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Feature/sckan-273 #354

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merged 5 commits into from
Nov 12, 2024
Merged

Feature/sckan-273 #354

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c87eafa
SCKAN-273 - (CS ingestion) change CS update logic if it has changes
D-GopalKrishna Nov 7, 2024
552c48f
SCKAN-273 - change permissions to move to exported from invalid
D-GopalKrishna Nov 12, 2024
9e26fce
SCKAN-273 - helper to move to exported state
D-GopalKrishna Nov 12, 2024
0b50d12
SCKAN-273 - change the state to EXPORTED (default) if no validation e…
D-GopalKrishna Nov 12, 2024
92d9f82
SCKAN-273 - do a get instead of filter first - since reference_uri is…
D-GopalKrishna Nov 12, 2024
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5 changes: 4 additions & 1 deletion backend/composer/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -634,7 +634,10 @@ def npo_approved(self, *args, **kwargs):

@transition(
field=state,
source=CSState.NPO_APPROVED,
source=[
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NOTE: allow to export from invalid.

CSState.NPO_APPROVED,
CSState.INVALID
],
target=CSState.EXPORTED,
conditions=[ConnectivityStatementStateService.is_valid],
permission=ConnectivityStatementStateService.has_permission_to_transition_to_exported,
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6 changes: 6 additions & 0 deletions backend/composer/services/cs_ingestion/helpers/notes_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,9 @@ def create_invalid_note(connectivity_statement: ConnectivityStatement, note: str
type=NoteType.ALERT,
note=f"Invalidated due to the following reason(s): {note}"
)


def do_transition_to_exported(connectivity_statement: ConnectivityStatement):
system_user = User.objects.get(username="system")
connectivity_statement.exported(by=system_user)
connectivity_statement.save()
13 changes: 8 additions & 5 deletions backend/composer/services/cs_ingestion/helpers/statement_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
from composer.services.cs_ingestion.helpers.getters import get_sex, get_circuit_type, get_functional_circuit_role, \
get_phenotype, get_projection_phenotype
from composer.services.cs_ingestion.helpers.notes_helper import do_transition_to_invalid_with_note, create_invalid_note, \
add_ingestion_system_note
add_ingestion_system_note, do_transition_to_exported
from composer.services.cs_ingestion.models import ValidationErrors


Expand All @@ -35,11 +35,11 @@ def create_or_update_connectivity_statement(statement: Dict, sentence: Sentence,
reference_uri=reference_uri,
defaults=defaults
)
if not created:
if not created:
if has_changes(connectivity_statement, statement, defaults):
ConnectivityStatement.objects.filter(reference_uri=reference_uri).update(**defaults)
fields_to_refresh = [field for field in defaults.keys() if field != 'state']
connectivity_statement.refresh_from_db(fields=fields_to_refresh)
defaults_without_state = {field: value for field, value in defaults.items() if field != 'state'}
ConnectivityStatement.objects.filter(reference_uri=reference_uri).update(**defaults_without_state)
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@D-GopalKrishna D-GopalKrishna Nov 8, 2024 •
edited
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@afonsobspinto - keeping the filter instead of the get here - since we cannot update a get (can only update a queryset)
AttributeError: 'ConnectivityStatement' object has no attribute 'update'

also doing connectivity_statement = ConnectivityStatement.objects.filter(reference_uri=reference_uri).first() since, we get

ConnectivityStatement.objects.filter(reference_uri=reference_uri).update(**defaults_without_state)
>>> 1

as return value after the update.

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I believe we could do:

        ```
        ConnectivityStatement.objects.filter(reference_uri=reference_uri).update(**defaults_without_state)
        connectivity_statement.refresh_from_db()
        ```

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Do you mean the following?

fields_to_refresh = [field for field in defaults.keys() if field != 'state']
connectivity_statement.refresh_from_db(fields=fields_to_refresh)

since the connectivity_statement.refresh_from_db() would lead to AttributeError: Direct state modification is not allowed.

connectivity_statement = ConnectivityStatement.objects.filter(reference_uri=reference_uri).first()
add_ingestion_system_note(connectivity_statement)

validation_errors = statement.get(VALIDATION_ERRORS, ValidationErrors())
Expand All @@ -50,6 +50,9 @@ def create_or_update_connectivity_statement(statement: Dict, sentence: Sentence,
do_transition_to_invalid_with_note(connectivity_statement, error_message)
else:
create_invalid_note(connectivity_statement, error_message)
else:
if connectivity_statement.state != CSState.EXPORTED:
do_transition_to_exported(connectivity_statement)
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move to EXPORTED state (default) if not in EXPORTED state - if there's no validation errors.

Reason to include this: (credit thanks - @afonsobspinto : ) )

If a statement was in INVALID state in the past; but if it has no validation errors when running it again in the future, then it should to be moved to EXPORTED state.

To cover the fourth edge case here - #354 (review)


update_many_to_many_fields(connectivity_statement, statement, update_anatomical_entities)
statement[STATE] = connectivity_statement.state
Expand Down