fix deprecations

Author: sphuber

aiida_common_workflows/cli/options.py

@@ -105,7 +105,12 @@ def convert(self, value, param, ctx):
                 f'file `{value}` could not be parsed into a `StructureData`: {exception}'
             ) from exception
 
-        duplicate = QueryBuilder().append(StructureData, filters={'extras._aiida_hash': structure._get_hash()}).first()  # pylint: disable=protected-access
+        duplicate = QueryBuilder().append(
+            StructureData,
+            filters={
+                'extras._aiida_hash': structure.base.caching._get_hash()  # pylint: disable=protected-access
+            }
+        ).first()
 
         if duplicate:
             return duplicate[0]  # pylint: disable=unsubscriptable-object

aiida_common_workflows/cli/plot.py

@@ -34,7 +34,7 @@ def cmd_plot_eos(workflow, precisions, print_table, output_file):
         echo.echo_critical(
             f'node {workflow.__class__.__name__}<{workflow.pk}> does not correspond to an EquationOfStateWorkChain.'
         )
-    outputs = workflow.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = workflow.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     missing_outputs = tuple(output for output in ('structures', 'total_energies') if output not in outputs)
     if missing_outputs:
@@ -107,7 +107,7 @@ def cmd_plot_dissociation_curve(workflow, precisions, print_table, output_file):
         echo.echo_critical(
             f'node {workflow.__class__.__name__}<{workflow.pk}> does not correspond to a DissociationCurveWorkChain.'
         )
-    outputs = workflow.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = workflow.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     missing_outputs = tuple(output for output in ('distances', 'total_energies') if output not in outputs)
     if missing_outputs:

aiida_common_workflows/cli/utils.py

@@ -16,7 +16,7 @@ def echo_process_results(node):
     from aiida.common.links import LinkType
 
     class_name = node.process_class.__name__
-    outputs = node.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
+    outputs = node.base.links.get_outgoing(link_type=(LinkType.CREATE, LinkType.RETURN)).all()
 
     if node.is_finished and node.exit_message:
         state = f'{node.process_state.value} [{node.exit_status}] `{node.exit_message}`'
@@ -78,13 +78,13 @@ def get_code_from_list_or_database(codes, entry_point: str):
     :param entry_point: calculation job entry point name.
     :return: a ``Code`` instance configured for the given entry point or ``None``.
     """
-    from aiida.orm import Code, QueryBuilder
+    from aiida.orm import AbstractCode, QueryBuilder
 
     for entry in codes:
-        if entry.get_attribute('input_plugin') == entry_point:
+        if entry.default_calc_job_plugin == entry_point:
             return entry
 
-    result = QueryBuilder().append(Code, filters={'attributes.input_plugin': entry_point}).first()
+    result = QueryBuilder().append(AbstractCode, filters={'attributes.default_calc_job_plugin': entry_point}).first()
 
     if result is not None:
         return result[0]

aiida_common_workflows/generators/ports.py

@@ -69,8 +69,8 @@ def validate(self, value: t.Any, breadcrumbs: t.Sequence[str] = ()) -> PortValid
         if result is not None:
             return result
 
-        if self.code_entry_point is not None and value.get_input_plugin_name() != self.code_entry_point:
-            return f'invalid entry point `{value.get_input_plugin_name()}` for `Code{value}`.'
+        if self.code_entry_point is not None and value.default_calc_job_plugin != self.code_entry_point:
+            return f'invalid entry point `{value.default_calc_job_plugin}` for `Code{value}`.'
 
         if value is not UNSPECIFIED and self.choices is not None and value not in self.choices:
             choices = [str(value) for value in self.choices]

aiida_common_workflows/workflows/dissociation.py

@@ -97,8 +97,8 @@ def set_distance(molecule: orm.StructureData, distance: orm.Float) -> orm.Struct
     versor_diff = vector_diff / np.linalg.norm(vector_diff)
     new_molecule = molecule.clone()
     new_position = (distance.value * versor_diff) / 2
-    new_molecule.attributes['sites'][0]['position'] = -new_position
-    new_molecule.attributes['sites'][1]['position'] = new_position
+    new_molecule.base.attributes.get('sites')[0]['position'] = -new_position
+    new_molecule.base.attributes.get('sites')[1]['position'] = new_position
     return new_molecule
 
