<commit_before># EXECUTION PROFILE
## "production" to keep track of half-executed jobs using a job repository database
## "test" to use an in-memory database that will record a single run
spring.profiles.active=production


# EXTERNAL APPLICATIONS
app.opencga.path=/path/to/opencga
app.vep.path=/path/to/variant_effect_predictor.pl
app.vep.num-forks=4


# STEPS MANAGEMENT
## Job repository database
job.repository.driverClassName=
job.repository.url=
job.repository.username=
job.repository.password=

## Repeat steps
## true: The already COMPLETEd steps will be rerun. This is restarting the job from the beginning
## false(default): if the job was aborted and is relaunched, COMPLETEd steps will NOT be done again
config.restartability.allow=false


# MONGO DATABASE
config.db.read-preference=primary
db.collections.features.name=features
db.collections.stats.name=populationStatistics


# LOGGING
# https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-logging.html
logging.level.uk.ac.ebi.eva=DEBUG
logging.level.org.opencb.opencga=DEBUG
logging.level.org.springframework=INFO<commit_msg>Database parameters added to application.properties<commit_after># EXECUTION PROFILE
## "production" to keep track of half-executed jobs using a job repository database
## "test" to use an in-memory database that will record a single run
spring.profiles.active=production


# EXTERNAL APPLICATIONS
app.opencga.path=/path/to/opencga
app.vep.path=/path/to/variant_effect_predictor.pl
app.vep.num-forks=4


# STEPS MANAGEMENT
## Job repository database
job.repository.driverClassName=
job.repository.url=
job.repository.username=
job.repository.password=

## Repeat steps
## true: The already COMPLETEd steps will be rerun. This is restarting the job from the beginning
## false(default): if the job was aborted and is relaunched, COMPLETEd steps will NOT be done again
config.restartability.allow=false


# MONGO DATABASE
spring.data.mongodb.host=
spring.data.mongodb.authentication-database=
spring.data.mongodb.username=
spring.data.mongodb.password=
spring.data.mongodb.database=
config.db.read-preference=primary
db.collections.features.name=features
db.collections.files.name=files
db.collections.stats.name=populationStatistics
db.collections.variants.name=variants


# LOGGING
# https://docs.spring.io/spring-boot/docs/current/reference/html/boot-features-logging.html
logging.level.uk.ac.ebi.eva=DEBUG
logging.level.org.opencb.opencga=DEBUG
logging.level.org.springframework=INFO
{'fraction_non_alphanumeric': 0.09996001599360256, 'fraction_numerical': 0.0007996801279488205, 'mean_word_length': 5.672, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 2, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '2623194', 'n_tokens_mistral': 805, 'n_tokens_neox': 775, 'n_words': 184}