## ----echo=FALSE--------------------------------------------------------------- source(system.file('vignettes_inc.R', package='biodb')) ## ----------------------------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- mybiodb <- biodb::newInst() ## ----------------------------------------------------------------------------- mybiodb$getConfig() ## ----------------------------------------------------------------------------- x <- mybiodb$getConfig()$listKeys() ## ----keysDf, echo=FALSE, results='asis'--------------------------------------- knitr::kable(x, "pipe", caption="List of keys with some of their parameters") ## ----------------------------------------------------------------------------- mybiodb$getConfig()$getDescription('useragent') ## ----------------------------------------------------------------------------- mybiodb$getConfig()$get('useragent') ## ----------------------------------------------------------------------------- mybiodb$getConfig()$set('useragent', 'My application ; wizard@of.oz') mybiodb$getConfig()$get('useragent') ## ----------------------------------------------------------------------------- mybiodb$getConfig()$enable('offline') mybiodb$getConfig()$disable('offline') ## ----------------------------------------------------------------------------- mybiodb$getConfig()$getDefaultValue('useragent') ## ----------------------------------------------------------------------------- mybiodb$getConfig()$getAssocEnvVar('useragent') ## ----------------------------------------------------------------------------- mybiodb$getDbsInfo() ## ----------------------------------------------------------------------------- mybiodb$getDbsInfo()$get('mass.csv.file') ## ----------------------------------------------------------------------------- mybiodb$getFactory() ## ----------------------------------------------------------------------------- chebi.tsv <- system.file("extdata", "chebi_extract.tsv", package='biodb') conn <- mybiodb$getFactory()$createConn('comp.csv.file', url=chebi.tsv) conn ## ----------------------------------------------------------------------------- conn$getEntry('1018') ## ----------------------------------------------------------------------------- conn$searchForEntries(list(monoisotopic.mass=list(value=136.05, delta=0.1))) ## ----echo=FALSE, results='asis'----------------------------------------------- make_vignette_ref('entries') ## ----------------------------------------------------------------------------- conn <- mybiodb$getFactory()$getConn('comp.csv.file') ## ----------------------------------------------------------------------------- mybiodb$getFactory()$deleteConn(conn) ## ----------------------------------------------------------------------------- compUrl <- system.file("extdata", "chebi_extract_custom.csv", package='biodb') compdb <- mybiodb$getFactory()$createConn('comp.csv.file', url=compUrl) compdb$setCsvSep(';') ## ----------------------------------------------------------------------------- compdb$getUnassociatedColumns() ## ----------------------------------------------------------------------------- compdb$getFieldsAndColumnsAssociation() ## ----------------------------------------------------------------------------- mybiodb$getFactory()$deleteConn(compdb) compdb <- mybiodb$getFactory()$createConn('comp.csv.file', url=compUrl) compdb$setCsvSep(';') compdb$setField('accession', 'ID') compdb$setField('kegg.compound.id', 'kegg') compdb$setField('monoisotopic.mass', 'mass') compdb$setField('molecular.mass', 'molmass') ## ----------------------------------------------------------------------------- compdb$getEntryIds() ## ----------------------------------------------------------------------------- compdb$getEntry('1018')$getFieldsAsDataframe() ## ----compTable, echo=FALSE, results='asis'------------------------------------ compDf <- read.table(compUrl, sep=";", header=TRUE, quote="") # Prevent RMarkdown from interpreting @ character as a reference: compDf$smiles <- vapply(compDf$smiles, function(s) paste0('`', s, '`'), FUN.VALUE='') knitr::kable(head(compDf), "pipe", caption="Excerpt from compound database CSV file.") ## ----------------------------------------------------------------------------- mybiodb$getEntryFields() ## ----------------------------------------------------------------------------- mybiodb$getEntryFields()$getFieldNames() ## ----------------------------------------------------------------------------- mybiodb$getEntryFields()$get('monoisotopic.mass') ## ----------------------------------------------------------------------------- mybiodb$getPersistentCache() ## ----echo=FALSE, results='asis'----------------------------------------------- make_vignette_ref('new_connector') ## ----------------------------------------------------------------------------- source(system.file("extdata", "ChebiExConn.R", package='biodb')) source(system.file("extdata", "ChebiExEntry.R", package='biodb')) mybiodb$loadDefinitions(system.file("extdata", "chebi_ex.yml", package='biodb')) conn <- mybiodb$getFactory()$createConn('chebi.ex') ## ----------------------------------------------------------------------------- entry <- conn$getEntry('17001') ## ----------------------------------------------------------------------------- mybiodb$getPersistentCache()$fileExist(conn$getCacheId(), name='17001', ext=conn$getEntryFileExt()) ## ----------------------------------------------------------------------------- mybiodb$getPersistentCache()$getFilePath(conn$getCacheId(), name='17001', ext=conn$getEntryFileExt()) ## ----------------------------------------------------------------------------- conn$deleteAllEntriesFromPersistentCache() ## ----------------------------------------------------------------------------- mybiodb$getPersistentCache()$fileExist(conn$getCacheId(), name='17001', ext=conn$getEntryFileExt()) ## ----------------------------------------------------------------------------- conn$deleteAllEntriesFromVolatileCache() ## ----------------------------------------------------------------------------- conn$deleteWholePersistentCache() ## ----------------------------------------------------------------------------- biodb::getLogger() ## ----------------------------------------------------------------------------- biodb::logInfo("%d entries have been processed.", 12) ## ----------------------------------------------------------------------------- biodb::logDebug("The file %s has been written.", 'myfile.txt') ## ----------------------------------------------------------------------------- biodb::logTrace("%d bytes written.", 1284902) ## ----------------------------------------------------------------------------- biodb::getLogger()$set_threshold(300) ## ----------------------------------------------------------------------------- biodb::logInfo("hello") ## ----------------------------------------------------------------------------- biodb::getLogger()$set_threshold(400) ## ----------------------------------------------------------------------------- biodb::logInfo("hello") ## ----------------------------------------------------------------------------- mybiodb$terminate() ## ----------------------------------------------------------------------------- sessionInfo()