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Commits on Feb 11, 2017
  1. Merge remote-tracking branch 'lawrence/feature-generic-errors'

    * lawrence/feature-generic-errors:
      Refactoring
      Removed the EXTENSION_FILE_NOT_FOUND class
      Removed the redundant DATABASE_DIR_NOT_FOUND class
      Removed the redundant BIN_DIR_NOT_FOUND class
      Replace EXTENSION_FILE_NOT_FOUND with ENOENT
      Replace DATABASE_DIR_NOT_FOUND with ENOENT
      Replace BIN_DIR_NOT_FOUND with ENOENT
      Added rescue block for ENOENT
    
    Signed-off-by: Anurag Priyam <anurag.priyam@qmul.ac.uk>
    Anurag Priyam committed Feb 11, 2017
Commits on Feb 1, 2017
  1. Merge remote-tracking branch 'lawrence/fix-assert-blast-installed'

    * lawrence/fix-assert-blast-installed:
      Rescue BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE
      Changed rescue behaviour
      Made class "BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE"
      Directly execute "blastdbcmd -version" using "sys"
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Feb 1, 2017
Commits on Jan 29, 2017
  1. Refactoring

    Changed 'puts e.to_s, ""' to 'puts e'
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 29, 2017
Commits on Jan 26, 2017
  1. Rescue BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE

    In bin/sequenceserver allowed the error
    BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE to be rescued. Edited the
    message in the rescue block to explain that a recent system update
    may have broken the user's NCBI BLAST+ installation.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 26, 2017
  2. Changed rescue behaviour

    Only a failed "sys" command needs to be re-raised in
    assert_blast_installed_and_compatible.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 26, 2017
  3. Made class "BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE"

    In lib/sequenceserver/exceptions.rb, made the class
    "BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE". This is part of a fix for
    a bug that precents SequenceServer from executing BLAST commands from
    the binary directory bin dir.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 26, 2017
  4. Directly execute "blastdbcmd -version" using "sys"

    In the method "assert_blast_installed_and_compatible" in
    lib/sequenceserver.rb, do not check whether "blastdbcmd" is
    available. Instead, directly execute "blastdbcmd -version" using
    "sys". Raise the error BLAST_NOT_INSTALLED_OR_NOT_EXECUTABLE if the
    BLAST version could not be determined.  This is part of a fix for a
    bug that prevents SequenceServer from executing BLAST commands from
    the binary directory bin dir.
    
    Signed-off-by: Lawrence <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 26, 2017
Commits on Jan 22, 2017
  1. Removed the EXTENSION_FILE_NOT_FOUND class

    Removed the redundant EXTENSION_FILE_NOT_FOUND error class and
    its rescue block. The ENOENT class will handle these errors.
    enjoyyourcopepods committed Jan 17, 2017
  2. Removed the redundant DATABASE_DIR_NOT_FOUND class

    Removed the redundant DATABASE_DIR_NOT_FOUND error class and its
    rescue block. The ENOENT class will handle these errors.
    enjoyyourcopepods committed Jan 17, 2017
  3. Removed the redundant BIN_DIR_NOT_FOUND class

    Removed the redundant BIN_DIR_NOT_FOUND error class and its rescue
    block. The ENOENT class will handle these errors.
    enjoyyourcopepods committed Jan 17, 2017
  4. Replace EXTENSION_FILE_NOT_FOUND with ENOENT

    Refactoring. Raise the error using the superclass ENOENT, not
    EXTENSION_FILE_NOT_FOUND.
    enjoyyourcopepods committed Jan 17, 2017
  5. Replace DATABASE_DIR_NOT_FOUND with ENOENT

    Refactoring. Raise the error using the superclass ENOENT, not
    DATABASE_DIR_NOT_FOUND.
    enjoyyourcopepods committed Jan 17, 2017
  6. Replace BIN_DIR_NOT_FOUND with ENOENT

    Refactoring. Raise the error using the superclass ENOENT, not
    BIN_DIR_NOT_FOUND.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 16, 2017
  7. Added rescue block for ENOENT

    Added to bin/sequenceserver a rescue block for the ENOENT error
    class.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 15, 2017
Commits on Jan 14, 2017
  1. Merge branch 'multifasta'

    Change alignment export format to multifasta.
    
