scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.1__py3-none-any.whl

pyworkflow/gui/project/viewprotocols.py

@@ -25,11 +25,11 @@
 import logging
 logger = logging.getLogger(__name__)
 
-from pyworkflow import Config, DEFAULT_EXECUTION_ACTION_ASK, DEFAULT_EXECUTION_ACTION_SINGLE
+from pyworkflow import Config, DEFAULT_EXECUTION_ACTION_ASK, DEFAULT_EXECUTION_ACTION_SINGLE, DOCSITEURLS
 from pyworkflow.gui import LIST_TREEVIEW, \
-    ShortCut, ToolTip, RESULT_RUN_ALL, RESULT_RUN_SINGLE, RESULT_CANCEL, BORDERLESS_TREEVIEW
+    ShortCut, ToolTip, RESULT_RUN_ALL, RESULT_RUN_SINGLE, RESULT_CANCEL, BORDERLESS_TREEVIEW, showInfo
 from pyworkflow.gui.project.constants import *
-from pyworkflow.protocol import SIZE_1MB, SIZE_1GB, SIZE_1TB
+from pyworkflow.protocol import SIZE_1MB, SIZE_1GB, SIZE_1TB, Protocol
 
 INIT_REFRESH_SECONDS = Config.SCIPION_GUI_REFRESH_INITIAL_WAIT
 
@@ -299,7 +299,7 @@ class ProtocolsView(tk.Frame):
         """ Call appropriate viewer for objId. """
         proj = self.project
         obj = proj.getObject(int(objId))
-        viewerClasses = self.domain.findViewers(obj.getClassName(), DESKTOP_TKINTER)
+        viewerClasses = self.domain.findViewers(obj, DESKTOP_TKINTER)
         if not viewerClasses:
             return  # TODO: protest nicely
         viewer = viewerClasses[0](project=proj, parent=self.window)
@@ -401,12 +401,12 @@ class ProtocolsView(tk.Frame):
     def _findProtocol(self, event=None):
         """ Find a desired protocol by typing some keyword. """
 
-        if event is not None and event.widget.widgetName=="canvas":
+        if event is not None and self._noSelection() and event.widget.widgetName=="canvas" and self:
             position = self.runsGraphCanvas.getCoordinates(event)
         else:
             position = None
 
-        window = SearchProtocolWindow(self.window, position=position)
+        window = SearchProtocolWindow(self.window, position=position, selectionGetter=self.getSelectedProtocol)
         window.show()
 
     def _locateProtocol(self, e=None):
@@ -1035,16 +1035,34 @@ class ProtocolsView(tk.Frame):
             self.viewButtons[ACTION_TREE].grid(row=0, column=1)
 
     def _protocolItemClick(self, e=None, position=None):
-        """ Callback for the window to add a new protocol."""
+        """ Callback for the window to add a new protocol.
+        """
 
         # Get the tree widget that originated the event
         # it could be the left panel protocols tree or just
-        # the search protocol dialog tree
+        # the search protocol dialog tree. In this case now non installed protocols are listed from the suggestions
         tree = e.widget
+
+        # Get the class name
         protClassName = tree.getFirst().split('.')[-1]
+
+        # Get the class: Now it may not be installed!!
         protClass = self.domain.getProtocols().get(protClassName)
-        prot = self.project.newProtocol(protClass)
-        self._openProtocolForm(prot, disableRunMode=True, position=position)
+
+        # If found continue to open the protocol form to ask for parameters
+        if protClass is not None:
+            prot = self.project.newProtocol(protClass)
+            self._openProtocolForm(prot, disableRunMode=True, position=position, previousProt=self.getSelectedProtocol())
+        # Missing class: probably not installed. Inform
+        else:
+            # Get the value as populated in pyworkflow.gui.project.searchprotocol.py:235 comming from SearchProtocolWindow.addSuggestions
+            rowValues = tree.item(protClassName)["values"]
+            prot_label = rowValues[0]
+            installedMsg = rowValues[2]
+            msg = ("%s %s To get it use the plugin manager or installation "
+                   "command and restart Scipion. See %s .") % (prot_label, installedMsg, DOCSITEURLS.PLUGIN_MANAGER)
+            showInfo("%s protocol is missing." % prot_label,
+                     msg, self)
 
     def _toggleColorScheme(self, e=None):
 
@@ -1332,13 +1350,20 @@ class ProtocolsView(tk.Frame):
         #
         # if update is not None: self._updateSelection()
 
