CsvFileConn: CSV File connector class.
In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases
CsvFileConn R Documentation
CSV File connector class.
Description
CSV File connector class.
CSV File connector class.
Details
This is the abstract connector class for all CSV file databases.
Super classes
biodb::BiodbConnBase -> biodb::BiodbConn -> CsvFileConn
Methods
Public methods
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Inherited methods
biodb::BiodbConnBase$getBaseUrl()biodb::BiodbConnBase$getConnClass()biodb::BiodbConnBase$getConnClassName()biodb::BiodbConnBase$getDbClass()biodb::BiodbConnBase$getEntryClass()biodb::BiodbConnBase$getEntryClassName()biodb::BiodbConnBase$getEntryContentType()biodb::BiodbConnBase$getEntryFileExt()biodb::BiodbConnBase$getEntryIdField()biodb::BiodbConnBase$getName()biodb::BiodbConnBase$getPropSlots()biodb::BiodbConnBase$getPropValSlot()biodb::BiodbConnBase$getPropertyValue()biodb::BiodbConnBase$getSchedulerNParam()biodb::BiodbConnBase$getSchedulerTParam()biodb::BiodbConnBase$getToken()biodb::BiodbConnBase$getUrl()biodb::BiodbConnBase$getUrls()biodb::BiodbConnBase$getWsUrl()biodb::BiodbConnBase$getXmlNs()biodb::BiodbConnBase$hasProp()biodb::BiodbConnBase$hasPropSlot()biodb::BiodbConnBase$isSlotProp()biodb::BiodbConnBase$propExists()biodb::BiodbConnBase$setBaseUrl()biodb::BiodbConnBase$setPropValSlot()biodb::BiodbConnBase$setPropertyValue()biodb::BiodbConnBase$setSchedulerNParam()biodb::BiodbConnBase$setSchedulerTParam()biodb::BiodbConnBase$setToken()biodb::BiodbConnBase$setUrl()biodb::BiodbConnBase$setWsUrl()biodb::BiodbConnBase$updatePropertiesDefinition()biodb::BiodbConn$addNewEntry()biodb::BiodbConn$allowEditing()biodb::BiodbConn$allowWriting()biodb::BiodbConn$annotateMzValues()biodb::BiodbConn$checkDb()biodb::BiodbConn$collapseResultsDataFrame()biodb::BiodbConn$correctIds()biodb::BiodbConn$deleteAllCacheEntries()biodb::BiodbConn$deleteAllEntriesFromPersistentCache()biodb::BiodbConn$deleteAllEntriesFromVolatileCache()biodb::BiodbConn$deleteWholePersistentCache()biodb::BiodbConn$disallowEditing()biodb::BiodbConn$disallowWriting()biodb::BiodbConn$download()biodb::BiodbConn$editingIsAllowed()biodb::BiodbConn$filterEntriesOnRt()biodb::BiodbConn$getAllCacheEntries()biodb::BiodbConn$getAllVolatileCacheEntries()biodb::BiodbConn$getBiodb()biodb::BiodbConn$getCacheFile()biodb::BiodbConn$getCacheId()biodb::BiodbConn$getChromCol()biodb::BiodbConn$getDownloadPath()biodb::BiodbConn$getEntry()biodb::BiodbConn$getEntryContent()biodb::BiodbConn$getEntryContentFromDb()biodb::BiodbConn$getEntryContentRequest()biodb::BiodbConn$getEntryIds()biodb::BiodbConn$getEntryImageUrl()biodb::BiodbConn$getEntryPageUrl()biodb::BiodbConn$getId()biodb::BiodbConn$getMatchingMzField()biodb::BiodbConn$getMzValues()biodb::BiodbConn$getNbEntries()biodb::BiodbConn$getNbPeaks()biodb::BiodbConn$getSearchableFields()biodb::BiodbConn$isCompounddb()biodb::BiodbConn$isDownloadable()biodb::BiodbConn$isDownloaded()biodb::BiodbConn$isEditable()biodb::BiodbConn$isExtracted()biodb::BiodbConn$isMassdb()biodb::BiodbConn$isRemotedb()biodb::BiodbConn$isSearchableByField()biodb::BiodbConn$isWritable()biodb::BiodbConn$makeRequest()biodb::BiodbConn$makesRefToEntry()biodb::BiodbConn$msmsSearch()biodb::BiodbConn$requiresDownload()biodb::BiodbConn$searchByName()biodb::BiodbConn$searchCompound()biodb::BiodbConn$searchForEntries()biodb::BiodbConn$searchForMassSpectra()biodb::BiodbConn$searchMsEntries()biodb::BiodbConn$searchMsPeaks()biodb::BiodbConn$searchMzRange()biodb::BiodbConn$searchMzTol()biodb::BiodbConn$setDownloadedFile()biodb::BiodbConn$setEditingAllowed()biodb::BiodbConn$setMatchingMzField()biodb::BiodbConn$setWritingAllowed()biodb::BiodbConn$write()biodb::BiodbConn$writingIsAllowed()
Method new()
New instance initializer. Connector classes must not be instantiated
directly. Instead, you must use the createConn() method of the factory class.
