15.4 Examples:

15.4.1 Prerequisites to interact with the PEcAn API Server

15.4.1.1 R Packages

15.4.1.2 Python Packages

Following are some example snippets to call the PEcAn API endpoints:

15.4.2 GET /api/ping

15.4.2.1 R Snippet

res <- httr::GET("http://localhost:8000/api/ping")
print(jsonlite::fromJSON(rawToChar(res$content)))
## $request
## [1] "ping"

## $response
## [1] "pong"

15.4.2.2 Python Snippet

response = requests.get("http://localhost:8000/api/ping")
print(json.dumps(response.json(), indent=2))
## {
##  "request": "ping",
##  "response": "pong"
## }

15.4.3 GET /api/status

15.4.3.1 R Snippet

res <- httr::GET("http://localhost:8000/api/status")
print(jsonlite::fromJSON(rawToChar(res$content)))
## $pecan_details$version
## [1] "1.7.0"

## $pecan_details$branch
## [1] "develop"

## $pecan_details$gitsha1
## [1] "unknown"

## $host_details$hostid
## [1] 99

## $host_details$hostname
## [1] ""

## $host_details$start
## [1] 99000000000

## $host_details$end
## [1] 99999999999

## $host_details$sync_url
## [1] ""

## $host_details$sync_contact
## [1] ""

15.4.3.2 Python Snippet

response = requests.get("http://localhost:8000/api/status")
print(json.dumps(response.json(), indent=2))
## {
##   "pecan_details": {
##     "version": "1.7.0",
##     "branch": "develop",
##     "gitsha1": "unknown"
##   },
##   "host_details": {
##     "hostid": 99,
##     "hostname": "",
##     "start": 99000000000,
##     "end": 99999999999,
##     "sync_url": "",
##     "sync_contact": ""
##   }
## }

15.4.4 GET /api/models/

15.4.4.1 R Snippet

# Search model(s) with `model_name` containing "sip" & `revision` containing "ssr"
res <- httr::GET(
         "http://localhost:8000/api/models/?model_name=sip&revision=ssr&ignore_case=TRUE",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $models
##     model_id model_name revision
## 1 1000000022     SIPNET      ssr

## $count
## [1] 1

15.4.4.2 Python Snippet

# Search model(s) with `model_name` containing "sip" & `revision` containing "ssr"
response = requests.get(
             "http://localhost:8000/api/models/?model_name=sip&revision=ssr&ignore_case=TRUE",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "models": [
##     {
##       "model_id": "1000000022",
##       "model_name": "SIPNET",
##       "revision": "ssr"
##     }
##   ],
##   "count": 1
## }

15.4.5 GET /api/models/{model_id}

15.4.5.1 R Snippet

# Fetch the details of PEcAn model with id = 1000000022
res <- httr::GET(
         "http://localhost:8000/api/models/1000000022",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $modeltype_id
## [1] 3

## $model_type
## [1] "SIPNET"

## $model_id
## [1] 1000000022

## $model_name
## [1] "SIPNET"

## $revision
## [1] "ssr"

## $inputs
##          input required
## 1          met     TRUE
## 2 poolinitcond    FALSE

15.4.5.2 Python Snippet

# Fetch the details of PEcAn model with id = 1000000022
response = requests.get(
             "http://localhost:8000/api/models/1000000022",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "model_id": "1000000022",
##   "model_name": "SIPNET",
##   "revision": "ssr",
##   "modeltype_id": 3,
##   "model_type": "SIPNET"
##   "inputs": [
##     {
##       "input": "met",
##       "required": TRUE
##     },
##     {
##       "input": "poolinitcond",
##       "required": FALSE
##     }
##   ]
## }

15.4.6 GET /api/sites/

15.4.6.1 R Snippet

# Search site(s) with `site_name` containing "willow"
res <- httr::GET(
         "http://localhost:8000/api/sites/?sitename=willow&ignore_case=TRUE",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $sites
##           id                                      sitename
## 1        676                         Willow Creek (US-WCr)
## 2       1108 Willow Creek (WC)-Chequamegon National Forest
## 3       1202                                  Tully_willow
## 4       1223                   Saare SRF willow plantation
## 5 1000005151                         Willow Creek (US-WCr)

