[Iplant-api-dev] Job management APIs

Rion Dooley dooley at tacc.utexas.edu
Tue Mar 3 15:29:29 MST 2015 

I think you probably just have the wrong path or hit the Data Store during maintenance today. Here are the URLs I used successfully to list your job output directory then download the error file.

https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/listings/?pretty=true

https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/media/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err
Downloading gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err

TLDR;

 Here is what I did to get the URLs and verify what you saw might just be a typo. I’ve used the CLI here with very verbose (-V) output enabled so you can see the full API URL called with each request. In the last call I use the print (-P) option, which tells the CLI to use curl’s default behavior and print the response (your downloaded error log file in this example) to stdout rather than saving it to a file.

$ jobs-output-list -V 0001425403186554-5056a550b8-0001-007
Calling curl -sk -H "Authorization: Bearer $AUTH_TOKEN" https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/listings/?pretty=true
{
  "status":"success",
  "message":null,
  "version":"2.1.0-r6d11c",
  "result":[
    {
      "name":".agave.archive",
      "path":"/.agave.archive",
      "lastModified":"2015-03-03T13:42:38.000-06:00",
      "length":7454,
      "permission":"NONE",
      "mimeType":"application/octet-stream",
      "format":"unknown",
      "type":"file",
      "_links":{
        "self":{
          "href":"https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/media/.agave.archive"
        },
        "system":{
          "href":"https://agave.iplantc.org/systems/v2/shabari-lonestar"
        },
        "parent":{
          "href":"https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007"
        }
      }
    },
    {
      "_links":{
        "parent":{
          "href":"https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007"
        },
        "self":{
          "href":"https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/media/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err"
        },
        "system":{
          "href":"https://agave.iplantc.org/systems/v2/shabari-lonestar"
        }
      },
      "format":"unknown",
      "lastModified":"2015-03-03T13:44:12.000-06:00",
      "length":646,
      "mimeType":"application/octet-stream",
      "name":"gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err",
      "path":"/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err",
      "permission":"NONE",
      "type":"file"
    }
  ]
}
$ jobs-output-get -V -P 0001425403186554-5056a550b8-0001-007 gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err
Calling curl -k -H "Authorization: Bearer $AUTH_TOKEN"    https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/media/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err
Downloading gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err ...
{
  "status" : "success",
  "message" : null,
  "version" : "2.1.0-r6d11c",
  "result" : { }
}
ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/GDB007gdna.fa does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/GDB007prot.fa does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/gth.lic does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
Warning: Permanently added 'c333-314.ls4.tacc.utexas.edu<http://c333-314.ls4.tacc.utexas.edu>' (RSA) to the list of known hosts.
{
  "status" : "success",
  "message" : null,
  "version" : "2.1.0-r6d11c",
  "result" : { }
}

—
Rion

On Mar 3, 2015, at 4:00 PM, Duvick, Jonathan P [GDCBS] <jduvick at iastate.edu<mailto:jduvick at iastate.edu>> wrote:

I can return file listings associated with a Lonestar job in progress using the '/outputs/listings/' API, e.g.

{"status":"success","message":null,"version":"2.1.0-r6d11c","result":[{"name":".agave.archive","path":"/.agave.archive","lastModified":"2015-03-03T13:42:38.000-06:00","length":7454,"permission":"NONE","mimeType":"application/octet-stream","format":"unknown","type":"file","_links":..... etc. etc.

but when I parse out ... '_links' :{'self':{ 'href': ...  for a single file and attempt to retrieve it with a second Curl command via '/ouputs/media/', I get this error:

Data: { "status" : "success", "message" : null, "version" : "2.1.0-r6d11c", "result" : { } }ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/GDB007gdna.fa does not exist ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/GDB007prot.fa does not exist ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR ERROR: resolveRodsTarget: srcPath /iplant/home/shabari/gth.lic does not exist ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR Warning: Permanently added 'c333-314.ls4.tacc.utexas.edu<http://c333-314.ls4.tacc.utexas.edu/>' (RSA) to the list of known hosts.

Here is the submitted href URL, attempting to retrieve an error file:

https://agave.iplantc.org/jobs/v2/0001425403186554-5056a550b8-0001-007/outputs/media/gth-gdb007-capsella-gth-test-0001425403186554-5056a550b8-0001-007.err

I'm referencing this documentation: http://preview.agaveapi.co/documentation/live-docs/#!/jobs/downloadOutput_get_14
Live Documentation – The Agave Platform
Science-as-a-Service API platform created by scientists exclusively for scientists
Read more...<http://preview.agaveapi.co/documentation/live-docs/#!/jobs/downloadOutput_get_14>


Jon Duvick
PlantGDB Manager
http://www.plantgdb.org/
Department of Genetics, Development and Cell Biology
2258 Molecular Biology Building
Iowa State University
Ames IA 50011

(515) 294-2360
(515) 294-6755 FAX
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