DHN-database/.example.env at main · DyHealthNet/DHN-database · GitHub

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# For docker swarm, do not use '' for the values, just the value itself
# Make this key unique and secure
SECRET_KEY=abc

# Match these values to the docker-compose.yml file
DATABASE_NAME=postgres
DATABASE_USER=postgres
DATABASE_PASS=password
DB_HOST=db
DB_PORT=5432

# path must refer to the path inside the container
# Phenotypes
PHENOTYPE_PATH=/data/DyHealthNet/chris_summary_data/fully_simulated/phenotypes_filtered_index_renamed.csv
PHENOTYPE_META_PATH=/data/DyHealthNet/chris_summary_data/phenotypes/pheno_meta_filtered.tsv
PHENOTYPE_LABEL_COLUMN=label
PHENOTYPE_TYPE_COLUMN=type
PHENOTYPE_DESCRIPTION_COLUMN=description
INPUT_DB_ID=SNOMED CT
PHENOTYPE_DP_NAME_COLUMN=snomed_term
PHENOTYPE_XREF_COLUMN=snomed_id

# Proteins
PROTEIN_PATH=/data/DyHealthNet/chris_summary_data/fully_simulated/proteins.csv
PROTEIN_META_PATH=/data/DyHealthNet/chris_summary_data/proteins/CHRIS_somalogic_descriptive_statistic.tsv
PROTEIN_LABEL_COLUMN=protein_id
PROTEIN_DESCRIPTION_COLUMN=Target
PROTEIN_DP_NAME_COLUMN=UniProt
PROTEIN_XREF_COLUMN=UniProt

# Metabolites
METABOLITE_PATH=/data/DyHealthNet/chris_summary_data/fully_simulated/metabolites.csv
METABOLITE_META_PATH=/data/DyHealthNet/chris_summary_data/metabolites/CHRIS_biocristes7500SumStats.txt
METABOLITE_LABEL_COLUMN=analyte_name
METABOLITE_DESCRIPTION_COLUMN=biochemical_name
METABOLITE_XREF_COLUMN=hmdb_id

# Genomic variants
GENOMIC_VARIANT_META_PATH=/data/DyHealthNet/chris_summary_data/variants/variants_meta.tsv
GWAS_STATS_PATH=/data/DyHealthNet/chris_summary_data/variants/fully_simulated_gwas.tsv


# whatever else
VAR_LABEL_MAPPING=/data/DyHealthNet/chris_baseline_codebook_public-ifb_20240809_category_coding.json

CALCULATED_EDGES_PATH=/data/DyHealthNet/scores.csv
DATA_DIR=/data

# Score calculation settings
PATIENT_ID_COLUMN=Patient ID
NUMBER_OF_WORKERS=16
TEST_TYPE=all

# For DEBUG stuff
DEBUG=False

# Define database creation settings
OBSERVATION_SOURCE=CHRIS
CHUNK_SIZE=
VISUALIZE=false

MAX_CONTEXT_PER_USER=5
FRONTEND_HOME_URL=http://192.168.1.10:9901
REDIS_URL=redis:6379

VITE_BACKEND_URL=http://localhost:8000