EDAM (Environmental Data Acquisition Module), is a template framework that facilitates timeseries data acquisition and integration. EDAM templates are written using programming language-agnostic semantics, and can be reused both for input and output, thus enabling data reuse via transformations across different formats.
This project runs on python3. Thus, python3 should be installed.
It is highly recommended installing the module via Python virtual environment You can install and run this version. Issue the followings:
pip install edam
Above command installs edam, which will be available to the virtual environment.
It also creates an .edam folder in your system's home directory.
All EDAM related documents are located in this folder.
User=drafted template and metadata, and input files should be placed
under these corresponding directories.
More information about the proposed workflow can be found in the proposed-workflow.
In the metadata file you can define observables, station and sensors.
An observable can have the following attributes:
- name (e.g. Wind)
- unit (e.g. direction km/h)
- observable_id (e.g. wind). This corresponds to the name one can use in the .tmpl
In a template one can use in a placeholder ({{}}) only the template_id's, which were defined in the metadata files.
A template_id can have certain attributes. These are:
- value (e.g.
{{wind.value}}) - timestamp. In case the table (csv) has a dedicated column which denotes the timestamp of a specific observable, this will be defined as
{{wind.timestamp.time}}(if it's in the hh:mm format). - In case the one column-timestamp refers to more than one observable (e.g. BoM wind_direction_max and wind_speed_max), this should be defined as
{{same_timestamp(windm_spd.timestamp.time, windm_dir.timestamp.time)}}
In case a column has the timestamp which corresponds to
all observables in each row, users will use the {{timestamp.}}.
- Edit
setting.yamlto correspond to your database system - Draft a metadata file and put it into metadata folder (
~/.edam/metadata) - Draft a template file (
~/.edam/templates) - Add your input csv file into inputs folder (
~/.edam/inputs)
After parsing datasets using edam command, you can issue viewer command
and a webservice starts on you computer. If no changes to settings.yaml
(check Proposed workflow) have been made, you can visit
http://127.0.0.1:5000 and view the data.
For more details about the edam command usage,
issue a edam --help in your terminal.
The Agricultural Model Intercomparison and Improvement Project (AgMIP) brought into the spotlight agricultural modelling data sharing. Within AgMIP, various agricultural models (such as the APSIM) were transformed into the AgMIP data scheme.
AgMIP and APSIM data files use different timestamp components. The challenge here is to compose these into one universal timestamp. APSIM uses julian dates and years, while AgMIP timestamp is represented through year, month, date components.
Another challenge was related with metadata encoded in the preamble of APSIM data files. Specifically, prior to the timeseries there are station metadata such as station name, location and others. The APSIM data files share the same structure, so these preamble-encoded metadata distinguish the different stations.
AgMIP dataset
@DATE YYYY MM DD SRAD TMAX TMIN RAIN WIND DEWP VPRS RHUM
1980001 1980 1 1 15.0 26.0 12.2 0.0 1.4 4.8 8.6 25
1980002 1980 1 2 6.9 21.2 9.5 0.0 1.6 8.1 10.8 42
1980003 1980 1 3 10.7 22.2 14.7 8.0 1.5 11.9 14.0 52
1980004 1980 1 4 15.6 24.0 10.0 0.0 2.9 9.2 11.7 39
1980005 1980 1 5 16.3 23.9 12.0 0.0 2.7 1.7 6.9 23
1980006 1980 1 6 15.0 23.0 11.8 0.0 2.7 2.8 7.5 26
1980007 1980 1 7 16.5 22.2 11.4 0.0 2.5 -0.5 5.9 22
AgMIP template