    * multifasta:
      edits in alignment_exporter
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 14, 2017
  2. edits in alignment_exporter

    Signed-off-by: aniarya82 <hiten.iitkgp@gmail.com>
    aniarya82 committed with yeban Jan 13, 2017
Commits on Jan 12, 2017
  1. Merge remote-tracking branch 'lawrence/feature-sys'

    Apply sys elsewhere throughout the code. We omit using it in
    bin/sequenceserver and for SequenceServer.which?.
    
    * lawrence/feature-sys:
      Allow "_make_blast_database" to puts output
      Revert use of 'sys' to run 'which' command
      Revert insertion of 'sys' into bin/sequenceserver
      Inserted the 'sys' method into more places
      Inserted the 'sys' method into more places
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 12, 2017
Commits on Jan 11, 2017
  1. Allow "_make_blast_database" to puts output

    Restore the ability of the "_make_blast_database" method to puts
    output to the console.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 11, 2017
  2. Revert use of 'sys' to run 'which' command

    The 'which' command will not be available in the SequenceServer
    binary directory.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 11, 2017
  3. Revert insertion of 'sys' into bin/sequenceserver

    "require 'sequenceserver'" placed here may cause
    SequenceServer to default to development mode.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 11, 2017
Commits on Jan 10, 2017
  1. Merge commit 'dc0fe9b72b5f1375c27afab93ed47777c981a686'

    * commit 'dc0fe9b72b5f1375c27afab93ed47777c981a686':
      Removed the redundant 'export_bin_dir' method
      Make the 'sys' method use the binary directory
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 10, 2017
  2. Build assets.

    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 10, 2017
  3. DOTDIR was defined twice. Define it only once, in sequenceserver.rb.

    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 10, 2017
Commits on Jan 9, 2017
  1. Removed the redundant 'export_bin_dir' method

    The 'export_bin_dir' method is no longer necessary if changing to
    the NCBI BLAST+ directory is handled by the 'sys' method.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 8, 2017
  2. Make the 'sys' method use the binary directory

    If a directory was given for NCBI BLAST+, the 'sys' method will
    set the PATH environment variable to this directory before
    executing a shell command, if no other path was given.
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 8, 2017
Commits on Jan 6, 2017
  1. Inserted the 'sys' method into more places

    Used the 'sys' method in several places where shell commands
    are run.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 6, 2017
  2. Inserted the 'sys' method into more places

    Used the 'sys' method in several places where shell commands
    are run.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 6, 2017
Commits on Jan 5, 2017
  1. sys: Provide base name to Tempfile.new.

    Looks like Tempfile.new takes a compulsory argument on older Rubies.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 5, 2017
  2. Try fixing Travis builds.

    - Nokogiri can no longer be installed on Ruby 2.0. Disabling testing on
    Ruby 2.0.
    - Travis is failing to install Ruby 2.3. Trying if specifying patch
    level will fix it.
    
    Otherwise tests are passing locally. Not sure what's causing them
    to fail on Travis.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 5, 2017
Commits on Jan 4, 2017
  1. Merge remote-tracking branch 'lawrence/forking-with-sys'

    sys: fork, change path, cwd and exec the command. In parent, wait2 on
    the child process. This ensures no concurrent parts of SequenceServer
    will be affected by change in path and cwd when executing a command.
    
    * lawrence/forking-with-sys:
      Reverted rubocop suggestion of zero? method
      Minor rubocop fixes
      Made 'sys' fork and use 'exec' to execute commands
      Removed parenthesis.
      Changed structure of fork in 'sys'.
      Added forking to 'sys' method.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
    yeban committed Jan 4, 2017
  2. Reverted rubocop suggestion of zero? method

    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 4, 2017
  3. Minor rubocop fixes

    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 4, 2017
  4. Made 'sys' fork and use 'exec' to execute commands

    Made 'sys' use fork and 'exec' to execute shell commands. This
    simplifies the code and allows greater flexibility.
    
    Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>
    enjoyyourcopepods committed Jan 4, 2017
  5. Merge remote-tracking branch 'upstream/master'

    Updates code relevant to the 'sys' method.
    enjoyyourcopepods committed Jan 4, 2017