BiodbEntry: The mother abstract class of all database entry classes.
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
BiodbEntry R Documentation
The mother abstract class of all database entry classes.
Description
The mother abstract class of all database entry classes.
The mother abstract class of all database entry classes.
Details
An entry is an element of a database, identifiable by its accession number.
Each contains a list of fields defined by a name and a value. The details of
all fields that can be set into an entry are defined inside the class
BiodbEntryFields. From this class are derived other abstract classes
for different types of entry contents: BiodbTxtEntry,
BiodbXmlEntry, BiodbCsvEntry, BiodbJsonEntry and
BiodbHtmlEntry. Then concrete classes are derived for each database:
CompCsvEntry, MassCsvEntry, etc. For biodb users, there is no
need to know this hierarchy; the knowledge of this class and its methods is
sufficient.
Methods
Public methods
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Method new()
New instance initializer. Entry objects must not be created directly.
Instead, they are retrieved through the connector instances.
Usage
BiodbEntry$new(parent)
Arguments
parentA valid BiodbConn instance.
Returns
Nothing.
Method parentIsAConnector()
Tests if the parent of this entry is a connector instance.
Usage
BiodbEntry$parentIsAConnector()
Returns
TRUE if this entry belongs to a connector, FALSE otherwise.
Method getParent()
Returns the parent instance (A BiodbConn or BiodbFactory object) to which
this object is attached.
Usage
BiodbEntry$getParent()
Returns
A BiodbConn instance or a BiodbFactory object.
Method getBiodb()
Returns the biodb main class instance to which this object is
attached.
Usage
BiodbEntry$getBiodb()
Returns
The main biodb instance.
Method cloneInstance()
Clones this entry.
Usage
BiodbEntry$cloneInstance(db.class = NULL)
Arguments
db.classThe database class (the Biodb database ID) of the
clone. By setting this parameter, you can specify a different database
for the clone, so you may clone an entry into another database if you
wish. By default the class of the clone will be the same as the
original entry.
Returns
The clone, as a new BiodbEntry instance.
Method getId()
Gets the entry ID.
Usage
BiodbEntry$getId()
Returns
the entry ID, which is the value if the accession field.
Method isNew()
Tests if this entry is new.
Usage
BiodbEntry$isNew()
Returns
TRUE if this entry was newly created, FALSE otherwise.
Method getDbClass()
Gets the ID of the database associated with this entry.
Usage
BiodbEntry$getDbClass()
Returns
The name of the database class associated with this entry.
Method setFieldValue()
Sets the value of a field. If the field is not already set for this
entry, then the field will be created. See BiodbEntryFields for a list of
possible fields in biodb.
Usage
BiodbEntry$setFieldValue(field, value)
Arguments
fieldThe name of a field.
valueThe value to set.
Returns
Nothing.
Method appendFieldValue()
Appends a value to an existing field. If the field is not defined for
this entry, then the field will be created and set to this value. Only
fields with a cardinality greater than one can accept multiple values.
Usage
BiodbEntry$appendFieldValue(field, value)
Arguments
fieldThe name of a field.
valueThe value to append.
Returns
Nothing.
Method getFieldNames()
Gets a list of all fields defined for this entry.
Usage
BiodbEntry$getFieldNames()
Returns
A character vector containing all field names defined in
this entry.
Method hasField()
Tests if a field is defined in this entry.
Usage
BiodbEntry$hasField(field)
Arguments
fieldThe name of a field.
Returns
TRUE if the specified field is defined in this entry,
FALSE otherwise.
Method removeField()
Removes the specified field from this entry.
Usage
BiodbEntry$removeField(field)
Arguments
fieldThe name of a field.
Returns
Nothing.
Method getFieldValue()
Gets the value of the specified field.
