sequenceserver 2.0.0.beta4 → 2.0.0.rc5

data/spec/database_spec.rb

@@ -16,44 +16,6 @@ module SequenceServer
       File.join(database_dir, 'sample')
     end
 
-    let 'database_dir_unformatted' do
-      File.join(database_dir, 'unformatted')
-    end
-
-    let 'fasta_file_prot_seqs' do
-      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.prot.subset.fasta')
-    end
-
-    let 'fasta_file_nucl_seqs' do
-      File.join(database_dir_sample, 'transcripts', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.cdna.subset.fasta')
-    end
-
-    let 'text_file' do
-      File.join(database_dir_sample, 'links.rb')
-    end
-
-    let 'binary_file' do
-      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
-                'Sinvicta2-2-3.prot.subset.fasta.phr')
-    end
-
-    let 'data_for_makeblastdb' do
-      [
-        File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
-                  'Cobs1.4.proteins.fa'),
-        :protein,
-        'Cobs 1.4 proteins',
-        true
-      ]
-    end
-
-    let 'makeblastdb_result_pattern' do
-      File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
-                'Cobs1.4.proteins.fa.*')
-    end
-
     before do
       SequenceServer.init
     end
@@ -64,20 +26,6 @@ module SequenceServer
       Database.clear
     end
 
-    it 'can tell FASTA file' do
-      Database.probably_fasta?(text_file).should be_falsey
-      Database.probably_fasta?(binary_file).should be_falsey
-      Database.probably_fasta?(fasta_file_prot_seqs).should be_truthy
-      Database.probably_fasta?(fasta_file_nucl_seqs).should be_truthy
-    end
-
-    it 'can tell type of sequences in FASTA file' do
-      Database.guess_sequence_type_in_fasta(fasta_file_prot_seqs)
-        .should eq :protein
-      Database.guess_sequence_type_in_fasta(fasta_file_nucl_seqs)
-        .should eq :nucleotide
-    end
-
     it 'can tell NCBI multipart database name' do
       sample_name1 = '/home/ben/pd.ben/sequenceserver/db/nr'
       sample_name2 = '/home/ben/pd.ben/sequenceserver/db/nr.00'
@@ -87,30 +35,6 @@ module SequenceServer
       Database.multipart_database_name?(sample_name3).should be_truthy
     end
 
-    it 'can tell FASTA files that are yet to be made into a BLAST+ database' do
-      SequenceServer.config[:database_dir] = database_dir_unformatted
-      # rubocop:disable Style/RescueModifier
-      Database.scan_databases_dir rescue NO_BLAST_DATABASE_FOUND
-      # rubocop:enable Style/RescueModifier
-      Database.unformatted_fastas.should_not be_empty
-    end
-
-    # it 'can make BLAST+ database from a FASTA file' do
-    #   Database._make_blast_database(*data_for_makeblastdb).should be_truthy
-    #   system "rm #{makeblastdb_result_pattern}"
-    # end
-
-    it 'can make intelligent database name suggestions' do
-      db_name_pairs = [['Si_gnf.fasta', 'Si gnf'],
-                       ['Aech.3.8.cds.fasta', 'Aech 3.8 cds'],
-                       ['Cobs1.4.proteins.fasta', 'Cobs 1.4 proteins'],
-                       ['S_inv.x.small.2.5.nucl.fa', 'S inv x small 2.5 nucl'],
-                       ['Sinvicta2-2-3.prot.fasta', 'Sinvicta 2-2-3 prot']]
-      db_name_pairs.each do |db|
-        Database.make_db_title(db[0]).should eql(db[1])
-      end
-    end
-
     let 'solenopsis_protein_database' do
       path = 'spec/database/sample/proteins/Solenopsis_invicta/'\
              'Sinvicta2-2-3.prot.subset.fasta'

