initial commit of basesite.

codingstrand · Apr 26, 2023 · b518c7f · b518c7f
commit b518c7f
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diff --git a/LICENSE b/LICENSE
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+MIT License
+
+Copyright (c) 2022 codingstrand
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
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+
+Use this repo to create repos for other sites.
diff --git a/breedbase_nginx.conf b/breedbase_nginx.conf
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+#
+server {
+
+       listen 80;
+
+	root /var/www/html;
+
+	server_name sample.breedbase.org;
+
+	client_max_body_size 1G;
+
+	location ~/brapi/ {
+	    auth_basic "off";
+            proxy_read_timeout 100m;
+            proxy_pass http://127.0.0.1:8080; 
+        }
+
+        location ~/user/login {
+           auth_basic "off";
+           proxy_pass http://127.0.0.1:8080;
+        }
+
+        location ~/.well-known/openid-configuration {
+           auth_basic "off";
+           proxy_pass http://127.0.0.1:8080;
+        }
+
+        location ~/brapi/authorize {
+           auth_basic "off";
+           proxy_pass http://127.0.0.1:8080;
+        }
+
+
+
+	location / {
+	    proxy_pass http://127.0.0.1:8080;
+            proxy_set_header  X-Real-IP  $remote_addr;
+            proxy_set_header  X-Forwarded-For  $proxy_add_x_forwarded_for;
+            proxy_set_header  Host $host;
+            proxy_read_timeout 100m;
+	    auth_basic "Restricted - Authorized Users Only";
+            auth_basic_user_file /etc/nginx/.htpasswd;
+	}
+
+
+}
+
diff --git a/crontab b/crontab
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+# /etc/crontab: system-wide crontab
+# Unlike any other crontab you don't have to run the `crontab'
+# command to install the new version when you edit this file
+# and files in /etc/cron.d. These files also have username fields,
+# that none of the other crontabs do.
+
+SHELL=/bin/sh
+PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin
+
+# m h dom mon dow user	command
+17 *	* * *	root    cd / && run-parts --report /etc/cron.hourly
+25 6	* * *	root	test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.daily )
+47 6	* * 7	root	test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.weekly )
+52 6	1 * *	root	test -x /usr/sbin/anacron || ( cd / && run-parts --report /etc/cron.monthly )
+#
+
+### BREEDBASE SPECIFIC CRONTAB ENTRIES:
+#
+30 00   * * *   root    /db_dumps/dump
+
+###* * * * *    root     date
diff --git a/docker-compose.yml b/docker-compose.yml
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+version: "3.7"
+
+services:
+  breedbase:
+    image: breedbase/breedbase:v0.70
+    depends_on:
+      - breedbase_db
+    container_name: breedbase_web
+    ports:
+      - 8080:8080
+      - 25:25
+    volumes:
+      - webdata:/home/production/volume
+      - type: bind
+        source: /home/production/basesite/empty_db_without.test_users.sql
+        target: /home/production/empty_dump.sql
+#      - type: bind
+#        source: /home/production/sgn
+#        target: /home/production/cxgn/sgn
+      - type: bind
+        source: /home/production/basesite.breedbase.org/sgn_local.conf
+        target: /home/production/cxgn/sgn/sgn_local.conf
+      - type: bind
+        source: /home/production/db_dumps
+        target: /db_dumps
+      - type: bind
+        source: /home/production/basesite/crontab
+        target: /etc/crontab
+
+  breedbase_db:
+    image: breedbase/pg:latest
+    container_name: breedbase_db
+    volumes:
+      - dbdata:/var/lib/postgresql/data
+
+volumes:
+  webdata:
+  dbdata:
+
+
+
diff --git a/dump b/dump
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+#!/bin/bash
+
+export DATE=`date --iso-8601`;
+
+echo "Dumping breedbase db, $DATE";
+
+rm $HOME/.pgpass
+
+echo "breedbase_db:5432:breedbase:postgres:postgres"> $HOME/.pgpass
+
