Difference between revisions of "CoGe v5"
From CoGepedia
| Line 13: | Line 13: | ||
* GenomeListConnector.pm | * GenomeListConnector.pm | ||
* FeatureListConnector.pm | * FeatureListConnector.pm | ||
| + | * ListAnnotation.pm | ||
====Deleted==== | ====Deleted==== | ||
| Line 42: | Line 43: | ||
* List.pm: changed relationship: list_group to list_colelction | * List.pm: changed relationship: list_group to list_colelction | ||
* List.pm: changed relationship: user to user_group | * 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 | * experiment_list_connector | ||
| Line 57: | Line 71: | ||
*Modify DatasetGroup.pm->user_groups() | *Modify DatasetGroup.pm->user_groups() | ||
| + | * Update List.pm: functions to access items in lists (genomes, features, experiments) | ||
| + | * | ||
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)
