diff --git a/src/components/Cytobands.js b/src/components/Cytobands.js new file mode 100644 index 00000000..ec431b06 --- /dev/null +++ b/src/components/Cytobands.js @@ -0,0 +1,914 @@ +export function Cytobands() { + return { + "chr1": [ + {"referenceName": "chr1", "start": 0, "end": 2300000, "cytoband": "p36.33", "stain": "gneg"}, + {"referenceName": "chr1", "start": 2300000, "end": 5300000, "cytoband": "p36.32", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 5300000, "end": 7100000, "cytoband": "p36.31", "stain": "gneg"}, + {"referenceName": "chr1", "start": 7100000, "end": 9100000, "cytoband": "p36.23", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 9100000, "end": 12500000, "cytoband": "p36.22", "stain": "gneg"}, + {"referenceName": "chr1", "start": 12500000, "end": 15900000, "cytoband": "p36.21", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 15900000, "end": 20100000, "cytoband": "p36.13", "stain": "gneg"}, + {"referenceName": "chr1", "start": 20100000, "end": 23600000, "cytoband": "p36.12", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 23600000, "end": 27600000, "cytoband": "p36.11", "stain": "gneg"}, + {"referenceName": "chr1", "start": 27600000, "end": 29900000, "cytoband": "p35.3", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 29900000, "end": 32300000, "cytoband": "p35.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 32300000, "end": 34300000, "cytoband": "p35.1", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 34300000, "end": 39600000, "cytoband": "p34.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 39600000, "end": 43700000, "cytoband": "p34.2", "stain": "gpos2512"}, + {"referenceName": "chr1", "start": 43700000, "end": 46300000, "cytoband": "p34.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 46300000, "end": 50200000, "cytoband": "p33", "stain": "gpos75"}, + {"referenceName": "chr1", "start": 50200000, "end": 55600000, "cytoband": "p32.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 55600000, "end": 58500000, "cytoband": "p32.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 58500000, "end": 60800000, "cytoband": "p32.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 60800000, "end": 68500000, "cytoband": "p31.3", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 68500000, "end": 69300000, "cytoband": "p31.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 69300000, "end": 84400000, "cytoband": "p31.1", "stain": "gpos100"}, + {"referenceName": "chr1", "start": 84400000, "end": 87900000, "cytoband": "p22.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 87900000, "end": 91500000, "cytoband": "p22.2", "stain": "gpos75"}, + {"referenceName": "chr1", "start": 91500000, "end": 94300000, "cytoband": "p22.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 94300000, "end": 99300000, "cytoband": "p21.3", "stain": "gpos75"}, + {"referenceName": "chr1", "start": 99300000, "end": 101800000, "cytoband": "p21.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 101800000, "end": 106700000, "cytoband": "p21.1", "stain": "gpos100"}, + {"referenceName": "chr1", "start": 106700000, "end": 111200000, "cytoband": "p13.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 111200000, "end": 115500000, "cytoband": "p13.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 115500000, "end": 117200000, "cytoband": "p13.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 117200000, "end": 120400000, "cytoband": "p12", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 120400000, "end": 121700000, "cytoband": "p11.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 121700000, "end": 123400000, "cytoband": "p11.1", "stain": "acen"}, + {"referenceName": "chr1", "start": 123400000, "end": 125100000, "cytoband": "q11", "stain": "acen"}, + {"referenceName": "chr1", "start": 125100000, "end": 143200000, "cytoband": "q12", "stain": "gvar"}, + {"referenceName": "chr1", "start": 143200000, "end": 147500000, "cytoband": "q21.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 147500000, "end": 150600000, "cytoband": "q21.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 150600000, "end": 155100000, "cytoband": "q21.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 155100000, "end": 156600000, "cytoband": "q22", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 156600000, "end": 159100000, "cytoband": "q23.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 159100000, "end": 160500000, "cytoband": "q23.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 160500000, "end": 165500000, "cytoband": "q23.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 165500000, "end": 167200000, "cytoband": "q24.1", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 167200000, "end": 170900000, "cytoband": "q24.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 170900000, "end": 173000000, "cytoband": "q24.3", "stain": "gpos75"}, + {"referenceName": "chr1", "start": 173000000, "end": 176100000, "cytoband": "q25.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 176100000, "end": 180300000, "cytoband": "q25.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 180300000, "end": 185800000, "cytoband": "q25.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 185800000, "end": 190800000, "cytoband": "q31.1", "stain": "gpos100"}, + {"referenceName": "chr1", "start": 190800000, "end": 193800000, "cytoband": "q31.2", "stain": "gneg"}, + {"referenceName": "chr1", "start": 193800000, "end": 198700000, "cytoband": "q31.3", "stain": "gpos100"}, + {"referenceName": "chr1", "start": 198700000, "end": 207100000, "cytoband": "q32.1", "stain": "gneg"}, + {"referenceName": "chr1", "start": 207100000, "end": 211300000, "cytoband": "q32.2", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 211300000, "end": 214400000, "cytoband": "q32.