CLI

This section describes EMHealth commands available through the command-line interface.

emhealth COMMAND arg1 arg2 ...

Main Tasks

Importing Data

Description

Import health monitor data from XML file. Compressed files (*.xml.gz) are also supported. Optional skip-duplicates argument is useful for small overlapping imports(e.g. automatic import of the last 1h of data every 30 min). If you are importing a large dataset, do not use this option as it will slow down the process significantly.

Syntax

emhealth import -i /path/to/file.xml.gz -s em_health/instruments.json [--skip-duplicates]

Create Windows Batch Script

Description

Create a Windows batch file to export Health Monitor data. Depending on the HM version, you may need to modify the executable path via -e option. The output export_hm_data.cmd file is created in the current directory.

Syntax

emhealth create-task [-e "C:\Program Files (x86)\Thermo Scientific Health Monitor\HealthMonitorCmd.exe"] -s em_health/instruments.json

Watchdog

Description

Watch directory for XML file changes and trigger import. The watchdog can import several files in parallel. Optional t argument specifies the polling interval in seconds, the default is 5 minutes.

Syntax

emhealth watch -i /path/to/xml/dir -s em_health/instruments.json [-t 300]

Update EMHealth

Description

Make sure to run git pull origin master from the installation folder before running this command. The update command below will migrate the databases schema to the latest version and update container images.

Syntax

emhealth update

Run tests

Description

Run unit tests to check the XML import parser and import functions. Also executes pgTAP tests on the database.

Syntax

emhealth test

Database Operations

Create Data Statistics

Description

This command is usually run after you have imported a large batch of historical data. It will aggregate daily statistics like autoloader counters, EPU/Tomo sessions etc that is used by various dashboards. You only need to run this command once, the statistics will be refreshed automatically.

Syntax

emhealth db -d tem create-stats

Backup

Description

Perform a logical backup of TimescaleDB (both TEM and SEM) or a physical backup of Grafana databases. The backups are saved into BACKUP_DIR folder.

Syntax

emhealth db -d tem backup
emhealth db -d grafana backup

Restore

Description

Restore either TimescaleDB or Grafana database from a backup file.

Syntax

emhealth db -d tem restore

Erase database

Description

ALL data will be removed from a specified database! Empty tables will be re-initialized.

Syntax

emhealth db -d tem erase

Remove Old Data

Description

Data older than X days will be removed from a database. Due to the database design, only the data chunks that are fully within the specified time range will be removed.

Syntax

emhealth db -d tem prune --days 360

Developer Tools

Reset performance stats

Description

The periodic database statistics collection is enabled by default. Below command can be used if you modify the pganalyze tables or functions and want to update the jobs. The output is used in dashboards under DB performance folder. Optional f flag will erase existing database statistics.

Syntax

emhealth dev -d tem pganalyze [-f]

Migrate database

Description

Migrate TimescaleDB schema to the latest version (if required).

Syntax

emhealth dev -d tem migrate

Import Alarms

Note

This functionality is currently under development

Universal Error Codes (UECs) or Alarms from an instrument are stored (from TEM server 6.2) in a database separate from Health Monitor events and can be typically displayed with UEC Viewer. If you have the credentials to access the MSSQL server on MPC, you can import UECs from MSSQL into EMHealth database. To make it work, MSSQL_USER and MSSQL_PASSWORD (in the docker/.env) have to be defined, as well as the server field with IP address for each instrument in the instruments.json.

emhealth dev -d tem import-uec