scipion-pyworkflow 3.10.6__py3-none-any.whl → 3.11.0__py3-none-any.whl

pyworkflow/gui/project/project.py

@@ -1,492 +0,0 @@
-#!/usr/bin/env python
-# **************************************************************************
-# *
-# * Authors:     J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [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
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * 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 <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-"""
-Main Project window implementation.
-It is composed by three panels:
-1. Left: protocol tree.
-2. Right upper: VIEWS (Data/Protocols)
-3. Summary/Details
-"""
-
-import logging
-from tkinter import Label
-
-from .. import askString
-
-logger = logging.getLogger(__name__)
-
-import os
-import threading
-import shlex
-import subprocess
-import socketserver
-
-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, getBigFont, ToolTip
-from pyworkflow.gui.browser import FileBrowserWindow
-
-from pyworkflow.gui.plotter import Plotter
-from pyworkflow.gui.text import _open_cmd, openTextFileEditor
-from pyworkflow.webservices import ProjectWorkflowNotifier, WorkflowRepository
-
-from .labels import LabelsDialog
-# Import possible Object commands to be handled
-from .base import ProjectBaseWindow, VIEW_PROTOCOLS, VIEW_PROJECTS
-
-
-class ProjectWindow(ProjectBaseWindow):
-    """ Main window for working in a Project. """
-    _OBJECT_COMMANDS = {}
-
-    def __init__(self, path, master=None):
-        # Load global configuration
-        self.projPath = path
-        self.project = self.loadProject()
-        self.projName = self.project.getShortName()
-
-        try:
-            projTitle = '%s (%s on %s)' % (self.projName,
-                                           pwutils.getLocalUserName(),
-                                           pwutils.getLocalHostName())
-        except Exception:
-            projTitle = self.projName 
-
-
-        # TODO: put the menu part more nicely. From here:
-        menu = MenuConfig()
-
-        projMenu = menu.addSubMenu('Project')
-        projMenu.addSubMenu('Browse files', 'browse',
-                            icon=Icon.FOLDER_OPEN)
-        projMenu.addSubMenu('Remove temporary files', 'delete',
-                            icon=Icon.ACTION_DELETE)
-        projMenu.addSubMenu('Toggle color mode', 'color_mode',
-                            shortCut="Ctrl+t", icon=Icon.ACTION_VISUALIZE)
-        projMenu.addSubMenu('Select all protocols', 'select all',
-                            shortCut="Ctrl+a", icon=Icon.SELECT_ALL)
-        projMenu.addSubMenu('Locate a protocol', 'locate protocol',
-                            shortCut="Ctrl+l")
-        projMenu.addSubMenu('', '')  # add separator
-        projMenu.addSubMenu('Import workflow', 'load_workflow',
-                            icon=Icon.DOWNLOAD)
-        projMenu.addSubMenu('Search workflow', 'search_workflow',
-                            icon=Icon.ACTION_SEARCH)
-
-        projMenu.addSubMenu('Configuration', 'configuration',
-                            icon=Icon.SETTINGS)
-
-        projMenu.addSubMenu('', '')  # add separator
-        projMenu.addSubMenu('Debug Mode', 'debug mode',
-                            shortCut="Ctrl+D", icon=Icon.DEBUG)
-        projMenu.addSubMenu('', '')  # add separator
-        projMenu.addSubMenu('Notes', 'notes', icon=Icon.ACTION_EDIT)
-        projMenu.addSubMenu('', '')  # add separator
-        projMenu.addSubMenu('Exit', 'exit', icon=Icon.ACTION_OUT)
-
-        helpMenu = menu.addSubMenu('Help')
-        helpMenu.addSubMenu('Online help', 'online_help',
-                            icon=Icon.ACTION_EXPORT)
-        helpMenu.addSubMenu('About', 'about',
-                            icon=Icon.ACTION_HELP)
-        helpMenu.addSubMenu('Contact support', 'contact_us',
-                            icon=Icon.ACTION_HELP)
-
-        self.menuCfg = menu
-
-        if self.project.openedAsReadOnly():
-            self.projName += "<READ ONLY>"
-
-        # 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)
-
-        OS.handler().maximizeWindow(self.root)
-
-        self.switchView(VIEW_PROTOCOLS)
-
-        self.initProjectTCPServer()  # Socket thread to communicate with clients
-
-        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
-    
-    def saveSettings(self):
-
-        try:
-            self.settings.write()
-        except Exception as ex:
-            logger.error(Message.NO_SAVE_SETTINGS, exc_info=ex)
-
-    def _onClosing(self):
-        if not self.project.openedAsReadOnly():
-            self.saveSettings()
-
-        ProjectBaseWindow._onClosing(self)
-     
-    def loadProject(self):
-        proj = pw.project.Project(pw.Config.getDomain(), self.projPath)
-        proj.configureLogging()
-        proj.load()
-
-        # Check if we have settings.sqlite, generate if not
-        settingsPath = os.path.join(proj.path, proj.settingsPath)
-        if os.path.exists(settingsPath):
-            self.settings = proj.getSettings()
-        else:
-            logger.info('Warning: settings.sqlite not found! '
-                  'Creating default settings..')
