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Refresh OPTIMADE aliases and update docstrings #3447

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Nov 1, 2023
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Refresh OPTIMADE aliases and update docstrings #3447

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25 changes: 14 additions & 11 deletions pymatgen/ext/optimade.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,9 +16,6 @@
from pymatgen.util.due import Doi, due
from pymatgen.util.provenance import StructureNL

# from retrying import retry


# TODO: importing optimade-python-tool's data structures will make more sense
Provider = namedtuple("Provider", ["name", "base_url", "description", "homepage", "prefix"])

Expand Down Expand Up @@ -46,7 +43,9 @@ class OptimadeRester:
# these aliases are provided as a convenient shortcut for users of the OptimadeRester class
aliases = {
"aflow": "http://aflow.org/API/optimade/",
"alexandria": "https://alexandria.odbx.science",
"cod": "https://www.crystallography.net/cod/optimade",
"cmr": "https://cmr-optimade.fysik.dtu.dk",
"mcloud.mc3d": "https://aiida.materialscloud.org/mc3d/optimade",
"mcloud.mc2d": "https://aiida.materialscloud.org/mc2d/optimade",
"mcloud.2dtopo": "https://aiida.materialscloud.org/2dtopo/optimade",
Expand All @@ -58,6 +57,7 @@ class OptimadeRester:
"mcloud.tin-antimony-sulfoiodide": "https://aiida.materialscloud.org/tin-antimony-sulfoiodide/optimade",
"mcloud.optimade-sample": "https://aiida.materialscloud.org/optimade-sample/optimade",
"mp": "https://optimade.materialsproject.org",
"mpdd": "http://mpddoptimade.phaseslab.org",
"mpds": "https://api.mpds.io",
"nmd": "https://nomad-lab.eu/prod/rae/optimade/",
"odbx": "https://optimade.odbx.science",
Expand Down Expand Up @@ -154,11 +154,8 @@ def describe(self):
provider_text = "\n".join(map(str, (provider for provider in self._providers.values() if provider)))
return f"OptimadeRester connected to:\n{provider_text}"

# @retry(stop_max_attempt_number=3, wait_random_min=1000, wait_random_max=2000)
def _get_json(self, url):
"""Retrieves JSON, will attempt to (politely) try again on failure subject to a
random delay and a maximum number of attempts.
"""
"""Retrieves and returns JSON resource from given url."""
return self.session.get(url, timeout=self._timeout).json()

@staticmethod
Expand Down Expand Up @@ -215,8 +212,11 @@ def get_structures(
elements: List of elements
nelements: Number of elements, e.g. 4 or [2, 5] for the range >=2 and <=5
nsites: Number of sites, e.g. 4 or [2, 5] for the range >=2 and <=5
chemical_formula_anonymous: Anonymous chemical formula
chemical_formula_hill: Chemical formula following Hill convention
chemical_formula_anonymous: The desired chemical formula in OPTIMADE anonymous formula format
(NB. The ordering is reversed from the pymatgen format, e.g., pymatgen "ABC2" should become "A2BC").
chemical_formula_hill: The desired chemical formula in the OPTIMADE take on the Hill formula format.
(NB. Again, this is different from the pymatgen format, as the OPTIMADE version is a reduced chemical
formula simply using the IUPAC/Hill ordering.)

Returns:
dict[str, Structure]: keyed by that database provider's id system
Expand Down Expand Up @@ -253,8 +253,11 @@ def get_snls(
elements: List of elements
nelements: Number of elements, e.g. 4 or [2, 5] for the range >=2 and <=5
nsites: Number of sites, e.g. 4 or [2, 5] for the range >=2 and <=5
chemical_formula_anonymous: Anonymous chemical formula
chemical_formula_hill: Chemical formula following Hill convention
chemical_formula_anonymous: The desired chemical formula in OPTIMADE anonymous formula format
(NB. The ordering is reversed from the pymatgen format, e.g., pymatgen "ABC2" should become "A2BC").
chemical_formula_hill: The desired chemical formula in the OPTIMADE take on the Hill formula format.
(NB. Again, this is different from the pymatgen format, as the OPTIMADE version is a reduced chemical
formula simply using the IUPAC/Hill ordering.)
additional_response_fields: Any additional fields desired from the OPTIMADE API,
these will be stored under the `'_optimade'` key in each `StructureNL.data` dictionary.

Expand Down