Results Resource¶
Resource URL: http://mytorrentserver/rundb/api/v1/results/
Schema URL: http://mytorrentserver/rundb/api/v1/results/schema/
Perform CRUD operations on results resources and data elements.
Fields table¶
| field | help text | default | nullable | readonly | blank | unique | type |
|---|---|---|---|---|---|---|---|
| reference | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| processedflows | Integer data. Ex: 2673 | n/a | false | false | false | false | integer |
| reportStatus | Unicode string data. Ex: “Hello World” | Nothing | true | false | false | false | string |
| reportstorage | A single related resource. Can be either a URI or set of nested resource data. | n/a | false | false | false | false | related |
| analysisVersion | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| runid | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| id | Integer data. Ex: 2673 | false | false | true | true | integer | |
| filesystempath | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| metaData | Unicode string data. Ex: “Hello World” | {} | false | false | true | false | string |
| log | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| timeStamp | A date & time as a string. Ex: “2010-11-10T03:07:43” | true | false | false | true | false | datetime |
| libmetrics | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| experiment | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | false | false | related |
| resultsName | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| status | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| planShortID | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| processedCycles | Integer data. Ex: 2673 | n/a | false | false | false | false | integer |
| bamLink | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| sffLink | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| representative | Boolean data. Ex: True | false | false | false | true | false | boolean |
| pluginState | A dictionary of data. Ex: {‘price’: 26.73, ‘name’: ‘Daniel’} | n/a | false | true | false | false | dict |
| qualitymetrics | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| diskusage | Integer data. Ex: 2673 | n/a | true | false | false | false | integer |
| eas | A single related resource. Can be either a URI or set of nested resource data. | n/a | true | false | true | false | related |
| tfSffLink | Unicode string data. Ex: “Hello World” | n/a | true | false | false | false | string |
| projects | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| pluginStore | A dictionary of data. Ex: {‘price’: 26.73, ‘name’: ‘Daniel’} | n/a | false | true | false | false | dict |
| resultsType | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| tfFastq | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| tfmetrics | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| parentIDs | Unicode string data. Ex: “Hello World” | false | false | true | false | string | |
| analysismetrics | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| timeToComplete | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| reportLink | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| fastqLink | Unicode string data. Ex: “Hello World” | n/a | false | false | false | false | string |
| pluginresults | Many related resources. Can be either a list of URIs or list of individually nested resource data. | n/a | false | false | false | false | related |
| framesProcessed | Integer data. Ex: 2673 | n/a | false | false | false | false | integer |
