Merge branch 'lis' of https://github.com/legumeinfo/sequenceserver in…

…to lis

.codeclimate.yml

@@ -7,25 +7,21 @@ checks:
   method-count:
     config:
       threshold: 50
-engines:
+plugins:
   rubocop:
     enabled: true
   eslint:
     enabled: true
-  csslint:
+  stylelint:
     enabled: true
-ratings:
-  paths:
-  - "**.rb"
-  - "**.js"
-  - "**.css"
-exclude_paths:
+exclude_patterns:
+- public/css/sequenceserver.min.css
+- public/sequenceserver-*.min.js
 - public/js/sequence.js
-- public/sequenceserver.min.css
-- public/sequenceserver.min.js
 - public/js/kablammo/*
 - public/vendor/**/*
 - node_modules/**/*
 - public/shims/**/*
 - public/vendor/*
 - spec/**/*
+- coverage/

.eslintrc.json

@@ -2,7 +2,8 @@
     "env": {
         "browser": true,
         "commonjs": true,
-        "es6": true
+        "es6": true,
+        "jquery": true
     },
     "extends": "eslint:recommended",
     "parserOptions": {
@@ -31,6 +32,13 @@
         "semi": [
             "error",
             "always"
+        ],
+        "no-unused-vars": [
+            "error",
+            {"args": "none"}
         ]
+    },
+    "globals": {
+        "d3": true
     }
-}
+}

.github/workflows/deploy.yml

@@ -0,0 +1,34 @@
+on:
+  push:
+    tags:
+      - '**'
+
+jobs:
+  build-and-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2 
+
+      - name: Add SSH key
+        env:
+            SSH_AUTH_SOCK: /tmp/ssh_agent.sock
+        run: |
+            chmod 700 ${HOME}
+            mkdir -m 700 -p ${HOME}/.ssh
+            echo '${{ secrets.DOCKER_SSH_CONFIG }}' > ${HOME}/.ssh/config
+            echo '${{ secrets.DOCKER_SSH_KNOWN_HOSTS }}' >> ${HOME}/.ssh/known_hosts
+            chmod 400 ${HOME}/.ssh/*
+            ssh-agent -a ${SSH_AUTH_SOCK} > /dev/null   
+            ssh-add - <<< '${{ secrets.DOCKER_HOST_SSH_PRIVATE_KEY }}'
+  
+      - name: Build container image and deploy image
+        env:
+            SSH_AUTH_SOCK: /tmp/ssh_agent.sock
+            DOCKER_BUILDKIT: 1
+            DOCKER_HOST: ssh://docker
+        run: docker compose up --detach --build --force-recreate --renew-anon-volumes
+

.mailmap

@@ -3,3 +3,10 @@ Ben J Woodcroft <donttrustben@gmail.com> Ben Woodcroft <donttrustben@gmail.com>
 Ben J Woodcroft <donttrustben@gmail.com> Ben J Woodcroft <donttrustben@gmail.com>
 Ben J Woodcroft <donttrustben@gmail.com> Ben J Woodcroft <gmail.com after donttrustben>
 Ben J Woodcroft <donttrustben@gmail.com> Ben J. Woodcroft <donttrustben near gmail.com>
+Hiten Chowdhary <hiten.iitkgp@gmail.com> aniarya82 <hiten.iitkgp@gmail.com>
+Esteban Gomez <eagomezc@unal.edu.co> eagomezc <eagomezc@unal.edu.co>
+Iwo Pieniak <ivo.pieniak@gmail.com> ivopieniak <ivo.pieniak@gmail.com>
+Iwo Pieniak <ivo.pieniak@gmail.com> ivopieniak <ivopieniak@gmail.com>
+Emeline Favreau <emeline.favreau@qmul.ac.uk> EmelineAurore <emeline.favreau@qmul.ac.uk>
+Lawrence <enjoyyourcopepods@gmx.com> emil <enjoyyourcopepods@gmx.com>
+Neel Kamath <neelkamathonline@gmail.com> neelkamath <neelkamath@icloud.com>