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 214400000, "end": 223900000, "cytoband": "q41", "stain": "gpos100"}, + {"referenceName": "chr1", "start": 223900000, "end": 224400000, "cytoband": "q42.11", "stain": "gneg"}, + {"referenceName": "chr1", "start": 224400000, "end": 226800000, "cytoband": "q42.12", "stain": "gpos25"}, + {"referenceName": "chr1", "start": 226800000, "end": 230500000, "cytoband": "q42.13", "stain": "gneg"}, + {"referenceName": "chr1", "start": 230500000, "end": 234600000, "cytoband": "q42.2", "stain": "gpos50"}, + {"referenceName": "chr1", "start": 234600000, "end": 236400000, "cytoband": "q42.3", "stain": "gneg"}, + {"referenceName": "chr1", "start": 236400000, "end": 243500000, "cytoband": "q43", "stain": "gpos75"}, + {"referenceName": "chr1", "start": 243500000, "end": 248956422, "cytoband": "q44", "stain": "gneg"} + ], + "chr10": [ + {"referenceName": "chr10", "start": 0, "end": 3000000, "cytoband": "p15.3", "stain": "gneg"}, + {"referenceName": "chr10", "start": 3000000, "end": 3800000, "cytoband": "p15.2", "stain": "gpos25"}, + {"referenceName": "chr10", "start": 3800000, "end": 6600000, "cytoband": "p15.1", "stain": "gneg"}, + {"referenceName": "chr10", "start": 6600000, "end": 12200000, "cytoband": "p14", "stain": "gpos75"}, + {"referenceName": "chr10", "start": 12200000, "end": 17300000, "cytoband": "p13", "stain": "gneg"}, + {"referenceName": "chr10", "start": 17300000, "end": 18300000, "cytoband": "p12.33", "stain": "gpos75"}, + {"referenceName": "chr10", "start": 18300000, "end": 18400000, "cytoband": "p12.32", "stain": "gneg"}, + {"referenceName": "chr10", "start": 18400000, "end": 22300000, "cytoband": "p12.31", "stain": "gpos75"}, + {"referenceName": "chr10", "start": 22300000, "end": 24300000, "cytoband": "p12.2", "stain": "gneg"}, + {"referenceName": "chr10", "start": 24300000, "end": 29300000, "cytoband": "p12.1", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 29300000, "end": 31100000, "cytoband": "p11.23", "stain": "gneg"}, + {"referenceName": "chr10", "start": 31100000, "end": 34200000, "cytoband": "p11.22", "stain": "gpos25"}, + {"referenceName": "chr10", "start": 34200000, "end": 38000000, "cytoband": "p11.21", "stain": "gneg"}, + {"referenceName": "chr10", "start": 38000000, "end": 39800000, "cytoband": "p11.1", "stain": "acen"}, + {"referenceName": "chr10", "start": 39800000, "end": 41600000, "cytoband": "q11.1", "stain": "acen"}, + {"referenceName": "chr10", "start": 41600000, "end": 45500000, "cytoband": "q11.21", "stain": "gneg"}, + {"referenceName": "chr10", "start": 45500000, "end": 48600000, "cytoband": "q11.22", "stain": "gpos25"}, + {"referenceName": "chr10", "start": 48600000, "end": 51100000, "cytoband": "q11.23", "stain": "gneg"}, + {"referenceName": "chr10", "start": 51100000, "end": 59400000, "cytoband": "q21.1", "stain": "gpos100"}, + {"referenceName": "chr10", "start": 59400000, "end": 62800000, "cytoband": "q21.2", "stain": "gneg"}, + {"referenceName": "chr10", "start": 62800000, "end": 68800000, "cytoband": "q21.3", "stain": "gpos100"}, + {"referenceName": "chr10", "start": 68800000, "end": 73100000, "cytoband": "q22.1", "stain": "gneg"}, + {"referenceName": "chr10", "start": 73100000, "end": 75900000, "cytoband": "q22.2", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 75900000, "end": 80300000, "cytoband": "q22.3", "stain": "gneg"}, + {"referenceName": "chr10", "start": 80300000, "end": 86100000, "cytoband": "q23.1", "stain": "gpos100"}, + {"referenceName": "chr10", "start": 86100000, "end": 87700000, "cytoband": "q23.2", "stain": "gneg"}, + {"referenceName": "chr10", "start": 87700000, "end": 91100000, "cytoband": "q23.31", "stain": "gpos75"}, + {"referenceName": "chr10", "start": 91100000, "end": 92300000, "cytoband": "q23.32", "stain": "gneg"}, + {"referenceName": "chr10", "start": 92300000, "end": 95300000, "cytoband": "q23.33", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 95300000, "end": 97500000, "cytoband": "q24.1", "stain": "gneg"}, + {"referenceName": "chr10", "start": 97500000, "end": 100100000, "cytoband": "q24.2", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 100100000, "end": 101200000, "cytoband": "q24.31", "stain": "gneg"}, + {"referenceName": "chr10", "start": 101200000, "end": 103100000, "cytoband": "q24.32", "stain": "gpos25"}, + {"referenceName": "chr10", "start": 103100000, "end": 104000000, "cytoband": "q24.33", "stain": "gneg"}, + {"referenceName": "chr10", "start": 104000000, "end": 110100000, "cytoband": "q25.1", "stain": "gpos100"}, + {"referenceName": "chr10", "start": 110100000, "end": 113100000, "cytoband": "q25.2", "stain": "gneg"}, + {"referenceName": "chr10", "start": 113100000, "end": 117300000, "cytoband": "q25.3", "stain": "gpos75"}, + {"referenceName": "chr10", "start": 117300000, "end": 119900000, "cytoband": "q26.11", "stain": "gneg"}, + {"referenceName": "chr10", "start": 119900000, "end": 121400000, "cytoband": "q26.12", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 121400000, "end": 125700000, "cytoband": "q26.13", "stain": "gneg"}, + {"referenceName": "chr10", "start": 125700000, "end": 128800000, "cytoband": "q26.2", "stain": "gpos50"}, + {"referenceName": "chr10", "start": 128800000, "end": 133797422, "cytoband": "q26.3", "stain": "gneg"} + ], + "chr11": [ + {"referenceName": "chr11", "start": 0, "end": 2800000, "cytoband": "p15.5", "stain": "gneg"}, + {"referenceName": "chr11", "start": 2800000, "end": 11700000, "cytoband": "p15.4", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 11700000, "end": 13800000, "cytoband": "p15.3", "stain": "gneg"}, + {"referenceName": "chr11", "start": 13800000, "end": 16900000, "cytoband": "p15.2", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 16900000, "end": 22000000, "cytoband": "p15.1", "stain": "gneg"}, + {"referenceName": "chr11", "start": 22000000, "end": 26200000, "cytoband": "p14.3", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 26200000, "end": 27200000, "cytoband": "p14.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 27200000, "end": 31000000, "cytoband": "p14.1", "stain": "gpos75"}, + {"referenceName": "chr11", "start": 31000000, "end": 36400000, "cytoband": "p13", "stain": "gneg"}, + {"referenceName": "chr11", "start": 36400000, "end": 43400000, "cytoband": "p12", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 43400000, "end": 48800000, "cytoband": "p11.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 48800000, "end": 51000000, "cytoband": "p11.12", "stain": "gpos75"}, + {"referenceName": "chr11", "start": 51000000, "end": 53400000, "cytoband": "p11.11", "stain": "acen"}, + {"referenceName": "chr11", "start": 53400000, "end": 55800000, "cytoband": "q11", "stain": "acen"}, + {"referenceName": "chr11", "start": 55800000, "end": 60100000, "cytoband": "q12.1", "stain": "gpos75"}, + {"referenceName": "chr11", "start": 60100000, "end": 61900000, "cytoband": "q12.