Devops deployment 6 create and test noctua developer deployment docs

docker-vars.yaml

@@ -11,7 +11,7 @@ tag: latest
 minerva_tag: v7
 
 # Ubuntu based image
-noctua_tag: v5
+noctua_tag: v6
 
 #docker_hub_user: "{{ lookup('env', 'USER')|lower }}"
 docker_hub_user: geneontology

production/config-stack.yaml.sample

@@ -25,27 +25,28 @@ stack:
 
      # download or create journal locally and specify full path here.
      # cd /tmp && wget http://skyhook.berkeleybop.org/blazegraph-20230611.jnl
+     # see production/gen_journal.sh.sample to generate one
      BLAZEGRAPH_JOURNAL: REPLACE_ME_FILE_PATH # /tmp/blazegraph-20230611.jnl
 
-     # HTTP OR HTTPS
-     noctua_host: REPLACE_ME # aes-test-noctua.geneontology.io
-     noctua_host_alias: REPLACE_ME
-     noctua_lookup_url: REPLACE_ME # https://golr-aux.geneontology.io/solr/
-     golr_neo_lookup_url: REPLACE_ME # https://aes-test-noctua.geneontology.io
+     # HTTPS
+     noctua_host: REPLACE_ME # noctua.geneontology.org or noctua.geneontology.io
+     noctua_host_alias: REPLACE_ME # noctua-production-2024-10-15.geneontology.org or aes-noctua-test-2024-10-15.geneontology.io
+     noctua_lookup_url: REPLACE_ME # https://noctua-production-2024-10-15.geneontology.org or https://aes-noctua-test-2024-10-15.geneontology.io
+     golr_neo_lookup_url: REPLACE_ME # https://golr-aux.geneontology.org/solr/ or https://golr-aux.geneontology.io/solr/
 
 
-     # HTTP OR HTTPS
+     # HTTPS
      github_client_id: 'REPLACE_ME'
      github_client_secret: 'REPLACE_ME'
-     github_callback_url: REPLACE_ME # https://aes-test-barista.geneontology.io/auth/github/callback
+     github_callback_url: REPLACE_ME # barista-production-2024-10-15.geneontology.org/auth/github/callback or https://aes-barista-test-2024-10-15.geneontology.io/auth/github/callback
 
-     # HTTP OR HTTPS
-     golr_lookup_url: REPLACE_ME # https://aes-test-golr.geneontology.io/solr
+     # HTTPS
+     golr_lookup_url: REPLACE_ME #  https://golr-aux.geneontology.org/solr/ or https://golr-aux.geneontology.io/solr/
 
      # HTTP OR HTTPS
-     barista_lookup_host: REPLACE_ME # aes-test-barista.geneontology.io
-     barista_lookup_host_alias: REPLACE_ME
-     barista_lookup_url: REPLACE_ME # https://aes-test-barista.geneontology.io
+     barista_lookup_host: REPLACE_ME # barista-production-2024-10-15.geneontology.org or aes-barista-test-2024-10-15.geneontology.io
+     barista_lookup_host_alias: REPLACE_ME barista-production-2024-10-15.geneontology.org or am-barista-test-2024-10-15.geneontology.io
+     barista_lookup_url: REPLACE_ME #  https://barista-production-2024-10-15.geneontology.org or https://am-barista-test-2024-10-15.geneontology.io
 
      USE_CLOUDFLARE: 0
    scripts: [ stage.yaml, start_services.yaml]

production/gen_journal.sh.sample

@@ -1,9 +1,17 @@
-# Modify java maximum heap based on your machine
+# Modify java maximum heap based on your machine and also update sdir such that it is same as path where git clone is executed.  Note, sdir has to be modified in export and docker run commands
+# If necessary, modify minerva version i.e. geneontology/minerva:v7
 export CMD="java -Xmx4G -jar minerva-cli.jar --import-owl-models -j /sdir/blazegraph.jnl -f /sdir/noctua-models/models"
 
