for searching in a list
     You are going to implement several elements:
@@ -874,7 +883,7 @@ class SearchBaseWindow(Window):
 
     def __init__(self, parentWindow, title="Search element", onClick=None, onDoubleClick=None, **kwargs):
         super().__init__(title=title,
-                              masterWindow=parentWindow)
+                         masterWindow=parentWindow)
 
         self.onClick = self._click if onClick is None else onClick
         self.onDoubleClick = self._double_click if onDoubleClick is None else onDoubleClick
@@ -905,8 +914,8 @@ class SearchBaseWindow(Window):
         entry.focus_set()
         entry.grid(row=0, column=1, sticky='nw')
         btn = widgets.IconButton(frame, "Search",
-                                       imagePath=Icon.ACTION_SEARCH,
-                                       command=self._onSearchClick)
+                                 imagePath=Icon.ACTION_SEARCH,
+                                 command=self._onSearchClick)
         btn.grid(row=0, column=2, sticky='nw')
 
         frame.grid(row=0, column=0, sticky='new', padx=5, pady=(10, 5))
@@ -947,7 +956,7 @@ class SearchBaseWindow(Window):
 
             if searchtext in linelower[index]:
                 # prioritize findings in label
-                weight += column[self.WEIGHT_INDEX]*2
+                weight += column[self.WEIGHT_INDEX] * 2
 
             elif " " in searchtext:
                 for word in searchtext.split():

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/gui/form.py

@@ -464,105 +464,12 @@ class SubclassesTreeProvider(TreeProvider):
         # Get the classes that are valid as input object in this Domain
         domain = pw.Config.getDomain()
         classes = [domain.findClass(c.strip()) for c in className.split(",")]
-        objects = []
-
-        # Do no refresh again and take the runs that are loaded
-        # already in the project. We will prefer to save time
-        # here than have the 'very last' version of the runs and objects
-        runs = project.getRuns(refresh=False)
-
-        for prot in runs:
-            # Make sure we don't include previous output of the same 
-            # protocol, it will cause a recursive loop
-            if prot.getObjId() != self.protocol.getObjId():
-                # Check if the protocol itself is one of the desired classes
-                if any(issubclass(prot.getClass(), c) for c in classes):
-                    p = pwobj.Pointer(prot)
-                    objects.append(p)
-
-                try:
-                    # paramName and attr must be set to None 
-                    # Otherwise, if a protocol has failed and the corresponding output object of type XX does not exist 
-                    # any other protocol that uses objects of type XX as input will not be able to choose then using
-                    # the magnifier glass (object selector of type XX)
-                    paramName = None
-                    attr = None
-                    for paramName, attr in prot.iterOutputAttributes(includePossible=True):
-                        def _checkParam(paramName, attr):
-                            # If attr is a sub-classes of any desired one, add it to the list
-                            # we should also check if there is a condition, the object
-                            # must comply with the condition
-                            p = None
-
-                            match = False
-                            cancelConditionEval = False
-                            possibleOutput = isinstance(attr, type)
-
-                            # Go through all compatible Classes coming from in pointerClass string
-                            for c in classes:
-                                # If attr is instance
-                                if isinstance(attr, c):
-                                    match = True
-                                    break
-                                # If it is a class already: "possibleOutput" case. In this case attr is the class and not
-                                # an instance of c. In this special case
-                                elif possibleOutput and attr == c:
-                                    match = True
-                                    cancelConditionEval = True
-
-                            # If attr matches the class
-                            if match:
-                                if cancelConditionEval or not condition or attr.evalCondition(condition):
-                                    p = pwobj.Pointer(prot, extended=paramName)
-                                    p._allowsSelection = True
-                                    objects.append(p)
-                                    return
-
-                            # JMRT: For all sets, we don't want to include the
-                            # subitems here for performance reasons (e.g SetOfParticles)
-                            # Thus, a Set class can define EXPOSE_ITEMS = True
-                            # to enable the inclusion of its items here
-                            if getattr(attr, 'EXPOSE_ITEMS', False) and not possibleOutput:
-                                # If the ITEM type match any of the desired classes
-                                # we will add some elements from the set
-                                if (attr.ITEM_TYPE is not None and
-                                        any(issubclass(attr.ITEM_TYPE, c) for c in classes)):
-                                    if p is None:  # This means the set have not be added
-                                        p = pwobj.Pointer(prot, extended=paramName)
-                                        p._allowsSelection = False
-                                        objects.append(p)
-                                    # Add each item on the set to the list of objects
-                                    try:
-                                        for i, item in enumerate(attr):
-                                            if i == self.maxNum:  # Only load up to NUM particles
-                                                break
-                                            pi = pwobj.Pointer(prot, extended=paramName)
-                                            pi.addExtended(item.getObjId())
-                                            pi._parentObject = p
-                                            objects.append(pi)
-                                    except Exception as ex:
-                                        print("Error loading items from:")
-                                        print("  protocol: %s, attribute: %s"
-                                              % (prot.getRunName(), paramName))
-                                        print("  dbfile: ",
-                                              os.path.join(project.getPath(),
-                                                           attr.getFileName()))
-                                        print(ex)
-
-                        _checkParam(paramName, attr)
-                        # The following is a dirty fix for the RCT case where there
-                        # are inner output, maybe we should consider extend this for
-                        # in a more general manner
-                        for subParam in ['_untilted', '_tilted']:
-                            if hasattr(attr, subParam):
-                                _checkParam('%s.%s' % (paramName, subParam),
-                                            getattr(attr, subParam))
-                except Exception as e:
-                    print("Cannot read attributes for %s (%s)" % (prot.getClass(), e))
+        # Obtaining only the outputs of the protocols that do not violate the sense of processing,
+        # thus avoiding circular references between protocols
+        objects = project.getProtocolCompatibleOutputs(self.protocol, classes, condition)
 