-            self.settings = proj.createSettings()
-
-        return proj
-
-    # The next functions are callbacks from the menu options.
-    # See how it is done in pyworkflow/gui/gui.py:Window._addMenuChilds()
-    #
-    def onBrowseFiles(self):
-        # Project -> Browse files
-        FileBrowserWindow("Browse Project files",
-                          self, self.project.getPath(''), 
-                          selectButton=None  # we will select nothing
-                          ).show()
-
-    def onDebugMode(self):
-        pw.Config.toggleDebug()
-
-    def onNotes(self):
-        notes_program = pw.Config.SCIPION_NOTES_PROGRAM
-        notes_args = pw.Config.SCIPION_NOTES_ARGS
-        args = []
-        notes_file = self.project.getPath('Logs', pw.Config.SCIPION_NOTES_FILE)
-
-        # If notesFile does not exist, it is created and an explanation/documentation comment is added at the top.
-        if not os.path.exists(notes_file):
-            f = open(notes_file, 'a')
-            f.write(pw.genNotesHeading())
-            f.close()
-
-        # Then, it will be opened as specified in the conf
-        if notes_program:
-            args.append(notes_program)
-            # Custom arguments
-            if notes_args:
-                args.append(notes_args)
-            args.append(notes_file)
-            subprocess.Popen(args)  # nonblocking
-        else:
-            # if no program has been selected
-            # xdg-open will try to guess but
-            # if the file does not exist it
-            # will return an error so If the file does
-            # not exist I will create an empty one
-            # 'a' will avoid accidental truncation
-            openTextFileEditor(notes_file)
-
-    def onRemoveTemporaryFiles(self):
-        # Project -> Remove temporary files
-        tmpPath = os.path.join(self.project.path, self.project.tmpPath)
-        n = 0
-        try:
-            for fname in os.listdir(tmpPath):
-                fpath = "%s/%s" % (tmpPath, fname)
-                if os.path.isfile(fpath):
-                    os.remove(fpath)
-                    n += 1
-                # TODO: think what to do with directories. Delete? Report?
-            self.showInfo("Deleted content of %s -- %d file(s)." % (tmpPath, n))
-        except Exception as e:
-            self.showError(str(e))
-        
-    def _loadWorkflow(self, obj):
-        try:
-            self.getViewWidget().info('Importing workflow %s' % obj.getPath())
-            self.project.loadProtocols(obj.getPath())
-            self.getViewWidget().updateRunsGraph(True)
-            self.getViewWidget().cleanInfo()
-        except Exception as ex:
-            self.showError(str(ex), exception=ex)
-            
-    def onImportWorkflow(self):
-        FileBrowserWindow("Select workflow .json file",
-                          self, self.project.getPath(''),
-                          onSelect=self._loadWorkflow,
-                          selectButton='Import'
-                          ).show()
-
-    def onSearchWorkflow(self):
-        WorkflowRepository().search()
-
-    def onToggleColorMode(self):
-        self.getViewWidget()._toggleColorScheme(None)
-
-    def onSelectAllProtocols(self):
-        self.getViewWidget()._selectAllProtocols(None)
-
-    def onLocateAProtocol(self):
-        self.getViewWidget()._locateProtocol(None)
-
-    def manageLabels(self):
-
-        labels = self.project.settings.getLabels()
-        dialog = LabelsDialog(self.root,
-                            labels,
-                            allowSelect=True)
-
-        # Scan for renamed labels to update node info...