## $count
## [1] 5

15.4.6.2 Python Snippet

# Search site(s) with `site_name` containing "willow"
response = requests.get(
             "http://localhost:8000/api/models/?sitename=willow&ignore_case=TRUE",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "sites": [
##     {
##       "id": 676,
##       "sitename": "Willow Creek (US-WCr)"
##     },
##     {
##       "id": 1108,
##       "sitename": "Willow Creek (WC)-Chequamegon National Forest"
##     },
##     {
##       "id": 1202,
##       "sitename": "Tully_willow"
##     },
##     {
##       "id": 1223,
##       "sitename": "Saare SRF willow plantation"
##     },
##     {
##       "id": 1000005151,
##       "sitename": "Willow Creek (US-WCr)"
##     }
##   ],
##   "count": 5
## }

15.4.7 GET /api/sites/{site_id}

15.4.7.1 R Snippet

# Fetch the details of PEcAn site with id = 676
res <- httr::GET(
         "http://localhost:8000/api/sites/676",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $id
## [1] 676

## $city
## [1] "Park Falls Ranger District"

## $state
## [1] "Wisconsin"

## $country
## [1] "US"

## $mat
## [1] 4

## $map
## [1] 815

## $soil
## [1] ""

## $som
## [1] "NA"

## $notes
## [1] "MF"

## $soilnotes
## [1] ""

## $sitename
## [1] "Willow Creek (US-WCr)"

## $greenhouse
[1] FALSE

## $sand_pct
## [1] 42.52

## $clay_pct
## [1] 20.17

## $time_zone
## [1] "America/Chicago"

15.4.7.2 Python Snippet

# Fetch the details of PEcAn site with id = 676
response = requests.get(
             "http://localhost:8000/api/sites/676",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "id": 676,
##   "city": "Park Falls Ranger District",
##   "state": "Wisconsin",
##   "country": "US",
##   "mat": 4,
##   "map": 815,
##   "soil": "",
##   "notes": "MF",
##   "soilnotes": "",
##   "sitename": "Willow Creek (US-WCr)",
##   "greenhouse": false,
##   "sand_pct": 42.52,
##   "clay_pct": 20.17,
##   "time_zone": "America/Chicago"
##  }

15.4.8 GET /api/pfts/

15.4.8.1 R Snippet

# Search pft(s) of "plant" type with `pft_name` containing "temperate" & belonging to `model_type` "SIPNET"
res <- httr::GET(
         "http://localhost:8000/api/pfts/?pft_name=temperate&pft_type=plant&model_type=sipnet&ignore_case=TRUE",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $pfts
##   model_type  pft_id          pft_name                       pft_type
##   <chr>       <S3: integer64> <chr>                          <chr>   
## 1 SIPNET              41      temperate.deciduous            plant   
## 2 SIPNET      1000000105      temperate.deciduous.IF         plant   
## 3 SIPNET      1000000107      temperate.deciduous_SDA        plant   
## 4 SIPNET      1000000115      temperate.deciduous.ALL        plant   
## 5 SIPNET      1000000118      temperate.deciduous.ALL.NORMAL plant   
## 6 SIPNET      2000000017      tundra.deciduous.NGEE_Arctic   plant   
## 7 SIPNET      2000000045      temperate.broadleaf.deciduous  plant

## $count
## [1] 7

15.4.8.2 Python Snippet

# Search pft(s) of "plant" type with `pft_name` containing "temperate" & belonging to `model_type` "SIPNET"
response = requests.get(
             "http://localhost:8000/api/pfts/?pft_name=temperate&pft_type=plant&model_type=sipnet&ignore_case=TRUE",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "pfts": [
##     {
##       "model_type": "SIPNET",
##       "pft_id": 41,
##       "pft_name": "temperate.deciduous",
##       "pft_type": "plant"
##     },
##     ...
##   ],
##   "count": 7
## }

15.4.9 GET /api/pfts/{pft_id}

15.4.9.1 R Snippet

# Fetch the details of PEcAn PFT with id = 2000000045
res <- httr::GET(
         "http://localhost:8000/api/pfts/2000000045",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $model_type
## [1] "SIPNET"

## $pft_id
## [1] 2000000045

## $pft_name
## [1] "temperate.broadleaf.deciduous"

## $definition
## [1] "SIPNET Temperate Deciduous PFT with priors on all parameters"

## $pft_type
## [1] "plant" 

15.4.9.2 Python Snippet

# Fetch the details of PEcAn PFT with id = 2000000045
response = requests.get(
             "http://localhost:8000/api/pfts/2000000045",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "model_type": "SIPNET",
##   "pft_id": 2000000045,
##   "pft_name": "temperate.broadleaf.deciduous",
##   "definition": "SIPNET Temperate Deciduous PFT with priors on all parameters",
##   "pft_type": "plant"
## }

