refactor: remove unused seqrepo configuration (#308)

README.md

@@ -18,7 +18,7 @@ cd fusion-curation
 Ensure that the following data sources are available:
 
 - the [VICC Gene Normalization](https://github.com/cancervariants/gene-normalization) database, accessible from a DynamoDB-compliant service. Set the endpoint address with environment variable `GENE_NORM_DB_URL`; default value is `http://localhost:8000`.
-- the [Biocommons SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database. Provide local path with environment variable `SEQREPO_DATA_PATH`; default value is `/usr/local/share/seqrepo/latest`.
+- the [Biocommons SeqRepo](https://github.com/biocommons/biocommons.seqrepo) database, used by `Cool-Seq-Tool`. The precise file location is configurable via the `SEQREPO_ROOT_DIR` variable, per the [documentation](https://coolseqtool.readthedocs.io/0.6.0/usage.html#environment-configuration).
 - the [Biocommons Universal Transcript Archive](https://github.com/biocommons/uta), by way of Genomic Med Lab's [Cool Seq Tool](https://github.com/GenomicMedLab/cool-seq-tool) package. Connection parameters to the Postgres database are set most easily as a [Libpq-compliant URL](https://www.postgresql.org/docs/current/libpq-connect.html#LIBPQ-CONNSTRING) under the environment variable `UTA_DB_URL`.
 
 Create a virtual environment for the server and install. Note: there's also a Pipfile so you can skip the virtualenv steps if you'd rather use a Pipenv instance instead of virtualenv/venv. I have been sticking with the latter because [Pipenv doesn't play well with entry points in development](https://stackoverflow.com/a/69225249), but if you aren't editing them in `setup.cfg`, then the former should be fine.

server/src/curfu/__init__.py

@@ -50,9 +50,6 @@
 else:
     UTA_DB_URL = "postgresql://uta_admin@localhost:5433/uta/uta_20210129"
 
-# get local seqrepo location
-SEQREPO_DATA_PATH = environ.get("SEQREPO_DATA_PATH", f"{APP_ROOT}/data/seqrepo/latest")
-
 
 class LookupServiceError(Exception):
     """Custom Exception to use when lookups fail in curation services."""

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: