Source code for pyworkflow.gui.project.viewprotocols

# -*- coding: utf-8 -*-
# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin ( [1]
# *
# * [1] SciLifeLab, Stockholm University
# *
# * This program is free software: you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation, either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program.  If not, see <>.
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address ''
# *
# **************************************************************************
import logging
import threading

from pyworkflow.gui import TextFileViewer, getDefaultFont, LIST_TREEVIEW, ShortCut
from pyworkflow.gui.project.constants import ACTION_REFRESH, ACTION_EDIT, ACTION_COPY, ACTION_DELETE, ACTION_STEPS, \


View with the protocols inside the main project window.

import os
import json
import re
import tempfile
from collections import OrderedDict
import tkinter as tk
import tkinter.ttk as ttk
import datetime as dt

from pyworkflow import Config, TK
import pyworkflow.utils as pwutils
import pyworkflow.protocol as pwprot
from pyworkflow.viewer import DESKTOP_TKINTER, ProtocolViewer
from import Color, KEYSYM, Icon, Message
from pyworkflow.webservices import WorkflowRepository

import pyworkflow.gui as pwgui
from pyworkflow.gui.form import FormWindow
from pyworkflow.gui.project.utils import getStatusColorFromNode, inspectObj
from pyworkflow.gui.project.searchprotocol import SearchProtocolWindow, ProtocolTreeProvider
from pyworkflow.gui.project.steps import StepsWindow
from pyworkflow.gui.project.viewprotocols_extra import RunIOTreeProvider, ProtocolTreeConfig
from pyworkflow.gui.project.searchrun import RunsTreeProvider, SearchRunWindow

logger = logging.getLogger(__name__)




[docs]class ScipionLogWindow(pwgui.Window): """Class that create a windows where the system log is display """ def __init__(self, parentWindow, **kwargs): pwgui.Window.__init__(self, title="Scipion log", masterWindow=parentWindow, minsize=(1000, 400)) content = tk.Frame(self.root) content.grid(row=0, column=0, sticky='news') pwgui.configureWeigths(content) self.showScipionLog = threading.Thread(name="scipion_log", target=self._showScipionLog, args=(content,)) self.showScipionLog.start() def _showScipionLog(self, content): """ Create a content of the system log window """ # Fill the Output Log terminal = tk.Frame(content) terminal.grid(row=0, column=0, sticky='news') pwgui.configureWeigths(terminal) self.textLog = TextFileViewer(terminal, font=getDefaultFont(), height=30, width=100) self.textLog.grid(row=0, column=0, sticky='news') fileLogPath = Config.SCIPION_LOG self.fileLog = open(fileLogPath, 'r') # Create a tab where the log will appear self.textLog.createWidgets([fileLogPath]) self.textLog.refreshAll(goEnd=True) # Refreshing the log every 3 seconds self.threadRefresh = threading.Thread(name="refresh_log", target=self._refreshLogComponent, args=(3,)) self.threadRefresh.start() def _refreshLogComponent(self, wait=3): """ Refresh the Plugin Manager log """ import time while True: time.sleep(wait) # Taking the vertical scroll position. If this action fail, assume # that the log window was closed and finalized the refresh thread try: vsPos = self.textLog.taList[0].getVScroll() if vsPos[1] == 1.0: self.textLog.refreshAll(goEnd=True) else: self.textLog.refreshAll(goEnd=False) except Exception: break
# noinspection PyAttributeOutsideInit
[docs]class ProtocolsView(tk.Frame): """ What you see when the "Protocols" tab is selected. In the main project window there are three tabs: "Protocols | Data | Hosts". This extended tk.Frame is what will appear when Protocols is on. """ RUNS_CANVAS_NAME = "runs_canvas" _protocolViews = None def __init__(self, parent, windows, **args): tk.Frame.__init__(self, parent, **args) # Load global configuration = windows self.project = windows.project self.domain = self.project.getDomain() self.root = windows.root self.getImage = windows.getImage self.protCfg = self.getCurrentProtocolView() self.settings = windows.getSettings() self.runsView = self.settings.getRunsView() self._loadSelection() self._items = {} self._lastSelectedProtId = None self._lastStatus = None self.selectingArea = False self._lastRightClickPos = None # Keep last right-clicked position = ttk.Style() self.root.bind("<F5>", self.refreshRuns) self.root.bind("<Control-f>", self._findProtocol) self.root.bind("<Control-a>", self._selectAllProtocols) self.root.bind("<Control-t>", self._toggleColorScheme) self.root.bind("<Control-d>", self._toggleDebug) self.root.bind("<Control-l>", self._locateProtocol) self.root.bind("<F2>", self._F2Pressed) if Config.debugOn(): self.root.bind("<Control-i>", self._inspectProtocols) # To bind key press to methods # Listen to any key: send event to keyPressed method self.root.bind("<Key>", self.keyPressed) self.keybinds = dict() # Register key binds self._bindKeyPress(KEYSYM.DELETE, self._onDelPressed) self.__autoRefresh = None self.__autoRefreshCounter = INIT_REFRESH_SECONDS # start by 3 secs self.refreshSemaphore = True self.repeatRefresh = False c = self.createContent() pwgui.configureWeigths(self) c.grid(row=0, column=0, sticky='news') def _bindKeyPress(self, key, method): self.keybinds[key] = method
[docs] def keyPressed(self, event): if event.keysym in self.keybinds: method = self.keybinds[event.keysym] method()
[docs] def createContent(self): """ Create the Protocols View for the Project. It has two panes: Left: containing the Protocol classes tree Right: containing the Runs list """ p = tk.PanedWindow(self, orient=tk.HORIZONTAL, bg='white') bgColor = Color.LIGHT_GREY_COLOR # Left pane, contains Protocols Pane leftFrame = tk.Frame(p, bg=bgColor) leftFrame.columnconfigure(0, weight=1) leftFrame.rowconfigure(1, weight=1) # Protocols Tree Pane protFrame = tk.Frame(leftFrame, width=300, height=500, bg=bgColor) protFrame.grid(row=1, column=0, sticky='news', padx=5, pady=5) protFrame.columnconfigure(0, weight=1) protFrame.rowconfigure(1, weight=1) self._createProtocolsPanel(protFrame, bgColor) self.updateProtocolsTree(self.protCfg) # Create the right Pane that will be composed by: # a Action Buttons TOOLBAR in the top # and another vertical Pane with: # Runs History (at Top) # Selected run info (at Bottom) rightFrame = tk.Frame(p, bg='white') rightFrame.columnconfigure(0, weight=1) rightFrame.rowconfigure(1, weight=1) # rightFrame.rowconfigure(0, minsize=label.winfo_reqheight()) # Create the Action Buttons TOOLBAR toolbar = tk.Frame(rightFrame, bg='white') toolbar.grid(row=0, column=0, sticky='news') pwgui.configureWeigths(toolbar) # toolbar.columnconfigure(0, weight=1) toolbar.columnconfigure(1, weight=1) self.runsToolbar = tk.Frame(toolbar, bg='white') self.runsToolbar.grid(row=0, column=0, sticky='sw') # On the left of the toolbar will be other # actions that can be applied to all runs (refresh, graph view...) self.allToolbar = tk.Frame(toolbar, bg='white') self.allToolbar.grid(row=0, column=10, sticky='se') self.createActionToolbar() # Create