Partial fix to #22. Laydi will require a project directory to run. If the

project directory does not exist, i.e. if a new project should be created, the
new -n switch is required. New syntax to run laydi is now
{{{
laydi [options] </path/to/project>
}}}

bin/laydi

@@ -3,7 +3,7 @@
 from getopt import getopt
 import os
 import sys
-from laydi import laydi, projectview, workflow, main
+from laydi import laydi, project, projectview, workflow, main
 #import workflows
 from laydi import cfgparse
 import optparse
@@ -73,11 +73,20 @@ def parse_options():
                  action='store_true',
                  help='Generate configuration file ~/.laydi if it does not exist.')
 
+    op.add_option('-n', '--new-project',
+                  action='store_true',
+                  help='Create new project directory.')
+
     for cf in conf_files:
         if os.path.isfile(cf):
             cp.add_file(cf)
 
-    return cp.parse(op)
+    options, params = cp.parse(op)
+    if len(params) != 1:
+        print "error: project directory must be specified."
+        sys.exit(1)
+        
+    return options, params
     
 if __name__ == '__main__':
     import gtk
@@ -86,6 +95,8 @@ if __name__ == '__main__':
     gnome.program_init(PROGRAM_NAME, VERSION)
 
     options, params = parse_options()
+
+    ## Workflow setup
     main.options = options
     
     for dir in main.options.workflowdir.split(';'):
@@ -112,8 +123,18 @@ if __name__ == '__main__':
     main.set_options(options)
     app = laydi.LaydiApp()
 
+    ## Project setup
+    prjroot = params[0]
+    if not project.is_project_directory(prjroot):
+        if options.new_project:
+            project.make_project_directory(prjroot)
+        else:
+            print "error: project directory not found: %s" % prjroot
+            print "notice: use the -n option to make a new project"
+            sys.exit(2)
+
     main.set_application(app)
-    main.set_projectview(projectview.ProjectView())
+    main.set_projectview(projectview.ProjectView(prjroot))
 
     app.set_projectview(main.projectview)
     app.show()

laydi/project.py

@@ -1,154 +1,305 @@
-import os
+import os, os.path
-import scipy
+import sys
-import gobject
+import configobj
-import gtk
+import time
-import laydi
-import logger, dataset, plots, main
 
-class Project:
+import dataset
-    """A Project contains datasets, selections etc.
+
-    The project, of which the application has only one at any given time,
+NAME = "laydi-cmd"
-    is the container for all datasets, plots and selections in use. The data
+VERSION = "0.1.0"
-    in the project is organized in a gtk.TreeStrore that is displayed in the
+PROJECT_VERSION_STRING = "Laydi project version 1"
-    navigator.
+
+def is_project_directory(dirname):
+    """Verifies that a directory is a laydi project"""
+
+    if not os.path.isdir(dirname):
+        return False
+    
+    ## Verify that the version is correct.
+    version_fn = os.path.join(dirname, "VERSION")
+    if not os.path.exists(version_fn):
+        return False
+    fd = open(version_fn)
+    line = fd.readline()
+    fd.close()
+
+    if line.strip() != PROJECT_VERSION_STRING:
+        return False
+
+    ## Require directories to be present.
+    if not os.path.isdir(os.path.join(dirname, "annotations")):
+        return False
+    if not os.path.isdir(os.path.join(dirname, "data")):
+        return False
+    if not os.path.isdir(os.path.join(dirname, "selections")):
+        return False
+    if not os.path.isdir(os.path.join(dirname, "exports")):
+        return False
+
+    ## If no tests failed, return True
+    return True
+
+
+def make_project_directory(dirname, force=False):
+    """Creates a project directory
+
+    force: ignore that directory exists and proceed anyway.
     """
+    if os.path.exists(dirname) and not force:
+        return False
 