15.4.10 GET /api/formats/

15.4.10.1 R Snippet

# Search format(s) with name containing 'ameriflux' & mime type containing 'csv'
res <- httr::GET(
         "http://localhost:8000/api/formats/?format_name=ameriflux&mimetype=csv&ignore_case=TRUE",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $formats
##   mimetype format_id        format_name
## 1 text/csv        19 AmeriFlux.level4.h
## 2 text/csv        20 AmeriFlux.level4.d
## 3 text/csv        21 AmeriFlux.level4.w
## 4 text/csv        22 AmeriFlux.level4.m
## 5 text/csv        35 AmeriFlux.level2.h
## 6 text/csv        36 AmeriFlux.level3.h

## $count
## [1] 6

15.4.10.2 Python Snippet

# # Search format(s) with name containing 'ameriflux' & mime type containing 'csv'
response = requests.get(
             "http://localhost:8000/api/formats/?format_name=ameriflux&mimetype=csv&ignore_case=TRUE",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "formats": [
##     {
##       "mimetype": "text/csv",
##       "format_id": 19,
##       "format_name": "AmeriFlux.level4.h"
##     },
##     {
##       "mimetype": "text/csv",
##       "format_id": 20,
##       "format_name": "AmeriFlux.level4.d"
##     },
##     ...
##   ],
##   "count": 6
## }
  

15.4.11 GET /api/formats/{format_id}

15.4.11.1 R Snippet

# Fetch the details of PEcAn format with id = 19
res <- httr::GET(
         "http://localhost:8000/api/formats/19",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $mimetype
## [1] "text/csv"

## $format_id
## [1] 19

## $name
## [1] "AmeriFlux.level4.h"

## $notes
## [1] "Half-hourly AmeriFlux level 4 gap filled, partitioned, and flagged flux tower data. Variables description:  Level 4 data are obtained from the level 3 products, data are ustar filtered, gap-filled using different methods (ANN and MDS) and partitioned (i.e. NEE, GPP, and Re). Flags with information regarding quality of the original and gapfilled data are added.  Missing values: -9999."

## $header
## [1] ""

## $format_variables
##                                                   description        name             unit
## 1                                            Latent heat flux        LE_f            W m-2
## 2                                          Sensible heat flux         H_f            W m-2
## 3                                             air temperature        Ta_f        degrees C
## 4                                      Vapor Pressure Deficit       VPD_f               Pa
## 5 Cumulative ecosystem respiration over a specified time step        Reco umol C02 m-2 s-1
## 6                                      Net ecosystem exchange NEE_st_fMDS   umol C m-2 s-1

15.4.11.2 Python Snippet

# Fetch the details of PEcAn format with id = 19
response = requests.get(
             "http://localhost:8000/api/formats/19",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "mimetype": "text/csv",
##   "format_id": 19,
##   "name": "AmeriFlux.level4.h",
##   "notes": "Half-hourly AmeriFlux level 4 gap filled, partitioned, and flagged flux tower data. Variables description:  ## Level 4 data are obtained from the level 3 products, data are ustar filtered, gap-filled using different methods (ANN and ## MDS) and partitioned (i.e. NEE, GPP, and Re). Flags with information regarding quality of the original and gapfilled data ## are added.  Missing values: -9999.",
##   "header": "",
##   "format_variables": [
##     {
##       "description": "Latent heat flux",
##       "name": "LE_f",
##       "unit": "W m-2"
##     },
##     ...
##   ]
## }

15.4.12 GET /api/inputs/

15.4.12.1 R Snippet

# Get the inputs needed for a workflow with model_id = 1000000022 & site_id = 676
res <- httr::GET(
         "http://localhost:8000/api/inputs/?model_id=1000000022&site_id=676",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $inputs
##                sitename model_name revision tag                      hostname file_name   format_name mimetype
## 1 Willow Creek (US-WCr)     SIPNET      ssr met ebi-forecast.igb.illinois.edu  wcr.clim Sipnet.climna text/csv
## 2 Willow Creek (US-WCr)     SIPNET      ssr met                        docker  wcr.clim Sipnet.climna text/csv
##                   file_path         id input_name          start_date            end_date
## 1 /home/share/data/dbfiles/        235            2000-01-01 06:00:00 2007-01-01 05:59:00
## 2        /data/sites/willow 2000000001            1998-01-01 00:00:00 2006-12-31 00:00:00

