def _on_database_select(self, _):
"""Load chosen database"""
self.structure_drop.reset()
if (self.database[1] is None
or getattr(self.database[1], "base_url", None) is None):
self.query_button.tooltip = "Search - No database chosen"
self.freeze()
else:
self.offset = 0
self.number = 1
self.structure_page_chooser.silent_reset()
try:
self.freeze()
self.query_button.description = "Updating ..."
self.query_button.icon = "cog"
self.query_button.tooltip = "Updating filters ..."
self._set_intslider_ranges()
self._set_version()
except Exception as exc: # pylint: disable=broad-except
LOGGER.error(
"Exception raised during setting IntSliderRanges: %s",
exc.with_traceback(),
)
finally:
self.query_button.description = "Search"
self.query_button.icon = "search"
self.query_button.tooltip = "Search"
self.sort_selector.valid_fields = sorted(
get_sortable_fields(self.database[1].base_url))
self.unfreeze()
def update_local_providers_json(response: dict) -> None:
"""Update local `providers.json` if necessary"""
# Remove dynamic fields
_response = response.copy()
for dynamic_field in (
"time_stamp",
"query",
"last_id",
"response_message",
"warnings",
):
_response.get("meta", {}).pop(dynamic_field, None)
if CACHED_PROVIDERS.exists():
try:
with open(CACHED_PROVIDERS, "r") as handle:
_file_response = json.load(handle)
except JSONDecodeError:
pass
else:
if _file_response == _response:
LOGGER.debug("Local %r is up-to-date", CACHED_PROVIDERS.name)
return
LOGGER.debug(
"Creating/updating local file of cached providers (%r).", CACHED_PROVIDERS.name
)
with open(CACHED_PROVIDERS, "w") as handle:
json.dump(_response, handle)
def _on_change_structure(self, change: dict):
"""Update widget when a new structure is chosen"""
if change["new"] is None:
LOGGER.debug(
"Got no new structure for DownloadChooser (change['new']=%s).",
change["new"],
)
self.reset()
else:
LOGGER.debug("Got new structure for DownloadChooser: id=%s",
change["new"].id)
self._update_options()
self.unfreeze()
# Auto-choose the first (available) option in the dropdown
available_formats = {
label: index
for index, (label, _) in enumerate(self._formats)
}
available_formats.pop(self._formats[0][0])
for label in self.dropdown.disabled_options:
available_formats.pop(label)
if available_formats:
new_index = min(available_formats.values())
self.dropdown.index = new_index
else:
self.dropdown.index = 0
def _set_version(self):
"""Set self.database_version from an /info query"""
base_url = self.database[1].base_url
if base_url not in self.__cached_versions:
# Retrieve and cache version
response = perform_optimade_query(
base_url=self.database[1].base_url, endpoint="/info")
msg, _ = handle_errors(response)
if msg:
raise QueryError(msg)
if "meta" not in response:
raise QueryError(
f"'meta' field not found in /info endpoint for base URL: {base_url}"
)
if "api_version" not in response["meta"]:
raise QueryError(
f"'api_version' field not found in 'meta' for base URL: {base_url}"
)
version = response["meta"]["api_version"]
if version.startswith("v"):
version = version[1:]
self.__cached_versions[base_url] = version
LOGGER.debug(
"Cached version %r for base URL: %r",
self.__cached_versions[base_url],
base_url,
)
self.database_version = self.__cached_versions[base_url]
def _observe_providers(self, change: dict):
"""Update child database dropdown upon changing provider"""
value = change["new"]
self.show_child_dbs.display = "none"
self.provider = value
if value is None or not value:
self.show_child_dbs.display = "none"
self.child_dbs.grouping = self.INITIAL_CHILD_DBS
self.providers.index = 0
self.child_dbs.index = 0
else:
self._initialize_child_dbs()
if sum([len(_[1]) for _ in self.child_dbs.grouping]) <= 2:
