scipion-pyworkflow 3.11.0__py3-none-any.whl → 3.11.1__py3-none-any.whl

pyworkflow/project/manager.py

@@ -0,0 +1,180 @@
+# **************************************************************************
+# *
+# * Authors:     J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
+# *
+# * 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, write to the Free Software
+# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+# * 02111-1307  USA
+# *
+# *  All comments concerning this program package may be sent to the
+# *  e-mail address 'scipion@cnb.csic.es'
+# *
+# **************************************************************************
+"""
+This modules handles the System management
+"""
+
+import os
+
+import pyworkflow as pw
+import pyworkflow.utils as pwutils
+from .project import Project
+
+
+class ProjectInfo(object):
+    """Class to store some information about the project"""
+    def __init__(self, projName, mTime, cTime, path):
+        """At least it receives the Project Name and its modification time"""
+        self.projName = projName
+        self.mTime = mTime
+        self.cTime = cTime
+        self.path = path
+
+    def __str__(self):
+        return "%s - %s" % (self.projName, self.path)
+
+    def getName(self):
+        return self.projName
+    
+    def getModificationTime(self):
+        return self.mTime
+
+    def getCreationTime(self):
+        return self.cTime
+
+    def isLink(self):
+        return os.path.islink(self.path)
+
+    def realPath(self):
+        return os.path.realpath(self.path)
+
+
+class Manager(object):
+    """ Manage all projects of a given workspace, for a given Domain.
+     (i.e, listing projects, creating, deleting or querying info)
+    """
+    def __init__(self, workspace=None):
+        """
+        Params:
+            workspace: path to where the user's workspace is. A subfolder
+            named 'projects' is expected. If workspace is None, the workspace
+            will be taken from the global configuration.
+        """
+        ws = workspace or pw.Config.SCIPION_USER_DATA
+        self.PROJECTS = os.path.join(ws, 'projects')
+
+    def getProjectPath(self, projectName):
+        """Return the project path given the name"""
+        return os.path.join(self.PROJECTS, projectName)
+        
+    def listProjects(self, sortByDate=True):
+        """Return a list with all existing projects
+        And some other project info
+        If sortByData is True, recently modified projects will be first"""
+        projList = []
+        pw.utils.makePath(self.PROJECTS)
+        for f in os.listdir(self.PROJECTS):
+            p = self.getProjectPath(f)
+            if os.path.isdir(p):
+                stat = os.stat(p)
+                projList.append(ProjectInfo(f, stat.st_mtime, stat.st_ctime, p))
+                
+        if sortByDate:
+            projList.sort(key=lambda k: k.mTime, reverse=True)
+        return projList
+    
+    def createProject(self, projectName, runsView=1, 
+                      hostsConf=None, protocolsConf=None, location=None, comment=None):
+        """Create a new project.
+        confs dict can contain customs .conf files
+        for: menus, protocols, or hosts
+        """
+        # Clean project name from undesired characters
+        projectName = Project.cleanProjectName(projectName)
+
+        # If location is not None create project on it (if exists)
+        if location is None:
+            projectPath = self.getProjectPath(projectName)
+        else:
+            projectPath = os.path.join(location, projectName)
+
+        # JMRT: Right now the project.create function change the current
+        # working dir (cwd) to the project location, let's store the cwd
+        # and restored after the creation
+        cwd = os.getcwd()
+        project = Project(pw.Config.getDomain(), projectPath)
+        project.create(runsView=runsView, 
+                       hostsConf=hostsConf, 
+                       protocolsConf=protocolsConf,
+                       comment=comment)
+        # If location is not the default one create a symlink on self.PROJECTS directory
+        if projectPath != self.getProjectPath(projectName):
+            # JMRT: Let's create the link to the absolute path, since relative
+            # can be broken in systems with different mount points
+            pw.utils.createAbsLink(os.path.abspath(projectPath),
+                                   self.getProjectPath(projectName))
+
+        os.chdir(cwd)  # Restore cwd before project creation
+
+        return project
+
+    def importProject(self, fromLocation, copyFiles=True, projectName=None, searchLocation=None):
+        """ Import a project that is somewhere else in the FS
+        Folder can be copied (default) or linked
+        Optionally a name can be specified, otherwise name will match location folder name
+        Project will always be created in the default project folder.
+        """
+        # If projectName is None...
+        if projectName is None:
+            # use same name as the import location
+            projectName = os.path.basename(fromLocation)
+
+        projectPath = self.getProjectPath(projectName)
+
+        # If need to copyFiles
+        if copyFiles:
+            # Copy the whole folder
+            pw.utils.copyTree(os.path.abspath(fromLocation), os.path.abspath(projectPath))
+
+        else:
+            # Link the folder
+            pw.utils.createAbsLink(os.path.abspath(fromLocation), projectPath)
+
+        project = self.loadProject(projectName)
+
+        if searchLocation:
+            project.fixLinks(searchLocation)
+
+        return project
+
+    def loadProject(self, projId, **kwargs):
+        """ Retrieve a project object, given its id. """
+        project = Project(pw.Config.getDomain(), self.getProjectPath(projId))
+        project.load(**kwargs)
+        return project
+
+    def deleteProject(self, projectName):
+        pw.utils.cleanPath(self.getProjectPath(projectName))
+
+    def renameProject(self, oldName, newName):
+        os.rename(self.getProjectPath(oldName), self.getProjectPath(newName))
+
+    def hasProject(self, projectName):
+        """Return True if exists a project with projectName"""
+        for projInfo in self.listProjects():
+            if projectName == projInfo.projName:
+                return True
+        return False