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remove spacy dependancy in pyproject.toml #913

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remove spacy dependancy in pyproject.toml #913

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838436e
remove spacy dependancy in pyproject.toml
madanucd Nov 26, 2024
ed1487c
Update poetry.lock to sync with pyproject.toml
madanucd Nov 26, 2024
fbc30a9
Merge branch 'main' into issue-809-dependency-update
madanucd Nov 26, 2024
c675d60
Revert merge commit from main
madanucd Nov 26, 2024
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82 changes: 34 additions & 48 deletions backend/poetry.lock
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6 changes: 2 additions & 4 deletions backend/pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -29,13 +29,11 @@ loguru = "*"
pystow = ">=0.5.4"
requests = "^2.31.0"
rich = "*"
typer = "^0.12.0"
typer = "^0.7.0"
typer-cli = "^0.0.13"
beautifulsoup4 = "^4.12.3"
spacy = "^3.7.6"

[tool.poetry.dependencies.en_core_sci_sm]
url = "https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.5.4/en_core_sci_sm-0.5.4.tar.gz"

[tool.poetry.group.dev.dependencies]
pytest = "^8.2.0"
mkdocs = ">=1.6.0"
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6 changes: 0 additions & 6 deletions backend/src/monarch_py/api/association.py
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Expand Up @@ -29,9 +29,6 @@ async def _get_associations(
object_taxon: Union[List[str], None] = Query(default=None),
entity: Union[List[str], None] = Query(default=None),
direct: bool = Query(default=False),
facet_fields: List[str] = Query(default_factory=list),
facet_queries: List[str] = Query(default_factory=list),
filter_queries: List[str] = Query(default_factory=list),
compact: bool = Query(default=False),
pagination: PaginationParams = Depends(),
format: OutputFormat = Query(
Expand All @@ -55,9 +52,6 @@ async def _get_associations(
object_namespace=object_namespace,
direct=direct,
compact=compact,
facet_fields=facet_fields,
facet_queries=facet_queries,
filter_queries=filter_queries,
offset=pagination.offset,
limit=pagination.limit,
)
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14 changes: 0 additions & 14 deletions backend/src/monarch_py/api/entity.py
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Expand Up @@ -86,17 +86,6 @@ def _association_table(
title="Only return direct associations",
examples=[True, False],
),
facet_fields: List[str] = Query(
default=None,
title="Facet fields to include in the response",
examples=["subject", "subject_taxon", "predicate"],
),
facet_queries: List[str] = Query(
default=None, title="Facet queries to include in the response", examples=['subject_category:"biolink:Gene"']
),
filter_queries: List[str] = Query(
default=None, title="Filter queries to limit the response", examples=['subject_category:"biolink:Gene"']
),
) -> Union[AssociationTableResults, str]:
"""
Retrieves association table data for a given entity and association type
Expand All @@ -116,9 +105,6 @@ def _association_table(
q=query,
traverse_orthologs=traverse_orthologs,
direct=direct,
facet_fields=facet_fields,
facet_queries=facet_queries,
filter_queries=filter_queries,
sort=sort,
offset=pagination.offset,
limit=pagination.limit,
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