Merge pull request #48 from albgar/FixData

Fix data

aiida_siesta/commands/data_psf.py

@@ -55,22 +55,14 @@ def psf_listfamilies(elements, with_description):
     """
     from aiida import orm
     from aiida.plugins import DataFactory
-    from aiida_siesta.data.psf import PSFGROUP_TYPE
+    from aiida_siesta.groups.pseudos import PsfFamily
 
     PsfData = DataFactory('siesta.psf')  # pylint: disable=invalid-name
     query = orm.QueryBuilder()
     query.append(PsfData, tag='psfdata')
     if elements is not None:
         query.add_filter(PsfData, {'attributes.element': {'in': elements}})
-    query.append(
-        orm.Group,
-        with_node='psfdata',
-        tag='group',
-        project=['label', 'description'],
-        filters={'type_string': {
-            '==': PSFGROUP_TYPE
-        }}
-    )
+    query.append(PsfFamily, with_node='psfdata', tag='group', project=['label', 'description'])
 
     query.distinct()
     if query.count() > 0:

aiida_siesta/commands/data_psml.py

@@ -55,22 +55,14 @@ def psml_listfamilies(elements, with_description):
     """
     from aiida import orm
     from aiida.plugins import DataFactory
-    from aiida_siesta.data.psml import PSMLGROUP_TYPE
+    from aiida_siesta.groups.pseudos import PsmlFamily
 
     PsmlData = DataFactory('siesta.psml')  # pylint: disable=invalid-name
     query = orm.QueryBuilder()
     query.append(PsmlData, tag='psmldata')
     if elements is not None:
         query.add_filter(PsmlData, {'attributes.element': {'in': elements}})
-    query.append(
-        orm.Group,
-        with_node='psmldata',
-        tag='group',
-        project=['label', 'description'],
-        filters={'type_string': {
-            '==': PSMLGROUP_TYPE
-        }}
-    )
+    query.append(PsmlFamily, with_node='psmldata', tag='group', project=['label', 'description'])
 
     query.distinct()
     if query.count() > 0:

aiida_siesta/data/psf.py

@@ -3,12 +3,9 @@
 """
 
 import io
-from aiida.common.utils import classproperty
 from aiida.common.files import md5_file
 from aiida.orm.nodes import SinglefileData
 
-PSFGROUP_TYPE = 'data.psf.family'
-
 
 def get_pseudos_from_structure(structure, family_name):
     """
@@ -64,6 +61,7 @@ def upload_psf_family(folder, group_label, group_description, stop_if_existing=T
     from aiida.common import AIIDA_LOGGER as aiidalogger
     from aiida.common.exceptions import UniquenessError
     from aiida.orm.querybuilder import QueryBuilder
+    from aiida_siesta.groups.pseudos import PsfFamily
 
     if not os.path.isdir(folder):
         raise ValueError("folder must be a directory")
@@ -79,9 +77,7 @@ def upload_psf_family(folder, group_label, group_description, stop_if_existing=T
     nfiles = len(files)
 
     automatic_user = orm.User.objects.get_default()
-    group, group_created = orm.Group.objects.get_or_create(
-        label=group_label, type_string=PSFGROUP_TYPE, user=automatic_user
-    )
+    group, group_created = PsfFamily.objects.get_or_create(label=group_label, user=automatic_user)
 
     if group.user.email != automatic_user.email:
         raise UniquenessError(
@@ -257,10 +253,6 @@ def get_or_create(cls, filename, use_first=False, store_psf=True):
 
         return (pseudos[0], False)
 
-    @classproperty
-    def psffamily_type_string(cls):  # pylint: disable=no-self-argument,no-self-use
-        return PSFGROUP_TYPE
-
     def store(self, *args, **kwargs):  # pylint: disable=arguments-differ
         """
         Store the node, reparsing the file so that the md5 and the element
@@ -327,9 +319,14 @@ def get_psf_family_names(self):
         """
         Get the list of all psf family names to which the pseudo belongs
         """
-        from aiida.orm import Group
+        from aiida.orm import QueryBuilder
+        from aiida_siesta.groups.pseudos import PsfFamily
 
-        return [_.name for _ in Group.query(nodes=self, type_string=self.psffamily_type_string)]
+        query = QueryBuilder()
+        query.append(PsfFamily, tag='group', project='label')
+        query.append(PsfData, filters={'id': {'==': self.id}}, with_group='group')
+
+        return [_[0] for _ in query.all()]
 