-    def _openProtocolForm(self, prot, disableRunMode=False, position=None):
-        """Open the Protocol GUI Form given a Protocol instance"""
+    def _openProtocolForm(self, prot, disableRunMode=False, position=None, previousProt=None):
+        """Open the Protocol GUI Form given a Protocol instance
+
+        :param prot: protocol to show and edit its parameters
+        :param disableRunMode: to show the form it in read only mode
+        :param position: Optional. Position to add the box once added to the graph.
+        :param previousProt: Optional. If passed it will try to link this protocol to the previous protocol.
+
+        """
 
         w = FormWindow(Message.TITLE_NAME_RUN + prot.getClassName(),
                        prot, self._executeSaveProtocol, self.window,
                        updateProtocolCallback=self._updateProtocol,
-                       disableRunMode=disableRunMode, position=position)
+                       disableRunMode=disableRunMode, position=position, previousProt=previousProt)
         w.adjustSize()
         w.show(center=True)
 
@@ -1495,7 +1520,7 @@ class ProtocolsView(tk.Frame):
 
     def _scheduleRunsUpdate(self, secs=1, position=None):
         # self.runsTree.after(secs*1000, self.refreshRuns)
-        self.window.enqueue(lambda : self.refreshRuns(position=position))
+        self.window.enqueue(lambda: self.refreshRuns(position=position))
 
     def executeProtocol(self, prot):
         """ Function to execute a protocol called not
@@ -1509,7 +1534,6 @@ class ProtocolsView(tk.Frame):
         if onlySave:
             self.project.saveProtocol(prot)
             msg = Message.LABEL_SAVED_FORM
-            # msg = "Protocol successfully saved."
 
         else:
             if doSchedule:
@@ -1596,7 +1620,6 @@ class ProtocolsView(tk.Frame):
     def _copyProtocolsToClipboard(self, e=None):
 
         protocols = self._getSelectedProtocols()
-
         jsonStr = self.project.getProtocolsJson(protocols)
 
         self.clipboard_clear()
@@ -1865,13 +1888,13 @@ class ProtocolsView(tk.Frame):
             self._lastStatus = None  # force logs to re-load
             self._scheduleRunsUpdate()
 
-    def _analyzeResults(self, prot, keyPressed):
-        viewers = self.domain.findViewers(prot.getClassName(), DESKTOP_TKINTER)
+    def _analyzeResults(self, prot:Protocol, keyPressed):
+        viewers = self.domain.findViewers(prot, DESKTOP_TKINTER)
         if len(viewers):
             # Instantiate the first available viewer
-            # TODO: If there are more than one viewer we should display
-            # TODO: a selection menu
-            firstViewer = viewers[0](project=self.project, protocol=prot,
+            viewer = viewers[0]
+            logger.info("Specific viewer found for protocol %s: %s" % (prot.getRunName, viewer))
+            firstViewer = viewer(project=self.project, protocol=prot,
                                      parent=self.window, keyPressed=keyPressed)
 
             if isinstance(firstViewer, ProtocolViewer):
@@ -1884,7 +1907,7 @@ class ProtocolsView(tk.Frame):
                 outputList.append(output)
 
             for output in outputList:
-                viewers = self.domain.findViewers(output.getClassName(), DESKTOP_TKINTER)
+                viewers = self.domain.findViewers(output, DESKTOP_TKINTER)
                 if len(viewers):
                     # Instantiate the first available viewer
                     # TODO: If there are more than one viewer we should display

pyworkflow/gui/project/viewprotocols_extra.py

@@ -27,8 +27,12 @@ import json
 import os
 from configparser import ConfigParser
 
+import logging
+logger = logging.getLogger(__name__)
+
+
 from pyworkflow import Config
-import  pyworkflow.gui as pwgui
+import pyworkflow.gui as pwgui
 import pyworkflow.object as pwobj
 import pyworkflow.utils as pwutils
 from pyworkflow.gui.project.utils import isAFinalProtocol
@@ -113,7 +117,7 @@ class RunIOTreeProvider(pwgui.tree.TreeProvider):
                                             % objLabel):
                 prot.getProject().deleteProtocolOutput(prot, obj)
                 self.parent._fillSummary()
-                self.parent.window.showInfo("Object *%s* successfully deleted."
+                logger.info("Object *%s* successfully deleted upon user request."
                                              % objLabel)
         except Exception as ex:
             self.parent.window.showError(str(ex))
@@ -138,7 +142,7 @@ class RunIOTreeProvider(pwgui.tree.TreeProvider):
             self._loggerCallback("Discovering viewers for the first time across all the plugins.")
 
