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

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

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)