# The provider either has 0 or 1 implementations
# or we have failed to retrieve any implementations.
# Automatically choose the 1 implementation (if there),
# while otherwise keeping the dropdown disabled.
self.show_child_dbs.display = "none"
try:
self.child_dbs.index = 1
LOGGER.debug("Changed child_dbs index. New child_dbs: %s",
self.child_dbs)
except IndexError:
pass
else:
self.show_child_dbs.display = None
def _on_database_change(self, change):
"""Update database summary, since self.database has been changed"""
LOGGER.debug("Database changed in summary. New value: %r",
change["new"])
if not change["new"] or change["new"] is None:
self.database_summary.value = ""
else:
self._update_database()
def _get_more_results(self, change):
"""Query for more results according to pageing"""
if not self.__perform_query:
self.__perform_query = True
LOGGER.debug(
"NOT going to perform query with change: name=%s value=%s",
change["name"],
change["new"],
)
return
pageing: Union[int, str] = change["new"]
LOGGER.debug(
"Updating results with pageing change: name=%s value=%s",
change["name"],
pageing,
)
if change["name"] == "page_offset":
self.offset = pageing
pageing = None
elif change["name"] == "page_number":
self.number = pageing
pageing = None
else:
# It is needed to update page_offset, but we do not wish to query again
with self.hold_trait_notifications():
self.__perform_query = False
self.structure_page_chooser.update_offset()
try:
# Freeze and disable list of structures in dropdown widget
# We don't want changes leading to weird things happening prior to the query ending
self.freeze()
# Update button text and icon
self.query_button.description = "Updating ... "
self.query_button.icon = "cog"
self.query_button.tooltip = "Please wait ..."
# Query database
response = self._query(pageing)
msg, _ = handle_errors(response)
if msg:
self.error_or_status_messages.value = msg
return
# Update list of structures in dropdown widget
self._update_structures(response["data"])
# Update pageing
self.structure_page_chooser.set_pagination_data(
links_to_page=response.get("links", {}), )
finally:
self.query_button.description = "Search"
self.query_button.icon = "search"
self.query_button.tooltip = "Search"
self.unfreeze()
def _on_provider_change(self, change: dict):
"""Update provider summary, since self.provider has been changed"""
LOGGER.debug("Provider changed in summary. New value: %r",
change["new"])
self.database_summary.value = ""
if not change["new"] or change["new"] is None:
self.provider_summary.value = ""
else:
self._update_provider()
def __init__(self, *args: Tuple[Any]):
LOGGER.warning(
"%s warned.\nWarning message: %s\nAbout this warning: %s",
args[0].__class__.__name__ if args
and isinstance(args[0], Exception) else self.__class__.__name__,
str(args[0]) if args else "",
args[0].__doc__
if args and isinstance(args[0], Exception) else self.__doc__,
)
super().__init__(*args)
def __getitem__(cls, name):
"""Log warning and default to "DEFAULT" if name is not valid"""
if name not in cls._member_map_:
LOGGER.warning(
"%r is not a valid button style. Setting button style to 'DEFAULT'. "
"Valid button styles: %s",
name,
list(cls._member_map_.keys()),
)
name = "DEFAULT"
return cls._member_map_[name]
def _get_file(filename: str) -> Union[str, bytes]:
"""Read and return file"""
path = Path(filename).resolve()
LOGGER.debug("Trying image file path: %s", str(path))
if path.exists() and path.is_file():
with open(path, "rb") as file_handle:
res = file_handle.read()
return res
LOGGER.debug("File %s either does not exist or is not a file",
str(path))
return ""
def __init__(self, *args: Tuple[Any]):
LOGGER.error(
"%s raised.\nError message: %s\nAbout this exception: %s",
args[0].__class__.__name__
if args and isinstance(args[0], Exception)
else self.__class__.__name__,
str(args[0]) if args else "",
args[0].__doc__
if args and isinstance(args[0], Exception)
else self.__doc__,
)
super().__init__(*args)