Usage
CsvFileConn$new(...)
Arguments
...All parameters are passed to the super class initializer.
Returns
Nothing.
Method getCsvQuote()
Gets the characters used to delimit quotes in the CSV database file.
Usage
CsvFileConn$getCsvQuote()
Returns
The characters used to delimit quotes as a single
character value.
Method setCsvQuote()
Sets the characters used to delimit quotes in the CSV database file.
Usage
CsvFileConn$setCsvQuote(quote)
Arguments
quoteThe characters used to delimit quotes as a single character
value.
Youmay specify several characters. Example \"\\"'\".
Returns
Nothing.
Method getCsvSep()
Gets the current CSV separator used for the database file.
Usage
CsvFileConn$getCsvSep()
Returns
The CSV separator as a character value.
Method setCsvSep()
Sets the CSV separator to be used for the database file. If this method is
called after the loading of the database, it will throw an error.
Usage
CsvFileConn$setCsvSep(sep)
Arguments
sepThe CSV separator as a character value.
Returns
Nothing.
Method getFieldNames()
Get the list of all biodb fields handled by this database.
Usage
CsvFileConn$getFieldNames()
Returns
A character vector of the biodb field names.
Method hasField()
Tests if a field is defined for this database instance.
Usage
CsvFileConn$hasField(field)
Arguments
fieldA valid Biodb entry field name.
Returns
TRUE of the field is defined, FALSE otherwise.
Method addField()
Adds a new field to the database. The field must not already exist. The
same single value will be set to all entries for this field. A new column
will be written in the memory data frame, containing the value given.
Usage
CsvFileConn$addField(field, value)
Arguments
fieldA valid Biodb entry field name.
valueThe value to set for this field.
Returns
Nothing.
Method getFieldColName()
Get the column name corresponding to a Biodb field.
Usage
CsvFileConn$getFieldColName(field)
Arguments
fieldA valid Biodb entry field name. This field must be defined for
this database instance.
Returns
The column name from the CSV file.
Method setField()
Sets a field by making a correspondence between a Biodb field and one or
more columns of the loaded data frame.
Usage
CsvFileConn$setField(field, colname, ignore.if.missing = FALSE)
Arguments
fieldA valid Biodb entry field name. This field must not be already
defined for this database instance.
colnameA character vector containing one or more column names from
the CSV file.
ignore.if.missingDeprecated parameter.
Returns
Nothing.
Method getFieldsAndColumnsAssociation()
Gets the association between biodb field names and CSV file column names.
Usage
CsvFileConn$getFieldsAndColumnsAssociation()
Returns
A list with names being the biodb field names and values being a
character vector of column names from the CSV file.
Method getUnassociatedColumns()
Gets the list of unassociated column names from the CSV file.
Usage
CsvFileConn$getUnassociatedColumns()
Returns
A character vector containing column names.
Method print()
Prints a description of this connector.
Usage
CsvFileConn$print()
Returns
Nothing.
Method setDb()
Sets the database directly from a data frame. You must not have set
the database previously with the URL parameter.
Usage
CsvFileConn$setDb(db)
Arguments
dbA data frame containing your database.
Returns
Nothing.
Method setIgnoreUnassignedColumns()
Tells the connector to ignore or not the columns found in the CSV file for
which no assignment were found.
Usage
CsvFileConn$setIgnoreUnassignedColumns(ignore)
Arguments
ignoreSet to TRUE to ignore the unassigned columns, and to FALSE
otherwise.
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
CsvFileConn$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
Super classes BiodbConn,
and sub-classes CompCsvFileConn,
MassCsvFileConn.
Examples
# Create an instance with default settings:
mybiodb <- biodb::newInst()
# Get a connector that inherits from CsvFileConn:
chebi_file <- system.file("extdata", "chebi_extract.tsv", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi_file)
# Get an entry
e <- conn$getEntry('1018')
# Terminate instance.
mybiodb$terminate()
pkrog/biodb documentation built on Nov. 29, 2022, 4:24 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| CsvFileConn | R Documentation |
CSV File connector class.
