Availableionchefplannedexperiment Resource¶
Resource URL: http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/
Schema URL: http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/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 | |
| 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 | 0.0 | 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 | false | 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 | |
| chefLastUpdate | A date & time as a string. Ex: “2010-11-10T03:07:43” | n/a | true | false | false | false | datetime |
| 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 | |
| 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 | |
| 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 |
| base_recalibrate | Boolean data. Ex: True | n/a | false | false | false | false | boolean |
| 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/availableionchefplannedexperiment/?format=json&limit=1
Python example¶
import requests
ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/availableionchefplannedexperiment/", params={"format": "json", "limit": 1})
ts_api_response = ts_api_request.json()
availableionchefplannedexperiments = ts_api_response["objects"]
for availableionchefplannedexperiment in availableionchefplannedexperiments:
print availableionchefplannedexperiment
Torrent Server response¶
{
"meta": {
"previous": null,
"total_count": 10,
"offset": 0,
"limit": 1,
"next": "/rundb/api/v1/availableionchefplannedexperiment/?offset=1&limit=1&format=json"
},
"objects": [
{
"planDisplayedName": "C18S2_package1_Thur_psp4",
"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 --calibration-training=100000 --flow-signals-type scaled-residual --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": [
"Chef_p1v2_dev_IE"
],
"notes": "148420",
"sequencekitname": "ProtonIIC200Kit",
"storageHost": null,
"expName": "",
"cycles": null,
"isReverseRun": false,
"storage_options": "A",
"thumbnailalignmentargs": "stage1 map4",
"chipType": "P1.1.17",
"chefProgress": 0.0,
"library": "hg19",
"reverselibrarykey": "",
"sampleTubeLabel": "00049613",
"seqKitBarcode": null,
"barcodeId": "IonXpress",
"chefLogPath": null,
"isPlanGroup": false,
"realign": false,
"sampleGroupingName": "",
"experiment": "/rundb/api/v1/experiment/23817/",
"bedfile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed",
"isReusable": false,
"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",
"chefLastUpdate": null,
"samplePrepKitName": "Ion AmpliSeq Exome Kit",
"applicationGroupDisplayedName": "DNA",
"metaData": {},
"sampleSet_uid": null,
"isFavorite": false,
"sampleSet_planIndex": 0,
"qcValues": [
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/",
"id": 266238,
"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/266238/"
},
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/",
"id": 266237,
"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/266237/"
},
{
"threshold": 30,
"plannedExperiment": "/rundb/api/v1/plannedexperiment/102054/",
"id": 266236,
"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/266236/"
}
],
"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 PI IC 200 Kit",
"runType": "AMPS_EXOME",
"username": "ionuser",
"planName": "C18S2_package1_Thur_psp4",
"sampleDisplayedName": "",
"prethumbnailbasecallerargs": "BaseCaller --barcode-filter 0.01 --barcode-filter-minreads 10 --keypass-filter on --phasing-residual-filter=2.0 --num-unfiltered 100000 --calibration-training=100000 --flow-signals-type scaled-residual",
"controlSequencekitname": "",
"chefMessage": "",
"childPlans": [],
"pairedEndLibraryAdapterName": "",
"runMode": "single",
"irworkflow": "",
"planExecuted": false,
"project": "Chef_p1v2_dev_IE",
"usePostBeadfind": false,
"runname": null,
"planGUID": "994fd167-7d5a-43e5-acca-c8ffa069350e",
"planShortID": "0KXAK",
"sampleSetGroupType": null,
