Revision history for Perl extension Genex.

2.6.0 Tue Feb 6 15:48:00 MST 2001

• XMLUtils.pm: Added the beginings of a real XML API, defining db2xml() and

  all2xml() for some classes Now defines Bio::Genex::GeneXML and ::GeneXML::USF helper

  classes Fixed pretty_print() to preserve whitespace

• DBUtils.pm: now has many more assert_* methods new helper method: fetch_db_ids_for_species() that does a

  join accross the USF, and ExternalDatabase tables

• Genex.pm: now has timestamp() helper method, so that all DB timestamps

  can be formatted identically

• GenexAdmin.pm: Class interface to new table. This enables a DB history mechanism to record changes to the DB installation
• get_objects() fixed for all classes
• db2xml.pl: fixed a BlastHits bug added pretty_print() again Fixed caching of control bundles, so that the <misc_list> is

  specific to each download

• cv-insert.pl: now records info into GenexAdmin now uses --name option to identify who made the changes uses --dbname to specify what DB to use
• status.pl: New CGI script that shows all version information pertinent to

  the server installation.

2.5.0 Fri Jan 26 02:38:59 MST 2001

• db2xml.pl: caching of experiment sets and control-bunldes implemented now has --no_cache option to avoid using or setting cache --user/--password now optional unless --authenticate is specified Removed citationlink() Fixed aweful citation bug that never showed up, because

  citationlink table was never populated

• Fixed API for get_objects() by creating new method

  get_all_objects().

• fixed bug in check_password()
• XMLUtils.pm.in Added new framework for implementing class-specific XML output. Implemented output for Chromosome, and partial output for Species

  (still needs USF for completeness).

• DBUtils.pm.in (Repository): Added new assert_* methods:

  assert_species assert_protocol assert_scanner assert_software assert_spotter assert_array assert_experiment check_password() no longer dies() with a bad password, instead it

  returns undef

• UserSequenceFeature, ExperimentSet and ArrayMeasurement now have

  provider_con_fk() and provider_con_obj() methods post_process() no longer automatically derefences the con_obj()

  from a us_obj, it first tests the definedness

• ExternalDatabase: Fixed full name
• list_tables.pl.in: Fixed name of HTML title

2.4.0 Tue Jan 16 09:50:56 MST 2001

• Changed to Bio::Genex namespace
• Now gets INSTALLSITELIB, INSTALLMAN1DIR, and INSTALLMAN3DIR from

  Config.PM

2.2.0 Sun Jan 14 16:37:46 MST 2001

• Is now compatible as part of complete GeneX installation or as update of just Genex.pm
• db2xml.pl can now use cached control bundle files
• example scripts now have more flexibility to choose a different DB if DEBUG is set.

2.1.2 Tue Jan 9 18:00:51 MST 2001

• Genex.pm is now included as part of the larger GeneX installation process
• Renamed GEML to GeneXML
• reorganization of directories (query and curation_tool removed, cgi renamed to samples).

2.1.1 Sat Dec 2 13:29:50 MST 2000

• Changed HTMLUtils::post_process(), it now is much more modular and handles errors more intelligently

2.1.0 Sun Nov 12 22:27:02 MST 2000

• Major upgrade for Bio::Genex::current_connection(). The $Bio::Genex::* global variables are still available, but current_connection() now takes key/value style arguments when making a connection. If given arguments, it checks their value against those of the current db handle and if any differ, it will invalidate the handle and create a new connection.
• DBUtils::check_password() enables checking username/password pairs from the UserSec table.
• UserSec table now stores passwords in crypt() format using the first two letters of the login as salt.
• Makefile.PL now sets four DB user variables: $Bio::Genex::RO_USERNAME $Bio::Genex::RO_PASSWORD $Bio::Genex::SU_USERNAME $Bio::Genex::SU_PASSWORD They are accessible by programs that don't want to hard-code usernames and passwords for the readonly => RO, and super-user => SU accounts.
• list_tables.pl and fetch_table.pl can now access alternate DB's by specifying the dbname parameter.
• HTMLUtils::post_process() now includes the raw fkey as well as the pretty printed name
• new geml.dtd (two minor #REQUIRED ==> #IMPLIED modifications)

2.0.8 Tue Oct 31 13:45:46 MST 2000

• Fixed linking table bug in get_objects().
• get_objects() API now resolved:
  • get_objects('ALL')
  • get_objects({column=>foo,value=>bar}) ==> no 'ALL'
  • get_objects(@ids)
• db2xml now handles treatments correctly
• minor geml.dtd modifications

2.0.7 Thu Oct 26 16:44:46 MST 2000

• Added new configuration parameters that enable installing the gxquery scripts and the curation-tool scripts properly
• Changes to data files

