sequenceserver 3.0.1 → 3.1.1

data/lib/sequenceserver/makeblastdb-modified-with-cache.rb

@@ -1,345 +0,0 @@
-require 'find'
-require 'forwardable'
-
-module SequenceServer
-  # Smart `makeblastdb` wrapper: recursively scans database directory determining
-  # which files need to be formatted or re-formatted.
-  #
-  # Example usage:
-  #
-  #   makeblastdb = MAKEBLASTDB.new(database_dir)
-  #   makeblastdb.scan && makeblastdb.run
-  #
-  class MAKEBLASTDB
-    extend Forwardable
-
-    def_delegators SequenceServer, :config, :sys, :logger
-
-    def initialize(database_dir)
-      @database_dir = database_dir
-    end
-
-    attr_reader :database_dir
-    attr_reader :formatted_fastas
-    attr_reader :fastas_to_format
-    attr_reader :fastas_to_reformat
-
-    # Scans the database directory to determine which FASTA files require
-    # formatting or re-formatting.
-    #
-    # Returns `true` if there are files to (re-)format, `false` otherwise.
-    def scan
-      # We need to know the list of formatted FASTAs as reported by blastdbcmd
-      # first. This is required to determine both unformatted FASTAs and those
-      # that require reformatting.
-      @formatted_fastas = []
-      determine_formatted_fastas
-
-      # Now determine FASTA files that are unformatted or require reformatting.
-      @fastas_to_format = []
-      determine_unformatted_fastas
-      @fastas_to_reformat = []
-      determine_fastas_to_reformat
-
-      # Return true if there are files to be (re-)formatted or false otherwise.
-      !@fastas_to_format.empty? || !@fastas_to_reformat.empty?
-    end
-
-    # Returns true if at least one database in database directory is formatted.
-    def any_formatted?
-      !@formatted_fastas.empty?
-    end
-
-    # Returns true if there is at least one unformatted FASTA in the databases
-    # directory.
-    def any_unformatted?
-      !@fastas_to_format.empty?
-    end
-
-    # Returns true if the databases directory contains one or more incompatible
-    # databases.
-    #
-    # Note that it is okay to only use V4 databases or only V5 databases.
-    # Incompatibility arises when they are mixed.
-    def any_incompatible?
-      return false if @formatted_fastas.all? { |ff| ff.v4? || ff.alias? }
-      return false if @formatted_fastas.all? { |ff| ff.v5? || ff.alias? }
-      true
-    end
-
-    # Runs makeblastdb on each file in `@fastas_to_format` and
-    # `@fastas_to_reformat`. Will do nothing unless `#scan`
-    # has been run before.
-    def run
-      format
-      reformat
-    end
-
-    # Format any unformatted FASTA files in database directory. Returns Array
-    # of files that were formatted.
-    def format
-      # Make the intent clear as well as ensure the program won't crash if we
-      # accidentally call format before calling scan.
-      return unless @fastas_to_format
-      @fastas_to_format.select do |path, title, type|
-        make_blast_database('format', path, title, type)
-      end
-    end
-
-    # Re-format databases that require reformatting. Returns Array of files
-    # that were reformatted.
-    def reformat
-      # Make the intent clear as well as ensure the program won't crash if
-      # we accidentally call reformat before calling scan.
-      return unless @fastas_to_reformat
-      @fastas_to_reformat.select do |path, title, type, non_parse_seqids|
-        make_blast_database('reformat', path, title, type, non_parse_seqids)
-      end
-    end
-
-    private
-
-    # Determines which FASTA files in the database directory are already
-    # formatted. Adds to @formatted_fastas.
-    def determine_formatted_fastas
-      blastdbcmd.each_line do |line|
-        path, *rest = line.chomp.split("\t")
-        next if multipart_database_name?(path)
-        rest << get_categories(path)
-        @formatted_fastas << Database.new(path, *rest)
-      end
-    end
-
-    # Determines which FASTA files in the database directory require
-    # reformatting. Adds to @fastas_to_format.
