ConfigurationKeys
- Configuration keys
- is this a production server?
| dbhost | the host for the database | localhost | | | dbname | the name of the database | fixture | | | dbuser | web_usr | the name of the postgres database user | usually either ```web_usr``` or ```postgres``` | | | dbpass | XYZ | the postgres database password for the dbuser | | |production_server | is this a production server? | 0 (not a production server), 1 (production server) | production servers do not send out emails for example | | ```rootpath``` | ```/home/production/cxgn/``` | | |
basepath /home/vagrant/cxgn/sgn
personalized_homepage 1 show_transplanting_date 0
python_executable /home/vagrant/.virtualenvs/cv/bin/python3.5 python_executable_maskrcnn_env /home/vagrant/.virtualenvs/cv/bin/python3.5
exclude_phenotype_outliers 0
image_analysis_services { "necrosis" : { "server_endpoint" : "http://unet.mcrops.org/api/", "image_type_name" : "image_analysis_necrosis_solomon_nsumba", "description" : "Necrosis Analysis, Makerere University", "service_traits" : { "CBSDpct|CO_334:0002078" : "Cassava" } }, "whitefly_count" : { "server_endpoint" : "http://18.216.149.204/home/api2/", "image_type_name" : "image_analysis_white_fly_count_solomon_nsumba", "description": "Whitefly count, Makarere University" }, "count_contours" : { "image_type_name" : "image_analysis_contours", "trait_name" : "count_contours", "script" : "GetContours.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Count Contours" }, "largest_contour_percent" : { "image_type_name" : "image_analysis_largest_contour", "trait_name" : "percent_largest_contour", "script" : "GetLargestContour.py", "input_image" : "image_path", "outfile_image" : "outfile_path", "results_outfile" : "results_outfile_path", "description" : "Largest Contour Percent" }, "count_sift" : { "image_type_name" : "image_analysis_sift", "trait_name" : "count_sift", "script" : "ImageProcess/CalculatePhenotypeSift.py", "input_image" : "image_paths", "outfile_image" : "outfile_paths", "results_outfile" : "results_outfile_path", "description" : "SIFT analysis" } }
- image_analysis_services { "plantcv_citrus_app": { "server_endpoint": "http://fake-image-analysis-service/", "image_type_name": "image_analysis_contours", "description": "Citrus Image Analysis (Mocked)", "service_traits": { "Fruit Diameter|INV:0000118": "INV" } } }
- For displaying ontologies in Ontology Browser
allow_trait_edits 1 allow_treatment_edits 0
- Marker Metadata Trait Categories
- Set the DB:Accession of the root term of the ontology used to define trait categories for marker metadata
- Seedlot Maintenance Events
- seedlot_maintenance_event_ontology_root
- The DB:Accession of the root term of the ontology used to define the Seedlot Maintenance categories, events, and values
- seedlot_maintenance_event_ontology_root SEEDLOT_MAINTENANCE:0000000
- seedlot_maintenance_info_cvterms
- The cvterm_id(s) of event(s) displayed as seedlot information on the record page
- seedlot_maintenance_info_cvterms 78211,78168
- seedlot material type options: seed, root, clone, plant, tissue culture or gametophyte
- default_seedlot_material_type seed
user_registration_join_breeding_programs 0 # when enabled, a new user can choose which breeding programs to join during registration user_registration_admin_confirmation 0 # when enabled, the new user confirmation message will be sent to the address(es) below instead of the user user_registration_admin_confirmation_email # a comma-separated list of email addresses to send new user confirmation messages to, when the above is enabled disable_login 0 default_login_janedoe 0 require_login 0
- Report parameters
brapi_require_login 1 brapi_observation_units_require_login 1 brapi_observations_require_login 1 brapi_post_variables 0 brapi_put_variables 0 brapi_images_require_login 1 brapi_variables_require_login 1 brapi_lists_require_login 1
- brapi_default_user admin
- brapi_default_user_role curator
- temporary feature flag until breedbase is storing treatments properly through brapi
allow_repeat_measures 0
- export trait names as synonyms (1) or the original trait name (0)
list_trait_require_id 1
- Cluster backend
- crossing prediction tool - should the sex of the plants be taken into account? (for diecieous plants such as Yam)
- if yes, provide the name of the variable that is used to score the sex of the plant
- the species that should be preselected in a list of species
- who is the web server user for chowning and emailing. need to set
- these manually under Apache mod_perl for example, because the server
- runs under a different user than when it starts.
