Tue Dec 12 15:03:39 MST 2000
* implement caching in control bundle retrieval

Sat Nov 11 14:22:16 MST 2000
Priority 1 
==========
* expset-login.pl CGI script needs to be updated to use cached data
* Hatfield ES in DB needs to have its AM's updated (at least adding a
  new AM for each data point w/o the spot reps separated out
* copyright and headers for all files
FIXED ==> * ensure all scripts that access UserSec:password use
  Bio::Genex::DBUtils::check_password() to crypt()/de-crypt() entries

Priority 2
==========
* DB schema to support security and updates
* DB schema to support separate one/two channel tables
* MGED XML
* checkin code to CVS - local
* checkin code to CVS - openqenex
* XDF
* XML dump for Brown Hatfield

Priority 3
==========
* addgroup CGI script
* test xml2db with output from db2xml
* fix Genex.pm install
* adduser CGI script
* last_updated fields in DB
* new DB security tables

Wed Nov  8 19:40:26 MST 2000
* create Bio::Genex::DBUtils::check_password()
* ensure that scripts that access UserSec:password use check_password()

Wed Nov  1 17:28:17 MST 2000
* fix current_connection() to take parameters. rename it to be
  connect()

Mon Oct 30 15:01:16 MST 2000
FIXED ==>  * All ratio AM's written to same <array>. Probably has to do with:
      Use of uninitialized value in hash element at
        ./scripts/db2xml.pl line 2320.
FIXED ==>  * ration AM's seem to be being given channels even though
    channel_name should be undefined: Use of uninitialized value in
       concatenation (.) at ./scripts/db2xml.pl line 2061. 
FIXED ==>  * cy5 channels have empty <measurement_factor_value_list/>'s
FIXED ==>  * each <treatment_list> has three empty <treatment/>'s
FIXED ==>  * all <treatment_factor>'s have value=1
FIXED ==>  * the non-empty <treatment>'s have empty <treatment_array_list/>'s
FIXED ==>  * use DBI::quote in get_objects()
FIXED ==>  * when calling get_objects({column=>foo, value=>bar,
    pkey_link=>baz}) $pkey_name should not get stomped on. Also, 'ALL'
    pkey_link=>should not be specified. 
FIXED ==>  * get_objects() should not have the same result as
    get_objects('ALL'), or it should give a warning.
  * XMLUtils::pretty_print() must not remove all newlines
FIXED ==>  * initialize() should only do DB query if the values have not been
    returned by a DB query.
  * fix get_objects(@id) so that it functions identical to
    get_objects('ALL') 

Mon Oct 23 16:48:31 MST 2000
FIXED ==> * num_chromosomes not getting written to control-bundle
FIXED ==> * protocol:text written as single line

Thu Oct 19 09:36:52 MST 2000
* for gxquery
FIXED ==>   * gxquery1.pl: providers are not being reported
FIXED ==>   * gxfetch_es1.pl: cit_fk not getting translated
FIXED ==>   * gxfetch_array1.pl: wants to be split into a download, and analysis
    page, type not getting translated

* Controlled Vocab issues
  * AL_DefaultSpotConcUnits.xml seems to be for individual spots not
    layout
  * AL_IdentifierCode.xml is stupid
  * CSF_Type.xml has extra terms
FIXED ==>  * ContactType.xml: technology_media, data_provider_protocol can't be
    used by DB; software_analysis overlaps with software_image
FIXED ==>  * EF_MajorCategory.xml and EF_MinorCategory.xml need to be looked at
FIXED ==>  * SW_Name.xml, SPT_ModelDescription.xml, SCN_ModelDescription.xml
    are creating too much work
  * SMP_GeneticStatus.xml is too generic, most terms overlap

Wed Oct  4 22:36:18 MST 2000
FIXED ==> * {USF,CSF}_ExternalDBLink has db_name() as an OO fkey method, it
  should have db_name_obj()

Tue Oct  3 12:35:33 MST 2000
* changes for xml2db.pl: 
  * remove hard-coded dates (line 249)
  * switch to create_{insert,select}_sql()
  * switch to fetch_last_value() (line 1232)
  * make error messages more verbose
  * why this? 'login => join('', split / /,
    $content{contact_person}),'
  * find better way to transmit usersec information than hardcoding
    login and password as Contact:contact_person
  * hard-coding of array_measurement type (line 997)

Tue Sep 26 21:40:19 MST 2000
* fix CSF_ExternalDBLink::db_name ==> two methods...
* fix CanonicalSequenceFeature::relatedcsf_fk ==> two methods...
* install_cgi only works with 5.6