data/spec/makeblastdb_spec.rb

@@ -0,0 +1,121 @@
+require 'spec_helper'
+require 'sequenceserver/database'
+
+# Test Database class.
+module SequenceServer
+  describe 'Database' do
+    let 'root' do
+      __dir__
+    end
+
+    let 'makeblastdb' do
+      SequenceServer.makeblastdb
+    end
+
+    let 'database_dir' do
+      File.join(root, 'database')
+    end
+
+    let 'database_dir_sample' do
+      File.join(database_dir, 'sample')
+    end
+
+    let 'database_dir_v4' do
+      File.join(database_dir, 'v4')
+    end
+
+    let 'database_dir_unformatted' do
+      File.join(database_dir, 'unformatted')
+    end
+
+    let 'database_dir_without_parse_seqids' do
+      File.join(database_dir, 'without_parse_seqids')
+    end
+
+    let 'fasta_file_prot_seqs' do
+      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
+                'Sinvicta2-2-3.prot.subset.fasta')
+    end
+
+    let 'fasta_file_nucl_seqs' do
+      File.join(database_dir_sample, 'transcripts', 'Solenopsis_invicta',
+                'Sinvicta2-2-3.cdna.subset.fasta')
+    end
+
+    let 'text_file' do
+      File.join(database_dir_sample, 'links.rb')
+    end
+
+    let 'binary_file' do
+      File.join(database_dir_sample, 'proteins', 'Solenopsis_invicta',
+                'Sinvicta2-2-3.prot.subset.fasta.phr')
+    end
+
+    let 'data_for_makeblastdb' do
+      [
+        File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
+                  'Cobs1.4.proteins.fa'),
+        :protein,
+        'Cobs 1.4 proteins',
+        true
+      ]
+    end
+
+    let 'makeblastdb_result_pattern' do
+      File.join(database_dir_unformatted, 'Cardiocondyla_obscurior',
+                'Cobs1.4.proteins.fa.*')
+    end
+
+    before do
+      SequenceServer.init
+    end
+
+    it 'can tell FASTA file' do
+      makeblastdb.send(:probably_fasta?, text_file).should be_falsey
+      makeblastdb.send(:probably_fasta?, binary_file).should be_falsey
+      makeblastdb.send(:probably_fasta?, fasta_file_prot_seqs).should be_truthy
+      makeblastdb.send(:probably_fasta?, fasta_file_nucl_seqs).should be_truthy
+    end
+
+    it 'can tell type of sequences in FASTA file' do
+      makeblastdb.send(:guess_sequence_type_in_fasta, fasta_file_prot_seqs).should eq :protein
+      makeblastdb.send(:guess_sequence_type_in_fasta, fasta_file_nucl_seqs).should eq :nucleotide
+    end
+
+    it 'can tell FASTA files that are yet to be made into a BLAST+ database' do
+      makeblastdb.instance_variable_set(:@database_dir, database_dir_unformatted)
+      makeblastdb.scan.should be_truthy
+    end
+
+    it 'can tell databases that require reformatting' do
+      # Control: shouldn't report sample v5 databases created using -parse_seqids
+      # as requiring reformatting.
+      makeblastdb.instance_variable_set(:@database_dir, database_dir_sample)
+      makeblastdb.scan.should be_falsey
+
+      # v4 databases require reformatting.
+      makeblastdb.instance_variable_set(:@database_dir, database_dir_v4)
+      makeblastdb.scan.should be_truthy
+
+      # non -parse_seqids databases require reformatting.
+      makeblastdb.instance_variable_set(:@database_dir, database_dir_without_parse_seqids)
+      makeblastdb.scan.should be_truthy
+    end
+
+    # it 'can make BLAST+ database from a FASTA file' do
+    #   Database._make_blast_database(*data_for_makeblastdb).should be_truthy
+    #   system "rm #{makeblastdb_result_pattern}"
+    # end
+
+    it 'can make intelligent database name suggestions' do
+      db_name_pairs = [['Si_gnf.fasta', 'Si gnf'],
+                       ['Aech.3.8.cds.fasta', 'Aech 3.8 cds'],
+                       ['Cobs1.4.proteins.fasta', 'Cobs 1.4 proteins'],
+                       ['S_inv.x.small.2.5.nucl.fa', 'S inv x small 2.5 nucl'],
+                       ['Sinvicta2-2-3.prot.fasta', 'Sinvicta 2-2-3 prot']]
+      db_name_pairs.each do |db|
+        makeblastdb.send(:make_db_title, db[0]).should eql(db[1])
+      end
+    end
+  end
+end

