Difference between revisions of "CoGe v5"

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Line 64: Line 64:
 
* user_group_data_connector
 
* user_group_data_connector
 
* list_connector
 
* list_connector
 +
* user_group_feature_list_permission_connector
  
 
====Rename====
 
====Rename====
Line 100: Line 101:
 
** feature_type_id -> int(11)
 
** feature_type_id -> int(11)
 
** dataset-id -> int(11)
 
** dataset-id -> int(11)
−
*feature_annotation: link -> text
+
*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
 +
 
  
  

Revision as of 18:31, 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)


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)
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