View source for CoGe v5

== Updating database: ==

Overview:  Major changes to have the database is structured.
* added section for experiment metadata
* updated how lists of data are managed in the system
* updated how user_groups connect to data (all through lists)


==Step-by-step modifications:==
===Modules===
====Additions====
* ExperimentListConnector.pm
* GenomeListConnector.pm
* FeatureListConnector.pm
* ListAnnotation.pm

====Deleted====
* ListConnector.pm
* Sequence.pm
* SequenceType.pm
* Quantitation.pm
* QuantitationExperiment.pm
* UserGroupDataConnector.pm

====Modified====
* Experiment.pm: deleted column "link"
* ExperimentAnnotation.pm added column "link"
* Feature.pm: delete relationship to sequences
* Feature.pm: delete relationship to quantiations
* Feature.pm: deleted sub seqs
* DatasetGroup.pm: remove relationship to UserGroupDatasetConnector
* List.pm: Added column "lock"
* List.pm: Added column "user_group_id"
* LIst.pm: Remove column "link"
* List.pm: Remove column "notes"
* List.pm: Remove column "user_id"
* List.pm: Changed column "list_group_id" to "list_collection_id"
* List.pm: Changed column "public" to "restricted"
* List.pm: added relationship: experiment_list_connectors
* List.pm: added relationship: genome_list_connectors
* List.pm: added relationship: feature_list_connectors
* List.pm: added relationship: list_annotations
* List.pm: changed relationship: list_group to list_colelction
* List.pm: changed relationship: user to user_group
* ListType.pm:  removed function groups
* ListGroup.pm:  Name Changed to List Collection
* ListCollections: Change Module header name: update all references to list_group
* ListCollections: Changed column list_group_id to list_connection_id
* ListCollections: Delete column user_id
* ListCollections: Changed column public to restricted
* AnnotationType:  added relationship to FeatureAnnotation
* Annotation renamed to FeatureAnnotation and updated
* ResultSet/Annotation renamed to ResultSet/FeatureAnnotation
* Feature: updated relationship annotations to feature_annotations
* UserGroup: removed relationship to user_group-data_connector
* UserGroup: added relationship to lists

===Tables===
====Delete====
* sequence
* sequence_type
* quantitation
* quantitation_experiment
* user_group_data_connector
* list_connector
* user_group_feature_list_permission_connector

====Rename====
 RENAME TABLE old_name TO new_name
* dataset_group to genome
* annotation to feature_annotation
* list_group to list_collection

====Modify tables====
*genome: change dataset_group_id to genome_id
*experiment: remove link
*experiment: dataset_group_id to genome_id
*genomic_sequence: dataset_group_id to genome_id
*dataset_connector: dataset_group_id to genome_id
*experiment: add link
*list:
** change list_group_id to list_connector_id
** remove notes
** remove link
** remove user_id
** change public to restrict
** add locked
* list_collection: 
** change public to restricted
**  change list_group_id to list_collection_id
** remove note
** remove user_id
'''table values'''
*data_source:  change int size for index to 11
*dataset
** change name size to 255
** change description size to 1024
* experiment_type: changed description type to varchar 1024
*feature:
** feature_id -> int(11)
** feature_type_id -> int(11)
** dataset-id -> int(11)
*feature_annotation: link -> text (Failed - table too big)
*feature_type: feature_type_id -> int(11)
*genome_sequence_type: id->int(11); name-> varchar 255
* image
** id-> int(11)
** name->255
** description -> 1024
* organism
** id-> int(11)
** name -> 255
*permission
** id-> 11
** name ->255
* user
** id->11
*user_group
** id->11
** name->255
** desc->1024
* user_group_connector
** all ids -> 11
* user_session
** ids->11
web_preferences
**id -> 11


'''Delayed changes''' (table are too big to do on SSD)
* location
* feature_annotation





====New====
* experiment_list_connector
* genome_list_connector
* feature_list_connector
* list_annotation



== Usage patterns ==

*New User:  During account creation:
** a Locked User Group belonging to the user is created with permission "Owner"
** a Locked List belonging to the Locked User Group is created.  The list_type for this group is "Owner"
** Neither of these may be deleted.  New data added by the user (or on the user's behalf by an Admin) is added to the locked list.

==To Do: ==

*Modify DatasetGroup.pm->user_groups()
* Update List.pm: functions to access items in lists (genomes, features, experiments)
*