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 61900000, "end": 63600000, "cytoband": "q12.3", "stain": "gpos25"}, + {"referenceName": "chr11", "start": 63600000, "end": 66100000, "cytoband": "q13.1", "stain": "gneg"}, + {"referenceName": "chr11", "start": 66100000, "end": 68700000, "cytoband": "q13.2", "stain": "gpos25"}, + {"referenceName": "chr11", "start": 68700000, "end": 70500000, "cytoband": "q13.3", "stain": "gneg"}, + {"referenceName": "chr11", "start": 70500000, "end": 75500000, "cytoband": "q13.4", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 75500000, "end": 77400000, "cytoband": "q13.5", "stain": "gneg"}, + {"referenceName": "chr11", "start": 77400000, "end": 85900000, "cytoband": "q14.1", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 85900000, "end": 88600000, "cytoband": "q14.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 88600000, "end": 93000000, "cytoband": "q14.3", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 93000000, "end": 97400000, "cytoband": "q21", "stain": "gneg"}, + {"referenceName": "chr11", "start": 97400000, "end": 102300000, "cytoband": "q22.1", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 102300000, "end": 103000000, "cytoband": "q22.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 103000000, "end": 110600000, "cytoband": "q22.3", "stain": "gpos100"}, + {"referenceName": "chr11", "start": 110600000, "end": 112700000, "cytoband": "q23.1", "stain": "gneg"}, + {"referenceName": "chr11", "start": 112700000, "end": 114600000, "cytoband": "q23.2", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 114600000, "end": 121300000, "cytoband": "q23.3", "stain": "gneg"}, + {"referenceName": "chr11", "start": 121300000, "end": 124000000, "cytoband": "q24.1", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 124000000, "end": 127900000, "cytoband": "q24.2", "stain": "gneg"}, + {"referenceName": "chr11", "start": 127900000, "end": 130900000, "cytoband": "q24.3", "stain": "gpos50"}, + {"referenceName": "chr11", "start": 130900000, "end": 135086622, "cytoband": "q25", "stain": "gneg"} + ], + "chr12": [ + {"referenceName": "chr12", "start": 0, "end": 3200000, "cytoband": "p13.33", "stain": "gneg"}, + {"referenceName": "chr12", "start": 3200000, "end": 5300000, "cytoband": "p13.32", "stain": "gpos25"}, + {"referenceName": "chr12", "start": 5300000, "end": 10000000, "cytoband": "p13.31", "stain": "gneg"}, + {"referenceName": "chr12", "start": 10000000, "end": 12600000, "cytoband": "p13.2", "stain": "gpos75"}, + {"referenceName": "chr12", "start": 12600000, "end": 14600000, "cytoband": "p13.1", "stain": "gneg"}, + {"referenceName": "chr12", "start": 14600000, "end": 19800000, "cytoband": "p12.3", "stain": "gpos100"}, + {"referenceName": "chr12", "start": 19800000, "end": 21100000, "cytoband": "p12.2", "stain": "gneg"}, + {"referenceName": "chr12", "start": 21100000, "end": 26300000, "cytoband": "p12.1", "stain": "gpos100"}, + {"referenceName": "chr12", "start": 26300000, "end": 27600000, "cytoband": "p11.23", "stain": "gneg"}, + {"referenceName": "chr12", "start": 27600000, "end": 30500000, "cytoband": "p11.22", "stain": "gpos50"}, + {"referenceName": "chr12", "start": 30500000, "end": 33200000, "cytoband": "p11.21", "stain": "gneg"}, + {"referenceName": "chr12", "start": 33200000, "end": 35500000, "cytoband": "p11.1", "stain": "acen"}, + {"referenceName": "chr12", "start": 35500000, "end": 37800000, "cytoband": "q11", "stain": "acen"}, + {"referenceName": "chr12", "start": 37800000, "end": 46000000, "cytoband": "q12", "stain": "gpos100"}, + {"referenceName": "chr12", "start": 46000000, "end": 48700000, "cytoband": "q13.11", "stain": "gneg"}, + {"referenceName": "chr12", "start": 48700000, "end": 51100000, "cytoband": "q13.12", "stain": "gpos25"}, + {"referenceName": "chr12", "start": 51100000, "end": 54500000, "cytoband": "q13.13", "stain": "gneg"}, + {"referenceName": "chr12", "start": 54500000, "end": 56200000, "cytoband": "q13.2", "stain": "gpos25"}, + {"referenceName": "chr12", "start": 56200000, "end": 57700000, "cytoband": "q13.3", "stain": "gneg"}, + {"referenceName": "chr12", "start": 57700000, "end": 62700000, "cytoband": "q14.1", "stain": "gpos75"}, + {"referenceName": "chr12", "start": 62700000, "end": 64700000, "cytoband": "q14.2", "stain": "gneg"}, + {"referenceName": "chr12", "start": 64700000, "end": 67300000, "cytoband": "q14.3", "stain": "gpos50"}, + {"referenceName": "chr12", "start": 67300000, "end": 71100000, "cytoband": "q15", "stain": "gneg"}, + {"referenceName": "chr12", "start": 71100000, "end": 75300000, "cytoband": "q21.1", "stain": "gpos75"}, + {"referenceName": "chr12", "start": 75300000, "end": 79900000, "cytoband": "q21.2", "stain": "gneg"}, + {"referenceName": "chr12", "start": 79900000, "end": 86300000, "cytoband": "q21.31", "stain": "gpos100"}, + {"referenceName": "chr12", "start": 86300000, "end": 88600000, "cytoband": "q21.32", "stain": "gneg"}, + 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"chr9", "start": 87800000, "end": 89200000, "cytoband": "q22.1", "stain": "gneg"}, + {"referenceName": "chr9", "start": 89200000, "end": 91200000, "cytoband": "q22.2", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 91200000, "end": 93900000, "cytoband": "q22.31", "stain": "gneg"}, + {"referenceName": "chr9", "start": 93900000, "end": 96500000, "cytoband": "q22.32", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 96500000, "end": 99800000, "cytoband": "q22.33", "stain": "gneg"}, + {"referenceName": "chr9", "start": 99800000, "end": 105400000, "cytoband": "q31.1", "stain": "gpos100"}, + {"referenceName": "chr9", "start": 105400000, "end": 108500000, "cytoband": "q31.2", "stain": "gneg"}, + {"referenceName": "chr9", "start": 108500000, "end": 112100000, "cytoband": "q31.3", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 112100000, "end": 114900000, "cytoband": "q32", "stain": "gneg"}, + {"referenceName": "chr9", "start": 114900000, "end": 119800000, "cytoband": "q33.1", "stain": "gpos75"}, + {"referenceName": "chr9", "start": 119800000, "end": 123100000, "cytoband": "q33.2", "stain": "gneg"}, + {"referenceName": "chr9", "start": 123100000, "end": 127500000, "cytoband": "q33.3", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 127500000, "end": 130600000, "cytoband": "q34.11", "stain": "gneg"}, + {"referenceName": "chr9", "start": 130600000, "end": 131100000, "cytoband": "q34.12", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 131100000, "end": 133100000, "cytoband": "q34.13", "stain": "gneg"}, + {"referenceName": "chr9", "start": 133100000, "end": 134500000, "cytoband": "q34.2", "stain": "gpos25"}, + {"referenceName": "chr9", "start": 134500000, "end": 138394717, "cytoband": "q34.3", "stain": "gneg"} + ], + "chrX": [ + {"referenceName": "chrX", "start": 0, "end": 4400000, "cytoband": "p22.33", "stain": "gneg"}, + {"referenceName": "chrX", "start": 4400000, "end": 6100000, "cytoband": "p22.32", "stain": "gpos50"}, + {"referenceName": "chrX", "start": 6100000, "end": 9600000, "cytoband": "p22.31", "stain": "gneg"}, + {"referenceName": "chrX", "start": 9600000, "end": 17400000, "cytoband": "p22.2", "stain": "gpos50"}, + {"referenceName": "chrX", "start": 17400000, "end": 19200000, "cytoband": "p22.13", "stain": "gneg"}, + {"referenceName": "chrX", "start": 19200000, "end": 21900000, "cytoband": "p22.12", "stain": "gpos50"}, + {"referenceName": "chrX", "start": 21900000, "end": 24900000, "cytoband": "p22.11", "stain": "gneg"}, + {"referenceName": "chrX", "start": 24900000, "end": 29300000, "cytoband": "p21.3", "stain": "gpos100"}, + {"referenceName": "chrX", "start": 29300000, "end": 31500000, "cytoband": "p21.2", "stain": "gneg"}, + {"referenceName": "chrX", "start": 31500000, "end": 37800000, "cytoband": "p21.1", "stain": "gpos100"}, + {"referenceName": "chrX", "start": 37800000, "end": 42500000, "cytoband": "p11.4", "stain": "gneg"}, + {"referenceName": "chrX", "start": 42500000, "end": 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{"referenceName": "chrX", "start": 74700000, "end": 76800000, "cytoband": "q13.3", "stain": "gneg"}, + {"referenceName": "chrX", "start": 76800000, "end": 85400000, "cytoband": "q21.1", "stain": "gpos100"}, + {"referenceName": "chrX", "start": 85400000, "end": 87000000, "cytoband": "q21.2", "stain": "gneg"}, + {"referenceName": "chrX", "start": 87000000, "end": 92700000, "cytoband": "q21.31", "stain": "gpos100"}, + {"referenceName": "chrX", "start": 92700000, "end": 94300000, "cytoband": "q21.32", "stain": "gneg"}, + {"referenceName": "chrX", "start": 94300000, "end": 99100000, "cytoband": "q21.33", "stain": "gpos75"}, + {"referenceName": "chrX", "start": 99100000, "end": 103300000, "cytoband": "q22.1", "stain": "gneg"}, + {"referenceName": "chrX", "start": 103300000, "end": 104500000, "cytoband": "q22.2", "stain": "gpos50"}, + {"referenceName": "chrX", "start": 104500000, "end": 109400000, "cytoband": "q22.3", "stain": "gneg"}, + {"referenceName": "chrX", "start": 109400000, "end": 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], + "chrY": [ + {"referenceName": "chrY", "start": 0, "end": 300000, "cytoband": "p11.32", "stain": "gneg"}, + {"referenceName": "chrY", "start": 300000, "end": 600000, "cytoband": "p11.31", "stain": "gpos50"}, + {"referenceName": "chrY", "start": 600000, "end": 10300000, "cytoband": "p11.2", "stain": "gneg"}, + {"referenceName": "chrY", "start": 10300000, "end": 10400000, "cytoband": "p11.1", "stain": "acen"}, + {"referenceName": "chrY", "start": 10400000, "end": 10600000, "cytoband": "q11.1", "stain": "acen"}, + {"referenceName": "chrY", "start": 10600000, "end": 12400000, "cytoband": "q11.21", "stain": "gneg"}, + {"referenceName": "chrY", "start": 12400000, "end": 17100000, "cytoband": "q11.221", "stain": "gpos50"}, + {"referenceName": "chrY", "start": 17100000, "end": 19600000, "cytoband": "q11.222", "stain": "gneg"}, + {"referenceName": "chrY", "start": 19600000, "end": 23800000, "cytoband": "q11.223", "stain": "gpos50"}, + {"referenceName": "chrY", "start": 23800000, "end": 26600000, "cytoband": "q11.23", "stain": "gneg"}, + {"referenceName": "chrY", "start": 26600000, "end": 57227415, "cytoband": "q12", "stain": "gvar"} + ] + } +} diff --git a/src/components/SubsetsHierarchyLoader.js b/src/components/SubsetsHierarchyLoader.js new file mode 100644 index 00000000..e6175743 --- /dev/null +++ b/src/components/SubsetsHierarchyLoader.js @@ -0,0 +1,42 @@ +import { useFilterTreesByType } from "../hooks/api" +import { WithData } from "./Loader" +import React from "react" +import { keyBy } from "lodash" +import { buildTree, TreePanel } from "./classificationTree/TreePanel" + +export default function SubsetsHierarchyLoader({ collationTypes, datasetIds, defaultTreeDepth }) { + const collationsHierarchyReply = useFilterTreesByType({ + datasetIds, + collationTypes + }) + + return ( + ( + + )} + /> + ) +} + +function SubsetsResponse({ collationsHierarchies, datasetIds, defaultTreeDepth }) { + const subsetById = keyBy(collationsHierarchies, "id") + const { tree, size } = buildTree(collationsHierarchies, subsetById) + + return ( + + ) +} diff --git a/src/components/SubsetsLoader.js b/src/components/SubsetsLoader.js index 227f23f6..d323e485 100644 --- a/src/components/SubsetsLoader.js +++ b/src/components/SubsetsLoader.js @@ -1,74 +1,111 @@ -import { useCollationsByType, useCollationsById } from "../hooks/api" -import { WithData } from "./Loader" -import React from "react" -import { keyBy, merge } from "lodash" +import { + SITE_DEFAULTS, + useServiceItemDelivery, + sampleSearchPageFiltersLink, + NoResultsHelp +} from "../hooks/api" +import { Loader } from "./Loader" import { SubsetHistogram } from "./SVGloaders" -import { buildTree, buildTreeForDetails, TreePanel } from "./classificationTree/TreePanel" +// import { ShowJSON } from "./RawData" +import { ExternalLink, InternalLink } from "./helpersShared/linkHelpers" -export default function SubsetsLoader({ collationTypes, datasetIds, defaultTreeDepth }) { - const bioSubsetsHierarchiesReply = useCollationsByType({ - datasetIds, - method: "paths", - collationTypes - }) +const service = "collations" - const allBioSubsetsReply = useCollationsById({ +export function SubsetLoader({ id, datasetIds }) { + const { data, error, isLoading } = useServiceItemDelivery( + id, + service, datasetIds - }) - + ) return ( - ( - ( - - )} - /> + + {data && ( + )} - /> + ) } -function SubsetsResponse({ bioSubsetsHierarchies, allBioSubsets, datasetIds, defaultTreeDepth }) { - const isDetailPage = bioSubsetsHierarchies.length === 1 - // We merge both subsets from hierarchies and subsets from allSubsets. - // This is because some children in the bioSubsetsHierarchies don't have labels or sample count information. - const subsetById = merge(keyBy(bioSubsetsHierarchies, "id"), allBioSubsets) - const { tree, size } = isDetailPage - ? buildTreeForDetails(bioSubsetsHierarchies, subsetById) - : buildTree(bioSubsetsHierarchies, subsetById) +function SubsetResponse({ response, datasetIds }) { + if (!response.response.results[0]) { + return NoResultsHelp("subsetdetails") + } + return +} +function Subset({ subset, datasetIds }) { + + const filters = subset.id + const sampleFilterScope = "allTermsFilters" + return ( +
+

