{ "info": { "author": "Argyrios Samourkasidis", "author_email": "argysamo@gmail.com", "bugtrack_url": null, "classifiers": [ "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6" ], "description": "[![PRs Welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg?style=flat-square)](http://makeapullrequest.com)\n\n# Table of contents\n\n- [Installation](#installation) \n- [Test cases](#test-cases) \n\t- [AgMIP and APSIM weather data files](#agmip-and-apsim-weather-data-files)\n\t\t- [AgMIP data files](#agmip-data-files)\n\t\t\t- [AgMIP dataset](#agmip-dataset)\n\t\t\t- [AgMIP template](#agmip-template)\n\t\t\t- [AgMIP metadata](#agmip-metadata)\n\t\t\t- [Parse AgMIP](#parse-agmip)\n\t\t- [APSIM station](#apsim-station)\n\t\t\t- [APSIM dataset](#apsim-dataset)\n\t\t\t- [APSIM template](#apsim-template)\n\t\t\t- [APSIM metadata](#apsim-metadata)\n\t\t\t- [Parse APSIM](#parse-apsim)\n[Template language](#template-language) \n[Proposed workflow](#proposed-workflow) \n \n# Installation\n\nThis project runs on **python3**. Thus, python3 should be installed. \n\nFor MacOS users issuing a `brew install python3` should do the trick. \nAbove command installs python3 (`/usr/local/bin/python3`) and pip3 (`/usr/local/bin/pip3`).\n\n\nYou can install and run this version. Issue the followings:\n\n`pip3 install edam`\n\nAbove commands install `edam` in your system. \nThey also create an **.edam** folder in your system's home directory. \nAll EDAM related documents are located in this folder. \nUser drafted *template* and *metadat* , and *input* files should be put in this folder. \n\nMore information about the proposed workflow can be found [here](#proposed-worflow). \n\n# Test cases\n\nAfter parsing datasets using `edam` command, you can issue `viewer` command \nand a webservice starts on you computer. If no changes to `settings.yaml` \n(check [Proposed workflow](#proposed-workflow)) have been made, you can visit \n`http://127.0.0.1:5000` and view the data. \n\nFor more details about the `edam` command usage, issue a `edam --help` in your terminal. \n\n## **AgMIP and APSIM weather data files**\n\nThe Agricultural Model Intercomparison and Improvement Project (AgMIP) brought into the spotlight agricultural modelling data sharing. \nWithin AgMIP, various agricultural models (such as the APSIM) were transformed into the AgMIP data scheme. \n\nAgMIP and APSIM data files use different *timestamp components*. \nThe challenge here is to compose these into one universal timestamp. \nAPSIM uses *julian dates* and *years*, while AgMIP timestamp is represented through *year*, *month*, *date* components. \n\nAnother challenge was related with metadata encoded in the preamble of APSIM data files. \nSpecifically, prior to the timeseries there are station metadata such as station name, location and others. \nThe APSIM data files share the same structure, so these preamble-encoded metadata distinguish the different stations. \n\n\n### AgMIP data files\n\n#### AgMIP dataset\n\n```csv\n@DATE YYYY MM DD SRAD TMAX TMIN RAIN WIND DEWP VPRS RHUM\n1980001 1980 1 1 15.0 26.0 12.2 0.0 1.4 4.8 8.6 25\n1980002 1980 1 2 6.9 21.2 9.5 0.0 1.6 8.1 10.8 42\n1980003 1980 