- when true, server removes its tempfiles when the app is started
show_grafting_interface 0 graft_separator_string "_on_"
solqtl /export/prod/tmp/solqtl/
- other config variables #####
#password set_this_please
dsn dbi:Pg:host=localhost;dbname=cxgn
user postgres
search_path public
search_path sgn
search_path annotation
search_path genomic
search_path insitu
search_path metadata
search_path pheno_population
search_path phenome
search_path physical
search_path tomato_gff
search_path biosource
search_path gem
search_path sgn_people
- Cview configuration parameters
cview_default_map_id 9
- Github access token used for contact form posting of issues
- NOAA National Climatic Data Center Access token
- captcha keys for the production site
- captcha_private_key 6Lc__9YSAAAAANcTczARhRnZRkKmzWjnhipyqI6f
- captcha_public_key 6Lc__9YSAAAAAH2ODL2FlR8jKa2Ms9i9d_0ziBWr
- backcompat variables for the various static content types
- relative URL and absolute path for static datasets
- relative URL and absoluate path for static site content
- this needs to be here rather than in the CGI controller itself to
- work around a bug in all but the most recent
- Catalyst::Controller::CGIBin
cgi_dir __path_to(cgi-bin)__
bac_publish_subdir tomato_genome/bacs
disposition host-header # application-wide
uri_class URI::SmartURI # by default
<default>
content_type text/plain
to sgn-bugs@solgenomics.net
from sgn-bugs@solgenomics.net
charset utf-8
</default>
dump_skip_class Catalyst Catalyst::Stats DBIx::Class::Schema DBIx::Class::ResultSet DBIx::Class::Row HTML::Mason::Interp
- should we send emails, if we are a production server? this can be
- used to turn off emails if we are being bombarded.
- External SMTP Server to send emails
- URL of the canonical, main production site
- is there a system message text file somewhere we should be displaying?
- defaults to /tmp/<user></user>/SGN-site
- tempfiles_base
- where to run cluster jobs - nothing means "batch" queue
- web_cluster_queue
- where to run cluster jobs
- is this a mirror of SGN, or the real thing?
- how to find cosii_files for markerinfo.pl
- log files, ABSOLUTE PATHS
- paths to stuff
- stock tempfiles (for downloading phenotype and genotype raw data)
- weblogo tempfiles for motifs finder tools
- currently our cookies encrypt stuff, so this is just a random string to use to do that
- where the genefamily info is stored
- stock properties that should be displayed and allowed to be edited in the "additional information" section and can be used in the accession file upload
editable_stock_props_definitions released_variety_name:offical variety name of the accession or stock,location_code:location code(s) for the accession,ploidy:a number(s) indicating the ploidy (e.g. 2 for diploid or 3 for triploid),genome_structure:genome structure(s) for accession which take into account ploidy and ancestral genome info e.g. AAA or AB,variety:variety(s) can be defined as a group of individuals or plants having similar traits that can be reproduced true to type from generation to generation,donor:the accession_name(s) of the donor accession and should be used in conjunction with donor institute and donor PUI,donor institute:the institute(s) of the donor accession(s),donor PUI:the permanent unique identifier(s) of the donor accession,country of origin:the country(s) of origin,state:the state(s) of origin,institute code: the institute code(s) of origin,institute name:the institute name(s) of origin,biological status of accession code:code(s) indicating the state of accession,notes:free text for notes,accession number:accession number(s) for accession from germplasm bank,PUI:permanent unique identifier(s) of the accession,seed source:origin(s) of seed source,type of germplasm storage code:code(s) indicating the type of germplasm storage,acquisition date:date(s) of acquisition YYYYMMDD for accession,transgenic:indicates if accession is transgenic. Please indicate 1 if transgenic and empty if otherwise.,introgression_parent:if the accession you are adding has an introgression that originated from one of the parents you can specify the parent here,introgression_backcross_parent:the backcross parent for introducing an introgression into the accession being added,introgression_map_version:the map version for identifying the start and stop position of the introgression. e.g. AGPv2,introgression_chromosome:the chromosome number that the introgression is on,introgression_start_position_bp:the start position of the introgression in base pairs,introgression_end_position_bp:the end position of the introgression in base pairs,number_of_insertions:number of transgene insertions in a transgenic plant,organization:the name(s) of the organization(s) which use this accession e.g. NARO,IITA
editable_vector_props Strain,CloningOrganism,InherentMarker,Backbone,SelectionMarker,CassetteName,VectorType,Gene,Promotors,Terminators,GenbankRecord,PlantAntibioticResistantMarker,BacterialResistantMarker
- Cross properties that should be displayed and allowed to be added to crosses on cross detail page.
