Ionchefplantemplate Resource¶

Resource URL: http://mytorrentserver/rundb/api/v1/ionchefplantemplate/

Schema URL: http://mytorrentserver/rundb/api/v1/ionchefplantemplate/schema/

Fields table¶

field	help text	default	nullable	readonly	blank	unique	type
planDisplayedName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
autoAnalyze	Boolean data. Ex: True	n/a	false	false	false	false	boolean
templatingKitBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
preAnalysis	Boolean data. Ex: True		false	false	true	false	boolean
chefStatus	Unicode string data. Ex: “Hello World”		false	false	true	false	string
applicationGroup	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
libkit	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
platform	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
categories	Unicode string data. Ex: “Hello World”		true	false	false	false	string
planPGM	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleSet_planTotal	Integer data. Ex: 2673	0	false	false	false	false	integer
projects	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
notes	Unicode string data. Ex: “Hello World”		true	false	true	false	string
sequencekitname	Unicode string data. Ex: “Hello World”		true	false	true	false	string
base_recalibration_mode	Unicode string data. Ex: “Hello World”		true	false	true	false	string
storageHost	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
expName	Unicode string data. Ex: “Hello World”		false	false	true	false	string
cycles	Integer data. Ex: 2673	n/a	true	false	false	false	integer
isReverseRun	Boolean data. Ex: True	false	false	false	true	false	boolean
storage_options	Unicode string data. Ex: “Hello World”	A	false	false	false	false	string
chipType	Unicode string data. Ex: “Hello World”		false	false	false	false	string
chefProgress	Floating point numeric data. Ex: 26.73	0	false	false	true	false	float
library	Unicode string data. Ex: “Hello World”		true	false	true	false	string
reverselibrarykey	Unicode string data. Ex: “Hello World”		false	true	false	false	string
sampleTubeLabel	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
seqKitBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
barcodeId	Unicode string data. Ex: “Hello World”		true	false	true	false	string
chefLogPath	Unicode string data. Ex: “Hello World”	n/a	true	false	true	false	string
isPlanGroup	Boolean data. Ex: True	false	false	false	true	false	boolean
realign	Boolean data. Ex: True	n/a	false	false	false	false	boolean
sampleGroupingName	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
experiment	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
bedfile	Unicode string data. Ex: “Hello World”		false	false	true	false	string
isReusable	Boolean data. Ex: True	false	false	false	true	false	boolean
isDuplicateReads	Boolean data. Ex: True	n/a	false	false	false	false	boolean
librarykitname	Unicode string data. Ex: “Hello World”		true	false	true	false	string
adapter	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
tfKey	Unicode string data. Ex: “Hello World”		false	false	true	false	string
parentPlan	Unicode string data. Ex: “Hello World”	None	false	false	true	false	string
forward3primeadapter	Unicode string data. Ex: “Hello World”		true	false	true	false	string
samplePrepKitName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
applicationGroupDisplayedName	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
metaData	Unicode string data. Ex: “Hello World”	{}	false	false	true	false	string
sampleSet_uid	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
isFavorite	Boolean data. Ex: True	false	false	false	true	false	boolean
sampleSet_planIndex	Integer data. Ex: 2673	0	false	false	false	false	integer
qcValues	Many related resources. Can be either a list of URIs or list of individually nested resource data.	n/a	true	false	true	false	related
planStatus	Unicode string data. Ex: “Hello World”		false	false	true	false	string
templatingKitName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
runType	Unicode string data. Ex: “Hello World”	GENS	false	false	false	false	string
username	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
planName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleDisplayedName	Unicode string data. Ex: “Hello World”		true	false	true	false	string
controlSequencekitname	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
chefMessage	Unicode string data. Ex: “Hello World”		false	false	true	false	string
templatingSize	Unicode string data. Ex: “Hello World”		true	false	false	false	string
childPlans	A list of data. Ex: [‘abc’, 26.73, 8]	[]	false	false	false	false	list
pairedEndLibraryAdapterName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
runMode	Unicode string data. Ex: “Hello World”		false	false	true	false	string
irworkflow	Unicode string data. Ex: “Hello World”		false	false	true	false	string
planExecuted	Boolean data. Ex: True	false	false	false	true	false	boolean
project	Unicode string data. Ex: “Hello World”	n/a	false	true	true	false	string
usePostBeadfind	Boolean data. Ex: True		false	false	true	false	boolean
libraryReadLength	Integer data. Ex: 2673	0	false	false	false	false	integer
runname	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
planGUID	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
planShortID	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
sampleSetGroupType	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
sample	Unicode string data. Ex: “Hello World”		true	false	true	false	string
planExecutedDate	A date & time as a string. Ex: “2010-11-10T03:07:43”	n/a	true	false	false	false	datetime
reverse_primer	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
id	Integer data. Ex: 2673		false	false	true	true	integer
barcodedSamples	Unicode string data. Ex: “Hello World”		true	false	true	false	string
regionfile	Unicode string data. Ex: “Hello World”		false	false	true	false	string
selectedPlugins	Unicode string data. Ex: “Hello World”		true	false	true	false	string
sampleSet	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
isSystemDefault	Boolean data. Ex: True	false	false	false	true	false	boolean
autoName	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
libraryKey	Unicode string data. Ex: “Hello World”		false	false	true	false	string
flows	Integer data. Ex: 2673	0	false	false	false	false	integer
date	A date & time as a string. Ex: “2010-11-10T03:07:43”	n/a	true	false	false	false	datetime
isSystem	Boolean data. Ex: True	false	false	false	true	false	boolean
variantfrequency	Unicode string data. Ex: “Hello World”		false	true	false	false	string
sampleSetDisplayedName	Unicode string data. Ex: “Hello World”	n/a	true	true	true	false	string
flowsInOrder	Unicode string data. Ex: “Hello World”		true	false	true	false	string
sampleGrouping	A single related resource. Can be either a URI or set of nested resource data.	n/a	true	false	true	false	related
chipBarcode	Unicode string data. Ex: “Hello World”	n/a	true	false	false	false	string
usePreBeadfind	Boolean data. Ex: True		false	false	true	false	boolean
resource_uri	Unicode string data. Ex: “Hello World”	n/a	false	true	false	false	string
reverse3primeadapter	Unicode string data. Ex: “Hello World”		false	true	false	false	string