.rspec

@@ -1,3 +1,4 @@
 --color
 --backtrace
 --require spec_helper.rb
+--pattern="spec/*_spec.rb","spec/blast_versions/blast_2.9.0/*.rb"

.stylelintrc.json

@@ -0,0 +1,6 @@
+{
+  "extends": "stylelint-config-standard",
+  "rules": {
+      "no-descending-specificity": null
+  }
+}

.travis.yml

@@ -2,7 +2,7 @@ language: ruby
 
 rvm:
   - 2.3
-  - 2.5
+  # - 2.5
 
 branches:
   only:
@@ -24,12 +24,12 @@ before_install:
   - wget -c "https://github.com/mozilla/geckodriver/releases/download/v0.24.0/geckodriver-v0.24.0-linux64.tar.gz" && tar xvf geckodriver-*.tar.gz -C bin
   # Download codeclimate test reporter to bin and make it executable
   - wget -c "https://codeclimate.com/downloads/test-reporter/test-reporter-latest-linux-amd64" -O bin/cc-test-reporter && chmod +x bin/cc-test-reporter
-  # Download and extract NCBI BLAST+ 2.10.0
-  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
+  # Download and extract NCBI BLAST+ 2.12.0
+  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz" && tar xvf ncbi-blast-*.tar.gz
   # Conclude installation by adding opt/bin/ containing codeclimate test reporter
-  # and geckodriver, and opt/ncbi-blast-2.10.0+/bin containing BLAST+ binaries to
+  # and geckodriver, and opt/ncbi-blast-2.12.0+/bin containing BLAST+ binaries to
   # PATH.
-  - export PATH="$PWD/bin:$PWD/ncbi-blast-2.10.0+/bin:$PATH"
+  - export PATH="$PWD/bin:$PWD/ncbi-blast-2.12.0+/bin:$PATH"
   # Reset working directory or subsequent steps may fail.
   - cd ..
   # Update bundler. Travis was using bundler 1.16.2 at the time of this writing
@@ -55,20 +55,20 @@ after_script:
       cc-test-reporter after-build --exit-code $TRAVIS_TEST_RESULT;
     fi
 
-jobs:
-  include:
-  # Each script listed below is automatically run by Travis in parallel, and only
-  # against Ruby 2.3 (because it is listed first in the rvm key), and after the
-  # main test stage. We use a glob pattern here instead of specifying just the
-  # directory name because capybara spec files in subfolders don't end with
-  # _spec.rb.
-  - stage: compatibility
-    script: bundle exec rspec spec/blast_versions/diamond_0.9.24/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.2.30/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.2.31/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.3.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.4.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.5.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.6.0/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.7.1/*
-  - script: bundle exec rspec spec/blast_versions/blast_2.8.1/*
+# jobs:
+#   include:
+#   # Each script listed below is automatically run by Travis in parallel, and only
+#   # against Ruby 2.3 (because it is listed first in the rvm key), and after the
+#   # main test stage. We use a glob pattern here instead of specifying just the
+#   # directory name because capybara spec files in subfolders don't end with
+#   # _spec.rb.
+#   - stage: compatibility
+#     script: bundle exec rspec spec/blast_versions/diamond_0.9.24/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.2.30/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.2.31/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.3.0/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.4.0/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.5.0/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.6.0/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.7.1/*
+#   - script: bundle exec rspec spec/blast_versions/blast_2.8.1/*

Dockerfile

@@ -1,6 +1,6 @@
 # Build variables. These need to be declared befored the first FROM
 # for the variables to be accessible in FROM instruction.
-ARG BLAST_VERSION=2.10.0
+ARG BLAST_VERSION=2.12.0
 
 ## Stage 1: gem dependencies.
 FROM ruby:2.7-slim-buster AS builder

README.md

@@ -1,10 +1,10 @@
 [![gem version](https://img.shields.io/badge/version-1.0.x%20(old%20stable)-green.svg)](http://rubygems.org/gems/sequenceserver)
-[![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png?branch=1.0.x)](https://travis-ci.org/wurmlab/sequenceserver)
+[![build status](https://www.travis-ci.com/wurmlab/sequenceserver.svg?branch=1.0.x)](https://travis-ci.com/wurmlab/sequenceserver)
 [![total downloads](http://ruby-gem-downloads-badge.herokuapp.com/sequenceserver?type=total&color=brightgreen)](http://rubygems.org/gems/sequenceserver)
 [![gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/wurmlab/sequenceserver)
 