the Run History tree v = ttk.PanedWindow(rightFrame, orient=tk.VERTICAL) # runsFrame = ttk.Labelframe(v, text=' History ', width=500, height=500) runsFrame = tk.Frame(v, bg='white') # runsFrame.grid(row=1, column=0, sticky='news', pady=5) self.runsTree = self.createRunsTree(runsFrame) pwgui.configureWeigths(runsFrame) self.createRunsGraph(runsFrame) if self.runsView == VIEW_LIST: treeWidget = self.runsTree else: treeWidget = self.runsGraphCanvas treeWidget.grid(row=0, column=0, sticky='news') # Create the Selected Run Info infoFrame = tk.Frame(v) infoFrame.columnconfigure(0, weight=1) infoFrame.rowconfigure(1, weight=1) # Create the info label self.infoLabel = tk.Label(infoFrame) self.infoLabel.grid(row=0, column=0, sticky='w', padx=3) # Create the Analyze results button self.btnAnalyze = pwgui.Button(infoFrame, text=Message.LABEL_ANALYZE, fg='white', bg=Color.RED_COLOR, image=self.getImage(Icon.ACTION_VISUALIZE), compound=tk.LEFT, activeforeground='white', activebackground='#A60C0C', command=self._analyzeResultsClicked) self.btnAnalyze.grid(row=0, column=0, sticky='ne', padx=15) #"W.TNotebook")#, background='white') tab = ttk.Notebook(infoFrame) # , style='W.TNotebook') # Summary tab dframe = tk.Frame(tab, bg='white') pwgui.configureWeigths(dframe, row=0) pwgui.configureWeigths(dframe, row=2) # Just configure the provider, later bellow, in updateSelection, it will be # provided with the protocols. provider = RunIOTreeProvider(self, None, self.project.mapper) rowheight = pwgui.getDefaultFont().metrics()['linespace']"NoBorder.Treeview", background='white', borderwidth=0,, rowheight=rowheight) self.infoTree = pwgui.browser.BoundTree(dframe, provider, height=6, show='tree', style="NoBorder.Treeview") self.infoTree.grid(row=0, column=0, sticky='news') label = tk.Label(dframe, text='SUMMARY', bg='white', label.grid(row=1, column=0, sticky='nw', padx=(15, 0)) hView = {'sci-open': self._viewObject, 'sci-bib': self._bibExportClicked} self.summaryText = pwgui.text.TaggedText(dframe, width=40, height=5, bg='white', bd=0,, handlers=hView) self.summaryText.grid(row=2, column=0, sticky='news', padx=(30, 0)) # Method tab mframe = tk.Frame(tab) pwgui.configureWeigths(mframe) # Methods text box self.methodText = pwgui.text.TaggedText(mframe, width=40, height=15, bg='white', handlers=hView) self.methodText.grid(row=0, column=0, sticky='news') # Reference export button # btnExportBib = pwgui.Button(mframe, text=Message.LABEL_BIB_BTN, # fg='white', bg=Color.RED_COLOR, # image=self.getImage(Icon.ACTION_BROWSE), # compound=tk.LEFT, # activeforeground='white', # activebackground='#A60C0C', # command=self._bibExportClicked) # btnExportBib.grid(row=2, column=0, sticky='w', padx=0) # Logs ologframe = tk.Frame(tab) pwgui.configureWeigths(ologframe) self.outputViewer = pwgui.text.TextFileViewer(ologframe, allowOpen=True, self.outputViewer.grid(row=0, column=0, sticky='news') = self._updateSelection() # Move to the selected protocol if self._isSingleSelection(): prot = self.getSelectedProtocol() node = self.runsGraph.getNode(str(prot.getObjId())) self._selectNode(node) # Add all tabs tab.add(dframe, text=Message.LABEL_SUMMARY) tab.add(mframe, text=Message.LABEL_METHODS) tab.add(ologframe, text=Message.LABEL_LOGS_OUTPUT) # tab.add(elogframe, text=Message.LABEL_LOGS_ERROR) # tab.add(slogframe, text=Message.LABEL_LOGS_SCIPION) tab.grid(row=1, column=0, sticky='news') v.add(runsFrame, weight=1) v.add(infoFrame, weight=20) v.grid(row=1, column=0, sticky='news') # Add sub-windows to PanedWindows p.add(leftFrame, padx=0, pady=0, sticky='news') p.add(rightFrame, padx=0, pady=0) p.paneconfig(leftFrame, minsize=5) leftFrame.config(width=235) p.paneconfig(rightFrame, minsize=10) return p
def _viewObject(self, objId): """ Call appropriate viewer for objId. """ proj = self.project obj = proj.getObject(int(objId)) viewerClasses = self.domain.findViewers(obj.getClassName(), DESKTOP_TKINTER) if not viewerClasses: return # TODO: protest nicely viewer = viewerClasses[0](project=proj, viewer.visualize(obj) def _loadSelection(self): """ Load selected items, remove if some do not exists. """ self._selection = self.settings.runSelection for protId in list(self._selection): if not self.project.doesProtocolExists(protId): self._selection.remove(protId) def _isMultipleSelection(self): return len(self._selection) > 1 def _isSingleSelection(self): return len(self._selection) == 1 def _noSelection(self): return len(self._selection) == 0
[docs] def info(self, message): self.infoLabel.config(text=message) self.infoLabel.update_idletasks()
[docs] def cleanInfo(self):"")
[docs] def refreshRuns(self, e=None, initRefreshCounter=True, checkPids=False): """ Refresh the protocol runs workflow. If the variable REFRESH_WITH_THREADS exits, then use a threads to refresh, i.o.c use normal behavior """ useThreads = Config.refreshInThreads() if useThreads: import threading # Refresh the status of displayed runs. if self.refreshSemaphore: # print("Launching a thread to refresh the runs...") threadRefreshRuns = threading.Thread(name="Refreshing runs", target=self.refreshDisplayedRuns, args=(e, initRefreshCounter, checkPids)) threadRefreshRuns.start() else: self.repeatRefresh = True else: self.refreshDisplayedRuns(e, initRefreshCounter, checkPids)
# noinspection PyUnusedLocal
[docs] def refreshDisplayedRuns(self, e=None, initRefreshCounter=True, checkPids=False): """ Refresh the status of displayed runs. Params: e: Tk event input initRefreshCounter: if True the refresh counter will be set to 3 secs then only case when False is from _automaticRefreshRuns where the refresh time is doubled each time to avoid refreshing too often. """ self.viewButtons[ACTION_REFRESH]['state'] = tk.DISABLED'Refreshing...') self.refreshSemaphore = False if Config.debugOn(): import psutil proc = psutil.Process(os.getpid()) mem = psutil.virtual_memory() logger.debug("------------- refreshing ---------- ") files = proc.open_files() logger.debug(" open files: %s" % len(files)) for f in files: logger.debug(" - %s, %s" % (f.path, f.fd)) logger.debug(" memory percent: %s" % proc.memory_percent()) if self.runsView == VIEW_LIST: self.updateRunsTree(True) else: self.updateRunsGraph(True, checkPids=checkPids) self._updateSelection() if initRefreshCounter: self.__autoRefreshCounter = INIT_REFRESH_SECONDS # start by 3 secs if self.__autoRefresh: self.runsTree.after_cancel(self.__autoRefresh) self.__autoRefresh = self.runsTree.after( self.__autoRefreshCounter * 1000, self._automaticRefreshRuns) self.refreshSemaphore = True if self.repeatRefresh: self.repeatRefresh = False self.refreshRuns() self.cleanInfo() self.viewButtons[ACTION_REFRESH]['state'] = tk.NORMAL
