How data import works in Baseline

Baseline allows data import via Excel files. Currently, only a single Excel format is supported - the one used for WES. For the description of the format, see the WES section.

Only data managed by Baseline system can be imported, e.g. patient data, samples, sequencing, therapies, etc. There is also other data accessible through Baseline but not managed by Baseline, such as mutational reports, BAMs, etc. These files are stored out of the Baseline database (secure storage) and Baseline only provides it on demand. Hence, this kind of data cannot be imported.

Import flow

The import flow is described in diagrams below. The flow is used for all supported data formats.

Excel table sent to server(user action via Baseline page)SeeValidity constraintsfor respectiveformats WES, WGS, TP53 etc.Table is validyesnoDatabase is emptyyesnoImport the whole tableStart merge flowreturn errorGet and store current database stateGet patient ID from Patients sheetPatient ID already present in databaseyesnoCompare all patient's data from Excel table to data in databaseAny difference foundyesnoAdd both current and new patient's data to difference listIgnore this patientLabel this patient for importAny Patients left?yesSeePending importsAdd 'pending import record' to pending imports tableImport data includes IDs of patientsto be imported (new ones) and listof differences for patients to be ovewritten.Return import data to clientno
Excel table sent to server(user action via Baseline page)SeeValidity constraintsfor respectiveformats WES, WGS, TP53 etc.Table is validyesnoDatabase is emptyyesnoImport the whole tableStart merge flowreturn errorGet and store current database stateGet patient ID from Patients sheetPatient ID already present in databaseyesnoCompare all patient's data from Excel table to data in databaseAny difference foundyesnoAdd both current and new patient's data to difference listIgnore this patientLabel this patient for importAny Patients left?yesSeePending importsAdd 'pending import record' to pending imports tableImport data includes IDs of patientsto be imported (new ones) and listof differences for patients to be ovewritten.Return import data to clientno