Usage
BiodbEntry$getFieldValue(
field,
compute = TRUE,
flatten = FALSE,
last = FALSE,
limit = 0,
withNa = TRUE,
duplicatedValues = TRUE
)
Arguments
fieldThe name of a field.
computeIf set to TRUE and a field is not defined, try to compute it
using internal defined computing rules. If set to FALSE, let the field
undefined.
flattenIf set to TRUE and a field's value is a vector of more than
one element, then export the field's value as a single string composed of
the field's value concatenated and separated by the character defined in the
'multival.field.sep' config key. If set to FALSE or the field contains only
one value, changes nothing.
lastIf set to TRUE and a field's value is a vector of more than one
element, then export only the last value. If set to FALSE, changes nothing.
limitThe maximum number of values to get in case the field contains
more than one value.
withNaIf set to TRUE, keep NA values. Otherwise filter out NAs
values in vectors.
duplicatedValuesIf set to TRUE, keeps duplicated values.
Returns
The value of the field.
Method getFieldsByType()
Gets the fields of this entry that have the specified type.
Usage
BiodbEntry$getFieldsByType(type)
Arguments
typeThe type of fields to retrieve.
Returns
A character vector containing the field names.
Method getFieldsAsDataframe()
Converts this entry into a data frame.
Usage
BiodbEntry$getFieldsAsDataframe(
only.atomic = TRUE,
compute = TRUE,
fields = NULL,
fields.type = NULL,
flatten = TRUE,
limit = 0,
only.card.one = FALSE,
own.id = TRUE,
duplicate.rows = TRUE,
sort = FALSE,
virtualFields = FALSE
)
Arguments
only.atomicIf set to TRUE, only export field's values that are atomic
computeIf set to TRUE and a field is not defined, try to compute it
using internal defined computing rules. If set to FALSE, let the field
undefined.
fieldsSet to character vector of field names in order to restrict
execution to this set of fields.
fields.typeIf set, output all the fields of the specified type.
flattenIf set to TRUE and a field's value is a vector of more than
one element, then export the field's value as a single string composed of
the field's value concatenated and separated by the character defined in the
'multival.field.sep' config key. If set to FALSE or the field contains only
one value, changes nothing.
limitThe maximum number of field values to write into new columns.
Used for fields that can contain more than one value.
only.card.oneIf set to TRUE, only fields with a cardinality of one
will be extracted.
own.idIf set to TRUE includes the database id field named
<database_name>.id whose values are the same as the accession field.
duplicate.rowsIf set to TRUE and merging field values with
cardinality greater than one, values will be duplicated.
sortIf set to TRUE sort the order of columns alphabetically,
otherwise do not sort.
virtualFieldsIf set to TRUE includes also virtual fields, otherwise
excludes them.
(i.e.of type vector).
Returns
A data frame containg the values of the fields.
Method getFieldsAsJson()
Converts this entry into a JSON string.
Usage
BiodbEntry$getFieldsAsJson(compute = TRUE)
Arguments
computeIf set to TRUE and a field is not defined, try to compute it
using internal defined computing rules. If set to FALSE, let the field
undefined.
Returns
A JSON object from jsonlite package.
Method parseContent()
Parses content string and set values accordingly for this entry's
fields. This method is called automatically and should be run directly
by users.
Usage
BiodbEntry$parseContent(content)
Arguments
contentA character string containing definition for an entry and
obtainedfrom a database. The format can be CSV, HTML, JSON,
XML, or just text.
Returns
Nothing.
Method computeFields()
Computes fields. Look at all missing fields, and try to compute them
using references to other databases, if a rule exists.
Usage
BiodbEntry$computeFields(fields = NULL)
Arguments
fieldsA list of fields to review for computing. By default all fields
will be reviewed.
Returns
TRUE if at least one field was computed successfully,
FALSE otherwise.
Method print()
Displays short information about this instance.
Usage
BiodbEntry$print()
Returns
Nothing.
Method getName()
Gets a short text describing this entry instance.
Usage
BiodbEntry$getName()
Returns
A character value concatenating the connector name with
the entry accession.
Method makesRefToEntry()
Tests if this entry makes reference to another entry.
Usage
BiodbEntry$makesRefToEntry(db, oid, recurse = FALSE)
Arguments
dbAnother database connector.
oidA entry ID from database db.
recurseIf set to TRUE, the algorithm will follow all references to
entries from other databases, to see if it can establish an indirect link to
oid.
