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initial commit of basesite.
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‎LICENSE

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MIT License
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Copyright (c) 2022 codingstrand
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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Use this repo to create repos for other sites.

‎breedbase_nginx.conf

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#
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server {
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listen 80;
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root /var/www/html;
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server_name sample.breedbase.org;
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client_max_body_size 1G;
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location ~/brapi/ {
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auth_basic "off";
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proxy_read_timeout 100m;
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proxy_pass http://127.0.0.1:8080;
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}
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location ~/user/login {
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auth_basic "off";
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proxy_pass http://127.0.0.1:8080;
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}
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location ~/.well-known/openid-configuration {
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auth_basic "off";
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proxy_pass http://127.0.0.1:8080;
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}
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location ~/brapi/authorize {
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auth_basic "off";
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proxy_pass http://127.0.0.1:8080;
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}
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location / {
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proxy_pass http://127.0.0.1:8080;
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proxy_set_header X-Real-IP $remote_addr;
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proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
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proxy_set_header Host $host;
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proxy_read_timeout 100m;
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auth_basic "Restricted - Authorized Users Only";
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auth_basic_user_file /etc/nginx/.htpasswd;
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}
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}
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‎crontab

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# /etc/crontab: system-wide crontab
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# Unlike any other crontab you don't have to run the `crontab'
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# command to install the new version when you edit this file
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# and files in /etc/cron.d. These files also have username fields,
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# that none of the other crontabs do.
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SHELL=/bin/sh
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PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
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# m h dom mon dow user command
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17 * * * * root cd / && run-parts --report /etc/cron.hourly
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25 6 * * * root test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.daily )
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47 6 * * 7 root test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.weekly )
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52 6 1 * * root test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.monthly )
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#
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### BREEDBASE SPECIFIC CRONTAB ENTRIES:
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#
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30 00 * * * root /db_dumps/dump
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###* * * * * root date

‎docker-compose.yml

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version: "3.7"
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services:
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breedbase:
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image: breedbase/breedbase:v0.70
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depends_on:
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- breedbase_db
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container_name: breedbase_web
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ports:
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- 8080:8080
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- 25:25
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volumes:
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- webdata:/home/production/volume
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- type: bind
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source: /home/production/basesite/empty_db_without.test_users.sql
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target: /home/production/empty_dump.sql
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# - type: bind
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# source: /home/production/sgn
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# target: /home/production/cxgn/sgn
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- type: bind
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source: /home/production/basesite.breedbase.org/sgn_local.conf
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target: /home/production/cxgn/sgn/sgn_local.conf
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- type: bind
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source: /home/production/db_dumps
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target: /db_dumps
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- type: bind
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source: /home/production/basesite/crontab
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target: /etc/crontab
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breedbase_db:
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image: breedbase/pg:latest
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container_name: breedbase_db
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volumes:
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- dbdata:/var/lib/postgresql/data
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volumes:
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webdata:
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dbdata:
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‎dump

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#!/bin/bash
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export DATE=`date --iso-8601`;
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echo "Dumping breedbase db, $DATE";
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rm $HOME/.pgpass
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echo "breedbase_db:5432:breedbase:postgres:postgres"> $HOME/.pgpass
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chmod 0600 $HOME/.pgpass
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ls -al $HOME/.pgpass
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pg_dump -h breedbase_db -U postgres -w -d breedbase > /db_dumps/breedbase_$DATE.sql
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‎firewall

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#!/bin/bash
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# Firewall that will prevent port 8080 and 5432 to be accessible from the outside world
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echo "1" > /proc/sys/net/ipv4/ip_forward
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iptables -I FORWARD -p tcp ! -i 0.0.0.0 --dport 8080 -j DROP # 8080 only accessible through localhost
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iptables -I FORWARD -p tcp ! -i 0.0.0.0 --dport 5432 -j DROP # postgres only accessible through localhost

‎sgn_local.conf

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dbhost breedbase_db
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dbname breedbase
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dbuser postgres
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dbpass postgres
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rootpath /home/production/cxgn
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basepath /home/production/cxgn/sgn
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#composable_cvs trait,toy # see below
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#composable_cvs_allowed_combinations Time Series|trait+toy
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homepage_files_dir /home/production/volume/public/static_content
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trial_download_logfile /home/production/volume/logs/cassava_trial_download_log
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static_datasets_url /data
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disable_login 0
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brapi_require_login 0
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require_login 1
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www_user www-data
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www_group www-data
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contact_form_email [email protected]
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error_log /var/log/sgn/error.log
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access_log /var/log/sgn/access.log
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python_executable python3
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preferred_species Manihot esculenta
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production_server 1
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image_dir /images/
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image_path /home/production/volume/public/images/
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cluster_shared_tempdir /home/production/volume/tmp
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tempfiles_base /home/production/volume/tmp/breedbase-site
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static_datasets_path /home/production/volume/public
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static_content_url /static_content
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static_content_path /home/production/volume/public/static_content
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main_production_site_url https://sample.breedbase.org
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# github token for contact form
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github_access_token 96d462a40bc3504f4768559e752f7eec16ff2bc1
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#Homepage controller customization
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homepage_display_phenotype_uploads 0
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# jbrowse path
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jbrowse_path /jbrowse_cassavabase/?data=data/json
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#path for archving uploaded files
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archive_path /home/production/volume/archive/breedbase/
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default_genotyping_protocol "GBS ApeKI Cassava genome v6_Oct2015"
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#default_genotyping_protocol "GBS ApeKI Cassava genome v5"
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identifier_prefix BB
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project_name Sample
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cview_db_backend Cassava
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# slurm config
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backend Slurm
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cluster_host ""
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cache_file_path /home/production/volume/cache
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solgs_dir /home/production/tmp/solgs/__USERNAME__
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trait_ontology_db_name CO_322
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trait_cv_name maize_trait
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#For display on onto tree
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#onto_root_namespaces NO (NCSU_ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
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#onto_root_namespaces CO_334 (Cassava Trait Ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology), DL_001 (Dawson Lab Ontology), TO (Time Ontology)
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onto_root_namespaces CO_322 (Maize Trait)
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#For display on trait search
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trait_variable_onto_root_namespaces CO_322 (Maize Trait), COMP (Composed Variables)
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composable_cvs trait,attribute
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composable_cvs_allowed_combinations trait+attribute+toy
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<Controller::Cview>
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cview_default_map_id 1
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</Controller::Cview>
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r_qtl_temp_path /export/prod/tmp/solqtl___USERNAME__
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submit_dir /home/production/public/submit-uploads
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blast_path ""
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blast_db_path /home/production/volume/blast/databases/current
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# path to our production_ftp site
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#
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ftpsite_root /home/production/volume/public
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<View::Mason>
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add_comp_root /home/production/cxgn/auburn/mason
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</View::Mason>
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<DatabaseConnection sgn_test>
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dsn dbi:Pg:host=localhost;dbname=cxgn
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user postgres
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password <your postgres user password>
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search_path public
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search_path sgn
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search_path annotation
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search_path genomic
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search_path insitu
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search_path metadata
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search_path pheno_population
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search_path phenome
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search_path physical
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search_path tomato_gff
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search_path biosource
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search_path gem
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</DatabaseConnection>

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