1 3 10.7 22.2 14.7 8.0 1.5 11.9 14.0 52\n1980004 1980 1 4 15.6 24.0 10.0 0.0 2.9 9.2 11.7 39\n1980005 1980 1 5 16.3 23.9 12.0 0.0 2.7 1.7 6.9 23\n1980006 1980 1 6 15.0 23.0 11.8 0.0 2.7 2.8 7.5 26\n1980007 1980 1 7 16.5 22.2 11.4 0.0 2.5 -0.5 5.9 22\n```\n\n#### AgMIP template\n\n```csv\n@DATE YYYY MM DD SRAD TMAX TMIN RAIN WIND DEWP VPRS RHUM\n{%for timestamp, srad, tmax, tmin, rain, wind, dewp, vprs, rhum in chunk%}\n1980001 {{timestamp.year}} {{timestamp.month}} {{timestamp.day}} {{srad.value}} {{tmax.value}} {{tmin.value}} {{rain.value}} {{wind.value}} {{dewp.value}} {{vprs.value}} {{rhum.value}}\n{%endfor%}\n```\n\n#### AgMIP metadata\n\n```yaml\nStation:\n name: Agmip\n mobile: False\n latitude: 23.200\n longitude: 89.330\n license: Attribution\n tags:\n key1: value1\n key2: value2\nObservables:\n - observable_id: tmin\n name: Temperature Min\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#min\n - observable_id: tmax\n name: Temperature Max\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#max\n - observable_id: rain\n name: Rain\n ontology: http://edam.gr#Rain\n - observable_id: srad\n name: Solar radiation\n ontology: http://edam.gr#SolarRadiation\n - observable_id: wind\n name: Wind\n ontology: http://edam.gr#WindSpeed\n - observable_id: rhum\n name: Humidity\n ontology: http://edam.gr#RelativeHumidity\n - observable_id: vprs\n name: Vprs\n ontology: http://edam.gr#VaporPressure\n - observable_id: dewp\n name: Dewing point\n ontology: http://edam.gr#DewingPoint\nUnits of Measurement:\n - name: Megajoule per square metre\n symbol: MJ/m^2\n relevant_observables: srad\n - name: Kilopascal\n symbol: kPa\n relevant_observables: vprs\n - name: Percent\n symbol: \\%\n relevant_observables: rhum\n - name: Celcius\n symbol: degC\n relevant_observables: tmin, tmax, dewp\n - name: Millimeters\n symbol: mm\n relevant_observables: rain\n - name: kilometers per hour\n symbol: km/hr\n relevant_observables: wind\n```\n\n#### Parse AgMIP\n\nFollowing command is executed in approximately 2 seconds:\n\n`edam --input Agmip.csv --template Agmip.tmpl --metadata Agmip.yaml --drop yes` \n\n\n### APSIM station\n\n#### APSIM dataset\n\n```csv\n[weather.met.weather]\n\nLatitude = 36.68\nlongitude = 116.98\ntav = 14.6 (oC) ! annual average ambient temperature\namp = 28.2 (oC) ! annual amplitude in mean monthly temperature\n!!!! 1/01/1961 to 31/12/2005\n day year radn maxt mint rain wind RH\n 273 2002 17.5 27.2 14.6 0 3.5 54\n 274 2002 13.6 23.1 14.7 0 5.3 40\n 275 2002 15.8 27.1 11.1 0 5.5 29\n 276 2002 15.5 25.8 16.5 0 3.8 39\n 277 2002 14.9 25.5 14.6 0 2.5 63\n 278 2002 15.2 23.1 15.2 0 3 47\n 279 2002 13.4 19.9 10.9 0 3 38\n 280 2002 15.7 19.3 8.2 0 2.5 47\n```\n\n#### APSIM template\n\n```csv\n[weather.met.weather]\n\nLatitude = {{station.latitude}}\nlongitude = {{station.longitude}}\ntav = {{station.tags.tav}}\namp = {{station.tags.amp}}\n!!!! 1/01/1961 to 31/12/2005\n day year radn maxt mint rain wind RH\n{%for timestamp, radn,maxt,mint,rain,wind,RH in chunk%}\n{{timestamp.dayofyear}} {{timestamp.year}} {{radn.value}} {{maxt.value}} {{mint.value}} {{rain.value}} {{wind.value}} {{RH.value}}\n{%endfor%}\n```\n\n#### APSIM