"sample": "",
"planExecutedDate": null,
"reverse_primer": null,
"id": 102054,
"barcodedSamples": {
"1": {
"barcodeSampleInfo": {
"IonXpress_001": {
"description": "",
"reference": "hg19",
"targetRegionBedFile": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed",
"hotSpotRegionBedFile": "",
"nucleotideType": "DNA",
"controlSequenceType": "",
"externalId": ""
}
},
"barcodes": [
"IonXpress_001"
]
}
},
"regionfile": "",
"selectedPlugins": {
"coverageAnalysis": {
"userInput": "",
"version": "4.2-r88700",
"features": [],
"name": "coverageAnalysis",
"id": 827
},
"validateVariantCaller": {
"userInput": {
"variant_caller_name": "variantCaller",
"truth_major_snp": "NA12878_NIST_NoChrY_SNP.bed",
"region": "NIST",
"sample": "NA12878",
"truth_minor_snp": "None",
"truth_major_indel": "NA12878_NIST_NoChrY_indel.bed",
"truth_minor_indel": "None"
},
"version": "0.2.1",
"features": [],
"name": "validateVariantCaller",
"id": 732
},
"variantCaller": {
"userInput": {
"torrent_variant_caller": {
"snp_min_allele_freq": "0.10000000000000001",
"snp_strand_bias": "0.97999999999999998",
"hotspot_min_coverage": 6,
"hotspot_min_cov_each_strand": 3,
"hotspot_min_allele_freq": "0.10000000000000001",
"snp_min_variant_score": 15,
"hotspot_strand_bias": "0.94999999999999996",
"hp_max_length": 8,
"filter_insertion_predictions": "0.20000000000000001",
"indel_min_variant_score": 20,
"indel_min_coverage": 10,
"heavy_tailed": 3,
"outlier_probability": "0.01",
"data_quality_stringency": 5,
"snp_min_cov_each_strand": 0,
"hotspot_min_variant_score": 10,
"indel_strand_bias": "0.90000000000000002",
"tvc_parameters_version": "germline_low_stringency_proton-3.6.66827",
"downsample_to_coverage": 400,
"filter_unusual_predictions": "0.25",
"indel_min_allele_freq": "0.14999999999999999",
"do_snp_realignment": 1,
"prediction_precision": 1,
"indel_min_cov_each_strand": 5,
"filter_deletion_predictions": "0.20000000000000001",
"suppress_recalibration": 0,
"snp_min_coverage": 5
},
"meta": {
"repository_id": "",
"ts_version": "4.0",
"name": "External file AmpliseqExome.germline_lowstringency_p1.4_0.20130920.parameters.json",
"user_selections": {
"chip": "proton_p1",
"frequency": "germline",
"library": "ampliseq",
"panel": "/rundb/api/v1/contentupload/53/"
},
"librarytype": "ampliseq",
"trimreads": true,
"tooltip": "Retrieved from external file",
"tvcargs": "tvc",
"built_in": false,
"configuration": "",
"compatibility": {}
},
"long_indel_assembler": {
"min_indel_size": 4,
"short_suffix_match": 5,
"output_mnv": 0,
"min_var_count": 5,
"min_var_freq": "0.14999999999999999",
"kmer_len": 19,
"max_hp_length": 8,
"relative_strand_bias": "0.80000000000000004"
},
"freebayes": {
"gen_min_coverage": 5,
"allow_mnps": 1,
"allow_complex": 0,
"read_max_mismatch_fraction": 1,
"read_mismatch_limit": 10,
"allow_indels": 1,
"min_mapping_qv": 4,
"gen_min_alt_allele_freq": "0.10000000000000001",
"allow_snps": 1,
"gen_min_indel_alt_allele_freq": "0.14999999999999999"
}
},
"version": "4.2-r88446",
"features": [],
"name": "variantCaller",
"id": 826
},
"AmpliconStats": {
"userInput": "",
"version": "0.4.5",
"features": [],
"name": "AmpliconStats",
"id": 774
}
},
"beadfindargs": "justBeadFind --beadfind-minlivesnr 3 --region-size=216,224 --total-timeout 600",
"sampleSet": null,
"isSystemDefault": false,
"autoName": null,
"libraryKey": "TCAG",
"flows": 520,
"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": "2014-06-26T04:47:43.000023+00:00",
"isSystem": false,
"variantfrequency": "",
"sampleSetDisplayedName": "",
"calibrateargs": "calibrate --skipDroop",
"flowsInOrder": "",
"sampleGrouping": null,
"base_recalibrate": true,
"chipBarcode": null,
"usePreBeadfind": true,
"resource_uri": "/rundb/api/v1/availableionchefplannedexperiment/102054/",
"reverse3primeadapter": ""
}
]
}
Allowed HTTP methods¶
- get
- post
- put
- delete
- patch