# noinspection PyUnusedLocal def _automaticRefreshRuns(self, e=None): """ Schedule automatic refresh increasing the time between refreshes. """ if pwutils.envVarOn('DO_NOT_AUTO_REFRESH'): return self.refreshRuns(initRefreshCounter=False, checkPids=True) secs = self.__autoRefreshCounter # double the number of seconds up to 30 min self.__autoRefreshCounter = min(2 * secs, 1800) self.__autoRefresh = self.runsTree.after(secs * 1000, self._automaticRefreshRuns) # noinspection PyUnusedLocal def _findProtocol(self, e=None): """ Find a desired protocol by typing some keyword. """ window = SearchProtocolWindow( def _locateProtocol(self, e=None): window = SearchRunWindow(, self.runsGraph, onDoubleClick=self._onRunClick) # self._moveCanvas(0,1) def _onRunClick(self, e=None): """ Callback to be called when a click happens o a run in the SearchRunWindow.tree""" tree = e.widget protId = tree.getFirst() node = self.runsGraph.getNode(protId) self._selectNode(node) def _selectNode(self, node): x = node.x y = node.y self._moveCanvas(x,y) # Select the protocol self._selectItemProtocol( self.refreshDisplayedRuns() def _moveCanvas(self, X, Y): self.runsGraphCanvas.moveTo(X, Y) def _scipionLog(self, e=None): windows = ScipionLogWindow(
[docs] def createActionToolbar(self): """ Prepare the buttons that will be available for protocol actions. """ self.actionButtons = {} self.actionList = [ACTION_EDIT, ACTION_COPY, ACTION_DELETE, ACTION_STEPS, ACTION_BROWSE, ACTION_DB, ACTION_STOP, ACTION_CONTINUE, ACTION_RESULTS, ACTION_EXPORT, ACTION_EXPORT_UPLOAD, ACTION_COLLAPSE, ACTION_EXPAND, ACTION_LABELS, ACTION_SEARCH] def addButton(action, text, toolbar): btn = tk.Label(toolbar, text=text, image=self.getImage(ActionIcons.get(action, None)), compound=tk.LEFT, cursor='hand2', bg='white') btn.bind(TK.LEFT_CLICK, lambda e: self._runActionClicked(action)) return btn for action in self.actionList: self.actionButtons[action] = addButton(action, action, self.runsToolbar) ActionIcons[ACTION_TREE] = RUNS_TREE self.viewButtons = {} # Add combo for switch between views viewFrame = tk.Frame(self.allToolbar) viewFrame.grid(row=0, column=0) self._createViewCombo(viewFrame) # Add refresh Tree button btn = addButton(ACTION_TREE, " ", self.allToolbar) pwgui.tooltip.ToolTip(btn, "Re-organize the node positions.", 1500) self.viewButtons[ACTION_TREE] = btn if self.runsView != VIEW_LIST: btn.grid(row=0, column=1) # Add refresh button btn = addButton(ACTION_REFRESH, ACTION_REFRESH, self.allToolbar) btn.grid(row=0, column=2) self.viewButtons[ACTION_REFRESH] = btn
def _createViewCombo(self, parent): """ Create the select-view combobox. """ label = tk.Label(parent, text='View:', bg='white') label.grid(row=0, column=0) viewChoices = ['List', 'Tree', 'Tree - small'] self.switchCombo = pwgui.widgets.ComboBox(parent, width=10, choices=viewChoices, values=[VIEW_LIST, VIEW_TREE, VIEW_TREE_SMALL], initial=viewChoices[self.runsView], onChange=lambda e: self._runActionClicked( ACTION_SWITCH_VIEW)) self.switchCombo.grid(row=0, column=1) def _updateActionToolbar(self): """ Update which action buttons should be visible. """ def displayAction(actionToDisplay, column, condition=True): """ Show/hide the action button if the condition is met. """ # If action present (set color is not in the toolbar but in the # context menu) action = self.actionButtons.get(actionToDisplay, None) if action is not None: if condition: action.grid(row=0, column=column, sticky='sw', padx=(0, 5), ipadx=0) else: action.grid_remove() for i, actionTuple in enumerate(self.provider.getActionsFromSelection()): action, cond = actionTuple displayAction(action, i, cond) def _createProtocolsTree(self, parent, show='tree', columns=None): t = pwgui.tree.Tree(parent, show=show, style=LIST_TREEVIEW, columns=columns) t.column('#0', minwidth=300) def configureTag(tag, img): # Protocol nodes t.tag_configure(tag, image=self.getImage(img)) t.tag_bind(tag, TK.LEFT_DOUBLE_CLICK, self._protocolItemClick) t.tag_bind(tag, TK.RETURN, self._protocolItemClick) t.tag_bind(tag, TK.ENTER, self._protocolItemClick) # Protocol nodes configureTag(ProtocolTreeConfig.TAG_PROTOCOL, 'python_file.gif') # New protocols configureTag(ProtocolTreeConfig.TAG_PROTOCOL_NEW, 'new.gif') # Beta protocols configureTag(ProtocolTreeConfig.TAG_PROTOCOL_BETA, 'beta.gif') # Disable protocols (not installed) are allowed to be added. configureTag(ProtocolTreeConfig.TAG_PROTOCOL_DISABLED, 'prot_disabled.gif') t.tag_configure('protocol_base', image=self.getImage('class_obj.gif')) t.tag_configure('protocol_group', image=self.getImage('class_obj.gif')) t.tag_configure('section', return t def _createProtocolsPanel(self, parent, bgColor): """Create the protocols Tree displayed in left panel""" comboFrame = tk.Frame(parent, bg=bgColor) tk.Label(comboFrame, text='View', bg=bgColor).grid(row=0, column=0, padx=(0, 5), pady=5) choices = self.getProtocolViews() initialChoice = self.settings.getProtocolView() combo = pwgui.widgets.ComboBox(comboFrame, choices=choices, initial=initialChoice) combo.setChangeCallback(self._onSelectProtocols) combo.grid(row=0, column=1) comboFrame.grid(row=0, column=0, padx=5, pady=5, sticky='nw') t = self._createProtocolsTree(parent) t.grid(row=1, column=0, sticky='news') # Program automatic refresh t.after(3000, self._automaticRefreshRuns) self.protTree = t
[docs] def getProtocolViews(self): if self._protocolViews is None: self._loadProtocols() return list(self._protocolViews.keys())
[docs] def getCurrentProtocolView(self): """ Select the view that is currently selected. Read from the settings the last selected view and get the information from the self._protocolViews dict. """ currentView = self.project.getProtocolView() if currentView in self.getProtocolViews(): viewKey = currentView else: viewKey = self.getProtocolViews()[0] self.project.settings.setProtocolView(viewKey) if currentView is not None: print("PROJECT: Warning, protocol view '%s' not found." % currentView) print(" Using '%s' instead." % viewKey) return self._protocolViews[viewKey]
def _loadProtocols(self): """ Load protocol configuration from a .conf file. """ # If the host file is not passed as argument... configProtocols = Config.SCIPION_PROTOCOLS localDir = Config.SCIPION_LOCAL_CONFIG protConf = os.path.join(localDir, configProtocols) self._protocolViews = ProtocolTreeConfig.load(self.project.getDomain(), protConf) def _onSelectProtocols(self, combo): """ This function will be called when a protocol menu is selected. The index of the new menu is passed. """ protView = combo.getText() self.settings.setProtocolView(protView) self.protCfg = self.getCurrentProtocolView() self.updateProtocolsTree(self.protCfg)
