Source code for aiidalab_widgets_base.databases
"""Widgets that allow to query online databases."""
import re
import ase
import ipywidgets as ipw
import requests
import traitlets as tl
TEMPLATE_PATTERN = re.compile(r"\{\{.*\}\}")
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class CodQueryWidget(ipw.VBox):
"""Query structures in Crystallography Open Database (COD)
Useful class members:
:ivar structure(Atoms): trait that contains the selected structure, None if structure is not selected.
"""
structure = tl.Instance(ase.Atoms, allow_none=True)
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def __init__(self, title="", **kwargs):
description = ipw.HTML(
"""<h3>Get crystal structures from
<a href="http://www.crystallography.net">Crystallography Open Database</a></h3>
<b>Queries by formula</b>
<br>
For the queries by formula please adhere to the Hill notation.
The chemical symbol of an element should be followed by its number in the structure,
except when there is only one atom.
When the structure does NOT contain carbon atoms, all the elements are listed alphabetically.
Example: <i>O2 Si</i>.
<br>
In case the structure DOES contain carbon atoms its number following the 'C' symbol is indicated first.
If hydrogen is also present in the structure then 'H' symbol and its number is indicated second.
The remaining elements are listed in the alphabetical order. Example: <i>C H4 N2 O</i>.
<br>
<b>Queries by the structure id number</b>
<br>
For the queries by structure id, plese provide the database id number. Example: <i>1008786</i>
"""
)
self.title = title
layout = ipw.Layout(width="400px")
style = {"description_width": "initial"}
self.inp_elements = ipw.Text(
description="",
value="",
placeholder="e.g.: Ni Ti or id number",
layout=layout,
style=style,
)
self.btn_query = ipw.Button(description="Query")
self.query_message = ipw.HTML("Waiting for input...")
self.drop_structure = ipw.Dropdown(
description="",
options=[("select structure", {"status": False})],
style=style,
layout=layout,
)
self.link = ipw.HTML("Link to the web-page will appear here")
self.btn_query.on_click(self._on_click_query)
self.drop_structure.observe(self._on_select_structure, names=["value"])
children = [
description,
ipw.HBox([self.btn_query, self.inp_elements]),
self.query_message,
ipw.HBox([self.drop_structure, self.link]),
]
super().__init__(children=children, **kwargs)
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@staticmethod
def _query(idn=None, formula=None):
"""Make the actual query."""
from aiida.tools.dbimporters.plugins.cod import CodDbImporter
importer = CodDbImporter()
if idn is not None:
return importer.query(id=idn)
if formula is not None:
return importer.query(formula=formula)
return None
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def _on_click_query(self, _=None):
"""Call query when the corresponding button is pressed."""
structures = [("select structure", {"status": False})]
idn = None
formula = None
self.query_message.value = "Quering the database ... "
try:
idn = int(self.inp_elements.value)
except ValueError:
formula = str(self.inp_elements.value)
for entry in self._query(idn=idn, formula=formula):
try:
entry_cif = entry.get_cif_node()
formula = entry_cif.get_ase().get_chemical_formula()
except Exception:
continue
entry_add = (
f"{formula} (id: {entry.source['id']})",
{
"status": True,
"cif": entry_cif,
"url": entry.source["uri"],
"id": entry.source["id"],
},
)
structures.append(entry_add)
self.query_message.value += f"{len(structures) - 1} structures found"
self.drop_structure.options = structures
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def _on_select_structure(self, change):
"""When a structure was selected."""
selected = change["new"]
if selected["status"] is False:
self.structure = None
return
self.structure = selected["cif"].get_ase()
struct_url = selected["url"].split(".cif")[0] + ".html"
self.link.value = (
f"""<a href="{struct_url}" target="_blank">COD entry {selected["id"]}</a>"""
)
@tl.default("structure")
def _default_structure(self):
return None
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class OptimadeQueryWidget(ipw.VBox):
"""AiiDAlab-specific OPTIMADE Query widget
Useful as a widget to integrate with the
:class:`aiidalab_widgets_base.structures.StructureManagerWidget`,
embedded into applications.