Returns
TRUE if this entry makes reference to the entry oid from database
db, FALSE otherwise.
Method getField()
DEPRECATED. Gets the value of a field.
Usage
BiodbEntry$getField(field)
Arguments
fieldThe name of the field.
Returns
The value of the field.
Method setField()
DEPRECATED. Sets the value of a field.
Usage
BiodbEntry$setField(field, value)
Arguments
fieldThe name of the field.
valueThe new value of the field.
Returns
Nothing.
Method getFieldClass()
Gets the class of a field.
Usage
BiodbEntry$getFieldClass(field)
Arguments
fieldThe name of the field.
Returns
The class of the field.
Method getFieldDef()
Gets the definition of an entry field.
Usage
BiodbEntry$getFieldDef(field)
Arguments
fieldThe name of the field.
Returns
An object BiodbEntryField which defines the field.
Method getFieldCardinality()
Gets the cardinality of the field.
Usage
BiodbEntry$getFieldCardinality(field)
Arguments
fieldThe name of the field.
Returns
The cardinality of the field.
Method fieldHasBasicClass()
DEPRECATED. Use BiodbEntryField::isVector() instead.
Usage
BiodbEntry$fieldHasBasicClass(field)
Arguments
fieldThe name of the field.
Returns
TRUE if the field as a basic type (logical, numeric, character, ...).
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbEntry$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbFactory, BiodbConn,
BiodbEntryFields.
Examples
# Create an instance with default settings:
mybiodb <- biodb::newInst()
# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')
# Get the connector of a compound database
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)
# Get an entry:
entry <- conn$getEntry(conn$getEntryIds(1))
# Get all defined fields:
entry$getFieldNames()
# Get a field value:
accession <- entry$getFieldValue('accession')
# Test if a field is defined:
if (entry$hasField('name'))
print(paste("The entry's name is ", entry$getFieldValue('name'),
'.', sep=''))
# Export an entry as a data frame:
df <- entry$getFieldsAsDataframe()
# You can set or reset a field's value:
entry$setFieldValue('mass', 1893.1883)
# Terminate instance.
mybiodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
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| BiodbEntry | R Documentation |
The mother abstract class of all database entry classes.
Description
The mother abstract class of all database entry classes.
The mother abstract class of all database entry classes.
Details
An entry is an element of a database, identifiable by its accession number.
Each contains a list of fields defined by a name and a value. The details of
all fields that can be set into an entry are defined inside the class
BiodbEntryFields. From this class are derived other abstract classes
for different types of entry contents: BiodbTxtEntry,
BiodbXmlEntry, BiodbCsvEntry, BiodbJsonEntry and
BiodbHtmlEntry. Then concrete classes are derived for each database:
CompCsvEntry, MassCsvEntry, etc. For biodb users, there is no
need to know this hierarchy; the knowledge of this class and its methods is
sufficient.
Methods
Public methods
Method new()
New instance initializer. Entry objects must not be created directly. Instead, they are retrieved through the connector instances.
Usage
BiodbEntry$new(parent)
Arguments
parentA valid BiodbConn instance.
Returns
Nothing.
Method parentIsAConnector()
Tests if the parent of this entry is a connector instance.
Usage
BiodbEntry$parentIsAConnector()
Returns
TRUE if this entry belongs to a connector, FALSE otherwise.
Method getParent()
Returns the parent instance (A BiodbConn or BiodbFactory object) to which this object is attached.
Usage
BiodbEntry$getParent()
Returns
A BiodbConn instance or a BiodbFactory object.
Method getBiodb()
Returns the biodb main class instance to which this object is attached.
Usage
BiodbEntry$getBiodb()
Returns
The main biodb instance.
Method cloneInstance()
Clones this entry.
Usage
BiodbEntry$cloneInstance(db.class = NULL)
Arguments
db.classThe database class (the Biodb database ID) of the clone. By setting this parameter, you can specify a different database for the clone, so you may clone an entry into another database if you wish. By default the class of the clone will be the same as the original entry.