[docs] def populateTree(self, tree, treeItems, prefix, obj, subclassedDict, level=0): # If node does not have leaves (protocols) do not add it if not obj.visible: return text = obj.text if text: value = obj.value if obj.value is not None else text key = '%s.%s' % (prefix, value) img = obj.icon if obj.icon is not None else '' tag = obj.tag if obj.tag is not None else '' if len(img): img = self.getImage(img) # If image is none img = img if img is not None else '' protClassName = value.split('.')[-1] # Take last part emProtocolsDict = self.domain.getProtocols() prot = emProtocolsDict.get(protClassName, None) if tag == 'protocol' and text == 'default': if prot is None: print("Protocol className '%s' not found!!!. \n" "Fix your config/protocols.conf configuration." % protClassName) return text = prot.getClassLabel() item = tree.insert(prefix, 'end', key, text=text, image=img, tags=tag) treeItems[item] = obj # Check if the attribute should be open or close openItem = getattr(obj, 'openItem', level < 2) if openItem: tree.item(item, open=openItem) # I think this mode is deprecated if obj.value is not None and tag == 'protocol_base': print('protocol_base tags are deprecated') # if prot is not None: # tree.item(item, image=self.getImage('class_obj.gif')) # # for k, v in emProtocolsDict.items(): # if (k not in subclassedDict and v is not prot and # issubclass(v, prot)): # key = '%s.%s' % (item, k) # t = v.getClassLabel() # tree.insert(item, 'end', key, text=t, tags='protocol') # else: # raise Exception("Class '%s' not found" % obj.value.get()) else: key = prefix for sub in obj: self.populateTree(tree, treeItems, key, sub, subclassedDict, level + 1)
[docs] def updateProtocolsTree(self, protCfg): try: self.protCfg = protCfg self.protTree.clear() self.protTree.unbind(TK.TREEVIEW_OPEN) self.protTree.unbind(TK.TREEVIEW_CLOSE) self.protTreeItems = {} subclassedDict = {} # Check which classes serve as base to not show them emProtocolsDict = self.domain.getProtocols() for _, v1 in emProtocolsDict.items(): for k2, v2 in emProtocolsDict.items(): if v1 is not v2 and issubclass(v1, v2): subclassedDict[k2] = True self.populateTree(self.protTree, self.protTreeItems, '', self.protCfg, subclassedDict) self.protTree.bind(TK.TREEVIEW_OPEN, lambda e: self._treeViewItemChange(True)) self.protTree.bind(TK.TREEVIEW_CLOSE, lambda e: self._treeViewItemChange(False)) except Exception as e: # Tree can't be loaded report back, but continue print("Protocols tree couldn't be loaded: %s" % e)
def _treeViewItemChange(self, openItem): item = self.protTree.focus() if item in self.protTreeItems: self.protTreeItems[item].openItem = openItem
[docs] def createRunsTree(self, parent): self.provider = RunsTreeProvider(self.project, self._runActionClicked) # This line triggers the getRuns for the first time. # Ne need to force the check pids here, temporary self.provider._checkPids = True t = pwgui.tree.BoundTree(parent, self.provider, style=LIST_TREEVIEW) self.provider._checkPids = False t.itemDoubleClick = self._runItemDoubleClick t.itemClick = self._runTreeItemClick return t
[docs] def updateRunsTree(self, refresh=False): self.provider.setRefresh(refresh) self.runsTree.update() self.updateRunsTreeSelection()
[docs] def updateRunsTreeSelection(self): for prot in self._iterSelectedProtocols(): treeId = self.provider.getObjectFromId(prot.getObjId())._treeId self.runsTree.selection_add(treeId)
[docs] def createRunsGraph(self, parent): self.runsGraphCanvas = pwgui.Canvas(parent, width=400, height=400, tooltipCallback=self._runItemTooltip, tooltipDelay=1000, name=ProtocolsView.RUNS_CANVAS_NAME, takefocus=True, highlightthickness=0) self.runsGraphCanvas.onClickCallback = self._runItemClick self.runsGraphCanvas.onDoubleClickCallback = self._runItemDoubleClick self.runsGraphCanvas.onRightClickCallback = self._runItemRightClick self.runsGraphCanvas.onControlClickCallback = self._runItemControlClick self.runsGraphCanvas.onAreaSelected = self._selectItemsWithinArea self.runsGraphCanvas.onMiddleMouseClickCallback = self._runItemMiddleClick parent.grid_columnconfigure(0, weight=1) parent.grid_rowconfigure(0, weight=1) self.settings.getNodes().updateDict() self.settings.getLabels().updateDict() self.updateRunsGraph()
[docs] def updateRunsGraph(self, refresh=False, reorganize=False, checkPids=False): self.runsGraph = self.project.getRunsGraph(refresh=refresh, checkPids=checkPids) self.drawRunsGraph(reorganize)
[docs] def drawRunsGraph(self, reorganize=False): # Check if there are positions stored if reorganize: # Create layout to arrange nodes as a level tree layout = pwgui.LevelTreeLayout() self.runsGraphCanvas.reorganizeGraph(self.runsGraph, layout) else: self.runsGraphCanvas.clear() layout = pwgui.LevelTreeLayout() if len( self.settings.getNodes()) == 0 else pwgui.BasicLayout() # Create empty nodeInfo for new runs for node in self.runsGraph.getNodes(): nodeId = if else 0 nodeInfo = self.settings.getNodeById(nodeId) if nodeInfo is None: self.settings.addNode(nodeId, x=0, y=0, expanded=True, visible=True) self.runsGraphCanvas.drawGraph(self.runsGraph, layout, drawNode=self.createRunItem, nodeList=self.settings.nodeList)
[docs] def createRunItem(self, canvas, node): nodeId = if else 0 nodeInfo = self.settings.getNodeById(nodeId) # Extend attributes: use some from nodeInfo node.expanded = nodeInfo.isExpanded() node.x, node.y = nodeInfo.getPosition() node.visible = nodeInfo.isVisible() nodeText = self._getNodeText(node) # Get status color statusColor = getStatusColorFromNode(node) # Get the box color (depends on color mode: label or status) boxColor = self._getBoxColor(nodeInfo, statusColor, node) # Draw the box item = RunBox(nodeInfo, self.runsGraphCanvas, nodeText, node.x, node.y, bgColor=boxColor, textColor='black') # No border item.margin = 0 # Paint the oval..if apply. self._paintOval(item, statusColor) # Paint the bottom line (for now only labels are painted there). self._paintBottomLine(item) item.setSelected(nodeId in self._selection) return item
def _getBoxColor(self, nodeInfo, statusColor, node): try: # If the color has to go to the box if self.settings.statusColorMode(): boxColor = statusColor elif self.settings.ageColorMode(): if # Project elapsed time elapsedTime = creationTime = # Get the latest activity timestamp ts = if elapsedTime is None or creationTime is None or ts is None: boxColor = DEFAULT_BOX_COLOR else: # tc closer to the end are younger protAge = ts - creationTime boxColor = self._ageColor('#6666ff', elapsedTime, protAge) else: boxColor = DEFAULT_BOX_COLOR # ... box is for the labels. elif self.settings.labelsColorMode(): # If there is only one label use the box for the color. if self._getLabelsCount(nodeInfo) == 1: labelId = nodeInfo.getLabels()[0] label = self.settings.getLabels().getLabel(labelId) # If there is no label (it has been deleted) if label is None: nodeInfo.getLabels().remove(labelId) boxColor = DEFAULT_BOX_COLOR else: boxColor = label.getColor() else: boxColor = DEFAULT_BOX_COLOR else: boxColor = DEFAULT_BOX_COLOR return boxColor except Exception as e: return DEFAULT_BOX_COLOR @staticmethod def _ageColor(rgbColor, projectAge, protocolAge): # Get the ratio ratio = protocolAge.seconds / float(projectAge.seconds) # Invert direction: older = white = 100%, newest = rgbColor = 0% ratio = 1 - ratio # There are cases coming with protocols older than the project. ratio = 0 if ratio < 0 else ratio return pwutils.rgb_to_hex(pwutils.lighter(pwutils.hex_to_rgb(rgbColor), ratio)) @staticmethod