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fixed to add the paper to the corpus when setting 'No TET data' statu… #842

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merged 1 commit into from
Feb 27, 2025
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Merged

fixed to add the paper to the corpus when setting 'No TET data' statu… #842

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47 changes: 29 additions & 18 deletions agr_literature_service/api/crud/topic_entity_tag_crud.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,27 +88,12 @@ def create_tag(db: Session, topic_entity_tag: TopicEntityTagSchemaPost, validate
new_db_obj = TopicEntityTagModel(**topic_entity_tag_data)

try:
mod_id = get_mod_id_from_mod_abbreviation(db, source.secondary_data_provider.abbreviation)
add_wft_141_bool = False
mod_corpus_association_db_obj = db.query(ModCorpusAssociationModel).filter_by(mod_id=mod_id, reference_id=reference_id).one_or_none()
if mod_corpus_association_db_obj is None:
add_wft_141_bool = True
new_mca = ModCorpusAssociationModel(reference_id=reference_id,
mod_id=mod_id,
corpus=True,
mod_corpus_sort_source='manual_creation')
db.add(new_mca)
elif mod_corpus_association_db_obj.corpus is not True:
add_wft_141_bool = True
mod_corpus_association_db_obj.corpus = True
mod_corpus_association_db_obj.mod_corpus_sort_source = "manual_creation"
if add_wft_141_bool:
new_wft = WorkflowTagModel(reference_id=reference_id, mod_id=mod_id, workflow_tag_id='ATP:0000141')
db.add(new_wft)

db.add(new_db_obj)
db.commit()
db.refresh(new_db_obj)

mod_id = get_mod_id_from_mod_abbreviation(db, source.secondary_data_provider.abbreviation)
add_paper_to_mod_if_not_already(db, reference_id, mod_id)
update_manual_indexing_workflow_tag(db, mod_id, reference_id, index_wft)
if validate_on_insert:
validate_tags(db=db, new_tag_obj=new_db_obj)
Expand All @@ -128,6 +113,7 @@ def set_indexing_status_for_no_tet_data(db: Session, mod_abbreviation, reference

reference_id = get_reference_id_from_curie_or_id(db, reference_curie)
mod_id = get_mod_id_from_mod_abbreviation(db, mod_abbreviation)
add_paper_to_mod_if_not_already(db, reference_id, mod_id)
update_manual_indexing_workflow_tag(db, mod_id, reference_id, "ATP:0000275")


Expand Down Expand Up @@ -155,6 +141,31 @@ def update_manual_indexing_workflow_tag(db: Session, mod_id, reference_id, index
db.commit()


def add_paper_to_mod_if_not_already(db: Session, reference_id, mod_id):

add_wft_141_bool = False
mca_db_obj = db.query(ModCorpusAssociationModel).filter_by(
mod_id=mod_id, reference_id=reference_id).one_or_none()
if mca_db_obj is None:
add_wft_141_bool = True
new_mca = ModCorpusAssociationModel(reference_id=reference_id,
mod_id=mod_id,
corpus=True,
mod_corpus_sort_source='manual_creation')
db.add(new_mca)
elif not mca_db_obj.corpus:
add_wft_141_bool = True
mca_db_obj.corpus = True
mca_db_obj.mod_corpus_sort_source = "manual_creation"
db.add(mca_db_obj)
if add_wft_141_bool:
new_wft = WorkflowTagModel(reference_id=reference_id,
mod_id=mod_id,
workflow_tag_id='ATP:0000141')
db.add(new_wft)
db.commit()


def calculate_validation_value_for_tag(topic_entity_tag_db_obj: TopicEntityTagModel, validation_type: str):
validating_tags_values = []
validating_tags_added_ids = set()
Expand Down
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