-    def determine_fastas_to_reformat
-      @formatted_fastas.each do |ff|
-        if ff.v4? || ff.non_parse_seqids?
-          @fastas_to_reformat << [ff.path, ff.title, ff.type, ff.non_parse_seqids?]
-        end
-      end
-    end
-
-    # Determines which FASTA files in the database directory are
-    # unformatted. Adds to @fastas_to_format.
-    def determine_unformatted_fastas
-      # Add a trailing slash to database_dir - Find.find doesn't work as
-      # expected without the trailing slash if database_dir is a symlink
-      # inside a docker container.
-      Find.find(database_dir + '/') do |path|
-        next if File.directory?(path)
-        next unless probably_fasta?(path)
-        next if @formatted_fastas.any? { |f| f[0] == path }
-
-        @fastas_to_format << [path,
-          make_db_title(path),
-          guess_sequence_type_in_fasta(path)]
-      end
-    end
-
-    # Runs `blastdbcmd` to determine formatted FASTA files in the database
-    # directory. Returns the output of `blastdbcmd`. This method is called
-    # by `determine_formatted_fastas`.
-    def blastdbcmd
-      # calculate checksum of database directory
-      current_db_checksum = Zlib::crc32(Dir.glob(File.join(config[:database_dir], '/**/*')).map {
-        |path| path.to_s + "_" + File.mtime(path).to_s + "_" + File.size(path).to_s
-      }.to_s)
-
-      checksum_path = config[:database_dir].chomp('/') + '.checksum'
-      index_path    = config[:database_dir].chomp('/') + '.index'
-
-      if File.exists?(checksum_path)
-        if current_db_checksum == File.read(checksum_path).to_i # db directory hasn't changed
-          if File.exists?(index_path) # lets use existing index
-            logger.info "Using existing database index: #{index_path}"
-            return File.read(index_path)
-          end
-        end
-      end rescue logger.error "Could not read: #{checksum_path} or #{index_path}"
-
-      # database directory has changed, or index file doesn't exist
-      # thus we run blastdbcmd to get formatted FASTA files
-      logger.info "Scanning for BLAST databases & creating index"
-      cmd = "blastdbcmd -recursive -list #{config[:database_dir]}" \
-            ' -list_outfmt "%f	%t	%p	%n	%l	%d	%v"'
-      out, err = sys(cmd, path: config[:bin])
-      errpat = /BLAST Database error/
-      fail BLAST_DATABASE_ERROR.new(cmd, err) if err.match(errpat)
-
-      # write checksum and index to file
-      File.open(checksum_path, 'w') { |f| f.write(current_db_checksum) } rescue
-         logger.error "Could not write database checksum to file" + checksum_path
-      File.open(index_path, 'w') { |f| f.write(out) } rescue
-         logger.error "Could not write database index to file" + index_path
-
-      return out
-    rescue CommandFailed => e
-      fail BLAST_DATABASE_ERROR.new(cmd, e.stderr)
-    end
-
-    # Create BLAST database, given FASTA file and sequence type in FASTA file.
-    def make_blast_database(action, file, title, type, non_parse_seqids = false)
-      return unless make_blast_database?(action, file, type)
-      title = confirm_database_title(title)
-      extract_fasta(file) unless File.exist?(file)
-      taxonomy = taxid_map(file, non_parse_seqids) || taxid
-      _make_blast_database(file, type, title, taxonomy)
-    end
-
-    # Show file path and guessed sequence type to the user and obtain a y/n
-    # response.
-    #
-    # Returns true if the user entered anything but 'n' or 'N'.
