scipion-pyworkflow 3.8.0__py3-none-any.whl → 3.9.0__py3-none-any.whl

pyworkflow/config.py

@@ -198,6 +198,7 @@ class Config:
 
     # Internal cached variables, use __ so they are not returned in getVars
     __activeColor = None
+    __defaultSpritesFile = _join(getResourcesPath(),'sprites.png')
 
     CONDA_ACTIVATION_CMD = _get(CONDA_ACTIVATION_CMD_VAR,'',
     "str: Command to activate/initialize conda itself. Do not confuse it with 'conda activate'. It should be defined at installation time. It looks like this: eval \"$(/extra/miniconda3/bin/conda shell.bash hook)\"")
@@ -299,7 +300,7 @@ class Config:
     SCIPION_CONTRAST_COLOR = _get('SCIPION_CONTRAST_COLOR', 'cyan',
     "Color used to highlight features over grayscaled images.", caster=validColor)
 
-    SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', _join(getResourcesPath(),'sprites.png'),
+    SCIPION_SPRITES_FILE = _get('SCIPION_SPRITES_FILE', __defaultSpritesFile,
     "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,
@@ -544,7 +545,12 @@ class Config:
             condaExe = os.path.join(envFolder, "bin", "python")
             return condaExe == getPython()
 
-
+    @classmethod
+    def getSpritesFile(cls):
+        if not os.path.exists(Config.SCIPION_SPRITES_FILE):
+            return cls.__defaultSpritesFile
+        else:
+            return Config.SCIPION_SPRITES_FILE
 
 
 # Add bindings folder to sys.path

pyworkflow/constants.py

@@ -43,7 +43,7 @@ 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 = '3.8.0'
+VERSION_3_0 = '3.9.0'
 
 # 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.
@@ -192,6 +192,7 @@ class DOCSITEURLS:
     WAIT_FOR = GUI + '#waiting-for-other-protocols'
     PLUGIN_MANAGER = USER + 'plugin-manager.html'
     HOST_CONFIG = DOCS + "scipion-modes/host-configuration.html"
+    THREADS_MPIS_AND_GPUS = USER + 'threads-mpi-gpus.html'
 
 
 # tkinter bind constants
@@ -211,3 +212,7 @@ DEFAULT_EXECUTION_ACTION_ASK = 1
 DEFAULT_EXECUTION_ACTION_SINGLE = 2
 DEFAULT_EXECUTION_ACTION_ALL = 3
 
+# Id field/attribute constants
+ID_COLUMN='id'
+ID_ATTRIBUTE='_objId'
+

pyworkflow/gui/canvas.py

@@ -82,8 +82,8 @@ class Canvas(tk.Canvas, Scrollable):
         self.bind("<Control-1>", self.onControlClick)
         # self.bind("<MouseWheel>", self.onScroll)
         # Scroll bindings in Linux
-        self.bind("<Shift-Button-4>", self.zoomerP)
-        self.bind("<Shift-Button-5>", self.zoomerM)
+        self.bind("<Control-Button-4>", self.zoomerP)
+        self.bind("<Control-Button-5>", self.zoomerM)
 
         self._tooltipId = None
         self._tooltipOn = False  # True if the tooltip is displayed
@@ -475,7 +475,7 @@ class Canvas(tk.Canvas, Scrollable):
             self.addItem(item)
 
             if getattr(node, 'expanded', True):
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if self.nodeList is None:
                         self._drawNodes(child, visitedDict)
                     elif self.nodeList.getNode(child.run.getObjId()).isVisible():
@@ -512,7 +512,7 @@ class Canvas(tk.Canvas, Scrollable):
         """
         Return a list with the visible parents of the node's children
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             parents = child.getParents()
             for parent in parents:
                 parentNode = self.nodeList.getNode(parent.run.getObjId())
@@ -525,7 +525,7 @@ class Canvas(tk.Canvas, Scrollable):
         the properties (width, height, x and y) is propagated
         to the hidden childs.
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             if child.getName() not in visitedDict:
                 child.width = node.width
                 child.height = node.height
@@ -544,7 +544,7 @@ class Canvas(tk.Canvas, Scrollable):
             item.moveTo(node.x, node.y)
 
             if getattr(node, 'expanded', True):
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if self.nodeList is None:
                         self.createEdge(item, child.item)
                         self._updatePositions(child, visitedDict, createEdges)

pyworkflow/gui/dialog.py

@@ -35,7 +35,7 @@ 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, ToolTip
+from . import gui, Window, widgets, configureWeigths, LIST_TREEVIEW, defineStyle, ToolTip, getDefaultFont
 from .tree import BoundTree, Tree
 from .text import Text, TaggedText
 