 **Beta version:** 
-[![new gem version](https://img.shields.io/badge/version-2.0%20(beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://secure.travis-ci.org/wurmlab/sequenceserver.png)](https://travis-ci.org/wurmlab/sequenceserver)
+[![new gem version](https://img.shields.io/badge/version-2.0%20(beta)-yellowgreen.svg)](http://rubygems.org/gems/sequenceserver) **GitHub Master:** [![build status](https://www.travis-ci.com/wurmlab/sequenceserver.svg?branch=master)](https://travis-ci.com/wurmlab/sequenceserver)
 
 
 
@@ -24,10 +24,10 @@ If you use SequenceServer, please cite:
   (2019).](https://doi.org/10.1093/molbev/msz185)
 
 
-## Stable (version 1.0.11)
+## Stable (version 1.0.14)
 
-- Release date: June 2017
-- Works with BLAST 2.2.30
+- Release date: May 2020
+- Works with BLAST 2.2.30 and higher
 
 ### Installation
 
@@ -120,7 +120,7 @@ To run all tests in a single file:
 
 To run all tests:
 
-    bundle exec rspec spec/**/*spec*
+    bundle exec rspec
 
 #### Getting code merged
 

bin/sequenceserver

@@ -308,34 +308,6 @@ begin
             exit! unless set?
           end
         end
-      rescue SequenceServer::INCOMPATIBLE_BLAST_DATABASES => e
-        unless list_databases? || make_blast_databases?
-          # Print error raised.
-          puts
-          puts e
-
-          # Offer user to format the FASTA files.
-          database_dir = SequenceServer.config[:database_dir]
-          puts
-          puts <<~MSG
-            Incompatible databases can cause BLAST searches and other features of
-            SequenceServer to fail unexpectedly.
-            You can view incompatible databases and choose to reformat them below.
-            Alternatively, please remove them from databases directory.
-
-            View incompatible databases? [y/n] (Default: y).
-          MSG
-          puts
-          print '>> '
-          response = STDIN.gets.to_s.strip
-          unless response =~ /^[n]$/i
-            reformatted = SequenceServer.makeblastdb.reformat
-            exit! if reformatted.empty? && !set?
-            redo unless set?
-          else
-            exit! unless set?
-          end
-        end
       rescue SequenceServer::ENOENT,
         SequenceServer::CONFIG_FILE_ERROR,
         SequenceServer::BLAST_DATABASE_ERROR,
@@ -382,8 +354,28 @@ begin
 
       if make_blast_databases?
         if SequenceServer.makeblastdb.scan
-          SequenceServer.makeblastdb.run
-        else
+          puts
+          puts <<~MSG
+          SequenceServer has scanned your databases directory and will now offer
+          to convert FASTA files into BLAST databases. It will also offer to
+          reformat any old-format BLAST databases and those created without
+          the -parse_seqids option of makeblastdb (-parse_seqids option is
+          required for sequence retrieval to correctly work).
+
+          Note that reformatting process can be slow large BLAST databases and
+          fail if sequence identifiers are longer than 50 characters. While we
+          exepect the reformatting process to work in most other cases, things
+          can inevitably go wrong. Thus, please back up your databases before
+          reformatting and post any issues to our Google Group/GitHub so that
+          we can all learn from it.
+
+          Proceed? [y/n] (Default: y).
+          MSG
+          puts
+          print '>> '
+          response = STDIN.gets.to_s.strip
+          SequenceServer.makeblastdb.run unless response =~ /^[n]$/i
+          else
           puts "All FASTA files in #{SequenceServer.config[:database_dir]} " \
                'are formatted.'
         end

db/Dockerfile

@@ -1,4 +1,4 @@
-FROM ncbi/blast:2.10.0
+FROM ncbi/blast:2.12.0
 
 WORKDIR /db
 VOLUME ["/db"]

lib/sequenceserver.rb

@@ -5,11 +5,7 @@
 # Top level module / namespace.
 module SequenceServer
   # The default version of BLAST that will be downloaded and configured for use.
-  BLAST_VERSION = '2.10.0+'.freeze
-  # The minimum version of BLAST that SequenceServer is happy to run with. This
-  # is for compatiblity with older database formats. Users will download BLAST
-  # themselves.
-  MIN_BLAST_VERSION = '2.9.0+'.freeze
+  BLAST_VERSION = '2.12.0+'.freeze
 
   # Default location of configuration file.
   DEFAULT_CONFIG_FILE = '~/.sequenceserver.conf'.freeze
@@ -78,9 +74,9 @@ def init(config = {})
       Thread.abort_on_exception = true if development?
 
       # Now locate binaries, scan databases directory, require any plugin files.
+      load_extension
       init_binaries
       init_database
-      load_extension
 
       # The above methods validate bin dir, database dir, and path to plugin
       # files. Port and host settings don't need to be validated: if running
@@ -141,7 +137,8 @@ def on_start
         puts "     -  http://#{ip_address}:#{config[:port]}"
         puts "     -  http://#{hostname}:#{config[:port]}" if hostname
         puts '   To share your setup with anyone in the world, ask your IT team'
-        puts '   for a public IP address.'
+        puts '   for a public IP address or consider the SequenceServer cloud'
+        puts '   hosting service: https://sequenceserver.com/cloud'
         puts '   To disable sharing, set :host: key in config file to 127.0.0.1'
         puts '   and restart server.'
       end
@@ -205,12 +202,19 @@ def init_database
 
       makeblastdb.scan
       fail NO_BLAST_DATABASE_FOUND, config[:database_dir] if !makeblastdb.any_formatted?
-      fail INCOMPATIBLE_BLAST_DATABASES, config[:database_dir] if makeblastdb.any_incompatible?
 
       Database.collection = makeblastdb.formatted_fastas
       Database.each do |database|
-        logger.debug("Found #{database.type} database '#{database.title}'" \
-                     " at '#{database.name}'")
+        logger.debug "Found #{database.type} database '#{database.title}' at '#{database.path}'"
+        if database.non_parse_seqids?
+          logger.warn "Database '#{database.title}' was created without using the" \
+                      ' -parse_seqids option of makeblastdb. FASTA download will' \
+                      " not work correctly (path: '#{database.path}')."
+        elsif database.v4?
+          logger.warn "Database '#{database.title}' is of older format. Mixing" \
+                      ' old and new format databases can be problematic' \
+                      "(path: '#{database.path}')."
+        end
       end
     end
 
@@ -245,7 +249,7 @@ def assert_blast_installed_and_compatible
       end
       version = out.split[1]
       fail BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE if version.empty?
-      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, MIN_BLAST_VERSION)
+      fail BLAST_NOT_COMPATIBLE, version unless is_compatible(version, BLAST_VERSION)
     end
 
     def server_url

lib/sequenceserver/api_errors.rb

@@ -41,7 +41,11 @@ def title
     def message
       <<~MSG
         Looks like there's a problem with one of the query sequences, selected
-        databases, or advanced parameters.
+        databases, or advanced parameters. Details of the error are included
+        below. Please ask on our
+        <a href="https://github.com/wurmlab/sequenceserver/issues" target="_blank">issue tracker</a>
+        or on our <a href="https://groups.google.com/g/sequenceserver">forum</a> if you are
+        not sure what the error message means, or if the error message is just a number.
       MSG
     end
 

lib/sequenceserver/blast/constants.rb

@@ -2,7 +2,7 @@
 module SequenceServer
   # Define constanst used by BLAST module.
   module BLAST
-    ERROR_LINE = /Error:\s(.*)/
+    ERROR_LINE = /Error:\s(.*)/i
 
     ALGORITHMS = %w[blastn blastp blastx tblastn tblastx].freeze