Mon Sep 25 14:54:58 MST 2000
FIXED ==> * make Bio::Genex::undefined call fetch_fkey_list() for all OTM types, and
  then have fetch_fkey_list() decide whether to call get_matrix() or
  not depending on the status of a class variable that defaults to
  true for the LT classes.
* Get rid of OTM_LT and OTM_LINK fkeys (and their _OO mirrors), and
  replace their usage with OTM fkeys. This should be simple after
  replacing the $lt_fkey usage in create_genex_class.pl
FIXED ==> * need to make MTO fkeys act like FKEY fkeys

Sun Sep 24 22:20:41 MST 2000
* documentation on attributes needs to be expanded

Sat Sep 23 16:22:05 MST 2000
* !!!HUGE MAJOR API CHANGE!!!
  Having these two fkey modes 'raw' and 'object' that allows the same
  method to be invoked in two different ways doesn't work. The code is
  broken and must be fixed. Instead raw fkey values will be accessed
  through the existing $obj->blah_fk() method, and objects are
  accessed through a new $obj->foo_obj() method.
FIXED ==> * fkey properties must be transferred to the OO method.
GONE ==> * get rid of recursive fetch
GONE ==> * get rid of no_fkey_objects
GONE ==> * get rid of fetch_fkey_fkeys, fetch_otm_fkeys 
FIXED ==> * fix get_objects(@id_list) so that bogus pkey values don't return
  objects
FIXED ==> * fix all code in create_genex_class.pl to use new OO fkey methods
FIXED ==> * fix all documentation in create_genex_class.pl
FIXED ==> * fix all code in Genex.pm to use new OO fkey methods
FIXED ==> * fix all code in DBUtils.pm, HTMLUtils.pm and XMLUtils.pm
  to use new OO fkey methods
FIXED ==> * fix all tests to use new OO fkey methods
FIXED * fix all code in scripts to use new OO fkey methods
FIXED ==> * fix all code in xml-write.pl to use new OO fkey methods

Fri Sep 22 11:27:26 MST 2000
FIXED ==> * Change the fkey code. The blah_fk() methods should always return
  *raw* fkey values. A corresponding blah() function is created that
  accesses the slot as OO interface.
* move Jiaye's XML2DB.pl to Genex.pm interface

Thu Sep 21 14:41:57 MST 2000
* fix length on ExternalDatabase:urls
FIXED ==> * why does pbrown experiment print 2 CSF tables

Wed Sep 20 14:40:31 MST 2000
FIXED ==> * CSF/USF files are printed in output even if not written
   (A. Thaliana) 

Tue Sep 19 13:46:48 MST 2000
FIXED ==> * multiple <groups> get written for same id
FIXED ==> * <treatment_factors> are written to <treatment_array_list>
FIXED ==> * all contacts are being written for do_experiments()
FIXED ==> * con_pk is being written out
FIXED ==> * multiple <experiment_factor_list> being written to same <array>
FIXED ==> * multiple <array_measurement_lists> are added to <array>
FIXED ==> * make sure local_accession gets written for <experiment_set>

Sat Sep 16 14:30:50 MST 2000
FIXED ==> * fix Makefile so that cgi scripts get installed on 'make
  install' and not on 'make' 
Fri Sep 15 19:43:24 MST 2000
FIXED ==> * change do_misc(), change user_name to be UserSec:login
FIXED ==> * change genex.ncgr.org DB experiment names

Thu Sep 14 16:22:35 MST 2000
FIXED ==> * treatment_factor_list apparently not being output for treatment
	elements
FIXED ==> * ensure that citation, software, scanner, and protocol are written
  out. 

Sat Sep  9 00:22:08 MST 2000
FIXED ==> * fix geml.dtd, so that <array> has all params

Thu Sep  7 15:10:23 MST 2000
* add checking to current_connection, so that if any of the connection
  parameters are different than the settings for the current dbh,
  close the current connection and open a new one.

Tue Sep  5 10:59:37 MST 2000
FIXED ==> * remove AM_Group
FIXED ==> * fix Makefile.PL so that prompt has default answer

Mon Sep  4 11:05:47 MST 2000
FIXED ==> * fix call to do_contacts() in do_experiment() so that it writes only
  the contacts for that experiment

Thu Aug 31 12:36:27 MST 2000
FIXED ==> * properly handle writing of multiple experiment sets

