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Merge pull request #513 from xchem/m2ms-1318-conf-site-tags
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Fixed tagging of site observations
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@kaliif
kaliif authored Feb 1, 2024
2 parents 9c74317 + ad8c45b commit 8e83d18
Showing 1 changed file with 82 additions and 102 deletions.
184 changes: 82 additions & 102 deletions viewer/target_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1059,11 +1059,11 @@ def process_canon_site_conf(
"canon_site": canon_site,
}

# members = extract(key="members")
members = extract(key="members")
ref_ligands = extract(key="reference_ligand_id")

index_fields = {
# "members": members,
"members": members,
"reference_ligands": ref_ligands,
}

Expand Down Expand Up @@ -1518,24 +1518,51 @@ def process_bundle(self):
canon_site_confs=canon_site_conf_objects,
)

tag_categories = (
"ConformerSites",
"CanonSites",
"XtalformSites",
"Quatassemblies",
"Xtalforms",
)

for cat in tag_categories:
self._tag_site_observations(site_observation_objects, cat)

# final remaining fk, attach reference site observation to canon_site_conf
for val in canon_site_conf_objects.values(): # pylint: disable=no-member
val.instance.ref_site_observation = site_observation_objects[
val.index_data["reference_ligands"]
].instance
val.instance.save()

# tag site observations
for val in canon_site_conf_objects.values(): # pylint: disable=no-member
tag = "conf_site: " + ",".join(val.instance.residues[:3])
so_list = [
site_observation_objects[k].instance for k in val.index_data["members"]
]
self._tag_observations(tag, "ConformerSites", so_list)

for val in canon_site_objects.values(): # pylint: disable=no-member
tag = "canon_site: " + ",".join(val.instance.residues[:3])
so_list = SiteObservation.objects.filter(
canon_site_conf__canon_site=val.instance
)
self._tag_observations(tag, "ConformerSites", so_list)

for val in xtalform_sites_objects.values(): # pylint: disable=no-member
tag = "xtalform_site: " + ",".join(val.instance.residues[:3])
so_list = [
site_observation_objects[k].instance for k in val.index_data["residues"]
]
self._tag_observations(tag, "ConformerSites", so_list)

for val in quat_assembly_objects.values(): # pylint: disable=no-member
tag = "quatassembly: " + val.instance.name
so_list = SiteObservation.objects.filter(
xtalform_site__xtalform__in=XtalformQuatAssembly.objects.filter(
quat_assembly=val.instance
).values("xtalform")
)
self._tag_observations(tag, "ConformerSites", so_list)

for val in xtalform_objects.values(): # pylint: disable=no-member
tag = "xtalform: " + val.instance.name
so_list = SiteObservation.objects.filter(
xtalform_site__xtalform=val.instance
)
self._tag_observations(tag, "ConformerSites", so_list)

def _load_yaml(self, yaml_file: Path) -> dict | None:
contents = None
try:
Expand Down Expand Up @@ -1592,96 +1619,49 @@ def _extract(

return result

def _tag_site_observations(self, site_observation_objects, category):
# this is an attempt to replicate tag creation from previous
# loader. as there are plenty of differences, I cannot just
# use the same functions..

logger.debug("Getting category %s", category)
groups: Dict[str, Any] = {}
for _, obj in site_observation_objects.items():
if category == "ConformerSites":
tags = [
"conf_site: " + ",".join(obj.instance.canon_site_conf.residues[:3]),
]
elif category == "CanonSites":
tags = [
"canon_site: "
+ ",".join(obj.instance.xtalform_site.canon_site.residues[:3]),
]
elif category == "XtalformSites":
tags = [
"xtalform_site: "
+ ",".join(obj.instance.xtalform_site.residues[:3]),
]
# tricky one. connected via m2m
elif category == "Quatassemblies":
tags = [
"quatassembly: " + qa.name
for qa in obj.instance.xtalform_site.xtalform.quat_assembly.all()
]

elif category == "Xtalforms":
tags = [
"xtalform: " + obj.instance.xtalform_site.xtalform.name,
]
else:
tags = [
"Unspecified",
]

for tag in tags:
if tag not in groups.keys():
groups[tag] = [obj.instance]
else:
groups[tag].append(obj.instance)

# I suspect I need to group them by site..
for tag, so_list in groups.items():
try:
# memo to self: description is set to tag, but there's
# no fk to tag, instead, tag has a fk to
# group. There's no uniqueness requirement on
# description so there's no certainty that this will
# be unique (or remain searchable at all because user
# is allowed to change the tag name). this feels like
# poor design but I don't understand the principles of
# this system to know if that's indeed the case or if
# it is in fact a truly elegant solution
so_group = SiteObservationGroup.objects.get(
target=self.target, description=tag
)
except SiteObservationGroup.DoesNotExist:
assert self.target
so_group = SiteObservationGroup(target=self.target)
so_group.save()
except MultipleObjectsReturned:
SiteObservationGroup.objects.filter(
target=self.target, description=tag
).delete()
assert self.target
so_group = SiteObservationGroup(target=self.target)
so_group.save()
def _tag_observations(self, tag, category, so_list):
try:
# memo to self: description is set to tag, but there's
# no fk to tag, instead, tag has a fk to
# group. There's no uniqueness requirement on
# description so there's no certainty that this will
# be unique (or remain searchable at all because user
# is allowed to change the tag name). this feels like
# poor design but I don't understand the principles of
# this system to know if that's indeed the case or if
# it is in fact a truly elegant solution
so_group = SiteObservationGroup.objects.get(
target=self.target, description=tag
)
except SiteObservationGroup.DoesNotExist:
assert self.target
so_group = SiteObservationGroup(target=self.target)
so_group.save()
except MultipleObjectsReturned:
SiteObservationGroup.objects.filter(
target=self.target, description=tag
).delete()
assert self.target
so_group = SiteObservationGroup(target=self.target)
so_group.save()

try:
so_tag = SiteObservationTag.objects.get(tag=tag, target=self.target)
# Tag already exists
# Apart from the new mol_group and molecules, we shouldn't be
# changing anything.
so_tag.mol_group = so_group
except SiteObservationTag.DoesNotExist:
so_tag = SiteObservationTag()
so_tag.tag = tag
so_tag.category = TagCategory.objects.get(category=category)
so_tag.target = self.target
so_tag.mol_group = so_group

so_tag.save()

for site_obvs in so_list:
logger.debug("site_obvs_id=%s", site_obvs.id)
so_group.site_observation.add(site_obvs)
so_tag.site_observations.add(site_obvs)
try:
so_tag = SiteObservationTag.objects.get(tag=tag, target=self.target)
# Tag already exists
# Apart from the new mol_group and molecules, we shouldn't be
# changing anything.
so_tag.mol_group = so_group
except SiteObservationTag.DoesNotExist:
so_tag = SiteObservationTag()
so_tag.tag = tag
so_tag.category = TagCategory.objects.get(category=category)
so_tag.target = self.target
so_tag.mol_group = so_group

so_tag.save()

so_group.site_observation.add(*so_list)
so_tag.site_observations.add(*so_list)

def _is_already_uploaded(self, target_created, project_created):
if target_created or project_created:
Expand Down

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