def _getLabelsCount(nodeInfo): return 0 if nodeInfo.getLabels() is None else len(nodeInfo.getLabels()) def _paintBottomLine(self, item): if self.settings.labelsColorMode(): self._addLabels(item) def _paintOval(self, item, statusColor): # Show the status as a circle in the top right corner if not self.settings.statusColorMode(): # Option: Status item. (topLeftX, topLeftY, bottomRightX, bottomRightY) = self.runsGraphCanvas.bbox( statusSize = 10 statusX = bottomRightX - (statusSize + 3) statusY = topLeftY + 3 pwgui.Oval(self.runsGraphCanvas, statusX, statusY, statusSize, color=statusColor, anchor=item) # in statusColorMode else: # Show a black circle if there is any label if self._getLabelsCount(item.nodeInfo) > 0: (topLeftX, topLeftY, bottomRightX, bottomRightY) = self.runsGraphCanvas.bbox( statusSize = 10 statusX = bottomRightX - (statusSize + 3) statusY = topLeftY + 3 pwgui.Oval(self.runsGraphCanvas, statusX, statusY, statusSize, color='black', anchor=item) def _getNodeText(self, node): nodeText = node.getLabel() # Truncate text to prevent overflow if len(nodeText) > 40: nodeText = nodeText[:37] + "..." if expandedStr = '' if node.expanded else '\n%s more' % str(node.countChilds({})) if self.runsView == VIEW_TREE_SMALL: nodeText = node.getName() + expandedStr else: nodeText += expandedStr + '\n' + if not expandedStr else expandedStr if nodeText += u' \u26a0' return nodeText 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: return # Get the positions of the box (topLeftX, topLeftY, bottomRightX, bottomRightY) = self.runsGraphCanvas.bbox( # Get the width of the box boxWidth = bottomRightX - topLeftX # Set the size marginV = 3 marginH = 2 labelWidth = (boxWidth - (2 * marginH)) / len(item.nodeInfo.getLabels()) labelHeight = 6 # Leave some margin on the right and bottom labelX = bottomRightX - marginH labelY = bottomRightY - (labelHeight + marginV) for index, labelId in enumerate(item.nodeInfo.getLabels()): # Get the label label = self.settings.getLabels().getLabel(labelId) # If not none if label is not None: # Move X one label to the left if index == len(item.nodeInfo.getLabels()) - 1: labelX = topLeftX + marginH else: labelX -= labelWidth pwgui.Rectangle(self.runsGraphCanvas, labelX, labelY, labelWidth, labelHeight, color=label.getColor(), anchor=item) else: item.nodeInfo.getLabels().remove(labelId)
[docs] def switchRunsView(self): viewValue = self.switchCombo.getValue() self.runsView = viewValue self.settings.setRunsView(viewValue) if viewValue == VIEW_LIST: self.runsTree.grid(row=0, column=0, sticky='news') self.runsGraphCanvas.frame.grid_remove() self.updateRunsTree() self.viewButtons[ACTION_TREE].grid_remove() self._lastRightClickPos = None else: self.runsTree.grid_remove() self.updateRunsGraph() self.runsGraphCanvas.frame.grid(row=0, column=0, sticky='news') self.viewButtons[ACTION_TREE].grid(row=0, column=1)
def _protocolItemClick(self, e=None): # Get the tree widget that originated the event # it could be the left panel protocols tree or just # the search protocol dialog tree tree = e.widget protClassName = tree.getFirst().split('.')[-1] protClass = self.domain.getProtocols().get(protClassName) prot = self.project.newProtocol(protClass) self._openProtocolForm(prot, disableRunMode=True) def _toggleColorScheme(self, e=None): currentMode = self.settings.getColorMode() if currentMode >= len(self.settings.COLOR_MODES) - 1: currentMode = -1 nextColorMode = currentMode + 1 self.settings.setColorMode(nextColorMode) self._updateActionToolbar() # self.updateRunsGraph() self.drawRunsGraph() def _toggleDebug(self, e=None): Config.toggleDebug() def _selectAllProtocols(self, e=None): self._selection.clear() # WHY GOING TO THE db? # Let's try using in memory data. # for prot in self.project.getRuns(): for prot in self.project.runs: self._selection.append(prot.getObjId()) self._updateSelection() # self.updateRunsGraph() self.drawRunsGraph() def _inspectProtocols(self, e=None): objs = self._getSelectedProtocols() # We will inspect the selected objects or # the whole project is no protocol is selected if len(objs) > 0: objs.sort(key=lambda obj: obj._objId, reverse=True) filePath = objs[0]._getLogsPath('inspector.csv') doInspect = True else: proj = self.project filePath = proj.getLogPath('inspector.csv') objs = [proj] doInspect = pwgui.dialog.askYesNo(Message.TITLE_INSPECTOR, Message.LABEL_INSPECTOR, self.root) if doInspect: inspectObj(objs, filePath) # we open the resulting CSV file with the OS default software pwgui.text.openTextFileEditor(filePath) # NOt used!: pconesa 02/11/2016. # def _deleteSelectedProtocols(self, e=None): # # for selection in self._selection: # self.project.getProtocol(self._selection[0]) # # # self._updateSelection() # self.updateRunsGraph() def _updateSelection(self): self._fillSummary() self._fillMethod() self._fillLogs() self._showHideAnalyzeResult() if self._isSingleSelection(): last = self.getSelectedProtocol() self._lastSelectedProtId = last.getObjId() if last else None self._updateActionToolbar() def _runTreeItemClick(self, item=None): self._selection.clear() for prot in self.runsTree.iterSelectedObjects(): self._selection.append(prot.getObjId()) self._updateSelection() def _selectItemProtocol(self, prot): """ Call this function when a new box (item) of a protocol is selected. It should be called either from itemClick or itemRightClick """ self._selection.clear() self.settings.dataSelection.clear() self._selection.append(prot.getObjId()) # Select output data too self.toggleDataSelection(prot, True) self._updateSelection() self.runsGraphCanvas.update_idletasks() def _deselectItems(self, item): """ Deselect all items except the item one """ g = self.project.getRunsGraph() for node in g.getNodes(): if and in self._selection: # This option is only for compatibility with all projects if hasattr(node, 'item'): node.item.setSelected(False) item.setSelected(True) def _runItemClick(self, item=None): # If click is in a empty area....start panning if item is None: print("Click on empty area") return self.runsGraphCanvas.focus_set() # Get last selected item for tree or graph if self.runsView == VIEW_LIST: prot = self.project.mapper.selectById(int(self.runsTree.getFirst())) else: prot = if prot is None: # in case it is the main "Project" node return self._deselectItems(item) self._selectItemProtocol(prot) def _runItemDoubleClick(self, e=None): if e.nodeInfo.isExpanded(): self._runActionClicked(ACTION_EDIT) def _runItemMiddleClick(self, e=None): self._runActionClicked(ACTION_SELECT_TO) def _runItemRightClick(self, item=None): prot = if prot is None: # in case it is the main "Project" node return n = len(self._selection) # Only select item with right-click if there is a single # item selection, not for multiple selection if n <= 1: self._deselectItems(item) self._selectItemProtocol(prot) self._lastRightClickPos = self.runsGraphCanvas.eventPos return self.provider.getObjectActions(prot) def _runItemControlClick(self, item=None): # Get last selected item for tree or graph if self.runsView == VIEW_LIST: # TODO: Prot is not used!! prot = self.project.mapper.selectById(int(self.runsTree.getFirst())) else: prot = protId = prot.getObjId() if protId in self._selection: item.setSelected(False) self._selection.remove(protId) # Remove data selected self.toggleDataSelection(prot, False) else: item.setSelected(True) if len(self._selection) == 1: # repaint first selected item firstSelectedNode = self.runsGraph.getNode(str(self._selection[0])) if hasattr(firstSelectedNode, 'item'): firstSelectedNode.item.setSelected(False) firstSelectedNode.item.setSelected(True) self._selection.append(prot.getObjId()) # Select output data too self.toggleDataSelection(prot, True) self._updateSelection()