 

aiida_common_workflows/workflows/relax/abinit/extractors.py

@@ -24,5 +24,5 @@ def get_ts_energy(common_relax_workchain: AbinitCommonRelaxWorkChain) -> float:
     if common_relax_workchain.process_class != AbinitCommonRelaxWorkChain:
         return ValueError('The input workchain is not a `AbinitCommonRelaxWorkChain`')
 
-    abinit_base_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    abinit_base_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     return -abinit_base_wc.outputs.output_parameters['e_entropy']

aiida_common_workflows/workflows/relax/abinit/generator.py

@@ -76,7 +76,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
 
         pseudo_family_label = protocol.pop('pseudo_family')
         try:
-            pseudo_family = orm.Group.objects.get(label=pseudo_family_label)
+            pseudo_family = orm.Group.collection.get(label=pseudo_family_label)
         except exceptions.NotExistent as exception:
             raise ValueError(
                 f'required pseudo family `{pseudo_family_label}` is not installed. '

aiida_common_workflows/workflows/relax/abinit/workchain.py

@@ -18,22 +18,22 @@
 def get_stress(parameters):
     """Return the stress array from the given parameters node."""
     stress = orm.ArrayData()
-    stress.set_array(name='stress', array=np.array(parameters.get_attribute('cart_stress_tensor')) * GPA_TO_EV_A3)
+    stress.set_array(name='stress', array=np.array(parameters.base.attributes.get('cart_stress_tensor')) * GPA_TO_EV_A3)
     return stress
 
 
 @calcfunction
 def get_forces(parameters):
     """Return the forces array from the given parameters node."""
     forces = orm.ArrayData()
-    forces.set_array(name='forces', array=np.array(parameters.get_attribute('forces')))
+    forces.set_array(name='forces', array=np.array(parameters.base.attributes.get('forces')))
     return forces
 
 
 @calcfunction
 def get_total_energy(parameters):
     """Return the total energy from the given parameters node."""
-    return orm.Float(parameters.get_attribute('energy'))
+    return orm.Float(parameters.base.attributes.get('energy'))
 
 
 @calcfunction

aiida_common_workflows/workflows/relax/castep/extractors.py

@@ -28,7 +28,7 @@ def get_ts_energy(common_relax_workchain):
     if common_relax_workchain.process_class != CastepCommonRelaxWorkChain:
         return ValueError('The input workchain is not a `CastepCommonRelaxWorkChain`')
 
-    castep_base_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    castep_base_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     e_ks = castep_base_wc.outputs.output_parameters['total energy']
     free_e = castep_base_wc.outputs.output_parameters['free energy']
 

aiida_common_workflows/workflows/relax/castep/generator.py

@@ -256,7 +256,7 @@ def generate_inputs(
     if isinstance(family_name, orm.Str):
         family_name = family_name.value
     try:
-        otfg_family = OTFGGroup.objects.get(label=family_name)
+        otfg_family = OTFGGroup.collection.get(label=family_name)
     except exceptions.NotExistent as exc:
         name = protocol['name']
         family = protocol['relax']['base']['pseudos_family']
@@ -424,7 +424,7 @@ def ensure_otfg_family(family_name, force_update=False):
     if isinstance(family_name, orm.Str):
         family_name = family_name.value
     try:
-        OTFGGroup.objects.get(label=family_name)
+        OTFGGroup.collection.get(label=family_name)
     except NotExistent:
         has_family = False
     else:

aiida_common_workflows/workflows/relax/castep/workchain.py

@@ -53,7 +53,7 @@ def get_free_energy(parameters):
     Return the free energy from the given parameters node.
     The free energy reported by CASTEP is the one that is consistent with the forces.
     """
-    return orm.Float(parameters.get_attribute('free_energy'))
+    return orm.Float(parameters.base.attributes.get('free_energy'))
 
