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Merged
github-actions merged 7 commits into from
Nov 12, 2021
Merged

[bot] Merge 21.11 to develop #263

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17b6055
Remove center-specific setup code (#258)
labkey-jeckels Nov 1, 2021
cf55aa4
log non-date and non-string type date values (#256)
ankurjuneja Nov 5, 2021
7a2dc40
TNPRC Issue 290: Method to edit legacy data via query module update r…
labkey-jeckels Nov 8, 2021
4323f7b
Support using linked schema in place of DB schema for testing purpose…
labkey-jeckels Nov 8, 2021
a20c36a
Merge 21.7 to 21.11
labkey-teamcity Nov 8, 2021
f67de55
Merge 21.7 to 21.11
labkey-teamcity Nov 11, 2021
c95dcd9
Merge 21.11 to develop
labkey-teamcity Nov 12, 2021
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3 changes: 3 additions & 0 deletions ehr/resources/queries/ehr_lookups/cage.js
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Expand Up @@ -14,6 +14,9 @@ function onUpsert(helper, scriptErrors, row, oldRow) {
row.location = row.room;
if (row.cage)
row.location += '-' + row.cage;
if (row.location.length > 24) {
console.log("Location is longer than allowed length: ", row.location);
}

//remove whitespace, normalize punctuation and pad digits
if (row.joinToCage){
Expand Down
21 changes: 12 additions & 9 deletions ehr/resources/scripts/ehr/utils.js
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Expand Up @@ -180,18 +180,21 @@ EHR.Server.Utils = new function(){
console.error('Unable to parse date string: ' + val);
}
}
else if (!isNaN(val)){
// NOTE: i'm not sure if we should really attempt this. this should really never happen,
// and it's probably an error if it does
normalizedVal = new Date(val);
}
else {
if (val['getTime']){
normalizedVal = new Date(val.getTime());
console.log('EHR trigger script is being passed a date with value: ' + val);
if (!isNaN(val)) {
// NOTE: i'm not sure if we should really attempt this. this should really never happen,
// and it's probably an error if it does
normalizedVal = new Date(val);
}
else {
if (!supppressErrors)
console.error('Unknown datatype for date value. Type was: ' + (typeof val) + ' and value was: ' + val);
if (val['getTime']) {
normalizedVal = new Date(val.getTime());
}
else {
if (!supppressErrors)
console.error('Unknown datatype for date value. Type was: ' + (typeof val) + ' and value was: ' + val);
}
}
}

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34 changes: 31 additions & 3 deletions ehr/src/org/labkey/ehr/EHRController.java
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Expand Up @@ -312,6 +312,7 @@ public ApiResponse execute(DiscardFormForm form, BindException errors)
public static class EHRQueryForm extends QueryForm
{
private boolean _showImport = false;
private boolean _queryUpdateURL = false;

public boolean isShowImport()
{
Expand All @@ -322,6 +323,16 @@ public void setShowImport(boolean showImport)
{
_showImport = showImport;
}

public boolean isQueryUpdateURL()
{
return _queryUpdateURL;
}

public void setQueryUpdateURL(boolean queryUpdateURL)
{
_queryUpdateURL = queryUpdateURL;
}
}

@RequiresPermission(UpdatePermission.class)
Expand Down Expand Up @@ -417,7 +428,24 @@ else if (isReactForm(form.getSchemaName(), form.getQueryName()))
}

DetailsURL updateUrl;
if (EHRServiceImpl.get().isUseFormEditUI(getContainer()) && null != ti.getColumn("taskid"))
if (form.isQueryUpdateURL())
{
// Send to the query controller's basic row-level update form
StringBuilder sb = new StringBuilder("query-updateQueryRow.view?schemaName=");
sb.append(ti.getUserSchema().getName());
sb.append("&queryName=");
sb.append(ti.getName());
for (String pk : pks)
{
sb.append("&");
sb.append(pk);
sb.append("=${");
sb.append(pk);
sb.append("}");
}
updateUrl = DetailsURL.fromString(sb.toString());
}
else if (EHRServiceImpl.get().isUseFormEditUI(getContainer()) && null != ti.getColumn("taskid"))
{
updateUrl = DetailsURL.fromString("/ehr/dataEntryForm.view?taskid=${taskid}&formType=${taskid/formType}");
}
Expand Down Expand Up @@ -1445,8 +1473,8 @@ public ModelAndView getView(EnterDataForm form, BindException errors)
{
if (form.getFormType() == null)
{
errors.reject(ERROR_MSG, "Must provide either the form type");
return null;
errors.reject(ERROR_MSG, "Must provide a form type");
return new SimpleErrorView(errors);
}

_def = DataEntryManager.get().getFormByName(form.getFormType(), getContainer(), getUser());
Expand Down
78 changes: 10 additions & 68 deletions ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java
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Expand Up @@ -142,7 +142,6 @@ abstract public class AbstractEHRTest extends BaseWebDriverTest implements Advan
protected List<Long> _saveRowsTimes;

protected abstract String getModuleDirectory();
private EHRSetupHelper _setupHelper = new EHRSetupHelper(this, getProjectName(), FOLDER_NAME, getModulePath(), getContainerPath());
protected EHRBillingHelper _billingHelper = new EHRBillingHelper(this, getProjectName(), FOLDER_NAME, getModulePath(), getContainerPath(),BILLING_FOLDER);