def _initialize_options(self) -> None:
"""Initialize options according to installed packages"""
for imported_object, adapter_format in [
(aseAtoms, "ase"),
(pymatgenStructure, "pymatgen"),
]:
if imported_object is None:
LOGGER.debug("%s not recognized to be installed.",
adapter_format)
self._formats = [
option for option in self._formats
if option[1].get("adapter_format", "") != adapter_format
]
def value(self) -> dict:
"""Return value for wrapped PTableWidget"""
LOGGER.debug(
"PeriodicTable: PTableWidget.selected_elements = %r",
self.ptable.selected_elements,
)
LOGGER.debug(
"PeriodicTable: Select ANY (True) or ALL (False) = %r",
self.select_any_all.value,
)
return not self.select_any_all.value, self.ptable.selected_elements.copy(
)
def _update_options(self) -> None:
"""Update options according to chosen structure"""
disabled_options = set()
if StructureFeatures.DISORDER in self.structure.structure_features:
# Disordered structures not usable with ASE
LOGGER.debug(
"'disorder' found in the structure's structure_features (%s)",
self.structure.structure_features,
)
disabled_options |= {
label
for label, value in self._formats
if value.get("adapter_format", "") == "ase"
}
if not self.structure.attributes.lattice_vectors:
LOGGER.debug("'lattice_vectors' not found for structure")
disabled_options |= {
label
for label, value in self._formats
if (value.get("adapter_format", "") == "ase"
and value.get("final_format", "") in ("struct", "vasp"))
}
if not self.structure.attributes.species:
LOGGER.debug("'species' not found for structure")
disabled_options |= {
label
for label, value in self._formats
if value.get("adapter_format", "") in ("cif", "pdb", "ase")
}
LOGGER.debug("Will disable the following dropdown options: %s",
disabled_options)
self.dropdown.disabled_options = list(disabled_options)
def _clear_cache(_):
"""Clear cached responses (not logs)"""
if str(LOG_DIR).startswith(str(CACHE_DIR)):
log_sub_dir = list(Path(str(LOG_DIR)[len(f"{CACHE_DIR}/"):]).parts)
LOGGER.debug(
"Cache dir: %s - Log dir: %s - Log sub dir parts: %s",
CACHE_DIR,
LOG_DIR,
log_sub_dir,
)
for dirpath, dirnames, filenames in os.walk(CACHE_DIR):
log_dir_part = log_sub_dir.pop(0) if log_sub_dir else ""
if not log_sub_dir:
LOGGER.debug(
"No more log sub directory parts. Removing %r from dirnames list.",
log_dir_part,
)
dirnames.remove(log_dir_part)
for directory in list(dirnames):
if directory == log_dir_part:
continue
LOGGER.debug("Removing folder: %s",
Path(dirpath).joinpath(directory).resolve())
shutil.rmtree(Path(dirpath).joinpath(directory).resolve(),
ignore_errors=True)
dirnames.remove(directory)
for filename in filenames:
LOGGER.debug("Removing file: %s",
Path(dirpath).joinpath(filename).resolve())
os.remove(Path(dirpath).joinpath(filename).resolve())
CACHE_DIR.mkdir(parents=True, exist_ok=True)
def _toggle_widget(self, change: dict):
"""Hide or show the widget according to the toggle button"""
if change["new"]:
# Show widget
LOGGER.debug("Show widget since toggle is %s", change["new"])
self.ptable_container.layout.visibility = "visible"
self.ptable_container.layout.height = "auto"
self.toggle_button.tooltip = "Hide Periodic Table"
self.toggle_button.description = "Hide Periodic Table"
else:
# Hide widget
LOGGER.debug("Hide widget since toggle is %s", change["new"])
self.ptable_container.layout.visibility = "hidden"
self.ptable_container.layout.height = "0px"
self.toggle_button.tooltip = "Show Periodic Table"
self.toggle_button.description = "Show Periodic Table"
def handle_errors(response: dict) -> Tuple[str, set]:
"""Handle any errors"""
if "data" not in response and "errors" not in response:
raise InputError(f"No data and no errors reported in response: {response}")
if "errors" in response:
LOGGER.error("Errored response:\n%s", json.dumps(response, indent=2))
if "data" in response:
msg = (
'<font color="red">Error(s) during querying,</font> but '
f"<strong>{len(response['data'])}</strong> structures found."
