<commit_before>aspiredb.ehcache.configfile.name=/ehcache.xml
aspiredb.runas.password=<PASSWORD>

aspiredb.download.path=/var/aspiredb.tmp


aspiredb.cli.variant.subjectid=subjectid
aspiredb.cli.variant.chrom=chrom
aspiredb.cli.variant.start=start
aspiredb.cli.variant.end=end

aspiredb.cli.variant.uservariantid=uservariantid
aspiredb.cli.variant.description=description
aspiredb.cli.variant.externalid=externalid

aspiredb.cli.variant.cnv.type=type
aspiredb.cli.variant.cnv.copynumber=copynumber
aspiredb.cli.variant.snv.referencebase=ref_base
aspiredb.cli.variant.snv.observedbase=obs_base
aspiredb.cli.variant.snv.dbsnpid=dbsnpid
aspiredb.cli.variant.indel.length=indel_length

# dbDirectory points to the directory that contains tables of function prediction 
aspiredb.cli.variant.functionalprediction.predictionColumn=LR_pred
aspiredb.cli.variant.functionalprediction.dbDirectory=/path/to/variant/function/prediction/directory
aspiredb.cli.variant.functionalprediction.dbPrefix=dbNSFP2.4_variant

# HTTPS SSL port. This should match your application server configuration.
aspiredb.sslPort=8443

# Maximum number of records allowed during upload
aspiredb.upload.maxRecords=30000

# Maximum number of records to show
aspiredb.view.maxRecords=50000

#####################################################
# EMAIL and URLS

# base url for the system, used in formed URLs
aspiredb.hosturl=http://www.chibi.ubc.ca/
aspiredb.appname=aspiredb
aspiredb.baseurl=${aspiredb.hosturl}${aspiredb.appname}/

# 'From' address for system notifications and SMTP server settings
aspiredb.admin.email=aspiredb
mail.host=localhost
mail.username=XXXXXX
mail.password=

# In ms, if the project upload time takes longer than this, send an email
aspiredb.uploadTimeThreshold=60000

# UCSC Genome Browser configs, e.g. http://genome.ucsc.edu/cgi-bin/hgCustom?clade=mammal&org=Human&db=hg19
aspiredb.ucsc.url=http://genome.ucsc.edu/cgi-bin/hgCustom
aspiredb.ucsc.clade=mammal
aspiredb.ucsc.db=hg19
aspiredb.ucsc.org=Human

# BioMart service to use
aspiredb.biomart.url=http://grch37.ensembl.org/biomart/martservice/results
# aspiredb.biomart.url=http://www.biomart.org/biomart/martservice/results<commit_msg>Switched over to new URL for BioMart web service; old URL (and others) down due to BioMart migrating hosting.<commit_after>aspiredb.ehcache.configfile.name=/ehcache.xml
aspiredb.runas.password=<PASSWORD>

aspiredb.download.path=/var/aspiredb.tmp


aspiredb.cli.variant.subjectid=subjectid
aspiredb.cli.variant.chrom=chrom
aspiredb.cli.variant.start=start
aspiredb.cli.variant.end=end

aspiredb.cli.variant.uservariantid=uservariantid
aspiredb.cli.variant.description=description
aspiredb.cli.variant.externalid=externalid

aspiredb.cli.variant.cnv.type=type
aspiredb.cli.variant.cnv.copynumber=copynumber
aspiredb.cli.variant.snv.referencebase=ref_base
aspiredb.cli.variant.snv.observedbase=obs_base
aspiredb.cli.variant.snv.dbsnpid=dbsnpid
aspiredb.cli.variant.indel.length=indel_length

# dbDirectory points to the directory that contains tables of function prediction 
aspiredb.cli.variant.functionalprediction.predictionColumn=LR_pred
aspiredb.cli.variant.functionalprediction.dbDirectory=/path/to/variant/function/prediction/directory
aspiredb.cli.variant.functionalprediction.dbPrefix=dbNSFP2.4_variant

# HTTPS SSL port. This should match your application server configuration.
aspiredb.sslPort=8443

# Maximum number of records allowed during upload
aspiredb.upload.maxRecords=30000

# Maximum number of records to show
aspiredb.view.maxRecords=50000

#####################################################
# EMAIL and URLS

# base url for the system, used in formed URLs
aspiredb.hosturl=http://www.chibi.ubc.ca/
aspiredb.appname=aspiredb
aspiredb.baseurl=${aspiredb.hosturl}${aspiredb.appname}/

# 'From' address for system notifications and SMTP server settings
aspiredb.admin.email=aspiredb
mail.host=localhost
mail.username=XXXXXX
mail.password=

# In ms, if the project upload time takes longer than this, send an email
aspiredb.uploadTimeThreshold=60000

# UCSC Genome Browser configs, e.g. http://genome.ucsc.edu/cgi-bin/hgCustom?clade=mammal&org=Human&db=hg19
aspiredb.ucsc.url=http://genome.ucsc.edu/cgi-bin/hgCustom
aspiredb.ucsc.clade=mammal
aspiredb.ucsc.db=hg19
aspiredb.ucsc.org=Human

# BioMart service to use
aspiredb.biomart.url=http://www.ensembl.org/biomart/martservice
# http://grch37.ensembl.org/biomart/martservice/results old url (and others) inaccessible January 2016 due to BioMart migrating hosting
# aspiredb.biomart.url=http://www.biomart.org/biomart/martservice/results
{'fraction_non_alphanumeric': 0.12110651274232194, 'fraction_numerical': 0.01263341319973862, 'mean_word_length': 6.527868852459016, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 5, 'xml': 2}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5003420', 'n_tokens_mistral': 1656, 'n_tokens_neox': 1544, 'n_words': 260}