diff --git a/server/pyproject.toml b/server/pyproject.toml index 84f70f77..a60a13fe 100644 --- a/server/pyproject.toml +++ b/server/pyproject.toml @@ -49,6 +49,7 @@ dev = [ "pre-commit>=3.7.1", "gene-normalizer ~= 0.1.39", "pydantic-to-typescript", + "cool-seq-tool >= 0.4.1" ] [project.scripts] diff --git a/server/src/curfu/devtools/build_gene_suggest.py b/server/src/curfu/devtools/build_gene_suggest.py index f4a1f449..54e8e581 100644 --- a/server/src/curfu/devtools/build_gene_suggest.py +++ b/server/src/curfu/devtools/build_gene_suggest.py @@ -7,10 +7,11 @@ import click from biocommons.seqrepo.seqrepo import SeqRepo +from cool_seq_tool.handlers.seqrepo_access import SEQREPO_ROOT_DIR from gene.database import create_db from gene.schemas import RecordType -from curfu import APP_ROOT, SEQREPO_DATA_PATH, logger +from curfu import APP_ROOT, logger class GeneSuggestionBuilder: @@ -22,7 +23,7 @@ class GeneSuggestionBuilder: def __init__(self) -> None: """Initialize class.""" self.gene_db = create_db() - self.sr = SeqRepo(SEQREPO_DATA_PATH) + self.sr = SeqRepo(SEQREPO_ROOT_DIR) self.genes = [] def _get_chromosome(self, record: dict) -> str | None: