PEcAn API library to be used in R applications. This will allow you to access the PEcAn REST endpoints and does not require access to the actual machines running PEcAn and their database.
License: MIT License
Is your feature request related to a problem? Please describe.
Currently we connect to the server without any input headers, which is fine for local development, but once we use runners like Github Actions, we need to specify headers for the host.
Describe the solution you'd like
A new connectHost function to accept the Host header
When attempting to use the rpecanapi package to connect to the PEcAn server, the functions ping() and get.status() return "Sorry! Server not responding.", which is the default error response in the tryCatch statement.
Steps to reproduce the behavior:
rpecanapi library.connect() function with the appropriate URL, username, and password.ping() or get.status() function.I expect the ping() and get.status() functions to return a response from the PEcAn server indicating its status as follows :
For the ping(server) command :
ping(server)
#> $request
#> [1] "ping"
#> $response
#> [1] "pong"For the get.status(server) command :
get.status(server)
#> $pecan_details$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] ""
#> $host_details$authentication_required
#> "TRUE"
I'm running the R session on a Linux machine and attempting to connect to a PEcAn server running locally on port 8000. The server is expected to be responsive as per its normal behavior.
This should work, whether or not there is a trailing slash:
IP <- "http://localhost:8000/"
server <- connect(IP, username = "carya", password = "illinois")
ping(server)
# Sorry! Server not responding.However, it currently only works if there is not a trailing slash (i.e., http://localhost:8000).
When we bring up the Docker stack in the Docker compose file locally by following the linked documentation and make an API POST request as follows:
The request from the Documentation is as follows:
# 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://pecan.localhost/api/workflows/",
httr::authenticate("carya", "illinois"),
httr::content_type("application/xml"),
body = xml_string
)
print(jsonlite::fromJSON(rawToChar(res$content)))We encounter the following error:
$error
[1] "500 - Internal server error"
$message
[1] "Error: $ operator is invalid for atomic vectors\n"Upon further inspection in the API container in Docker Desktop, we can see the logs as below:
2023-06-27 17:14:54
2023-06-27 17:14:54 Attaching package: ‘dplyr’
2023-06-27 17:14:54
2023-06-27 17:14:54 The following objects are masked from ‘package:stats’:
2023-06-27 17:14:54
2023-06-27 17:14:54 filter, lag
2023-06-27 17:14:54
2023-06-27 17:14:54 The following objects are masked from ‘package:base’:
2023-06-27 17:14:54
2023-06-27 17:14:54 intersect, setdiff, setequal, union
2023-06-27 17:14:54
2023-06-27 17:14:56 Running plumber API at http://0.0.0.0:8000
2023-06-27 17:14:56 Running swagger Docs at http://127.0.0.1:8000/__docs__/
2023-06-27 17:19:23 2023-06-27 11:49:23 DEBUG [insert.workflow] :
2023-06-27 17:19:23 INSERT INTO workflows (site_id, model_id, folder, hostname, start_date,
2023-06-27 17:19:23 end_date, advanced_edit, started_at) VALUES ($1, $2, $3, $4, $5, $6, $7,
2023-06-27 17:19:23 $8) RETURNING id
2023-06-27 17:19:24 2023-06-27 11:49:24 DEBUG [insert.workflow] :
2023-06-27 17:19:24 Running workflow ID: 99000000087
2023-06-27 17:19:25 Warning in result_fetch(res@ptr, n = n) :
2023-06-27 17:19:25 Don't need to call dbFetch() for statements, only for queries
2023-06-27 17:19:25 2023-06-27 11:49:25 INFO [rabbitmq_create_queue] :
2023-06-27 17:19:25 creating queue pecan in rabbitmq
2023-06-27 17:19:25 2023-06-27 11:49:25 ERROR [rabbitmq_send_message] :
2023-06-27 17:19:25 error sending message to rabbitmq [ 405 ]
2023-06-27 17:19:25 <simpleError: $ operator is invalid for atomic vectors>
The api.sipnet.xml file is as follows:
<?xml version="1.0"?>
<pecan>
<pfts>
<pft>
<name>temperate.coniferous</name>
</pft>
</pfts>
<meta.analysis>
<iter>3000</iter>
<random.effects>FALSE</random.effects>
<threshold>1.2</threshold>
<update>AUTO</update>
</meta.analysis>
<ensemble>
<variable>NPP</variable>
</ensemble>
<sensitivity.analysis>
<quantiles>
<sigma>-1</sigma>
<sigma>1</sigma>
</quantiles>
<variable>NPP</variable>
</sensitivity.analysis>
<model>
<type>SIPNET</type>
<revision>r136</revision>
<id>1000000014</id>
</model>
<run>
<site>
<id>772</id>
</site>
<inputs>
<met>
<id>99000000003</id>
</met>
</inputs>
<start.date>2002-01-01 00:00:00</start.date>
<end.date>2005-12-31 00:00:00</end.date>
<dbfiles>pecan/dbfiles</dbfiles>
</run>
</pecan>
Upon further inspection, even if we use the csv file in the Pecan-Status-Board repository, we encounter the same error.
The workflow should be successfully submitted and tests should be performed against the given data
/assign @robkooper
While running the "run-test-list.R," the following error can be encountered:
Error: Problem with `mutate()` column `pfts`.
ℹ `pfts = strsplit(pfts, "|", fixed = TRUE)`.
x non-character argument
The lead cause of this issue is because of the strsplit function, as it only takes character strings as input.
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