[docs] def toggleDataSelection(self, prot, append): # Go through the data selection for paramName, output in prot.iterOutputAttributes(): if append: self.settings.dataSelection.append(output.getObjId()) else: self.settings.dataSelection.remove(output.getObjId())
def _runItemTooltip(self, tw, item): """ Create the contents of the tooltip to be displayed for the given item. Params: tw: a tk.TopLevel instance (ToolTipWindow) item: the selected item. """ prot = if prot: tm = '*%s*\n' % prot.getRunName() tm += 'Identifier :%s\n' % prot.getObjId() 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)) if not hasattr(tw, 'tooltipText'): frame = tk.Frame(tw) frame.grid(row=0, column=0) tw.tooltipText = pwgui.dialog.createMessageBody(frame, tm, None, textPad=0, textBg=Color.LIGHT_GREY_COLOR_2) tw.tooltipText.config(bd=1, relief=tk.RAISED) else: pwgui.dialog.fillMessageText(tw.tooltipText, tm) @staticmethod def _selectItemsWithinArea(x1, y1, x2, y2, enclosed=False): """ Parameters ---------- x1: x coordinate of first corner of the area y1: y coordinate of first corner of the area x2: x coordinate of second corner of the area y2: y coordinate of second corner of the area enclosed: Default True. Returns enclosed items, overlapping items otherwise. Returns ------- Nothing """ return # NOT working properly: Commented for the moment. # if enclosed: # items = self.runsGraphCanvas.find_enclosed(x1, y1, x2, y2) # else: # items = self.runsGraphCanvas.find_overlapping(x1, y1, x2, y2) # # update = False # # for itemId in items: # if itemId in self.runsGraphCanvas.items: # # item = self.runsGraphCanvas.items[itemId] # if not item.node.isRoot(): # item.setSelected(True) # self._selection.append(itemId) # update = True # # if update is not None: self._updateSelection() def _openProtocolForm(self, prot, disableRunMode=False): """Open the Protocol GUI Form given a Protocol instance""" w = FormWindow(Message.TITLE_NAME_RUN + prot.getClassName(), prot, self._executeSaveProtocol,, hostList=self.project.getHostNames(), updateProtocolCallback=self._updateProtocol, disableRunMode=disableRunMode) w.adjustSize() def _browseSteps(self): """ Open a new window with the steps list. """ window = StepsWindow(Message.TITLE_BROWSE_DATA,, self.getSelectedProtocol()) def _browseRunData(self): provider = ProtocolTreeProvider(self.getSelectedProtocol()) window = pwgui.browser.BrowserWindow(Message.TITLE_BROWSE_DATA, window.setBrowser(pwgui.browser.ObjectBrowser(window.root, provider)) window.itemConfig(self.getSelectedProtocol(), open=True) def _browseRunDirectory(self): """ Open a file browser to inspect the files generated by the run. """ protocol = self.getSelectedProtocol() workingDir = protocol.getWorkingDir() if os.path.exists(workingDir): protFolderShortCut = ShortCut.factory(workingDir,name="Protocol folder", icon=None ,toolTip="Protocol directory") window = pwgui.browser.FileBrowserWindow("Browsing: " + workingDir,, path=workingDir, shortCuts=[protFolderShortCut]) else:"Protocol working dir does not exists: \n %s" % workingDir) def _iterSelectedProtocols(self): for protId in sorted(self._selection): prot = self.project.getRunsGraph().getNode(str(protId)).run if prot: yield prot def _getSelectedProtocols(self): return [prot for prot in self._iterSelectedProtocols()] def _iterSelectedNodes(self): for protId in sorted(self._selection): node = self.settings.getNodeById(protId) yield node def _getSelectedNodes(self): return [node for node in self._iterSelectedNodes()]
[docs] def getSelectedProtocol(self): if self._selection: return self.project.getProtocol(self._selection[0]) return None
def _showHideAnalyzeResult(self): if self._selection: self.btnAnalyze.grid() else: self.btnAnalyze.grid_remove() def _fillSummary(self): self.summaryText.setReadOnly(False) self.summaryText.clear() self.infoTree.clear() n = len(self._selection) if n == 1: prot = self.getSelectedProtocol() if prot: provider = RunIOTreeProvider(self, prot, self.project.mapper) self.infoTree.setProvider(provider) self.infoTree.grid(row=0, column=0, sticky='news') self.infoTree.update_idletasks() # Update summary self.summaryText.addText(prot.summary()) else: self.infoTree.clear() elif n > 1: self.infoTree.clear() for prot in self._iterSelectedProtocols(): self.summaryText.addLine('> _%s_' % prot.getRunName()) for line in prot.summary(): self.summaryText.addLine(line) self.summaryText.addLine('') self.summaryText.setReadOnly(True) def _fillMethod(self): try: self.methodText.setReadOnly(False) self.methodText.clear() self.methodText.addLine("*METHODS:*") cites = OrderedDict() for prot in self._iterSelectedProtocols(): self.methodText.addLine('> _%s_' % prot.getRunName()) for line in prot.getParsedMethods(): self.methodText.addLine(line) cites.update(prot.getCitations()) cites.update(prot.getPackageCitations()) self.methodText.addLine('') if cites: self.methodText.addLine('*REFERENCES:* ' ' [[sci-bib:][<<< Open as bibtex >>>]]') for cite in cites.values(): self.methodText.addLine(cite) self.methodText.setReadOnly(True) except Exception as e: self.methodText.addLine('Could not load all methods:' + str(e)) def _fillLogs(self): try: prot = self.getSelectedProtocol() if not self._isSingleSelection() or not prot: self.outputViewer.clear() self._lastStatus = None elif prot.getObjId() != self._lastSelectedProtId: self._lastStatus = prot.getStatus() i = self.outputViewer.getIndex() self.outputViewer.clear() # Right now skip the err tab since we are redirecting # stderr to stdout out, err, schedule = prot.getLogPaths() self.outputViewer.addFile(out) self.outputViewer.addFile(err) if os.path.exists(schedule): self.outputViewer.addFile(schedule) elif i == 2: i = 0 self.outputViewer.setIndex(i) # Preserve the last selected tab self.outputViewer.selectedText().goEnd() # when there are not logs, force re-load next time if (not os.path.exists(out) or not os.path.exists(err)): self._lastStatus = None elif prot.isActive() or prot.getStatus() != self._lastStatus: doClear = self._lastStatus is None self._lastStatus = prot.getStatus() self.outputViewer.refreshAll(clear=doClear, goEnd=doClear) except Exception as e:"Something went wrong filling %s's logs: %s. Check terminal for details" % (prot, e)) import traceback traceback.print_exc() def _scheduleRunsUpdate(self, secs=1): # self.runsTree.after(secs*1000, self.refreshRuns)
