1.1.0.beta12

Changelog

• Write default BLAST options that were previously defined only in the code
  to config file during setup. Since old config files won't have this info
  available, retain the old behaviour of automatically adding '-task blastn'
  to BLASTN searches and log this during startup.
  (issue raised by Niek Art)
• Multipart database volumes can have 3 digit suffixes (e.g.
  refseq_genomic.100). Our regex allowed for only 2 digit
  suffixes (e.g. nr.00). Fixed that.
  (issue raised by Niek Art)
• Show location of config file by default during startup
• Code-style improvements.
  (credit: Emeline Favreau, Esteban Gomez)

1.1.0.beta11

• Display of large results are handled by rendering results of fifty queries at
  a time. However, in each cycle of update, instead of focusing only on the
  next fifty queries, React would automatically also check if previously
  rendered queries needed to be updated as well. This resulted in each cycle of
  update to take more and more time. Prevent that by returning false from
  shouldComponentUpdate lifecycle method if the query is already rendered.
• Kablammo / graphical HSP overview:
  • Reverse order of HSPs for drawing so that the HSP with stronger evalue
    are drawn last, and thus end up on top of HSP with weaker evalue if
    overlapping.
  • Handle hover events more efficiently.
• Copy-pasting hit sequence from sequence viewer should eliminate whitespace
  introduced by grouping of residues, but it didn't. So disabled grouping of
  residues in sequence viewer so that the sequence can be copy-pasted as it
  is.
• SVG and PNG download links would break into two lines on smaller windows.
  Fixed that.
• Do not change padding when hit is selected. Further, apply orange border
  to selected hits only on the left side instead of on all sides.
• Downloading alignments of selected hits wouldn’t work if sequence ids
  included a pipe character. Fixed this.
• Last line of the alignment would sometimes not be shown. Fixed that.
• Expanded error handling:
  • Inform user if BLAST's XML output is invalid, and suggest deduplicating
    sequence ids or rerunning with a single database (issue #194) (credits:
    Ben Woodcroft, Tomáš Pluskal, and others).
  • Inform user if BLAST ran out of memory and ask to retry with smaller
    query. Should be rare, but is good to know when this happens.
  • Inform user if SequenceServer doesn't have permission to create job
    directory. Should be particularly helpful when setting up with
    Apache.
  • Inform user if SequenceServer/BLAST runs out of disk space.
  • Inform user if BLAST produced empty output.
• Update Dockerfile so that docker image is built from the source. This
  ensures that the tag applied to docker image and software version are
  in sync. (credit: Michał T. Lorenc)
• Don't use symlinks inside of the repository as symlinks are not
  supported on all platform and can thus cause installation to
  fail.
• Ensure the new version can be deployed to a suburi.

1.1.0.beta10

Features

• Added a button to select all databases.
• Meta data on top of report page now includes date (as well as labels
  for program, databases, parameters).
• Reduce overall amount of vertical space on the report page so that more
  results fit in the same height.
• Detailed space reduction effort were needed for pairwise alignments,
  which now use almost 2x less vertical space. Importantly, alignments are
  now "pretty formatted" in the browser instead of on the server so that all
  available horizontal space is known beforehand. Previously we were restricted
  to assuming 60 characters per line.
• For displaying pairwise alignments we previously used nested tables. We now
  use list of divs and pre tags. This reduces memory usage and increases speed
  (crucial for large reports).
• Eliminate borders from around graphs to reduce clutter and free up vertical
  space.
• Add % sign for when identity, gaps, positive are shown as percentage.
• Use more meaningful headers for hits and hsp overview graphs.

Bug fixes

• Consecutive blank spaces in the middle line of the alignment were truncated
  while parsing BLAST’s XML output. Fix it.

1.1.0.beta8

• Fix programming errors in Report.fetchResults.
• Change title of hits overview to matching sequences.

1.1.0.beta7

• Add Kablammo (http://kablammo.wasmuthlab.org) to visualise HSPs per hit
  (credit: Alekhya Munagala).
• Ensure all scripting of results HTML (such as binding event handlers)
  is done at appropriate stages of rendering process.
• Report page repeatedly pings the server for results. The frequency of
  pings was meant to decrease with time. However, a bug in the code
  resulted in frequency of pinging to remain the same. Fix that.
• When there are too many hits to create circos visualisation, show a
  message explaining the same (credit: Hiten Chowdhary).
• Do not add circos visualisation to page if there are no hits to
  visualise (credit: Hiten Chowdhary).