@@ -443,7 +443,8 @@ class EntryDialog(Dialog):
         label = tk.Label(bodyFrame, text=self.entryLabel, bg=Config.SCIPION_BG_COLOR, bd=0)
         label.grid(row=row, column=0, sticky='nw', padx=(15, 10), pady=15)
         self.entry = tk.Entry(bodyFrame, bg=gui.cfgEntryBgColor,
-                              width=self.entryWidth, textvariable=self.tkvalue)
+                              width=self.entryWidth, textvariable=self.tkvalue,
+                              font=getDefaultFont())
         self.entry.grid(row=row, column=1, sticky='new', padx=(0, 15), pady=15)
         self.initial_focus = self.entry
 

pyworkflow/gui/form.py

@@ -1698,14 +1698,19 @@ class FormWindow(Window):
                 c2 = 0
                 sticky = 'e'
 
+                helpMessage = pwutils.Message.HELP_PARALLEL_HEADER
+
                 if mode == pwprot.STEPS_PARALLEL:
                     if allowThreads and numberOfThreads > 0:
                         prot.numberOfMpi.set(1)
-                        self._createHeaderLabel(procFrame, pwutils.Message.LABEL_THREADS,
+                        self._createHeaderLabel(procFrame, pwutils.Message.LABEL_SCIPION_THREADS,
                                                 sticky=sticky, row=r2, column=c2,
                                                 pady=0)
                         entry = self._createBoundEntry(procFrame,
                                                        pwutils.Message.VAR_THREADS)
+
+                        helpMessage += pwutils.Message.HELP_SCIPION_THREADS
+
                         entry.grid(row=r2, column=c2 + 1, padx=(0, 5), sticky='w')
                     elif allowMpi and numberOfMpi > 1:
                         self.showError("MPI parameter is deprecated for protocols "
@@ -1728,6 +1733,8 @@ class FormWindow(Window):
                         # Modify values to be used in MPI entry
                         c2 += 2
                         sticky = 'w'
+
+                        helpMessage += pwutils.Message.HELP_PARALLEL_THREADS
                     # ---- MPI ----
                     if allowMpi:
                         self._createHeaderLabel(procFrame, pwutils.Message.LABEL_MPI,
@@ -1736,11 +1743,14 @@ class FormWindow(Window):
                         entry = self._createBoundEntry(procFrame, pwutils.Message.VAR_MPI)
                         entry.grid(row=r2, column=c2 + 1, padx=(0, 5), sticky='w')
 
+                        helpMessage += pwutils.Message.HELP_PARALLEL_MPI
+
+
                 btnHelp = IconButton(procFrame, pwutils.Message.TITLE_COMMENT,
                                      pwutils.Icon.ACTION_HELP,
                                      highlightthickness=0,
                                      command=self._createHelpCommand(
-                                         pwutils.Message.HELP_MPI_THREADS))
+                                         helpMessage))
                 btnHelp.grid(row=0, column=4, padx=(5, 0), pady=2, sticky='e')
 
                 procFrame.columnconfigure(0, minsize=60)

pyworkflow/gui/graph.py

@@ -85,7 +85,7 @@ class LevelTree(object):
         nextLevel = level + 1
         if nextLevel > self.maxLevel:
             return
-        for child in node.getChilds():
+        for child in node.getChildren():
             if nextLevel > getattr(child, 'level', 0):
                 self._setLevel(child, nextLevel, node)
 
@@ -97,7 +97,7 @@ class LevelTree(object):
         if level > self.maxLevel:
             return
 