-    def __init__(self, name="Testing"):
+    rootdir = dirname
-        self.data_tree = gtk.TreeStore(str,
+    anndir = os.path.join(dirname, "annotations")
-                                       str,
+    seldir = os.path.join(dirname, "selections")
-                                       object, 
+    datadir = os.path.join(dirname, "data")
-                                       str,
+    exportdir = os.path.join(dirname, "exports")
-                                       str,
+    version_file_path = os.path.join(dirname, "VERSION")
-                                       gobject.TYPE_OBJECT, 
-                                       float)
         
+    os.makedirs(rootdir)
+    for d in [anndir, seldir, datadir, exportdir]:
+        os.mkdir(d)
+
+    fd = open(version_file_path, "w")
+    print >> fd, PROJECT_VERSION_STRING
+    fd.close()
+
+
+
+class Universe(object):
+    """A Universe is a collection of all existing identifiers in a set of datasets"""
+
+    def __init__(self):
+        self.refcount = {}
+
+    def register_dim(self, dim):
+        """Increase reference count for identifiers in Dimension object dim"""
+        d = self.refcount.get(dim.name, None)
+        if d == None:
+            d = {}
+            self.refcount[dim.name] = d
+        for i in dim:
+            d[i] = d.get(i, 0) + 1
+        
+    def register_ds(self, ds):
+        """Increase reference count for identifiers in all Dimensions of dataset ds"""
+        for dim in ds.dims:
+            self.register_dim(dim)
+
+    def unregister_dim(self, dim):
+        """Update reference count for identifiers in Dimension object dim
+           Update reference count for identifiers in Dimension object dim, and remove all
+           identifiers with a reference count of 0, as they do not (by definition) exist 
+           any longer.
+        """
+        ids = self.refcount[dim.name]
+        for i in dim:
+            refcount = ids[i]
+            if refcount == 1:
+                ids.pop(i)
+            else:
+                ids[i] -= 1
+        if len(ids) == 0:
+            self.refcount.pop(dim.name)
+
+
+    def unregister_ds(self, ds):
+        """Update reference count for identifiers along Dimensions in Dataset ds.
+	   Update reference count for identifiers along all Dimensions in
+	   Dataset ds, and remove all identifiers with a reference count of 0,
+           as they do not (by definition) exist any longer.
+        """
+        for dim in ds:
+            self.register_dim(dim)
+
+    def register(self, obj):
+        if isinstance(obj, Dataset):
+            self.register_ds(obj)
+        else:
+            self.register_dim(obj)
+
+    def unregister(self, obj):
+        if isinstance(obj, Dataset):
+            self.unregister_ds(obj)
+        else:
+            self.unregister_dim(obj)
+
+    def __getent___(self, dimname):
+        return set(self.references[dimname].keys())
+
+    def __iter__(self):
+        return self.references.keys().__iter__()
+
+
+class Dimension(object):
+    """A Dimension represents the set of identifiers an object has along an axis.
+    """
+    def __init__(self, name, ids=[]):
         self.name = name
-        self.dim_names = []
+        self.idset = set(ids)
-        self._selection_observers = []
+        self.idlist = list(ids)
-        self._dataset_observers = []
-        self.current_data = []
-        self.datasets = []
-        self.sel_obj = dataset.Selection('Current Selection')
-        self.selections = []
-        self._last_selection = None
-        self._dataset_iter_map = {}
 
-    def add_selection_observer(self, observer):
+        if len(self.idset) != len(self.idlist):
-        self._selection_observers.append(observer)
+            raise Exception("Duplicate identifiers are not allowed")
-        observer.selection_changed(None, self.get_selection())
 
-    def notify_selection_listeners(self, dim_name):
+    def __getitem__(self, element):
-        """Notifies observers"""
+        return self.idlist[element]
-        for observer in self._selection_observers:
-            observer.selection_changed(dim_name, self.get_selection())
 
-    def add_dataset_observer(self, observer):
+    def __getslice__(self, start, end):
-        self._dataset_observers.append(observer)
+        return self.idlist[start:end]
-        observer.dataset_changed()
 
-    def notify_dataset_listeners(self):
+    def __contains__(self, element):
-        """Notifies observers when new datasets are added"""
+        return self.idset.__contains__(element)
-        for observer in self._dataset_observers:
-            observer.dataset_changed()
         
-    def set_selection(self, dim_name, selection):
+    def __str__(self):
-        """Sets a current selection and notify observers"""
+        return "%s: %s" % (self.name, str(self.idlist))
-        self.sel_obj[dim_name] = set(selection)
-        self.notify_selection_listeners(dim_name)
-        self._last_selection = selection
 
-    def get_selection(self):
+    def __len__(self):
-        """Returns the current selection object"""
+        return len(self.idlist)
-        return self.sel_obj
 
-    def delete_data(self, it):
+    def __iter__(self):
-        """Delete elements from the project."""
+        return iter(self.idlist)
-        child = self.data_tree.iter_children(it)
-        while child != None:
-            c = self.data_tree.iter_next(child)
-            self.delete_data(child)
-            child = c
-        main.application.main_view.remove_view(self.data_tree.get(it, 2)[0])
-        self.data_tree.remove(it)
 
-    def add_data(self, parents, data, fun='Function'):
+    def intersection(self, dim):
-        """Adds a set of data and plots to the navigator.
+        return self.idset.intersection(dim.idset)
 
-        This method is usually called after a Function in a workflow
+    def as_tuple(self):
-        has finished and returns its output."""
+        return (self.name, self.idlist)
 
-        if len(parents) > 0: 
+
-            parent_iter = self._dataset_iter_map[parents[0]]
+class Directory(object):
+    def __init__(self, path):
+        self.path = path
+        self.files = set()
+        self.timestamp = -1
+        self.update()
+
+    def update(self):
+        now = time.time()
+        newfiles = set(os.listdir(self.path))
+        for fn in newfiles - self.files:
+            if os.path.isdir(os.path.join(self.path, fn)):
+                self.dir_created(fn)
             else:
-            parent_iter = None
+                self.file_created(fn)
-
+        for fn in self.files - newfiles:
-        # Add the function node to the tree
+            if os.path.isdir(os.path.join(self.path, fn)):
-        icon = laydi.icon_factory.get("folder_grey")
+                self.dir_deleted(fn)
-        it = self.data_tree_insert(parent_iter, fun, None, None, "black", icon)
-        
-        # Add all returned datasets/plots/selections
-        for d in data:
-            # Any kind of dataset
-            if isinstance(d, dataset.Dataset):
-                if isinstance(d, dataset.GraphDataset):
-                    icon = laydi.icon_factory.get("graph_dataset")
-                elif isinstance(d, dataset.CategoryDataset):
-                    icon = laydi.icon_factory.get("category_dataset")
             else:
-                    icon = laydi.icon_factory.get("dataset")
+                self.file_removed(fn)
+        for fn in self.files.intersection(newfiles):
+            filepath = os.path.join(self.path, fn)
+            if os.path.getctime(filepath) >= self.timestamp:
+                if os.path.isdir(filepath):
+                    self.dir_changed(fn)
+                else:
+                    self.file_changed(fn)
+        self.files = newfiles
+        self.timestamp = now
             
-                self.add_dataset(d)
+    def file_created(self, fn):
-                self.data_tree_insert(it, d.get_name(), d, None, "black", icon) 
+        print "file created: %s" % fn
+        pass
 
-            # Any kind of plot
+    def file_changed(self, fn):
-            elif isinstance(d, plots.Plot):
+        print "file changed: %s" % fn
-                icon = laydi.icon_factory.get("line_plot")
+        pass
-                self.data_tree_insert(it, d.get_title(), d, None, "black", icon)
-                d.set_selection_listener(self.set_selection)
-                self._selection_observers.append(d)
 
-            # Selections are not added to the data tree
+    def file_removed(self, fn):
-            elif isinstance(d, dataset.Selection):
+        print "file removed: %s" % fn
-                self.add_selection(d)
+        pass
 
