From 290c14324a707a7fc2309559d664080a9a46b753 Mon Sep 17 00:00:00 2001 From: sckott Date: Wed, 10 Jan 2024 19:29:06 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20getwilds?= =?UTF-8?q?/proofr@0711db2a0f1d6a02a06649da73f1c41a5824aabc=20=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgdown.yml | 2 +- reference/index.html | 7 ++++++- reference/proof_authenticate.html | 4 ++-- reference/proof_cancel.html | 18 +++++------------- reference/proof_header.html | 6 +++--- reference/proof_start.html | 7 +++---- reference/proof_status.html | 13 +++++++++---- search.json | 2 +- 8 files changed, 30 insertions(+), 29 deletions(-) diff --git a/pkgdown.yml b/pkgdown.yml index a595da8..f18396f 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: proofr: proofr.html -last_built: 2024-01-08T19:45Z +last_built: 2024-01-10T19:29Z urls: reference: http://getwilds.org/proofr/reference article: http://getwilds.org/proofr/articles diff --git a/reference/index.html b/reference/index.html index d982b4d..fddf8b2 100644 --- a/reference/index.html +++ b/reference/index.html @@ -63,7 +63,12 @@

All functionsproof_cancel() -
Delete PROOF Cromwell server
+
Cancel/stop PROOF Cromwell server
+
+ + proof_header() +
+
Get header for PROOF API calls
proof_start() diff --git a/reference/proof_authenticate.html b/reference/proof_authenticate.html index c0c945c..32d2fbc 100644 --- a/reference/proof_authenticate.html +++ b/reference/proof_authenticate.html @@ -1,5 +1,5 @@ -Authenticate with PROOF API — proof_authenticate • proofrAuthenticate with PROOF API — proof_authenticate • proofr @@ -46,7 +46,7 @@
-

Authenticates with HutchNet credentials, returns PROOF API token

+

Authenticate with PROOF API

diff --git a/reference/proof_cancel.html b/reference/proof_cancel.html index ea1cee1..bc767cb 100644 --- a/reference/proof_cancel.html +++ b/reference/proof_cancel.html @@ -1,5 +1,5 @@ -Delete PROOF Cromwell server — proof_cancel • proofrCancel/stop PROOF Cromwell server — proof_cancel • proofr @@ -40,13 +40,13 @@
-

Delete PROOF Cromwell server

+

Cancel/stop PROOF Cromwell server

Source: R/cancel.R
proof_cancel.Rd
-

Delete PROOF Cromwell server

+

Cancel/stop PROOF Cromwell server

@@ -58,16 +58,8 @@

Usage

Value

-

A list with fields job_id and info

- - -

-
-

Details

-

Does not return PROOF/Cromwell server URL, for that you have to -periodically call proof_status(), or wait for the email from the -PROOF API

-
+

A list with a single field:

  • message (character)

    • +

References

https://github.com/FredHutch/proof-api#delete-cromwell-server

diff --git a/reference/proof_header.html b/reference/proof_header.html index d545175..8dc9494 100644 --- a/reference/proof_header.html +++ b/reference/proof_header.html @@ -1,5 +1,5 @@ -Get header for PROOF API calls — proof_header • proofrGet header for PROOF API calls — proof_header • proofr @@ -46,7 +46,7 @@
-

Utility method to get header for PROOF API calls

+

Get header for PROOF API calls

@@ -57,7 +57,7 @@

Usage

Arguments

token
-

PROOF API token

+

(character) PROOF API token. optional

diff --git a/reference/proof_start.html b/reference/proof_start.html index 5d37cf3..e6683a5 100644 --- a/reference/proof_start.html +++ b/reference/proof_start.html @@ -65,10 +65,9 @@

ArgumentsValue

-

A list with fields job_id and info

- - -
+

A list with fields:

  • job_id (character)

    • +

  • info (character)

    • +

Details

Does not return PROOF/Cromwell server URL, for that you have to diff --git a/reference/proof_status.html b/reference/proof_status.html index b5c2cf3..71c80e8 100644 --- a/reference/proof_status.html +++ b/reference/proof_status.html @@ -41,7 +41,7 @@

Get PROOF API job status - is job running, what's its URL...