         # Sort objects before returning them
         self._sortObjects(objects)
-
         return objects
 
     def _sortObjects(self, objects):
@@ -654,7 +561,7 @@ class SubclassesTreeProvider(TreeProvider):
         viewers = domain.findViewers(obj.getClassName(), DESKTOP_TKINTER)
         proj = self.protocol.getProject()
         for v in viewers:
-            actions.append(('Open with %s' % v.__name__,
+            actions.append((v.getName(),
                             lambda: v(project=proj).visualize(obj)))
         return actions
 
@@ -2242,6 +2149,11 @@ class FormWindow(Window):
             errors, resultAction = ProtocolsView._launchSubWorkflow(self.protocol,
                                                                     mode, self.root,
                                                                     askSingleAll=True)
+
+            if errors:
+                self.showInfo(errors)
+                return
+
         if resultAction == RESULT_CANCEL:
             return
         elif resultAction == RESULT_RUN_ALL:

{scipion-pyworkflow-3.3.1 → scipion-pyworkflow-3.5.0}/pyworkflow/gui/graph_layout.py

@@ -88,9 +88,10 @@ class LevelTreeLayout(GraphLayout):
         # Setup empty layout for each node
         for node in graph.getNodes():
             node._layout = {}
-            
+
+        visitDict = dict()
         # Do some level initialization on each node
-        self._setLayoutLevel(rootNode,  1, None)
+        self._setLayoutLevel(rootNode,  1, None, visitDict)
         self._computeNodeOffsets(rootNode, 1)
         # Compute extreme left limit
         m = 9999
@@ -106,36 +107,46 @@ class LevelTreeLayout(GraphLayout):
     def _isNewNode(self, node):
         return node.x == 0 or node.y == 0 or node.isRoot()
         
-    def _setLayoutLevel(self, node, level, parent):
+    def _setLayoutLevel(self, node, level, parent, visitDict=None, ancestors=[]):
         """ Iterate over all nodes and set _layout dict.
         Also set the node level, which is defined
         as the max level of a parent + 1
         """
-        if level > self.maxLevel:
-            return 
-        
-        layout = node._layout
-        
-        if level > layout.get('level', 0):
-            # Calculate the y-position depending on the level
-            # and the delta-Y (DY)
-            if not self.partial or self._isNewNode(node):
-                node.y = level * self.getY()
-            layout['level'] = level
-            layout['parent'] = parent
-            if hasattr(node, 'width'):
-                half = node.width / 2
-            else:
-                half = 50
-            layout['half'] = half
-            layout['hLimits'] = [[-half, half]]
-            layout['offset'] = 0
-    
-            if self.__isNodeExpanded(node):
-                for child in node.getChilds():
-                    if Config.debugOn():
-                        print("%s: Setting layout for child %s" % ("-" * level, child), flush=True)
-                    self._setLayoutLevel(child, level+1, node)
+        if visitDict is None:
+            visitDict = {}
+
+        if node.getName() not in visitDict:
+            visitDict[node.getName()] = True
+
+            if level > self.maxLevel:
+                return
+
+            layout = node._layout
+
+            if level > layout.get('level', 0):
+                # Calculate the y-position depending on the level
+                # and the delta-Y (DY)
+                if not self.partial or self._isNewNode(node):
+                    node.y = level * self.getY()
+                layout['level'] = level
+                layout['parent'] = parent
+                if hasattr(node, 'width'):
+                    half = node.width / 2
+                else:
+                    half = 50
+                layout['half'] = half
+                layout['hLimits'] = [[-half, half]]
+                layout['offset'] = 0
+
+                if self.__isNodeExpanded(node):
+                    ancestors.append(node.getName())
+                    for child in node.getChilds():
+                        if child.getName() in ancestors:
+                            logger.warning("WARNING: There might be a cyclic redundancy error in this protocol: %s (%s)" %(child.getLabel(),
+                                                                                                                           child.getName()))
+                        if Config.debugOn():
+                            print("%s: Setting layout for child %s" % ("-" * level, child), flush=True)
+                        self._setLayoutLevel(child, level+1, node, visitDict, ancestors.copy())
 
     def __isNodeExpanded(self, node):
         """ Check if the status of the node is expanded or collapsed. """