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refactor: remove unused seqrepo configuration (#308)
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jsstevenson authored Aug 12, 2024
1 parent 5e8d941 commit 8c1fc23
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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.
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3 changes: 0 additions & 3 deletions server/src/curfu/__init__.py
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Expand Up @@ -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."""
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5 changes: 3 additions & 2 deletions server/src/curfu/devtools/build_gene_suggest.py
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Expand Up @@ -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:
Expand All @@ -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:
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