-    def data_tree_insert(self, parent, text, data, bg, fg, icon, selected = 0):
+    def dir_created(self, fn):
-        """Inserts data into the tree view.
+        print "directory created: %s" % fn
-        @param text: The title of the object.
+        pass
-        @param data: A dataset, plot or function object.
+
-        @param bg: Background color.
+    def dir_changed(self, fn):
-        @param fg: Foreground (font) color.
+        print "directory changed: %s" % fn
-        @param icon: Pixmap icon.
+        pass
+
+    def dir_removed(self, fn):
+        print "directory removed: %s" % fn
+        pass
+
+
+class DataDirectory(Directory):
+    def __init__(self, dirname, project):
+        self.project = project
+        self.datasets= []
+        self.dsfiles = {}
+        Directory.__init__(self, dirname)
+
+    def file_created(self, fn):
+        """Called from update() when new files are created.
+
+           Load new datasets that have appeared since last update.
         """
-        tree = self.data_tree
+        filepath = os.path.join(self.path, fn)
-        it = tree.append(parent)
+        name, ext = os.path.splitext(fn)
-        tree[it] = [text, type(data), data, bg, fg, icon, selected]
+        if ext == ".ftsv":
-        self._dataset_iter_map[data] = it
+            ds = dataset.read_ftsv(filepath)
-        return it
+            self.datasets.append(ds)
+            self.dsfiles[fn] = ds
 
-    def add_dataset(self, dataset):
+    def file_changed(self, fn):
-        """Appends a new Dataset to the project."""
+        """Called from update() when files are changed.
-        logger.log('debug','Adding dataset: %s' %dataset.get_name())
-        self.datasets.append(dataset)
-        for dim_name in dataset.get_all_dims():
-            if dim_name not in self.dim_names:
-                self.dim_names.append(dim_name)
-                self.sel_obj[dim_name] = set()
-                self.notify_selection_listeners(dim_name)
-        self.notify_dataset_listeners()
 
-    def add_selection(self, selection):
+           Delete old dataset and load the new one when dataset files 
-        """Adds a new selection to the project."""
+           have been changed.
-        self.selections.append(selection)
+        """
-        self.notify_dataset_listeners()
+        filepath = os.path.join(self.path, fn)
+        name, ext = os.path.splitext(fn)
+        print self.datasets
+        if ext == ".ftsv":
+            oldds = self.dsfiles[fn]
+            self.datasets.remove(oldds)
             
-    def object_at(self, path):
+            ds = dataset.read_ftsv(filepath)
-        """Returns the object at a given path in the tree."""
+            self.datasets.append(ds)
-        it = self.get_iter(path)
-        obj = self[it][2]
-        if obj:
-            obj.show()
-        return obj
 
-    #def set_current_data(self, obj):
+            self.dsfiles[fn] = ds
-    #    self.current_data = obj
+        print self.datasets
+
+    def file_removed(self, fn):
+        """Called from update() when a file is deleted
+
+           Removes the associated dataset if a dataset file is removed.
+        """
+        filepath = os.path.join(self.path, fn)
+        name, ext = os.path.splitext(fn)
+        if ext == ".ftsv":
+            ds = self.dsfiles[fn]
+            self.datasets.remove(ds)
+            self.dsfiles.pop(fn)
+
+    def dir_created(self, fn):
+        """Called from update() when a subdirectory is created.
+
+           Instantiate new handlers for the directory if possible.
+        """
+        filepath = os.path.join(self.path, fn)
+        
+
+def SelectionDirectory(object):
+    def __init__(self, dirname):
+        pass
+
+class Project(object):
+    def __init__(self, dirname):
+        """Opens a project directory. The directory must exist and be a valid project."""
+        
+        ## Set path names.
+        self.rootdir = dirname
+        self.anndir = os.path.join(dirname, "annotations")
+        self.seldir = os.path.join(dirname, "selections")
+        self.datadir = os.path.join(dirname, "data")
+        self.exportdir = os.path.join(dirname, "exports")
+        version_file_path = os.path.join(dirname, "VERSION")
+
+        self.universe = Universe()
+        
+        self.data = DataDirectory(self.datadir, self)
+
+    def update(self):
+        print "updating project"
+        self.data.update()