- Source: R/job_status.R + Source: R/status.R
proof_status.Rd
@@ -58,9 +58,14 @@

Usage

Value

-

A list with slots:

  • canJobStart

    • -

  • jobStatus

    • -

  • cromwellUrl

    • +

    A list with fields:

    • canJobStart (logical): can a job to make a Cromwell server be started? +FALSE if server already running; TRUE if server not running

      • +

    • jobStatus (character): status of the job that controls the Cromwell +server. e.g., "RUNNING". NULL if server not running

      • +

    • cromwellUrl (character): the URL for the Cromwell server. NULL if +server not running

      • +

    • jobInfo (list): metadata on the Cromwell server. All slots NULL +if server not running

References

diff --git a/search.json b/search.json index a973cd5..89a504c 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"http://getwilds.org/proofr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 proofr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"authenticate-with-the-proof-api","dir":"Articles","previous_headings":"","what":"Authenticate with the PROOF API","title":"Getting Started","text":"Run function proof_authenticate(), calls PROOF API username password, returns API token (alphanumeric string). (note: token real token) token returned set environment variable within R session. important ’s good security practice pass secrets API tokens parameters functions. say, please save API token environment variable somewhere computer, shouldn’t need running proof_authenticate() ’ll look environment variable.","code":"proof_authenticate(\"username\", \"password\") #> xyGKibGctQ92rmMKKb39q43XgPxGCmrWoX7NZtamTjDP"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"start-a-cromwell-server","dir":"Articles","previous_headings":"","what":"Start a Cromwell Server","title":"Getting Started","text":"Start server Get URL","code":"proof_start() metadata <- proof_status() cromwell_url <- metadata$cromwellUrl cromwell_url"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"rcromwell-setup","dir":"Articles","previous_headings":"","what":"rcromwell setup","title":"Getting Started","text":"Load rcromwell Set Cromwell server URL recognized rcromwell Set Authorization HTTP header used rcromwell HTTP requests now able interact Cromwell server authentication details retrieved via proofr package!","code":"library(rcromwell) library(httr) cromwell_config(cromwell_url) httr::set_config(proof_header())"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"interact-with-the-cromwell-server","dir":"Articles","previous_headings":"","what":"Interact with the Cromwell server","title":"Getting Started","text":"Now, check version Cromwell server","code":"cromwell_version()"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"done","dir":"Articles","previous_headings":"","what":"Done!","title":"Getting Started","text":"’re now setup interact Cromwell server. See rcromwell package docs get started.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Scott Chamberlain. Author, maintainer.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Chamberlain S (2024). proofr: Client PROOF API. R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel), http://getwilds.org/proofr/ (website)https://github.com/getwilds/proofr (devel).","code":"@Manual{, title = {proofr: Client for the PROOF API}, author = {Scott Chamberlain}, year = {2024}, note = {R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, url = {http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, }"},{"path":"http://getwilds.org/proofr/index.html","id":"proofr","dir":"","previous_headings":"","what":"Client for the PROOF API","title":"Client for the PROOF API","text":"R client PROOF API PROOF API https://github.com/FredHutch/proof-api","code":""},{"path":"http://getwilds.org/proofr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Client for the PROOF API","text":"can install development version proofr GitHub :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/proofr\")"},{"path":"http://getwilds.org/proofr/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Client for the PROOF API","text":"get started proofr, see Getting Started vignette.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"Authenticate with PROOF API — proof_authenticate","title":"Authenticate with PROOF API — proof_authenticate","text":"Authenticates HutchNet credentials, returns PROOF API token","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"proof_authenticate(username, password)"},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Authenticate with PROOF API — proof_authenticate","text":"username (character) HutchNet username password (character) HutchNet password","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Authenticate with PROOF API — proof_authenticate","text":"single token (character) bearer authentication PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"# Sys.getenv(\"PROOF_TOKEN\") # x <- proof_authenticate() # Sys.getenv(\"PROOF_TOKEN\")"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Delete PROOF Cromwell server — proof_cancel","title":"Delete PROOF Cromwell server — proof_cancel","text":"Delete PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Delete PROOF Cromwell server — proof_cancel","text":"","code":"proof_cancel()"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Delete PROOF Cromwell server — proof_cancel","text":"list fields job_id info","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Delete