| autoExempt | Boolean data. Ex: True | false | false | false | true | false | boolean |
| resource_uri | Unicode string data. Ex: “Hello World” | n/a | false | true | false | false | string |
Example request¶
Request URL: http://mytorrentserver/rundb/api/v1/results/?format=json&limit=1
Python example¶
import requests
ts_api_request = requests.get("http://mytorrentserver/rundb/api/v1/results/", params={"format": "json", "limit": 1})
ts_api_response = ts_api_request.json()
resultss = ts_api_response["objects"]
for results in resultss:
print results
Torrent Server response¶
{
"meta": {
"previous": null,
"total_count": 43354,
"offset": 0,
"limit": 1,
"next": "/rundb/api/v1/results/?offset=1&limit=1&format=json"
},
"objects": [
{
"reference": "hg19",
"processedflows": 0,
"reportStatus": "Nothing",
"reportstorage": {
"name": "Home",
"default": true,
"webServerPath": "/output",
"dirPath": "/results/analysis/output",
"id": 1,
"resource_uri": ""
},
"analysisVersion": "db:4.1.21+2-1,an:4.1.24+0-1,",
"runid": "DGMU8",
"id": 293943,
"filesystempath": "/results/analysis/output/Home/Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446_293943",
"metaData": {},
"log": "/output/Home/Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446_293943/log.html",
"timeStamp": "2014-01-23T07:39:52.000803+00:00",
"libmetrics": [
"/rundb/api/v1/libmetrics/32368/"
],
"experiment": "/rundb/api/v1/experiment/17446/",
"resultsName": "Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446",
"status": "Completed",
"planShortID": "ONPK8",
"processedCycles": 0,
"bamLink": "/output/Home/Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446_293943/R_2014_01_22_16_30_23_user_D1--632--R54651-p8s2_827b2_20m_man-cf_Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446.bam",
"sffLink": null,
"representative": false,
"pluginState": {
"coverageAnalysisLite": "Completed",
"SystematicErrorAnalysis": "Completed",
"1_Torrent_Accuracy": "Error",
"duplicateReads_useZC": "Completed",
"autoCal": "Completed",
"variantCaller": "Completed",
"ConversionRate": "Completed",
"validateVariantCaller": "Completed",
"timingPerformance": "Completed",
"coverageAnalysis": "Completed",
"VariantQC": "Completed"
},
"qualitymetrics": [
"/rundb/api/v1/qualitymetrics/31678/"
],
"diskusage": 151,
"eas": "/rundb/api/v1/experimentanalysissettings/18714/",
"tfSffLink": null,
"projects": [
"/rundb/api/v1/project/1080/"
],
"pluginStore": {
"coverageAnalysisLite": {
"Non-duplicate": "",
"barcoded": "true",
"Uniquely mapped": "No",
"Targetted regions": "/results/uploads/BED/46/hg19/merged/plain/AmpliSeqExome.20131001.designed.bed",
"Target padding": "0",
"barcodes": {
"IonXpress_033": {
"Bases in target regions": "57742646",
"Number of mapped reads": "41517304",
"Targeted Regions": "AmpliSeqExome.20131001.designed",
"Percent reads on target": "94.39%",
"Average base coverage depth": "112.4",
"Reference (File)": "hg19",
"Coverage Analysis Lite Report": "N/A",
"Target base coverage at 100x": "51.05%",
"Target base coverage at 20x": "94.26%",
"Uniformity of base coverage": "93.56%",
"Target base coverage at 1x": "98.53%",
"Using": "All Mapped Reads",
"Target base coverage at 500x": "0.10%",
"Alignments": "IonXpress_033_R_2014_01_22_16_30_23_user_D1--632--R54651-p8s2_827b2_20m_man-cf_Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446",
"Total base reads on target": "6490060189"
},
"IonXpress_034": {
"Bases in target regions": "57742646",
"Number of mapped reads": "48026110",
"Targeted Regions": "AmpliSeqExome.20131001.designed",