     @property
     def element(self):
@@ -383,9 +380,9 @@ def get_psf_group(cls, group_label):
         """
         Return the PsfFamily group with the given name.
         """
-        from aiida.orm import Group
+        from aiida_siesta.groups.pseudos import PsfFamily
 
-        return Group.get(label=group_label, type_string=cls.psffamily_type_string)
+        return PsfFamily.get(label=group_label)
 
     @classmethod
     def get_psf_groups(cls, filter_elements=None, user=None):
@@ -400,25 +397,22 @@ def get_psf_groups(cls, filter_elements=None, user=None):
                If defined, it should be either a DbUser instance, or a string
                for the username (that is, the user email).
         """
-        from aiida.orm import Group
+        from aiida.orm import QueryBuilder
+        from aiida.orm import User
+        from aiida_siesta.groups.pseudos import PsfFamily
 
-        group_query_params = {"type_string": cls.psffamily_type_string}
+        query = QueryBuilder()
+        query.append(PsfFamily, tag='group', project='*')
 
-        if user is not None:
-            group_query_params['user'] = user
+        if user:
+            query.append(User, filters={'email': {'==': user}}, with_group='group')
 
         if isinstance(filter_elements, str):
             filter_elements = [filter_elements]
 
         if filter_elements is not None:
-            actual_filter_elements = {_.capitalize() for _ in filter_elements}
-
-            group_query_params['node_attributes'] = {'element': actual_filter_elements}
+            query.append(PsfData, filters={'attributes.element': {'in': filter_elements}}, with_group='group')
 
-        all_psf_groups = Group.query(**group_query_params)
+        query.order_by({PsfFamily: {'id': 'asc'}})
 
-        groups = [(g.name, g) for g in all_psf_groups]
-        # Sort by name
-        groups.sort()
-        # Return the groups, without name
-        return [_[1] for _ in groups]
+        return [_[0] for _ in query.all()]

aiida_siesta/data/psml.py

@@ -2,13 +2,12 @@
 This module manages the PSML pseudopotentials in the local repository.
 """
 
-from aiida.common.utils import classproperty
 from aiida.common.files import md5_file
 from aiida.orm.nodes import SinglefileData
 
 # See LICENSE.txt and AUTHORS.txt
 
-PSMLGROUP_TYPE = 'data.psml.family'
+#PSMLGROUP_TYPE = 'data.psml.family'
 
 
 def get_pseudos_from_structure(structure, family_name):
@@ -65,6 +64,7 @@ def upload_psml_family(folder, group_label, group_description, stop_if_existing=
     from aiida.common import AIIDA_LOGGER as aiidalogger
     from aiida.common.exceptions import UniquenessError
     from aiida.orm.querybuilder import QueryBuilder
+    from aiida_siesta.groups.pseudos import PsmlFamily
 
     if not os.path.isdir(folder):
         raise ValueError("folder must be a directory")
@@ -80,9 +80,10 @@ def upload_psml_family(folder, group_label, group_description, stop_if_existing=
     nfiles = len(files)
 
     automatic_user = orm.User.objects.get_default()
-    group, group_created = orm.Group.objects.get_or_create(
-        label=group_label, type_string=PSMLGROUP_TYPE, user=automatic_user
-    )
+    #group, group_created = orm.Group.objects.get_or_create(
+    #    label=group_label, type_string=PSMLGROUP_TYPE, user=automatic_user
+    #)
+    group, group_created = PsmlFamily.objects.get_or_create(label=group_label, user=automatic_user)
 
     if group.user.email != automatic_user.email:
         raise UniquenessError(
@@ -258,9 +259,9 @@ def get_or_create(cls, filename, use_first=False, store_psml=True):
 
         return (pseudos[0], False)
 
-    @classproperty
-    def psmlfamily_type_string(cls):  # pylint: disable=no-self-argument,no-self-use
-        return PSMLGROUP_TYPE
+    #@classproperty
+    #def psmlfamily_type_string(cls):  # pylint: disable=no-self-argument,no-self-use
+    #    return PSMLGROUP_TYPE
 
     def store(self, *args, **kwargs):  # pylint: disable=arguments-differ
         """
@@ -328,9 +329,15 @@ def get_psml_family_names(self):
         """
         Get the list of all psml family names to which the pseudo belongs
         """
-        from aiida.orm import Group
+        #from aiida.orm import Group
+        from aiida.orm import QueryBuilder
+        from aiida_siesta.groups.pseudos import PsmlFamily
 