@DATE YYYY MM DD SRAD TMAX TMIN RAIN WIND DEWP VPRS RHUM
{%for timestamp, srad, tmax, tmin, rain, wind, dewp, vprs, rhum in chunk%}
1980001 {{timestamp.year}} {{timestamp.month}} {{timestamp.day}} {{srad.value}} {{tmax.value}} {{tmin.value}} {{rain.value}} {{wind.value}} {{dewp.value}} {{vprs.value}} {{rhum.value}}
{%endfor%}
AgMIP metadata
Station:
name: Agmip
mobile: False
latitude: 23.200
longitude: 89.330
license: Attribution
tags:
key1: value1
key2: value2
Observables:
- observable_id: tmin
name: Temperature Min
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#min
- observable_id: tmax
name: Temperature Max
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#max
- observable_id: rain
name: Rain
ontology: https://edam.org#Rain
- observable_id: srad
name: Solar radiation
ontology: https://edam.org#SolarRadiation
- observable_id: wind
name: Wind
ontology: https://edam.org#WindSpeed
- observable_id: rhum
name: Humidity
ontology: https://edam.org#RelativeHumidity
- observable_id: vprs
name: Vprs
ontology: https://edam.org#VaporPressure
- observable_id: dewp
name: Dewing point
ontology: https://edam.org#DewingPoint
Units of Measurement:
- name: Megajoule per square metre
symbol: MJ/m^2
relevant_observables: srad
- name: Kilopascal
symbol: kPa
relevant_observables: vprs
- name: Percent
symbol: \%
relevant_observables: rhum
- name: Celcius
symbol: degC
relevant_observables: tmin, tmax, dewp
- name: Millimeters
symbol: mm
relevant_observables: rain
- name: kilometers per hour
symbol: km/hr
relevant_observables: windFollowing command is executed in approximately 2 seconds:
edam --input Agmip.csv --template Agmip.tmpl --metadata Agmip.yaml
APSIM dataset
[weather.met.weather]
Latitude = 36.68
longitude = 116.98
tav = 14.6 (oC) ! annual average ambient temperature
amp = 28.2 (oC) ! annual amplitude in mean monthly temperature
!!!! 1/01/1961 to 31/12/2005
day year radn maxt mint rain wind RH
273 2002 17.5 27.2 14.6 0 3.5 54
274 2002 13.6 23.1 14.7 0 5.3 40
275 2002 15.8 27.1 11.1 0 5.5 29
276 2002 15.5 25.8 16.5 0 3.8 39
277 2002 14.9 25.5 14.6 0 2.5 63
278 2002 15.2 23.1 15.2 0 3 47
279 2002 13.4 19.9 10.9 0 3 38
280 2002 15.7 19.3 8.2 0 2.5 47
APSIM template
[weather.met.weather]
Latitude = {{station.latitude}}
longitude = {{station.longitude}}
tav = {{station.tags.tav}}
amp = {{station.tags.amp}}
!!!! 1/01/1961 to 31/12/2005
day year radn maxt mint rain wind RH
{%for timestamp, radn,maxt,mint,rain,wind,RH in chunk%}
{{timestamp.dayofyear}} {{timestamp.year}} {{radn.value}} {{maxt.value}} {{mint.value}} {{rain.value}} {{wind.value}} {{RH.value}}
{%endfor%}
APSIM metadata
Station:
name: Yucheng
license: Attribution
Observables:
- observable_id: mint
name: Temperature
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#min
- observable_id: maxt
name: Max Temperature
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#max
- observable_id: rain
name: Rain
ontology: https://edam.org#Rain
- observable_id: radn
name: Solar radiation
ontology: https://edam.org#SolarRadiation
- observable_id: wind
name: Wind
ontology: https://edam.org#WindSpeed
- observable_id: RH
name: Relative humidity
ontology: https://edam.org#RelativeHumidity
Units of Measurement:
- name: Millijoule per square meters
symbol: mJ/m^2
relevant_observables: radn
- name: Percent
symbol: \%
relevant_observables: RH
- name: Celcius
symbol: degC
relevant_observables: mint, maxt
- name: Millimeters
symbol: mm
relevant_observables: rain
- name: Meters per second
symbol: m/s
relevant_observables: windFollowing command is executed in less than 1 second:
edam --input Yucheng.met --template Yucheng.tmpl --metadata Yucheng.yaml
In the context of Open Data, the UK Meteorological Office, reports historical
observations of 27 weather stations.