"Percent reads on target": "94.01%",
"Average base coverage depth": "130.8",
"Reference (File)": "hg19",
"Coverage Analysis Lite Report": "N/A",
"Target base coverage at 100x": "61.01%",
"Target base coverage at 20x": "94.93%",
"Uniformity of base coverage": "93.55%",
"Target base coverage at 1x": "98.55%",
"Using": "All Mapped Reads",
"Target base coverage at 500x": "0.22%",
"Alignments": "IonXpress_034_R_2014_01_22_16_30_23_user_D1--632--R54651-p8s2_827b2_20m_man-cf_Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446",
"Total base reads on target": "7552568443"
}
}
},
"SystematicErrorAnalysis": {
"qts_peak": "NaN",
"indel-5-per-mb": "10626.700000000001",
"positions-with-sse": "0.0080719999999999993",
"qts_base": "NaN",
"barcoded": "true",
"positions-with-sse-d15": "0.0080719999999999993",
"Target-regions_file": "/results/uploads/BED/46/hg19/merged/plain/AmpliSeqExome.20131001.designed.bed",
"stb-95-per-mb": "67945.399999999994",
"positions-with-sse-i5": "0.0073000000000000001",
"positions-with-sse-d5": "0.023935000000000001",
"positions-with-sse-i15": "0.0018799999999999999",
"indel-15-per-mb": "3118.8000000000002",
"barcodes": {
"IonXpress_033": {
"indel-5-per-mb": "10600.3",
"positions-with-sse": "0.007770",
"positions-with-sse-d15": "0.007770",
"stb-95-per-mb": "68851.0",
"positions-with-sse-i5": "0.007519",
"positions-with-sse-d5": "0.022925",
"positions-with-sse-i15": "0.001964",
"indel-15-per-mb": "3126.1"
},
"IonXpress_034": {
"indel-5-per-mb": "10653.1",
"positions-with-sse": "0.008373",
"positions-with-sse-d15": "0.008373",
"stb-95-per-mb": "67039.8",
"positions-with-sse-i5": "0.007080",
"positions-with-sse-d5": "0.024945",
"positions-with-sse-i15": "0.001796",
"indel-15-per-mb": "3111.5"
}
}
},
"1_Torrent_Accuracy": {},
"duplicateReads_useZC": {
"adapter_found_rate_chr1": "0.89400000000000002",
"duplicate_reads_chr1": 673650,
"duprate_at_725k_chr1": "0.89300000000000002",
"duplicate_rate_chr1": "0.89200000000000002",
"total_reads_chr1": 754826
},
"autoCal": {
"dc_range": 0
},
"variantCaller": {
"barcodes": {
"IonXpress_033": {
"hotspots": {},
"variants": {
"no_call": 0,
"homo_snps": 18047,
"het_snps": 31409,
"other": 1321,
"variants": 54343,
"het_indels": 2444,
"homo_indels": 1122
}
},
"IonXpress_034": {
"hotspots": {},
"variants": {
"no_call": 0,
"homo_snps": 18134,
"het_snps": 31524,
"other": 1308,
"variants": 54522,
"het_indels": 2422,
"homo_indels": 1134
}
}
},
"barcoded": "true",
"targets_bed": "/results/uploads/BED/46/hg19/unmerged/detail/AmpliSeqExome.20131001.designed.bed",
"Target Regions": "AmpliSeqExome.20131001.designed",
"Trim Reads": true,
"Target Loci": "Not using",
"Configuration": "Germ Line - Proton - Low Stringency",
"Aligned Reads": "R_2014_01_22_16_30_23_user_D1--632--R54651-p8s2_827b2_20m_man-cf",
"Library Type": "AmpliSeq"
},
"ConversionRate": {},
"validateVariantCaller": {
"SNP_FP-ConfidentPos": 5410,
"InDel_AmbPos-AllPos": 0,
"SNP_PPV>=30x": "96.7228784857032",
"InDel_FN>=100x": 930,
"SNP_FN>=100x": 896,
"InDel_TP-AllPos": 2591,
"InDel_FP>=30x": 1689,
"SNP_FN>=30x": 2004,
"SNP_FP>=1000x": 0,
"SNP_ConsensusAccuracy-AllPos": "0.999914181450164",
"InDel_NoCalls-AllPos": 894775,
"InDel_FP-AllPos": 2681,
"InDel_FP_50x-100x": 695,
"InDel_Sensitivity>=20x": "47.7212806026365",
"SNP_TP>=500x": 132,
"SNP_Sensitivity>=100x": "98.2144280589877",
"SNP_Sensitivity>=500x": "99.2481203007519",
"InDel_ConsensusAccuracy-AllPos": "0.999949885886992",
"SNP_ConsensusAccuracy>=50x": "0.999971537775062",
"InDel_FN>=20x": 2776,
"SNP_FP>=50x": 1762,