-        return [_.name for _ in Group.query(nodes=self, type_string=self.psmlfamily_type_string)]
+        query = QueryBuilder()
+        query.append(PsmlFamily, tag='group', project='label')
+        query.append(PsmlData, filters={'id': {'==': self.id}}, with_group='group')
+
+        return [_[0] for _ in query.all()]
 
     @property
     def element(self):
@@ -385,9 +392,10 @@ def get_psml_group(cls, group_label):
         """
         Return the PsmlFamily group with the given name.
         """
-        from aiida.orm import Group
+        #from aiida.orm import Group
+        from aiida_siesta.groups.pseudos import PsmlFamily
 
-        return Group.get(label=group_label, type_string=cls.psmlfamily_type_string)
+        return PsmlFamily.get(label=group_label)
 
     @classmethod
     def get_psml_groups(cls, filter_elements=None, user=None):
@@ -402,25 +410,25 @@ def get_psml_groups(cls, filter_elements=None, user=None):
                If defined, it should be either a DbUser instance, or a string
                for the username (that is, the user email).
         """
-        from aiida.orm import Group
+        #from aiida.orm import Group
+        from aiida.orm import QueryBuilder
+        from aiida.orm import User
+        from aiida_siesta.groups.pseudos import PsmlFamily
+
+        query = QueryBuilder()
+        #filters = {'type_string': {'==': cls.psmlfamily_type_string}}
 
-        group_query_params = {"type_string": cls.psmlfamily_type_string}
+        query.append(PsmlFamily, tag='group', project='*')
 
-        if user is not None:
-            group_query_params['user'] = user
+        if user:
+            query.append(User, filters={'email': {'==': user}}, with_group='group')
 
         if isinstance(filter_elements, str):
             filter_elements = [filter_elements]
 
         if filter_elements is not None:
-            actual_filter_elements = {_.capitalize() for _ in filter_elements}
-
-            group_query_params['node_attributes'] = {'element': actual_filter_elements}
+            query.append(PsmlData, filters={'attributes.element': {'in': filter_elements}}, with_group='group')
 
-        all_psml_groups = Group.query(**group_query_params)
+        query.order_by({PsmlFamily: {'id': 'asc'}})
 
-        groups = [(g.name, g) for g in all_psml_groups]
-        # Sort by name
-        groups.sort()
-        # Return the groups, without name
-        return [_[1] for _ in groups]
+        return [_[0] for _ in query.all()]

aiida_siesta/groups/pseudos.py

@@ -0,0 +1,9 @@
+from aiida.orm.groups import Group
+
+
+class PsfFamily(Group):
+    """Group that represents a pseudo potential family containing `PsfData` nodes."""
+
+
+class PsmlFamily(Group):
+    """Group that represents a pseudo potential family containing `PsmlData` nodes."""

setup.json

@@ -55,6 +55,10 @@
         "aiida.cmdline.data": [
             "psf = aiida_siesta.commands.data_psf:psfdata",
             "psml = aiida_siesta.commands.data_psml:psmldata"
-        ]
+        ],
+	"aiida.groups": [
+      	    "data.psf.family = aiida_siesta.groups.pseudos:PsfFamily",
+            "data.psml.family = aiida_siesta.groups.pseudos:PsmlFamily"
+    	]
     }
 }

tests/data/test_pseudos.py

@@ -0,0 +1,24 @@
+def test_pseudos_classmethods(generate_psf_data, generate_psml_data):
+
+    from aiida_siesta.data.psml import PsmlData
+    from aiida_siesta.data.psf import PsfData
+
+    assert PsfData.get_psf_groups() == []
+    assert PsmlData.get_psml_groups() == []
+
+    #get_psf_group(cls, group_label)
+
+    #from_md5
+
+    #get_or_create
+
+def test_pseudo(generate_psf_data, generate_psml_data):
+
+    psf = generate_psf_data('Si')
+    psml = generate_psml_data('Si')
+
+    assert psf.get_psf_family_names() == []
+    assert psml.get_psml_family_names() == []
+
+    #set_file
+    #assert 'md5' in psf.attributes