data/views/layout.erb

@@ -29,7 +29,7 @@
       <a
         class="navbar-brand"
         href="http://sequenceserver.com" target="_blank">
-        SequenceServer
+        <img class="logo" src="SequenceServer_logo.png" alt="sequenceserver_logo">
         <small>
           <%= SequenceServer::VERSION %>
         </small>
@@ -74,6 +74,10 @@
           href='http://www.sequenceserver.com'>
           <%=
             quote = [
+              "Run BLAST on local computer.",
+              "Custom BLAST search.",
+              "Install blast on Mac.",
+              "Perform BLAST analyses with SequenceServer.",
               "Custom BLAST web interface by SequenceServer.",
               "SequenceServer: Local BLAST with bespoke html interface.",
               "Set up custom BLAST interface with SequenceServer.",

metadata

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: sequenceserver
 version: !ruby/object:Gem::Version
-  version: 2.0.0.beta4
+  version: 2.0.0.rc5
 platform: ruby
 authors:
 - Anurag Priyam
 - Ben J Woodcroft
 - Vivek Rai
 - Yannick Wurm
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2019-12-13 00:00:00.000000000 Z
+date: 2020-06-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: json_pure
@@ -247,6 +247,7 @@ files:
 - ".bootstrap/config.json"
 - ".codeclimate.yml"
 - ".csslintrc"
+- ".dockerignore"
 - ".eslintignore"
 - ".eslintrc.json"
 - ".gitignore"
@@ -284,6 +285,7 @@ files:
 - lib/sequenceserver/job_remover.rb
 - lib/sequenceserver/links.rb
 - lib/sequenceserver/logger.rb
+- lib/sequenceserver/makeblastdb.rb
 - lib/sequenceserver/pool.rb
 - lib/sequenceserver/report.rb
 - lib/sequenceserver/routes.rb
@@ -292,6 +294,7 @@ files:
 - lib/sequenceserver/sys.rb
 - lib/sequenceserver/version.rb
 - package.json
+- public/SequenceServer_logo.png
 - public/config.js
 - public/css/fonts.css
 - public/css/grapher.css
@@ -315,18 +318,23 @@ files:
 - public/fonts/fontawesome-webfont.woff2
 - public/js/alignment_exporter.js
 - public/js/circos.js
+- public/js/download_fasta.js
 - public/js/error_modal.js
 - public/js/exporter.js
 - public/js/grapher.js
+- public/js/hit.js
 - public/js/hits_overview.js
 - public/js/hsp.js
+- public/js/jquery_world.js
 - public/js/kablammo.js
 - public/js/kablammo/alignment_viewer.js
 - public/js/length_distribution.js
+- public/js/query.js
 - public/js/report.js
 - public/js/search.js
 - public/js/sequence.js
-- public/js/sequenceserver.js
+- public/js/sequence_modal.js
+- public/js/sidebar.js
 - public/js/svgExporter.js
 - public/js/utils.js
 - public/js/visualisation_helpers.js
@@ -3772,45 +3780,95 @@ files:
 - spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsd
 - spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsi
 - spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsq
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ndb
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog
-- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd
-- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nos
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.not
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.ntf
+- spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nto
 - spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt
 - spec/database/sample/links.rb
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pdb
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog
-- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd
-- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pos
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pot
 - spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.ptf
+- spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pto
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pdb
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog
-- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd
-- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pos
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pot
 - spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.ptf
+- spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pto
 - spec/database/sample/proteins/uniprot/URL
 - spec/database/sample/si_uniprot_idmap.yml
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ndb
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog
-- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd
-- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nos
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.not
 - spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.ntf
+- spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nto
 - spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq
+- spec/database/v4/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt
+- spec/database/v4/links.rb
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phi
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi
+- spec/database/v4/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi
+- spec/database/v4/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq
+- spec/database/v4/proteins/uniprot/URL
+- spec/database/v4/si_uniprot_idmap.yml
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhd
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhi
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi
+- spec/database/v4/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq
 - spec/database/without_parse_seqids/without_parse_seqids.fa
 - spec/database/without_parse_seqids/without_parse_seqids.fa.phr
 - spec/database/without_parse_seqids/without_parse_seqids.fa.pin
@@ -3937,6 +3995,7 @@ files:
 - spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml
 - spec/download_helper.rb
 - spec/empty_config.yml
+- spec/makeblastdb_spec.rb
 - spec/routes_spec.rb
 - spec/sample.conf
 - spec/sequence_spec.rb
@@ -4016,9 +4075,10 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: 1.3.1
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.5.2.3
-signing_key: 
+rubyforge_project:
+rubygems_version: 2.7.6.2
+signing_key:
 specification_version: 4
 summary: BLAST search made easy!
 test_files: []
+...