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.

1.1.0.beta

Features

• Update to BLAST 2.6.0+
• We put a customizable default parameter in BLAST searches to only return hits with evalues stronger than 1e-5 (BLAST's default of evalue 10 includes too many spurious hits that are confusing to junior users)
• We make it explicit that '-task blastn' option is used for BLASTN (instead of BLASTN's default behaviour of running megablast)
• Stable URL for results: meaning that results page can now be bookmarked, shared, or linked to from your lab notebook
• "Download FASTA of all" link in the sidebar can handle many sequences (previously it was disabled if >30 hits)
• Ability to download individual or all alignments in FASTA format (code from Kablammo project at http://kablammo.wasmuthlab.org/)
• Ability to download alignment overview in SVG and PNG image (code from Kablammo project at http://kablammo.wasmuthlab.org/)
• Use a, b, c numbering for HSPs to distinguish easily from hits
• Show summary of BLAST database and search parameters at top of results page
• Show coverage and identity in hits table
• results can be opened in a new tab by pressing 'Cmd' / 'Ctrl' button while clicking on the submit button (like any other link).
• Drop support for Ruby older than 2.3. This allows SequenceServer to be embedded in Rails 5, means we benefit from performance improvements in new Ruby, and importantly makes code and dependencies easier to maintain and test
• If BLAST was downloaded by SequenceServer or path to BLAST binaries was explicitly provided by the user, BLAST searches are run in "sandbox mode". In sandbox mode, SequenceServer cannot access any other system command. This increases security.
• We no longer require BLAST databases to have been created with -parse_seqids option of makeblastdb

Bugfixes

• Alignment overview: colour each HSP by its evalue (instead using the evalue of the hit)
• Fix crash when downloading amino acid sequences that include stop codons (*)
• All code and fonts (except Twitter badge) are loaded locally

Known issues

As this is beta software, a few things may not work as expected. Following is a list of known issues that we are currently working on:

• Performance with many number of hits: e.g., sequenceserver doesnt load the results of BLASTing a 300 kilobase file including >1000 queries against itself fails.
• Deploying on suburi (e.g., antgenomes.org/sequenceserver) currently doesn't work
• Hits table can look jumbled up if BLAST search returns multiple hits with same evalue
• Sidebar height is not appropriately constrained
• 6 tests fail on the Travis code checker

Under the hood changes

• We now use browser's default form submission behavior instead of using AJAX. This allows results to be opened in a new tab by pressing 'Cmd' / 'Ctrl' button while clicking on the submit button (like any other link).
• Previously, submitting the search form and obtaining results from the server would be accomplished in one long HTTP request. This was problematic for long running BLAST searches as production servers (e.g., Nginx, Apache) drop connections after a set interval. Now search form submission creates a 'job' (with a unique identifier) whose status is queried repeatedly by the result page. Such 'asynchronous' approach is more scalable and should also work well with job schedulers like qsub and bsub.
• The server now returns results in JSON format instead of HTML format. We use the React framework along with JSX to generate HTML results directly in the browser. Access to raw results directly in the browser has enabled us to test a few different visualisations for BLAST results (not part of this release). This approach also allows the use of 'curl' to obtain results in command line and process the results in any scripting language.

1.0.11

Changed how docker images are automatically built. Everything is same as the previous release.

1.0.10 (important)

Issue fixed: Whitespaces in the XML returned by BLAST were ignored during parsing in some cases, leading to the middle line of the alignment getting truncated.

1.0.9 (important)

• Fixes misleading prettification of evalue in hits table.
• Evalue 0.00 was shown as 0.00x10⁺⁰⁰ in hsp stats table. Fix that.