"InDel_PPV-AllPos": "49.1464339908953",
"InDel_ConsensusAccuracy>=30x": "0.999964918459836",
"InDel_FP-ncRNA": 18,
"InDel_ReferenceCalls-AllPos": 0,
"Target-regions_file": "/results/analysis/output/Home/Auto_user_D1--632--R54651-p8s2_827b2_20m_man-cf_17446_293943/plugin_out/validateVariantCaller_out.570190/../variantCaller_out.564691/AmpliSeqExome.20131001.designed.bed",
"SNP_TP-AllPos": 87058,
"InDel_Sensitivity>=30x": "49.0349819059107",
"InDel_FN>=500x": 3,
"InDel_FP_20x-50x": 827,
"InDel_FP-ConfidentPos": 2681,
"InDel_FN-AllPos": 3353,
"SNP_HP11-AllPos": 0,
"InDel_FN>=50x": 2041,
"SNP_Sensitivity-AllPos": "94.6478076994162",
"Truth-major_SNP_file": "NA12878_NIST_NoChrY_SNP.bed",
"InDel_Sensitivity-AllAnnotations": "87.1800314804519",
"SNP_FP_200x-300x": 84,
"InDel_FP>=20x": 2020,
"SNP_FN>=500x": 1,
"Combined Variant Positive Predictive Value for All Bases at >=20x": "94.0001",
"SNP_Sensitivity>=1000x": 100,
"InDel_FP_700x-1000x": 0,
"SNP_FP>=30x": 2777,
"SNP_FP_700x-1000x": 0,
"SNP_ConsensusAccuracy>=20x": "0.999952352557784",
"InDel_TP>=30x": 2439,
"SNP_AmbPos-AllPos": 0,
"Truth-minor_InDel_file": "None",
"SNP_FP_500x-700x": 1,
"SNP_FP_50x-100x": 1095,
"InDel_ConsensusAccuracy>=20x": "0.999960167834606",
"InDel_FP-Exons": 1062,
"SNP_TP>=30x": 81962,
"SNP_ReferenceCalls-AllPos": 0,
"InDel_FP_500x-700x": 1,
"InDel_FP_200x-300x": 65,
"barcoded": "true",
"SNP_FP_20x-50x": 1773,
"SNP_FP>=100x": 667,
"SNP_Sensitivity>=20x": "97.4601197273262",
"InDel_FP_300x-400x": 9,
"SNP_FP_100x-200x": 565,
"barcodes": {
"IonXpress_033": {
"SNP_FP-ConfidentPos": "2733",
"InDel_AmbPos-AllPos": "0",
"SNP_PPV>=30x": "96.7970258096804",
"InDel_FN>=100x": "411",
"SNP_FN>=100x": "406",
"InDel_TP-AllPos": "1281",
"InDel_FP>=30x": "838",
"SNP_FN>=30x": "1006",
"SNP_FP>=1000x": "0",
"SNP_ConsensusAccuracy-AllPos": "0.999912578529413",
"InDel_NoCalls-AllPos": "450359",
"InDel_FP-AllPos": "1375",
"InDel_FP_50x-100x": "369",
"InDel_Sensitivity>=20x": "47.4402730375427",
"SNP_TP>=500x": "44",
"SNP_Sensitivity>=100x": "98.2229614391386",
"SNP_Sensitivity>=500x": "100",
"InDel_ConsensusAccuracy-AllPos": "0.999949088579261",
"SNP_ConsensusAccuracy>=50x": "0.999972775263102",
"InDel_FN>=20x": "1386",
"SNP_FP>=50x": "829",
"InDel_PPV-AllPos": "48.230421686747",
"InDel_ConsensusAccuracy>=30x": "0.99996518422908",
"InDel_FP-ncRNA": "9",
"InDel_ReferenceCalls-AllPos": "0",
"SNP_TP-AllPos": "43461",
"InDel_Sensitivity>=30x": "48.7158581328985",
"InDel_FN>=500x": "1",
"InDel_FP_20x-50x": "437",
"InDel_FP-ConfidentPos": "1375",
"InDel_FN-AllPos": "1690",
"SNP_HP11-AllPos": "0",
"InDel_FN>=50x": "977",
"SNP_Sensitivity-AllPos": "94.4989237024635",
"InDel_Sensitivity-AllAnnotations": "43.1167956916863",
"SNP_FP_200x-300x": "34",
"InDel_FP>=20x": "1013",
"SNP_FN>=500x": "0",
"Combined Variant Positive Predictive Value for All Bases at >=20x": "94.022600",
"SNP_Sensitivity>=1000x": "0",
"InDel_FP_700x-1000x": "0",
"SNP_FP>=30x": "1344",
"SNP_FP_700x-1000x": "0",
"SNP_ConsensusAccuracy>=20x": "0.999952742906361",
"InDel_TP>=30x": "1195",
"SNP_AmbPos-AllPos": "0",
"SNP_FP_500x-700x": "0",
"SNP_FP_50x-100x": "536",
"InDel_ConsensusAccuracy>=20x": "0.999960151224028",
"InDel_FP-Exons": "537",
"SNP_TP>=30x": "40617",
"SNP_ReferenceCalls-AllPos": "0",
"InDel_FP_500x-700x": "0",
"InDel_FP_200x-300x": "29",
"SNP_FP_20x-50x": "911",
"SNP_FP>=100x": "293",
"SNP_Sensitivity>=20x": "97.439640391121",
"InDel_FP_300x-400x": "0",
"SNP_FP_100x-200x": "255",
"SNP_Sensitivity-AllAnnotations": "94.4989237024635",
"InDel_FP_400x-500x": "2",