Returns
The clone, as a new BiodbEntry instance.
Method getId()
Gets the entry ID.
Usage
BiodbEntry$getId()
Returns
the entry ID, which is the value if the accession field.
Method isNew()
Tests if this entry is new.
Usage
BiodbEntry$isNew()
Returns
TRUE if this entry was newly created, FALSE otherwise.
Method getDbClass()
Gets the ID of the database associated with this entry.
Usage
BiodbEntry$getDbClass()
Returns
The name of the database class associated with this entry.
Method setFieldValue()
Sets the value of a field. If the field is not already set for this entry, then the field will be created. See BiodbEntryFields for a list of possible fields in biodb.
Usage
BiodbEntry$setFieldValue(field, value)
Arguments
fieldThe name of a field.
valueThe value to set.
Returns
Nothing.
Method appendFieldValue()
Appends a value to an existing field. If the field is not defined for this entry, then the field will be created and set to this value. Only fields with a cardinality greater than one can accept multiple values.
Usage
BiodbEntry$appendFieldValue(field, value)
Arguments
fieldThe name of a field.
valueThe value to append.
Returns
Nothing.
Method getFieldNames()
Gets a list of all fields defined for this entry.
Usage
BiodbEntry$getFieldNames()
Returns
A character vector containing all field names defined in this entry.
Method hasField()
Tests if a field is defined in this entry.
Usage
BiodbEntry$hasField(field)
Arguments
fieldThe name of a field.
Returns
TRUE if the specified field is defined in this entry, FALSE otherwise.
Method removeField()
Removes the specified field from this entry.
Usage
BiodbEntry$removeField(field)
Arguments
fieldThe name of a field.
Returns
Nothing.
Method getFieldValue()
Gets the value of the specified field.
Usage
BiodbEntry$getFieldValue( field, compute = TRUE, flatten = FALSE, last = FALSE, limit = 0, withNa = TRUE, duplicatedValues = TRUE )
Arguments
fieldThe name of a field.
computeIf set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.
flattenIf set to TRUE and a field's value is a vector of more than one element, then export the field's value as a single string composed of the field's value concatenated and separated by the character defined in the 'multival.field.sep' config key. If set to FALSE or the field contains only one value, changes nothing.
lastIf set to TRUE and a field's value is a vector of more than one element, then export only the last value. If set to FALSE, changes nothing.
limitThe maximum number of values to get in case the field contains more than one value.
withNaIf set to TRUE, keep NA values. Otherwise filter out NAs values in vectors.
duplicatedValuesIf set to TRUE, keeps duplicated values.
Returns
The value of the field.
Method getFieldsByType()
Gets the fields of this entry that have the specified type.
Usage
BiodbEntry$getFieldsByType(type)
Arguments
typeThe type of fields to retrieve.
Returns
A character vector containing the field names.
Method getFieldsAsDataframe()
Converts this entry into a data frame.
Usage
BiodbEntry$getFieldsAsDataframe( only.atomic = TRUE, compute = TRUE, fields = NULL, fields.type = NULL, flatten = TRUE, limit = 0, only.card.one = FALSE, own.id = TRUE, duplicate.rows = TRUE, sort = FALSE, virtualFields = FALSE )
Arguments
only.atomicIf set to TRUE, only export field's values that are atomic
computeIf set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.
fieldsSet to character vector of field names in order to restrict execution to this set of fields.
fields.typeIf set, output all the fields of the specified type.
flattenIf set to TRUE and a field's value is a vector of more than one element, then export the field's value as a single string composed of the field's value concatenated and separated by the character defined in the 'multival.field.sep' config key. If set to FALSE or the field contains only one value, changes nothing.
limitThe maximum number of field values to write into new columns. Used for fields that can contain more than one value.
only.card.oneIf set to TRUE, only fields with a cardinality of one will be extracted.
own.idIf set to TRUE includes the database id field named
<database_name>.idwhose values are the same as theaccessionfield.duplicate.rowsIf set to TRUE and merging field values with cardinality greater than one, values will be duplicated.
sortIf set to TRUE sort the order of columns alphabetically, otherwise do not sort.
virtualFieldsIf set to TRUE includes also virtual fields, otherwise excludes them.