 
 @calcfunction
@@ -62,7 +62,7 @@ def get_total_magnetization(parameters):
     Return the free energy from the given parameters node.
     The free energy reported by CASTEP is the one that is consistent with the forces.
     """
-    return orm.Float(parameters.get_attribute('spin_density'))
+    return orm.Float(parameters.base.attributes.get('spin_density'))
 
 
 class CastepCommonRelaxWorkChain(CommonRelaxWorkChain):

aiida_common_workflows/workflows/relax/cp2k/generator.py

@@ -334,7 +334,7 @@ def _get_kpoints(kpoints_distance, structure, reference_workchain):
         if reference_workchain and 'cp2k__kpoints' in reference_workchain.inputs:
             kpoints_mesh = KpointsData()
             kpoints_mesh.set_cell_from_structure(structure)
-            kpoints_mesh.set_kpoints_mesh(reference_workchain.inputs.cp2k__kpoints.get_attribute('mesh'))
+            kpoints_mesh.set_kpoints_mesh(reference_workchain.inputs.cp2k__kpoints.base.attributes.get('mesh'))
             return kpoints_mesh
 
         if kpoints_distance:

aiida_common_workflows/workflows/relax/cp2k/workchain.py

@@ -22,7 +22,7 @@
 @calcfunction
 def get_total_energy(parameters):
     """Return the total energy from the given parameters node."""
-    return orm.Float(parameters.get_attribute('energy') * HA_TO_EV)
+    return orm.Float(parameters.base.attributes.get('energy') * HA_TO_EV)
 
 
 @calcfunction

aiida_common_workflows/workflows/relax/fleur/extractors.py

@@ -25,7 +25,7 @@ def get_ts_energy(common_relax_workchain):
     if common_relax_workchain.process_class != WorkflowFactory('common_workflows.relax.fleur'):
         return ValueError('The input workchain is not a `FleurCommonRelaxWorkChain`')
 
-    fleur_relax_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    fleur_relax_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     fleur_calc_out = fleur_relax_wc.outputs.last_scf.last_calc
 
     output_parameters = fleur_calc_out.output_parameters

aiida_common_workflows/workflows/relax/fleur/workchain.py

@@ -24,13 +24,13 @@ def get_forces_from_trajectory(trajectory):  # pylint: disable=unused-argument
 @calcfunction
 def get_total_energy(parameters):
     """Calcfunction to get total energy from relax output"""
-    return orm.Float(parameters.get_attribute('energy'))
+    return orm.Float(parameters.base.attributes.get('energy'))
 
 
 @calcfunction
 def get_total_magnetization(parameters):
     """Return the total magnetic moment of the cell from the given parameters node."""
-    return orm.Float(parameters.get_attribute('total_magnetic_moment_cell'))
+    return orm.Float(parameters.base.attributes.get('total_magnetic_moment_cell'))
 
 
 class FleurCommonRelaxWorkChain(CommonRelaxWorkChain):

aiida_common_workflows/workflows/relax/gaussian/generator.py

@@ -80,7 +80,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
         magnetization_per_site = kwargs.get('magnetization_per_site', None)
         threshold_forces = kwargs.get('threshold_forces', None)
 
-        if any(structure.get_attribute_many(['pbc1', 'pbc2', 'pbc3'])):
+        if any(structure.base.attributes.get_many(['pbc1', 'pbc2', 'pbc3'])):
             print('Warning: PBC detected in input structure. It is not supported and thus ignored.')
 
         # -----------------------------------------------------------------

aiida_common_workflows/workflows/relax/gpaw/generator.py

@@ -117,7 +117,9 @@ def _construct_builder( # pylint: disable=arguments-differ,too-many-locals
         kpoints.set_cell_from_structure(structure)
         if reference_workchain:
             previous_kpoints = reference_workchain.inputs.kpoints
-            kpoints.set_kpoints_mesh(previous_kpoints.get_attribute('mesh'), previous_kpoints.get_attribute('offset'))
+            kpoints.set_kpoints_mesh(
+                previous_kpoints.base.attributes.get('mesh'), previous_kpoints.base.attributes.get('offset')
+            )
         else:
             kpoints.set_kpoints_mesh_from_density(protocol['kpoint_distance'])
 

aiida_common_workflows/workflows/relax/gpaw/workchain.py

@@ -21,7 +21,7 @@ def extract_forces_from_array(array):
 @calcfunction
 def extract_total_energy_from_parameters(parameters):
     """Return the total energy from the given parameters node."""
-    energy_cont = parameters.get_attribute('energy_contributions')
+    energy_cont = parameters.base.attributes.get('energy_contributions')
     total_energy = energy_cont['xc'] + energy_cont['local'] + energy_cont['kinetic']
     total_energy += energy_cont['external'] + energy_cont['potential'] + energy_cont['entropy (-st)']
     return orm.Float(total_energy)

aiida_common_workflows/workflows/relax/orca/generator.py

@@ -16,7 +16,7 @@
 
 __all__ = ('OrcaCommonRelaxInputGenerator',)
 
-StructureData = DataFactory('structure')
+StructureData = DataFactory('core.structure')
 
 
 class OrcaCommonRelaxInputGenerator(CommonRelaxInputGenerator):
@@ -72,7 +72,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
         magnetization_per_site = kwargs.get('magnetization_per_site', None)
 
