Module detail: DB.pm

NAME

ArrayExpress::AutoSubmission::DB - Class::DBI based interface to the autosubmissions tracking database.

SYNOPSIS

 use ArrayExpress::AutoSubmission::DB::Experiment;
 my $expt = ArrayExpress::AutoSubmission::DB::Experiment->retrieve( $id );

DESCRIPTION

This module is the abstract superclass for a set of Class::DBI - based modules, which are used as an object-relational mapping to the underlying submissions tracking database (currently implemented using MySQL). You should not use this class directly; rather, you should use the relevant table subclasses to query the database (see SYNOPSIS for an example). Please refer to the Class::DBI documentation for information on query syntax.

TABLES

Included below are auto-generated descriptions of the MySQL tables. This listing was generated using the SQL::Translator::Producer::POD module.

array_designs

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

miamexpress_subid

• int(11)
• Default 'NULL'
• Nullable 'Yes'

accession

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

miamexpress_login

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

status

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

data_warehouse_ready

• char(15)
• Default 'NULL'
• Nullable 'Yes'

date_last_processed

• datetime
• Default 'NULL'
• Nullable 'Yes'

comment

• text(65535)
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

miame_score

• int(11)
• Default 'NULL'
• Nullable 'Yes'

in_data_warehouse

• int(11)
• Default 'NULL'
• Nullable 'Yes'

annotation_source

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

annotation_version

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

biomart_table_name

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

release_date

• datetime
• Default 'NULL'
• Nullable 'Yes'

is_released

• int(11)
• Default 'NULL'
• Nullable 'Yes'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = miamexpress_subid

array_designs_experiments

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

array_design_id

• int(11)
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = array_design_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = array_design_id
• Reference Table = array_designs
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

array_designs_organisms

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

organism_id

• int(11)
• Nullable 'No'

array_design_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = organism_id

NORMAL

• Fields = array_design_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = organism_id
• Reference Table = organisms
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = array_design_id
• Reference Table = array_designs
• Reference Fields = id
• On delete = CASCADE

categories

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

ontology_term

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

display_label

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

is_common

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_bmc

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_fv

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

categories_designs

FIELDS

category_id

• int(11)
• Nullable 'No'

design_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = category_id

NORMAL

• Fields = design_id

CONSTRAINTS

FOREIGN KEY

• Fields = category_id
• Reference Table = categories
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = design_id
• Reference Table = designs
• Reference Fields = id
• On delete = CASCADE

categories_materials

FIELDS

category_id

• int(11)
• Nullable 'No'

material_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = category_id

NORMAL

• Fields = material_id

CONSTRAINTS

FOREIGN KEY

• Fields = category_id
• Reference Table = categories
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = material_id
• Reference Table = materials
• Reference Fields = id
• On delete = CASCADE

categories_taxons

FIELDS

category_id

• int(11)
• Nullable 'No'

taxon_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = category_id

NORMAL

• Fields = taxon_id

CONSTRAINTS

FOREIGN KEY

• Fields = category_id
• Reference Table = categories
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = taxon_id
• Reference Table = taxons
• Reference Fields = id
• On delete = CASCADE

data_files

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

is_unpacked

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id

data_formats

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(50)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = name

design_instances

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

design_id

• int(11)
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = design_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = design_id
• Reference Table = designs
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

designs

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

display_label

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

ontology_category

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

ontology_value

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

design_type

• char(15)
• Nullable 'No'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

events

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

array_design_id

• int(11)
• Default 'NULL'
• Nullable 'Yes'

experiment_id

• int(11)
• Default 'NULL'
• Nullable 'Yes'

event_type

• varchar(50)
• Nullable 'No'

was_successful

• int(11)
• Default 'NULL'
• Nullable 'Yes'

source_db

• varchar(30)
• Default 'NULL'
• Nullable 'Yes'

target_db

• varchar(30)
• Default 'NULL'
• Nullable 'Yes'

start_time

• datetime
• Default 'NULL'
• Nullable 'Yes'

end_time

• datetime
• Default 'NULL'
• Nullable 'Yes'

machine

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

operator

• varchar(30)
• Default 'NULL'
• Nullable 'Yes'

log_file

• varchar(511)
• Default 'NULL'
• Nullable 'Yes'

jobregister_dbid

• int(15)
• Default 'NULL'
• Nullable 'Yes'

comment

• text(65535)
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = array_design_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = array_design_id
• Reference Table = array_designs
• Reference Fields = id

