Addressing code review comments

aiida/backends/tests/export_and_import.py

@@ -1808,11 +1808,6 @@ def test_links_for_workflows(self):
             o1.add_link_from(w1, 'output', link_type=LinkType.CREATE)
             o1.add_link_from(w1, 'return', link_type=LinkType.RETURN)
 
-            uuids_wanted = set(_.uuid for _ in (w1,o1,i1))
-            # links_wanted = [l for l in self.get_all_node_links() if l[3] in
-            #                 ('createlink', 'inputlink', 'returnlink', 'calllink')]
-            # links_wanted = self.get_all_node_links()
-
             links_wanted = [l for l in self.get_all_node_links() if l[3] in
                             (LinkType.CREATE.value,
                              LinkType.INPUT.value,

aiida/cmdline/commands/exportfile.py

@@ -39,20 +39,20 @@ def cli(self, *args):
     help='Export the given computers by pk')
 @click.option('-G', '--groups', multiple=True, type=int,
     help='Export the given groups by pk')
-@click.option('-g', '--group_names', multiple=True, type=str,
+@click.option('-g', '--group-names', multiple=True, type=str,
     help='Export the given groups by group name')
-@click.option('-IF', '--input_forward', is_flag=True, default=False,
-    help='Follow forward INPUT links (recursively) when calculating the node '
-         "set to export. By default this is switched off.")
-@click.option('-CrR', '--create_reversed', is_flag=True, default=True,
-    help='Follow reverse CREATE links (recursively) when calculating the node '
-         'set to export. By default this is switched on.')
-@click.option('-RR', '--return_reversed', is_flag=True, default=False,
-    help='Follow reverse RETURN links (recursively) when calculating the node '
-         'set to export. By default this is switched off.')
-@click.option('-CaR', '--call_reversed', is_flag=True, default=False,
-    help='Follow reverse CALL links (recursively) when calculating the node '
-         'set to export. By default this is switched off.')
+@click.option('-I', '--input-forward', is_flag=True, default=False,
+    show_default=True, help='Follow forward INPUT links (recursively) when '
+                            'calculating the node set to export.')
+@click.option('-C', '--create-reversed', is_flag=True, default=True,
+    show_default=True, help='Follow reverse CREATE links (recursively) when '
+                            'calculating the node set to export.')
+@click.option('-R', '--return-reversed', is_flag=True, default=False,
+    show_default=True, help='Follow reverse RETURN links (recursively) when '
+                            'calculating the node set to export.')
+@click.option('-X', '--call-reversed', is_flag=True, default=False,
+    show_default=True, help='Follow reverse CALL links (recursively) when '
+                            'calculating the node set to export.')
 @click.option('-f', '--overwrite', is_flag=True, default=False,
     help='Overwrite the output file, if it exists')
 @click.option('-a', '--archive-format',
@@ -66,6 +66,8 @@ def create(outfile, computers, groups, nodes, group_names, input_forward,
     """
     import sys
     from aiida.backends.utils import load_dbenv, is_dbenv_loaded
+    # TODO: Replace with aiida.cmdline.utils.decorators.with_dbenv decocator
+    # TODO: when we merge to develop
     if not is_dbenv_loaded():
         load_dbenv()
     from aiida.orm import Group, Node, Computer

aiida/cmdline/commands/importfile.py

@@ -31,6 +31,7 @@ def run(self, *args):
 
         from aiida.common.folders import SandboxFolder
         from aiida.orm.importexport import get_valid_import_links, import_data
+        from aiida.common.exceptions import ContentNotExistent
 
         parser = argparse.ArgumentParser(
             prog=self.get_full_command_name(),
@@ -82,7 +83,10 @@ def run(self, *args):
         for filename in files:
             try:
                 print "**** Importing file {}".format(filename)
-                import_data(filename)
+                try:
+                    import_data(filename)
+                except ContentNotExistent as ce:
+                    print ce
             except Exception:
                 traceback.print_exc()
 

aiida/orm/data/__init__.py

@@ -97,8 +97,6 @@ def add_link_from(self, src, label=None, link_type=LinkType.UNSPECIFIED):
 
         if link_type is LinkType.CREATE and \
                         len(self.get_inputs(link_type=LinkType.CREATE)) > 0:
-            for l in self.get_inputs(link_type=LinkType.CREATE):
-                print "=====> ", l, l.dbnode
             raise ValueError("At most one CREATE node can enter a data node")
 
         if not isinstance(src, Calculation):

aiida/orm/importexport.py

@@ -387,9 +387,9 @@ def import_data_dj(in_path,ignore_unknown_nodes=False,
                                  "nor a zip file.")
 
         if not folder.get_content_list():
-            print "The provided file/folder is empty. Exiting silently"
-            return
-
+            from aiida.common.exceptions import ContentNotExistent
+            raise ContentNotExistent("The provided file/folder ({}) is empty"
+                                     .format(in_path))
         try:
             with open(folder.get_abs_path('metadata.json')) as f:
                 metadata = json.load(f)
@@ -869,7 +869,6 @@ def import_data_sqla(in_path, ignore_unknown_nodes=False, silent=False):
 
     from aiida.orm import Node, Group
     from aiida.common.archive import extract_tree, extract_tar, extract_zip, extract_cif
-    from aiida.common.links import LinkType
     from aiida.common.folders import SandboxFolder, RepositoryFolder
     from aiida.common.utils import get_object_from_string
     from aiida.common.datastructures import calc_states
@@ -910,6 +909,10 @@ def import_data_sqla(in_path, ignore_unknown_nodes=False, silent=False):
                                  "is neither a (possibly compressed) tar "
                                  "file, nor a zip file.")
 