2.0.6 Tue Oct 24 16:50:40 MST 2000

• included query/Makefile.PL which slipped through the cracks

2.0.5 Tue Oct 24 16:05:40 MST 2000

• Changed URL in HTMLUtils.pm to point to sample scripts
• added new configuration options that query for the directories to install the sample cgi scripts and the query cgi scripts
• added Makefile.PL to query and install_query target to primary Makefile, and query/Makefile

2.0.4 Tue Oct 24 15:56:40 MST 2000

• added new configuration option for locating the analysis tools

2.0.3 Tue Oct 24 15:22:40 MST 2000

• added new configuration options for placing the query iterface and the sample CGI scripts in different directories

2.0.2 Tue Oct 24 14:22:40 MST 2000

• updated controlled vocabulary XML
• add new data XML files in data/db_tables
• added gxquery/
• minor fixes to db2xml.pl

2.0.1 Wed Oct 18 22:13:38 MST 2000

• Added db2xml.pl.in
• All dtd's now have versions
• eliminated numerous warnings from all modules
• xml-write.pl renamed to db2xml.pl
• new functionality for create_insert_sql() for creating SQL without placeholders
• Made error messages more verbose
• use of DBUtils::fetch_fkey_list() is depricated, use get_objects() instead

2.0.0 Tue Sep 26 20:56:00 MST 2000

• Fkey interface revamped. Now each foreign key has a raw interface that accesses the values as stored in the DB, and an object oriented interface that retrieves an object of foreign class. This also obsoleted many of the old confusing flags to new(), such as: 'no_fkey_objects', 'recursive_fetch', 'fetch_fkey_fkeys', and 'fetch_otm_fkeys'
• application startup time is much quicker. Classes no longer declare 'use' pragmas for all fkeys.
• created data directory where XML versions of some tables are stored: external_database, and controlled vocabularies.
• also all MANY_TO_ONE fkeys now leave methods in the calling class, for example 'spc_fk' in Chromosome. This provides both parent and child links to DB objects in MANY_TO_ONE relationships.
• xml-write now has friendlier command line option interface
• all internal methods now have better DBI error messages
• get_objects() no longer returns bogus objects.
• new example script: list_tables.pl that is the main entry point from browsing the DB, table-by-table
• example cgi scripts are now only installed during 'make install'
• more example scripts for using XML to insert data into the DB: cv-insert.pl, contact-insert.pl, security-insert.pl

1.0.5 Fri Sep 22 19:41:44 MST 2000

• Bug fix for xml-write: if USF/CSF entries not present, no external_file reference is created.
• Bug fix for make process: cgi scripts are now installed in $CGDIR only during 'make install'
• minor bug fixes for entire make process, and general cleanup of Makefile.PL

1.0.4 Wed Sep 20 14:50:41 MST 2000

• Fixed linking table bug that caused only a single entry to be retrieved for any fkey access.
• Final version of xml-write.pl. Species can now be specified by comma-delimited list (--species=4,5,6), as can experiments. New option for limiting what arrays are output by specifying array type (--am-types=primary_raw,derived_ratio). New tables supported include GroupSec, TL_FactorValues, Treatment_AMs, Sample, and Citation.

1.0.3 Sat Sep 16 14:18:02 MST 2000

• Bug fix in create_genex_class.pl for linking tables ==> %TABLE2PKEY was improperly generated
• moved DTD's into distribution
• new scripts directory
• Makefile.PL has nicer interface
• numerous additions to xml-write: control bundle can now include all contacts in DB, info has been normalized between <array> and <array_measurement>, <citation> support added, controlled vocab terms no longer use white-space,

1.0.2 Thu Sep 7 17:00:58 MST 2000

• created scripts directory
• moved assert_element() to XMLUtils.pm
• more refinements to xml-write.pl

1.0.1 Tue Sep 5 12:28:31 MST 2000

• xml-write.pl now can output complete experiment sets
• All subclasses of Bio::Genex::ControlledVocab are now part of the ControlledVocab.pm file
• Removed AM_Group class

1.0 Thu Jun 16 18:11:07 MDT 2000

• first official release

0.29 Thu Jun 15 18:11:07 MDT 2000

• added scripts for creating control bundle
• fixed controlled vocab table bugs

0.28 Thu Jun 15 16:41:29 MDT 2000

• new controlled vocab tables

0.27 Thu Jun 15 15:20:15 MDT 2000

• changed interface to get_objects(), it now accepts an optional hashref as the first parameter, e.g. my @objs = $class->get_objects({no_fkey_objects=>},'ALL')

0.26 Tue Jun 13 15:24:07 MDT 2000

• Fixed CACHE bug in Makefile.PL
• added xml-write.pl.in, write-con-vocab.pl.in, and pretty-print.pl.in

0.25 Tue Jun 13 13:37:07 MDT 2000

• removed %%GENEX-EXTRALIBS%% this broke make test because the use 'lib' made perl find those libs before the new ones in blib.