- Cross properties for cassavabase
- Cross properties for yambase
- cross_properties Number of Flowers,Pollination Date,Harvest Date,Number of Seeds Harvested,Days to Maturity,Seed Extraction Date,Number of Seeds Extracted,Number of Viable Seeds,Number of Nonviable Seeds, Days from Harvest to Extraction
- Cross properties for musabase
- cross_properties First Pollination Date,Repeat Pollination Date,Harvest Date,Seed Extraction Date,Number of Seeds Extracted,Embryo Rescue Good Seeds,Embryo Rescue Bad Seeds,Embryo Rescue Total Seeds,Embryo Rescue Date,Subculture Date,Subcultures Count,Subcultures Multiplication Number,Rooting Date,Rooting Plantlet,Germinating After 2 Weeks Date,Active Germinating After 2 Weeks,Germinating Afte 8 Weeks Date,Active Germinating After 8 Weeks,Screenhouse Transfer Date,Hardening Date
- Cross additional info
- properties for ordering system (required 2 sets of order properties: order_properties and order_properties_dialog)
- customized dropdown menu can be included in the order_properties_dialog. Dropdown menu can be linked with each property by using ":"
- for example Facility and Experiment Type properties have customized dropdown menu:
- order_properties Quantity,Facility,Scientist,Required by Date,Experiment Name,Experiment Type
- order_properties_dialog Quantity,Facility:green house:growth chamber,Scientist,Required by Date,Experiment Name,Experiment Type:seed production:experimentation
- for setting up a single step submission use the following:
- ordering_type single_step
- two steps (adding to your cart first) is by default
- for connecting orders with tracking activity project
- for connecting transformation with tracking activity project
tracking_activities subculture_count,rooted_count,hardened_count tracking_activities_header Subculture Count,Rooted Count,Hardened Count
tracking_transformation_info coculture_date,number_of_transformants tracking_transformation_info_header Co-culture Date, Number of Transformants
tracking_tissue_culture_info subculture_count,rooted_count,hardened_count tracking_tissue_culture_info_header Subculture Count,Rooted Count,Hardened Count
- Whether obsoleted accessions are allowed to include in new trials
enabled 1
</feature> <feature>
enabled 1
</feature>
- default GBrowse2 configuration, for a Debian gbrowse2 installation
enabled 1
perl_inc /usr/local/share/website/gbrowse/lib/perl5
tmp_dir /usr/local/share/website/tmp/gbrowse
cgi_url /gbrowse/bin
static_url /gbrowse/static
run_mode fastcgi
cgi_bin /usr/lib/cgi-bin/gbrowse
static_dir /usr/local/share/website/gbrowse/htdocs
</feature>
- default ITAG config
enabled 1
pipeline_base /export/shared/tomato_genome/itagpipeline/itag
releases_base /export/prod/private/genomes/solanum_lycopersicum/annotation
</feature>
- how to find blast stuff
- Set the the Blast DB (by species and reference genome) used for getting the marker flanking sequence
- flanking_sequence_blast_db Triticum aestivum|RefSeq_v1|4,Triticum durum|Triticum durum|5
- bin directory used by cluster nodes
- the shared temp directory used by cluster nodes
cluster_host ""
- how verbose we want the warnings to be in the apache error log
- Insitu file locations
- path to our production_ftp site
- path to the pucebaboon temperature sensor file:
- path for archving uploaded files
- path for Cache::File system. used by CXGN::Dataset::Cache
- cache_file_path /export/prod/sgn_cache
- site overall identifier prefix used for site specific data
- such as stocks, unignes (yet to be implemented) and other datatypes
- for example, uploading barcode phenotyping data will not work without this key (see L )
- default genotyping protocol to use:
genotyping_server_host NULL genotyping_server_username NULL genotyping_server_password NULL genotyping_server_token NULL
- HIDAP Shiny Server Support
- BrAPI params
- Expression Atlas Connection
- Sampling trial tissue types
- Homepage controller customization
- banana ordering system
- ODK Services
- Transcriptomics protocol options
- Authorized Clients for SSO
simsearch_datadir /home/production/simsearch_data
version sgn-311.0-236 version_updated 2021-12-23T19:04:41Z
- <oidc_client>
- # Create OAuth client ID in the cloud console: https://console.cloud.google.com/apis/credentials
- # Authorized JavaScript origins: https://<BREEDBASE DOMAIN>
- # Authorized redirect URIs: https://<BREEDBASE DOMAIN>/authenticate/oidc/google/callback
- <google>
- client_id <YOUR CLIENT_ID HERE>.apps.googleusercontent.com # [REQUIRED] Client ID in google (XXX.apps.googleusercontent.com)
- client_secret <YOUR CLIENT_SECRET HERE> # [REQUIRED] Client Secret in google
- well_known_url https://accounts.google.com/.well-known/openid-configuration # [REQUIRED] Well Known Configuration
- auto_provision 0 # [OPTIONAL] If email does not exist in database, don't create new user
- </google>
- <keycloak>
- client_id <KEYCLOAK CLIENT ID> # [REQUIRED] Client ID in keycloak
- client_secret <KEYCLOAK CLIENT SECRET> # [REQUIRED] Client ID in keycloak
- well_known_url https://<KEYCLOAK DOMAIN>/auth/realms/<REALM>/.well-known/openid-configuration # [REQUIRED] Well Known Configuration
- code_challenge_method S256 # [OPTIONAL] PKCE code challenge method
- auto_provision 1 # [OPTIONAL] If email does not exist in database, do create new user
- </keycloak>
- </oidc_client>
