Difference between revisions of "CoGe v5"

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(Created page with ' == 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 sys...')
 
(→‎Modify tables)
 
(11 intermediate revisions by the same user not shown)
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== Updating database: ==
+
== Updating database: ==
  
 
Overview:  Major changes to have the database is structured.
 
Overview:  Major changes to have the database is structured.
Line 13: Line 13:
 
* GenomeListConnector.pm
 
* GenomeListConnector.pm
 
* FeatureListConnector.pm
 
* FeatureListConnector.pm
 +
* ListAnnotation.pm
  
 
====Deleted====
 
====Deleted====
Line 28: Line 29:
 
* Feature.pm: delete relationship to quantiations
 
* Feature.pm: delete relationship to quantiations
 
* Feature.pm: deleted sub seqs
 
* 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
 +
* list_group_image_connector to list_collection_image_connector
 +
 +
====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
 +
** added user_group_id
 +
** add locked
 +
* list_collection:
 +
** change public to restricted
 +
**  change list_group_id to list_collection_id
 +
** remove note
 +
** remove user_id
 +
*list_collection_image_connector: updated id
 +
*user: add locked
 +
 +
'''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
 
* experiment_list_connector
 
* genome_list_connector
 
* genome_list_connector
 
* feature_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)
 +
* if ($obj->restricted && !$obj->has_access($user) {#skip}

Latest revision as of 14:26, 3 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
  • list_group_image_connector to list_collection_image_connector

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
    • added user_group_id
    • add locked
  • list_collection:
    • change public to restricted
    • change list_group_id to list_collection_id
    • remove note
    • remove user_id
  • list_collection_image_connector: updated id
  • user: add locked

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)
  • if ($obj->restricted && !$obj->has_access($user) {#skip}
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