From fd8c3cc0198ed63ab7527d3601cbcda481ee7c2d Mon Sep 17 00:00:00 2001 From: Kevin Krouse Date: Thu, 27 May 2021 01:46:55 +0800 Subject: [PATCH] merge AP053 and PassFail query updates into 21.3 (#66) * Ticket 42753: AP053 new query (#64) * 42776: pass-fail query for AP050 and AP053 (#65) --- hvtnFlow/plans/AP-053.tsv | 185 ++++++++++++++++++ .../queries/flow/AnalysisPlan052.sql | 2 +- .../queries/flow/AnalysisPlan053.sql | 69 +++++++ .../queries/flow/PassFailDetails.sql | 36 +++- 4 files changed, 285 insertions(+), 7 deletions(-) create mode 100644 hvtnFlow/plans/AP-053.tsv create mode 100644 hvtnFlow/resources/queries/flow/AnalysisPlan053.sql diff --git a/hvtnFlow/plans/AP-053.tsv b/hvtnFlow/plans/AP-053.tsv new file mode 100644 index 00000000..1bf9febd --- /dev/null +++ b/hvtnFlow/plans/AP-053.tsv @@ -0,0 +1,185 @@ +analysisPlanSort analysisPlanId description NAME1 STAT1 +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time:Count Time:Count +AP-053 53 27-color ICS for VIR 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53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/8+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/8+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/27+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/27+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/28+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/28+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/57+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/57+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/69+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/69+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/95+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/95+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/107a+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/107a+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/153+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/153+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/154+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/154+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/CCR7+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/CCR7+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/CM:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/CM:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/EM:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/EM:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/GzB+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/GzB+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNgIL2TNF153154MIP1BIL17aIL17F:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNgIL2TNF153154MIP1BIL17aIL17F:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_AND_154:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_AND_154:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_or_IL2:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_or_IL2:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_OR_IL2_AND_154:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_OR_IL2_AND_154:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_OR_IL2_OR_TNF_OR_154:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IFNg_OR_IL2_OR_TNF_OR_154:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IL2+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IL2+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IL17a_OR_IL17F+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/IL17a_OR_IL17F+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/Ki67+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/Ki67+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/MIP1B+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/MIP1B+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/N:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/N:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/NKG2C+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/NKG2C+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/RA+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/RA+:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/TD:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/TD:Count +AP-053 53 27-color ICS for VIR CMV vector vaccine studies Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/TNF+:Count Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3-/Total NK/TNF+:Count diff --git a/hvtnFlow/resources/queries/flow/AnalysisPlan052.sql b/hvtnFlow/resources/queries/flow/AnalysisPlan052.sql index 33e6f1c5..3f8cf5a8 100644 --- a/hvtnFlow/resources/queries/flow/AnalysisPlan052.sql +++ b/hvtnFlow/resources/queries/flow/AnalysisPlan052.sql @@ -65,5 +65,5 @@ A.RELIABLE, A.COMMENTS, A._well @hidden, A._fcsfile @hidden, A._sample @hidden -FROM AnalysisPlanTemplate_AP051 A +FROM AnalysisPlanTemplate A WHERE A.ANALYSIS_PLAN_ID = '52' diff --git a/hvtnFlow/resources/queries/flow/AnalysisPlan053.sql b/hvtnFlow/resources/queries/flow/AnalysisPlan053.sql new file mode 100644 index 00000000..cd3d364a --- /dev/null +++ b/hvtnFlow/resources/queries/flow/AnalysisPlan053.sql @@ -0,0 +1,69 @@ +/* + * Copyright (c) 2015 LabKey Corporation + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + */ +SELECT +--A._sample.property.NETWORK as NETWORK, +A.NETWORK, +A.PROTOCOL, +A.LABID, +A.ASSAY, +A.ASSAY_METHOD, +A.ASSAYID, +A._well.Run AS FLOWJO_XML_FILENAME, +A._well AS FCS_FILENAME, +A.SPECROLE, +A.PTID, +A.SID, +A.GUSPEC, +--A._sample.property.PTIDTYPE as PTIDTYPE, +A.PTIDTYPE, +A.SPECTYPE, +A.ISOLATION, +A.ADDITIVE, +A.CRYOSTAT, +A.CTRSAMPNAME, +A.STDY_DESC, +A.VISITNO, +A.DRAWDT, +A.TESTDT, +A.PLATE, +A.SAMP_ORD, +A.WELL_ID, +A.WELLROLE, +A.ANTIGEN, +NULL AS ANTIGENID, +A.NREPL, +A.ANALYSIS_PLAN_ID, +A.EXP_ASSAY_ID, +A.COLLECTCT, +A.SUBSET1 AS SUBSET, +A.SUBSET1_NUM AS SUBSET_NUM, + +A.NUMVIALS, +A.RUNGROUPID AS GUAVA_MUSE_ID, +A.VIABL1, +A.RECOVR1, +A.VIABL2, +A.RECOVR2, +A.METHOD AS COUNT_METHOD, +A.REPLACE, +A.MODDT, +A.RUNNUM, +A.RELIABLE, +A.COMMENTS, +A._well @hidden, A._fcsfile @hidden, A._sample @hidden + +FROM AnalysisPlanTemplate A +WHERE A.ANALYSIS_PLAN_ID = '53' diff --git a/hvtnFlow/resources/queries/flow/PassFailDetails.sql b/hvtnFlow/resources/queries/flow/PassFailDetails.sql index 0ee0bb70..ce3b7c88 100644 --- a/hvtnFlow/resources/queries/flow/PassFailDetails.sql +++ b/hvtnFlow/resources/queries/flow/PassFailDetails.sql @@ -63,7 +63,11 @@ FROM A.Statistic('S/Exclude/14-/Lv/L/3+/4+:Count'), A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/4+:Count'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+:Count') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+:Count'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/4+:Count'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/4+:Count') ) AS CD4_Count, COALESCE(A.Statistic('S/Lv/L/3+/8+:Count'), @@ -73,7 +77,11 @@ FROM A.Statistic('S/Exclude/14-/Lv/L/3+/8+:Count'), A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/8+:Count'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+:Count') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+:Count'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/8+:Count'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/8+:Count') ) AS CD8_Count, COALESCE(A.Statistic('S/Lv/L/3+/4+/IFNg\IL2:Count'), @@ -94,7 +102,11 @@ FROM A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/4+/IFNg_OR_IL2:Count'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+/IFNg_OR_IL2:Count') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+/IFNg_OR_IL2:Count'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/4+/IFNg_OR_IL2:Count'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/4+/IFNg_or_IL2:Count') ) AS CD4_Resp_Count, COALESCE(A.Statistic('S/Lv/L/3+/8+/IFNg\IL2:Count'), @@ -115,7 +127,11 @@ FROM A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/8+/IFNg_OR_IL2:Count'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+/IFNg_OR_IL2:Count') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+/IFNg_OR_IL2:Count'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/8+/IFNg_OR_IL2:Count'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/8+/IFNg_or_IL2:Count') ) AS CD8_Resp_Count, COALESCE(A.Statistic('S/Lv/L/3+/4+/IFNg\IL2:Freq_Of_Parent'), @@ -136,7 +152,11 @@ FROM A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/4+/IFNg_OR_IL2:Freq_Of_Parent'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+/IFNg_OR_IL2:Freq_Of_Parent') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/4+/IFNg_OR_IL2:Freq_Of_Parent'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/4+/IFNg_OR_IL2:Freq_Of_Parent'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/4+/IFNg_or_IL2:Freq_Of_Parent') ) AS CD4_Resp, COALESCE(A.Statistic('S/Lv/L/3+/8+/IFNg\IL2:Freq_Of_Parent'), @@ -157,7 +177,11 @@ FROM A.Statistic('S/Time/Lv/14-SSlo/Keeper/L/16-56-/8+/IFNg_OR_IL2:Freq_Of_Parent'), -- AP048 - A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+/IFNg_OR_IL2:Freq_Of_Parent') + A.Statistic('Time/S/K1/K2/K3/K4/K5/K6/Lv/14-/S/L/DR-/3+/3+excl16br/16-56-/8+/IFNg_OR_IL2:Freq_Of_Parent'), + -- AP050 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/S/L/19-/3+/3+excl 16br/56-16-/8+/IFNg_OR_IL2:Freq_Of_Parent'), + -- AP053 + A.Statistic('Time/Lv/K1/K2/K3/K4/K5/K6/K7/K8/14-/L/S/19-/3+/3+excl 16br/56-16-/8+/IFNg_or_IL2:Freq_Of_Parent') ) AS CD8_Resp, FROM FCSAnalyses AS A