## $count
## [1] 2
# Get the inputs needed for a workflow with format_id = 5000000002 (AMERIFLUX_BASE_HH) & host_id = 99000000001 (docker)
res <- httr::GET(
         "http://localhost:8000/api/inputs/?format_id=5000000002&host_id=99000000001",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $inputs
##                                sitename mimetype       format_name hostname               file_name
## 1 Niwot Ridge Forest/LTER NWT1 (US-NR1) text/csv AMERIFLUX_BASE_HH   docker AMF_US-NR1_BASE_HH_15-5
##                               file_path         id              input_name start_date   end_date
## 1 /data/dbfiles/AmerifluxLBL_site_0-772 1000011238 AmerifluxLBL_site_0-772 1998-01-01 2016-12-31

## $count
## [1] 1

15.4.12.2 Python Snippet

# Get the inputs needed for a workflow with model_id = 1000000022 & site_id = 676
response = requests.get(
             "http://localhost:8000/api/inputs/?model_id=1000000022&site_id=676",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "inputs": [
##     {
##       "sitename": "Willow Creek (US-WCr)",
##       "model_name": "SIPNET",
##       "revision": "ssr",
##       "tag": "met",
##       "hostname": "ebi-forecast.igb.illinois.edu",
##       "file_name": "wcr.clim",
##       "format_name": "Sipnet.climna",
##       "mimetype": "text/csv",
##       "file_path": "/home/share/data/dbfiles/",
##       "id": 235,
##       "input_name": "",
##       "start_date": "2000-01-01 06:00:00",
##       "end_date": "2007-01-01 05:59:00"
##     },
##     ...
##   ],
##   "count": 2
## }
# Get the inputs needed for a workflow with format_id = 5000000002 (AMERIFLUX_BASE_HH) & host_id = 99000000001 (docker)
response = requests.get(
             "http://localhost:8000/api/inputs/?format_id=5000000002&host_id=99000000001",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "inputs": [
##     {
##       "sitename": "Niwot Ridge Forest/LTER NWT1 (US-NR1)",
##       "hostname": "docker",
##       "file_name": "AMF_US-NR1_BASE_HH_15-5",
##       "format_name": "AMERIFLUX_BASE_HH",
##       "mimetype": "text/csv",
##       "file_path": "/data/dbfiles/AmerifluxLBL_site_0-772",
##       "id": 1000011238,
##       "input_name": "AmerifluxLBL_site_0-772",
##       "start_date": "1998-01-01",
##       "end_date": "2016-12-31"
##     }
##   ],
##   "count": 1,
## }

15.4.13 GET /api/inputs/{input_id}

15.4.13.1 R Snippet

# Download the input file with id = 99000000003
res <- httr::GET(
         "http://localhost:8000/api/inputs/99000000003",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.2002.nc")

# Download the file 'fraction.plantation' from the input directory with id = 295
res <- httr::GET(
         "http://localhost:8000/api/inputs/295?filename=fraction.plantation",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.fraction.plantation")

15.4.13.2 Python Snippet

# Download the input file for with id = 99000000003
response = requests.get(
             "http://localhost:8000/api/inputs/99000000003",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.2002.nc", "wb") as file:
  file.write(response.content)
  
# Download the file 'fraction.plantation' from the input directory with id = 295
response = requests.get(
             "http://localhost:8000/api/inputs/295?filename=fraction.plantation",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.2002.nc", "wb") as file:
  file.write(response.content)

15.4.14 GET /api/workflows/

15.4.14.1 R Snippet

# Get workflow(s) that use `model_id` = 1000000022 [SIPNET] & `site_id` = 676 [Willow Creek (US-WCr)]
res <- httr::GET(
         "http://localhost:8000/api/workflows/?model_id=1000000022&site_id=676",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $workflows
##           id                             folder          started_at site_id   model_id          hostname start_date   end_date
## 1 1000009900 /fs/data2/output//PEcAn_1000009900 2018-11-09 08:56:37     676 1000000022        geo.bu.edu 2004-01-01 2004-12-31
## 2 1000009172 /fs/data2/output//PEcAn_1000009172 2018-04-11 18:14:52     676 1000000022 test-pecan.bu.edu 2004-01-01 2004-12-31
## ...