-        childs = [c for c in node.getChilds() if c.parent is node]
+        childs = [c for c in node.getChildren() if c.parent is node]
         n = len(childs)
 
         if n > 0:
@@ -174,7 +174,7 @@ class LevelTree(object):
         for each level of the tree
         """
         node.hLimits = [[-node.half, node.half]]
-        childs = [c for c in node.getChilds() if c.parent is node]
+        childs = [c for c in node.getChildren() if c.parent is node]
         for child in childs:
             count = 1
             if not hasattr(child, 'hLimits'):
@@ -221,7 +221,7 @@ class LevelTree(object):
         if node.level == self.maxLevel:
             return
 
-        for c in node.getChilds():
+        for c in node.getChildren():
             if c.parent is node:
                 self._createEdges(c, nx)
             self.createEdge(node.item, c.item)
@@ -230,7 +230,7 @@ class LevelTree(object):
         """ Paint nodes using its position. """
         self._paintNode(node, None)
 
-        for child in node.getChilds():
+        for child in node.getChildren():
             # parent = None for nodes that have been not traversed
             parent = getattr(child, 'parent', None)
             if parent is None:
@@ -241,7 +241,7 @@ class LevelTree(object):
         """ Paint only the edges between nodes, assuming they are
         already well positioned. 
         """
-        for child in node.getChilds():
+        for child in node.getChildren():
             if child.parent is node:
                 self._paintEdges(child)
             self.createEdge(node.item, child.item)

pyworkflow/gui/graph_layout.py

@@ -132,7 +132,7 @@ class LevelTreeLayout(GraphLayout):
 
             if self.__isNodeExpanded(node):
                 ancestors.append(node.getName())
-                for child in node.getChilds():
+                for child in node.getChildren():
                     if child.getName() in ancestors:
                         logger.warning("WARNING: There might be a cyclic redundancy error in this protocol: %s (%s)" %(child.getLabel(),
                                                                                                                        child.getName()))
@@ -155,7 +155,7 @@ class LevelTreeLayout(GraphLayout):
         visited by this node first (its 'parent')
         """
         if self.__isNodeExpanded(node):
-            return [c for c in node.getChilds() if c._layout['parent'] is node]
+            return [c for c in node.getChildren() if c._layout['parent'] is node]
         else:
             return []  # treat collapsed nodes as if they have no childs
         

pyworkflow/gui/project/base.py

@@ -28,7 +28,7 @@ import webbrowser
 import tkinter as tk
 
 import pyworkflow as pw
-from pyworkflow.gui import Window, Message, Color, getBigFont, defineStyle
+from pyworkflow.gui import Window, Message, Color, getBigFont, defineStyle, ToolTip
 from pyworkflow.gui.widgets import GradientFrame
 from pyworkflow.utils.properties import Icon
 from pyworkflow.gui.project.variables import VariablesDialog
@@ -98,18 +98,18 @@ class ProjectBaseWindow(Window):
                                 bg=pw.Config.SCIPION_BG_COLOR)
         versionLabel.grid(row=0, column=1, sticky='sw', pady=20)
         
-        # Create the Project Name label
-        projName = getattr(self, 'projName', '')
-        projLabel = tk.Label(header, text=projName, font=getBigFont(),
-                             borderwidth=0, anchor='nw', bg=pw.Config.SCIPION_BG_COLOR,
-                             fg=Color.ALT_COLOR_DARK)
-        projLabel.grid(row=0, column=2, sticky='sw', padx=(20, 5), pady=10)
+        self.customizeheader(header)
+
         # Create gradient
         GradientFrame(header, height=8, borderwidth=0).grid(row=1, column=0,
                                                             columnspan=3,
                                                             sticky='new')
         return header
 
