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@@ -1,5 +1,5 @@
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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@@ -1,5 +1,5 @@
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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@@ -1,6 +1,6 @@
<%
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<%
/*
* Copyright (c) 2020 LabKey Corporation
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT "Physical Exam".ParticipantID, ROUND(AVG("Physical Exam".Temp_C), 1) AS AverageTemp,
FROM "Physical Exam"
GROUP BY "Physical Exam".ParticipantID
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT COUNT(Demographics.ParticipantId) AS "Count",
Demographics.Gender,
Demographics.Country,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT Demographics.ParticipantId,
Demographics.date,
Demographics.StartDate,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT ELISpotAssay.ParticipantId,
ELISpotAssay.SampleDescription,
ELISpotAssay.SpecimenID,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT "Physical Exam".ParticipantId,
"Physical Exam".SequenceNum,
"Physical Exam".Date,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT "Physical Exam + AverageTemp".ParticipantId,
"Physical Exam + AverageTemp".SequenceNum,
"Physical Exam + AverageTemp".Date,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT "Physical Exam".ParticipantId,
"Physical Exam".SequenceNum,
"Physical Exam".Date,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
# Caveats for these plots:
# - Y Axis. The left-most y axis insists on having the largest maximum.
# --- In the first plot, Viral Load has the largest max (and thus is
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
library(Cairo);
Cairo(file="${imgout:labkeyl_cairo.png}", type="png");
options(echo=TRUE);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
names(labkey.data)

library(Cairo);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
names(labkey.data)

library(Cairo);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
library(Cairo);
Cairo(file="${imgout:labkeyl_cairo.png}", type="png");
options(echo=TRUE);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 LabKey Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
##
library(Cairo);
data_means <- aggregate(labkey.data, list(ParticipantID =
labkey.data$participantid), mean, na.rm = TRUE);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
library(lattice);
png(filename="${imgout:a}", width=900);
plot.new();
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 LabKey Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
##
library(Cairo);
Cairo(file="${imgout:diastol_v_systol_figure.png}", type="png");
plot(labkey.data$diastolicbloodpressure, labkey.data$systolicbloodpressure,
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 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.
##
data_means <- aggregate(labkey.data, list(ParticipantID =
labkey.data$participantid), mean, na.rm = TRUE);
library(Cairo);
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Original file line number Diff line number Diff line change
@@ -1,3 +1,18 @@
##
# Copyright (c) 2020-2026 LabKey Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
##
# This sample code returns the query data in tab-separated values format, which LabKey then
# renders as HTML. Replace this code with your R script. See the Help tab for more details.
write.table(labkey.data, file = "${tsvout:tsvfile}", sep = "\t", qmethod = "double", col.names=NA)
Original file line number Diff line number Diff line change
@@ -1 +1,6 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT * FROM AssayList
2 changes: 1 addition & 1 deletion data/api/domainTest.js
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2011-2019 LabKey Corporation
* Copyright (c) 2011-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/COMP.sql
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@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
A.Name AS First,
B.Name AS Second,
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/Comparison.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
C.First, C.Second,
C.FirstRowId, C.SecondRowId,
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/DeviationFromMean.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT Single.RowId,
MAX(Single.FCSFile) AS FCSFile,
COUNT(Mean.RowId) AS NumberAveraged,
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/DeviationFromMean2.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT
Single.RowId,
Single.FCSFile,
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/PassFail.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT Min(D.Key) AS Key,
CASE WHEN (Count(D.LO_CD4) = 0 AND
COUNT(D.LO_CD8) = 0 AND
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5 changes: 5 additions & 0 deletions data/flow/flowjoquery/query/PassFailDetails.sql
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
/*
* Copyright (c) 2020-2026 LabKey Corporation
*
* Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
*/
SELECT B.RowId AS FCSAnalysis,
B.Stim,
B.CD4_Count,
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15 changes: 15 additions & 0 deletions data/pgrestore/cleanPgDump.sh
Original file line number Diff line number Diff line change
@@ -1,5 +1,20 @@
#!/usr/bin/env bash

#
# Copyright (c) 2023-2026 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.
#
set -eu

export PGHOST=${PGHOST:-localhost}
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2 changes: 1 addition & 1 deletion data/qc/assayTransformError.R
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
##
# Copyright (c) 2015-2019 LabKey Corporation
# Copyright (c) 2020-2026 LabKey Corporation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
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