DHN-docker/.env.chris at main · DyHealthNet/DHN-docker · 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
ADMIN_USER=admin
ADMIN_PASS=CHANGEME

# This needs to correspond to the url you are accessing the site with
FRONTEND_HOME_URL=http://192.168.1.10:9901

# 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=/home/scratch/larend/DyHealthNet/platform_data/chris_data/phenotypes_data.csv
PHENOTYPE_META_PATH=/scratch/larend/DyHealthNet/platform_data/chris_data/phenotypes_meta.csv
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=/scratch/larend/DyHealthNet/platform_data/chris_data/proteomics_data.csv
PROTEIN_META_PATH=/scratch/larend/DyHealthNet/platform_data/chris_data/proteomics_meta.csv
PROTEIN_LABEL_COLUMN=protein_id
PROTEIN_DESCRIPTION_COLUMN=Target
PROTEIN_DP_NAME_COLUMN=UniProt
PROTEIN_XREF_COLUMN=UniProt

# Metabolites
METABOLITE_PATH=/scratch/larend/DyHealthNet/platform_data/chris_data/metabolomics_data.csv
METABOLITE_META_PATH=/scratch/larend/DyHealthNet/platform_data/chris_data/metabolomics_meta.csv
METABOLITE_LABEL_COLUMN=analyte_name
METABOLITE_DESCRIPTION_COLUMN=biochemical_name
METABOLITE_XREF_COLUMN=hmdb_id

# Genomic variants
GENOMIC_VARIANT_META_PATH=
GWAS_STATS_PATH=

# Other options
VAR_LABEL_MAPPING=/home/larend/DyHealthNet/data/chris_data/phenotypes_var_label_mapping.csv
CALCULATED_EDGES_PATH=/scratch/larend/DyHealthNet/platform_data/scores.csv
DATA_DIR=/scratch/larend/DyHealthNet/platform_data
MAX_CONTEXT_PER_USER=5
REDIS_URL=redis:6379

# Score calculation settings
PATIENT_ID_COLUMN=aid
NUMBER_OF_WORKERS=16
NAN_VALUE=-89
TEST_TYPE=all

# Number of Contexts a User is allowed to create and least number of patients required to create a context
MAX_CONTEXT_PER_USER=5
CRITICAL_NUMBER=5

# OAuth Settings - add the credentials of the GitHub App here
OAUTH_GITHUB_CLIENT_ID=Iv23lisNNMDVIxgKnygz
OAUTH_GITHUB_SECRET=678d6d57c095ad08d5e77d80d04f2280c6dddca8

# For DEBUG stuff
DEBUG=False

# Define database creation settings
OBSERVATION_SOURCE=CHRIS
VISUALIZE=false