-    def make_blast_database?(action, file, type)
-      puts
-      puts
-      puts "FASTA file to #{action}: #{file}"
-      puts "FASTA type: #{type}"
-      print 'Proceed? [y/n] (Default: y): '
-      response = STDIN.gets.to_s.strip
-      !response.match(/n/i)
-    end
-
-    # Show the database title that we are going to use to the user for
-    # confirmation.
-    #
-    # Returns user input if any. Auto-determined title otherwise.
-    def confirm_database_title(default)
-      print "Enter a database title or will use '#{default}': "
-      from_user = STDIN.gets.to_s.strip
-      from_user.empty? && default || from_user
-    end
-
-    # Check if a '.taxid_map.txt' file exists. If not, try getting it
-    # using blastdbcmd.
-    def taxid_map(db, non_parse_seqids)
-      return if non_parse_seqids
-      taxid_map = db.sub(/#{File.extname(db)}$/, '.taxid_map.txt')
-      extract_taxid_map(db, taxid_map) if !File.exist?(taxid_map)
-      "-taxid_map #{taxid_map}" if !File.zero?(taxid_map)
-    end
-
-    # Get taxid from the user. Returns user input or 0.
-    #
-    # Using 0 as taxid is equivalent to not setting taxid for the database
-    # that will be created.
-    def taxid
-      default = 0
-      print 'Enter taxid (optional): '
-      user_response = STDIN.gets.strip
-      "-taxid #{user_response.empty? && default || Integer(user_response)}"
-    rescue ArgumentError # presumably from call to Interger()
-      puts 'taxid should be a number'
-      retry
-    end
-
-    def _make_blast_database(file, type, title, taxonomy)
-      cmd = "makeblastdb -parse_seqids -hash_index -in '#{file}'" \
-            " -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
-            " #{taxonomy}"
-      out, err = sys(cmd, path: config[:bin])
-      puts out.strip
-      puts err.strip
-      return true
-    rescue CommandFailed => e
-      puts <<~MSG
-        Could not create BLAST database for: #{file}
-        Tried: #{cmd}
-        stdout: #{e.stdout}
-        stderr: #{e.stderr}
-      MSG
-      exit!
-    end
-
-    # Extract FASTA file from BLAST database.
-    #
-    # Invoked while reformatting a BLAST database if the corresponding
-    # FASTA file does not exist.
-    def extract_fasta(db)
-      puts
-      puts 'Extracting sequences ...'
-      cmd = "blastdbcmd -entry all -db #{db}"
-      sys(cmd, stdout: db, path: config[:bin])
-    rescue CommandFailed => e
-      puts <<~MSG
-        Could not extract sequences from: #{db}
-        Tried: #{cmd}
-        stdout: #{e.stdout}
-        stderr: #{e.stderr}
-      MSG
-      exit!
-    end
-
-    def extract_taxid_map(db, taxmap_file)
-      cmd = "blastdbcmd -entry all -db #{db} -outfmt '%i %T'"
-      sys(cmd, stdout: taxmap_file, path: config[:bin])
-    rescue CommandFailed => e
-      # silence error
-    end
-
-    # Returns true if the database name appears to be a multi-part database
-    # name.
-    #
-    # e.g.
-    # /home/ben/pd.ben/sequenceserver/db/nr.00 => yes
-    # /home/ben/pd.ben/sequenceserver/db/nr => no
-    # /home/ben/pd.ben/sequenceserver/db/img3.5.finished.faa.01 => yes
-    # /home/ben/pd.ben/sequenceserver/db/nr00 => no
-    # /mnt/blast-db/refseq_genomic.100 => yes
-    def multipart_database_name?(db_name)
-      !(db_name.match(%r{.+/\S+\.\d{2,3}$}).nil?)
-    end
-
-    def get_categories(path)
-      path
-        .gsub(config[:database_dir], '') # remove database_dir from path
-        .split('/')
-        .reject(&:empty?)[0..-2] # the first entry might be '' if database_dir does not end with /
-    end
-
-    # Returns true if first character of the file is '>'.
