CHANGES.rst

Changelog

This is a record of changes made between each Mutalyzer release.

Version 2.0.14

Released on November 9th 2015.

• E-mail address is now optional in batch job website interface (#119).
• Use Mailcheck in the batch jobs form (#107).
• Optional email for batch jobs from webservices (#104).
• Process batch jobs grouped by email address (#101).
• Use interval binning scheme on transcript mappings (#100).
• Back translator interface (#74).
• Transcript-protein links are now cached in Redis (#94).
• Added Ter as a valid amino acid in the HGVS grammar (#90).
• Refactoring of unit tests (#88, #89).

Version 2.0.13

Released on October 1st 2015.

• Fix query bug in update transcript-protein links (#85).

Version 2.0.12

Released on September 30th 2015.

• Fix off-by-one in slicing chromosome by gene name (#79).
• Document scheme used for all positions and ranges (#79).
• Show diff for variant protein from non-reference start codon (#78).
• Visualise protein change, also with alternative start (#72).
• Translate alternative start to M, also in variant (#72).
• Added Baker's yeast (SacCer_Apr2011/sacCer3) assembly (#73).

Version 2.0.11

Released on August 6th 2015.

• Fix bug in recognizing p.(=) (was reported as p.?) (#65).

Version 2.0.10

Released on July 21st 2015.

• Don't crash the position converter on transcript mappings containing no exons (#63).
• Use the notation for an uncertain stop codon, e.g., p.(Gln730Profs*?) instead of p.(Gln730Profs*96) when a variant results in a frame shift or extension and we don't see a new stop codon in the RNA (#57).
• Added Dog (Broad CanFam3.1/canFam3) assembly for position converter (#56).

Version 2.0.9

Released on July 9th 2015.

• Improvements in encoding detection of uploaded batch files (#52, #53).
• Usability improvements in reading DNA for description extractor (#54).

Version 2.0.8

Released on May 27th 2015.

• The HGVS variant description extractor package is available through the Description Extractor interface (#1).
• GitHub project moved from LUMC/mutalyzer to mutalyzer/mutalyzer.

Version 2.0.7

Released on March 27th 2015.

• Return fault code and description on RPC service errors (#31).
• Use esummary 2.0 response format (#32).

Version 2.0.6

Released on February 10th 2015.

• Added getGeneLocation webservice method. Given a gene symbol and optional genome build, it returns the location of the gene (#28).
• Discard incomplete genes in genbank reference files (#26).

Version 2.0.5

Released on December 16th 2014.

• New website layout by Landscape (GitLab!26).
• Source code moved from GitLab to GitHub.
• Automated unit tests on Travis CI (#16).
• Developer documentation hosted on Read the Docs (#17).

Version 2.0.4

Released on November 19th 2014.

• Many string encoding related fixes. Summarizing, Mutalyzer should now be completely aware of input and output string encodings, in all interfaces. Internally, all strings are unicode strings. This comes with minor changes in the webservice definitions, which most clients will probably not notice (GitLab!25).
• Don't crash on mail errors in the batch scheduler (GitLab#30).
• Fix importing transcript mappings from UCSC database (GitLab#9).
• Rename GRCh36 to NCBI36 (GitLab#8).
• Updated all Python dependencies to their latest versions.
• Mutalyzer is now Open Source! Source code is available under the AGPL and documentation under the CC-by-sa license.

Version 2.0.3

Released on September 20th 2014.

• Fix several error cases in LOVD2 view on the name checker.

Version 2.0.2

Released on October 9th 2014.

• Fix incorrect GRCm38 chromosome accession number versions.
• Fix crash in position converter batch jobs.
• Upgrade the webservice library we use (Spyne, from 2.10.10 to 2.11.0). This potentially affects behaviour of both our SOAP and HTTP/RPC+JSON webservices, although our tests did not show any problems.

Version 2.0.1

Released on September 27th 2014.

• Fix POST requests to the HTTP/RPC+JSON webservice. This was a regression from version 2.0.beta-33. Thanks to Ken Doig for reporting the issue.

Version 2.0.0

Released on September 26th 2014.

This release does not bring many new features, but comes with significant changes to the technical infrastructure. GitLab!6 tracks most of this.

Some highlights especially users of the webservices should be aware of:

• HTTP/RPC+JSON webservice has changed response format (wrapper object removed). See below for an :ref:`example <changelog_200_example>`.
• No more plain HTTP access, only redirects to HTTPS.
• Many website entrypoints have changed URLs and form parameter names (the old ones have HTTP redirects).
• Removed old redirects from paths starting with /2.0/.
• In maintenance mode, all requests get a Service Temporarily Unavailable response with status code 503.

Other changes:

• Upload a genbank file using the SOAP webservice (uploadGenBankLocalFile).
• Do not cleanup the cache during request handling (GitLab#18).
• Add GRCh38 (hg38) assembly (GitLab!20).
• Move from nose to pytest for unit tests (GitLab!23).
• Fix running Mutalyzer in a virtual environment and have an up-to-date requirements.txt for pip (GitLab!4).
• Switch from TAL to Jinja2 (GitLab!3).
• Refactor user interfaces (GitLab!5).
• Move from configobj to Python module based config (GitLab!7).
• Use SQLAlchemy as ORM (GitLab!8).
• Use Redis for stat counters (GitLab!10).
• Port website from web.py to Flask (GitLab!11).
• Isolated unit tests using fixtures and an in-memory database (GitLab!12).
• Display announcement on website (GitLab!14).
• Database migrations with Alembic (GitLab!15).
• Update documentation and use Sphinx (GitLab!16).
• Move to semantic versioning, starting with version 2.0.0 (GitLab!22).
• Add 404 not found page.
• Don't auto remove comma characters in syntax checker.
• Add a dash (-) as an allowed character in the gene name.
• Range, reverse complement range, and compound insertions/insertion-deletions.

The wrapper object has been removed from the HTTP/RPC+JSON webservice response format. As an example, consider an old response format for the checkSyntax method:

{
  "checkSyntaxResponse": {
    "checkSyntaxResult": {
      "valid": true,
      "messages": {
        "SoapMessage": []
      }
    }
  }
}

The new response format is:

{
  "valid": true,
  "messages": []
}

Version 2.0.beta-33

Released on August 19th 2014.

• Link to Upcoming server update announcement.

Version 2.0.beta-32

Released on June 26th 2014.

• Link to Visual interface for Variant Description Extractor announcement.

Version 2.0.beta-31

Released on March 27th 2014.

• Due to incorrect interpretation, temporarily only support one CDS per transcript (ignore all others) in LRG.
• Due to incorrect interpretation, temporarily ignore transcripts without a fixed id.

Version 2.0.beta-30

Released on February 18th 2014.

• Handle NCBI Entrez response validation errors (fixes, among other things, LOVD Trac#29).
• Loosen error severity when CDS cannot be translated.
• Mutalyzer development migrated from Subversion to Git for version control.

Version 2.0.beta-29

Released on October 11th 2013.

• Add Jonathan Vis attribution and COMMIT logo to about page.