NOTE: `embedded` for `OptimadeQueryFilterWidget` was introduced in `optimade-client`
version 2020.11.5.
:param embedded: Whether or not to show extra database and provider information.
When set to `True`, the extra information will be hidden, this is useful
in situations where the widget is used in a Tab or similar, e.g., for the
class :class:`aiidalab_widgets_base.structures.StructureManagerWidget`.
:type embedded: bool
:param title: Title used for Tab header if employed in
:class:`aiidalab_widgets_base.structures.StructureManagerWidget`.
:type title: str
"""
structure = tl.Instance(ase.Atoms, allow_none=True)
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def __init__(
self,
embedded=True,
title=None,
**kwargs,
) -> None:
try:
from ipyoptimade import default_parameters, query_filter, query_provider
except ImportError:
super().__init__(
[
ipw.HTML(
"""
<div style="margin: 10px 0; padding: 10px; background-color: #ffcc00; color: black; border-left: 6px solid #ffeb3b;">
<i class="fa fa-exclamation-triangle" aria-hidden="true"></i>
This widget requires the <code>optimade-client</code> package to be installed.
Please run <code>pip install optimade-client</code> to install the missing package.
</div>"""
)
]
)
return
providers_header = ipw.HTML("<h4>Select a provider</h4>")
providers = query_provider.OptimadeQueryProviderWidget(
embedded=embedded,
width_ratio=kwargs.pop("width_ratio", None),
width_space=kwargs.pop("width_space", None),
database_limit=kwargs.pop("database_limit", None),
disable_providers=kwargs.pop(
"disable_providers", default_parameters.DISABLE_PROVIDERS
),
skip_databases=kwargs.pop(
"skip_databases", default_parameters.SKIP_DATABASE
),
skip_providers=kwargs.pop(
"skip_providers", default_parameters.SKIP_DATABASE
),
provider_database_groupings=kwargs.pop(
"provider_database_groupings",
default_parameters.PROVIDER_DATABASE_GROUPINGS,
),
)
filters = query_filter.OptimadeQueryFilterWidget(
embedded=embedded,
button_style=kwargs.pop("button_style", None),
result_limit=kwargs.pop("results_limit", None),
subparts_order=kwargs.pop("subparts_order", None),
)
ipw.dlink((providers, "database"), (filters, "database"))
filters.observe(self._update_structure, names="structure")
self.title = title or "OPTIMADE"
layout = kwargs.pop("layout", {"width": "auto", "height": "auto"})
super().__init__(
children=(providers_header, providers, filters),
layout=layout,
**kwargs,
)
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def _update_structure(self, change: dict) -> None:
"""New structure chosen"""
self.structure = (
change["new"].as_aiida_structuredata.get_ase() if change["new"] else None
)
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class ComputationalResourcesDatabaseWidget(ipw.VBox):
"""Extract the setup of a known computer from the AiiDA code registry."""
_default_database_source = (
"https://aiidateam.github.io/aiida-resource-registry/database.json"
)
database_source = tl.Unicode(allow_none=True)
computer_setup = tl.Dict()
computer_configure = tl.Dict()
code_setup = tl.Dict()
STYLE = {"description_width": "180px"}
LAYOUT = {"width": "400px"}
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def __init__(
self,
default_calc_job_plugin=None,
database_source=None,
show_reset_button=True,
**kwargs,
):
if database_source is None:
database_source = self._default_database_source
self.default_calc_job_plugin = default_calc_job_plugin
# Select domain.
self.domain_selector = ipw.Dropdown(
options=(),
description="Domain:",
disabled=False,
layout=self.LAYOUT,
style=self.STYLE,
)
self.domain_selector.observe(self._domain_changed, names=["value", "options"])
# Select computer.
self.computer_selector = ipw.Dropdown(
options=(),
description="Computer:",
disabled=False,
layout=self.LAYOUT,
style=self.STYLE,
)
self.computer_selector.observe(
self._computer_changed, names=["value", "options"]
)
# Select code.
self.code_selector = ipw.Dropdown(
options=(),
description="Code:",
disabled=False,
layout=self.LAYOUT,
style=self.STYLE,
)
self.code_selector.observe(self._code_changed, names=["value", "options"])
reset_button = ipw.Button(description="Reset")
reset_button.on_click(self.reset)
if show_reset_button is False:
reset_button.layout.display = "none"
super().__init__(
children=[
self.domain_selector,
self.computer_selector,
self.code_selector,
reset_button,
],
**kwargs,
)
self.database_source = database_source
self.reset()
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def reset(self, _=None):
"""Reset widget and traits"""
with self.hold_trait_notifications():
self.domain_selector.value = None
self.computer_selector.value = None
self.code_selector.value = None
@tl.observe("database_source")
def _database_source_changed(self, _=None):
self.database = self._database_generator(
self.database_source, self.default_calc_job_plugin
)
# Update domain selector.
self.domain_selector.options = self.database.keys()
self.reset()
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@staticmethod
def _database_generator(database_source, default_calc_job_plugin):
"""From database source JSON and default calc job plugin, generate resource database"""
try:
database = requests.get(database_source).json()
except Exception:
database = {}
if default_calc_job_plugin is None:
return database
# filter database by default calc job plugin
for domain, domain_value in database.copy().items():
for computer, computer_value in domain_value.copy().items():
if computer == "default":
# skip default computer
continue
for code, code_value in list(computer_value["codes"].items()):
# check if code plugin matches default plugin
# if not, remove code
plugin = re.sub(
TEMPLATE_PATTERN, r".*", code_value["default_calc_job_plugin"]
)
if re.match(plugin, default_calc_job_plugin) is None:
del computer_value["codes"][code]
if len(computer_value["codes"]) == 0:
# remove computer since no codes defined in this computer source
del domain_value[computer]
if domain_value.get("default") == computer:
# also remove default computer from domain
del domain_value["default"]
if len(domain_value) == 0:
# remove domain since no computers with required codes defined in this domain source
del database[domain]
continue
if domain_value["default"] not in domain_value:
# make sure default computer is still points to existing computer
domain_value["default"] = sorted(domain_value.keys() - {"default"})[0]
return database
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def _domain_changed(self, change=None):
"""callback when new domain selected"""
with self.hold_trait_notifications(): # To prevent multiple calls to callbacks
if change["new"] is None:
self.computer_selector.options = ()
self.computer_selector.value = None
self.code_selector.options = ()
self.code_selector.value = None
return
else:
selected_domain = self.domain_selector.value
with self.hold_trait_notifications():
self.computer_selector.options = tuple(
key
for key in self.database.get(selected_domain, {}).keys()
if key != "default"
)
self.computer_selector.value = self.database.get(
selected_domain, {}
).get("default")
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def _computer_changed(self, change=None):
"""callback when new computer selected"""
with self.hold_trait_notifications():
if change["new"] is None:
self.code_selector.options = ()
self.code_selector.value = None
self.computer_setup, self.computer_configure = {}, {}
return
else:
self.code_selector.value = None
selected_computer = self.computer_selector.value
selected_domain = self.domain_selector.value
computer_dict = self.database.get(selected_domain, {}).get(
selected_computer, {}
)
self.code_selector.options = list(computer_dict.get("codes", {}).keys())
self.code_selector.value = None
computer_setup = computer_dict.get("computer", {}).get("computer-setup", {})
computer_configure = computer_dict.get("computer", {}).get(
"computer-configure", {}
)
if "hostname" in computer_setup:
computer_configure["hostname"] = computer_setup.get("hostname")
self.computer_setup = computer_setup
self.computer_configure = computer_configure
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def _code_changed(self, change=None):
"""Update code settings."""
if change["new"] is None:
self.code_setup = {}
return
else:
selected_code = self.code_selector.value
selected_domain = self.domain_selector.value
selected_computer = self.computer_selector.value
self.code_setup = (
self.database.get(selected_domain, {})
.get(selected_computer, {})
.get("codes", {})
.get(selected_code, {})
)