metadata\n\n```yaml\nStation:\n name: Yucheng\n license: Attribution\nObservables:\n - observable_id: mint\n name: Temperature\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#min\n - observable_id: maxt\n name: Max Temperature\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#max\n - observable_id: rain\n name: Rain\n ontology: http://edam.gr#Rain\n - observable_id: radn\n name: Solar radiation\n ontology: http://edam.gr#SolarRadiation\n - observable_id: wind\n name: Wind\n ontology: http://edam.gr#WindSpeed\n - observable_id: RH\n name: Relative humidity\n ontology: http://edam.gr#RelativeHumidity\nUnits of Measurement:\n - name: Millijoule per square meters\n symbol: mJ/m^2\n relevant_observables: radn\n - name: Percent\n symbol: \\%\n relevant_observables: RH\n - name: Celcius\n symbol: degC\n relevant_observables: mint, maxt\n - name: Millimeters\n symbol: mm\n relevant_observables: rain\n - name: Meters per second\n symbol: m/s\n relevant_observables: wind\n```\n\n#### Parse APSIM\n\nFollowing command is executed in less than 1 second:\n\n`edam --input Yucheng.met --template Yucheng.tmpl --metadata Yucheng.yaml --drop yes` \n\n\n## **UK Meteorological Office**\n\nIn the context of Open Data, the UK Meteorological Office, reports historical observations of 27 weather stations. \nFor every station, monthly observations are stored in one text document. \nNew observations are appended every month and each weather station can be found on a certain URI. \nURI follows the pattern: \n`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. \n\nData points reported in Met Office weather stations' documents have special markers. \nThe challenge here is concerned with establishing a relation among markers and attributes. \nThis relation, expressed using natural language, is defined in each document's preamble. \nFor example, \"estimated data is marked with a * after the value\". \nThese types of metadata are essential, so they have to be parsed and stored. \n\n### UK Met dataset\n\n```csv\nCwmystwyth\nLocation: 277300E 274900N, Lat 52.358 Lon -3.802, 301 metres amsl\nEstimated data is marked with a * after the value.\nMissing data (more than 2 days missing in month) is marked by ---.\nSunshine data taken from an automatic Kipp & Zonen sensor marked with a #, otherwise sunshine data taken from a Campbell Stokes recorder.\n yyyy mm tmax tmin af rain sun\n degC degC days mm hours\n 1959 1 4.5 -1.9 20 --- 57.2\n 1959 2 7.3 0.9 15 --- 87.2\n 1959 3 8.4 3.1 3 --- 81.6\n 1959 4 10.8 3.7 1 --- 107.4\n 1959 5 15.8 5.8 1 --- 213.5\n 1959 6 16.9 8.2 0 --- 209.4\n 1959 7 18.5 9.5 0 --- 167.8\n 1959 8 19.0 10.5 0 --- 164.8\n 1959 9 18.3 5.9 0 --- 196.5\n 1959 10 14.8 7.9 1 --- 101.1\n 1959 11 8.8 3.9 3 --- 38.9\n 1959 12 7.2 2.5 3 --- 19.2\n```\n\n### UK Met template\n\n```csv\n{{station.name}}\nLocation:{{station.location}}, Lat {{station.latitude}} Lon {{station.longitude}}, {{station.tags.altitude}}\nEstimated data is marked with a * after the value.\nMissing data (more than 2 days missing in month) is marked by ---.\nSunshine data taken from an automatic Kipp & Zonen sensor marked with a #, otherwise sunshine data taken from a Campbell Stokes recorder.