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Merged
labkey-martyp merged 5 commits into from
Aug 3, 2026
Merged

Weights and species reports #13

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61dcc6d
Re-declare ehr wrapped lookup columns in NBRI query metadata
labkey-martyp Aug 2, 2026
a9bde65
Key NBRI weight ranges on species codes and load species lookups
labkey-martyp Aug 2, 2026
433b995
Use species codes in NBRI test subjects for weight range validation
labkey-martyp Aug 2, 2026
1dd9c36
Use species and gender codes in NBRI reference sample data
labkey-martyp Aug 2, 2026
0dc868e
Shorten re-declaration comments in NBRI query metadata
labkey-martyp Aug 2, 2026
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2 changes: 2 additions & 0 deletions nbri_ehr/resources/data/lookupsManifest.tsv
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Expand Up @@ -111,6 +111,8 @@ routes
sib_score
source
snomed
species
species_codes
skin_problem
status_codes
stool_score
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6 changes: 4 additions & 2 deletions nbri_ehr/resources/data/weight_ranges.tsv
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@@ -1,3 +1,5 @@
Species Min Weight Max Weight
Cynomolgus 0.0 20.0
Rhesus 0.0 35.0
CMO 0.04 2.2
MCY 0.2 16.0
MMU 0.2 30.0
MNE 0.2 30.0
19 changes: 19 additions & 0 deletions nbri_ehr/resources/queries/ehr_lookups/weight_ranges.query.xml
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@@ -0,0 +1,19 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="weight_ranges" tableDbType="TABLE">
<columns>
<column columnName="species">
<columnTitle>Species</columnTitle>
<fk>
<fkDbSchema>ehr_lookups</fkDbSchema>
<fkTable>species_codes</fkTable>
<fkColumnName>code</fkColumnName>
<fkDisplayColumnName>common_name</fkDisplayColumnName>
</fk>
</column>
</columns>
</table>
</tables>
</metadata>
</query>
12 changes: 12 additions & 0 deletions nbri_ehr/resources/queries/study/assignment.query.xml
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Expand Up @@ -21,6 +21,18 @@
<column columnName="taskid">
<isHidden>true</isHidden>
</column>
<!-- Re-declared from ehr/queries/study/assignment.query.xml; this file

@labkey-bpatel labkey-bpatel Aug 3, 2026

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what is re-declared, the "CoAssignments" column?
"this file" as in assignment.query.xml?

there are more such comments in .query.xml files below - wondering if they are necessary.

@labkey-martyp labkey-martyp Aug 3, 2026

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yeah I actually trimmed down those comments a lot. They were a lot longer. It's just redeclaring since this overrides the EHR version of this .query.xml. I'll shorten them further.

