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Merged
github-actions merged 8 commits into from
Dec 17, 2025
Merged

[bot] Fast-forward for 25.12.0 #912

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2bfdcfa
Add new tests to hematology bulk upload (#900)
LeviCameron1 Nov 25, 2025
0a03523
TB Dashboard Access Report Upload (#898)
LeviCameron1 Nov 25, 2025
62acf47
25.7 fb workdaychanges (#901)
dnicolalde Nov 28, 2025
45c5ac3
Merge 25.7 to 25.11
labkey-teamcity Dec 1, 2025
1034262
Merge 25.11 to 25.12
labkey-teamcity Dec 2, 2025
25cfda4
Test failure fix related to query validation during folder import (#907)
labkey-bpatel Dec 9, 2025
e0aa7f9
Merge 25.7 to 25.11
labkey-teamcity Dec 15, 2025
3e9cbcc
Merge 25.11 to 25.12
labkey-teamcity Dec 16, 2025
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90 changes: 21 additions & 69 deletions WNPRC_Compliance/resources/queries/wnprc_compliance/MostRecentAccessReportSummary.sql
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,70 +1,22 @@
SELECT
ar.date as report_date,

card_info.card_id,
cards.exempt,
cards.exempt_reason,
personsList.lastTbClearance,
personsList.measles_required,
personsList.isArchived,

card_info.first_name,
card_info.last_name,
card_info.middle_name,

access_info.access_levels,

persons_to_cards.personid

FROM (
SELECT
report_id,
card_id,
GROUP_CONCAT(access_level, ';') as access_levels


FROM (
SELECT
reports.report_id,
report_data.card_id,
report_data.access_level,


FROM wnprc_compliance.access_reports reports, wnprc_compliance.access_report_data report_data
WHERE (
reports.date = (SELECT MAX(date) FROM wnprc_compliance.access_reports)
AND (
report_data.report_id = reports.report_id
)
)
)

GROUP BY report_id, card_id
) as access_info

LEFT JOIN wnprc_compliance.card_info card_info
on (
access_info.card_id = card_info.card_id
AND
access_info.report_id = card_info.report_id
)

LEFT JOIN wnprc_compliance.cards cards
ON (
cards.card_id = access_info.card_id
)

LEFT JOIN wnprc_compliance.persons_to_cards persons_to_cards
ON (
persons_to_cards.cardid = access_info.card_id
)

LEFT JOIN wnprc_compliance.personsList personsList
ON (
personsList.personid = persons_to_cards.personid
)

LEFT JOIN wnprc_compliance.access_reports ar
ON (
ar.report_id = access_info.report_id
)
ar.date as report_date,
card_info.card_id,
cards.exempt,
cards.exempt_reason,
personsList.lastTbClearance,
personsList.measles_required,
personsList.isArchived,
card_info.first_name,
card_info.last_name,
card_info.middle_name,
persons_to_cards.personid
FROM wnprc_compliance.access_reports ar
INNER JOIN wnprc_compliance.card_info card_info
ON ar.report_id = card_info.report_id
LEFT JOIN wnprc_compliance.cards cards
ON cards.card_id = card_info.card_id
LEFT JOIN wnprc_compliance.persons_to_cards persons_to_cards
ON persons_to_cards.cardid = card_info.card_id
LEFT JOIN wnprc_compliance.personsList personsList
ON personsList.personid = persons_to_cards.personid
WHERE ar.date = (SELECT MAX(date) FROM wnprc_compliance.access_reports)
84 changes: 30 additions & 54 deletions WNPRC_Compliance/src/org/labkey/wnprc_compliance/AccessReportRowParser.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,14 +25,13 @@
*/
public class AccessReportRowParser {
enum ColumnName {
FIRST_NAME (false, "Name (Last, First, Middle)"),
LAST_NAME (false, "Name (Last, First, Middle)"),
MIDDLE_NAME (false, "Name (Last, First, Middle)"),
CARD_NUMBER (true, "Badge ID(Issue)"),
CARD_ISSUED (false, "Badge Active"),
CARD_EXPIRE (false, "Badge Deactive"),
FIRST_NAME (false, "First Name"),
LAST_NAME (false, "Last Name"),
MIDDLE_NAME (false, "Middle Name"),
CARD_NUMBER (true, "Badge ID"),
CARD_ISSUED (false, "Badge Activate"),
CARD_EXPIRE (false, "Badge Deactivate"),
BADGE_TYPE (false, "Badge Type"),
CARD_ISSUE_CODE (false, "Badge Id(Issue)"),
;

boolean required;
Expand Down Expand Up @@ -87,7 +86,7 @@ public AccessReportRowParser(Row headerRow) throws MalformedReportException {
}
}

public Pair<CardInfo, AccessInfo> parseRow(String reportId, Row row, Container container) throws ParseException
public CardInfo parseRow(Row row) throws ParseException
{
Map<ColumnName, Object> values = new HashMap<>();