(i.e.of type vector).
Returns
A data frame containg the values of the fields.
Method getFieldsAsJson()
Converts this entry into a JSON string.
Usage
BiodbEntry$getFieldsAsJson(compute = TRUE)
Arguments
computeIf set to TRUE and a field is not defined, try to compute it using internal defined computing rules. If set to FALSE, let the field undefined.
Returns
A JSON object from jsonlite package.
Method parseContent()
Parses content string and set values accordingly for this entry's fields. This method is called automatically and should be run directly by users.
Usage
BiodbEntry$parseContent(content)
Arguments
contentA character string containing definition for an entry and
obtainedfrom a database. The format can be CSV, HTML, JSON, XML, or just text.
Returns
Nothing.
Method computeFields()
Computes fields. Look at all missing fields, and try to compute them using references to other databases, if a rule exists.
Usage
BiodbEntry$computeFields(fields = NULL)
Arguments
fieldsA list of fields to review for computing. By default all fields will be reviewed.
Returns
TRUE if at least one field was computed successfully, FALSE otherwise.
Method print()
Displays short information about this instance.
Usage
BiodbEntry$print()
Returns
Nothing.
Method getName()
Gets a short text describing this entry instance.
Usage
BiodbEntry$getName()
Returns
A character value concatenating the connector name with the entry accession.
Method makesRefToEntry()
Tests if this entry makes reference to another entry.
Usage
BiodbEntry$makesRefToEntry(db, oid, recurse = FALSE)
Arguments
dbAnother database connector.
oidA entry ID from database db.
recurseIf set to TRUE, the algorithm will follow all references to entries from other databases, to see if it can establish an indirect link to
oid.
Returns
TRUE if this entry makes reference to the entry oid from database db, FALSE otherwise.
Method getField()
DEPRECATED. Gets the value of a field.
Usage
BiodbEntry$getField(field)
Arguments
fieldThe name of the field.
Returns
The value of the field.
Method setField()
DEPRECATED. Sets the value of a field.
Usage
BiodbEntry$setField(field, value)
Arguments
fieldThe name of the field.
valueThe new value of the field.
Returns
Nothing.
Method getFieldClass()
Gets the class of a field.
Usage
BiodbEntry$getFieldClass(field)
Arguments
fieldThe name of the field.
Returns
The class of the field.
Method getFieldDef()
Gets the definition of an entry field.
Usage
BiodbEntry$getFieldDef(field)
Arguments
fieldThe name of the field.
Returns
An object BiodbEntryField which defines the field.
Method getFieldCardinality()
Gets the cardinality of the field.
Usage
BiodbEntry$getFieldCardinality(field)
Arguments
fieldThe name of the field.
Returns
The cardinality of the field.
Method fieldHasBasicClass()
DEPRECATED. Use BiodbEntryField::isVector() instead.
Usage
BiodbEntry$fieldHasBasicClass(field)
Arguments
fieldThe name of the field.
Returns
TRUE if the field as a basic type (logical, numeric, character, ...).
Method clone()
The objects of this class are cloneable with this method.
Usage
BiodbEntry$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
BiodbFactory, BiodbConn,
BiodbEntryFields.
Examples
# Create an instance with default settings:
mybiodb <- biodb::newInst()
# Get a compound CSV file database
chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb')
# Get the connector of a compound database
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv)
# Get an entry:
entry <- conn$getEntry(conn$getEntryIds(1))
# Get all defined fields:
entry$getFieldNames()
# Get a field value:
accession <- entry$getFieldValue('accession')
# Test if a field is defined:
if (entry$hasField('name'))
print(paste("The entry's name is ", entry$getFieldValue('name'),
'.', sep=''))
# Export an entry as a data frame:
df <- entry$getFieldsAsDataframe()
# You can set or reset a field's value:
entry$setFieldValue('mass', 1893.1883)
# Terminate instance.
mybiodb$terminate()
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