## $count
## [1] 5

15.4.14.2 Python Snippet

# Get workflow(s) that use `model_id` = 1000000022 [SIPNET] & `site_id` = 676 [Willow Creek (US-WCr)]
response = requests.get(
             "http://localhost:8000/api/workflows/?model_id=1000000022&site_id=676",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "workflows": [
##     {
##       "id": 1000009172,
##       "folder": "/fs/data2/output//PEcAn_1000009900",
##       "started_at": "2018-11-09 08:56:37",
##       "site_id": 676,
##       "model_id": 1000000022,
##       "hostname": "geo.bu.edu",
##       "start_date": "2004-01-01",
##       "end_date": "2004-12-31"
##     },
##     ...
##   ],
##   "count": 5
## }

15.4.15 POST /api/workflows/

15.4.15.1 R Snippet

# Submit a workflow in XML format for execution
xmlFile <- "pecan/tests/api.sipnet.xml"
xml_string <- paste0(xml2::read_xml(xmlFile))
res <- httr::POST(
         "http://localhost:8000/api/workflows/",
         httr::authenticate("carya", "illinois"),
         httr::content_type("application/xml"),
         body = xml_string
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $workflow_id
## [1] 99000000001

## $status
## [1] "Submitted successfully"

15.4.15.2 Python Snippet

# Submit a workflow in XML format for execution
xml_file = "pecan/tests/api.sipnet.xml"
root = xml.etree.ElementTree.parse(xml_file).getroot()
response = requests.post(
             "http://localhost:8000/api/workflows/",
             auth=HTTPBasicAuth('carya', 'illinois'),
             headers = {'Content-Type': 'application/xml'},
             data = xml.etree.ElementTree.tostring(root, encoding='unicode', method='xml')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "workflow_id": "99000000001",
##   "status": "Submitted successfully"
## }

15.4.16 GET /api/workflows/{id}

15.4.16.1 R Snippet

# Get details of workflow with `id` = '1000009172'
res <- httr::GET(
         "http://localhost:8000/api/workflows/1000009172",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $id
## [1] "1000009172"

## $folder
## [1] "/fs/data2/output//PEcAn_1000009172"

## $hostname
## [1] "test-pecan.bu.edu"

## $user_id
## [1] "NA"

## $properties
## $properties$end
## [1] "2004/12/31"

## $properties$pft
## $properties$pft[[1]]
## [1] "soil.IF"

## $properties$pft[[2]]
## [1] "temperate.deciduous.IF"


## $properties$email
## [1] ""

## $properties$notes
## [1] ""

## $properties$start
## [1] "2004/01/01"

## $properties$siteid
## [1] "676"

## $properties$modelid
## [1] "1000000022"

## $properties$hostname
## [1] "test-pecan.bu.edu"

## $properties$sitename
## [1] "WillowCreek(US-WCr)"

## $properties$input_met
## [1] "AmerifluxLBL.SIPNET"

## $properties$pecan_edit
## [1] "on"

## $properties$sitegroupid
## [1] "1000000022"

## $properties$fluxusername
## [1] "pecan"

## $properties$input_poolinitcond
## [1] "-1"

15.4.16.2 Python Snippet

# Get details of workflow with `id` = '1000009172'
response = requests.get(
             "http://localhost:8000/api/workflows/1000009172",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "id": "1000009172",
##   "folder": "/fs/data2/output//PEcAn_1000009172",
##   "hostname": "test-pecan.bu.edu",
##   "user_id": "NA",
##   "properties": {
##     "end": "2004/12/31",
##     "pft": [
##       "soil.IF",
##       "temperate.deciduous.IF"
##     ],
##     "email": "",
##     "notes": "",
##     "start": "2004/01/01",
##     "siteid": "676",
##     "modelid": "1000000022",
##     "hostname": "test-pecan.bu.edu",
##     "sitename": "WillowCreek(US-WCr)",
##     "input_met": "AmerifluxLBL.SIPNET",
##     "pecan_edit": "on",
##     "sitegroupid": "1000000022",
##     "fluxusername": "pecan",
##     "input_poolinitcond": "-1"
##   }
## }

15.4.17 GET /api/workflows/{id}/status

15.4.17.1 R Snippet

# Get list of run belonging to the workflow with `workflow_id` = '99000000001'
res <- httr::GET(
         "http://localhost:8000/api/workflows/99000000001/status",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $workflow_id
## [1] "99000000001"

