<commit_before># importer database settings
db.user=cbio
db.password=<PASSWORD>
db.host=miso-dev.cbio.mskcc.org
db.portal_db_name=ben_sandbox
db.importer_db_name=ben_cgds_importer
db.driver=com.mysql.jdbc.Driver
db.connection_string=jdbc:mysql://localhost/
db.portal_schema=$PORTAL_HOME/core/src/main/resources/db/cgds.sql

# google docs credentials
google.id=gdac.portal
google.pw=<PASSWORD>

# google docs user access settings
users.spreadsheet=gdac.portal
users.worksheet=bob789rye

# google docs importer configuration settings
importer.spreadsheet_service_appname=cBio Portal Importer Tool
importer.spreadsheet=portal_importer_configuration
importer.cancer_studies_worksheet=cancer_studies
importer.case_id_filters_worksheet=case_id_filters-default
importer.case_lists_worksheet=case_lists
importer.clinical_attributes_namespace_worksheet=clinical_attributes_namespace
importer.clinical_attributes_worksheet=clinical_attributes
importer.datatypes_worksheet=datatypes
importer.data_sources_worksheet=data_sources
importer.portals_worksheet=portals
importer.reference_data_worksheet=reference_data
importer.tumor_types_worksheet=tumor_types
importer.foundation_worksheet=foundation
importer.icgc_worksheet=icgc

# mail
mail.server=cbio.mskcc.org
mail.triage_portal.update.message.sender=cbioportal
mail.triage_portal.update.message.recipient=cbioportal
mail.triage_portal.update.message.subject=cbioportal
mail.triage_portal.update.message.body=cbioportal
mail.production_portal.update.message.sender=cbioportal
mail.production_portal.update.message.recipient=cbioportal
mail.production_portal.update.message.subject=cbioportal
mail.production_portal.update.message.body=cbioportal
mail.redeploy.message.sender=cbioportal
mail.redeploy.message.recipient=cbioportal
mail.redeploy.message.subject=cbioportal
mail.redeploy.message.body=cbioportal

# sftp on production server (for redeploy war)
production.sftp.host=placeholder.org
production.sftp.username=placeholder
production.sftp.password=<PASSWORD>

# annotation database - should be removed after
annotate.db.user=cbio
annotate.db.password=<PASSWORD>
annotate.db.host=localhost
annotate.db.name=oncotator

# NCI's clinical trial information
nci.cancer.ftp.user=mskccbio
nci.cancer.ftp.password=<PASSWORD>
nci.cancer.sftp.user=mskccbio
nci.cancer.sftp.password=<PASSWORD>
sshpass.path=/data/local/bin/sshpass

# firehose_get script
firehose_get_script=$PORTAL_HOME/importer/src/main/scripts/firehose_get

# liftover tool
liftover_binary=/home/grossb/local/bin/liftOver
liftover_chain_file=/home/grossb/local/bin/hg18ToHg19.over.chain

# tcga clinical data
tcga.clinical.url=https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<TUMOR_TYPE>/bcr/nationwidechildrens.org/bio/clin/
tcga.clinical.filename=nationwidechildrens.org_<TUMOR_TYPE>.bio.Level_2.0.<REVISION>.0.tar.gz
nci.cadsr.url=http://cadsrapi.nci.nih.gov/cadsrapi40/GetXML?query=
nci.cadsr.query=DataElement[@publicId=CDE_ID:]<commit_msg>added annotator tool properties into importer.properties<commit_after># importer database settings
db.user=cbio
db.password=cbio
db.host=miso-dev.cbio.mskcc.org
db.portal_db_name=ben_sandbox
db.importer_db_name=ben_cgds_importer
db.driver=com.mysql.jdbc.Driver
db.connection_string=jdbc:mysql://localhost/
db.portal_schema=$PORTAL_HOME/core/src/main/resources/db/cgds.sql

# google docs credentials
google.id=gdac.portal
google.pw=<PASSWORD>

# google docs user access settings
users.spreadsheet=gdac.portal
users.worksheet=bob789rye

# google docs importer configuration settings
importer.spreadsheet_service_appname=cBio Portal Importer Tool
importer.spreadsheet=portal_importer_configuration
importer.cancer_studies_worksheet=cancer_studies
importer.case_id_filters_worksheet=case_id_filters-default
importer.case_lists_worksheet=case_lists
importer.clinical_attributes_namespace_worksheet=clinical_attributes_namespace
importer.clinical_attributes_worksheet=clinical_attributes
importer.datatypes_worksheet=datatypes
importer.data_sources_worksheet=data_sources
importer.portals_worksheet=portals
importer.reference_data_worksheet=reference_data
importer.tumor_types_worksheet=tumor_types
importer.foundation_worksheet=foundation
importer.icgc_worksheet=icgc

# mail
mail.server=cbio.mskcc.org
mail.triage_portal.update.message.sender=cbioportal
mail.triage_portal.update.message.recipient=cbioportal
mail.triage_portal.update.message.subject=cbioportal
mail.triage_portal.update.message.body=cbioportal
mail.production_portal.update.message.sender=cbioportal
mail.production_portal.update.message.recipient=cbioportal
mail.production_portal.update.message.subject=cbioportal
mail.production_portal.update.message.body=cbioportal
mail.redeploy.message.sender=cbioportal
mail.redeploy.message.recipient=cbioportal
mail.redeploy.message.subject=cbioportal
mail.redeploy.message.body=cbioportal

# sftp on production server (for redeploy war)
production.sftp.host=placeholder.org
production.sftp.username=placeholder
production.sftp.password=<PASSWORD>

# annotation database - should be removed after
annotate.db.user=cbio
annotate.db.password=<PASSWORD>
annotate.db.host=localhost
annotate.db.name=oncotator

# annotator tool
annotator.maf2maf=/ssd-data/cmo/opt/vcf2maf/maf2maf.pl
annotator.vcf2maf=/ssd-data/cmo/opt/vcf2maf/vcf2maf.pl
annotator.vep_path=/ssd-data/cmo/opt/vep
annotator.vep_data=/ssd-data/cmo/opt/vep
annotator.ref_fasta=/ssd-data/cmo/srv/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
annotator.exclude_cols=oncotator
annotator.intermediate_maf=/tmp/annotator_out.maf

# NCI's clinical trial information
nci.cancer.ftp.user=mskccbio
nci.cancer.ftp.password=<PASSWORD>
nci.cancer.sftp.user=mskccbio
nci.cancer.sftp.password=<PASSWORD>
sshpass.path=/data/local/bin/sshpass

# firehose_get script
firehose_get_script=$PORTAL_HOME/importer/src/main/scripts/firehose_get

# liftover tool
liftover_binary=/home/grossb/local/bin/liftOver
liftover_chain_file=/home/grossb/local/bin/hg18ToHg19.over.chain

# tcga clinical data
tcga.clinical.url=https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/<TUMOR_TYPE>/bcr/nationwidechildrens.org/bio/clin/
tcga.clinical.filename=nationwidechildrens.org_<TUMOR_TYPE>.bio.Level_2.0.<REVISION>.0.tar.gz
nci.cadsr.url=http://cadsrapi.nci.nih.gov/cadsrapi40/GetXML?query=
nci.cadsr.query=DataElement[@publicId=CDE_ID:]
{'fraction_non_alphanumeric': 0.09894934922377294, 'fraction_numerical': 0.0053316606554806335, 'mean_word_length': 8.434911242603551, 'pattern_counts': {'":': 0, '<': 20, '<?xml version=': 0, '>': 20, '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': '4808994', 'n_tokens_mistral': 2438, 'n_tokens_neox': 2320, 'n_words': 219}