\n yyyy mm tmax tmin af rain sun\n degC degC days mm hours\n{%for timestamp, tmax,tmin,af,rain,sun in chunk%}\n{{timestamp.year}} {{timestamp.month}} {{tmax.value}} {{tmin.value}} {{af.value}} {{rain.value}} {{sun.value}}\n{%endfor%}\n```\n\n### UK Met metadata\n\n```yaml\nStation:\n license: Attribution\n region: United Kingdom\n url: http://www.metoffice.gov.uk/\n tags:\n key1:value1\n key2:value2\nObservables:\n - observable_id: tmin\n name: Temperature minimum\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#min\n - observable_id: tmax\n name: Temperature Max\n ontology: http://edam.gr#Temperature\n qualifiers: http://edam.gr#max\n - observable_id: rain\n name: Rain\n ontology: http://edam.gr#Rain\n - observable_id: af\n name: Days of air frost\n ontology: http://edam.gr#AirFrostDays\n - observable_id: sun\n name: Sunshine duration\n ontology: http://edam.gr#SunShineDuration\nUnits of Measurement:\n - name: Days\n symbol: D\n relevant_observables: af, sun\n - name: Celcius\n symbol: degC\n relevant_observables: tmin, tmax\n - name: Millimeters\n symbol: mm\n relevant_observables: rain\n```\n\n### Parse all UK Met weather stations\n\nFollowing command downloads and stores data from 27 weather stations. \nIt is executed in approximately 9 seconds. \n\n`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\" --drop yes`\n\n## **Australian Bureau of Meteorology (Online)**\n\nBureau of Meteorology (BoM) in Australia offers historical timeseries from a number of weather stations. \nThey concern *daily* observations which are published every month in HTML documents. \nThese share the same structure and semantics, and are available online. \nUsers can access the timeseries by crafting URLs which comprise of information about the requested station id, and month/year. \nFor example, the URL for the meteorological data about Adelaide station (*5002* station id) for *October 2017* is: \n[http://www.bom.gov.au/climate/dwo/**201710**/text/IDCJDW**5002**.**201710**.csv](http://www.bom.gov.au/climate/dwo/201710/text/IDCJDW5002.201710.csv)\n\nThe challenge in curating BoM timeseries was regarded with their structure. \nIn most other cases, every data-row corresponds to *one observation* for a *given timestamp*. \nHowever, each BoM row has *two observations* for the *same* daily-sampled timestamp. \nThese two observations are taken during different time of a day. \nThis *sampling hour*, which will complement the *daily-sampled timestamp* for the bi-daily observations, is encoded in the dataset's header.\n\n### BoM dataset\n\n```csv\n\"Daily Weather Observations for Elliston, South Australia for July 2017\"\n\"Prepared at 13:05 GMT on Monday 21 August 2017 IDCJDW5017.201707\"\n\"Copyright 2003 Commonwealth Bureau of Meteorology\"\n\"Observations were drawn from Elliston {station 018069}\"\n\n,\"Date\",\"Minimum temperature (\u00b0C)\",\"Maximum temperature (\u00b0C)\",\"Rainfall (mm)\",\"Evaporation (mm)\",\"Sunshine (hours)\",\"Direction of maximum wind gust \",\"Speed of maximum wind gust (km/h)\",\"Time of maximum wind gust\",\"9am Temperature (\u00b0C)\",\"9am relative humidity (%)\",\"9am cloud amount (oktas)\",\"9am wind