         # Checks
-        if any(structure.get_attribute_many(['pbc1', 'pbc2', 'pbc2'])):
+        if any(structure.base.attributes.get_many(['pbc1', 'pbc2', 'pbc2'])):
             warnings.warn('PBC detected in the input structure. It is not supported and thus is ignored.')
 
         if protocol not in self.get_protocol_names():

aiida_common_workflows/workflows/relax/quantum_espresso/extractors.py

@@ -27,5 +27,5 @@ def get_ts_energy(common_relax_workchain: QuantumEspressoCommonRelaxWorkChain) -
     if common_relax_workchain.process_class != QuantumEspressoCommonRelaxWorkChain:
         return ValueError('The input workchain is not a `QuantumEspressoCommonRelaxWorkChain`')
 
-    qe_relax_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    qe_relax_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     return -qe_relax_wc.outputs.output_parameters['energy_smearing']

aiida_common_workflows/workflows/relax/quantum_espresso/generator.py

@@ -197,7 +197,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
             builder.base['pw']['parameters'] = orm.Dict(dict=parameters)
 
         if reference_workchain:
-            relax = reference_workchain.get_outgoing(node_class=orm.WorkChainNode).one().node
+            relax = reference_workchain.base.links.get_outgoing(node_class=orm.WorkChainNode).one().node
             base = sorted(relax.called, key=lambda x: x.ctime)[-1]
             calc = sorted(base.called, key=lambda x: x.ctime)[-1]
             kpoints = calc.inputs.kpoints

aiida_common_workflows/workflows/relax/quantum_espresso/workchain.py

@@ -30,8 +30,8 @@ def extract_from_trajectory(trajectory):
 @calcfunction
 def extract_from_parameters(parameters):
     """Return the total energy and optionally the total magnetization from the given parameters node."""
-    total_energy = parameters.get_attribute('energy')
-    total_magnetization = parameters.get_attribute('total_magnetization', None)
+    total_energy = parameters.base.attributes.get('energy')
+    total_magnetization = parameters.base.attributes.get('total_magnetization', None)
 
     results = {'total_energy': orm.Float(total_energy)}
 

aiida_common_workflows/workflows/relax/siesta/extractors.py

@@ -22,7 +22,7 @@ def get_ts_energy(common_relax_workchain):
     if common_relax_workchain.process_class != WorkflowFactory('common_workflows.relax.siesta'):
         return ValueError('The input workchain is not a `CommonWorkflowSiestaWorkChain`')
 
-    siesta_base_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    siesta_base_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     e_ks = siesta_base_wc.outputs.output_parameters['E_KS']
     free_e = siesta_base_wc.outputs.output_parameters['FreeE']
 

aiida_common_workflows/workflows/relax/siesta/generator.py

@@ -98,7 +98,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
 
         pseudo_family = self._protocols[protocol]['pseudo_family']
         try:
-            orm.Group.objects.get(label=pseudo_family)
+            orm.Group.collection.get(label=pseudo_family)
         except exceptions.NotExistent as exc:
             raise ValueError(
                 f'protocol `{protocol}` requires `pseudo_family` with name {pseudo_family} '
@@ -213,8 +213,8 @@ def _get_param(self, key, structure, reference_workchain):  # pylint: disable=to
         #the underline SiestaBaseWorkChain.
         if reference_workchain is not None:
             from aiida.orm import WorkChainNode
-            siesta_base_outs = reference_workchain.get_outgoing(node_class=WorkChainNode).one().node.outputs
-            mesh = siesta_base_outs.output_parameters.attributes['mesh']
+            siesta_base_outs = reference_workchain.base.links.get_outgoing(node_class=WorkChainNode).one().node.outputs
+            mesh = siesta_base_outs.output_parameters.base.attributes.get('mesh')
             parameters['mesh-sizes'] = f'[{mesh[0]} {mesh[1]} {mesh[2]}]'
             parameters.pop('mesh-cutoff', None)
 