-    def probably_fasta?(file)
-      return false unless file.match(/((cds)|(fasta)|(fna)|(pep)|(cdna)|(fa)|(prot)|(fas)|(genome)|(nuc)|(dna)|(nt))$/i)
-      File.read(file, 1) == '>'
-    end
-
-    # Suggests improved titles when generating database names from files
-    # for improved apperance and readability in web interface.
-    # For example:
-    # Cobs1.4.proteins.fasta -> Cobs 1.4 proteins
-    # S_invicta.xx.2.5.small.nucl.fa -> S invicta xx 2.5 small nucl
-    def make_db_title(path)
-      db_name = File.basename(path)
-      db_name.tr!('"', "'")
-      # removes .fasta like extension names
-      db_name.gsub!(File.extname(db_name), '')
-      # replaces _ with ' ',
-      db_name.gsub!(/(_)/, ' ')
-      # replaces '.' with ' ' when no numbers are on either side,
-      db_name.gsub!(/(\D)\.(?=\D)/, '\1 ')
-      # preserves version numbers
-      db_name.gsub!(/\W*(\d+([.-]\d+)+)\W*/, ' \1 ')
-      db_name
-    end
-
-    # Guess whether FASTA file contains protein or nucleotide sequences by
-    # sampling a few few characters of the file.
-    def guess_sequence_type_in_fasta(file)
-      sequences = sample_sequences(file)
-      sequence_types = sequences.map { |seq| Sequence.guess_type(seq) }
-      sequence_types = sequence_types.uniq.compact
-      (sequence_types.length == 1) && sequence_types.first
-    end
-
-    # Read first 1,048,576 characters of the file, split the read text on
-    # fasta def line pattern and return.
-    #
-    # If the given file is FASTA, returns Array of as many different
-    # sequences in the portion of the file read. Returns the portion
-    # of the file read wrapped in an Array otherwise.
-    def sample_sequences(file)
-      File.read(file, 1_048_576).split(/^>.+$/).delete_if(&:empty?)
-    end
-  end
-end

data/public/js/tests/advanced_parameters.spec.js

@@ -1,36 +0,0 @@
-/* eslint-disable no-unused-vars */
-/* eslint-disable no-undef */
-import { render, screen, fireEvent } from '@testing-library/react';
-import { Form } from '../form';
-import { AMINO_ACID_SEQUENCE } from './mock_data/sequences';
-import data from './mock_data/databases.json';
-import userEvent from '@testing-library/user-event';
-import '@testing-library/jest-dom/extend-expect';
-import '@testing-library/react/dont-cleanup-after-each';
-
-export const setMockJSONResult = (result) => {
-    global.$.getJSON = (_, cb) => cb(result);
-};
-describe('ADVANCED PARAMETERS', () => {
-    const getInputElement = () => screen.getByRole('textbox', { name: '' });
-    test('should not render the link to advanced parameters modal if blast algorithm is unknown', () => {
-        setMockJSONResult(data);
-        const {container } =render(<Form onSequenceTypeChanged={() => { }
-        } />);
-        const modalButton = container.querySelector('[data-target="#help"]');
-        expect(modalButton).toBeNull();
-    });
-    test('should render the link to advanced parameters modal if blast algorithm is known', () => {
-        setMockJSONResult(data);
-        const {container } =render(<Form onSequenceTypeChanged={() => { }
-        } />);
-        
-        const inputEl = getInputElement();
-        // populate search and select dbs to determine blast algorithm
-        fireEvent.change(inputEl, { target: { value: AMINO_ACID_SEQUENCE } });
-        const proteinSelectAllBtn = screen.getByRole('heading', { name: /protein databases/i }).parentElement.querySelector('button');
-        fireEvent.click(proteinSelectAllBtn);
-        const modalButton = container.querySelector('[data-target="#help"]');
-        expect(modalButton).not.toBeNull();
-    });
-});