 
-        viewers = Config.getDomain().findViewers(obj.getClassName(), DESKTOP_TKINTER)
+        viewers = Config.getDomain().findViewers(obj, DESKTOP_TKINTER)
 
         def viewerCallback(viewer):
             return lambda: self._visualizeObject(viewer, obj)
@@ -191,7 +195,7 @@ class RunIOTreeProvider(pwgui.tree.TreeProvider):
             try:
                 value = str(label)
             except Exception as e:
-                print("Can not convert object %s - %s to string." % (key, name))
+                logger.info("Can not convert object %s - %s to string." % (key, name))
                 value = str(e)
 
             return value
@@ -502,8 +506,7 @@ class ProtocolTreeConfig:
                     cls.__addProtocolsFromConf(protocols, protocolsConfPath)
 
             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, pluginName))
+                logger.info(f'Failed to read protocols.conf from {pluginName}. The reported error was:\n  {e}\n')
 
         # Clean empty sections
         cls._hideEmptySections(protocols)

pyworkflow/gui/widgets.py

@@ -281,8 +281,8 @@ class GradientFrame(tk.Canvas):
 
     def __init__(self, parent, **args):
         tk.Canvas.__init__(self, parent, **args)
-        self._color1 = Config.SCIPION_BG_COLOR #"#d2a7a7"
-        self._color2 = Config.SCIPION_MAIN_COLOR #"#820808"
+        self._color1 = Config.SCIPION_BG_COLOR
+        self._color2 = Config.SCIPION_MAIN_COLOR
         self.bind("<Configure>", self._draw_gradient)
 
     def _draw_gradient(self, event=None):

pyworkflow/mapper/sqlite.py

@@ -1543,18 +1543,18 @@ class SqliteFlatDb(SqliteDb):
         return self._results(iterate=False)
 
     def count(self):
-        """ Return the number of element in the table. """
-        self.executeCommand(self.selectCmd('1').replace('*', 'COUNT(id)'))
+        """ Return the number of elements in the table. """
+        self.executeCommand(self.selectCmd(None, orderByStr="").replace('*', 'COUNT(*)'))
         return self.cursor.fetchone()[0]
 
     def maxId(self):
         """ Return the maximum id from the Objects table. """
-        self.executeCommand(self.selectCmd('1').replace('*', 'MAX(id)'))
+        self.executeCommand(self.selectCmd(None, orderByStr="").replace('*', 'MAX(id)'))
         return self.cursor.fetchone()[0]
 
     # FIXME: Seems to be duplicated and a subset of selectAll
     def selectObjectsBy(self, iterate=False, **args):
-        """More flexible select where the constrains can be passed
+        """More flexible select where the constraints can be passed
         as a dictionary, the concatenation is done by an AND"""
         whereList = ['%s=?' % k for k in args.keys()]
         whereStr = ' AND '.join(whereList)

pyworkflow/plugin.py

@@ -28,6 +28,7 @@
 # **************************************************************************
 import logging
 import sys
+from functools import lru_cache
 
 from pyworkflow import Variable, VariablesRegistry, VarTypes
 from .protocol import Protocol
@@ -79,6 +80,9 @@ class Domain:
     _viewers = {}
     _wizards = {}
 
+    # Preferred viewers:
+    _preferred_viewers = None
+
     @classmethod
     def registerPlugin(cls, name):
         """ Register a new plugin. This function should only be called when
@@ -113,15 +117,17 @@ class Domain:
 
         # Catch any import exception, warn about it but continue.
         except ModuleNotFoundError as e:
+
+            logger.debug("Module %s not found: %s" %(name, e))
             if e.name == name:
                 # This is probably due to a priority package like pwchem not being installed
-                pass
+                logger.debug("Name is different!!: e.name='%s', name='%s'" %( e.name , name))
             else:
                 logger.warning("Plugin '%s' has import errors: %s. Maybe a missing dependency?. "
                                "Is it devel mode and need to be reinstalled?. Ignoring it and continuing." % (name, str(e)))
         except Exception as e:
 