PROOF Cromwell server — proof_cancel","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Delete PROOF Cromwell server — proof_cancel","text":"https://github.com/FredHutch/proof-api#delete-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Get header for PROOF API calls — proof_header","title":"Get header for PROOF API calls — proof_header","text":"Utility method get header PROOF API calls","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get header for PROOF API calls — proof_header","text":"","code":"proof_header(token = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get header for PROOF API calls — proof_header","text":"token PROOF API token","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get header for PROOF API calls — proof_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":null,"dir":"Reference","previous_headings":"","what":"Start PROOF Cromwell server — proof_start","title":"Start PROOF Cromwell server — proof_start","text":"Start PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start PROOF Cromwell server — proof_start","text":"","code":"proof_start(pi_name = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start PROOF Cromwell server — proof_start","text":"pi_name (character) PI name form last_f; needed user one SLURM account","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start PROOF Cromwell server — proof_start","text":"list fields job_id info","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start PROOF Cromwell server — proof_start","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Start PROOF Cromwell server — proof_start","text":"https://github.com/FredHutch/proof-api#post-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PROOF API job status - is job running, what's its URL... — proof_status","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"Get PROOF API job status - job running, URL...","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"","code":"proof_status()"},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"list slots: canJobStart jobStatus cromwellUrl","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"https://github.com/FredHutch/proof-api#get-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"proofr: Client for the PROOF API — proofr-package","title":"proofr: Client for the PROOF API — proofr-package","text":"Client PROOF API.","code":""},{"path":[]},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proofr: Client for the PROOF API — proofr-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID)","code":""}] +[{"path":"http://getwilds.org/proofr/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 proofr authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"authenticate-with-the-proof-api","dir":"Articles","previous_headings":"","what":"Authenticate with the PROOF API","title":"Getting Started","text":"Run function proof_authenticate(), calls PROOF API username password, returns API token (alphanumeric string). (note: token real token) token returned set environment variable within R session. important ’s good security practice pass secrets API tokens parameters functions. say, please save API token environment variable somewhere computer, shouldn’t need running proof_authenticate() ’ll look environment variable.","code":"proof_authenticate(\"username\", \"password\") #> xyGKibGctQ92rmMKKb39q43XgPxGCmrWoX7NZtamTjDP"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"start-a-cromwell-server","dir":"Articles","previous_headings":"","what":"Start a Cromwell Server","title":"Getting Started","text":"Start server Get URL","code":"proof_start() metadata <- proof_status() cromwell_url <- metadata$cromwellUrl cromwell_url"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"rcromwell-setup","dir":"Articles","previous_headings":"","what":"rcromwell setup","title":"Getting Started","text":"Load rcromwell Set Cromwell server URL recognized rcromwell Set Authorization HTTP header used rcromwell HTTP requests now able interact Cromwell server authentication details retrieved via proofr package!","code":"library(rcromwell) library(httr) cromwell_config(cromwell_url) httr::set_config(proof_header())"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"interact-with-the-cromwell-server","dir":"Articles","previous_headings":"","what":"Interact with the Cromwell server","title":"Getting Started","text":"Now, check version Cromwell server","code":"cromwell_version()"},{"path":"http://getwilds.org/proofr/articles/proofr.html","id":"done","dir":"Articles","previous_headings":"","what":"Done!","title":"Getting Started","text":"’re now setup interact Cromwell server. See rcromwell package docs get started.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Scott Chamberlain. Author, maintainer.","code":""},{"path":"http://getwilds.org/proofr/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Chamberlain S (2024). proofr: Client PROOF API. R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel), http://getwilds.org/proofr/ (website)https://github.com/getwilds/proofr (devel).","code":"@Manual{, title = {proofr: Client for the PROOF API}, author = {Scott Chamberlain}, year = {2024}, note = {R package version 0.0.0.91http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, url = {http://getwilds.org/proofr/ (website) https://github.com/getwilds/proofr (devel)}, }"},{"path":"http://getwilds.org/proofr/index.html","id":"proofr","dir":"","previous_headings":"","what":"Client for the PROOF API","title":"Client for the PROOF API","text":"R client PROOF API PROOF API https://github.com/FredHutch/proof-api","code":""},{"path":"http://getwilds.org/proofr/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Client for the PROOF API","text":"can install development version proofr GitHub :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/proofr\")"},{"path":"http://getwilds.org/proofr/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Client for the PROOF API","text":"get started proofr, see Getting Started vignette.