gochado

type ChadoHelper struct {
	*Database
	// contains filtered or unexported fields
}

type ChadoLoader interface {
	// To prepare involved chado tables for bulk load, such as
	// disabling indexes and/or foreign keys if needed
	AlterTables()
	// Primarilly to complement the AlterTables method, put back the chaged tables
	// in its pristine states. Could also be used to re-calcualate statistics
	// on tables that has inserts after bulk load.
	ResetTables()
	// Actual data loading by running a series of sql statements that transfers
	// data from staging tables.
	BulkLoad()
}

type Cv struct {
	CvId       int64 `primary_key:"cv_id"`
	Name       string
	Definition string
	Cvterms    []Cvterm
}

type Cvterm struct {
	CvtermId           int64 `primary_key:"cvterm_id"`
	Name               string
	Definition         string
	IsObsolete         bool
	IsRelationshiptype bool

	//Foreign keys
	CvId     int64
	Cv       Cv
	DbxrefId int64
	Dbxref   Dbxref
}

type DataBucket struct {
	// contains filtered or unexported fields
}

type DataCache struct {
	sync.RWMutex
	// contains filtered or unexported fields
}

type Database struct {
	ChadoHandler *sqlx.DB
}

type Db struct {
	DbId        int64 `primary_key:"db_id"`
	Name        string
	Description string
	Urlprefix   string
	Url         string
	// has_many relations
	Dbxrefs []Dbxref
}

type Dbxref struct {
	DbxrefId    int64 `primary_key:"dbxref_id"`
	Accession   string
	Version     string
	Description string
	//Foreign key
	DbId int64
	// Embedded struct belongs_to relation
	Db Db
	//has_many relations
	FeatureDbxrefs []FeatureDbxref
}

type Feature struct {
	FeatureId        int64 `primary_key:"feature_id"`
	Name             string
	Uniquename       string
	Residues         string
	Seqlen           int64
	Md5checksum      string
	IsAnalysis       bool
	IsObsolete       bool
	Timeaccessioned  time.Time
	Timelastmodified time.Time

	//foreign keys
	OrganismId int64
	Organism   Organism
	DbxrefId   int64
	Dbxref     Dbxref
	TypeId     int64
	Type       Cvterm

	//has_many relations
	FeatureCvterms []FeatureCvterm
	FeatureDbxrefs []FeatureDbxref
}

type FeatureCvterm struct {
	FeatureCvtermId int64 `primary_key:"feature_cvterm_id"`
	IsNot           bool
	Rank            int64
	//foreign keys
	FeatureId int64
	Feature   Feature
	CvtermId  int64
	Cvterm    Cvterm
	PubId     int64
	Pub       Pub
}

type FeatureDbxref struct {
	FeatureDbxrefId int64 `primary_key:"feature_dbxref_id"`
	FeatureId       int64
	DbxrefId        int64
	Feature         Feature
	Dbxref          Dbxref
}

type GpadFixtureLoader struct {
	// contains filtered or unexported fields
}

type Organism struct {
	OrganismId   int64 `primary_key:"organism_id"`
	Abbreviation string
	Genus        string
	Species      string
	CommonName   string
	Comment      string
	Features     []Feature
}

type Pub struct {
	PubId       int64 `primary_key:"pub_id"`
	Title       string
	Volumetitle string
	Volume      string
	SeriesName  string
	Issue       string
	Pyear       string
	Pages       string
	Miniref     string
	Uniquename  string
	Publisher   string
	Pubplace    string
	IsObsolete  bool
	//foreign key
	TypeId int64
	Type   Cvterm
}

type SqlParser struct {
	// contains filtered or unexported fields
}

type StagingLoader interface {
	// Add a row of unprocessed data to the staging cache
	AddDataRow(string)
	// Create temporary staging tables
	CreateTables()
	// Drop the staging tables
	DropTables()
	// Alteration in the staging tables, for example creating indexes
	AlterTables()
	// Bulk upload data from staging cache to the staging tables
	BulkLoad()
}