Example request¶

Request URL: http://mytorrentserver/rundb/api/v1/ionchefplantemplate/?format=json&limit=1

Python example¶

import requests

ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/ionchefplantemplate/", params={"format": "json", "limit": 1})
ts_api_response = ts_api_request.json()

ionchefplantemplates = ts_api_response["objects"]

for ionchefplantemplate in ionchefplantemplates:
    print ionchefplantemplate

Torrent Server response¶

{
    "meta": {
        "previous": null,
        "total_count": 17,
        "offset": 0,
        "limit": 1,
        "next": "/rundb/api/v1/ionchefplantemplate/?offset=1&limit=1&format=json"
    },
    "objects": [
        {
            "planDisplayedName": "IC_P1v2_VAL_ccp",
            "autoAnalyze": true,
            "templatingKitBarcode": null,
            "preAnalysis": true,
            "chefStatus": "",
            "applicationGroup": "/rundb/api/v1/applicationgroup/1/",
            "libkit": null,
            "platform": "",
            "categories": "",
            "planPGM": null,
            "prebasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --max-phasing-levels 2",
            "alignmentargs": "stage1 map4",
            "thumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000",
            "sampleSet_planTotal": 0,
            "projects": [
                "IC_P1v2_val"
            ],
            "notes": "",
            "sequencekitname": "IonProtonIHiQ",
            "base_recalibration_mode": "no_recal",
            "storageHost": null,
            "expName": "",
            "cycles": null,
            "isReverseRun": false,
            "storage_options": "A",
            "thumbnailalignmentargs": "stage1 map4",
            "chipType": "P1.1.17",
            "chefProgress": 0,
            "library": "hg19",
            "reverselibrarykey": "",
            "sampleTubeLabel": "",
            "seqKitBarcode": null,
            "barcodeId": "IonXpress",
            "chefLogPath": null,
            "isPlanGroup": false,
            "realign": false,
            "sampleGroupingName": "",
            "experiment": "/rundb/api/v1/experiment/32917/",
            "bedfile": "/results/uploads/BED/44/hg19/unmerged/detail/CCP.20131001.designed.bed",
            "isReusable": true,
            "isDuplicateReads": false,
            "thumbnailbeadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=100,100 --beadfind-thumbnail 1",
            "librarykitname": "Ion AmpliSeq 2.0 Library Kit",
            "adapter": null,
            "basecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 1000 --barcode-filter-postpone 1",
            "tfKey": "ATCG",
            "parentPlan": null,
            "forward3primeadapter": "ATCACCGACTGCCCATAGAGAGGCTGAGAC",
            "planStatus": "pending",
            "samplePrepKitName": "",
            "applicationGroupDisplayedName": "DNA",
            "metaData": {},
            "sampleSet_uid": null,
            "isFavorite": true,
            "sampleSet_planIndex": 0,
            "qcValues": [
                {
                    "threshold": 30,
                    "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/",
                    "id": 289314,
                    "qcType": {
                        "description": "",
                        "minThreshold": 0,
                        "maxThreshold": 100,
                        "defaultThreshold": 30,
                        "qcName": "Usable Sequence (%)",
                        "id": 3,
                        "resource_uri": "/rundb/api/v1/qctype/3/"
                    },
                    "resource_uri": "/rundb/api/v1/plannedexperimentqc/289314/"
                },
                {
                    "threshold": 30,
                    "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/",
                    "id": 289313,
                    "qcType": {
                        "description": "",
                        "minThreshold": 1,
                        "maxThreshold": 100,
                        "defaultThreshold": 30,
                        "qcName": "Key Signal (1-100)",
                        "id": 2,
                        "resource_uri": "/rundb/api/v1/qctype/2/"
                    },
                    "resource_uri": "/rundb/api/v1/plannedexperimentqc/289313/"
                },
                {
                    "threshold": 30,
                    "plannedExperiment": "/rundb/api/v1/plannedexperiment/111154/",
                    "id": 289312,
                    "qcType": {
                        "description": "",
                        "minThreshold": 0,
                        "maxThreshold": 100,
                        "defaultThreshold": 30,
                        "qcName": "Bead Loading (%)",
                        "id": 1,
                        "resource_uri": "/rundb/api/v1/qctype/1/"