1.1.0.beta6

• Show length distribution of hits per query (credit: Hiten Chowdhary). Like circos, this visualisation is drawn only when user clicks the corresponding button.
• Do not draw alignments overview (per query) on page load if number of queries is >250. In this case, the user must click the corresponding button to render the visualisation.
• Once all results have been retrieved from the server, update the page with results of 50 queries every 500 ms. Along with the optimisation above, this allows us to render large results - tested up to 1200 queries and 1500 hits. The page remains responsive (e.g., scrolling) while it is being updated and after, however, there are two caveats still when viewing large results:
  • Some features, such as selecting hits for download, ability to download FASTA and pairwise alignments for a single hit, and affixing of sidebar are not activated till the entire result has been rendered and currently there is no clear way to communicate this to the user.
  • Visualisations are slow to render and hide on click.
• Displaying of appropriate error messages when BLAST failed was broken due to a typo in the code. Fixed it (credit: Tomáš Pluskal).
• Make entering taxid optional again when creating BLAST databases from FASTA file (reported by: Tomáš Pluskal)

1.1.0.beta5

Changelog

• Enable Circos visualisation (experimental). The visualisation is drawn
  specifically on clicking the ‘CIRCOS’ link on the report page. Works
  best when total number of matching hits and hsps is small.
• Entering non-numeric taxid when creating BLAST databases would cause
  SequenceServer to crash. Instead, it now prompts user to re-input
  taxid.
• Anchor tags as well as buttons are used on the report page for different
  actions. Ensure both are consistently styled.
• We use SauceLabs browser testing platform for testing the user-interface.
  Duly credit SauceLabs in README by linking to their website.

Roadmap (comments welcome)

https://docs.google.com/document/d/1Vt2MmaD5h5oN8XrmokLVnjUfRLWqKVWeEja3w9SIeBw

1.1.0.beta4

Changelog

• Retain the order in which hits and hsps are returned by BLAST. In previous
  beta releases, hits and hsps were sorted by evalue, which didn't work well
  when multiple evalues were similar.
• Show error message (SystemError) if no permission to create job
  directory, or no disk space.
• By default, delete finished jobs after 30 days instead of 7 days.
• Ensure browser cache is refreshed for new releases.
• Do not show backtrace when job not found.
• Refactoring in previous beta release had broken XML and tabular
  report download link on the results page - fix it.
• Slightly modify citation line.

1.1.0.beta3

Changelog

• Expanded User Interface (UI) testing to cover more scenarios:
  • All five basic BLAST algorithms are now tested using a multi-fasta query
    with no defline for the first sequence, and at least two databases.
    UI tests previously covered selected BLAST algorithms and were
    restricted to single query sequence and single database.
• Expanded platforms on which automated UI tests are run (powered by:
  SauceLabs) -
  • Latest Chrome and Firefox on Linux, macOS 10.13, and Windows 10
  • Latest Safari on macOS 10.13
  • Latest Edge on Windows 10
    Previously we tested only on latest Firefox on Linux.
• Update error handling mechanism to work with the new asynchronous nature
  of running BLAST searches (credit: Hiten Chowdhary).
• Improve error reporting:
  • Fix parsing of error message when BLAST exit status is 1 (incorrect
    advanced params or weird error in query sequence)
  • BLAST results are deleted after 7 days. If user attempts to access
    a deleted job, show 'job not found' message instead of treating it
    like other errors.

For those interested in using SequenceServer API to run BLAST searches using
curl or so,

• Errors are now reported in JSON format as well instead of HTML (error body
  may still contain HTML links)

1.1.0.beta2

Changelog

• Addressed all the failing tests - all tests now pass! Thanks to Hiroyuki
  Nakamura for fixing Travis test script.
• Show the clickable list of query ids in the sidebar for only up to 8
  queries, so that the sidebar doesn't spill over onto the footer.
• Update to Sinatra 2.0, so that SequenceServer can be embedded in
  Rails 5 (credit Hiroyuki Nakamura).
• Speed up page load time by compressing server's response on the go. Both
  the search form and short BLAST results now load significantly (5x) faster.