)
elif isinstance(response["errors"], dict) and "detail" in response["errors"]:
msg = (
'<font color="red">Error(s) during querying. '
f"Message from server:<br>{response['errors']['detail']!r}.</font>"
)
elif isinstance(response["errors"], list) and any(
["detail" in _ for _ in response["errors"]]
):
details = [_["detail"] for _ in response["errors"] if "detail" in _]
msg = (
'<font color="red">Error(s) during querying. Message(s) from server:<br> - '
f"{'<br> - '.join(details)!r}</font>"
)
else:
msg = (
'<font color="red">Error during querying, '
"please try again later.</font>"
)
http_errors = set()
for raw_error in response.get("errors", []):
try:
error = OptimadeError(**raw_error)
status = int(error.status)
except (ValidationError, TypeError, ValueError):
status = 400
http_errors.add(status)
return msg, http_errors
return "", set()
def _uses_new_structure_features(self) -> bool:
"""Check whether self.database_version is >= v1.0.0-rc.2"""
critical_version = SemanticVersion("1.0.0-rc.2")
version = SemanticVersion(self.database_version)
LOGGER.debug("Semantic version: %r", version)
if version.base_version > critical_version.base_version:
return True
if version.base_version == critical_version.base_version:
if version.prerelease:
return version.prerelease >= critical_version.prerelease
# Version is bigger than critical version and is not a pre-release
return True
# Major.Minor.Patch is lower than critical version
return False
def _goto_last(self, _):
"""Go to last page of results"""
if self.pages_links.get("last", False):
for pageing in self.SUPPORTED_PAGEING:
self._cache[pageing] = self._parse_pageing(
self.pages_links["last"], pageing)
LOGGER.debug("Go to last page of results - using link: %s",
self.pages_links["last"])
self.page_link = self.pages_links["last"]
else:
self._cache["page_offset"] = self._last_page_offset
self._cache["page_number"] = self._last_page_number
LOGGER.debug(
"Go to last page of results - using offset: %d",
self._cache["page_offset"],
)
self.page_offset = self._cache["page_offset"]
def elements(
value: Tuple[bool, Dict[str, int]]
) -> Tuple[Union[List[str], List[Tuple[str]]], List[str]]:
"""Extract included and excluded elements"""
use_all = value[0]
ptable_value = value[1]
include = []
exclude = []
for element, state in ptable_value.items():
if state == 0:
# Include
include.append(element)
elif state == 1:
# Exclude
exclude.append(element)
LOGGER.debug(
"elements: With value %r the following are included: %r. And excluded: %r",
value,
include,
exclude,
)
values = []
operators = []
if exclude:
elements = ",".join([f'"{element}"' for element in exclude])
values.append(("NOT", elements))
operators.append(" HAS ANY ")
if include:
include_elements = ",".join(
[f'"{element}"' for element in include])
values.append(include_elements)
operators.append(" HAS ALL " if use_all else " HAS ANY ")
LOGGER.debug(
"elements: Resulting parsed operator(s): %r and value(s): %r",
operators,
values,
)
return values, operators
def get_entry_endpoint_schema(base_url: str, endpoint: str = None) -> dict:
"""Retrieve provider's entry endpoint schema (default: /structures)."""