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id

experiments

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

accession

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

user_id

• int(11)
• Default 'NULL'
• Nullable 'Yes'

checker_score

• int(11)
• Default 'NULL'
• Nullable 'Yes'

software

• varchar(100)
• Default 'NULL'
• Nullable 'Yes'

status

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

data_warehouse_ready

• int(11)
• Default 'NULL'
• Nullable 'Yes'

date_last_edited

• datetime
• Default 'NULL'
• Nullable 'Yes'

date_submitted

• datetime
• Default 'NULL'
• Nullable 'Yes'

date_last_processed

• datetime
• Default 'NULL'
• Nullable 'Yes'

in_curation

• int(11)
• Default 'NULL'
• Nullable 'Yes'

curator

• char(30)
• Default 'NULL'
• Nullable 'Yes'

comment

• text(65535)
• Nullable 'Yes'

experiment_type

• char(30)
• Default 'NULL'
• Nullable 'Yes'

miamexpress_login

• char(30)
• Default 'NULL'
• Nullable 'Yes'

miamexpress_subid

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_affymetrix

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_mx_batchloader

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

miame_score

• int(11)
• Default 'NULL'
• Nullable 'Yes'

in_data_warehouse

• int(11)
• Default 'NULL'
• Nullable 'Yes'

num_submissions

• int(11)
• Default 'NULL'
• Nullable 'Yes'

submitter_description

• text(65535)
• Nullable 'Yes'

curated_name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

num_samples

• int(11)
• Default 'NULL'
• Nullable 'Yes'

num_hybridizations

• int(11)
• Default 'NULL'
• Nullable 'Yes'

has_raw_data

• int(11)
• Default 'NULL'
• Nullable 'Yes'

has_processed_data

• int(11)
• Default 'NULL'
• Nullable 'Yes'

release_date

• datetime
• Default 'NULL'
• Nullable 'Yes'

is_released

• int(11)
• Default 'NULL'
• Nullable 'Yes'

ae_miame_score

• int(11)
• Default 'NULL'
• Nullable 'Yes'

ae_data_warehouse_score

• int(11)
• Default 'NULL'
• Nullable 'Yes'

INDICES

NORMAL

• Fields = user_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = user_id
• Reference Table = users
• Reference Fields = id

experiments_factors

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

factor_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = experiment_id

NORMAL

• Fields = factor_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = factor_id
• Reference Table = factors
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

experiments_loaded_data

FIELDS

experiment_id

• int(11)
• Nullable 'No'

loaded_data_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = experiment_id

NORMAL

• Fields = loaded_data_id

CONSTRAINTS

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = loaded_data_id
• Reference Table = loaded_data
• Reference Fields = id
• On delete = CASCADE

experiments_quantitation_types

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

quantitation_type_id

• int(11)
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = quantitation_type_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = quantitation_type_id
• Reference Table = quantitation_types
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

factors

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(128)
• Nullable 'No'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

loaded_data

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

identifier

• varchar(255)
• Nullable 'No'

md5_hash

• char(35)
• Nullable 'No'

data_format_id

• int(11)
• Nullable 'No'

is_deleted

• int(11)
• Nullable 'No'

platform_id

• int(11)
• Default 'NULL'
• Nullable 'Yes'

needs_metrics_calculation

• int(11)
• Nullable 'No'

date_hashed

• datetime
• Default 'NULL'
• Nullable 'Yes'

INDICES

NORMAL

• Fields = data_format_id

NORMAL

• Fields = platform_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = platform_id
• Reference Table = platforms
• Reference Fields = id

