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Structure download section: add extxyz and xsf formats #501

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merged 3 commits into from
Aug 17, 2023
Merged

Structure download section: add extxyz and xsf formats #501

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a31b480
Structure download section: add extxyz and xsf formats.
yakutovicha Aug 16, 2023
49dae8a
Add test to the `_prepare_payload` method.
yakutovicha Aug 17, 2023
6e4f1fc
Test `_prepare_payload` with several formats
yakutovicha Aug 17, 2023
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21 changes: 17 additions & 4 deletions aiidalab_widgets_base/viewers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -452,7 +452,14 @@ def _download_tab(self):

# 1. Choose download file format.
self.file_format = ipw.Dropdown(
options=["xyz", "cif"],
label="Extended xyz",
# File extension and format may be differen. Therefore, we define both.
options=(
("xyz", {"extension": "xyz", "format": "xyz"}),
("cif", {"extension": "cif", "format": "cif"}),
("Extended xyz", {"extension": "xyz", "format": "extxyz"}),
("xsf", {"extension": "xsf", "format": "xsf"}),
),
layout={"width": "200px"},
description="File format:",
)
Expand Down Expand Up @@ -710,10 +717,13 @@ def apply_displayed_selection(self, _=None):

def download(self, change=None): # pylint: disable=unused-argument
"""Prepare a structure for downloading."""
suffix = f"-pk-{self.pk}" if self.pk else ""
payload = self._prepare_payload()
if payload is None:
return
suffix = f"pk-{self.pk}" if self.pk else "not-stored"
self._download(
payload=self._prepare_payload(),
filename=f"structure{suffix}.{self.file_format.value}",
filename=f"""structure-{suffix}.{self.file_format.value["extension"]}""",
)

@staticmethod
Expand All @@ -737,7 +747,10 @@ def _prepare_payload(self, file_format=None):
"""Prepare binary information."""
from tempfile import NamedTemporaryFile

file_format = file_format if file_format else self.file_format.value
if not self.structure:
return None

file_format = file_format if file_format else self.file_format.value["format"]
tmp = NamedTemporaryFile()
self.structure.write(tmp.name, format=file_format) # pylint: disable=no-member
with open(tmp.name, "rb") as raw:
Expand Down
28 changes: 24 additions & 4 deletions tests/test_viewers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,22 +67,42 @@ def test_structure_data_viwer(structure_data_object):

# Selection of atoms.

# Direct selection
# Direct selection.
v._selected_atoms.value = "1..2"
v.apply_displayed_selection()
assert v.selection == [0, 1]

# x coordinate lower than 0.5
# The x coordinate lower than 0.5.
v._selected_atoms.value = "x<0.5"
v.apply_displayed_selection()
assert v.selection == [0]

# id of the second atom
# The id of the second atom
v._selected_atoms.value = "id > 1"
v.apply_displayed_selection()
assert v.selection == [1]

# or of the two selections
# or of the two selections.
v._selected_atoms.value = "x>0.5 or x<0.5"
v.apply_displayed_selection()
assert v.selection == [0, 1]

# Check the `_prepare_payload` function used for downloading.
format_cases = [
(
"Extended xyz",
"""MgpMYXR0aWNlPSIzLjg0NzM3IDAuMCAwLjAgMS45MjM2ODUgMy4zMzE5MiAwLjAgMS45MjM2ODUgMS4xMTA2NCAzLjE0MTM2NCIgUHJvcGVydGllcz1zcGVjaWVzOlM6MTpwb3M6UjozOm1hc3NlczpSOjEgcGJjPSJUIFQgVCIKU2kgICAgICAgMC4wMDAwMDAwMCAgICAgICAwLjAwMDAwMDAwICAgICAgIDAuMDAwMDAwMDAgICAgICAyOC4wODU1MDAwMApTaSAgICAgICAxLjkyMzY4NTAwICAgICAgIDEuMTEwNjQwMDAgICAgICAgMC43ODUzNDEwMCAgICAgIDI4LjA4NTUwMDAwCg==""",
),
(
"xsf",
"""Q1JZU1RBTApQUklNVkVDCiAzLjg0NzM3MDAwMDAwMDAwIDAuMDAwMDAwMDAwMDAwMDAgMC4wMDAwMDAwMDAwMDAwMAogMS45MjM2ODUwMDAwMDAwMCAzLjMzMTkyMDAwMDAwMDAwIDAuMDAwMDAwMDAwMDAwMDAKIDEuOTIzNjg1MDAwMDAwMDAgMS4xMTA2NDAwMDAwMDAwMCAzLjE0MTM2NDAwMDAwMDAwClBSSU1DT09SRAogMiAxCiAxNCAgICAgMC4wMDAwMDAwMDAwMDAwMCAgICAgMC4wMDAwMDAwMDAwMDAwMCAgICAgMC4wMDAwMDAwMDAwMDAwMAogMTQgICAgIDEuOTIzNjg1MDAwMDAwMDAgICAgIDEuMTEwNjQwMDAwMDAwMDAgICAgIDAuNzg1MzQxMDAwMDAwMDAK""",
),
(
"cif",
"""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""",
),
]

for fmt, out in format_cases:
v.file_format.label = fmt
assert v._prepare_payload() == out
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