[GMOD-devel] CMap 0.06 Released

[Ken Y. C. <kc...@cs...>]

All,

Version 0.06 of CMap has been released and is available for download
from the GMOD/Sourceforge site:

    http://sourceforge.net/project/showfiles.php?group_id=27707

This constitutes quite an upgrade from version 0.05 and includes many
schema changes.  Please report any problems via the bug tracking tool:

    http://sourceforge.net/tracker/?func=browse&group_id=27707&atid=511220

From the Changes file:

-   Fixed bug (#657917) where last page of features on map view in web
    admin tool was showing too many rows in feature table
-   Added separate BUGS and TODO files so they are not lost in the
    Changes file
-   Added a generic feature search to web admin tool
-   Added new "paginate" sub to Utils for creating pages of recordsets
    for web navigation, added better and more standard paging to
    user feature search and most of the admin pages that return what
    could be a large recordset
-   Fixed bug (#660483) where "IO::Tee=GLOB(0x4d7900)" was being
    printed while exporting data as SQL statements in cmap_admin.pl
-   Added a DESTROY method to base class to disconnect database so
    that "Database handle destroyed without explicit disconnect" error
    messages wouldn't appear
-   Cleaned up many of the admin templates to make them more
    consistent
-   Added "is_enabled" field to "cmap_feature_correspondence" to allow
    a curator to permanently disable a feature correspondence record
-   Added "drawing_lane" field to cmap_feature_type so that a curator
    can determine the lane for drawing features (thereby placing some
    feature types closer to the map)
-   Added "drawing_priority" field to cmap_feature_type so that a
    curator can determine the order for drawing features within a lane
-   Added conditions to SQL for the matrix that all the map sets
    selected must have "is_enabled=1"
-   Changed label distribution on maps to wait until after all the
    features for a lane have been drawn, then sort by position,
    whether the feature is highlighted, and whether the feature has a
    correspondence
-   Added new DATA_CURATION document in "docs" directory to describe
    how to curate data using CMap tools
-   Added a legend to explain feature glyphs
-   Added watermark of "CMap" version number in lower-right corner of
    legend hyperlinked to the GMOD-CMap website
-   Added code to allow a dbxref with only a name to be accepted (so a
    curator can block out an cross-reference on a feature with "Not
    available")
-   Added ability to search for multiple features in the admin tool
-   Added ability to choose quote escaping style in cmap_admin.pl when
    exporting data as SQL INSERT statements
-   Fixed bug (#665326) where SQL for finding map features was missing
    spanning features (with both start and stop positions) when the
    given range started after the feature's start position
-   Changed ambiguously named element "include_features" on main CMap
    form to "label_features" in preparation for allowing users to
    actually choose which feature types to show.  Be sure to use the new
    "cmap.conf" if you're upgrading (or change "include_features" to
    "label_features")
-   Added restriction by feature type to map detail page
-   Changed link to map details page for non-relational maps to be a
    question mark underneath the map rather than a click on the whole
    map;  this is less ambiguous and also frees up the map for clicking
    to zoom on specific areas
-   Added ability to restrict correspondences by type
-   Changed "score" in "cmap_correspondence_evidence" to a float
-   Added "line_color" to "cmap_evidence_type" table
-   Added "title" attribute to map areas on templates for viewing maps
-   Changed "truncate table" in SQL for reloading of correpsondence
    matrix to be a more simple unqualified "delete from" in order to
    get around permissions in PostgreSQL (there was also some
    complaint earlier that this didn't work with some earlier version
    of MySQL)
-   Added "display_order" fields to "cmap_map"
-   Fixed bug (#677777) where feature search in the web admin tool
    wasn't case-insensitive
-   Added trimming of whitespace on column names in data import
-   Added pagination to map set info page
-   Added coloring of correspondence lines based on evidence
-   Added new feature glyphs: up-arrow, down-arrow, double-arrow,
    filled-box, in-triangle, and out-triangle
-   Expanded legend into feature types and evidence types
-   Added support for multiple data sources
-   Added option to not overwrite map info when importing via
    cmap_admin.pl
-   Added exporting of feature correspondence via cmap_admin.pl
-   Added dbxref_name and dbxref_url to feature export in
    cmap_admin.pl
-   Added cmap-schema.png, a diagram of the tables
-   Removed DATA_IMPORT, DATA_CURATION from docs, consolidated into new
    ADMINSTRATION document
-   Fixed bug in user feature search where "All" choice for features
    types and species wasn't working
-   Added acceptance of multiple evidence codes (separated by commas) in
    feature correspondence import file
-   Removed Bio::GMOD::CMap::Drawer::Feature
-   Added minimum number of correspondences restriction
-   Added deleting of maps and map sets to cmap_admin.pl
-   Added view of color palette in web admin tool
-   Added ability to create automated name-based correspondences between
    features of different types via cmap.conf options
-   Added quoted string support to feature search
-   Increased size of all "double" fields (in MySQL declarations) from
    8 to 11
-   Added experimental throttling measures (see ADMINISTRATION)
-   Added ability to highlight features by primary name, alternate
    name or accesssion ID
-   Added ability to highlight features with embedded spaces in the
    name

Enjoy,

ky