+chmod 0600 $HOME/.pgpass
+
+ls -al $HOME/.pgpass
+
+pg_dump -h breedbase_db -U postgres -w -d breedbase > /db_dumps/breedbase_$DATE.sql
+
diff --git a/firewall b/firewall
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+#!/bin/bash
+
+# Firewall that will prevent port 8080 and 5432 to be accessible from the outside world
+
+echo "1" > /proc/sys/net/ipv4/ip_forward
+
+iptables -I FORWARD -p tcp ! -i 0.0.0.0 --dport 8080 -j DROP # 8080 only accessible through localhost
+iptables -I FORWARD -p tcp ! -i 0.0.0.0 --dport 5432 -j DROP # postgres only accessible through localhost
diff --git a/sgn_local.conf b/sgn_local.conf
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+dbhost breedbase_db
+dbname breedbase
+dbuser postgres
+dbpass postgres
+
+rootpath /home/production/cxgn
+basepath /home/production/cxgn/sgn
+
+#composable_cvs trait,toy   # see below
+#composable_cvs_allowed_combinations Time Series|trait+toy
+
+homepage_files_dir        /home/production/volume/public/static_content
+
+trial_download_logfile /home/production/volume/logs/cassava_trial_download_log
+static_datasets_url /data
+disable_login 0
+brapi_require_login 0
+require_login 1
+
+www_user www-data
+www_group www-data
+
+contact_form_email       info@codingstrand.com
+
+error_log                 /var/log/sgn/error.log
+access_log                /var/log/sgn/access.log
+
+python_executable python3
+
+preferred_species Manihot esculenta
+
+production_server 1
+image_dir /images/
+image_path /home/production/volume/public/images/
+cluster_shared_tempdir /home/production/volume/tmp
+tempfiles_base /home/production/volume/tmp/breedbase-site
+static_datasets_path /home/production/volume/public
+static_content_url  /static_content
+static_content_path /home/production/volume/public/static_content
+
+main_production_site_url https://sample.breedbase.org
+
+# github token for contact form
+github_access_token 96d462a40bc3504f4768559e752f7eec16ff2bc1
+
+#Homepage controller customization
+homepage_display_phenotype_uploads 0
+
+# jbrowse path
+jbrowse_path              /jbrowse_cassavabase/?data=data/json
+
+#path for archving uploaded files
+archive_path    /home/production/volume/archive/breedbase/
+
+default_genotyping_protocol "GBS ApeKI Cassava genome v6_Oct2015"
+#default_genotyping_protocol "GBS ApeKI Cassava genome v5"
+
+identifier_prefix BB
+project_name Sample
+cview_db_backend Cassava        
+
+# slurm config
+backend Slurm
+cluster_host ""
+cache_file_path /home/production/volume/cache
+solgs_dir        /home/production/tmp/solgs/__USERNAME__
+
+trait_ontology_db_name CO_322
+
+trait_cv_name maize_trait
+
+#For display on onto tree
+#onto_root_namespaces  NO (NCSU_ontology), GO (Gene Ontology), PO (Plant Ontology), SO (Sequence Ontology), PATO (Phenotype and Trait Ontology)
+#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)
+onto_root_namespaces CO_322 (Maize Trait)
+
+#For display on trait search
+trait_variable_onto_root_namespaces CO_322 (Maize Trait), COMP (Composed Variables)
+
+composable_cvs trait,attribute
+composable_cvs_allowed_combinations trait+attribute+toy
+
+<Controller::Cview>     
+        cview_default_map_id 1
+</Controller::Cview>
+
+r_qtl_temp_path /export/prod/tmp/solqtl___USERNAME__
+
+submit_dir                /home/production/public/submit-uploads
+
+blast_path                ""
+blast_db_path             /home/production/volume/blast/databases/current
+
+# path to our production_ftp site
+#
+ftpsite_root              /home/production/volume/public
+
+<View::Mason>
+  add_comp_root /home/production/cxgn/auburn/mason
+</View::Mason>
+
+<DatabaseConnection sgn_test>
+  dsn dbi:Pg:host=localhost;dbname=cxgn
+  user postgres
+  password <your postgres user password>
+
+  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
+
+</DatabaseConnection>
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		Use this repo to create repos for other sites.