Changelog for Bio::MAGETAB -------------------------- 1.31 Bio::MAGETAB-1.31.tar.gz Replacing the old DateTime::Format::DateManip module with DateTime::Format::Flexible, which appears to be maintained more responsively. 1.30 Bio::MAGETAB-1.30.tar.gz Fix for FactorValue and Characteristics Measurement bug (https://rt.cpan.org/Public/Bug/Display.html?id=94398). 1.28 Bio::MAGETAB-1.28.tar.gz Minor bug fixes for assorted test case failures; no substantive changes in code behaviour. 1.27 Bio::MAGETAB-1.27.tar.gz Change to the default v1.1 SDRF export such that all assays are represented by "Assay Name" columns, and all Assay and Hybridization Name columns will include Technology Type. The v1.0 export remains unchanged. Added the EFO term "array assay" to the Technology Type terms recognised as being attached to hybridisations. 1.26 Bio::MAGETAB-1.26.tar.gz Re-release incorporating Module::Install 1.06 to fix a known bug when installing using perl 5.16. No other code changes. 1.25 Bio::MAGETAB-1.25.tar.gz Fixing SDRF parser to correctly recognise Array Design columns associated with Assay Name. 1.24 Bio::MAGETAB-1.24.tar.gz Making the parsed MAGE-TAB document version attribute accessible from in the Reader classes. 1.23 Bio::MAGETAB-1.23.tar.gz Several important bug fixes provided by Anna Farne. 1.22 Bio::MAGETAB-1.22.tar.gz Another attempt to solve the error reporting problem, newly reintroduced by the loss of previously-documented functions from Parse::RecDescent (see below). Improved error message formatting. 1.21 Bio::MAGETAB-1.21.tar.gz Fixed redirection of Parse::RecDescent error reporting to use the now-documented mechanisms for doing so. 1.20 Bio::MAGETAB-1.20.tar.gz Added the option to link from ParameterValue to ControlledTerm as per June 2009 v1.1 MAGE-TAB specification. Default search path for SDRF/ADF/DataMatrix switched from current working directory to IDF directory. Tests added for Bio::MAGETAB::Util::Reader class. Possible fix for URI test errors when running on MSWin32. 1.13 Bio::MAGETAB-1.13.tar.gz Fixed minor FileHandle type coercion bug which led to an unsightly verbose warning in Moose::Meta::Attribute. 1.12 Bio::MAGETAB-1.12.tar.gz Migrated from the deprecated Moose::Policy module to using MooseX::FollowPBP. 1.11 Bio::MAGETAB-1.11.tar.gz Minor fixes to IDF and SDRF export to comply with a stricter interpretation of the MAGE-TAB specification. 1.10 Bio::MAGETAB-1.10.tar.gz Added export_version attribute to the Writer classes to support export of either MAGE-TAB v1.0 or MAGE-TAB v1.1. Corrected the behaviour of the ADF Writer class when exporting [mapping] sections. 1.00 Bio::MAGETAB-1.00.tar.gz Bug fix for export of IDF containing no multi-value fields. Minor POD fixes. 0.99 Bio::MAGETAB-0.99.tar.gz Added support for IDF "MAGE-TAB Version" tag. Now compliant with the second draft of the MAGE-TAB v1.1 specification document. 0.98 Bio::MAGETAB-0.98.tar.gz Minor fixes to enable Bio::MAGETAB::Types to work with the most recent Moose and MooseX::Types modules. 0.97 Bio::MAGETAB-0.97.tar.gz Merged magetab and magetab-util packages together for convenience (see below for old Bio::MAGETAB::Util changelog). Minor bug fixes. New class to automate fixes to ArrayExpress MAGE-TAB documents. 0.96 Bio::MAGETAB-0.96.tar.gz Made LabeledExtract->label attribute optional. This better agrees with the MAGE-TAB specification, even if it doesn't make much sense in reality. This change makes SDRF parsing slightly simpler. 0.95 Bio::MAGETAB-0.95.tar.gz Added BaseClass to the MagicDraw UML model document. Renamed Feature blockColumn and column attributes to blockCol and col respectively; this avoids naming conflicts in some ORM implementations. Renamed all "type" attributes, similarly to avoid conflicts. Converted Source providers and ProtocolApplication performers to fully-fledged Contact objects. Relaxed requirement for measurement on ParameterValue. Added POD coverage tests. 0.91 Bio::MAGETAB-0.91.tar.gz Added class documentation (POD). 0.9 Bio::MAGETAB-0.9.tar.gz Initial public release; API almost finalised. Changelog for Bio::MAGETAB::Util, prior to merging with Bio::MAGETAB -------------------------------------------------------------------- 0.4 Bio-MAGETAB-Util-0.4.tar.gz Added ADF, IDF and SDRF export functions. Improved GraphViz visualisation API. Minor parser bug fixes. 0.31 Bio-MAGETAB-Util-0.31.tar.gz Various bug fixes based on tests with real-world IDFs and SDRFs. Improved object identity heuristics. Full MySQL database schema and unloader script. 0.3 Bio-MAGETAB-Util-0.3.tar.gz Initial public release