+ {subset.label} ({subset.id}) +

+ + {subset.type && ( <> - {isDetailPage && ( -
- Subset Type +
    +
  • + {subset.type}{" "} + -
- )} - + + + )} + +
Sample Counts
+
    +
  • {subset.count} samples
    • +
  • {subset.codeMatches} direct {subset.id} code matches
    • + {subset.cnvAnalyses && ( +
  • {subset.cnvAnalyses} CNV analyses
    • + )} + {subset.frequencymapCnvAnalyses && ( +
  • + {subset.frequencymapCnvAnalyses} {" CNV analyses used in frequency calculations"} +
    • + )} +
+
CNV Histogram
+
+ +
+ +
+ +
+

+ Download CNV frequency data for genomic 1Mb bins. +

+ +
+ +
+

+ Select samples through the search form, e.g. by querying for specific + genomic variants or phenotypes. +

+ + {/**/} + +
) } diff --git a/src/components/classificationTree/SubsetsTree.js b/src/components/classificationTree/SubsetsTree.js index c0c1ee92..fdc7f9ab 100644 --- a/src/components/classificationTree/SubsetsTree.js +++ b/src/components/classificationTree/SubsetsTree.js @@ -6,10 +6,10 @@ import { FaAngleDown, FaAngleRight } from "react-icons/fa" import Tippy from "@tippyjs/react" import { FixedSizeTree as VTree } from "react-vtree" import useDebounce from "../../hooks/debounce" -import { min } from "lodash" +// import { min } from "lodash" import { filterNode } from "./tree" -const ROW_HEIGHT = 30 +const ROW_HEIGHT = 28 export function SubsetsTree({ tree, @@ -18,8 +18,7 @@ export function SubsetsTree({ datasetIds, checkedSubsets, checkboxClicked, - sampleFilterScope, - defaultTreeDepth + sampleFilterScope }) { const { searchInput, @@ -27,7 +26,7 @@ export function SubsetsTree({ filteredTree, debouncedSearchInput } = useFilterTree(tree) - const [levelSelector, setLevelSelector] = useState(defaultTreeDepth) + const [levelSelector, setLevelSelector] = useState(3) // console.log(filteredTree) @@ -43,7 +42,7 @@ export function SubsetsTree({
setSearchInput(e.target.value)} /> @@ -87,7 +86,7 @@ export function SubsetsTree({ )} {checkedSubsets.map((subset) => (
  • - {subset.label} ({subset.count}) + {subset.label ? subset.label : subset.id} ({subset.count})
    • ))} @@ -166,7 +165,6 @@ function Tree({ // Node component receives all the data we created in the `treeWalker` + // internal openness state (`isOpen`), function to change internal openness // state (`toggle`) and `style` parameter that should be added to the root div. - function Node({ data: { isLeaf, subsetId, subset, nestingLevel }, treeData: { @@ -180,9 +178,9 @@ function Node({ style, setOpen }) { - const isSearchPossible = subset && canSearch(subset) + const isSearchPossible = true // subset && canSearch(subset) const even = index % 2 === 0 - const detailsPage = subsetId.match("cellosaurus") ? "cellline" : "subset" + const detailsPage = "subset" return (
    )} - + <> {(subset?.label && ( - {subset.label} + + {subset.label}: {subsetId} + + )) + || + + + {subsetId}: {subsetId} - )) ||  } - + } + - : {subsetId} {isSearchPossible ? ( hp.depth)) - : 999 - return minDepth >= 2 -} +// function canSearch(subset) { +// // Only necessary for NCIT +// if (!subset.id.includes("NCIT:")) return true +// const minDepth = subset.hierarchyPaths +// ? min(subset.hierarchyPaths?.map((hp) => hp.depth)) +// : 999 +// return minDepth >= 2 +// } diff --git a/src/components/classificationTree/TreePanel.js b/src/components/classificationTree/TreePanel.js index 243ba05a..292eacd6 100644 --- a/src/components/classificationTree/TreePanel.js +++ b/src/components/classificationTree/TreePanel.js @@ -1,7 +1,7 @@ import React, { useState } from "react" import { SubsetsTree } from "./SubsetsTree" import { sortBy } from "lodash" -import { getOrMakeChild, getOrMakeNode } from "./tree" +import { getOrMakeNode } from "./tree" export function TreePanel({ tree, @@ -9,7 +9,6 @@ export function TreePanel({ subsetById, datasetIds, sampleFilterScope, - defaultTreeDepth, isFlat }) { const [checkedIds, setCheckedIds] = useState({}) @@ -34,7 +33,6 @@ export function TreePanel({ checkedSubsets={checkedSubsets} checkboxClicked={checkboxClicked} sampleFilterScope={sampleFilterScope} - defaultTreeDepth={defaultTreeDepth} isFlat={isFlat} />
    @@ -63,23 +61,5 @@ export function buildTree(response, subsetById) { return { tree, size } } -export function buildTreeForDetails(response, subsetById) { - const rootSubset = response[0] - const tree = { id: "root", children: [], path: ["root"] } - let size = 1 - const rootNode = getOrMakeChild(tree, rootSubset.id) - rootNode.subset = rootSubset - const childTerms = rootSubset.childTerms - childTerms.forEach((c) => { - // some subsets have themselves in the children list - if (rootSubset.code !== c) { - const node = getOrMakeChild(rootNode, c, randomStringGenerator) - node.subset = subsetById[node.id] - size++ - } - }) - return { tree, size } -} - // We generate random UID because a tree contains several nodes with the same ids const randomStringGenerator = () => Math.random().toString(36).substring(2, 15) diff --git a/src/components/searchForm/BiosamplesSearchForm.js b/src/components/searchForm/BiosamplesSearchForm.js index 358913c6..a1163a49 100644 --- a/src/components/searchForm/BiosamplesSearchForm.js +++ b/src/components/searchForm/BiosamplesSearchForm.js @@ -720,7 +720,6 @@ function useFilteringTerms(watchForm, ct) { const datasetIds = watchForm("datasetIds") return useFiltersByType({ datasetIds, - method: "counts", collationTypes: ct }) } diff --git a/src/components/searchForm/BiosamplesSearchPanel.js b/src/components/searchForm/BiosamplesSearchPanel.js index b4e12933..c05b96bd 100644 --- a/src/components/searchForm/BiosamplesSearchPanel.js +++ b/src/components/searchForm/BiosamplesSearchPanel.js @@ -17,7 +17,6 @@ export default function BiosamplesSearchPanel({ parametersConfig, beaconQueryTypes, requestTypeExamples, - cytoBands, collapsed }) { const [query, setQuery] = useState(null) // actual valid query @@ -67,7 +66,6 @@ export default function BiosamplesSearchPanel({ } > {shouldDisplay && ( )} + {shouldDisplayMate && ( + + )}
    ) } diff --git a/src/components/searchResults/VariantsDataTable.js b/src/components/searchResults/VariantsDataTable.js index 5d2ce9bc..91193d9a 100644 --- a/src/components/searchResults/VariantsDataTable.js +++ b/src/components/searchResults/VariantsDataTable.js @@ -19,8 +19,8 @@ export default function VariantsDataTable({ apiReply, datasetId }) { accessor: "variation.variantLevelData.clinicalInterpretations[0].clinicalRelevance" }, { - Header: "Variant Effect", - accessor: "variation.molecularAttributes.molecularEffects[0].label" + Header: "Variant type", + accessor: "variation.type" }, { Header: TooltipHeader( @@ -31,13 +31,21 @@ export default function VariantsDataTable({ apiReply, datasetId }) { Cell: ({ value: caseLevelData }) => caseLevelData.map((cld, i) => ( )) } @@ -50,7 +58,9 @@ export default function VariantsDataTable({ apiReply, datasetId }) { apiReply={apiReply} render={(response) => (
    - + {response.response?.resultSets[0]?.results && ( +
    + )} )} /> diff --git a/src/hooks/api.js b/src/hooks/api.js index af05a6c8..0899d4c2 100644 --- a/src/hooks/api.js +++ b/src/hooks/api.js @@ -284,7 +284,7 @@ export function useServiceItemDelivery(id, entity, datasetIds) { } export function getServiceItemUrl(id, collection, datasetIds) { - return `${SITE_DEFAULTS.API_PATH}services/${collection}?id=${id}&datasetIds=${datasetIds}` + return `${SITE_DEFAULTS.API_PATH}services/${collection}/${id}?datasetIds=${datasetIds}` } export function NoResultsHelp(id, entity) { @@ -361,8 +361,14 @@ export function useCollations({ datasetIds, method, filters }) { return useProgenetixApi(url) } -export function useFiltersByType({ datasetIds, method, collationTypes }) { - const url = `${SITE_DEFAULTS.API_PATH}beacon/filtering_terms/?datasetIds=${datasetIds}&method=${method}&collationTypes=${collationTypes}` +export function useFiltersByType({ datasetIds, collationTypes }) { + // TODO: construct URL w/o optional parameters if empty + const url = `${SITE_DEFAULTS.API_PATH}beacon/datasets/${datasetIds}/filtering_terms/?collationTypes=${collationTypes}` + return useProgenetixApi(url) +} + +export function useFilterTreesByType({ datasetIds, collationTypes }) { + const url = `${SITE_DEFAULTS.API_PATH}beacon/datasets/${datasetIds}/filtering_terms?collationTypes=${collationTypes}&mode=termTree` return useProgenetixApi(url) } diff --git a/src/modules/data-pages/NCIT_SubsetsPage.js b/src/modules/data-pages/NCIT_SubsetsPage.js deleted file mode 100644 index 81095af0..00000000 --- a/src/modules/data-pages/NCIT_SubsetsPage.js +++ /dev/null @@ -1,28 +0,0 @@ -import React from "react" -import { Layout } from "../../components/Layout" -import { SITE_DEFAULTS } from "../../hooks/api" -import SubsetsLoader from "../../components/SubsetsLoader" - -const INITIAL_TREE_LEVEL = 2 - -export default function NCIT_SubsetsPage() { - return ( - -
    -