replaces ehr's rather than merging with it. See weight.query.xml. -->
<column columnName="CoAssignments" wrappedColumnName="lsid">
<columnTitle>CoAssignments</columnTitle>
<isHidden>false</isHidden>
<isUnselectable>true</isUnselectable>
<fk>
<fkDbSchema>study</fkDbSchema>
<fkTable>assignmentTotalCoAssigned</fkTable>
<fkColumnName>lsid</fkColumnName>
</fk>
</column>
</columns>
</table>
</tables>
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14 changes: 13 additions & 1 deletion nbri_ehr/resources/queries/study/chemistryResults.query.xml
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@@ -1,7 +1,7 @@
<query xmlns="http://labkey.org/data/xml/query">
<metadata>
<tables xmlns="http://labkey.org/data/xml">
<table tableName="serology" tableDbType="TABLE" useColumnOrder="true">
<table tableName="chemistryResults" tableDbType="TABLE" useColumnOrder="true">
<tableUrl />
<insertUrl />
<importUrl />
Expand All @@ -15,6 +15,18 @@
<column columnName="type">
<columnTitle>Type</columnTitle>
</column>
<!-- Re-declared from ehr/queries/study/chemistryResults.query.xml; this file
replaces ehr's rather than merging with it. See weight.query.xml. -->
<column columnName="refRange" wrappedColumnName="lsid">
<columnTitle>Ref Range</columnTitle>
<isUnselectable>true</isUnselectable>
<isHidden>false</isHidden>
<fk>
<fkDbSchema>study</fkDbSchema>
<fkTable>chemistryRefRange</fkTable>
<fkColumnName>lsid</fkColumnName>
</fk>
</column>
</columns>
</table>
</tables>
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13 changes: 13 additions & 0 deletions nbri_ehr/resources/queries/study/housing.query.xml
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Expand Up @@ -45,6 +45,19 @@
<column columnName="remark"/>
<column columnName="performedBy">
</column>
<!-- Re-declared because this file replaces ehr's metadata rather than merging
with it. Keyed on lsid, not ehr's objectid: housingTotalRoommates selects
only lsid, so objectid leaves the join silently unresolved. -->
<column columnName="TotalRoommates" wrappedColumnName="lsid">
<columnTitle>Total Cagemates</columnTitle>
<isHidden>false</isHidden>
<isUnselectable>true</isUnselectable>
<fk>
<fkDbSchema>study</fkDbSchema>
<fkTable>housingTotalRoommates</fkTable>
<fkColumnName>lsid</fkColumnName>
</fk>
</column>
</columns>
</table>
</tables>
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22 changes: 22 additions & 0 deletions nbri_ehr/resources/queries/study/weight.query.xml
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Expand Up @@ -29,6 +29,28 @@
</fk>
</column>
<column columnName="performedBy" />
<!-- Re-declared because this file replaces ehr's metadata rather than merging
with it; without these the ehr "Percent Change" view cannot resolve. -->
<column columnName="percentChange" wrappedColumnName="lsid">
<columnTitle>Percent Change</columnTitle>
<isHidden>false</isHidden>
<isUnselectable>true</isUnselectable>
<fk>
<fkDbSchema>study</fkDbSchema>
<fkTable>weightPctChange</fkTable>
<fkColumnName>lsid</fkColumnName>
</fk>
</column>
<column columnName="relChange" wrappedColumnName="lsid">
<columnTitle>Relative Change</columnTitle>
<isHidden>false</isHidden>
<isUnselectable>true</isUnselectable>
<fk>
<fkDbSchema>study</fkDbSchema>
<fkTable>weightRelChange</fkTable>
<fkColumnName>lsid</fkColumnName>
</fk>
</column>
</columns>
</table>
</tables>
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26 changes: 13 additions & 13 deletions nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetDemographics.tsv
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
objectid Id QCStateLabel date birth death calculated_status gender sire dam species origin performedby
1 44444 Completed -1381d -1381d Alive 1 44442 44443 10 00001 1004
2 44446 Completed -1406d -1406d Alive 1 44442 44443 10 00003 1004
3 44445 Completed -1414d -1414d -726d Dead 2 44442 44443 10 00004 1004
4 TEST6390238 Completed -3923d -3923d Shipped 2 3565069 5250080 9 00002 1004
5 TEST5904521 Completed -5431d -5431d Shipped 1 8377984 9 00004 1004
6 TEST3804589 Completed -5806d -5806d Shipped 1 493957 9749422 9 00005 1004
7 TEST2312318 Completed -8069d -8069d Shipped 1 5748235 8739374 9 00002 1004
8 TEST1993532 Completed -11808d -11808d -2259d Dead 2 5409336 3784452 9 00003 1004
9 TEST4551032 Completed -6362d -6362d Alive 1 5030167 8416939 9 00001 1004
11 44442 Completed -6100d -6100d Alive 1 8377984 10 00004 1004
12 44443 Completed -6100d -6100d Alive 1 8377984 10 00004 1004
13 44447 Completed -2600d -2600d Alive 1 8377984 10 00004 1004
14 8377984 Completed -2600d -2600d Alive 1 8377984 10 00004 1004
1 44444 Completed -1381d -1381d Alive M 44442 44443 MNE 00001 1004
2 44446 Completed -1406d -1406d Alive M 44442 44443 MNE 00003 1004
3 44445 Completed -1414d -1414d -726d Dead F 44442 44443 MNE 00004 1004
4 TEST6390238 Completed -3923d -3923d Shipped F 3565069 5250080 MMU 00002 1004
5 TEST5904521 Completed -5431d -5431d Shipped M 8377984 MMU 00004 1004
6 TEST3804589 Completed -5806d -5806d Shipped M 493957 9749422 CMO 00005 1004
7 TEST2312318 Completed -8069d -8069d Shipped M 5748235 8739374 MMU 00002 1004
8 TEST1993532 Completed -11808d -11808d -2259d Dead F 5409336 3784452 MMU 00003 1004
9 TEST4551032 Completed -6362d -6362d Alive M 5030167 8416939 MMU 00001 1004
11 44442 Completed -6100d -6100d Alive M 8377984 MNE 00004 1004
12 44443 Completed -6100d -6100d Alive F 8377984 MNE 00004 1004
13 44447 Completed -2600d -2600d Alive M 8377984 MNE 00004 1004
14 8377984 Completed -2600d -2600d Alive F 8377984 MNE 00004 1004
4 changes: 2 additions & 2 deletions nbri_ehr/test/sampledata/nbri_ehr/study/study/datasets/datasetWeight.tsv
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@@ -1,6 +1,6 @@
objectid Id date weight remark QCStateLabel units performedby
1 TEST3804589 -5735d 0.037 vel praesent tincidunt Completed 1004
2 TEST3804589 -5730d 0.035 erat et convallis Completed 1004
1 TEST3804589 -5735d 0.040 vel praesent tincidunt Completed 1004
2 TEST3804589 -5730d 0.040 erat et convallis Completed 1004
3 TEST3804589 -5727d 0.041 egestas pharetra Completed 1004
4 TEST3804589 -5722d 0.045 sed dui suscipit Completed 1004
5 TEST3804589 -5714d 0.058 a aliquet et tempus Completed 1004
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37 changes: 19 additions & 18 deletions nbri_ehr/test/src/org.labkey.test/tests.nbri_ehr/NBRI_EHRTest.java
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Expand Up @@ -407,25 +407,27 @@ protected void createTestSubjects() throws Exception

