Package index • ntsportal

analysis-linearRegression module

Functions for updating linear regression tables

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

Functions for saving user credentials for the elasticsearch connection

connectNtsportal(): Set ElasticSearch credentials and create ElasticSearch connection object
resetConnectionCredentials(): Create connection with new credentials
setCredNonInteractive(): Set credentials for accessing NTSPortal ElasticSearch

Functions for updating structural formula images for dashboards

createAllStructures(): Create images of structural formulae from the spectral library
checkPngAvailability(): Check that all structural formula PNGs have been created
removeRedundantPngs(): Delete redundant PNGs
checkPngSyncronization(): Check synchronization with the picture server

Functions for updating enrich policies

High-level functions for retrieving data from NTSPortal

Low level Generics for database communication

addValueToArray(): Add value to an array field
deleteTable(): Delete a table
DbComm-class: DbComm interface
getDbComm(): Make a DbComm interface object
getNrow(): Get the number of rows in a table
getTableAsRecords(): Get a table as a list of ntspRecords
getUniqueValues(): Get unique values in a field of a table
isTable(): Does a table exist?
ping(): Test the DB-Connection
PythonDbComm(): Build Python DB communications interface
PythonDbComm-class: A DbComm interface using the Python back-end
removeValueFromArray(): Remove a value from an array field
removeFieldFromTable(): Remove a field from a Table
replaceValueInField(): Replace a value in a field Will replace all occurrences of this value in the specified field. There is no way to restrict the change to specific records. For that purpose, use `setValueInField()`.
setValueInField(): Set the value of a field in a table

Functions for updating ingest pipelines

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

Functions for adding metadata entries to msrawfiles tables

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

Functions for manipulating msrawfiles tables

addRawfiles(): Add new records for MS measurement files to msrawfiles index
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
createBackupMsrawfiles(): Create a backup of an msrawfiles index
findTemplateId(): Get ID based on search parameters
msrawfilesSetVersion(): Change msrawfiles to a new version

Functions for validating records

Functions for file processing and ingesting records

convertToRecord(): Convert the result of file scanning to a list of feature records Compound and sample metadata, including spectra are collected from the `scanResult`, from the linked raw measurement files, or from `msrawfileRecords`
ingestFeatureRecords(): Ingest featureRecords into Elasticsearch
scanBatch(): Extract features from measurement files with an algorithm
screeningSelectedBatches(): Process measurement files in selected batch directories
screeningOneBatch(): Process one batch of measurement files
screeningSelectedBatchesSlurm(): Process batches using SLURM by selecting directories

Functions for updating spectral library table

Miscellaneous and package initialization functions

esSearchPaged(): Get search results for more than 10000 docs by pagination.
makeMappingsTbl(): Turn mappings into a tibble for documentation
ntsportal: ntsportal: A package for non-target data management