[docs] def executeProtocol(self, prot): """ Function to execute a protocol called not directly from the Form "Execute" button. """ # We need to equeue the execute action # to be executed in the same thread self._executeSaveProtocol(prot))
def _executeSaveProtocol(self, prot, onlySave=False, doSchedule=False): if onlySave: self.project.saveProtocol(prot) msg = Message.LABEL_SAVED_FORM # msg = "Protocol successfully saved." else: if doSchedule: self.project.scheduleProtocol(prot) else: self.project.launchProtocol(prot) # Select the launched protocol to display its summary, methods..etc self._selection.clear() self._selection.append(prot.getObjId()) self._updateSelection() self._lastStatus = None # clear lastStatus to force re-load the logs msg = "" # Update runs list display, even in save we # need to get the updated copy of the protocol self._scheduleRunsUpdate() self._selectItemProtocol(prot) return msg def _updateProtocol(self, prot): """ Callback to notify about the change of a protocol label or comment. """ self._scheduleRunsUpdate() def _continueProtocol(self, prot): self.project.continueProtocol(prot) self._scheduleRunsUpdate() def _onDelPressed(self): # This function will be connected to the key 'Del' press event # We need to check if the canvas have the focus and then # proceed with the delete action # get the widget with the focus widget = self.focus_get() # Call the delete action only if the widget is the canvas if str(widget).endswith(ProtocolsView.RUNS_CANVAS_NAME): try: self._deleteProtocol() except Exception as ex: def _deleteProtocol(self): protocols = self._getSelectedProtocols() if len(protocols) == 0: return protStr = '\n - '.join(['*%s*' % p.getRunName() for p in protocols]) if pwgui.dialog.askYesNo(Message.TITLE_DELETE_FORM, Message.LABEL_DELETE_FORM % protStr, self.root):'Deleting protocols...') self.project.deleteProtocol(*protocols) self._selection.clear() self._updateSelection() self._scheduleRunsUpdate() self.cleanInfo() def _F2Pressed(self, event): """ Invoked then F2 if pressed: Protocol rename""" self._runActionClicked(ACTION_RENAME) def _editProtocol(self, protocol): disableRunMode = False if protocol.isSaved(): disableRunMode = True self._openProtocolForm(protocol, disableRunMode=disableRunMode) def _copyProtocols(self): protocols = self._getSelectedProtocols() if len(protocols) == 1: newProt = self.project.copyProtocol(protocols[0]) if newProt is None:"Error copying protocol.!!!") else: self._openProtocolForm(newProt, disableRunMode=True) else:'Copying the protocols...') self.project.copyProtocol(protocols) self.refreshRuns() self.cleanInfo() def _stopWorkFlow(self, action): protocols = self._getSelectedProtocols() workflowProtocolList, activeProtList = self.project._getWorkflowFromProtocol(protocols[0], False) if activeProtList: errorProtList = [] if pwgui.dialog.askYesNo(Message.TITLE_STOP_WORKFLOW_FORM, Message.TITLE_STOP_WORKFLOW, self.root):'Stopping the workflow...') errorProtList = self.project.stopWorkFlow(activeProtList) self.cleanInfo() self.refreshRuns() if errorProtList: msg = '\n' for prot in errorProtList: msg += str(prot.getObjLabel()) + '\n' pwgui.dialog.MessageDialog( self, Message.TITLE_STOPPED_WORKFLOW_FAILED, Message.TITLE_STOPPED_WORKFLOW_FAILED + ' with: ' + msg, 'fa-times-circle_alert.gif') def _resetWorkFlow(self, action): protocols = self._getSelectedProtocols() errorProtList = [] if pwgui.dialog.askYesNo(Message.TITLE_RESET_WORKFLOW_FORM, Message.TITLE_RESET_WORKFLOW, self.root):'Resetting the workflow...') workflowProtocolList, activeProtList = self.project._getWorkflowFromProtocol(protocols[0]) errorProtList = self.project.resetWorkFlow(workflowProtocolList) self.cleanInfo() self.refreshRuns() if errorProtList: msg = '\n' for prot in errorProtList: msg += str(prot.getObjLabel()) + '\n' pwgui.dialog.MessageDialog( self, Message.TITLE_RESETED_WORKFLOW_FAILED, Message.TITLE_RESETED_WORKFLOW_FAILED + ' with: ' + msg, 'fa-times-circle_alert.gif') def _launchWorkFlow(self, action): """ This function can launch a workflow from a selected protocol in two modes depending on the 'action' value (RESTART, CONTINUE) """ protocols = self._getSelectedProtocols() errorList = [] defaultMode = pwprot.MODE_RESUME workflowProtocolList, activeProtList = self.project._getWorkflowFromProtocol(protocols[0]) # Check if exists active protocols if activeProtList: msg = '\n' for activeProt in activeProtList: msg += str(activeProt.getObjLabel()) + '\n' pwgui.dialog.MessageDialog( self, Message.TITLE_LAUNCHED_WORKFLOW_FAILED_FORM, Message.TITLE_LAUNCHED_WORKFLOW_FAILED + "\n" + Message.TITLE_ACTIVE_PROTOCOLS + "\n" + msg, 'fa-times-circle_alert.gif') elif action == ACTION_RESTART_WORKFLOW: if pwgui.dialog.askYesNo(Message.TITLE_RESTART_WORKFLOW_FORM, Message.TITLE_RESTART_WORKFLOW, self.root): defaultMode = pwprot.MODE_RESTART'Restarting...') errorList = self.project.launchWorkflow(workflowProtocolList, defaultMode) self.cleanInfo() elif action == ACTION_CONTINUE_WORKFLOW:'Continuing...') errorList = self.project.launchWorkflow(workflowProtocolList, defaultMode) self.cleanInfo() if errorList: msg = '' for errorProt in errorList: msg += str(errorProt) + '\n' pwgui.dialog.MessageDialog( self, Message.TITLE_LAUNCHED_WORKFLOW_FAILED_FORM, Message.TITLE_LAUNCHED_WORKFLOW_FAILED + "\n" + msg, 'fa-times-circle_alert.gif') self.refreshRuns() def _selectLabels(self): selectedNodes = self._getSelectedNodes() if selectedNodes: dlg = if dlg.resultYes(): for node in selectedNodes: node.setLabels([label.getName() for label in dlg.values]) # self.updateRunsGraph() self.drawRunsGraph() def _selectAncestors(self): self._selectNodes(down=False) def _selectDescendants(self): self._selectNodes(down=True) def _selectNodes(self, down=True, fromRun=None): """ Selects all nodes in the specified direction, defaults to down.""" nodesToSelect = [] # If parent param not passed... if fromRun is None: # ..use selection, must be first call for protId in self._selection: run = self.runsGraph.getNode(str(protId)) nodesToSelect.append(run) else: name = fromRun.getName() if not name.isdigit(): return else: name = int(name) # If already selected (may be this should be centralized) if name not in self._selection: nodesToSelect = (fromRun,) self._selection.append(name) # Go in the direction . for run in nodesToSelect: # Choose the direction: down or up. direction = run.getChilds if down else run.getParents # Select himself plus ancestors for parent in direction(): self._selectNodes(down, parent) # Only update selection at the end, avoid recursion if fromRun is None: self._lastSelectedProtId = None self._updateSelection() self.drawRunsGraph() def _exportProtocols(self, defaultPath=None, defaultBasename=None): protocols = self._getSelectedProtocols() def _export(obj): filename = os.path.join(browser.getCurrentDir(), browser.getEntryValue()) try: if (not os.path.exists(filename) or"File already exists", "*%s* already exists, do you want " "to overwrite it?" % filename)): self.project.exportProtocols(protocols, filename)"Workflow successfully saved to '%s' " % filename) else: # try again self._exportProtocols(defaultPath=browser.getCurrentDir(), defaultBasename=browser.getEntryValue()) except Exception as ex: import traceback traceback.print_exc() browser = pwgui.browser.FileBrowserWindow( "Choose .json file to save workflow",, path=defaultPath or self.project.getPath(''), onSelect=_export, entryLabel='File ', entryValue=defaultBasename or 'workflow.json') def _exportUploadProtocols(self): try: jsonFn = os.path.join(tempfile.mkdtemp(), 'workflow.json') self.project.exportProtocols(self._getSelectedProtocols(), jsonFn) WorkflowRepository().upload(jsonFn) pwutils.cleanPath(jsonFn) except Exception as ex:"Error connecting to workflow repository:\n" + str(ex)) def _stopProtocol(self, prot): if pwgui.dialog.askYesNo(Message.TITLE_STOP_FORM, Message.LABEL_STOP_FORM, self.root): self.project.stopProtocol(prot) self._lastStatus = None # force logs to re-load self._scheduleRunsUpdate() def _analyzeResults(self, prot): viewers = self.domain.findViewers(prot.getClassName(), 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, if isinstance(firstViewer, ProtocolViewer): firstViewer.visualize(prot, else: firstViewer.visualize(prot) else: outputList = [] for _, output in prot.iterOutputAttributes(): outputList.append(output) for output in outputList: viewers = self.domain.findViewers(output.getClassName(), 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 viewerclass = viewers[0] firstViewer = viewerclass(project=self.project, protocol=prot, # FIXME:Probably o longer needed protocol on args, already provided on init firstViewer.visualize(output,, protocol=prot) def _analyzeResultsClicked(self, e=None): """ Function called when button "Analyze results" is called. """ prot = self.getSelectedProtocol() # Nothing selected if prot is None: return if os.path.exists(prot._getPath()): self._analyzeResults(prot) else:"Selected protocol hasn't been run yet.") def _bibExportClicked(self, e=None): try: bibTexCites = OrderedDict() for prot in self._iterSelectedProtocols(): bibTexCites.update(prot.getCitations(bibTexOutput=True)) bibTexCites.update(prot.getPackageCitations(bibTexOutput=True)) if bibTexCites: with tempfile.NamedTemporaryFile(suffix='.bib') as bibFile: for refId, refDict in bibTexCites.items(): # getCitations does not always return a dictionary # if the citation is not found in the bibtex file it adds just # the refId: like "Ramirez-Aportela-2019" # we need to exclude this if isinstance(refDict, dict): refType = refDict['ENTRYTYPE'] # remove 'type' and 'id' keys refDict = {k: v for k, v in refDict.items() if k not in ['ENTRYTYPE', 'ID']} jsonStr = json.dumps(refDict, indent=4, ensure_ascii=False)[1:] jsonStr = jsonStr.replace('": "', '"= "') jsonStr = re.sub('(?<!= )"(\S*?)"', '\\1', jsonStr) jsonStr = jsonStr.replace('= "', ' = "') refStr = '@%s{%s,%s\n\n' % (refType, refId, jsonStr) bibFile.write(refStr.encode('utf-8')) else: print("WARNING: reference %s not properly defined or unpublished." % refId) # flush so we can see content when opening bibFile.flush() pwgui.text.openTextFileEditor( except Exception as ex: return def _renameProtocol(self, prot): """ Open the EditObject dialog to edit the protocol name. """ kwargs = {} if self._lastRightClickPos: kwargs['position'] = self._lastRightClickPos dlg = pwgui.dialog.EditObjectDialog(self.runsGraphCanvas, Message.TITLE_EDIT_OBJECT, prot, self.project.mapper, **kwargs) if dlg.resultYes(): self._updateProtocol(prot) def _runActionClicked(self, action): prot = self.getSelectedProtocol() if prot: try: if action == ACTION_DEFAULT: pass elif action == ACTION_EDIT: self._editProtocol(prot) elif action == ACTION_RENAME: self._renameProtocol(prot) elif action == ACTION_COPY: self._copyProtocols() elif action == ACTION_DELETE: self._deleteProtocol() elif action == ACTION_STEPS: self._browseSteps() elif action == ACTION_BROWSE: self._browseRunDirectory() elif action == ACTION_DB: self._browseRunData() elif action == ACTION_STOP: self._stopProtocol(prot) elif action == ACTION_CONTINUE: self._continueProtocol(prot) elif action == ACTION_RESULTS: self._analyzeResults(prot) elif action == ACTION_EXPORT: self._exportProtocols(defaultPath=pwutils.getHomePath()) elif action == ACTION_EXPORT_UPLOAD: self._exportUploadProtocols() elif action == ACTION_COLLAPSE: node = self.runsGraph.getNode(str(prot.getObjId())) nodeInfo = self.settings.getNodeById(prot.getObjId()) nodeInfo.setExpanded(False) self.setVisibleNodes(node, visible=False) self.updateRunsGraph(True, reorganize=False) self._updateActionToolbar() elif action == ACTION_EXPAND: node = self.runsGraph.getNode(str(prot.getObjId())) nodeInfo = self.settings.getNodeById(prot.getObjId()) nodeInfo.setExpanded(True) self.setVisibleNodes(node, visible=True) self.updateRunsGraph(True, reorganize=False) self._updateActionToolbar() elif action == ACTION_LABELS: self._selectLabels() elif action == ACTION_SELECT_FROM: self._selectDescendants() elif action == ACTION_SELECT_TO: self._selectAncestors() elif action == ACTION_RESTART_WORKFLOW: self._launchWorkFlow(action) elif action == ACTION_CONTINUE_WORKFLOW: self._launchWorkFlow(action) elif action == ACTION_STOP_WORKFLOW: self._stopWorkFlow(action) elif action == ACTION_RESET_WORKFLOW: self._resetWorkFlow(action) elif action == ACTION_SEARCH: self._searchProtocol() except Exception as ex: if Config.debugOn(): import traceback traceback.print_exc() # Following actions do not need a select run if action == ACTION_TREE: self.drawRunsGraph(reorganize=True) elif action == ACTION_REFRESH: self.refreshRuns(checkPids=True) elif action == ACTION_SWITCH_VIEW: self.switchRunsView()
[docs] def setVisibleNodes(self, node, visible=True): hasParentHidden = False for child in node.getChilds(): prot = nodeInfo = self.settings.getNodeById(prot.getObjId()) if visible: hasParentHidden = self.hasParentHidden(child) if not hasParentHidden: nodeInfo.setVisible(visible) self.setVisibleNodes(child, visible)
[docs] def hasParentHidden(self, node): for parent in node.getParents(): prot = nodeInfo = self.settings.getNodeById(prot.getObjId()) if not nodeInfo.isVisible() or not nodeInfo.isExpanded(): return True return False
[docs]class RunBox(pwgui.TextBox): """ Just override TextBox move method to keep track of position changes in the graph. """ def __init__(self, nodeInfo, canvas, text, x, y, bgColor, textColor): pwgui.TextBox.__init__(self, canvas, text, x, y, bgColor, textColor) self.nodeInfo = nodeInfo canvas.addItem(self)
[docs] def move(self, dx, dy): pwgui.TextBox.move(self, dx, dy) self.nodeInfo.setPosition(self.x, self.y)
[docs] def moveTo(self, x, y): pwgui.TextBox.moveTo(self, x, y) self.nodeInfo.setPosition(self.x, self.y)