result = {}
endpoint = endpoint if endpoint is not None else "structures"
endpoint = f"/info/{endpoint.strip('/')}"
response = perform_optimade_query(endpoint=endpoint, base_url=base_url)
msg, _ = handle_errors(response)
if msg:
LOGGER.error(
"Could not retrieve information about entry-endpoint %r.\n Message: %r\n Response:"
"\n%s",
endpoint[len("/info/") :],
msg,
response,
)
return result
return response.get("data", {}).get("properties", {})
def _goto_next(self, _):
"""Go to next page of results"""
if self.pages_links.get("next", False):
for pageing in self.SUPPORTED_PAGEING:
self._cache[pageing] = self._parse_pageing(
self.pages_links["next"], pageing)
LOGGER.debug("Go to next page of results - using link: %s",
self.pages_links["next"])
self.page_link = self.pages_links["next"]
else:
self._cache["page_offset"] += self._page_limit
self._cache["page_number"] += 1
LOGGER.debug(
"Go to next page of results - using pageing:\n page_offset=%d\n page_number=%d",
self._cache["page_offset"],
self._cache["page_number"],
)
self.page_offset = self._cache["page_offset"]
self.page_number = self._cache["page_number"]
def _query(self, link: str = None) -> dict:
"""Query helper function"""
# If a complete link is provided, use it straight up
if link is not None:
try:
link = ordered_query_url(link)
response = SESSION.get(link, timeout=TIMEOUT_SECONDS)
if response.from_cache:
LOGGER.debug("Request to %s was taken from cache !", link)
response = response.json()
except (
requests.exceptions.ConnectTimeout,
requests.exceptions.ConnectionError,
requests.exceptions.ReadTimeout,
) as exc:
response = {
"errors": {
"msg": "CLIENT: Connection error or timeout.",
"url": link,
"Exception": repr(exc),
}
}
except JSONDecodeError as exc:
response = {
"errors": {
"msg": "CLIENT: Could not decode response to JSON.",
"url": link,
"Exception": repr(exc),
}
}
return response
# Avoid structures with null positions and with assemblies.
add_to_filter = 'NOT structure_features HAS ANY "assemblies"'
if not self._uses_new_structure_features():
add_to_filter += ',"unknown_positions"'
optimade_filter = self.filters.collect_value()
optimade_filter = ("( {} ) AND ( {} )".format(optimade_filter,
add_to_filter)
if optimade_filter and add_to_filter else
optimade_filter or add_to_filter or None)
LOGGER.debug("Querying with filter: %s", optimade_filter)
# OPTIMADE queries
queries = {
"base_url": self.database[1].base_url,
"filter": optimade_filter,
"page_limit": self.page_limit,
"page_offset": self.offset,
"page_number": self.number,
"sort": self.sorting,
}
LOGGER.debug(
"Parameters (excluding filter) sent to query util func: %s",
{key: value
for key, value in queries.items() if key != "filter"},
)
return perform_optimade_query(**queries)
def update_old_links_resources(resource: dict) -> Union[LinksResource, None]:
"""Try to update to resource to newest LinksResource schema"""
try:
res = LinksResource(**resource)
except ValidationError:
LOGGER.debug(
"Links resource could not be cast to newest LinksResource model. Resource: %s",
resource,
)
resource["attributes"]["link_type"] = resource["type"]
resource["type"] = "links"
LOGGER.debug(
"Trying casting to LinksResource again with the updated resource: %s",
resource,
)
try:
res = LinksResource(**resource)
except ValidationError:
LOGGER.debug(
"After updating 'type' and 'attributes.link_type' in resource, "
"it still fails to cast to LinksResource model. Resource: %s",
resource,
)
return None
else:
return res
else:
return res
def update_ranged_inputs(self, change: dict):
"""Update ranged inputs' min/max values"""
ranges = change["new"]
if not ranges or ranges is None:
return
for field, config in ranges.items():
if field not in self.query_fields:
raise ParserError(
field=field,
value="N/A",
extras=[
("config", config),
("self.query_fields.keys", self.query_fields.keys()),
],
msg=
"Provided field is unknown. Can not update range for unknown field.",
)
widget = self.query_fields[field].input_widget
cached_value: Tuple[int, int] = widget.value
for attr in ("min", "max"):
if attr in config and config[attr] is not None:
try:
new_value = int(config[attr])
except (TypeError, ValueError) as exc:
raise ParserError(
field=field,
value=cached_value,
extras=[("attr", attr),
("config[attr]", config[attr])],
msg=
f"Could not cast config[attr] to int. Exception: {exc!s}",
) from exc
LOGGER.debug(
"Setting %s for %s to %d.\nWidget immediately before: %r",
attr,
field,
new_value,
widget,
)
