From a427ca3fc94733322a7acf39b22bcc7bdb6ac64f Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Tue, 23 Apr 2019 12:21:02 +0200
Subject: [PATCH] Fixed bug with searching multi quantities (atoms,
quantities).
---
nomad/api/info.py | 2 +-
nomad/datamodel/base.py | 10 +++++-----
nomad/datamodel/dft.py | 4 ++--
nomad/search.py | 13 ++++++-------
4 files changed, 14 insertions(+), 15 deletions(-)
diff --git a/nomad/api/info.py b/nomad/api/info.py
index 983636ebf3..35cc9408e8 100644
--- a/nomad/api/info.py
+++ b/nomad/api/info.py
@@ -66,7 +66,7 @@ class InfoResource(Resource):
'normalizers': [normalizer.__name__ for normalizer in normalizing.normalizers],
'domain': {
'name': datamodel.Domain.instance.name,
- 'quantities': datamodel.Domain.instance.quantities,
+ 'quantities': [quantity for quantity in datamodel.Domain.instance.quantities.values()],
'metrics_names': datamodel.Domain.instance.metrics_names,
'aggregations_names': datamodel.Domain.instance.aggregations_names
},
diff --git a/nomad/datamodel/base.py b/nomad/datamodel/base.py
index ad8ae4fc7a..dae862ecd2 100644
--- a/nomad/datamodel/base.py
+++ b/nomad/datamodel/base.py
@@ -225,7 +225,7 @@ class Domain:
self.name = name
self.domain_entry_class = domain_entry_class
- self.quantities: List[DomainQuantity] = []
+ self.quantities: Dict[str, DomainQuantity] = {}
self.root_sections = root_sections
reference_domain_calc = domain_entry_class()
@@ -239,13 +239,13 @@ class Domain:
quantities[quantity_name] = quantity
quantity.name = quantity_name
quantity.multi = isinstance(value, list)
- self.quantities.append(quantity)
+ self.quantities[quantity.name] = quantity
for quantity_name in quantities.keys():
assert hasattr(reference_domain_calc, quantity_name) and not hasattr(reference_general_calc, quantity_name), \
'quantity does not exist or overrides general non domain quantity'
- assert any(quantity.order_default for quantity in Domain.instances[name].quantities), \
+ assert any(quantity.order_default for quantity in Domain.instances[name].quantities.values()), \
'you need to define a order default quantity'
@property
@@ -255,7 +255,7 @@ class Domain:
"""
return {
quantity.metric[0]: (quantity.metric[1], quantity.name)
- for quantity in self.quantities
+ for quantity in self.quantities.values()
if quantity.metric is not None
}
@@ -272,7 +272,7 @@ class Domain:
"""
return {
quantity.name: quantity.aggregations
- for quantity in self.quantities
+ for quantity in self.quantities.values()
if quantity.aggregations > 0
}
diff --git a/nomad/datamodel/dft.py b/nomad/datamodel/dft.py
index 844bc62fb3..0a9c25b591 100644
--- a/nomad/datamodel/dft.py
+++ b/nomad/datamodel/dft.py
@@ -157,7 +157,7 @@ Domain('DFT', DFTCalcWithMetadata, quantities=dict(
atoms=DomainQuantity(
'The atom labels of all atoms in the simulated system.',
# aggregations=len(ase.data.chemical_symbols)),
- aggregations=200), # quickfix for bad atom labels
+ aggregations=200, multi=True), # quickfix for bad atom labels
basis_set=DomainQuantity(
'The used basis set functions.', aggregations=10),
xc_functional=DomainQuantity(
@@ -176,7 +176,7 @@ Domain('DFT', DFTCalcWithMetadata, quantities=dict(
),
quantities=DomainQuantity(
'All quantities that are used by this calculation',
- metric=('quantities', 'value_count')
+ metric=('quantities', 'value_count'), multi=True
),
n_total_energies=DomainQuantity(
'Number of total energy calculations',
diff --git a/nomad/search.py b/nomad/search.py
index 2d0edc4c7a..9dd8aed5e7 100644
--- a/nomad/search.py
+++ b/nomad/search.py
@@ -71,7 +71,7 @@ class Dataset(InnerDoc):
class WithDomain(IndexMeta):
""" Override elasticsearch_dsl metaclass to sneak in domain specific mappings """
def __new__(cls, name, bases, attrs):
- for quantity in datamodel.Domain.instance.quantities:
+ for quantity in datamodel.Domain.instance.quantities.values():
attrs[quantity.name] = quantity.elastic_mapping
return super(WithDomain, cls).__new__(cls, name, bases, attrs)
@@ -143,8 +143,8 @@ class Entry(Document, metaclass=WithDomain):
self.references = [ref.value for ref in source.references]
self.datasets = [Dataset.from_dataset_popo(ds) for ds in source.datasets]
- for quantity in datamodel.Domain.instance.quantities:
- setattr(self, quantity.name, getattr(source, quantity.name))
+ for quantity in datamodel.Domain.instance.quantities.keys():
+ setattr(self, quantity, getattr(source, quantity))
def delete_upload(upload_id):
@@ -196,7 +196,7 @@ The available search quantities in :func:`aggregate_search` as tuples with *sear
elastic field and description.
"""
-for quantity in datamodel.Domain.instance.quantities:
+for quantity in datamodel.Domain.instance.quantities.values():
search_spec = ('term', quantity.name, quantity.description)
search_quantities[quantity.name] = search_spec
@@ -218,7 +218,7 @@ metrics_names = list(metric for metric in metrics.keys())
order_default_quantity = None
-for quantity in datamodel.Domain.instance.quantities:
+for quantity in datamodel.Domain.instance.quantities.values():
if quantity.order_default:
order_default_quantity = quantity.name
@@ -243,8 +243,7 @@ def _construct_search(q: Q = None, time_range: Tuple[datetime, datetime] = None,
values = [value]
for item in values:
- if key == 'atoms':
- # TODO This should be configurable and not specific to atoms
+ if datamodel.Domain.instance.quantities[key].multi:
items = item.split(',')
else:
items = [item]
--
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