"InDel_FP>=50x": "576",
"SNP_FN-AllAnnotations": "2530",
"SNP_FP-AllPos": "2733",
"SNP_PPV-AllPos": "94.0836472269126",
"SNP_FP>=20x": "1740",
"InDel_Sensitivity>=1000x": "0",
"InDel_ConsensusAccuracy>=50x": "0.999974203772787",
"InDel_TP>=100x": "616",
"SNP_TP>=50x": "36440",
"SNP_ConsensusAccuracy>=30x": "0.999960965142337",
"InDel_Sensitivity-AllPos": "43.1167956916863",
"InDel_TP>=20x": "1251",
"InDel_AmbNotDetected-AllPos": "0",
"SNP_FP>=500x": "0",
"% Callable Bases": "99.161500",
"SNP_FN>=20x": "1105",
"InDel_FP>=1000x": "0",
"SNP_Sensitivity>=30x": "97.5830670542729",
"InDel_FN>=1000x": "0",
"InDel_FP>=500x": "0",
"SNP_FP_400x-500x": "2",
"InDel_HP11-AllPos": "0",
"Combined Variant Positive Predictive Value for All Bases at all coverages": "91.590500",
"SNP_FN>=1000x": "0",
"SNP_FN>=50x": "810",
"InDel_TP>=500x": "2",
"InDel_PPV>=30x": "58.780127889818",
"InDel_TP>=1000x": "0",
"SNP_FP_300x-400x": "2",
"SNP_Sensitivity>=50x": "97.8255033557047",
"Combined Variant Sensitivity for All Bases at >= 20x": "94.560500",
"SNP_TP>=100x": "22441",
"InDel_FP>=100x": "207",
"SNP_NoCalls-AllPos": "56910",
"InDel_Sensitivity>=500x": "66.6666666666667",
"SNP_TP>=20x": "42053",
"InDel_Sensitivity>=50x": "52.3182040019522",
"InDel_FN-AllAnnotations": "1690",
"InDel_TP>=50x": "1072",
"SNP_TP>=1000x": "0",
"InDel_FN>=30x": "1258",
"SNP_AmbNotDetected-AllPos": "0",
"SNP_FP-ncRNA": "28",
"SNP_FN-AllPos": "2530",
"InDel_Sensitivity>=100x": "59.9805258033106",
"InDel_FP_100x-200x": "176",
"SNP_FP-Exons": "993",
"Combined Variant Sensitivity for All Bases at all coverages": "91.381000"
},
"IonXpress_034": {
"SNP_FP-ConfidentPos": "2677",
"InDel_AmbPos-AllPos": "0",
"SNP_PPV>=30x": "96.6501472719622",
"InDel_FN>=100x": "519",
"SNP_FN>=100x": "490",
"InDel_TP-AllPos": "1310",
"InDel_FP>=30x": "851",
"SNP_FN>=30x": "998",
"SNP_FP>=1000x": "0",
"SNP_ConsensusAccuracy-AllPos": "0.999915784370915",
"InDel_NoCalls-AllPos": "444416",
"InDel_FP-AllPos": "1306",
"InDel_FP_50x-100x": "326",
"InDel_Sensitivity>=20x": "47.9985035540591",
"SNP_TP>=500x": "88",
"SNP_Sensitivity>=100x": "98.2072952109172",
"SNP_Sensitivity>=500x": "98.876404494382",
"InDel_ConsensusAccuracy-AllPos": "0.999950683194723",
"SNP_ConsensusAccuracy>=50x": "0.999970300287021",
"InDel_FN>=20x": "1390",
"SNP_FP>=50x": "933",
"InDel_PPV-AllPos": "50.0764525993884",
"InDel_ConsensusAccuracy>=30x": "0.999964652690593",
"InDel_FP-ncRNA": "9",
"InDel_ReferenceCalls-AllPos": "0",
"SNP_TP-AllPos": "43597",
"InDel_Sensitivity>=30x": "49.3454978183261",
"InDel_FN>=500x": "2",
"InDel_FP_20x-50x": "390",
"InDel_FP-ConfidentPos": "1306",
"InDel_FN-AllPos": "1663",
"SNP_HP11-AllPos": "0",
"InDel_FN>=50x": "1064",
"SNP_Sensitivity-AllPos": "94.7966949336812",
"InDel_Sensitivity-AllAnnotations": "44.0632357887656",
"SNP_FP_200x-300x": "50",
"InDel_FP>=20x": "1007",
"SNP_FN>=500x": "1",
"Combined Variant Positive Predictive Value for All Bases at >=20x": "93.977600",
"SNP_Sensitivity>=1000x": "100",
"InDel_FP_700x-1000x": "0",
"SNP_FP>=30x": "1433",
"SNP_FP_700x-1000x": "0",
"SNP_ConsensusAccuracy>=20x": "0.999951962209208",
"InDel_TP>=30x": "1244",
"SNP_AmbPos-AllPos": "0",
"SNP_FP_500x-700x": "1",
"SNP_FP_50x-100x": "559",
"InDel_ConsensusAccuracy>=20x": "0.999960184445184",
"InDel_FP-Exons": "525",
"SNP_TP>=30x": "41345",
"SNP_ReferenceCalls-AllPos": "0",
"InDel_FP_500x-700x": "1",
"InDel_FP_200x-300x": "36",
"SNP_FP_20x-50x": "862",
"SNP_FP>=100x": "374",
"SNP_Sensitivity>=20x": "97.4804198534647",
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