+    def customizeheader(self, headerFrame):
+        """ Implement in children classes to customize it: e.g.: Project name in project window"""
+        pass
+
     def addViewList(self, header):
         """Create the view selection frame (Protocols|Data) in the header.
         """

pyworkflow/gui/project/project.py

@@ -31,6 +31,10 @@ It is composed by three panels:
 """
 
 import logging
+from tkinter import Label
+
+from .. import askString
+
 logger = logging.getLogger(__name__)
 
 import os
@@ -43,7 +47,7 @@ import pyworkflow as pw
 import pyworkflow.utils as pwutils
 from pyworkflow.gui.project.utils import OS
 from pyworkflow.project import MenuConfig
-from pyworkflow.gui import Message, Icon
+from pyworkflow.gui import Message, Icon, getBigFont, ToolTip
 from pyworkflow.gui.browser import FileBrowserWindow
 
 from pyworkflow.gui.plotter import Plotter
@@ -61,7 +65,10 @@ class ProjectWindow(ProjectBaseWindow):
 
     def __init__(self, path, master=None):
         # Load global configuration
-        self.projName = os.path.basename(path)
+        self.projPath = path
+        self.project = self.loadProject()
+        self.projName = self.project.getShortName()
+
         try:
             projTitle = '%s (%s on %s)' % (self.projName,
                                            pwutils.getLocalUserName(),
@@ -69,8 +76,6 @@ class ProjectWindow(ProjectBaseWindow):
         except Exception:
             projTitle = self.projName 
 
-        self.projPath = path
-        self.project = self.loadProject()
 
         # TODO: put the menu part more nicely. From here:
         menu = MenuConfig()
@@ -119,6 +124,8 @@ class ProjectWindow(ProjectBaseWindow):
         # Notify about the workflow in this project
         self.selectedProtocol = None
         self.showGraph = False
+        self.commentTT = None  # Tooltip to store the project description
+
         Plotter.setBackend('TkAgg')
         ProjectBaseWindow.__init__(self, projTitle, master,
                                    minsize=(90, 50), icon=Icon.SCIPION_ICON_PROJ, _class=self.projName)
@@ -131,12 +138,30 @@ class ProjectWindow(ProjectBaseWindow):
 
         ProjectWorkflowNotifier(self.project).notifyWorkflow()
 
+
     def createHeaderFrame(self, parent):
         """Create the header and add the view selection frame at the right."""
         header = ProjectBaseWindow.createHeaderFrame(self, parent)
         self.addViewList(header)
         return header
 
+    def customizeheader(self, headerFrame):
+        """ Adds the Project name in the header frame"""
+        # Create the Project Name label
+
+        projLabel = Label(headerFrame, text=self.projName, font=getBigFont(),
+                             borderwidth=0, anchor='nw', bg=pw.Config.SCIPION_BG_COLOR,
+                             fg=pw.Color.ALT_COLOR_DARK)
+        projLabel.bind("<Button-1>", self.setComment)
+        projLabel.grid(row=0, column=2, sticky='sw', padx=(20, 5), pady=10)
+
+        self.commentTT = ToolTip(projLabel, self.project.getComment(), 200)
+    def setComment(self, e):
+
+        newComment = askString("Change project description", "Description", self.root, entryWidth=100, defaultValue=self.project.getComment())
+        self.commentTT.configure(text=newComment)
+        self.project.setComment(newComment)
+        self.project._storeCreationTime()  # Comment is stored as creation time comment for now
     def getSettings(self):
         return self.settings
     
@@ -334,30 +359,6 @@ class ProjectWindow(ProjectBaseWindow):
 
         except Exception as ex:
             logger.error("There was an error executing object command !!!:", exc_info=ex)
-    
-    def recalculateCTF(self, inputObjId, sqliteFile):
-        """ Load the project and launch the protocol to
-        create the subset.
-        """
-        # Retrieve project, input protocol and object from db
-        project = self.project
-        inputObj = project.mapper.selectById(int(inputObjId))
-        parentProtId = inputObj.getObjParentId()
-        parentProt = project.mapper.selectById(parentProtId)
-        protDep = project._getProtocolsDependencies([parentProt])
-        if protDep:
-            prot = project.copyProtocol(parentProt)
-            prot.continueRun.set(parentProt)
-        else:
-            prot = parentProt
-            prot.isFirstTime.set(True)
-        
-        # Define the input params of the new protocol
-        prot.recalculate.set(True)
-        prot.sqliteFile.set(sqliteFile)
-        # Launch the protocol
-        self.getViewWidget().executeProtocol(prot)
-
 
