Difference between revisions of "CoGe v5"

Revision as of 17:47, 31 July 2012

== 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

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

• experiment_list_connector
• genome_list_connector
• feature_list_connector

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()