Ion Torrent™ Server API Quick Reference

REST request format

Syntax

http://[<username>:<password>@]
        <host>/rundb/api/<version>/<resource>?format=json
        [[&<filter>{=<value> | __<qualifier>=<value>}]...][&order_by=[-]<filter>]

Examples

http://ionuser:ionuser@ionwest.itw/rundb/api/v1/experiment
        ?format=json&expName__startswith=R_2010_11&order_by=date

curl --user ionuser:ionuser --header "Content-Type: application/json"
        --location 'http://ionwest.itw/rundb/api/v1/results'

REST methods

Method	Function	Element URI	List URI
POST	Create	Create new entry in element	Create new entry in list
GET	Read	Get URI content	List URI members
PUT	Update	Replace URI content	Replace URI members
DELETE	Delete	Delete URI element	Delete list members

HTTP status codes

Method	Code	Meaning
GET	200	Resource exists
	301	Permanently moved
	401	Authorization err or
	404	Not found
	410	No longer exists
PUT/POST	200	Resource replaced
	201	Resource created
	204	No response
	301	Redirect
	400	Invalid data
	401	Authorization error
	409	Resource state conflict
	500	Internal error
	501	Method not implemented
DELETE	200	Resource deleted
	400	Resource not deleted
	401	Authorization error

Top-level requests

URI	Scope
/rundb/api/v1/	Resource list
/rundb/api/v1/ <resource>/	Resource element list (default limit: 20)
/rundb/api/v1/ <resource>?limit =0	Resource element list; all elements
/rundb/api/v1/ <resource>/<key>/	Resrouce element
/rundb/api/v1/ <resource>/set/ <key>;<key>;.../	Multiple resource elements
/rundb/api/v1/ <resource>/schema	Resource schema

Resources

• ++ indicates PUT/POST/DELETE permitted
• Bold type indicates KEY field

analysismetrics

amb, bead, dud, empty, excluded, id, ignored, keypass_all_beads, lib, libFinal, libKp, libLive, libMix, lib_pass_basecaller, lib_pass_cafie, live, pinned, report, sysCF, sysDR, sysIE, tf, tfFinal, tfKp, tfLive, tfMix, washout, washout_ambiguous, washout_dud, washout_library, washout_live, washout_test_fragment

dnabarcode ++

adapter, annotation, floworder, id, index, length, name, sequence, type

experiment ++

autoAnalyze, backup, barcodeId, baselineRun, chipBarcode, chipType, cycles, date, expCompInfo, expDir, expName, flows, flowsInOrder, ftpStatus, id, library, libraryKey, log, metaData, notes, pgmName, project, reagentBarcode, results, sample, seqKitBarcode, star, storageHost, storage_options, unique, usePreBeadfind

fileserver

comments, filesPrefix, id, location, name

globalconfig

default_command_line, default_flow_order, default_library_key, default_plugin_script, default_storage_options, default_test_fragment_key, fasta_path, id, name, plugin_folder, plugin_output_folder, records_to_display, reference_path, selected, sfftrim, sfftrim_args, site_name, web_root

libmetrics

See Filters (continued)

location

comments, id, name

plugin

autorun, chipType, date, id, libraryName, name, path, project, sample, selected, version

qualitymetrics

id, q0_100bp_reads, q0_15bp_reads, q0_50bp_reads, q0_bases, q0_max_read_length, q0_mean_read_length, q0_reads, q17_100bp_reads, q17_150bp_reads, q17_50bp_reads, q17_bases, q17_max_read_length, q17_mean_read_length, q17_reads, q20_100bp_reads, q20_150bp_reads, q20_50bp_reads, q20_bases, q20_max_read_length, q20_mean_read_length, q20_reads, report

referencegenome

bled, id, index_version, name, notes, reference_path, short_name, source, species, status, verbose_error, version

results ++

analysisVersion, analysismetrics, experiment, fastqLink, framesProcessed, id, libmetrics, log, metaData, pluginState, pluginStore, processedCycles, qualitymetrics, reportLink, reportstorage, resultsName, sffLink, status, tfFastq, tfSffLink, tfmetrics, timeStamp, timeToComplete

rig ++

alarms, comments, ftppassword, ftprootdir, ftpserver, ftpusername, last_clean_date, last_experiment, last_init_date, location, name, <nameValue>/status, state, updateflag, updatehome, version

runtype ++

barcode, description, id, runType

tfmetrics

See Filters (continued)

Extended resources

Plugins

POST:

Request Header:

Content-Type: application/json

Request Body:

{"plugin":["<pluginName>"]}

or

{"plugin":["<pluginName>"], pluginconfig : { json params } }

http://myhost/rundb/api/v1/results/<key>/plugin?format=json

Files

Example:

1. From results resource response:

   {"log": "/output/Home/Auto_B15-45_4_013/log.html"}
   

2. Get file:

   http://myhost/output/Home/Auto_B15-45_4_013/log.html
   

Filter qualifiers

Usage: <field>__<qualifier>=<value>

Example: library__contains=coli

contains	icontains	istartswith	search
day	iendswith	lt	startswith
endswith	iexact	lte	week_day
exact	in	month	year
gt	iregex	range
gte	isnull	regex

Sort parameter

Usage: order_by=[-]<filter>

Examples:

(ascending) order_by=date

(descending) order_by=-date

Data format parameter

Format	Parameter	Note
JSON	?format=json
XML	?format=xml	Not supported

Supported run types (>= 3.x)

Run Type	Description
RunType.FULLCHIP	Whole chip PGM run.
RunType.THUMB	Thumbnail run.
RunType.COMPOSITE	Proton run.

Supported run levels (>= 3.x)

Run Level	Description
RunLevel.PRE	Runs after all analysis jobs have been submitted, but before any finish.
RunLevel.BLOCK	Runs when an individual block finishes analysis. Occurs once for each block.
RunLevel.POST	Runs after all blocks are done processing.
RunLevel.LAST	Runs after everything, including other plugins. Multiple plugins w/ LAST will run at the same time.
RunLevel.DEFAULT	Default run level, generally PGM runs.