## $status
## [1] "TRAIT  2020-07-22 07:02:33  2020-07-22 07:02:35  DONE  "      
## [2] "META  2020-07-22 07:02:35  2020-07-22 07:02:38  DONE  "       
## [3] "CONFIG  2020-07-22 07:02:38  2020-07-22 07:02:40  DONE  "     
## [4] "MODEL  2020-07-22 07:02:40  2020-07-22 07:04:07  DONE  "      
## [5] "OUTPUT  2020-07-22 07:04:07  2020-07-22 07:04:08  DONE  "     
## [6] "ENSEMBLE  2020-07-22 07:04:08  2020-07-22 07:04:09  DONE  "   
## [7] "SENSITIVITY  2020-07-22 07:04:09  2020-07-22 07:04:16  DONE  "
## [8] "FINISHED  2020-07-22 07:04:16  2020-07-22 07:04:16  DONE  "

15.4.17.2 Python Snippet

# Get list of run belonging to the workflow with `workflow_id` = '99000000001'
response = requests.get(
             "http://localhost:8000/api/workflows/99000000001/status",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "workflow_id": "99000000001",
##   "status": [
##     "TRAIT  2020-07-22 07:02:33  2020-07-22 07:02:35  DONE  ",
##     "META  2020-07-22 07:02:35  2020-07-22 07:02:38  DONE  ",
##     "CONFIG  2020-07-22 07:02:38  2020-07-22 07:02:40  DONE  ",
##     "MODEL  2020-07-22 07:02:40  2020-07-22 07:04:07  DONE  ",
##     "OUTPUT  2020-07-22 07:04:07  2020-07-22 07:04:08  DONE  ",
##     "ENSEMBLE  2020-07-22 07:04:08  2020-07-22 07:04:09  DONE  ",
##     "SENSITIVITY  2020-07-22 07:04:09  2020-07-22 07:04:16  DONE  ",
##     "FINISHED  2020-07-22 07:04:16  2020-07-22 07:04:16  DONE  "
##   ]
## }

15.4.18 GET /api/workflows/{id}/file/{filename}

15.4.18.1 R Snippet

# Download the 'ensemble.ts.99000000017.NPP.2002.2002.Rdata' output file for the workflow with id = 99000000031
res <- httr::GET(
         "http://localhost:8000/api/workflows/99000000031/file/ensemble.ts.99000000017.NPP.2002.2002.Rdata",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.ensemble.ts.99000000017.NPP.2002.2002.Rdata")

15.4.18.2 Python Snippet

# Download the 'ensemble.ts.99000000017.NPP.2002.2002.Rdata' output file for the workflow with id = 99000000031
response = requests.get(
             "http://localhost:8000/api/workflows/99000000031/file/ensemble.ts.99000000017.NPP.2002.2002.Rdata",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.ensemble.ts.99000000017.NPP.2002.2002.Rdata", "wb") as file:
  file.write(response.content)

15.4.19 GET /api/runs/

15.4.19.1 R Snippet

# Get list of run belonging to the workflow with `workflow_id` = '1000009172'
res <- httr::GET(
         "http://localhost:8000/api/runs/?workflow_id=1000009172",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $runs
##    runtype  ensemble_id    workflow_id    id            model_id     site_id      parameter_list start_time        
## finish_time    
##  1 ensemble 1000017624     1000009172     1002042201    1000000022   796          ensemble=1     2005-01-01 
## 00:00:00 2011-12-31 00:00:00
##  ...

## $count
## [1] 50

15.4.19.2 Python Snippet

# Get list of run belonging to the workflow with `workflow_id` = '1000009172'
response = requests.get(
             "http://localhost:8000/api/runs/?workflow_id=1000009172",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "runs": [
##     {
##       "runtype": "ensemble",
##       "ensemble_id": 1000017624,
##       "workflow_id": 1000009172,
##       "id": 1002042201,
##       "model_id": 1000000022,
##       "site_id": 796,
##       "parameter_list": "ensemble=1",
##       "start_time": "2005-01-01",
##       "finish_time": "2011-12-31"
##     },
##     ...
##   ]
##   "count": 50,
##   "next_page": "http://localhost:8000/api/workflows/?workflow_id=1000009172&offset=50&limit=50"
## }