Wed Aug 30 16:19:32 MST 2000
FIXED ==> * fix classes so that a lookup on an fkey that results in only
  whitespace returns undef and not an object 
FIXED ==> * include dtd in xml files
FIXED ==> * accept dir_name for writing, return file list
FIXED ==> * add experiment names to control bundle
FIXED ==> * get do_control_bundle() to output CSF
FIXED ==> * File name convention ==> control-bundle.xml
                           control-bundle_{ALS,CSF,USF}NN.ext
                           exp-set-name.xml
                           exp-set-name_{AMS,ALS,CSF,USF}NN.ext

Tue Aug 29 10:18:13 MST 2000
FIXED ==> * make do_al() callable by do_array() when needed
FIXED ==> * Ensure that all elements that have ID attributes call create_id() (TIME => 2h)
FIXED ==> * Ensure that all elements that have IDREF attributes call lookup_id() (TIME => 2h)
FIXED ==> * Rewrite lookup_id(). If it detects that the ID being requested is
  not yet stored in the XML file, it should fetch it from the DB and
  store it, before returning the ID. (TIME => 4h) 
FIXED ==> * Remove debugging code in do_usf() and do_al() that sets _LIMIT. (TIME => 30m)
FIXED ==> * Fix hard coded USF names in xml-write.pl line 994. Instead must
  decide whether usf_name is gene_name or serial_orf dynamically. (TIME => 1h)

Sun Aug 27 19:47:28 MST 2000
FIXED ==> * rewrite Bio::Genex::undefined() so that a Bio::Genex::Fkey object is
  called to dispatch the fetching of the data.

Tue Aug 22 19:34:07 MST 2000
* document one-to-many-link fkeys in create-genex-class.pl

Sun Jun 18 10:35:20 MDT 2000
FIXED ==> * change $_USE_CACHE ==> $USE_CACHE and $_LIMIT ==> $LIMIT
FIXED ==> * add HTMLUtils::objs2html()
FIXED ==> * add {column=>$col,value=>$val} options to get_objects().

Tue Jun 13 22:39:16 MDT 2000
FIXED ==> * add OTM_LINK fkey, so that Bio::Genex::undefined() can call
  fetch_fkey_list with the proper info and not call classname->pkey_name
				   
Fri Jun  9 12:15:45 MDT 2000
FIXED ==> * Add dbms(), db_name(), db_host() methods to Bio::Genex::Connect()
FIXED ==> * Require a Bio::Genex::Connect in DBUtils
FIXED ==> * write an assert_dbh() method for DBUtils so that all the error
  checking is in one function

Thu Jun  8 09:59:35 MDT 2000
FIXED ==> * Fix Makefile.PL so that there is a default on the extra library
  question.
FIXED ==> * fix DBUtils::create_insert_sql() to accept values as well as
  placeholders 

Wed Jun  7 19:41:55 MDT 2000
FIXED ==> * add a fetch_es_spot_values() helper function to DBUtils that fetches
  all array and spot data for a given experiment set
FIXED ==> * get rid of 'recursive_fetch'
FIXED ==> * implement object caching in Classes
FIXED ==> * add $LIMIT to all classes
FIXED ==> * add LIMIT clause to create_select_sql
* test linking table classes better
* test lookup table classes better
				   
Mon Jun  5 21:32:54 MDT 2000
FIXED ==> * Fix LOOKUP_TABLE fkey, there needs to be a OTM_LT fkey
FIXED ==> * Need a better way to specify which types of fkey_objects get fetched
  during a fetch(), in undefined(), or with fetch_fkey_list(), or
  get_objects() . One idea was to add three attributes: fetch_fkey,
  fetch_lt_fkey, fetch_otm_fkey. The values of these are used to
  determine what is fetched. 

Sun Jun  4 16:29:52 MDT 2000
FIXED ==> * eliminate 'delayed_fetch' by making it always on
FIXED ==> * add LOOKUP_TABLE fkeys
FIXED ==> * move fetch_otm_list() from create_genex_class.pl to DBUtils
FIXED ==> * deal properly with fkey_accessors in Bio::Genex::undefined

Sat Jun  3 10:18:20 MDT 2000
FIXED ==> * Add tests for get_objects()
FIXED ==> * redo attributes() call in create_genex_class.pl so that we have
  attributes that are not automatically looked-up, and those that
  are. 
FIXED ==> * add @COLUMN_NAMES TO create_genex_class.pl
FIXED ==> * redo Bio::Genex::undefined so that it handles attributes that aren't
  looked up automatically

Fri Jun  2 11:05:04 MDT 2000
FIXED ==> * Fix documentation bug for fkey methods
FIXED ==> * fix bug in ObjectTemplate where calling foo(undef) calls
   setter and triggers undefined(); 
* Document MANIFEST to let people know what the files are
FIXED ==> * Deal with linking tables
FIXED ==> * It should not be an error to call an fkey accessor with delayed
  fetch, it should work if 'id' is set, or else it should be a warning