direction\",\"9am wind speed (km/h)\",\"9am MSL pressure (hPa)\",\"3pm Temperature (\u00b0C)\",\"3pm relative humidity (%)\",\"3pm cloud amount (oktas)\",\"3pm wind direction\",\"3pm wind speed (km/h)\",\"3pm MSL pressure (hPa)\"\n,2017-07-1,6.4,18.4,0,,,,,,10.0,74,0,,,1024.3,,,,,,\n,2017-07-2,10.1,16.6,0,,,,,,12.0,64,0,NNW,19,1014.1,,,,,,\n,2017-07-3,7.5,17.3,8.8,,,,,,10.0,90,8,NNW,33,1005.9,,,,,,\n,2017-07-4,9.8,16.4,14.2,,,,,,13.4,92,8,NNW,15,1014.1,,,,,,\n,2017-07-5,10.5,17.5,27.8,,,,,,14.4,83,6,WSW,17,1017.0,,,,,,\n,2017-07-6,5.6,16.1,0.2,,,,,,9.7,68,0,NNW,11,1012.8,,,,,,\n,2017-07-7,9.1,15.8,9.2,,,,,,12.6,75,6,SW,37,1015.1,,,,,,\n,2017-07-8,8.4,15.7,4.6,,,,,,10.8,97,8,WNW,7,1019.7,,,,,,\n,2017-07-9,7.6,15.7,5.0,,,,,,10.8,96,6,NNE,2,1023.2,,,,,,\n,2017-07-10,6.9,16.8,0.8,,,,,,11.0,97,6,NNE,2,1027.1,,,,,,\n,2017-07-11,5.5,18.6,0,,,,,,9.9,82,1,NNE,4,1030.6,,,,,,\n,2017-07-12,8.7,21.2,0,,,,,,12.2,51,6,N,22,1024.5,,,,,,\n,2017-07-13,10.0,18.7,0,,,,,,11.9,80,8,NNE,2,1018.0,,,,,,\n,2017-07-14,10.6,16.8,3.4,,,,,,13.9,78,7,SSW,11,1020.6,,,,,,\n,2017-07-15,8.9,16.0,1.4,,,,,,11.0,82,8,NNW,15,1023.8,,,,,,\n,2017-07-16,9.1,15.4,0.2,,,,,,11.7,78,8,N,15,1013.2,,,,,,\n,2017-07-17,11.0,15.9,9.4,,,,,,14.5,69,4,WSW,33,1011.2,,,,,,\n,2017-07-18,11.0,15.8,5.0,,,,,,12.0,87,8,SSW,28,1018.9,,,,,,\n,2017-07-19,11.1,15.2,2.6,,,,,,13.5,72,8,SSE,15,1026.8,,,,,,\n,2017-07-20,5.1,14.1,0,,,,,,8.2,84,8,ENE,7,1024.5,,,,,,\n,2017-07-21,7.3,22.9,0,,,,,,12.5,60,3,NNE,22,1018.2,,,,,,\n,2017-07-22,8.9,20.5,0,,,,,,13.0,61,0,NNW,4,1016.6,,,,,,\n,2017-07-23,12.9,18.0,0,,,,,,15.5,86,0,NNW,11,1020.2,,,,,,\n,2017-07-24,6.1,21.5,0,,,,,,11.9,89,0,NNE,4,1021.3,,,,,,\n,2017-07-25,5.4,18.0,0,,,,,,14.4,99,7,NW,11,1020.2,,,,,,\n,2017-07-26,8.3,18.9,0.2,,,,,,10.1,97,2, ,Calm,1025.6,,,,,,\n,2017-07-27,6.7,18.4,0,,,,,,16.4,61,8,NNW,22,1016.5,,,,,,\n,2017-07-28,4.2,25.6,0.6,,,,,,10.6,89,7,NNE,9,1019.8,,,,,,\n,2017-07-29,10.1,17.4,0,,,,,,16.8,70,8,WNW,22,1007.0,,,,,,\n,2017-07-30,11.3,16.8,3.6,,,,,,13.1,86,2,WSW,11,1015.9,,,,,,\n,2017-07-31,10.3,16.9,5.0,,,,,,12.4,82,6,SSW,22,1022.7,,,,,,\n```\n\n### BoM template\n\n```csv\n\"Daily Weather Observations for {{station.name}}, {{station.region}} for July 2017\"\n\"Prepared at 16:06 GMT on Monday 7 August 2017 IDCJDW5002.201701\"\n\"Copyright 2003 Commonwealth Bureau of Meteorology\"\n\"The \"official\" Adelaide site is now at West Terrace / ngayirdapira.\"\n\"The \"official\" Adelaide weather observations site is now at West Terrace / ngayirdapira {site number 023000}. This Kent Town site is about 2 km east of the city centre.\"\n\"Observations were drawn from Adelaide (Kent Town) {station 023090}\"\n\n,\"Date\",\"Minimum temperature (\u00b0C)\",\"Maximum temperature (\u00b0C)\",\"Rainfall (mm)\",\"Evaporation (mm)\",\"Sunshine (hours)\",\"Direction of maximum wind gust \",\"Speed of maximum wind gust (km/h)\",\"Time of maximum wind gust\",{% set hour=9 %},{% set hour=9 %},{% set hour=9 %},{% set hour=9 %},{% set hour=9 %},{%set hour=9 %},{% set hour=15 %},{% set hour=15 %},{%set hour=15 %},{% set hour=15 %},{% set hour=15 %},{% set hour=15 %}\n{%for temp, wind, timestamp, windm_spd, windm_dir, wind_spd, wind_dir, rain, evap, sun, humidity, cloud, mlsp, tempMIN, tempMAX