                    },
                    "resource_uri": "/rundb/api/v1/plannedexperimentqc/289312/"
                }
            ],
            "analysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=216,224 --bkg-bfmask-update false --gpuWorkLoad 1 --total-timeout 600 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json",
            "thumbnailcalibrateargs": "calibrate --skipDroop",
            "templatingKitName": "Ion PROTON IC v2 Universal",
            "runType": "AMPS",
            "username": "ionuser",
            "planName": "IC_P1v2_VAL_ccp",
            "sampleDisplayedName": "",
            "prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000",
            "controlSequencekitname": "",
            "chefMessage": "",
            "templatingSize": "200",
            "childPlans": [],
            "pairedEndLibraryAdapterName": "",
            "runMode": "single",
            "irworkflow": "",
            "planExecuted": false,
            "project": "IC_P1v2_val",
            "usePostBeadfind": false,
            "libraryReadLength": 200,
            "runname": null,
            "planGUID": "b55face2-df5f-434c-89df-210f384170cb",
            "planShortID": "IL9TF",
            "sampleSetGroupType": null,
            "sample": "",
            "planExecutedDate": null,
            "reverse_primer": null,
            "id": 111154,
            "barcodedSamples": {},
            "regionfile": "/results/uploads/BED/47/hg19/unmerged/detail/CCP.20131001.hotspots.bed",
            "selectedPlugins": {
                "SystematicErrorAnalysis": {
                    "userInput": "",
                    "version": "0.8.5",
                    "features": [],
                    "name": "SystematicErrorAnalysis",
                    "id": 734
                },
                "IonReporterUploader": {
                    "userInput": {
                        "accountName": "None",
                        "userInputInfo": "",
                        "accountId": "0"
                    },
                    "version": "4.4.0.2",
                    "features": [
                        "export"
                    ],
                    "name": "IonReporterUploader",
                    "id": 993
                },
                "variantCaller": {
                    "userInput": {
                        "torrent_variant_caller": {
                            "snp_min_allele_freq": "0.02",
                            "snp_strand_bias": "0.95",
                            "hotspot_min_coverage": 6,
                            "hotspot_min_cov_each_strand": 2,
                            "position_bias": "0.75",
                            "hotspot_min_allele_freq": "0.01",
                            "snp_min_variant_score": 6,
                            "mnp_min_variant_score": 400,
                            "hotspot_strand_bias": "0.95",
                            "hp_max_length": 8,
                            "filter_insertion_predictions": "0.2",
                            "indel_min_variant_score": 6,
                            "indel_min_coverage": 15,
                            "heavy_tailed": 3,
                            "outlier_probability": "0.005",
                            "position_bias_ref_fraction": "0.05",
                            "indel_strand_bias_pval": 1,
                            "data_quality_stringency": "6.5",
                            "snp_min_cov_each_strand": 0,
                            "indel_as_hpindel": 0,
                            "snp_strand_bias_pval": 1,
                            "mnp_strand_bias": "0.95",
                            "mnp_strand_bias_pval": 1,
                            "hotspot_strand_bias_pval": 1,
                            "hotspot_min_variant_score": 6,
                            "do_mnp_realignment": 1,
                            "indel_strand_bias": "0.9",
                            "downsample_to_coverage": 2000,
                            "filter_unusual_predictions": "0.3",
                            "indel_min_allele_freq": "0.05",
                            "mnp_min_allele_freq": "0.02",
                            "mnp_min_coverage": 6,
                            "do_snp_realignment": 1,
                            "mnp_min_cov_each_strand": 0,
                            "snp_min_coverage": 6,
                            "prediction_precision": 1,
                            "indel_min_cov_each_strand": 2,
                            "filter_deletion_predictions": "0.2",
                            "realignment_threshold": 1,
                            "suppress_recalibration": 0,
                            "position_bias_pval": "0.05",
                            "use_position_bias": 0
                        },
                        "meta": {