-        labelsRenamed = dict()
-        for label in labels:
-            if label.hasOldName():
-                oldName = label.getOldName()
-                newName = label.getName()
-                logger.info("Label %s renamed to %s" % (oldName, newName))
-                labelsRenamed[oldName] = newName
-                label.clearOldName()
-
-        # If there are labels renamed
-        if labelsRenamed:
-            logger.info("Updating labels of protocols after renaming.")
-            labels.updateDict()
-
-            for node in self.project.settings.getNodes():
-                nodeLabels = node.getLabels()
-                for index, nodeLabel in enumerate(nodeLabels):
-
-                    newLabel = labelsRenamed.get(nodeLabel, None)
-                    if newLabel is not None:
-                        logger.info("Label %s found in %s. Updating it to %s" % (nodeLabel,node, newLabel))
-                        nodeLabels[index] = newLabel
-
-        return dialog
-
-    def initProjectTCPServer(self):
-        server = ProjectTCPServer((self.project.address, self.project.port),
-                                  ProjectTCPRequestHandler)
-        server.project = self.project
-        server.window = self
-        server_thread = threading.Thread(name="projectTCPserver", target=server.serve_forever)
-        # Exit the server thread when the main thread terminates
-        server_thread.daemon = True
-        server_thread.start()
-
-    # Seems it is not used and should be in scipion-em
-    # Not within scipion but used from ShowJ
-    def schedulePlot(self, path, *args):
-        # FIXME: This import should not be here
-        from pwem.viewers import EmPlotter
-        self.enqueue(lambda: EmPlotter.createFromFile(path, *args).show())
-
-    @classmethod
-    def registerObjectCommand(cls, cmd, func):
-        """ Register an object command to be handled when receiving the
-        action from showj. """
-        cls._OBJECT_COMMANDS[cmd] = func
-
-    def runObjectCommand(self, cmd, inputStrId, objStrId):
-        try:
-            objId = int(objStrId)
-            project = self.project
-
-            if os.path.isfile(inputStrId) and os.path.exists(inputStrId):
-                from pwem.utils import loadSetFromDb
-                inputObj = loadSetFromDb(inputStrId)
-            else:
-                inputId = int(inputStrId)
-                inputObj = project.mapper.selectById(inputId)
-
-            func = self._OBJECT_COMMANDS.get(cmd, None)
-
-            if func is None:
-                logger.info("Error, command '%s' not found. " % cmd)
-            else:
-                def myfunc():
-                    func(inputObj, objId)
-                    inputObj.close()
-                self.enqueue(myfunc)
-
-        except Exception as ex:
-            logger.error("There was an error executing object command !!!:", exc_info=ex)
-
-class ProjectManagerWindow(ProjectBaseWindow):
-    """ Windows to manage all projects. """
-    # To allow plugins to add their own menus
-    _pluginMenus = dict()
-
-    def __init__(self, **kwargs):
-
-        # TODO: put the menu part more nicely. From here:
-        menu = MenuConfig()
-
-        fileMenu = menu.addSubMenu('File')
-        fileMenu.addSubMenu('Browse files', 'browse', icon=Icon.FOLDER_OPEN)
-        fileMenu.addSubMenu('Exit', 'exit', icon=Icon.ACTION_OUT)
-
-        confMenu = menu.addSubMenu('Configuration')
-        if os.path.exists(pw.Config.SCIPION_CONFIG):
-            confMenu.addSubMenu('General', 'general')
-        confMenu.addSubMenu('Hosts', 'hosts')
-        if os.path.exists(pw.Config.SCIPION_PROTOCOLS):
-            confMenu.addSubMenu('Protocols', 'protocols')
-        if os.path.exists(pw.Config.SCIPION_LOCAL_CONFIG):
-            confMenu.addSubMenu('User', 'user')
-
-        helpMenu = menu.addSubMenu('Help')
-        helpMenu.addSubMenu('Online help', 'online_help', icon=Icon.ACTION_EXPORT)
-        helpMenu.addSubMenu('About', 'about', icon=Icon.ACTION_HELP)
-
-        self.menuCfg = menu
-
-        try:
-            title = '%s (%s on %s)' % (Message.LABEL_PROJECTS, 
-                                       pwutils.getLocalUserName(),
-                                       pwutils.getLocalHostName())
-        except Exception:
-            title = Message.LABEL_PROJECTS
-        
-        ProjectBaseWindow.__init__(self, title, minsize=(750, 500),
-                                   icon=Icon.SCIPION_ICON_PROJS, **kwargs)
-        self.manager = pw.project.Manager()
-        self.switchView(VIEW_PROJECTS)
-
-    #
-    # The next functions are callbacks from the menu options.