Description
CSV File connector class.
CSV File connector class.
Details
This is the abstract connector class for all CSV file databases.
Super classes
biodb::BiodbConnBase -> biodb::BiodbConn -> CsvFileConn
Methods
Public methods
Inherited methods
biodb::BiodbConnBase$getBaseUrl()biodb::BiodbConnBase$getConnClass()biodb::BiodbConnBase$getConnClassName()biodb::BiodbConnBase$getDbClass()biodb::BiodbConnBase$getEntryClass()biodb::BiodbConnBase$getEntryClassName()biodb::BiodbConnBase$getEntryContentType()biodb::BiodbConnBase$getEntryFileExt()biodb::BiodbConnBase$getEntryIdField()biodb::BiodbConnBase$getName()biodb::BiodbConnBase$getPropSlots()biodb::BiodbConnBase$getPropValSlot()biodb::BiodbConnBase$getPropertyValue()biodb::BiodbConnBase$getSchedulerNParam()biodb::BiodbConnBase$getSchedulerTParam()biodb::BiodbConnBase$getToken()biodb::BiodbConnBase$getUrl()biodb::BiodbConnBase$getUrls()biodb::BiodbConnBase$getWsUrl()biodb::BiodbConnBase$getXmlNs()biodb::BiodbConnBase$hasProp()biodb::BiodbConnBase$hasPropSlot()biodb::BiodbConnBase$isSlotProp()biodb::BiodbConnBase$propExists()biodb::BiodbConnBase$setBaseUrl()biodb::BiodbConnBase$setPropValSlot()biodb::BiodbConnBase$setPropertyValue()biodb::BiodbConnBase$setSchedulerNParam()biodb::BiodbConnBase$setSchedulerTParam()biodb::BiodbConnBase$setToken()biodb::BiodbConnBase$setUrl()biodb::BiodbConnBase$setWsUrl()biodb::BiodbConnBase$updatePropertiesDefinition()biodb::BiodbConn$addNewEntry()biodb::BiodbConn$allowEditing()biodb::BiodbConn$allowWriting()biodb::BiodbConn$annotateMzValues()biodb::BiodbConn$checkDb()biodb::BiodbConn$collapseResultsDataFrame()biodb::BiodbConn$correctIds()biodb::BiodbConn$deleteAllCacheEntries()biodb::BiodbConn$deleteAllEntriesFromPersistentCache()biodb::BiodbConn$deleteAllEntriesFromVolatileCache()biodb::BiodbConn$deleteWholePersistentCache()biodb::BiodbConn$disallowEditing()biodb::BiodbConn$disallowWriting()biodb::BiodbConn$download()biodb::BiodbConn$editingIsAllowed()biodb::BiodbConn$filterEntriesOnRt()biodb::BiodbConn$getAllCacheEntries()biodb::BiodbConn$getAllVolatileCacheEntries()biodb::BiodbConn$getBiodb()biodb::BiodbConn$getCacheFile()biodb::BiodbConn$getCacheId()biodb::BiodbConn$getChromCol()biodb::BiodbConn$getDownloadPath()biodb::BiodbConn$getEntry()biodb::BiodbConn$getEntryContent()biodb::BiodbConn$getEntryContentFromDb()biodb::BiodbConn$getEntryContentRequest()biodb::BiodbConn$getEntryIds()biodb::BiodbConn$getEntryImageUrl()biodb::BiodbConn$getEntryPageUrl()biodb::BiodbConn$getId()biodb::BiodbConn$getMatchingMzField()biodb::BiodbConn$getMzValues()biodb::BiodbConn$getNbEntries()biodb::BiodbConn$getNbPeaks()biodb::BiodbConn$getSearchableFields()biodb::BiodbConn$isCompounddb()biodb::BiodbConn$isDownloadable()biodb::BiodbConn$isDownloaded()biodb::BiodbConn$isEditable()biodb::BiodbConn$isExtracted()biodb::BiodbConn$isMassdb()biodb::BiodbConn$isRemotedb()biodb::BiodbConn$isSearchableByField()biodb::BiodbConn$isWritable()biodb::BiodbConn$makeRequest()biodb::BiodbConn$makesRefToEntry()biodb::BiodbConn$msmsSearch()biodb::BiodbConn$requiresDownload()biodb::BiodbConn$searchByName()biodb::BiodbConn$searchCompound()biodb::BiodbConn$searchForEntries()biodb::BiodbConn$searchForMassSpectra()biodb::BiodbConn$searchMsEntries()biodb::BiodbConn$searchMsPeaks()biodb::BiodbConn$searchMzRange()biodb::BiodbConn$searchMzTol()biodb::BiodbConn$setDownloadedFile()biodb::BiodbConn$setEditingAllowed()biodb::BiodbConn$setMatchingMzField()biodb::BiodbConn$setWritingAllowed()biodb::BiodbConn$write()biodb::BiodbConn$writingIsAllowed()
Method new()
New instance initializer. Connector classes must not be instantiated directly. Instead, you must use the createConn() method of the factory class.
