Difference between revisions of "CoGe v5"
From CoGepedia
| Line 1: | Line 1: | ||
| − | + | = Updating database: == | |
Overview: Major changes to have the database is structured. | Overview: Major changes to have the database is structured. | ||
Revision as of 07:56, 1 August 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)
Contents
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
- 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()
- Update List.pm: functions to access items in lists (genomes, features, experiments)