-    # See how it is done in pyworkflow/gui/gui.py:Window._addMenuChilds()
-    #
-    def onBrowseFiles(self):
-        # File -> Browse files
-        FileBrowserWindow("Browse files", self,
-                          pw.Config.SCIPION_USER_DATA,
-                          selectButton=None).show()
-
-    def onGeneral(self):
-        # Config -> General
-        self._openConfigFile(pw.Config.SCIPION_CONFIG)
-
-    @staticmethod
-    def _openConfigFile(configFile):
-        """ Open an Scipion configuration file, if the user have one defined,
-        also open that one with the defined text editor.
-        """
-        _open_cmd(configFile)
-
-    @staticmethod
-    def onHosts():
-        # Config -> Hosts
-        ProjectManagerWindow._openConfigFile(pw.Config.SCIPION_HOSTS)
-
-    @staticmethod
-    def onProtocols():
-        ProjectManagerWindow._openConfigFile(pw.Config.SCIPION_PROTOCOLS)
-
-    @staticmethod
-    def onUser():
-        ProjectManagerWindow._openConfigFile(pw.Config.SCIPION_LOCAL_CONFIG)
-
-
-class ProjectTCPServer(socketserver.ThreadingMixIn, socketserver.TCPServer):
-    pass
-
-
-class ProjectTCPRequestHandler(socketserver.BaseRequestHandler):
-
-    def handle(self):
-        try:
-            project = self.server.project
-            window = self.server.window
-            msg = self.request.recv(1024)
-            msg = msg.decode()
-            tokens = shlex.split(msg)
-            if msg.startswith('run protocol'):
-                
-                logger.debug("run protocol messaged arrived: %s" % msg)
-                protocolName = tokens[2]
-                protocolClass = pw.Config.getDomain().getProtocols()[protocolName]
-                # Create the new protocol instance and set the input values
-                protocol = project.newProtocol(protocolClass)
-
-                for token in tokens[3:]:
-                    param, value = token.split('=')
-                    attr = getattr(protocol, param, None)
-                    if param == 'label':
-                        protocol.setObjLabel(value)
-                    elif attr.isPointer():
-                        obj = project.getObject(int(value))
-                        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
-                # access to the project sqlite database
-                window.getViewWidget().executeProtocol(protocol)
-            elif msg.startswith('run function'):
-                functionName = tokens[2]
-                functionPointer = getattr(window, functionName)
-                functionPointer(*tokens[3:])
-            else:
-                answer = b'no answer available\n'
-                self.request.sendall(answer)
-        except Exception as e:
-            print(e)
-            import traceback
-            traceback.print_stack()

pyworkflow/gui/project/searchprotocol.py

@@ -1,154 +0,0 @@
-# -*- coding: utf-8 -*-
-# **************************************************************************
-# *
-# * Authors:     Pablo Conesa [1]
-# *
-# * [1] Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
-# *
-# * 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
-# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# * 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 <https://www.gnu.org/licenses/>.