15.4.20 GET /api/runs/{run_id}

15.4.20.1 R Snippet

# Get details of run belonging with `id` = '99000000282'
res <- httr::GET(
         "http://localhost:8000/api/runs/99000000282",
         httr::authenticate("carya", "illinois")
       )
print(jsonlite::fromJSON(rawToChar(res$content)))
## $runtype
## [1] "sensitivity analysis"

## $ensemble_id
## [1] 99000000016

## $workflow_id
## [1] 99000000031

## $id
## [1] 99000000282

## $model_id
## [1] 1000000014

## $site_id
## [1] 772

## $start_time
## [1] "2002-01-01"

## $finish_time
## [1] "2002-12-31"

## $parameter_list
## [1] "quantile=MEDIAN,trait=all,pft=temperate.coniferous"

## $started_at
## [1] "2020-07-22 07:02:40"

## $finished_at
## [1] "2020-07-22 07:02:57"

## $inputs
## $inputs$info
## [1] "README.txt"

## $inputs$others
## [1] "sipnet.clim"          "sipnet.in"            "sipnet.param"         "sipnet.param-spatial"

## $outputs
## $outputs$logfile
## [1] "logfile.txt"

## $outputs$info
## [1] "README.txt"

## $outputs$years
## $outputs$years$`2002`
## $outputs$years$`2002`$data
## [1] "2002.nc"

## $outputs$years$`2002`$variables
## $outputs$years$`2002`$variables$GPP
## [1] "Gross Primary Productivity"

## $outputs$years$`2002`$variables$NPP
## [1] "Net Primary Productivity"

## ...

15.4.20.2 Python Snippet

# Get details of run with `id` = '1002042201'
response = requests.get(
             "http://localhost:8000/api/runs/1002042201",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
print(json.dumps(response.json(), indent=2))
## {
##   "runtype": "ensemble",
##   "ensemble_id": 1000017624,
##   "workflow_id": 1000009172,
##   "id": 1002042201,
##   "model_id": 1000000022,
##   "site_id": 796,
##   "parameter_list": "ensemble=1",
##   "start_time": "2005-01-01",
##   "finish_time": "2011-12-31",
##   "inputs": {
##     "info": "README.txt",
##     "others": [
##       "sipnet.clim",
##       "sipnet.in",
##       "sipnet.param",
##       "sipnet.param-spatial"
##     ]
##   }
##   "outputs": {
##     "logfile": "logfile.txt",
##     "info": "README.txt",
##     "years": {
##       "2002": {
##         "data": "2002.nc",
##         "variables": {
##           "GPP": "Gross Primary Productivity",
##           "NPP": "Net Primary Productivity",
##           ...
##         }
##       }
##     }
##   }
## }

15.4.21 GET /api/runs/{run_id}/input/{filename}

15.4.21.1 R Snippet

# Download the 'sipnet.in' input file for the run with id = 99000000282
res <- httr::GET(
         "http://localhost:8000/api/runs/99000000282/input/sipnet.in",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.sipnet.in")

15.4.21.2 Python Snippet

# Download the 'sipnet.in' input file for the run with id = 99000000282
response = requests.get(
             "http://localhost:8000/api/runs/99000000282/input/sipnet.in",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.sipnet.in", "wb") as file:
  file.write(response.content)

15.4.22 GET /api/runs/{run_id}/output/{filename}

15.4.22.1 R Snippet

# Download the '2002.nc' output file for the run with id = 99000000282
res <- httr::GET(
         "http://localhost:8000/api/runs/99000000282/output/2002.nc",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.2002.nc")

15.4.22.2 Python Snippet

# Download the '2002.nc' output file for the run with id = 99000000282
response = requests.get(
             "http://localhost:8000/api/runs/99000000282/output/2002.nc",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.2002.nc", "wb") as file:
  file.write(response.content)

15.4.23 GET /api/runs/{run_id}/graph/{year}/{y_var}

15.4.23.1 R Snippet

# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
res <- httr::GET(
         "http://localhost:8000/api/runs/99000000282/graph/2002/GPP",
         httr::authenticate("carya", "illinois")
       )
writeBin(res$content, "test.png")

15.4.23.2 Python Snippet

# Plot the Gross Primary Productivity vs Time for the run with ID `99000000282` for the year 2002
response = requests.get(
             "http://localhost:8000/api/runs/99000000282/graph/2002/GPP",
             auth=HTTPBasicAuth('carya', 'illinois')
           )
with open("test.png", "wb") as file:
  file.write(response.content)