Expand All @@ -96,23 +95,16 @@ public Pair<CardInfo, AccessInfo> parseRow(String reportId, Row row, Container c
for (ColumnName columnName : cellIndexLookup.keySet()) {
Cell cell = row.getCell(cellIndexLookup.get(columnName));
if (cell != null ) {
if (columnName.headerText.equals(ColumnName.FIRST_NAME.headerText))
{
if (cell.getCellType() == CellType.STRING && !cell.getStringCellValue().isEmpty())
{
Matcher matcher = Pattern.compile("^(.*?),\\s+(\\w+)(?:\\s+(\\w+))?$").matcher(cell.getStringCellValue());

if (matcher.find())
{
values.put(ColumnName.FIRST_NAME, matcher.group(2));
values.put(ColumnName.LAST_NAME, matcher.group(1));
values.put(ColumnName.MIDDLE_NAME, matcher.group(3));
}
}

if(columnName == ColumnName.FIRST_NAME){
values.put(ColumnName.FIRST_NAME, cell.getStringCellValue());
}

if (columnName.headerText.equals(ColumnName.CARD_ISSUED.headerText))
else if (columnName == ColumnName.MIDDLE_NAME){
values.put(ColumnName.MIDDLE_NAME, cell.getStringCellValue());
}else if (columnName == ColumnName.LAST_NAME){
values.put(ColumnName.LAST_NAME, cell.getStringCellValue());
}else if (columnName == ColumnName.BADGE_TYPE){
values.put(ColumnName.BADGE_TYPE, cell.getStringCellValue());
}else if (columnName == ColumnName.CARD_ISSUED)
{
if (!cell.toString().isEmpty())
{
Expand All @@ -121,42 +113,32 @@ public Pair<CardInfo, AccessInfo> parseRow(String reportId, Row row, Container c
values.put(ColumnName.CARD_ISSUED, d);

}
}
if (columnName.headerText.equals(ColumnName.CARD_EXPIRE.headerText))
}else if (columnName == ColumnName.CARD_EXPIRE)
{
if (!cell.toString().isEmpty())
{
DateFormat df = new SimpleDateFormat("dd-MMM-yyyy");
Date d = df.parse(cell.toString());
values.put(ColumnName.CARD_EXPIRE, d);
}
}else if (columnName == ColumnName.CARD_NUMBER)
{
values.put(ColumnName.CARD_NUMBER, cell.getStringCellValue());
}

if (columnName.headerText.equals(ColumnName.CARD_NUMBER.headerText))
{

if (cell.getCellType() == CellType.STRING && !cell.getStringCellValue().isEmpty())
{
Matcher matcher = Pattern.compile("(\\d+)\\s*\\((\\d+)\\)").matcher(cell.getStringCellValue());
if (matcher.find())
{
values.put(ColumnName.CARD_NUMBER, matcher.group(1));
values.put(ColumnName.CARD_ISSUE_CODE, matcher.group(2));
}
}
}

String value = "";
if (cell.getCellType() == CellType.STRING) {
value = cell.getStringCellValue();
}
if (!values.containsKey(columnName))
values.put(columnName, value);

}
}

Pair<CardInfo, AccessInfo> pair = new Pair<>(new CardInfo(values), new AccessInfo(values));
return pair;
return new CardInfo(values);
}

public static class CardInfo {
Expand Down Expand Up @@ -187,9 +169,6 @@ public Date getCardIssued() {
public Date getCardExpire() {
return (Date) this.values.get(ColumnName.CARD_EXPIRE);
}
public String getIssueCode() {
return (String) this.values.get(ColumnName.CARD_ISSUE_CODE);
}
public String getCardType() {
return (String) this.values.get(ColumnName.BADGE_TYPE);
}
Expand All @@ -200,24 +179,16 @@ public Map<ColumnName, Object> getValues() {

}

public static class AccessInfo {
private Map<ColumnName, Object> values;

public AccessInfo(Map<ColumnName, Object> values) {
this.values = values;
}

}

public static class MalformedReportException extends Exception {
public MalformedReportException(String message) {
super(message);
}
}

public static Date parseDate(String dateString) {
SimpleDateFormat dateFormat = new SimpleDateFormat("MM/dd/yyyy hh:mm:ssa");
SimpleDateFormat dateFormat = new SimpleDateFormat("MM.dd.yy");
SimpleDateFormat shortDateFormat = new SimpleDateFormat("MM/dd/yyyy");
SimpleDateFormat fullDateFormat = new SimpleDateFormat("MM/dd/yyyy hh:mm:ssa");

Date date;

Expand All @@ -229,7 +200,12 @@ public static Date parseDate(String dateString) {
date = shortDateFormat.parse(dateString);
}
catch(ParseException e2) {
throw new ApiUsageException("Unrecognized Date format: " + dateString);
try {
date = fullDateFormat.parse(dateString);
}
catch(ParseException e3) {
throw new ApiUsageException("Unrecognized Date format: " + dateString);
}
}
}