-# *
-# *  All comments concerning this program package may be sent to the
-# *  e-mail address 'scipion@cnb.csic.es'
-# *
-# **************************************************************************
-""" This modules hosts code provider and window to search for a protocol"""
-import tkinter as tk
-
-from pyworkflow import Config
-import  pyworkflow.gui as pwgui
-import pyworkflow.object as pwobj
-from pyworkflow.gui.dialog import SearchBaseWindow
-
-from pyworkflow.gui.project.utils import isAFinalProtocol
-from pyworkflow.gui.project.viewprotocols_extra import ProtocolTreeConfig
-
-UPDATED = "updated"
-
-NEW = "new"
-
-BETA = "beta"
-
-
-class ProtocolTreeProvider(pwgui.tree.ObjectTreeProvider):
-    """Create the tree elements for a Protocol run"""
-
-    def __init__(self, protocol):
-        self.protocol = protocol
-        # This list is create to group the protocol parameters
-        # in the tree display
-        self.status = pwobj.List(objName='_status')
-        self.params = pwobj.List(objName='_params')
-        self.statusList = ['status', 'initTime', 'endTime', 'error',
-                           'interactive', 'mode']
-
-        objList = [] if protocol is None else [protocol]
-        pwgui.tree.ObjectTreeProvider.__init__(self, objList)
-
-
-
-class SearchProtocolWindow(SearchBaseWindow):
-
-    columnConfig = {
-        '#0': ('Status', {'width': 50, 'minwidth': 50, 'stretch': tk.NO}, 5),
-        # Heading, tree column kwargs, casting for sorting
-        'protocol': ('Protocol', {'width': 300, 'stretch': tk.FALSE}, 10),
-        'streaming': ('Streamified', {'width': 100, 'stretch': tk.FALSE}, 5),
-        'installed': ('Installation', {'width': 110, 'stretch': tk.FALSE}, 5),
-        'help': ('Help', {'minwidth': 300, 'stretch': tk.YES}, 5),
-        'score': ('Score', {'width': 50, 'stretch': tk.FALSE}, 5, int)
-    }
-
-    def __init__(self, parentWindow, position=None):
-
-        posStr = "" if position is None else " at (%s,%s)" % position
-        self.position = position
-        super().__init__(parentWindow,
-                         title="Add a protocol" + posStr)
-
-    def _createResultsTree(self, frame, show, columns):
-        return self.master.getViewWidget()._createProtocolsTree(frame, show=show, columns=columns, position=self.position)
-
-    def _onSearchClick(self, e=None):
-
-        self._resultsTree.clear()
-
-        protList = self.scoreProtocols()
-
-        # Sort by weight
-        protList.sort(reverse=True, key=lambda x: x[8])
-
-        self._addProtocolToTree(protList)
-
-    def scoreProtocols(self):
-
-        keyword = self._searchVar.get().lower().strip()
-        emProtocolsDict = Config.getDomain().getProtocols()
-        protList = []
-
-        for key, prot in emProtocolsDict.items():
-            if isAFinalProtocol(prot, key):
-                label = prot.getClassLabel().lower()
-                line = (key, label,
-                        "installed" if prot.isInstalled() else "missing installation",
-                        prot.getHelpText().strip().replace('\r', '').replace('\n', '').lower(),
-                        "streamified" if prot.worksInStreaming() else "static",
-                        BETA if prot.isBeta() else "",
-                        NEW if prot.isNewDev() else "",
-                        UPDATED if prot.isUpdated() else "")
-
-                line = self._addSearchWeight(line, keyword)
-                # something was found: weight > 0
-                if line[8] != 0:
-                    protList.append(line)
-
-        return protList
-
-    @staticmethod
-    def _addSearchWeight(line2Search, searchtext):
-        # Adds a weight value for the search
-        weight = 0
-
-        # prioritize findings in label
-        if searchtext in line2Search[1]:
-            weight += 10
-
-        for value in line2Search[2:]:
-            weight += 5 if searchtext in value else 0
-
-        if " " in searchtext:
-            for word in searchtext.split():
-                if word in line2Search[1]:
-                    weight += 3
-
-                for value in line2Search[2:]:
-                    weight += 1 if word in value else 0
-
-        return line2Search + (weight,)
-
-    def _addProtocolToTree(self, protList):
-        """ Adds the items in protList to the tree
-
-        :param protList: List of tuples with all the values/columns used in the search search to show in the tree"""
-
-        for key, label, installed, help, streamified, beta, new, updated, weight in protList:
-            tag = ProtocolTreeConfig.getProtocolTag(installed == 'installed',
-                                                    beta == BETA,
-                                                    new == NEW,
-                                                    updated == UPDATED)
-
-            self._resultsTree.insert(
-                '', 'end', key, text="", tags=tag,
-                values=(label, streamified, installed, help, weight))
-
-