Package: biodb 1.13.0

Pierrick Roger

biodb: biodb, a library and a development framework for connecting to chemical and biological databases

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

Authors:Pierrick Roger [aut, cre], Alexis Delabrière [ctb]

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biodb.pdf |biodb.html✨
biodb/json (API)
NEWS

# Install 'biodb' in R:
install.packages('biodb', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pkrog/biodb/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:biodb-1.13.0(bioc 3.20)biodb-1.12.0(bioc 3.19)

bioconductor-package

85 exports 2.22 score 70 dependencies 8 dependents

Last updated 2 months agofrom:e265a9ae67

Exports:abstractClassBiodbBiocPersistentCacheBiodbConfigBiodbConnBiodbConnBaseBiodbCsvEntryBiodbCustomPersistentCacheBiodbDbInfoBiodbDbsInfoBiodbEntryBiodbEntryFieldBiodbEntryFieldsBiodbFactoryBiodbHtmlEntryBiodbJsonEntryBiodbListEntryBiodbMainBiodbPersistentCacheBiodbRequestBiodbRequestSchedulerBiodbSdfEntryBiodbTxtEntryBiodbUrlBiodbXmlEntrycheckDeprecatedCacheFoldersCompCsvFileConnCompCsvFileEntryCompSqliteConnCompSqliteEntrycreateBiodbTestInstanceCsvFileConndf2strerrorerror0ExtConnClassExtCppExtDefinitionsExtDescriptionFileExtEntryClassExtFileGeneratorExtGeneratorExtGitignoreExtLicenseExtMakefileExtPackageExtPackageFileExtRbuildignoreExtReadmeExtTestsExtTravisFileExtVignettegenNewExtPkggetConnClassNamegetConnTypesgetDefaultCacheDirgetEntryClassNamegetEntryTypesgetLicensesgetLoggergetPkgNamegetReposNamegetTestOutputDirlistTestRefEntrieslogDebuglogDebug0logInfologInfo0logTracelogTrace0lst2strMassCsvFileConnMassCsvFileEntryMassSqliteConnMassSqliteEntrynewInstProgressRangerunGenericTestsSqliteConntestContextTestRefEntriestestThatupgradeExtPkgwarnwarn0

Dependencies:askpassBiocFileCachebitbit64bitopsblobbriocachemcallrchkclicpp11crayoncurlDBIdbplyrdescdiffobjdigestdplyrevaluatefansifastmapfilelockfsgenericsgit2rgluehmshttrjsonlitelgrlifecyclemagrittrmemoisemimeopensslpillarpkgbuildpkgconfigpkgloadplogrplyrpraiseprettyunitsprocessxprogresspspurrrR6rappdirsRcppRCurlrematch2rlangrprojrootRSQLitestringistringrsystestthattibbletidyrtidyselectutf8vctrswaldowithrXMLyaml

Creating a new connector.

Pierrick Roger

Rendered fromnew_connector.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2022-02-16
Started: 2020-05-29

Creating a new field for entries.

Pierrick Roger

Rendered fromnew_entry_field.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2021-10-12
Started: 2019-05-28

Details on biodb

Pierrick Roger

Rendered fromdetails.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2022-04-02
Started: 2020-11-28

An introduction to biodb

Pierrick Roger

Rendered frombiodb.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2022-04-02
Started: 2021-05-06

Manipulating entry objects

Pierrick Roger

Rendered fromentries.Rmdusingknitr::rmarkdownon Jun 11 2024.