//insert into demographics
log("Creating test subjects");
// demographics.species holds an ehr_lookups.species_codes code, and ehr_lookups.weight_ranges is keyed
// on that same code, so weight validation only fires for animals given a real code here.
fields = new String[]{"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"};
data = new Object[][]{
{SUBJECTS[0], "Rhesus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[1], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[2], "Marmoset", (new Date()).toString(), getFemale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[3], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[4], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
{SUBJECTS[0], "MMU", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[1], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[2], "CAE", (new Date()).toString(), getFemale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[3], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{SUBJECTS[4], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
};
insertCommand = getApiHelper().prepareInsertCommand("study", "demographics", "lsid", fields, data);
getApiHelper().deleteAllRecords("study", "demographics", new Filter("Id", StringUtils.join(SUBJECTS, ";"), Filter.Operator.IN));
getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), insertCommand, getExtraContext());

//for simplicity, also create the animals from MORE_ANIMAL_IDS right now
data = new Object[][]{
{MORE_ANIMAL_IDS[0], "Rhesus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[1], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[2], "Marmoset", (new Date()).toString(), getFemale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[3], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[4], "Cynomolgus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
{MORE_ANIMAL_IDS[0], "MMU", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[1], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[2], "CAE", (new Date()).toString(), getFemale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[3], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004},
{MORE_ANIMAL_IDS[4], "MNE", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
};
insertCommand = getApiHelper().prepareInsertCommand("study", "demographics", "lsid", fields, data);
getApiHelper().deleteAllRecords("study", "demographics", new Filter("Id", StringUtils.join(MORE_ANIMAL_IDS, ";"), Filter.Operator.IN));
Expand Down Expand Up @@ -478,7 +480,7 @@ protected void createTestSubjects() throws Exception
log("Creating task grouping test subject");
fields = new String[]{"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"};
data = new Object[][]{
{taskGroupAnimalId, "Rhesus", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
{taskGroupAnimalId, "MMU", (new Date()).toString(), getMale(), new Date(), "Alive", UUID.randomUUID().toString(), 1004}
};
insertCommand = getApiHelper().prepareInsertCommand("study", "demographics", "lsid", fields, data);
getApiHelper().deleteAllRecords("study", "demographics", new Filter("Id", taskGroupAnimalId));
Expand Down Expand Up @@ -535,7 +537,7 @@ public void testWeightValidation()
};
Map<String, List<String>> expected = new HashMap<>();
expected.put("weight", Arrays.asList(
"WARN: Weight above the allowable value of 20.0 kg for Cynomolgus",
"WARN: Weight above the allowable value of 30.0 kg for MNE",
"INFO: Weight gain of >10%. Last weight 12 kg")
);
getApiHelper().testValidationMessage(DATA_ADMIN.getEmail(), "study", "weight", getWeightFields(), data, expected);
Expand Down Expand Up @@ -1217,9 +1219,9 @@ public void createSubjectsForDeathForm() throws IOException, CommandException
getApiHelper().doSaveRows(DATA_ADMIN.getEmail(), getApiHelper().prepareInsertCommand("study", "birth", "lsid",
new String[]{"Id", "Date", "gender", "QCStateLabel", "performedby"},
new Object[][]{
{aliveAnimalId, LocalDateTime.now().minusDays(30), "f", "Completed", 1004},
{deadAnimalId, LocalDateTime.now().minusDays(30), "m", "Completed", 1004},
{departedAnimalId, LocalDateTime.now().minusDays(30), "m", "Completed", 1004},
{aliveAnimalId, LocalDateTime.now().minusDays(30), getFemale(), "Completed", 1004},
{deadAnimalId, LocalDateTime.now().minusDays(30), getMale(), "Completed", 1004},
{departedAnimalId, LocalDateTime.now().minusDays(30), getMale(), "Completed", 1004},
}
), getExtraContext());

Expand Down Expand Up @@ -1703,9 +1705,8 @@ private int countLines(File file) throws Exception
}
}

// Creates the parents of a conception. They need a species from the ehr_lookups.species list because the
// Start with Conception window copies the dam's species onto the newborn, and the reference study's
// demographics data carries placeholder species values that no lookup entry matches.
// Creates the parents of a conception. They need an ehr_lookups.species_codes code because the Start with
// Conception window copies the dam's species onto the newborn, and the test asserts the resulting record.
private void createBreedingPair(String damId, String sireId, String species) throws Exception
{
String[] fields = new String[]{"Id", "Species", "Birth", "Gender", "date", "calculated_status", "objectid", "performedby"};
Expand Down