0.20 Tue Jun 6 16:57:40 MDT 2000

• DBUtils.pm: Moved all functions in @EXPORT to @EXPORT_OK. Added fetch_fkey_list(). Added caching to assert_table_defined() ==> much faster for repetitive asserts.
• Genex.pm: undefined() handles fetching fkeys as objects.
• All classes: new fkey type: LOOKUP_TABLE fkeys. delayed_fetch flag is gone, instead it works by default Added fkey_objects, fetch_all, fetch_fkey_fkeys, fetch_lt_fkeys, fetch_otm_fkeys flags. Cleaned up fetching of fkeys as objects. Documented in comments and pod.
• new classes:

  UserSequenceFeature.pm ExternalDatabase.pm ExperimentFactors.pm CanonicalSequenceFeature.pm BlastHits.pm

• fetch_es.pl: Added security check to make sure that CGI parameters haven't been modified. Now use filtering on technology types. Had to add DISTINCT flag to select statement, and prepend table name to columns requested.
• fetch_array.pl: Added security check to make sure that CGI parameters haven't been modified.
• fetch_spot.pl.in: Added security check to make sure that CGI parameters haven't been modified.
• query-intro.pl.in: Technology types are now fetched from DB. Values are now sorted so defaults come to the top.
• DBUtils.pm.in: Added a DISTINCT option to create_select_sql().

0.18 Wed May 31 16:34:48 MDT 2000

• DBUtils.pm.in: Added three new helper functions:

  fetch_es_ids -- gets a list of all available experiment set ids

  from the DB. fetch_am_ids -- gets a list of all available array measurement

  ids for a given experiment from the DB. output_spot_data -- writes all spot data for a given experiment

  set to a filehandle.

0.17 Fri May 26 16:34:48 MDT 2000

• added fetch_spot.pl for retrieval of spot data in downloadable tab delimited files
• Added ONLY_ONE_ES parameter to enable a generic interface to the combination of query-intro.pl/fetch_es.pl/fetch_array.pl
• query-intro.pl can now filter on species
• fetch_es.pl can now filter on array type
• HTMLUtils::post_process() now filters out logins and passwords
• All objects can be called in a recursive fetch mode. If fetch is called with a numeric parameter (e.g. $array->fetch(2)), that parameter is used to specify the depth of the recursive fetch -- this is used for following fkeys.
• renamed mksub.pl to create_genex_class.pl
• Added classes:

  Spotter.pm Software.pm Scanner.pm Sample.pm Protocol.pm ExperimentSet.pm ArrayMeasurement.pm ArrayLayout.pm

0.16 Tue May 23 13:51:28 MDT 2000

• fixed dangerous problem with caching the current database handle => calling disconnect() didn't undefine the handle, just removed the backend connection.
• fixed dangerous bug in Bio::Genex::undefined()
• fixed grammar bug in cgi scripts

0.15 Mon May 22 16:58:30 MDT 2000

• added changes for latest ObjectTemplate.pm
• added Genex.t regression tests
• added HTMLUtils.t regression tests
• added DBUtils.t regression tests
• now HTMLUTils::post_process() uses autofetch on all attributes.

0.14 Thu May 18 17:36:08 MDT 2000

• Modified HTMLUtils::post_process() to use the object interface instead of using DBI queries ==> WOW!!

0.13 Thu May 18 16:47:29 MDT 2000

• Added trial sytle sheet, used it in query-intro.pl
• added get_groups() to mksub.pl
• fetch_table.pl now used instead of other scripts
• modified fetch_table.pl to use object interface instead of rolling it's own DBI queries.

0.12 Wed May 17 17:46:14 MDT 2000

• bug fix in fetch_table.pl to print out the header using the table name. Also added defaults for all parameters

0.11 Wed May 17 16:16:48 MDT 2000

• Makefile.PL now puts Genex.pm in the right place
• Added DBUtils.pm.in
• Added HTMLUtils.pm.in
• moved post_process() to HTMLUtils
• created fetch_table.pl to handle generic tables
• added UserSec.pm and GroupSec.pm

0.10 Tue May 16 13:12:02 MDT 2000

• Makefile.PL now queries user if environment variables are not defined
• Makefile.PL now saves cache of user data

0.01 Sat Feb 5 10:11:52 2000

• original version; created by h2xs 1.19

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