Usage
CsvFileConn$new(...)
Arguments
...All parameters are passed to the super class initializer.
Returns
Nothing.
Method getCsvQuote()
Gets the characters used to delimit quotes in the CSV database file.
Usage
CsvFileConn$getCsvQuote()
Returns
The characters used to delimit quotes as a single character value.
Method setCsvQuote()
Sets the characters used to delimit quotes in the CSV database file.
Usage
CsvFileConn$setCsvQuote(quote)
Arguments
quoteThe characters used to delimit quotes as a single character value.
Youmay specify several characters. Example \"\\"'\".
Returns
Nothing.
Method getCsvSep()
Gets the current CSV separator used for the database file.
Usage
CsvFileConn$getCsvSep()
Returns
The CSV separator as a character value.
Method setCsvSep()
Sets the CSV separator to be used for the database file. If this method is called after the loading of the database, it will throw an error.
Usage
CsvFileConn$setCsvSep(sep)
Arguments
sepThe CSV separator as a character value.
Returns
Nothing.
Method getFieldNames()
Get the list of all biodb fields handled by this database.
Usage
CsvFileConn$getFieldNames()
Returns
A character vector of the biodb field names.
Method hasField()
Tests if a field is defined for this database instance.
Usage
CsvFileConn$hasField(field)
Arguments
fieldA valid Biodb entry field name.
Returns
TRUE of the field is defined, FALSE otherwise.
Method addField()
Adds a new field to the database. The field must not already exist. The same single value will be set to all entries for this field. A new column will be written in the memory data frame, containing the value given.
Usage
CsvFileConn$addField(field, value)
Arguments
fieldA valid Biodb entry field name.
valueThe value to set for this field.
Returns
Nothing.
Method getFieldColName()
Get the column name corresponding to a Biodb field.
Usage
CsvFileConn$getFieldColName(field)
Arguments
fieldA valid Biodb entry field name. This field must be defined for this database instance.
Returns
The column name from the CSV file.
Method setField()
Sets a field by making a correspondence between a Biodb field and one or more columns of the loaded data frame.
Usage
CsvFileConn$setField(field, colname, ignore.if.missing = FALSE)
Arguments
fieldA valid Biodb entry field name. This field must not be already defined for this database instance.
colnameA character vector containing one or more column names from the CSV file.
ignore.if.missingDeprecated parameter.
Returns
Nothing.
Method getFieldsAndColumnsAssociation()
Gets the association between biodb field names and CSV file column names.
Usage
CsvFileConn$getFieldsAndColumnsAssociation()
Returns
A list with names being the biodb field names and values being a character vector of column names from the CSV file.
Method getUnassociatedColumns()
Gets the list of unassociated column names from the CSV file.
Usage
CsvFileConn$getUnassociatedColumns()
Returns
A character vector containing column names.
Method print()
Prints a description of this connector.
Usage
CsvFileConn$print()
Returns
Nothing.
Method setDb()
Sets the database directly from a data frame. You must not have set the database previously with the URL parameter.
Usage
CsvFileConn$setDb(db)
Arguments
dbA data frame containing your database.
Returns
Nothing.
Method setIgnoreUnassignedColumns()
Tells the connector to ignore or not the columns found in the CSV file for which no assignment were found.
Usage
CsvFileConn$setIgnoreUnassignedColumns(ignore)
Arguments
ignoreSet to TRUE to ignore the unassigned columns, and to FALSE otherwise.
Returns
Nothing.
Method clone()
The objects of this class are cloneable with this method.
Usage
CsvFileConn$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
Super classes BiodbConn,
and sub-classes CompCsvFileConn,
MassCsvFileConn.
Examples
# Create an instance with default settings:
mybiodb <- biodb::newInst()
# Get a connector that inherits from CsvFileConn:
chebi_file <- system.file("extdata", "chebi_extract.tsv", package="biodb")
conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi_file)
# Get an entry
e <- conn$getEntry('1018')
# Terminate instance.
mybiodb$terminate()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.