 git clone https://github.com/geneontology/noctua-models.git
-docker pull geneontology/minerva:v2
-echo docker run --rm -v $PWD:/sdir -t geneontology/minerva:v2  $CMD
-docker run --rm -v $PWD:/sdir -t geneontology/minerva:v2  $CMD
+# If above command takes long to run or is unsuccessful, retrieve a shallow copy
+# For testing puroses, only a subset of models in directory 'noctua-models/models' are required.  Therefore, only about a ~1000 .ttl files are necessary in directory  'noctua-models/models'
+#git clone https://github.com/geneontology/noctua-models.git --depth 1   
+docker pull geneontology/minerva:v7
+
+# Modify sdir
+echo docker run --rm -v $PWD:/sdir -t geneontology/minerva:v7  $CMD
+
+# Modify sdir
+docker run --rm -v $PWD:/sdir -t geneontology/minerva:v7  $CMD
 exit 1
 

templates/httpd-vhosts-prod-barista.conf

@@ -3,10 +3,9 @@
     ServerName {{ barista_lookup_host  }}
     ServerAlias {{ barista_lookup_host_alias }}
 
-    Alias /robots.txt /var/www/html/robots.txt
-    RewriteEngine On
-    RewriteRule ^/robots.txt /robots.txt
-
+    #Do not use permanent for testing Redirect permanent / https://{{barista_lookup_host_alias}}/
+    Redirect / https://{{barista_lookup_host_alias}}/ 
+
     ## Get aggressive with badly behaving bots.
     RewriteCond %{HTTP_USER_AGENT}  ^.*Adsbot.*$ [OR]
     RewriteCond %{HTTP_USER_AGENT}  ^.*AhrefsBot.*$ [OR]
@@ -21,14 +20,9 @@
     RewriteCond %{HTTP_USER_AGENT}  ^.*semrush.*$ [OR]
     RewriteCond %{HTTP_USER_AGENT}  ^.*WhatWeb.*$ [OR]
     RewriteCond %{HTTP_USER_AGENT}  ^.*WhatWeb.*$
-    RewriteRule . - [R=403,L]
+    RewriteRule . - [R=403,L]    
+
+
 
 
-    ErrorLog "/var/log/apache2/barista-error.log"
-    CustomLog "/var/log/apache2/barista-access.log" common
-    ## Proxy.
-    ProxyPreserveHost On
-    ProxyRequests Off
-    ProxyPass / http://barista:3400/
-    ProxyPassReverse / http://barista:3400/
 </VirtualHost>

templates/httpd-vhosts-prod-noctua.conf

@@ -3,11 +3,8 @@
     ServerName {{ noctua_host }}
     ServerAlias {{ noctua_host_alias }}
 
-    ## Setup robots.txt.
-    DocumentRoot /var/www/html
-    Alias /robots.txt /var/www/html/robots.txt
-    RewriteEngine On
-    RewriteRule ^/robots.txt /robots.txt
+    #Do not use permanent for testing Redirect permanent / https://{{noctua_host_alias}}/
+    Redirect / https://{{noctua_host_alias}}/
 
     ## Get aggressive with badly behaving bots.
     RewriteCond %{HTTP_USER_AGENT}  ^.*Adsbot.*$ [OR]
@@ -23,15 +20,6 @@
     RewriteCond %{HTTP_USER_AGENT}  ^.*semrush.*$ [OR]
     RewriteCond %{HTTP_USER_AGENT}  ^.*WhatWeb.*$ [OR]
     RewriteCond %{HTTP_USER_AGENT}  ^.*WhatWeb.*$
-    RewriteRule . - [R=403,L]
+    RewriteRule . - [R=403,L]    
 
-
-    ErrorLog "/var/log/apache2/noctua-error.log"
-    CustomLog "/var/log/apache2/noctua-access.log" common
-
-    ## Proxy.
-    ProxyPreserveHost On
-    ProxyRequests Off
-    ProxyPass / http://noctua:8910/
-    ProxyPassReverse / http://noctua:8910/
 </VirtualHost>