in chunk%}\n,{{timestamp.date()}},{{tempMIN.value}},{{tempMAX.value}},{{rain.value}},{{evap.value}},{{sun.value}},{{windm_dir.value}},{{windm_spd.value}},{{same_timestamp(windm_spd.timestamp.time, windm_dir.timestamp.time)}},{{temp.value}},{{humidity.value}},{{cloud.value}},{{wind_dir.value}},{{wind_spd.value}},{{mlsp.value}},{{temp.value}},{{humidity.value}},{{cloud.value}},{{wind_dir.value}},{{wind_spd.value}},{{mlsp.value}}\n{%endfor%}\n```\n\n### Bom metadata\n\n```yaml\nStation:\n url: http://www.bom.gov.au\n license: Attribution\nObservables:\n - observable_id: temp\n name: Temperature above sea level\n - observable_id: tempMIN\n name: Temperature Min\n - observable_id: tempMAX\n name: Temperature Max\n - observable_id: rain\n name: Rain\n - observable_id: evap\n name: Evapotranspiration\n - observable_id: sun\n name: Sunlight\n - observable_id: windm_dir\n name: Wind max direction\n - observable_id: windm_spd\n name: Wind max speed\n - observable_id: wind_dir\n name: Wind direction\n - observable_id: wind_spd\n name: Wind speed\n - observable_id: humidity\n name: Humidity\n - observable_id: cloud\n name: Cloud\n - observable_id: mlsp\n name: Pressure\nUnits of Measurement:\n - name: Celcius\n symbol: C\n relevant_observables: temp, tempMIN, tempMAX\n - name: Millimeters\n symbol: mm\n relevant_observables: rain, evap\n - name: hours\n symbol: hr\n relevant_observables: sun\n - name: hectoPascal\n symbol: hPa\n relevant_observables: mlsp\n - name: eights\n symbol: 8th\n relevant_observables: cloud\n - name: Percent\n symbol: \\%\n relevant_observables: humidity\n - name: Wind speed\n symbol: km/h\n relevant_observables: wind_spd\n - name: Wind direction\n symbol:\n relevant_observables: windm_dir\n```\n\n### Parse all BoM stations for July 2017\n\nThe following command will generate the URLs for 574 stations, download, and store them. \nUltimately 478 stations exist. \nThis command takes some time to be executed (aprox. 5 minutes). \n\n`edam --input \"http://www.bom.gov.au/climate/dwo/201707/text/IDCJDW{2-8}0{01-82}.201707.csv\" --template bom.tmpl --metadata bom.yaml --drop yes` \n\n# EDAM template language\n\n## Metadata file\n\nIn the metadata file you can define *observables*, *station* and *sensors*. \n\nAn *observable* can have the following attributes: \n1. name (e.g. Wind)\n2. unit (e.g. direction km/h)\n3. observable_id (e.g. wind). This corresponds to the name one can use in the .tmpl\n\n## Template\n\nIn a template one can use in a *placeholder (**{{}}**)* only the *template_id*'s, which were defined in the metadata files. \n\nA *template_id* can have certain attributes. \nThese are:\n1. value (e.g.`{{wind.value}}`)\n2. 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).\n3. In case the one column-timestamp refers to more than one observables (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)}}`\n\nIn case a column has the timestamp which corresponds to **all observables in each row**, users will use the `{{timestamp.}}`. \n\n# Proposed workflow\n\n1. Edit `setting.yaml` to correspond to your database system \n1. 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