    - The cancer samples in Progenetix are mapped to several classification - systems. For each of the classes, aggregated date is available by - clicking the code. Additionally, a selection of the corresponding - samples can be initiated by clicking the sample number or selecting - one or more classes through the checkboxes. -

    -

    - Sample selection follows a hierarchical system in which samples - matching the child terms of a selected class are included in the - response. -

    -
    - -     - ) -} diff --git a/src/modules/data-pages/celllines_dataPage.js b/src/modules/data-pages/celllines_dataPage.js deleted file mode 100644 index f7a19224..00000000 --- a/src/modules/data-pages/celllines_dataPage.js +++ /dev/null @@ -1,20 +0,0 @@ -import React from "react" -import { Layout } from "../../components/Layout" -import parametersConfig from "../../config/beaconSearchParameters.yaml" -import beaconQueryTypes from "../../config/beaconQueryTypes.yaml" -import requestTypeExamples from "../../config/celllines_searchExamples.yaml" -import BiosamplesSearchPanel from "../../components/searchForm/BiosamplesSearchPanel" - -export default function cellLines_dataPage({ cytoBands }) { - return ( - - - - ) -} diff --git a/src/modules/data-pages/cellosaurus_SubsetsPage.js b/src/modules/data-pages/cellosaurus_SubsetsPage.js deleted file mode 100644 index f4f6f9e1..00000000 --- a/src/modules/data-pages/cellosaurus_SubsetsPage.js +++ /dev/null @@ -1,33 +0,0 @@ -import React from "react" -import { Layout } from "../../components/Layout" -import { SITE_DEFAULTS } from "../../hooks/api" -import SubsetsLoader from "../../components/SubsetsLoader" -import Panel from "../../components/Panel" - -const INITIAL_TREE_LEVEL = 0 - -export default function cellosaurus_SubsetsPage() { - return ( - -
    -

    - The cancer cell lines in cancercelllines.org are labeled - by their Cellosaurus IDs as the primary identifier. Cell lines are - arranged hierarchially: Daughter cell lines are displayed below the - primary cell lines they were derived from; i.e. HeLa S3 (CVCL_0058) - is shown as a daughter cell line of HeLa (CVCL_0030) and so forth. -

    -

    - Sample selection follows a hierarchical system in which samples - matching the child terms of a selected class are included in the - response. This means that one can retrieve all instances and daughter - cell lines of a given cell line in a id-based search (i.e. searching for - HeLa will also return the daughter lines by default - but optionally). -

