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.
This syntax is deprecated, you must add <<#LightBlue>> at the end of the line, after the ';' This syntax is deprecated, you must add <<#Gold>> at the end of the line, after the ';' This syntax is deprecated, you must add <<#Salmon>> at the end of the line, after the ';' Excel table sent to server (user action via Baseline page) See Validity constraints for respective formats WES, WGS, TP53 etc. Table is valid yes no Database is empty yes no Import the whole table Start merge flow return error Get and store current database state Get patient ID from Patients sheet Patient ID already present in database yes no Compare all patient's data from Excel table to data in database Any difference found yes no Add both current and new patient's data to difference list Ignore this patient Label this patient for import Any Patients left? yes See Pending imports Add 'pending import record' to pending imports table Import data includes IDs of patients to be imported (new ones) and list of differences for patients to be ovewritten. Return import data to client no This syntax is deprecated, you must add <<#LightBlue>> at the end of the line, after the ';' This syntax is deprecated, you must add <<#Gold>> at the end of the line, after the ';' This syntax is deprecated, you must add <<#Salmon>> at the end of the line, after the ';' Excel table sent to server (user action via Baseline page) See Validity constraints for respective formats WES, WGS, TP53 etc. Table is valid yes no Database is empty yes no Import the whole table Start merge flow return error Get and store current database state Get patient ID from Patients sheet Patient ID already present in database yes no Compare all patient's data from Excel table to data in database Any difference found yes no Add both current and new patient's data to difference list Ignore this patient Label this patient for import Any Patients left? yes See Pending imports Add 'pending import record' to pending imports table Import data includes IDs of patients to be imported (new ones) and list of differences for patients to be ovewritten. Return import data to client no