                            "ts_version": "4.4",
                            "name": "Generic - Proton - Somatic - Low Stringency",
                            "user_selections": {
                                "chip": "proton_p1",
                                "frequency": "somatic",
                                "library": "ampliseq",
                                "panel": "/rundb/api/v1/contentupload/48/"
                            },
                            "librarytype": "ampliseq",
                            "trimreads": true,
                            "tooltip": "Parameter settings optimized for low frequency variants and minimum false negatives on Proton chips",
                            "tvcargs": "tvc",
                            "barcode_mode": "match",
                            "based_on": "ampliseqexome_somatic_lowstringency_p1_parameters.json",
                            "built_in": true,
                            "configuration": "somatic_low_stringency_proton",
                            "compatibility": {
                                "chip": [
                                    "proton_p1"
                                ],
                                "frequency": [
                                    "somatic"
                                ],
                                "stringency": [
                                    "low"
                                ],
                                "library": [
                                    "wholegenome",
                                    "ampliseq",
                                    "targetseq"
                                ]
                            }
                        },
                        "long_indel_assembler": {
                            "min_indel_size": 4,
                            "short_suffix_match": 5,
                            "output_mnv": 0,
                            "min_var_count": 5,
                            "min_var_freq": "0.15",
                            "kmer_len": 19,
                            "max_hp_length": 8,
                            "relative_strand_bias": "0.8"
                        },
                        "freebayes": {
                            "gen_min_coverage": 6,
                            "allow_mnps": 1,
                            "allow_complex": 0,
                            "read_snp_limit": 10,
                            "read_max_mismatch_fraction": 1,
                            "allow_indels": 1,
                            "min_mapping_qv": 4,
                            "gen_min_alt_allele_freq": "0.035",
                            "allow_snps": 1,
                            "gen_min_indel_alt_allele_freq": "0.1"
                        }
                    },
                    "version": "4.4.0.6",
                    "features": [],
                    "name": "variantCaller",
                    "id": 994
                },
                "validateVariantCaller": {
                    "userInput": "",
                    "version": "0.2.1",
                    "features": [],
                    "name": "validateVariantCaller",
                    "id": 732
                },
                "validateVariantCaller-Lite": {
                    "userInput": "",
                    "version": "1.1.6",
                    "features": [],
                    "name": "validateVariantCaller-Lite",
                    "id": 964
                },
                "coverageAnalysis": {
                    "userInput": "",
                    "version": "4.4.0.12",
                    "features": [],
                    "name": "coverageAnalysis",
                    "id": 995
                }
            },
            "beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600",
            "sampleSet": null,
            "isSystemDefault": false,
            "autoName": null,
            "libraryKey": "TCAG",
            "flows": 400,
            "thumbnailanalysisargs": "Analysis --from-beadfind --clonal-filter-bkgmodel true --region-size=100,100 --bkg-bfmask-update false --gpuWorkLoad 1 --bkg-debug-param 1 --beadfind-thumbnail 1 --gopt /opt/ion/config/gopt_p1.1.17_ampliseq_exome.param.json",
            "date": "2015-01-28T19:57:42.000445+00:00",
            "isSystem": false,
            "variantfrequency": "",
            "sampleSetDisplayedName": "",
            "calibrateargs": "calibrate --skipDroop",
            "flowsInOrder": "",
            "sampleGrouping": null,
            "chipBarcode": null,
            "usePreBeadfind": true,
            "resource_uri": "/rundb/api/v1/ionchefplantemplate/111154/",
            "reverse3primeadapter": ""
        }
    ]
}

Allowed HTTP methods¶

get
post
put
delete
patch

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