FOREIGN KEY

• Fields = data_format_id
• Reference Table = data_formats
• Reference Fields = id

loaded_data_quality_metrics

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

value

• decimal(12,5)
• Default 'NULL'
• Nullable 'Yes'

quality_metric_id

• int(11)
• Nullable 'No'

loaded_data_id

• int(11)
• Nullable 'No'

date_calculated

• datetime
• Default 'NULL'
• Nullable 'Yes'

INDICES

NORMAL

• Fields = quality_metric_id

NORMAL

• Fields = loaded_data_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = loaded_data_id
• Reference Table = loaded_data
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = quality_metric_id
• Reference Table = quality_metrics
• Reference Fields = id
• On delete = CASCADE

material_instances

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

material_id

• int(11)
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = material_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = material_id
• Reference Table = materials
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

materials

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

display_label

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

ontology_category

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

ontology_value

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

meta

FIELDS

name

• varchar(128)
• PRIMARY KEY
• Default ''
• Nullable 'No'

value

• varchar(128)
• Default ''
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = name

organism_instances

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

organism_id

• int(11)
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = organism_id

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = organism_id
• Reference Table = organisms
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id
• On delete = CASCADE

organisms

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

scientific_name

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

common_name

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

accession

• int(11)
• Default 'NULL'
• Nullable 'Yes'

taxon_id

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = taxon_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = taxon_id
• Reference Table = taxons
• Reference Fields = id

permissions

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(40)
• Nullable 'No'

info

• varchar(80)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

permissions_roles

FIELDS

role_id

• int(11)
• Nullable 'No'

permission_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = role_id

NORMAL

• Fields = permission_id

CONSTRAINTS

FOREIGN KEY

• Fields = role_id
• Reference Table = roles
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = permission_id
• Reference Table = permissions
• Reference Fields = id
• On delete = CASCADE

platforms

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(50)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = name

protocols

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

accession

• char(15)
• Default 'NULL'
• Nullable 'Yes'

user_accession

• varchar(100)
• Default 'NULL'
• Nullable 'Yes'

expt_accession

• char(15)
• Default 'NULL'
• Nullable 'Yes'

name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

date_last_processed

• datetime
• Default 'NULL'
• Nullable 'Yes'

comment

• text(65535)
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = accession

quality_metrics

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

type

• varchar(50)
• Nullable 'No'

description

• text(65535)
• Nullable 'Yes'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = type

quantitation_types

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(128)
• Nullable 'No'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

roles

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

name

• varchar(40)
• Nullable 'No'

info

• varchar(80)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

roles_users

FIELDS

user_id

• int(11)
• Nullable 'No'

role_id

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = user_id

NORMAL

• Fields = role_id

CONSTRAINTS

FOREIGN KEY

• Fields = user_id
• Reference Table = users
• Reference Fields = id
• On delete = CASCADE

FOREIGN KEY

• Fields = role_id
• Reference Table = roles
• Reference Fields = id
• On delete = CASCADE

spreadsheets

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

experiment_id

• int(11)
• Nullable 'No'

name

• varchar(255)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

INDICES

NORMAL

• Fields = experiment_id

CONSTRAINTS

PRIMARY KEY

• Fields = id

FOREIGN KEY

• Fields = experiment_id
• Reference Table = experiments
• Reference Fields = id

taxons

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

scientific_name

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

common_name

• varchar(50)
• Default 'NULL'
• Nullable 'Yes'

accession

• int(11)
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

users

FIELDS

id

• int(11)
• PRIMARY KEY
• Nullable 'No'

login

• varchar(40)
• Nullable 'No'

name

• varchar(40)
• Default 'NULL'
• Nullable 'Yes'

password

• varchar(40)
• Nullable 'No'

email

• varchar(100)
• Default 'NULL'
• Nullable 'Yes'

modified_at

• datetime
• Default 'NULL'
• Nullable 'Yes'

created_at

• datetime
• Default 'NULL'
• Nullable 'Yes'

access

• datetime
• Default 'NULL'
• Nullable 'Yes'

is_deleted

• int(11)
• Nullable 'No'

CONSTRAINTS

PRIMARY KEY

• Fields = id

UNIQUE

• Fields = login

PRODUCED BY

SQL::Translator::Producer::POD

AUTHOR

Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2004.

Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.