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"Authenticate with PROOF API — proof_authenticate","title":"Authenticate with PROOF API — proof_authenticate","text":"Authenticate PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"proof_authenticate(username, password)"},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Authenticate with PROOF API — proof_authenticate","text":"username (character) HutchNet username password (character) HutchNet password","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Authenticate with PROOF API — proof_authenticate","text":"single token (character) bearer authentication PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Authenticate with PROOF API — proof_authenticate","text":"","code":"# Sys.getenv(\"PROOF_TOKEN\") # x <- proof_authenticate() # Sys.getenv(\"PROOF_TOKEN\")"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":null,"dir":"Reference","previous_headings":"","what":"Cancel/stop PROOF Cromwell server — proof_cancel","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"Cancel/stop PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"","code":"proof_cancel()"},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"list single field: message (character)","code":""},{"path":"http://getwilds.org/proofr/reference/proof_cancel.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Cancel/stop PROOF Cromwell server — proof_cancel","text":"https://github.com/FredHutch/proof-api#delete-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":null,"dir":"Reference","previous_headings":"","what":"Get header for PROOF API calls — proof_header","title":"Get header for PROOF API calls — proof_header","text":"Get header PROOF API calls","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get header for PROOF API calls — proof_header","text":"","code":"proof_header(token = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get header for PROOF API calls — proof_header","text":"token (character) PROOF API token. optional","code":""},{"path":"http://getwilds.org/proofr/reference/proof_header.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get header for PROOF API calls — proof_header","text":"request S3 class HTTP header can passed httr::GET(), httr::POST(), etc.","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":null,"dir":"Reference","previous_headings":"","what":"Start PROOF Cromwell server — proof_start","title":"Start PROOF Cromwell server — proof_start","text":"Start PROOF Cromwell server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start PROOF Cromwell server — proof_start","text":"","code":"proof_start(pi_name = NULL)"},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start PROOF Cromwell server — proof_start","text":"pi_name (character) PI name form last_f; needed user one SLURM account","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Start PROOF Cromwell server — proof_start","text":"list fields: job_id (character) info (character)","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start PROOF Cromwell server — proof_start","text":"return PROOF/Cromwell server URL, periodically call proof_status(), wait email PROOF API","code":""},{"path":"http://getwilds.org/proofr/reference/proof_start.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Start PROOF Cromwell server — proof_start","text":"https://github.com/FredHutch/proof-api#post-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":null,"dir":"Reference","previous_headings":"","what":"Get PROOF API job status - is job running, what's its URL... — proof_status","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"Get PROOF API job status - job running, URL...","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"","code":"proof_status()"},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"list fields: canJobStart (logical): can job make Cromwell server started? FALSE server already running; TRUE server running jobStatus (character): status job controls Cromwell server. e.g., \"RUNNING\". NULL server running cromwellUrl (character): URL Cromwell server. NULL server running jobInfo (list): metadata Cromwell server. slots NULL server running","code":""},{"path":"http://getwilds.org/proofr/reference/proof_status.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Get PROOF API job status - is job running, what's its URL... — proof_status","text":"https://github.com/FredHutch/proof-api#get-cromwell-server","code":""},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":null,"dir":"Reference","previous_headings":"","what":"proofr: Client for the PROOF API — proofr-package","title":"proofr: Client for the PROOF API — proofr-package","text":"Client PROOF API.","code":""},{"path":[]},{"path":"http://getwilds.org/proofr/reference/proofr-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"proofr: Client for the PROOF API — proofr-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID)","code":""}]