 class ProjectManagerWindow(ProjectBaseWindow):
     """ Windows to manage all projects. """
@@ -466,6 +467,13 @@ class ProjectTCPRequestHandler(socketserver.BaseRequestHandler):
                         attr.set(obj)
                     elif value:
                         attr.set(value)
+
+                if protocol.useQueue():
+                    # Do not use the queue in this case otherwise we need to ask for queue parameters.
+                    # Maybe something to do in the future. But now this logic is in form.py.
+                    logger.warning('Cancelling launching protocol "%s" to the queue.' % protocol)
+                    protocol._useQueue.set(False)
+
                 # project.launchProtocol(protocol)
                 # We need to enqueue the action of execute a new protocol
                 # to be run in the same GUI thread and avoid concurrent

pyworkflow/gui/project/steps.py

@@ -30,7 +30,6 @@ import pyworkflow.protocol as pwprot
 import  pyworkflow.gui as pwgui
 import pyworkflow.utils as pwutils
 
-
 from pyworkflow import TK
 from pyworkflow.utils import Icon
 
@@ -59,11 +58,17 @@ class StepsTreeProvider(pwgui.tree.TreeProvider):
         return info
 
     @staticmethod
-    def getObjectPreview(obj):
+    def getObjectPreview(obj: pwprot.Step):
 
         args = json.loads(obj.argsStr.get())
         msg = "*Prerequisites*: %s \n" % str(obj._prerequisites)
-        msg += "*Arguments*: " + '\n  '.join([str(a) for a in args])
+
+        msg += ("*Arguments*:\n")
+        for arg in args:
+            msg += " %s\n" % arg
+
+        msg += "*Needs GPU*: %s" % obj.needsGPU()
+
         if hasattr(obj, 'resultFiles'):
             results = json.loads(obj.resultFiles.get())
             if len(results):

pyworkflow/gui/project/viewdata.py

@@ -55,7 +55,7 @@ def populateTree(tree, elements, parentId=''):
                 t += ' (%d)' % node.count
             node.nodeId = tree.insert(parentId, 'end', node.getName(),
                                       text=t, tags=DATA_TAG)
-            populateTree(tree, node.getChilds(), node.nodeId)
+            populateTree(tree, node.getChildren(), node.nodeId)
             if node.count:
                 tree.see(node.nodeId)
                 tree.item(node.nodeId, tags=('non-empty', DATA_TAG))

pyworkflow/gui/project/viewprotocols.py

@@ -808,7 +808,7 @@ class ProtocolsView(tk.Frame):
         item.margin = 0
 
         # Paint the oval..if apply.
-        self._paintOval(item, statusColor)
+        #self._paintOval(item, statusColor)
 
         # Paint the bottom line (for now only labels are painted there).
         self._paintBottomLine(item)
@@ -821,7 +821,7 @@ class ProtocolsView(tk.Frame):
         try:
 
             # If the color has to go to the box
-            if self.settings.statusColorMode():
+            if self.settings.statusColorMode() or self.settings.labelsColorMode():
                 boxColor = statusColor
 
             elif self.settings.ageColorMode():
@@ -931,7 +931,7 @@ class ProtocolsView(tk.Frame):
 
     def _paintBottomLine(self, item):
 
-        if self.settings.labelsColorMode():
+        if self.settings.labelsColorMode() or self.settings.statusColorMode():
             self._addLabels(item)
 
     def _paintOval(self, item, statusColor):
@@ -967,7 +967,7 @@ class ProtocolsView(tk.Frame):
             nodeText = nodeText[:37] + "..."
 
