Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
Commits on Mar 3, 2015
  1. Merge pull request #149 from vivekiitkgp/patch

    authored
    [WIP] Fix bootlint errors and search form validation
  2. Vivek Rai

    Fix bootlint errors and search form validation

    vivekiitkgp authored
    Closes #148
    
    Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
  3. Merge pull request #147 from vivekiitkgp/patch

    authored
    Fix error in gemspec file as reported by @gusevfe
  4. Vivek Rai

    Fix error in gemspec file as reported by @gusevfe

    vivekiitkgp authored
    Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Commits on Feb 24, 2015
  1. Anurag Priyam

    Fix build.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Commits on Feb 23, 2015
  1. Anurag Priyam

    Merge remote-tracking branch 'wwood/curl'

    yeban authored
    * wwood/curl:
      use curl instead of wget so OSX is supported, fix #139
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  2. Anurag Priyam

    Include public/dist in the repo.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    Switch to GNU AGPL version 3.

    yeban authored
    * Include a COPYRIGHT file on lines of
      https://raw.githubusercontent.com/diaspora/diaspora/develop/COPYRIGHT to
      attribute software we depend on.
    * Include LICENSE.d3.js because minified version of d3 does not contain
      copyright and license notice.
    * Mention at top of public/js/sequence.js that it has been modified to
      comply with Apache license.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Commits on Feb 21, 2015
  1. Ben J Woodcroft
  2. Anurag Priyam

    Release 1.0.0.pre.5.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    Fix error due to SequenceServer#[] being undefined.

    yeban authored
    Culprit - abaed27.
    
    close #137
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  4. Anurag Priyam

    Fixes for Ruby 1.8.7.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  5. Vivek Rai

    Lookbehind not available in Ruby1.8.7. Fix that.

    vivekiitkgp authored
    Signed-off-by: Vivek Rai <vivekraiiitkgp@gmail.com>
Commits on Feb 20, 2015
  1. Anurag Priyam

    Ensure full tabular report is indeed full tabular report.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  2. Anurag Priyam

    Release 1.0.0.pre.4.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    Update Rubies to test on, on Travis.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  4. Anurag Priyam

    Hold a reference to up to 100 search results.

    yeban authored
    To avoid the associated tempfile from being GCed.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  5. Anurag Priyam

    Do not activate DnD if a modal is active.

    yeban authored
    Because it doesn't make sense to do so.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  6. Anurag Priyam

    Change CONFIG_FILE_ERROR message to "Error reading config file".

    yeban authored
    From "Error in config file".
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  7. Anurag Priyam

    Print "incorrect number of sequences" message only when relevant.

    yeban authored
    Missed to add a guard clause in 02e87da somehow.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Commits on Feb 19, 2015
  1. Anurag Priyam

    Gem version and total downloads badge.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  2. Anurag Priyam

    Add instructions to setup development environment to README.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    Rename App to Routes and move to routes.rb.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  4. Anurag Priyam

    Update BLAST::Report API. Fix NCBI link generator.

    yeban authored
    An HSP now holds a pointer to the Hit object it belongs to. Hit to Query. And
    Query to Report. Leveraging this, we define Hit#querydb which simply forwards
    to Report#querydb, move Report#which_blastdb to Hit#whichdb, and extend Hit
    class with Links module instead of Report. This approach feels "just right".
    
    Update link generators accordingly, fix NCBI link generator while at it (which
    was broken because we had begun using Hit#accession instead of Hit#id several
    commits back and thus couldn't infer if the hit was from nr database), and
    simplify Report a bit.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  5. Anurag Priyam

    Include "incorrect number of sequences retrieved" message in download…

    yeban authored
    …ed FASTA.
    
    Followed with some refactoring to show the same message in downloaded FASTA
    file and sequence viewer.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  6. Anurag Priyam

    Fix minor breakage to search summary at the bottom of the HTML report.

    yeban authored
    We changed Report#stats to return a Hash instead of Array in SHA b9bf84d, but
    missed to update search summary accordingly.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  7. Anurag Priyam

    Ajaxify single FASTA download link.

    yeban authored
    Just like all the download links in sidebar. So that we can provide error
    feedback to the user if need be.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Commits on Feb 18, 2015
  1. Anurag Priyam

    Do not add timestamp to downloads.

    yeban authored
    * Makes the file name too big.
    * Timestamp will be in server's time zone which may different from that of
      client's, in which case timestamp will serve to confuse a user than help.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  2. Anurag Priyam

    Extract sequence retrieval code from get_sequence route to Sequence::…

    yeban authored
    …Retriever.
    
    Like BLAST::Formatter.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    Update .rubocop.yml.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  4. Anurag Priyam

    Refactor BLAST module.

    yeban authored
    * Simplify and document BLAST::Report.
    * Standardise names for report downloads.
    * Move `blast_formatter` functionality BLAST::Formatter from BLAST.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Commits on Feb 16, 2015
  1. Anurag Priyam

    Add Help & Support link to the header.

    yeban authored
    Link to http://www.sequenceserver.com/#support.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  2. Anurag Priyam

    Say upfront that we accept query sequences in FASTA format only.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  3. Anurag Priyam

    SHA 2d5bdf8 broke method chaining in a few functions. Fix it.

    yeban authored
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
  4. Anurag Priyam

    Further assist user with intelligent tooltips on BLAST button.

    yeban authored
    * Ask user to select a database if none selected.
    * If user hovers on BLAST button for a second, he is clearly unsure what to do.
      In that case, say 'Click to BLAST or press Ctrl-Enter.' Additionally, if more
      than one BLAST algorithms are possible, tell them how to find it.
    
    Signed-off-by: Anurag Priyam <anurag08priyam@gmail.com>
Something went wrong with that request. Please try again.