For every station, monthly observations are stored in one text document.
New observations are appended every month and each weather station can be
found on a certain URI.
URI follows the pattern:
http://www.metoffice.gov.uk/pub/data/weather/uk/climate/stationdata/{station name}data.txt,
where {station name} is replaced with an actual station name.
Data points reported in Met Office weather stations' documents have special markers. The challenge here is concerned with establishing a relation among markers and attributes. This relation, expressed using natural language, is defined in each document's preamble. For example, "estimated data is marked with a * after the value". These types of metadata are essential, so they have to be parsed and stored.
UK Met dataset
Cwmystwyth
Location: 277300E 274900N, Lat 52.358 Lon -3.802, 301 metres amsl
Estimated data is marked with a * after the value.
Missing data (more than 2 days missing in month) is marked by ---.
Sunshine data taken from an automatic Kipp & Zonen sensor marked with a #, otherwise sunshine data taken from a Campbell Stokes recorder.
yyyy mm tmax tmin af rain sun
degC degC days mm hours
1959 1 4.5 -1.9 20 --- 57.2
1959 2 7.3 0.9 15 --- 87.2
1959 3 8.4 3.1 3 --- 81.6
1959 4 10.8 3.7 1 --- 107.4
1959 5 15.8 5.8 1 --- 213.5
1959 6 16.9 8.2 0 --- 209.4
1959 7 18.5 9.5 0 --- 167.8
1959 8 19.0 10.5 0 --- 164.8
1959 9 18.3 5.9 0 --- 196.5
1959 10 14.8 7.9 1 --- 101.1
1959 11 8.8 3.9 3 --- 38.9
1959 12 7.2 2.5 3 --- 19.2
UK Met template
{{station.name}}
Location:{{station.location}}, Lat {{station.latitude}} Lon {{station.longitude}}, {{station.tags.altitude}}
Estimated data is marked with a * after the value.
Missing data (more than 2 days missing in month) is marked by ---.
Sunshine data taken from an automatic Kipp & Zonen sensor marked with a #, otherwise sunshine data taken from a Campbell Stokes recorder.
yyyy mm tmax tmin af rain sun
degC degC days mm hours
{%for timestamp, tmax,tmin,af,rain,sun in chunk%}
{{timestamp.year}} {{timestamp.month}} {{tmax.value}} {{tmin.value}} {{af.value}} {{rain.value}} {{sun.value}}
{%endfor%}
UK Met metadata
Station:
license: Attribution
region: United Kingdom
url: http://www.metoffice.gov.uk/
tags:
key1:value1
key2:value2
Observables:
- observable_id: tmin
name: Temperature minimum
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#min
- observable_id: tmax
name: Temperature Max
ontology: https://edam.org#Temperature
qualifiers: https://edam.org#max
- observable_id: rain
name: Rain
ontology: https://edam.org#Rain
- observable_id: af
name: Days of air frost
ontology: https://edam.org#AirFrostDays
- observable_id: sun
name: Sunshine duration
ontology: https://edam.org#SunShineDuration
Units of Measurement:
- name: Days
symbol: D
relevant_observables: af, sun
- name: Celcius
symbol: degC
relevant_observables: tmin, tmax
- name: Millimeters
symbol: mm
relevant_observables: rainFollowing command downloads and stores data from 27 weather stations. It is executed in approximately 9 seconds.
edam --input "http://www.metoffice.gov.uk/pub/data/weather/uk/climate/stationdata/{_var_}data.txt" --template uk.tmpl --metadata uk.yaml --var "aberporth,armagh, ballypatrick, camborne, cambridge, cardiff, chivenor, cwmystwyth, dunstaffnage, durham, eastbourne, eskdalemuir"