# Since "min" is always set first, to be able to set "min" to a valid value,
# "max" is first set to the new "min" value + 1 IF the new "min" value is
# larger than the current "max" value, otherwise there is no reason,
# and it may indeed lead to invalid attribute setting, if this is done.
# For "max", coming last, this should then be fine, as the new "min" and "max"
# values should never be an invalid pair.
if attr == "min" and new_value > cached_value[1]:
widget.max = new_value + 1
setattr(widget, attr, new_value)
LOGGER.debug("Updated widget %r:\n%r", attr, widget)
widget.value = (widget.min, widget.max)
LOGGER.debug("Final state, updated widget:\n%r", widget)
def ranged_int(
field: str, value: Tuple[Union[int, None],
Union[int, None]]) -> Union[str, List[str]]:
"""Turn IntRangeSlider widget value into OPTIMADE filter string"""
LOGGER.debug("ranged_int: Received value %r for field %r", value,
field)
low, high = value
res = ""
if low is None or high is None:
if low is not None:
res = f">={low}"
if high is not None:
res = f"<={high}"
elif low == high:
# Exactly N of property
res = f"={low}"
else:
# Range of property
res = [f">={low}", f"<={high}"]
LOGGER.debug("ranged_int: Concluded the response is %r", res)
return res
def _toggle_debug_logging(self, change: dict):
"""Set logging level depending on toggle button"""
if change["new"]:
# Set logging level DEBUG
WIDGET_HANDLER.setLevel(logging.DEBUG)
LOGGER.info("Set log output in widget to level DEBUG")
LOGGER.debug("This should now be shown")
# Show debug buttons
self.clear_cache.layout.visibility = "visible"
self.clear_logs.layout.visibility = "visible"
else:
# Set logging level to INFO
WIDGET_HANDLER.setLevel(logging.INFO)
LOGGER.info("Set log output in widget to level INFO")
LOGGER.debug("This should now NOT be shown")
# Hide debug buttons
self.clear_cache.layout.visibility = "hidden"
self.clear_logs.layout.visibility = "hidden"
def ordered_query_url(url: str) -> str:
"""Decode URL, sort queries, re-encode URL"""
LOGGER.debug("Ordering URL: %s", url)
parsed_url = urlparse(url)
queries = parse_qs(parsed_url.query)
LOGGER.debug("Queries to sort and order: %s", queries)
sorted_keys = sorted(queries.keys())
res = OrderedDict()
for key in sorted_keys:
# Since the values are all lists, we also sort these
res[key] = sorted(queries[key])
res = urlencode(res, doseq=True)
res = (
f"{parsed_url.scheme}://{parsed_url.netloc}{parsed_url.path};{parsed_url.params}?{res}"
f"#{parsed_url.fragment}"
)
LOGGER.debug("Newly ordered URL: %s", res)
LOGGER.debug("Treated URL after unparse(parse): %s", urlunparse(urlparse(res)))
return urlunparse(urlparse(res))
def fetch_providers(providers_urls: Union[str, List[str]] = None) -> list:
"""Fetch OPTIMADE database providers (from Materials-Consortia)
:param providers_urls: String or list of strings with versioned base URL(s)
to Materials-Consortia providers database
"""
if providers_urls and not isinstance(providers_urls, (list, str)):
raise TypeError("providers_urls must be a string or list of strings")
if not providers_urls:
providers_urls = PROVIDERS_URLS
elif not isinstance(providers_urls, list):
providers_urls = [providers_urls]
for providers_url in providers_urls:
providers = perform_optimade_query(base_url=providers_url, endpoint="")
msg, _ = handle_errors(providers)
if msg:
LOGGER.warning("%r returned error(s).", providers_url)
else:
break
else:
if CACHED_PROVIDERS.exists():
# Load local cached providers file
LOGGER.warning(
"Loading local, possibly outdated, list of providers (%r).",
CACHED_PROVIDERS.name,
)
with open(CACHED_PROVIDERS, "r") as handle:
providers = json.load(handle)
else:
LOGGER.error(
"Neither any of the provider URLs: %r returned a valid response, "
"and the local cached file of the latest valid response does not exist.",
providers_urls,
)
providers = {}
update_local_providers_json(providers)
return providers.get("data", [])