+        if not folder.get_content_list():
+            from aiida.common.exceptions import ContentNotExistent
+            raise ContentNotExistent("The provided file/folder ({}) is empty"
+                                     .format(in_path))
         try:
             with open(folder.get_abs_path('metadata.json')) as f:
                 metadata = json.load(f)
@@ -1683,10 +1686,10 @@ def export_tree(what, folder,allowed_licenses=None, forbidden_licenses=None,
                 silent=False, input_forward=False, create_reversed=True,
                 return_reversed=False, call_reversed=False, **kwargs):
     """
-    Export the DB entries passed in the 'what' list to a file tree.
+    Export the entries passed in the 'what' list to a file tree.
     :todo: limit the export to finished or failed calculations.
-    :param what: a list of Django database entries; they can belong to
-    different models.
+    :param what: a list of entity instances; they can belong to
+    different models/entities.
     :param folder: a :py:class:`Folder <aiida.common.folders.Folder>` object
     :param input_forward: Follow forward INPUT links (recursively) when
     calculating the node set to export.
@@ -1733,7 +1736,7 @@ def export_tree(what, folder,allowed_licenses=None, forbidden_licenses=None,
     given_node_entry_ids = set()
     given_group_entry_ids = set()
 
-    # I store a list of the actual dbnodes
+    # I keep the pks of the given entities
     for entry in what:
         if issubclass(entry.__class__, Group):
             given_group_entry_ids.add(entry.pk)
@@ -1908,7 +1911,6 @@ def export_tree(what, folder,allowed_licenses=None, forbidden_licenses=None,
         else:
             curr_node_id = to_be_visited[Data].pop()
             # If it is already visited continue to the next node
-            # If it is already visited continue to the next node
             if curr_node_id in to_be_exported:
                 continue
             # Otherwise say that it is a node to be exported
@@ -2599,16 +2601,29 @@ def export_zip(what, outfile = 'testzip', overwrite = False,
         print "File written in {:10.3g} s.".format(time.time() - t)
 
 
-def export(what, outfile='export_data.aiida.tar.gz', overwrite=False, silent=False, **kwargs):
+def export(what, outfile='export_data.aiida.tar.gz', overwrite=False,
+           silent=False, **kwargs):
     """
-    Export the DB entries passed in the 'what' list on a file.
-
+    Export the entries passed in the 'what' list to a file tree.
     :todo: limit the export to finished or failed calculations.
-
-    :param what: a list of Django database entries; they can belong to different
-      models.
-    :param also_parents: if True, also all the parents are stored (from the transitive closure)
-    :param also_calc_outputs: if True, any output of a calculation is also exported
+    :param what: a list of entity instances; they can belong to
+    different models/entities.
+    :param input_forward: Follow forward INPUT links (recursively) when
+    calculating the node set to export.
+    :param create_reversed: Follow reversed CREATE links (recursively) when
+    calculating the node set to export.
+    :param return_reversed: Follow reversed RETURN links (recursively) when
+    calculating the node set to export.
+    :param call_reversed: Follow reversed CALL links (recursively) when
+    calculating the node set to export.
+    :param allowed_licenses: a list or a function. If a list, then checks
+    whether all licenses of Data nodes are in the list. If a function,
+    then calls function for licenses of Data nodes expecting True if
+    license is allowed, False otherwise.
+    :param forbidden_licenses: a list or a function. If a list, then checks
+    whether all licenses of Data nodes are in the list. If a function,
+    then calls function for licenses of Data nodes expecting True if
+    license is allowed, False otherwise.
     :param outfile: the filename of the file on which to export
     :param overwrite: if True, overwrite the output file without asking.
         if False, raise an IOError in this case.
@@ -2635,25 +2650,17 @@ def export(what, outfile='export_data.aiida.tar.gz', overwrite=False, silent=Fal
     if not silent:
         print "COMPRESSING..."
 
-    # PAX_FORMAT: virtually no limitations, better support for unicode
-    #   characters
-    # dereference=True: at the moment, we should not have any symlink or
-    #   hardlink in the AiiDA repository; therefore, do not store symlinks
-    #   or hardlinks, but store the actual destinations.
-    #   This also simplifies the checks on import.
     t3 = time.time()
     with tarfile.open(outfile, "w:gz", format=tarfile.PAX_FORMAT,
                       dereference=True) as tar:
         tar.add(folder.abspath, arcname="")
-
-        #        import shutil
-        #        shutil.make_archive(outfile, 'zip', folder.abspath)#, base_dir='aiida')
     t4 = time.time()
 
     if not silent:
         filecr_time = t2-t1
         filecomp_time = t4-t3
-        print "Exported in {:6.2g}s, compressed in {:6.2g}s, total: {:6.2g}s.".format(filecr_time, filecomp_time, filecr_time + filecomp_time)
+        print("Exported in {:6.2g}s, compressed in {:6.2g}s, total: {:6.2g}s."
+              .format(filecr_time, filecomp_time, filecr_time + filecomp_time))
 
     if not silent:
         print "DONE."