    -
    - - - -     - ) -} diff --git a/src/modules/data-pages/icdom_SubsetsPage.js b/src/modules/data-pages/icdom_SubsetsPage.js deleted file mode 100644 index 7f58a47f..00000000 --- a/src/modules/data-pages/icdom_SubsetsPage.js +++ /dev/null @@ -1,28 +0,0 @@ -import React from "react" -import { Layout } from "../../components/Layout" -import { SITE_DEFAULTS } from "../../hooks/api" -import SubsetsLoader from "../../components/SubsetsLoader" - -const INITIAL_TREE_LEVEL = 2 - -export default function icdom_SubsetsPage() { - return ( - -
    -

    - The cancer samples in Progenetix are mapped to several classification - systems. For each of the classes, aggregated date is available by - clicking the code. Additionally, a selection of the corresponding - samples can be initiated by clicking the sample number or selecting - one or more classes through the checkboxes. -

    -

    - Sample selection follows a hierarchical system in which samples - matching the child terms of a selected class are included in the - response. -

    -
    - -     - ) -} diff --git a/src/pages/biosamples.js b/src/pages/biosamples.js deleted file mode 100644 index c10c11e7..00000000 --- a/src/pages/biosamples.js +++ /dev/null @@ -1,12 +0,0 @@ -import Page from "../modules/data-pages/celllines_dataPage" -import { getCytoBands } from "../utils/genome" -export default Page - -// This function gets called at build time on server-side. -export const getStaticProps = async () => ({ - props: { - cytoBands: await getCytoBands() - } -}) - -// This page is an alias for search.js since /biosamples has been shared berfore... \ No newline at end of file diff --git a/src/pages/cellline.js b/src/pages/cellline.js index e84b8799..a015b152 100644 --- a/src/pages/cellline.js +++ b/src/pages/cellline.js @@ -1,2 +1,293 @@ -import Page from "../modules/details-pages/celllinePage" -export default Page +import React, { useEffect, useState } from "react" +import { + SITE_DEFAULTS, + useProgenetixApi, + sampleSearchPageFiltersLink, + NoResultsHelp +} from "../hooks/api" +import { Loader } from "../components/Loader" +import { Layout } from "../components/Layout" +import Panel from "../components/Panel" +import { AncestryData } from "../components/AncestryData" +import { LiteratureSearch } from "../components/LiteratureSearch" +// import { ShowJSON } from "../components/RawData" +import { SubsetHistogram } from "../components/SVGloaders" +import { ExternalLink, InternalLink } from "../components/helpersShared/linkHelpers" +import { withUrlQuery } from "../hooks/url-query" +import VariantsDataTable from "../components/searchResults/VariantsDataTable" + +const exampleId = "cellosaurus:CVCL_0023" +const searchPage = "filterSearch" + +const CellLineDetailsPage = withUrlQuery(({ urlQuery }) => { + var { id, datasetIds } = urlQuery + if (!datasetIds) { + datasetIds = SITE_DEFAULTS.DATASETID + } + const hasAllParams = id && datasetIds + const [plotGeneSymbols, setGeneSymbols] = useState(""); + const [plotCytoregionLabels, setCytoregionSymbols] = useState(""); + + const aURL = `${SITE_DEFAULTS.API_PATH}beacon/genomicVariations/?filters=${id}&datasetIds=${datasetIds}&variantType=SO:0001059&paginateResults=false` + const variantsReply = useProgenetixApi( aURL ) + + const iURL = `${SITE_DEFAULTS.API_PATH}beacon/individuals/?filters=${id}&datasetIds=${datasetIds}&limit=1` + var [individual, setIndividual] = useState([]); + useEffect(() => { + fetch( iURL ) + .then((response) => response.json()) + .then((data) => { + console.log(data.response.resultSets[0].results[0]); + setIndividual(data.response.resultSets[0].results[0]) + }) + .catch((err) => { + console.log(err.message); + }); + }, [setIndividual]); + + return ( + + {!hasAllParams ? ( + NoResultsHelp(exampleId, "subsetdetails") + ) : ( + <> + + + + + + + + + + +

    The graph shows the copy number gains (up, blue) and losses (down, orange) + as percentage of the cell line instances they were observed in. Off note, since + all instances arose from the same donor cell line one would expect all genomic + regions to be either 0 or 100 percent. Regions with diverging values are either + due to clonal divergence/progression and/or to experimental variability. +

    +
    + +
    +     + + + + + + + )} +     + ) +}) + +export default CellLineDetailsPage + +/*============================================================================*/ +/*============================================================================*/ +/*============================================================================*/ + +function ThisSubsetLoader({ id, individual, datasetIds }) { + + const sURL = `${SITE_DEFAULTS.API_PATH}services/collations/${id}?datasetIds=${datasetIds}` + + const { data, error, isLoading } = useProgenetixApi(sURL) + + return ( + + {data && ( + + )} + + ) +} + +/*============================================================================*/ + +function SubsetResponse({ id, response, individual, datasetIds }) { + if (!response.response?.results[0]) { + return NoResultsHelp(exampleId, "subsetdetails") + } + return +} + +/*============================================================================*/ + +function Subset({ id, subset, individual, datasetIds }) { + + const filters = id + const sampleFilterScope = "allTermsFilters" + const [showAll, setShowAll] = useState(false); + // console.log(individual); + // console.log(Object.keys(individual)); + + return ( + + +
    + +

    {subset.label} ({subset.id})