-            (pwutils.yellow("WARNING!!: Plugin containing module %s does not import properly. "
+            logger.info(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))
@@ -390,56 +396,99 @@ class Domain:
     @classmethod
     def getPreferredViewers(cls, className):
         """ Find and import the preferred viewers for this class. """
-        viewerNames = pw.Config.VIEWERS.get(className, [])
-        if not isinstance(viewerNames, list):
-            viewerNames = [viewerNames]
-        viewers = []  # we will try to import them and store here
-        for prefViewerStr in viewerNames:
-            try:
-                viewerModule, viewerClassName = prefViewerStr.rsplit('.', 1)
-                prefViewer = cls.importFromPlugin(viewerModule,
-                                                  viewerClassName,
-                                                  doRaise=True)
-                viewers.append(prefViewer)
-            except Exception as e:
-                logger.error("Couldn't load \"%s\" as preferred viewer for %s.\n"
-                      "There might be a typo in your VIEWERS variable "
-                      "or an error in the viewer's plugin installation"
-                      % (prefViewerStr, className), exc_info=e)
-        return viewers
+
+        if cls._preferred_viewers is None:
+            logger.info("Caching preferred viewers from VIEWERS config variable.")
+            cls._preferred_viewers = dict()
+
+            for target, viewerNames in pw.Config.VIEWERS.items():
+                viewers = []
+                for prefViewerStr in viewerNames:
+                    try:
+                        viewerModule, viewerClassName = prefViewerStr.rsplit('.', 1)
+                        prefViewer = cls.importFromPlugin(viewerModule,
+                                                          viewerClassName,
+                                                          doRaise=True)
+                        viewers.append(prefViewer)
+                    except Exception as e:
+                        logger.error("Couldn't load \"%s\" as preferred viewer for %s.\n"
+                              "There might be a typo in your VIEWERS variable "
+                              "or an error in the viewer's plugin installation"
+                              % (prefViewerStr, className), exc_info=e)
+
+                cls._preferred_viewers[target] = viewers
+
+        return cls._preferred_viewers.get(className, [])
+
+    @classmethod
+    @lru_cache
+    def getViewersSorted(cls):
+        """ Returns all viewers sorted by its class name"""
+
+        viewers = cls.getViewers()
+        return [viewers[key] for key in sorted(viewers)]
 
     @classmethod
-    def findViewers(cls, className, environment):
-        """ Find the available viewers in this Domain for this class. """
+    def findViewers(cls, target, environment):
+        """ Find the available viewers in this Domain for this target.
+
+        Sorting criteria:
+
+        1st Will appear those viewers in VIEWERS variable (preferred viewers) in appearance order
+        2nd Viewers targeting specifically the target and not any super class of it
+        3rd rest.
+
+        In 2nd and 3rd case the order viewers are added depends on the alphabetical order the viewer when discovered.
+        This usually matches the viewer class name, but could be fine tune using import aliases like:
+
+        from my_viewer import MyViewer as AAAMyViewer in the viewers folder of the plugin.
+
+        In case viewers is a file and not a folder with an __init__, I'm afraid class name is what is taken into account
+
+        The import order is not possible to use since python sort them automatically.
+
+        """
         viewers = []
         try:
-            clazz = cls.findClass(className)
+            instance = None
+            if isinstance(target, str):
+                logger.warning("DEVELOPERS: pass the instance/object instead of the class. This mode will be deprecated soon")
+                className = target
+                clazz = cls.findClass(className)
+            else:
+                className = target.__class__.__name__
+                clazz = target.__class__
+                instance = target
+
             baseClasses = clazz.mro()
-            preferredViewers = cls.getPreferredViewers(className)
-            preferedFlag = 0
 
-            for viewer in cls.getViewers().values():
-                viewerAdded=False
+            # Add preferred viewers
+            preferred_viewers = []
+            available_preferred_viewers = cls.getPreferredViewers(className)
+            for prefViewer in available_preferred_viewers:
+                if prefViewer.can_handle_this(baseClasses, instance=instance):
+                    preferred_viewers.append(prefViewer)
+
+
+            specific_viewers = []
+            other_viewers=[]
+            # get all the viewers available
+
+            for viewer in cls.getViewersSorted():
+
                 if environment in viewer._environments:
-                    for t in viewer._targets:
-                        if t in baseClasses:
-                            for prefViewer in preferredViewers:
-                                if viewer is prefViewer:
-                                    viewers.insert(0, viewer)
-                                    viewerAdded=True
-                                    preferedFlag = 1
-                                    break
+
+                    if viewer not in preferred_viewers:
+
+                        t = viewer.can_handle_this(baseClasses, target)
+                        if t is not None:
+                            if t == clazz:
+                                specific_viewers.append(viewer)
+
                             else:
-                                if t == clazz:
-                                    viewers.insert(preferedFlag, viewer)
-                                    viewerAdded = True
-                                else:
-                                    viewers.append(viewer)
-                                    viewerAdded = True
-                                break
-
-                        if viewerAdded:
-                            break
+                                other_viewers.append(viewer)
+
+            viewers = preferred_viewers + specific_viewers + other_viewers
 
         except Exception as e:
             # Catch if there is a missing plugin, we will get Legacy which triggers and Exception