From b5fa1318e10edf0b30cd76ae251ad700c3796c04 Mon Sep 17 00:00:00 2001
From: adf <adf@ncgr.org>
Date: Tue, 24 Sep 2024 17:14:02 -0400
Subject: [PATCH] tweaks for a version of sequence server that the mines can
 post sequences to

---
 .env                         |  3 ++-
 compose.yml                  |  2 +-
 db/Dockerfile                |  2 +-
 lib/sequenceserver/config.rb |  2 +-
 lib/sequenceserver/links.rb  | 14 ++++++++++----
 lib/sequenceserver/routes.rb |  2 +-
 public/js/form.js            |  3 +--
 7 files changed, 17 insertions(+), 11 deletions(-)

diff --git a/.env b/.env
index 514542da8..f0fe340b7 100644
--- a/.env
+++ b/.env
@@ -1 +1,2 @@
-COMPOSE_PROJECT_NAME=lis-blast
+COMPOSE_PROJECT_NAME=all-genera-blast3
+REVERSE_PROXY_PORT=8010
diff --git a/compose.yml b/compose.yml
index bcb20820d..c737403fe 100644
--- a/compose.yml
+++ b/compose.yml
@@ -14,4 +14,4 @@ services:
     healthcheck:
       test: ["CMD-SHELL", "{ curl -qo /dev/null http://localhost:4567/searchdata.json || exit 1; } && [ $$(ps -p $$(pgrep --parent 1 --ful sequenceserver) -o rss=) -lt 4000000 ] || kill 1"]
     ports:
-      - "4567:4567"
+      - "${REVERSE_PROXY_PORT}:4567"
diff --git a/db/Dockerfile b/db/Dockerfile
index f1e71850c..ec4e40ab4 100644
--- a/db/Dockerfile
+++ b/db/Dockerfile
@@ -1,7 +1,6 @@
 FROM ncbi/blast-static:2.14.1
 
 WORKDIR /db
-VOLUME ["/db"]
 
 ENV DATA_STORE=https://data.legumeinfo.org
 RUN printf '#!/bin/bash\nset -o pipefail -o errexit -o nounset; curl ${DATA_STORE}/${1} | gzip -dc | makeblastdb -parse_seqids -hash_index -dbtype ${2} -taxid ${3} -title "${4}" -out $(basename ${1#.f*.gz})\n' > /usr/local/bin/mkblastdb \
@@ -109,3 +108,4 @@ RUN mkblastdb Vigna/angularis/annotations/Gyeongwon.gnm3.ann1.3Nz5/vigan.Gyeongw
 RUN mkblastdb Vigna/radiata/annotations/VC1973A.gnm7.ann1.RWBG/vigra.VC1973A.gnm7.ann1.RWBG.protein.faa.gz prot 157791 'Vigna radiata VC1973A v7.1 proteins'
 RUN mkblastdb Vigna/unguiculata/annotations/IT97K-499-35.gnm1.ann2.FD7K/vigun.IT97K-499-35.gnm1.ann2.FD7K.protein_primary.faa.gz prot 3917 'Vigna unguiculata IT97K-499-35 v1.2 proteins'
 
+VOLUME ["/db"]
diff --git a/lib/sequenceserver/config.rb b/lib/sequenceserver/config.rb
index 297645ef8..1e8a3c3cd 100644
--- a/lib/sequenceserver/config.rb
+++ b/lib/sequenceserver/config.rb
@@ -130,7 +130,7 @@ def defaults
           }
         },
         num_threads: 1,
-        num_jobs: 1,
+        num_jobs: 5,
         job_lifetime: 43_200,
         # Set cloud_share_url to 'disabled' to disable the cloud sharing feature
         cloud_share_url: 'https://share.sequenceserver.com/api/v1/shared-job',
diff --git a/lib/sequenceserver/links.rb b/lib/sequenceserver/links.rb
index 3dc228714..dcfbfc11b 100644
--- a/lib/sequenceserver/links.rb
+++ b/lib/sequenceserver/links.rb
@@ -87,8 +87,10 @@ def jbrowse
       end
 
       # Prepare other fields besides sessionTracks
-      locStart = coordinates[1][0].to_s()
-      locEnd = coordinates[1][1].to_s()
+      #locStart = coordinates[1][0].to_s()
+      #locEnd = coordinates[1][1].to_s()
+      locStart = hsps[0].sstart.to_s()
+      locEnd = hsps[0].send.to_s()
       assembly = id.match('^.+gnm\d+')[0]
       tracks = 'sequenceserver_track'
 
@@ -134,8 +136,12 @@ def jbrowse
       sessionTracks << ']}}]'
 
       # Assemble the JBrowse link URL from the fields above
-      url = 'https://dev.peanutbase.org/tools/jbrowse2/'
-      url << '?loc=' + id + ':' + locStart + '-' + locEnd
+      url = 'https://all-genera.lis.ncgr.org/tools/jbrowse2/'
+      if locStart <= locEnd
+        url << '?loc=' + id + ':' + locStart + '-' + locEnd
+      else
+        url << '?loc=' + id + ':' + locEnd + '-' + locStart
+      end
       url << '&assembly=' + assembly
       url << '&tracks=' + tracks
       url << '&sessionTracks=' + sessionTracks
diff --git a/lib/sequenceserver/routes.rb b/lib/sequenceserver/routes.rb
index 9effe1966..5873118cd 100644
--- a/lib/sequenceserver/routes.rb
+++ b/lib/sequenceserver/routes.rb
@@ -66,7 +66,7 @@ class Routes < Sinatra::Base
         secret: ENV.fetch('SESSION_SECRET') { SecureRandom.alphanumeric(64) }
       )
 
-      use Rack::Csrf, raise: true, skip: ['POST:/cloud_share']
+      #use Rack::Csrf, raise: true, skip: ['POST:/cloud_share']
     end
 
     unless ENV['SEQUENCE_SERVER_COMPRESS_RESPONSES'] == 'false'
diff --git a/public/js/form.js b/public/js/form.js
index 2ab4b3e34..ff4602ddb 100644
--- a/public/js/form.js
+++ b/public/js/form.js
@@ -203,7 +203,6 @@ export class Form extends Component {
                 </div>
 
                 <form id="blast" ref={this.formRef} onSubmit={this.handleFormSubmission}>
-                    <input type="hidden" name="_csrf" value={document.querySelector('meta[name="_csrf"]').content} />
                     <div className="px-4">
                         <SearchQueryWidget ref="query" onSequenceTypeChanged={this.handleSequenceTypeChanged} onSequenceChanged={this.handleSequenceChanged}/>
 
@@ -305,4 +304,4 @@ class MixedNotification extends Component {
             </div>
         );
     }
-}
\ No newline at end of file
+}