@@ -281,7 +281,9 @@ def _get_kpoints(self, key, structure, reference_workchain):
             kpoints_mesh = KpointsData()
             kpoints_mesh.set_cell_from_structure(structure)
             previous_wc_kp = reference_workchain.inputs.kpoints
-            kpoints_mesh.set_kpoints_mesh(previous_wc_kp.get_attribute('mesh'), previous_wc_kp.get_attribute('offset'))
+            kpoints_mesh.set_kpoints_mesh(
+                previous_wc_kp.base.attributes.get('mesh'), previous_wc_kp.base.attributes.get('offset')
+            )
             return kpoints_mesh
 
         if 'kpoints' in self._protocols[key]:

aiida_common_workflows/workflows/relax/siesta/workchain.py

@@ -57,6 +57,6 @@ def convert_outputs(self):
         res_dict = get_forces_and_stress(self.ctx.workchain.outputs.forces_and_stress)
         self.out('forces', res_dict['forces'])
         self.out('stress', res_dict['stress'])
-        if 'stot' in self.ctx.workchain.outputs.output_parameters.attributes:
+        if 'stot' in self.ctx.workchain.outputs.output_parameters.base.attributes.all:
             self.out('total_magnetization', get_magn(self.ctx.workchain.outputs.output_parameters))
         self.out('remote_folder', self.ctx.workchain.outputs.remote_folder)

aiida_common_workflows/workflows/relax/vasp/extractors.py

@@ -19,7 +19,7 @@ def get_ts_energy(common_relax_workchain):
     if common_relax_workchain.process_class != WorkflowFactory('common_workflows.relax.vasp'):
         return ValueError('The input workchain is not a `VaspCommonRelaxWorkChain`')
 
-    vasp_wc = common_relax_workchain.get_outgoing(link_type=LinkType.CALL_WORK).one().node
+    vasp_wc = common_relax_workchain.base.links.get_outgoing(link_type=LinkType.CALL_WORK).one().node
     energies = vasp_wc.outputs.energies
     energy_free = energies.get_array('energy_free_electronic')[0]
     energy_no_entropy = energies.get_array('energy_no_entropy')[0]

aiida_common_workflows/workflows/relax/vasp/generator.py

@@ -188,7 +188,9 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
         kpoints.set_cell_from_structure(structure)
         if reference_workchain:
             previous_kpoints = reference_workchain.inputs.kpoints
-            kpoints.set_kpoints_mesh(previous_kpoints.get_attribute('mesh'), previous_kpoints.get_attribute('offset'))
+            kpoints.set_kpoints_mesh(
+                previous_kpoints.base.attributes.get('mesh'), previous_kpoints.base.attributes.get('offset')
+            )
         else:
             kpoints.set_kpoints_mesh_from_density(protocol['kpoint_distance'])
         builder.kpoints = kpoints

aiida_common_workflows/workflows/relax/wien2k/generator.py

@@ -84,7 +84,7 @@ def _construct_builder(self, **kwargs) -> engine.ProcessBuilder:
             inpdict['-nometal'] = True
         if reference_workchain:  # ref. workchain is passed as input
             # derive Rmt's from the ref. workchain and pass as input
-            w2k_wchain = reference_workchain.get_outgoing(node_class=orm.WorkChainNode).one().node
+            w2k_wchain = reference_workchain.base.links.get_outgoing(node_class=orm.WorkChainNode).one().node
             ref_wrkchn_res_dict = w2k_wchain.outputs.workchain_result.get_dict()
             rmt = ref_wrkchn_res_dict['Rmt']
             atm_lbl = ref_wrkchn_res_dict['atom_labels']

docs/source/workflows/composite/dc.rst

@@ -103,7 +103,7 @@ A template script to retrieve the results follows:
 
     node = load_node(<IDN>) # <IDN> is an identifier (PK, uuid, ..) of a completed DC workchain
 
-    outputs = node.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = node.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     distances = []
     energies = []

docs/source/workflows/composite/eos.rst

@@ -103,7 +103,7 @@ A template script to retrieve the results follows:
 
     node = load_node(<IDN>) # <IDN> is an identifier (PK, uuid, ..) of a completed EoS workchain
 
-    outputs = node.get_outgoing(link_type=LinkType.RETURN).nested()
+    outputs = node.base.links.get_outgoing(link_type=LinkType.RETURN).nested()
 
     volumes = []
     energies = []