Wed May 31 16:30:49 MDT 2000
FIXED ==> * Fix security bug, input from HTML form is being used directly in SQL query. 
FIXED ==> * change all the sql WHERE list generating code to use join() per
  Andrew's suggestion  

Thu May 25 16:06:51 MDT 2000
FIXED ==> * Add filter to fetch_es.pl that enables only selection of:
  - primary_raw
  - background_corrected
  - derived_ratio
FIXED ==> * modify fetch_array.pl to include the array fkey as "es_fk:array_pk"
  so that fetch_spot.pl can write the arrays to different output
  files. 
FIXED ==> * modify query-intro.pl, fetch_es.pl, and fetch_arry.pl to accept an
  'ONLY_ONE_ES' parameter. This will cause fetch_array.pl to signal an
  error if it receives more than one exp_set.
FIXED ==> * create fetch_spot.pl
* Add link table between ExperimentSet and Species
FIXED ==> * Can fudge Species filter in fetch_es.pl by:
  - SELECT am_pk FROM ArrayMeasurement WHERE primary_es_fk = $es_pk LIMIT 1
  - SELECT usf_fk FROM AM_spots WHERE am_fk = $am_pk LIMIT 1
  - SELECT spc_fk FROM UserSequenceFeature WHERE usf_pk = $usf_fk

Wed May 24 17:57:33 MDT 2000
FIXED ==> * Add new .t files for all modules
FIXED ==> * Add new tests for recursion fetch

Tue May 23 11:24:13 MDT 2000
FIXED ==> * Add data retreival button to fetch_array.pl
FIXED ==> * add xml writing capability for entire experiment set.
* add xml writing capability for individual data pieces.
FIXED ==> * add TAB writing capability for entire array
FIXED ==> * Fix grammer error in fetch_* pages. If table name ends in 's', no
  's' should be added to plural.
FIXED ==> * Fix query-intro.pl to use Species to restrict query
FIXED ==> * Fix query-intro.pl to properly show technology types
FIXED ==> * Fix problem with calling disconnect() on a handle stored by
  Bio::Genex::current_connection();

Mon May 22 16:58:30 MDT 2000
FIXED ==> * find out why the Pat Brown user and group links don't work
FIXED ==> * fix the trailing '/' problem on the Make parameters
* Add these fkeys to HTMLUtils::post_process()
FIXED  - ams_fk
FIXED  - als_fk
FIXED  - tl_fk
FIXED  - sptr_fk
FIXED  - scn_fk
FIXED  - prt_fk
FIXED  - ef_fk
FIXED  - db_name
FIXED  - smp_fk
FIXED  - owner_us_fk
FIXED  - primary_es_fk
FIXED  - al_fk
FIXED  - image_anal_sw_fk
FIXED  - spotter_sw_fk
FIXED  - scan_sw_fk
FIXED  - csf1_csf_fk
FIXED  - csf2_csf_fk
FIXED  - csf_fk
FIXED  - putative_csf_fk
FIXED  - es_fk
FIXED  - ratio_am_fk
FIXED  - am_fk

* Add new modules: 
FIXED  - ExperimentSet.pm
FIXED  - ArrayMeasurement.pm
FIXED  - AM_Group.pm
FIXED  - ArrayLayout.pm
FIXED  - Sample.pm
FIXED  - UserSequenceFeature.pm
FIXED  - CanonicalSequenceFeature.pm
FIXED  - Scanner.pm
FIXED  - Spotter.pm
FIXED  - Software.pm
FIXED  - ExternalDatabase.pm
FIXED  - BlastHits.pm
FIXED  - SampleProtocols.pm => LINK
FIXED  - Protocol.pm
FIXED  - HotSpots.pm => LINK
FIXED  - ExperimentFactors.pm
FIXED  - AM_FactorValues.pm => LINK
FIXED  - TL_FactorValues.pm => LINK
FIXED  - TreatmentLevel.pm
FIXED  - GroupLink.pm ==> array of groups/users
FIXED  - USF_ExternalDBLink.pm ==> array of DB/SF
FIXED  - CSF_ExternalDBLink.pm ==> array of DB/SF
FIXED  - RelatedCSF.pm ==> array of CSF
FIXED  - Treatment_AMs.pm ==> array of TreatmentLevels/ArrayMeasurements
FIXED  - AM_Spots.pm
FIXED  - AL_Spots.pm

Thu May 18 18:22:46 MDT 2000
FIXED ==> * Fix ObjectTemplate so that autofetch works again


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