//xpath fragment
Expand Down Expand Up @@ -221,7 +220,7 @@ protected void createTestSubjects() throws Exception
{
String[] fields;
Object[][] data;
PostCommand insertCommand;
PostCommand<?> insertCommand;

//insert into demographics
log("Creating test subjects");
Expand Down Expand Up @@ -376,22 +375,26 @@ protected void createProjectAndFolders(String type)
_containerHelper.createSubfolder(getProjectName(), getProjectName(), FOLDER_NAME, type, null);
}

/** Hook for center-specific setup that needs to happen after the containers are created but before the study is imported */
protected void doExtraPreStudyImportSetup()
{

}

@LogMethod
protected void initProject() throws Exception
{
initProject("EHR");
}

@LogMethod
protected void initProject(String type) throws Exception
{
createProjectAndFolders(type);
setFormatStrings();
setEHRModuleProperties();
createUsersandPermissions();//note: we create the users prior to study import, b/c that user is used by TableCustomizers
if(type.equals("TNPRC EHR"))
_setupHelper.loadEHRTableDefinitions();
if(type.equals("ONPRC EHR"))
onprcSetupBeforeStudyUpload(); //this needs to happen before import study() below so that 'Validation Queries' step doesn't fail since the queries depend on setup in this method.

doExtraPreStudyImportSetup();

populateInitialData();
defineQCStates();
Expand All @@ -406,67 +409,6 @@ protected void initProject(String type) throws Exception
primeCaches();
}

private void onprcSetupBeforeStudyUpload()
{
//create onprc_billing_public linked schema
beginAt(getProjectName());
SchemaHelper schemaHelper = new SchemaHelper(this);
schemaHelper.createLinkedSchema(this.getProjectName(), null, "onprc_billing_public", "/" + this.getContainerPath(), "onprc_billing_public", null, null, null);

//create Labfee_NoChargeProjects
beginAt(getProjectName());

ListHelper.ListColumn projectCol= new ListHelper.ListColumn("project", ListHelper.ListColumnType.Integer);
ListHelper.ListColumn startDateCol= new ListHelper.ListColumn("startDate", ListHelper.ListColumnType.DateAndTime);
ListHelper.ListColumn dateDisabledCol= new ListHelper.ListColumn("dateDisabled", ListHelper.ListColumnType.DateAndTime);
ListHelper.ListColumn createdDbCol= new ListHelper.ListColumn("Createdb", ListHelper.ListColumnType.Integer);
ListHelper.ListColumn notesCol= new ListHelper.ListColumn("Notes", ListHelper.ListColumnType.String);
_listHelper.createList(getProjectName(), "Labfee_NoChargeProjects", ListHelper.ListColumnType.Integer, "key", projectCol, startDateCol, dateDisabledCol, createdDbCol, notesCol);

_listHelper.createList(getProjectName(), "GeneticValue", ListHelper.ListColumnType.String, "Id",
new ListHelper.ListColumn("meanKinship", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("zscore", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("genomeUniqueness", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("totalOffspring", ListHelper.ListColumnType.Integer),
new ListHelper.ListColumn("livingOffspring", ListHelper.ListColumnType.Integer),
new ListHelper.ListColumn("assignments", ListHelper.ListColumnType.Integer),
new ListHelper.ListColumn("condition", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("import", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("value", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("rank", ListHelper.ListColumnType.Integer)
);

_listHelper.createList(getProjectName(), "Special_Aliases", ListHelper.ListColumnType.AutoInteger, "Key",
new ListHelper.ListColumn("Category", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("Alias", ListHelper.ListColumnType.String));

// Fake up an external schema connection for "dbo" via a list and a linked schema
_listHelper.createList(getProjectName(), "Rpt_ChargesProjection", ListHelper.ListColumnType.AutoInteger, "RowId",
new ListHelper.ListColumn("ChargeId", ListHelper.ListColumnType.Integer),
new ListHelper.ListColumn("UnitCost", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year1", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year2", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year3", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year4", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year5", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year6", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year7", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("year8", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate1", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate2", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate3", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate4", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate5", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate6", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate7", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate8", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("Aprate9", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("PostedDate", ListHelper.ListColumnType.DateAndTime)
);
schemaHelper.createLinkedSchema(this.getProjectName(), null, "dbo", "/" + this.getContainerPath(), null, "lists", null, null);

}

@LogMethod(quiet = true)
protected void populate(@LoggedParam String tableLabel)
{
Expand Down
2 changes: 1 addition & 1 deletion ehr/test/src/org/labkey/test/tests/ehr/AbstractGenericEHRTest.java
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Expand Up @@ -221,7 +221,7 @@ public void testCustomButtons()
recallLocation();
List<String> submenuItems = dr.getHeaderMenuOptions("More Actions");
List<String> expectedSubmenu = Arrays.asList("Jump To History", "Return Distinct Values","Show Record History","Compare Weights","Edit Records");
Assert.assertEquals("More actions menu did not contain expected options",expectedSubmenu, submenuItems);
Assert.assertTrue("More actions menu did not contain expected options. Expected: " + expectedSubmenu + ", but found: " + submenuItems, submenuItems.containsAll(expectedSubmenu));
}

private void testUserAgainstAllStates(@LoggedParam EHRUser user)
Expand Down
60 changes: 0 additions & 60 deletions ehr/test/src/org/labkey/test/tests/ehr/EHRSetupHelper.java
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