    + + {subset?.parentTerms?.length > 1 && ( + <> +
    Parental Cell Lines
    +
      + {subset.parentTerms + .map(pt => + ).reduce((prev, curr) => [prev, ' ⇒ ', curr])} +
    + + )} + + + {subset?.childTerms?.length > 1 && ( + <> +
    Derived Cell Lines
    +
      + {subset.childTerms.slice(0, showAll ? subset.childTerms.length : 5).map(pt => + + )} +
    + {subset.childTerms.length > 5 && ( + + + + )} + + )} + + +
    Donor Details
    + +
      + + {individual?.indexDisease?.diseaseCode && ( +
    • + Diagnosis{": "} + {individual.indexDisease.diseaseCode.id}{" ("} + {individual.indexDisease.diseaseCode?.label}{")"} +
      • + + )} + + {individual?.description && ( +
    • + Description{": "} + {individual.description} +
      • + )} + + {individual?.sex && ( +
    • + Genotypic Sex{": "} + {individual?.sex?.label} ({individual.sex.id}) +
      • + )} + + {individual?.indexDisease?.onset && ( +
    • + Age at Collection{": "} + {individual.indexDisease.onset.age} +
      • + )} + +
    + + {individual?.genomeAncestry && individual?.genomeAncestry?.length > 0 && ( + <> +
    Genomic Ancestry
    + + + )} + +
    Samples
    + +{/* + {individual.biosamples && individual.biosamples.length > 0 && + <> +
    Biosamples
    +
      + {individual.biosamples.map((bs, i) => ( +
    • + +
      • + ))} +
    + + } +*/} + +
      +
    • + {subset.count} samples ( + {subset.codeMatches} direct {subset.id} matches;{" "} + {subset.cnvAnalyses} CNV analyses) +
      • +
    • Select {subset.id} samples in the{" "} + {" "}Search Form + +
      • +
    + +
    More Information
    +
      +
    • + Cellosaurus{": "} +
      • +
    + + {/**/} + +
    + ) +} + +/*============================================================================*/ + + diff --git a/src/pages/index.js b/src/pages/index.js index 426f6726..517036eb 100644 --- a/src/pages/index.js +++ b/src/pages/index.js @@ -25,6 +25,8 @@ export default function Index({ subsetsResponse.response.results.filter((s) => s.cnvAnalyses > 1) ) + console.log(randomSubset) + return ( @@ -45,9 +47,11 @@ export default function Index({ of the overall more than 16‘000 cell lines, cancercelllines.org provides a unique entry point for the comparative analysis of genomic variants in cell lines as well as for the exploration of related publications. + +

    - - +*/}

    In cancercelllines.org genomic variation data collected from a variaty of external resources and from original data (re-) analyses has @@ -101,14 +105,14 @@ export default function Index({ } export const getStaticProps = async () => { - const subsetsReply = await tryFetch( - `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=cellosaurus,NCIT&deliveryKeys=count,id,label` - ) const cellosaurusCountReply = await tryFetch( - `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&method=codematches&collationTypes=cellosaurus` + `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=cellosaurus&requestedGranularity=count` ) const ncitCountReply = await tryFetch( - `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&method=codematches&collationTypes=NCIT` + `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=NCIT&includeDescendantTerms=false&requestedGranularity=count` + ) + const subsetsReply = await tryFetch( + `${SITE_DEFAULTS.PREFETCH_PATH}services/collations/?datasetIds=${SITE_DEFAULTS.DATASETID}&collationTypes=cellosaurus&deliveryKeys=count,id,label,cnv_analyses` ) return { props: { diff --git a/src/pages/search.js b/src/pages/search.js index 4bdc300e..1448c6a4 100644 --- a/src/pages/search.js +++ b/src/pages/search.js @@ -1,10 +1,19 @@ -import Page from "../modules/data-pages/celllines_dataPage" -import { getCytoBands } from "../utils/genome" -export default Page +import React from "react" +import { Layout } from "../components/Layout" +import BiosamplesSearchPanel from "../components/searchForm/BiosamplesSearchPanel" +import parametersConfig from "../config/beaconSearchParameters.yaml" +import beaconQueryTypes from "../config/beaconQueryTypes.yaml" +import requestTypeExamples from "../config/celllines_searchExamples.yaml" -// This function gets called at build time on server-side. -export const getStaticProps = async () => ({ - props: { - cytoBands: await getCytoBands() - } -}) +export default function Page() { + return ( + + + + ) +} diff --git a/src/pages/subsets/NCIT-subsets.js b/src/pages/subsets/NCIT-subsets.js index d6e573a6..abef61d0 100644 --- a/src/pages/subsets/NCIT-subsets.js +++ b/src/pages/subsets/NCIT-subsets.js @@ -1,2 +1,26 @@ -import Page from "../../modules/data-pages/NCIT_SubsetsPage" -export default Page +import React from "react" +import { Layout } from "../../components/Layout" +import SubsetsHierarchyLoader from "../../components/SubsetsHierarchyLoader" +import { SITE_DEFAULTS } from "../../hooks/api" + +export default function ncit_SubsetsPage() { + return ( + +

    +

    + The cancer samples in Progenetix are mapped to several classification + systems. For each of the classes, aggregated date is available by + clicking the code. Additionally, a selection of the corresponding + samples can be initiated by clicking the sample number or selecting + one or more classes through the checkboxes. +

    +

    + Sample selection follows a hierarchical system in which samples + matching the child terms of a selected class are included in the + response. +

    +
    + +     + ) +} diff --git a/src/pages/subsets/cellosaurus-subsets.js b/src/pages/subsets/cellosaurus-subsets.js index e3ad2caf..8f917439 100644 --- a/src/pages/subsets/cellosaurus-subsets.js +++ b/src/pages/subsets/cellosaurus-subsets.js @@ -1,2 +1,28 @@ -import Page from "../../modules/data-pages/cellosaurus_SubsetsPage" -export default Page +import React from "react" +import { Layout } from "../../components/Layout" +import SubsetsHierarchyLoader from "../../components/SubsetsHierarchyLoader" +import { SITE_DEFAULTS } from "../../hooks/api" + +export default function cellosaurus_SubsetsPage() { + return ( + +
    +

    + The cancer cell lines in cancercelllines.org are labeled + by their Cellosaurus IDs as the primary identifier. Cell lines are + arranged hierarchially: Daughter cell lines are displayed below the + primary cell lines they were derived from; i.e. HeLa S3 (CVCL_0058) + is shown as a daughter cell line of HeLa (CVCL_0030) and so forth. +

    +

    + Sample selection follows a hierarchical system in which samples + matching the child terms of a selected class are included in the + response. This means that one can retrieve all instances and daughter + cell lines of a given cell line in a id-based search (i.e. searching for + HeLa will also return the daughter lines by default - but optionally). +

    +
    + +     + ) +} diff --git a/src/pages/subsets/icdom-subsets.js b/src/pages/subsets/icdom-subsets.js index 244813b9..5816115d 100644 --- a/src/pages/subsets/icdom-subsets.js +++ b/src/pages/subsets/icdom-subsets.js @@ -1,2 +1,26 @@ -import Page from "../../modules/data-pages/icdom_SubsetsPage" -export default Page +import React from "react" +import { Layout } from "../../components/Layout" +import SubsetsHierarchyLoader from "../../components/SubsetsHierarchyLoader" +import { SITE_DEFAULTS } from "../../hooks/api" + +export default function icdom_SubsetsPage() { + return ( + +
    +

    + The cancer samples in Progenetix are mapped to several classification + systems. For each of the classes, aggregated date is available by + clicking the code. Additionally, a selection of the corresponding + samples can be initiated by clicking the sample number or selecting + one or more classes through the checkboxes. +

    +

    + Sample selection follows a hierarchical system in which samples + matching the child terms of a selected class are included in the + response. +

    +
    + +     + ) +}