         if node.run:
-            expandedStr = '' if node.expanded else '\n ➕ %s more' % str(node.countChilds({}))
+            expandedStr = '' if node.expanded else '\n ➕ %s more' % str(node.countChildren({}))
             if self.runsView == VIEW_TREE_SMALL:
                 nodeText = node.getName() + expandedStr
             else:
@@ -978,7 +978,7 @@ class ProtocolsView(tk.Frame):
 
     def _addLabels(self, item):
         # If there is only one label it should be already used in the box color.
-        if self._getLabelsCount(item.nodeInfo) < 2:
+        if self._getLabelsCount(item.nodeInfo) < 1:
             return
         # Get the positions of the box
         (topLeftX, topLeftY, bottomRightX,
@@ -1056,7 +1056,7 @@ class ProtocolsView(tk.Frame):
         nextColorMode = currentMode + 1
 
         self.settings.setColorMode(nextColorMode)
-        self._updateActionToolbar()
+        # WHY? self._updateActionToolbar()
         # self.updateRunsGraph()
         self.drawRunsGraph()
         self._infoAboutColorScheme()
@@ -1283,7 +1283,7 @@ class ProtocolsView(tk.Frame):
             tm += 'Status: %s\n' % prot.getStatusMessage()
             tm += 'Wall time: %s\n' % pwutils.prettyDelta(prot.getElapsedTime())
             tm += 'CPU time: %s\n' % pwutils.prettyDelta(dt.timedelta(seconds=prot.cpuTime))
-            tm += 'Folder size: %s\n' % pwutils.prettySize(prot.getSize())
+            # tm += 'Folder size: %s\n' % pwutils.prettySize(prot.getSize())
 
             if not hasattr(tw, 'tooltipText'):
                 frame = tk.Frame(tw)
@@ -1805,7 +1805,7 @@ class ProtocolsView(tk.Frame):
         # Go in the direction .
         for run in nodesToSelect:
             # Choose the direction: down or up.
-            direction = run.getChilds if down else run.getParents
+            direction = run.getChildren if down else run.getParents
 
             # Select himself plus ancestors
             for parent in direction():
@@ -2054,7 +2054,7 @@ class ProtocolsView(tk.Frame):
 
     def setVisibleNodes(self, node, visible=True):
         hasParentHidden = False
-        for child in node.getChilds():
+        for child in node.getChildren():
             prot = child.run
             nodeInfo = self.settings.getNodeById(prot.getObjId())
             if visible:

pyworkflow/gui/project/viewprotocols_extra.py

@@ -245,7 +245,7 @@ class RunIOTreeProvider(pwgui.tree.TreeProvider):
         if obj is None or not obj.hasValue():
             return None
 
-        if isinstance(obj, pwobj.String):
+        if isinstance(obj, pwobj.String) and not obj.getName():
             info = stringToInfo()
         else:
             # All attributes are considered output, unless they are pointers
@@ -504,7 +504,7 @@ class ProtocolTreeConfig:
 
             except Exception as e:
                 print('Failed to read settings. The reported error was:\n  %s\n'
-                      'To solve it, fix %s and run again.' % e)
+                      'To solve it, fix %s and run again.' % (e, pluginName))
 
         # Clean empty sections
         cls._hideEmptySections(protocols)
@@ -557,4 +557,4 @@ class ProtocolConfig(MenuConfig):
         return MenuConfig.addSubMenu(self, text, value, **args)
 
     def __str__(self):
-        return self.text
+        return self.text

pyworkflow/gui/widgets.py

@@ -161,8 +161,8 @@ class Scrollable(object):
         widget.bind("<Button-4>", self.scrollV)
         widget.bind("<Button-5>", self.scrollV)
 
-        widget.bind("<Control-Button-4>", self.scrollH)
-        widget.bind("<Control-Button-5>", self.scrollH)
+        widget.bind("<Shift-Button-4>", self.scrollH)
+        widget.bind("<Shift-Button-5>", self.scrollH)
 
 
     def getVScroll(self):

pyworkflow/mapper/sqlite.py

@@ -27,12 +27,12 @@ logger = logging.getLogger(__name__)
 import re
 from collections import OrderedDict
 
-from pyworkflow import Config
+from pyworkflow import Config, ID_ATTRIBUTE, ID_COLUMN
 from pyworkflow.utils import replaceExt, joinExt, valueToList
 from .sqlite_db import SqliteDb, OperationalError
 from .mapper import Mapper
 
