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Graceful handling of files from RCSB PDB (issue 1282) #567

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merged 2 commits into from
Mar 26, 2024
Merged

Graceful handling of files from RCSB PDB (issue 1282) #567

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fd9fd08
stashing
kaliif Mar 22, 2024
816145c
Target loader now accepts experiments marked as 'manual'
kaliif Mar 26, 2024
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65 changes: 38 additions & 27 deletions viewer/target_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,10 @@
# assemblies and xtalforms
XTALFORMS_FILE = "assemblies.yaml"

# holding horses for now
# # assigned xtalforms, not all are referenced in meta_aligner
# ASSIGNED_XTALFORMS_FILE = "assigned_xtalforms.yaml"

# target name, nothing else
CONFIG_FILE = "config*.yaml"

Expand Down Expand Up @@ -737,9 +741,6 @@ def process_experiment(
logger.debug("incoming data: %s", item_data)
experiment_name, data = item_data

if "aligned_files" not in data.keys():
return None

extract = functools.partial(
self._extract,
data=data,
Expand Down Expand Up @@ -1480,7 +1481,7 @@ def process_bundle(self):
self.report.log(logging.ERROR, msg)
raise FileExistsError(msg)

if project_created and committer.pk == settings.ANONYMOUS_USER:
if project_created and self.project.title in settings.PUBLIC_TAS_LIST: # type: ignore[attr-defined]
assert self.project
self.project.open_to_public = True
self.project.save()
Expand Down Expand Up @@ -1694,35 +1695,45 @@ def process_bundle(self):
# memo to self: there used to be some code to test the
# position of the iterator in existing entries. This
# was because it was assumed, that when adding v2
# uploads, it can bring a long new observations under
# uploads, it can bring along new observations under
# existing experiment. Following discussions with
# Conor, it seems that this will not be the case. But
# should it agin be, this code was deleted on
# 2024-03-04, if you need to check

for so in so_group.filter(code__isnull=True):
code_prefix = experiment_objects[so.experiment.code].index_data[
"code_prefix"
]
# iter_pos = next(suffix)
# code = f"{code_prefix}{so.experiment.code.split('-')[1]}{iter_pos}"
code = (
f"{code_prefix}{so.experiment.code.split('-')[1]}{next(suffix)}"
)

# test uniqueness for target
# TODO: this should ideally be solved by db engine, before
# rushing to write the trigger, have think about the
# loader concurrency situations
if SiteObservation.objects.filter(
experiment__experiment_upload__target=self.target,
code=code,
).exists():
msg = (
f"short code {code} already exists for this target; "
+ "specify a code_prefix to resolve this conflict"
)
self.report.log(logging.ERROR, msg)
if so.experiment.type == 1:
# manual. code is pdb code
code = f"{so.experiment.code}-{next(suffix)}"
# NB! at the time of writing this piece of
# code, I haven't seen an example of the data
# so I only have a very vague idea how this is
# going to work. The way I understand it now,
# they cannot belong to separate groups so
# there's no need for different iterators. But
# could be I need to split them up
else:
# model building. generate code
code_prefix = experiment_objects[so.experiment.code].index_data[
"code_prefix"
]
# iter_pos = next(suffix)
# code = f"{code_prefix}{so.experiment.code.split('-')[1]}{iter_pos}"
code = f"{code_prefix}{so.experiment.code.split('-')[1]}{next(suffix)}"

# test uniqueness for target
# TODO: this should ideally be solved by db engine, before
# rushing to write the trigger, have think about the
# loader concurrency situations
if SiteObservation.objects.filter(
experiment__experiment_upload__target=self.target,
code=code,
).exists():
msg = (
f"short code {code} already exists for this target; "
+ "specify a code_prefix to resolve this conflict"
)
self.report.log(logging.ERROR, msg)

so.code = code
so.save()
Expand Down