Package index • ntsportal

All functions

addRawfiles(): Add new records for MS measurement files to msrawfiles index

addValueToArray(): Add value to an array field

changeAliasAddress(): Change alias of an index to a new index.

changeMsrawfileFilename(): Change filename in the msrawfiles-db and on the filesystem

changeMsrawfilePath(): Change the path of one document in msrawfiles

checkMsrawfiles(): Check `msrawfiles` for validity

checkPngAvailability(): Check that all structural formula PNGs have been created

checkPngSyncronization(): Check synchronization with the picture server

connectNtsportal(): Set ElasticSearch credentials and create ElasticSearch connection object

convertToRecord(<dbasResult>): Convert a `dbasResult` to a `list` of `featureRecord`s

createAllStructures(): Create images of structural formulae from the spectral library

createBackupMsrawfiles(): Create a backup of an msrawfiles index

dbaScreeningNewBatches(): Process all measurement files which have not yet been processed by DBAS

dbaScreeningOneBatch(): Process one batch of measurement files by DBAS

dbaScreeningSelectedBatches(): DBAS process selected measurement files via batch directory

dbaScreeningSelectedBatchesSlurm(): Process batches (DBAS) using SLURM by selecting directories

dbaScreeningUnprocessedBatchesSlurm(): Process new batches (DBAS) using SLURM

DbComm-class: DbComm interface

deleteTable(): Delete a table

esSearchPaged(): Get search results for more than 10000 docs by pagination.

executeEnrichPolicy(): Refresh an existing enrich policy

findTemplateId(): Get ID based on search parameters

getDbComm(): Make a DbComm interface object

getNrow(): Get the number of rows in a table

getTableAsRecords(): Get a table as a list of ntspRecords

getTableAsTibble(): Get a table as a tibble

ingest(): Ingest featureRecords into Elasticsearch

isTable(): Does a table exist?

msrawfilesSetVersion(): Change msrawfiles to a new version

ntsportal: ntsportal: A package for non-target data management

ping(): Test the DB-Connection

PythonDbComm-class: A DbComm interface using the Python back-end

PythonDbComm(): Build Python DB communications interface

removeRedundantPngs(): Delete redundant PNGs

removeValueFromArray(): Remove a value from an array field

resetConnectionCredentials(): Create connection with new credentials

scanBatchDbas(): Scan measurement files for known compounds

setCredNonInteractive(): Set credentials for accessing NTSPortal ElasticSearch

setValueInField(): Set the value of a field in a table

updateEnrichPolicies(): Update enrich policies in Elasticsearch

updateIngestPipelines(): Update Ingest Pipelines needed for ntsportal on the elasticsearch cluster

updateLinearRegressionTable(): Update the "analysis_dbas" table for Time Series SPM dashboard

updateSpectralLibrary(): Update the CSL spectral library on ntsportal

validateRecord(): Validate that a `*record` is correctly formated