-ID = 'id'
+ID = ID_COLUMN
 CREATION = 'creation'
 PARENT_ID = 'parent_id'
 CLASSNAME = 'classname'
@@ -210,7 +210,7 @@ class SqliteMapper(Mapper):
         rowId = objRow[ID]
         rowName = self._getStrValue(objRow['name'])
 
-        if not hasattr(obj, '_objId'):
+        if not hasattr(obj, ID_ATTRIBUTE):
             raise Exception("Entry '%s' (id=%s) in the database, stored as '%s'"
                             ", is being mapped to %s object. " %
                             (rowName, rowId,
@@ -1356,8 +1356,8 @@ class SqliteFlatDb(SqliteDb):
     def addCommonFieldsToMap(self):
 
         # Add common fields to the mapping
-        self._columnsMapping["id"] = "id"
-        self._columnsMapping["_objId"] = "id"
+        self._columnsMapping[ID_COLUMN] = ID_COLUMN
+        self._columnsMapping[ID_ATTRIBUTE] = ID_COLUMN
 
     def getClassRows(self):
         """ Create a dictionary with names of the attributes

pyworkflow/object.py

@@ -66,7 +66,7 @@ class Object(object):
             self._objId =  None  # Unique identifier of this object in some context
             self._objParentId =  None  # identifier of the parent object
             self._objName = ''  # The name of the object will contains the whole path of ancestors
-            self._objLabel =  ''  # This will serve to label the objects
+            self._objLabel = ''  # This will serve to label the objects
             self._objComment = ''
             # Performance: self._objTag =  None  # This attribute serve to make some annotation on the object.
             self._objDoStore = True

pyworkflow/plugin.py

@@ -124,6 +124,7 @@ class Domain:
             (pwutils.yellow("WARNING!!: Plugin containing module %s does not import properly. "
                                  "All its content will be missing in this execution." % name))
             logger.info("Please, contact developers at %s and send this ugly information below. They'll understand it!." % DOCSITEURLS.CONTACTUS)
+            logger.info("Error message: %s"% str(e))
             logger.info(pwutils.yellow(traceback.format_exc()))
 
     @classmethod

pyworkflow/project/config.py

@@ -40,7 +40,7 @@ class ProjectSettings(pwobj.Object):
     COLOR_MODE_LABELS = 1
     COLOR_MODE_AGE = 2
     COLOR_MODE_SIZE = 3
-    COLOR_MODES = (COLOR_MODE_STATUS, COLOR_MODE_LABELS, COLOR_MODE_AGE, COLOR_MODE_SIZE)
+    COLOR_MODES = (COLOR_MODE_STATUS, COLOR_MODE_LABELS, COLOR_MODE_AGE)  # This has poor performance many cases, COLOR_MODE_SIZE)
 
     def __init__(self, confs={}, **kwargs):
         super().__init__(**kwargs)
@@ -112,6 +112,9 @@ class ProjectSettings(pwobj.Object):
     def setColorMode(self, colorMode):
         """ Set the color mode to use when drawing the graph.
         """
+        # Skip LABELS color mode to avoid double iteration
+        if colorMode == self.COLOR_MODE_LABELS:
+            colorMode+=1
         self.colorMode.set(colorMode)
 
     def statusColorMode(self):

pyworkflow/project/manager.py

@@ -97,9 +97,9 @@ class Manager(object):
         return projList
     
     def createProject(self, projectName, runsView=1, 
-                      hostsConf=None, protocolsConf=None, location=None):
+                      hostsConf=None, protocolsConf=None, location=None, comment=None):
         """Create a new project.
-        confs dict can contains customs .conf files 
+        confs dict can contain customs .conf files
         for: menus, protocols, or hosts
         """
         # Clean project name from undesired characters
@@ -118,7 +118,8 @@ class Manager(object):
         project = Project(pw.Config.getDomain(), projectPath)
         project.create(runsView=runsView, 
                        hostsConf=hostsConf, 
-                       protocolsConf=protocolsConf)
+                       protocolsConf=protocolsConf,
+                       comment=comment)
         # If location is not the default one create a symlink on self.PROJECTS directory
         if projectPath != self.getProjectPath(projectName):
             # JMRT: Let's create the link to the absolute path, since relative