Last update: 2021-10-12
Started: 2020-11-28

Readme and manuals

Help Manual

Help pageTopics
biodb: biodb, a library and a development framework for connecting to chemical and biological databasesbiodb-package biodb
Declares a class as abstract.abstractClass
Declares a method as abstractabstractMethod
A persistent cache implementation that uses BiocCache package.BiodbBiocPersistentCache
A class for storing configuration values.BiodbConfig
The mother abstract class of all database connectors.BiodbConn
Base class of 'BiodbConn' for encapsulating all needed information for database access.BiodbConnBase
Entry class for content in CSV format.BiodbCsvEntry
A biodb custom persistent cache implementation.BiodbCustomPersistentCache
A class for describing the characteristics of a database.BiodbDbInfo
A class for describing the available databases.BiodbDbsInfo
The mother abstract class of all database entry classes.BiodbEntry
A class for describing an entry field.BiodbEntryField
A class for handling description of all entry fields.BiodbEntryFields
A class for constructing biodb objects.BiodbFactory
Entry class for content in HTML format.BiodbHtmlEntry
Entry class for content in JSON format.BiodbJsonEntry
Entry class for content in list format.BiodbListEntry
The central class of the biodb package.BiodbMain
The abstract class for handling file caching.BiodbPersistentCache
Class Request.BiodbRequest
Class for handling requests.BiodbRequestScheduler
Scheduler rule class.BiodbRequestSchedulerRule
Entry class for content in SDF format.BiodbSdfEntry
This class represents an SQL binary operator.BiodbSqlBinaryOp
The SQL Expression abstact class.BiodbSqlExpr
This class represents an SQL field.BiodbSqlField
This class represents an SQL list.BiodbSqlList
This class represents an SQL logical operator.BiodbSqlLogicalOp
This class handles an SQL Query.BiodbSqlQuery
This class represents an SQL value.BiodbSqlValue
A class for acknowledging messages during tests.BiodbTestMsgAck
Entry class for content in text format.BiodbTxtEntry
Class URL.BiodbUrl
Entry class for content in XML format.BiodbXmlEntry
Check deprecated default cache folders.checkDeprecatedCacheFolders
Close match PPMcloseMatchPpm
Compound CSV File connector class.CompCsvFileConn
Compound CSV File entry class.CompCsvFileEntry
Class for handling a Compound database in SQLite format.CompSqliteConn
Compound SQLite entry class.CompSqliteEntry
Convert connector name into class prefix.connNameToClassPrefix
Creating a BiodbMain instance for tests.createBiodbTestInstance
CSV File connector class.CsvFileConn
Convert a data.frame into a string.df2str
Test if a URL is valid according to RCurldoesRCurlRequestUrlExist
Throw an error and log it too.error
Throw an error and log it too.error0
Extension connector clasExtConnClass
Extension C++ code classExtCpp
Extension defintions file classExtDefinitions
Extension DESCRIPTION fileExtDescriptionFile
Extension entry classExtEntryClass
Extension file generator abstract classExtFileGenerator
Extension generator abstract classExtGenerator
Extension Gitignore file classExtGitignore
Extension licenseExtLicense
Extension MakefileExtMakefile
Extension package classExtPackage
Extension package file class.ExtPackageFile
Extension Rbuildignore file classExtRbuildignore
Extension README file classExtReadme
Extension tests classExtTests
Extension Travis YAML file generator classExtTravisFile
Extension vignette classExtVignette
File template class.FileTemplate
Generate a new extension package for biodb.genNewExtPkg
Get URL content using base::url().getBaseUrlContent
Get URL request result using base::url().getBaseUrlRequestResult
Get connector class name.getConnClassName
Get connector types.getConnTypes
Get default cache folder.getDefaultCacheDir
Get entry class name.getEntryClassName
Get entry types.getEntryTypes
Get the available licenses for extension packages.getLicenses
Get the main package logger.getLogger
Get the package name from a package folder path.getPkgName
Get URL content using RCurl::getURL().getRCurlContent
Get URL request result using RCurcl::getURL().getRCurlRequestResult
Extract the repository name from a package folder.getReposName
Get the test output directory.getTestOutputDir
Get a URL content.getUrlContent
Send a request and get results.getUrlRequestResult
List test reference entries.listTestRefEntries
Loads the contents of files in memory.loadFileContents
Log debug message.logDebug
Log debug message.logDebug0
Log information message.logInfo
Log information message.logInfo0
Log trace message.logTrace
Log trace message.logTrace0
Convert a list into a string.lst2str
Build an RCurl::CURLOptions object.makeRCurlOptions
Mass CSV File connector class.MassCsvFileConn
Mass CSV File entry class.MassCsvFileEntry
Class for handling a Mass spectrometry database in SQLite format.MassSqliteConn
Mass spectra SQLite entry class.MassSqliteEntry
Create a new BiodbMain instance.newInst
Prepares file contents for saving.prepareFileContents
Progress class.Progress
Range class.Range
Class RequestResult.RequestResult
Run generic tests.runGenericTests
Saves contents to files.saveContentsToFiles
SQLite connector class.SqliteConn
Set a test context.testContext
A class for accessing the test reference entries.TestRefEntries
Run a test.testThat
Upgrading an existing extension package for biodb.upgradeExtPkg
Throw a warning and log it too.warn
Throw a warning and log it too.warn0