Data

Data Format

LEAF converts measurement data into Influx timeseries databases (InfluxDB) Line Protocol data format by default, meaning that the data can be easily inserted into InfluxDB or any other timeseries database.

InfluxDB Line Protocol

Line protocol is a text based data model format that is designed for efficiently writing time-series data. This data model organizes timeseries data and data points into four components:

• measurement: The identity of the measurement set and referring to the table that data is stored in. Note that later InfluxDB versions refer to this as table.
• tag sets: Optional key-value pair(s) that can be used as, or hold, the metadata to describe the data.
• field sets: Key-value pair(s) representing the data and its value (e.g., temperature=10)
• timestamp : Optional unix timestamp

Format

These four components: timestamps;, measurement names; fields (key-value pairs representing the data); and tags (optional key-value pairs used to store metadata that describes the data) are arranged in a single line. A typical line in this format looks like this:

measurementName,tagKey=tagValue fieldKey="fieldValue" 1465839830100400200

Where:

• measurementName: Identifies the measurement.
• tagKey=tagValue: Zero or more tag sets separated by commas. Tags are optional but recommended for indexing.
• fieldKey=“fieldValue”: At least one field set, with multiple fields separated by commas. Fields are the actual data points.
• 1465839830100400200: An optional timestamp for the data point. If not specified, depending upon the recipient, the server’s current time is used.

measurementName,tagKey1=tagValue1,tagKey2=tagValue2 fieldKey1="fieldValue1",fieldKey2="fieldValue2" 1465839830100400200

This format is highly optimized for time-series data, enabling quick parsing and writing as:

• everything before the first comma is a measurement
• everything between the first comma and the first white space is tag, with distinct tag being separated by a comma
• everything between the first white space and the second white space is field, with distinct field being separated by a comma
• everything after the second comma is timestamp represented as an integer

Each line is then separated by \n.

Example

Example 1: Abundance

As an example, say if we have a timeseries dataset where we count the occurrence (or abundance) of two species (G. ruber and G. bulloides) this would be represented tabularly as:

AbundanceCounts

Time	Sample	Location	Analyst	Abundance: G. ruber	Abundance: G. bulloides
1465839830100400200	T86_5P#6_DIS_0_1cm	NAtl	BM	50	76
1465839830100400800	T86_5P#6_DIS_1_2cm	NAtl	JK	47	81
1465839830100401200	T86_5P#6_DIS_2_3cm	NAtl	JK	31	99

With the data (Abundance: G. ruber and Abundance: G. bulloides) and metadata (Sample, Location, Analyst) being found on individual rows with a timestamp index (Time). In line protocol this table would be:

AbundanceCounts,sample=T86_5P#6_DIS_0_1cm,location=NAtl,analyst=BM G_ruber=50,G_bulloides=76 1465839830100400200
AbundanceCounts,sample=T86_5P#6_DIS_1_2cm,location=NAtl,analyst=JK G_ruber=47,G_bulloides=81 1465839830100400800
AbundanceCounts,sample=T86_5P#6_DIS_2_3cm,location=NAtl,analyst=BM G_ruber=31,G_bulloides=99 1465839830100401200

To make cleaner we could make it one message per analysis:

AbundanceCounts,sample=T86_5P#6_DIS_0_1cm,location=NAtl,analyst=BM G_ruber=50 1465839830100400200
AbundanceCounts,sample=T86_5P#6_DIS_0_1cm,location=NAtl,analyst=BM G_bulloides=76 1465839830100400200
AbundanceCounts,sample=T86_5P#6_DIS_1_2cm,location=NAtl,analyst=JK G_ruber=47 1465839830100400800
AbundanceCounts,sample=T86_5P#6_DIS_1_2cm,location=NAtl,analyst=JK G_bulloides=81 1465839830100400800
AbundanceCounts,sample=T86_5P#6_DIS_2_3cm,location=NAtl,analyst=BM G_ruber=31 1465839830100401200
AbundanceCounts,sample=T86_5P#6_DIS_2_3cm,location=NAtl,analyst=BM G_bulloides=99 1465839830100401200

To further simplify the line protocol and make it less dependent upon specific field keys we could add the species being counted as a separate field:

AbundanceCounts,sample=T86_5P#6_DIS_0_1cm,location=NAtl,analyst=BM counted=G_ruber,count=50 1465839830100400200
AbundanceCounts,sample=T86_5P#6_DIS_0_1cm,location=NAtl,analyst=BM counted=G_bulloides,count=76 1465839830100400200
AbundanceCounts,sample=T86_5P#6_DIS_1_2cm,location=NAtl,analyst=JK counted=G_ruber,count=47 1465839830100400800
AbundanceCounts,sample=T86_5P#6_DIS_1_2cm,location=NAtl,analyst=JK counted=G_bulloides,count=81 1465839830100400800
AbundanceCounts,sample=T86_5P#6_DIS_2_3cm,location=NAtl,analyst=BM counted=G_ruber,count=31 1465839830100401200
AbundanceCounts,sample=T86_5P#6_DIS_2_3cm,location=NAtl,analyst=BM counted=G_bulloides,count=99 1465839830100401200

By making the line protocol more generic additional datasets could be stored alongside this one from different locations, analysts, or even samples.

Example 2: Environmental variables

A timeseries database of a sensor that measures rainfall and temperature would for example look like the following table:

EnvironmentalVariables

Time	Location	Entity	Rainfall	Temperature
1465839830100400200	WUR Campus	Sensor1	0	22.4
1465839830100400800	WUR Campus	Sensor1	0	21.7
1465839830100401200	WUR Campus	Sensor1	0	21.9

This could be translated into:

EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=temperature,value=22.4 1465839830100400200
EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=rainfall,value=0 1465839830100400200
EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=temperature,value=21.7 1465839830100400800
EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=rainfall,value=0 1465839830100400800
EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=temperature,value=21.9 1465839830100401200
EnvironmentalVariables,location="WUR Campus",entity=Sensor1 measurement=rainfall,value=0 1465839830100401200

Python Package: InfluxObject

To convert datasets into Line Protocol, LEAF uses the Python Package InfluxObject. This package can be independently installed by entering the following command in the terminal:

pip install influxobject

The package contains the following commands:

x = influxobject.InfluxPoint()
x.
    x.add_field(..., ...)
    x.from_json(...)
    x.remove_field(...)
    x.set_measurement(...)
    x.to_line_protocol()
    x.add_tag(..., ...)
    x.remove_tag(...)
    x.set_tags(...)
    x.validate()
    x.parse_line_protocol(...)
    x.set_fields(...)
    x.set_timestamp(...)
    x.to_json()

which can be used like so:

from influxobject.influxpoint import InfluxPoint

influx_point = InfluxPoint()
influx_point.set_measurement("measurement")
influx_point.set_tags({"tag1": "value1"})
influx_point.set_fields({"field1": 1, "field2": 2})
influx_point.set_timestamp(datetime.datetime(2021, 1, 1))\

# JSON and Line Protocol outputs
print(influx_point.to_json())
print(influx_point.to_line_protocol())

JSON representation:

{
    "measurement": "measurement",
    "tags": {"tag1": "value1"},
    "fields": {"field1": 1, "field2": 2},
    "timestamp": 1609455600,
}

Line Protocol representation:

"measurement,tag1=value1 field1=1,field2=2 1609455600"