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Merged
labkey-jeckels merged 3 commits into from
Nov 1, 2021
Merged

Remove center-specific setup code #258

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b762637
Fix ONPRC test query validation errors by adding missing column and e…
Oct 29, 2021
81326b0
Alternate approach for mocking up ONPRC environment for geneticscore
Oct 29, 2021
0adb6e3
Delete problematic RandData_MHCData.sql as it references tables and q…
Oct 30, 2021
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78 changes: 10 additions & 68 deletions ehr/test/src/org/labkey/test/tests/ehr/AbstractEHRTest.java
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Original file line number Diff line number Diff line change
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
60 changes: 0 additions & 60 deletions ehr/test/src/org/labkey/test/tests/ehr/EHRSetupHelper.java
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76 changes: 74 additions & 2 deletions ehr/test/src/org/labkey/test/tests/onprc_ehr/AbstractGenericONPRC_EHRTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,19 +25,19 @@
import org.labkey.remoteapi.query.SaveRowsResponse;
import org.labkey.remoteapi.query.SelectRowsCommand;
import org.labkey.remoteapi.query.SelectRowsResponse;
import org.labkey.test.Locator;
import org.labkey.test.ModulePropertyValue;
import org.labkey.test.TestFileUtils;
import org.labkey.test.WebTestHelper;
import org.labkey.test.tests.ehr.AbstractGenericEHRTest;
import org.labkey.test.util.Ext4Helper;
import org.labkey.test.util.ListHelper;
import org.labkey.test.util.LogMethod;
import org.labkey.test.util.PasswordUtil;
import org.labkey.test.util.SchemaHelper;
import org.labkey.test.util.SqlserverOnlyTest;
import org.labkey.test.util.ehr.EHRClientAPIHelper;
import org.labkey.test.util.ext4cmp.Ext4CmpRef;
import org.labkey.test.util.ext4cmp.Ext4FieldRef;
import org.openqa.selenium.WebElement;

import java.io.File;
import java.text.SimpleDateFormat;
Expand Down Expand Up @@ -114,6 +114,78 @@ protected void importStudy()
importStudyFromPath(1);
}

@Override
protected void doExtraPreStudyImportSetup()
{
//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)
);

// Mock up a table in the geneticscore schema instead of needing to mock up all of the geneticscore dependencies too
_listHelper.createList(getProjectName(), "mhc_data", ListHelper.ListColumnType.AutoInteger, "RowId",
new ListHelper.ListColumn("subjectId", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("datatype", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("marker", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("result", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("score", ListHelper.ListColumnType.Decimal),
new ListHelper.ListColumn("assaytype", ListHelper.ListColumnType.String),
new ListHelper.ListColumn("totalTests", ListHelper.ListColumnType.Integer));

schemaHelper.createLinkedSchema(this.getProjectName(), "dbo", "/" + this.getContainerPath(), null, "lists", null, null);
}

@Override
@LogMethod
protected void initProject() throws Exception
Expand Down