Expand Down
91 changes: 16 additions & 75 deletions WNPRC_Compliance/src/org/labkey/wnprc_compliance/AccessReportService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,19 +54,25 @@ public AccessReportService(User user, Container container) {
this.container = container;
}

public void importReport(InputStream stream) throws IOException, AccessReportRowParser.MalformedReportException, ParseException
public void importReport(InputStream stream, String filename) throws IOException, AccessReportRowParser.MalformedReportException, ParseException
{
String reportid = UUID.randomUUID().toString().toUpperCase();
Sheet sheet = new ExcelLoader(stream,false, null).getSheet();

Row titleRow = sheet.getRow(1);
if (!titleRow.getCell(0).getStringCellValue().equalsIgnoreCase("Access Level Assignments to Cardholders")) {
// Ensure all necessary columns are present in an uploaded report
Row columnHeaderRow = sheet.getRow(0);
if(!columnHeaderRow.getCell(3).getStringCellValue().equalsIgnoreCase("Last Name")
|| !columnHeaderRow.getCell(5).getStringCellValue().equalsIgnoreCase("First Name")
|| !columnHeaderRow.getCell(7).getStringCellValue().equalsIgnoreCase("Middle Name")
|| !columnHeaderRow.getCell(23).getStringCellValue().equalsIgnoreCase("Badge Type")
|| !columnHeaderRow.getCell(25).getStringCellValue().equalsIgnoreCase("Badge ID")
|| !columnHeaderRow.getCell(30).getStringCellValue().equalsIgnoreCase("Badge Activate")
|| !columnHeaderRow.getCell(32).getStringCellValue().equalsIgnoreCase("Badge Deactivate")){
throw new ApiUsageException("You can only upload area rights reports here.");
}

Row dateRow = sheet.getRow(6);
//the report created date is the 13th column over
Matcher matcher = Pattern.compile("Report\\s+Date:\\s*(\\d{2}/\\d{2}/\\d{4}\\s+\\d{1,2}:\\d{2}:\\d{2}[AP]M)").matcher(dateRow.getCell(14).getStringCellValue());
//the report created is in the file name
Matcher matcher = Pattern.compile("(\\d{1,2}\\.\\d{1,2}\\.\\d{2})").matcher(filename);
String reportDateTime;
Date generatedOn;
if (matcher.find())
Expand All @@ -88,73 +94,20 @@ public void importReport(InputStream stream) throws IOException, AccessReportRow
}

Map<String, JSONObject> cardInfos = new HashMap<>();
List<Map<String, Object>> accessData = new ArrayList<>();


//if the cell contains Prim and Barrier
Pattern accessLevelPattern = Pattern.compile("Access Level:\\s*");

Iterator<Row> rows = sheet.rowIterator();
AccessReportRowParser rowParser = null;
String accessLevel = "";
outer:
AccessReportRowParser rowParser = new AccessReportRowParser(columnHeaderRow);
while (rows.hasNext()) {
Row currentRow = rows.next();
//don't parse items until we reach the main block
if (currentRow.getRowNum() < 8)
{
continue;
}
if (currentRow.getCell(4) == null)
{
// Skip header row
if(currentRow.getRowNum() == 0){
continue;
}
String firstCellText = currentRow.getCell(0).getStringCellValue();

Matcher accessLevelMatcher = accessLevelPattern.matcher(firstCellText);
//we've encountered an access level block of text
//we can grab the header and skip a row
if (accessLevelMatcher.matches())
{
accessLevel = currentRow.getCell(4).getStringCellValue();

// We are about to go into a block of values. First, eat the blank line
rows.next();

// Now eat the header line
Row headerRow = rows.next();
//sets up the column names from the header row?

//
rowParser = new AccessReportRowParser(headerRow);

currentRow = rows.next();
}
if (rowParser == null)
{
continue;
}
Pair<AccessReportRowParser.CardInfo, AccessReportRowParser.AccessInfo> results = rowParser.parseRow(reportid, currentRow, container);
AccessReportRowParser.CardInfo cardInfo = results.first;
AccessReportRowParser.AccessInfo accessInfo = results.second;
AccessReportRowParser.CardInfo cardInfo = rowParser.parseRow(currentRow);

if (cardInfo.getValues().isEmpty())
continue;


//end of spreadsheet pattern
Pattern endOfSheetPattern = Pattern.compile("Total Badges Required for Download:");
if (endOfSheetPattern.matcher(cardInfo.getFirstName()).matches())
{
int getNumCards = (int) currentRow.getCell(10).getNumericCellValue();
if (cardInfos.size() != getNumCards)
{
throw new RuntimeException("Card number does not equal total badge count in sheet, upload failed.");
}
break;
}


String cardNumber = cardInfo.getCardNumber();
if (cardNumber == null || cardNumber.equals(""))
{
Expand All @@ -171,19 +124,10 @@ public void importReport(InputStream stream) throws IOException, AccessReportRow
cardInfoJSON.put("middle_name", cardInfo.getMiddleName());
cardInfoJSON.put("date_issued", cardInfo.getCardIssued());
cardInfoJSON.put("date_expire", cardInfo.getCardExpire());
cardInfoJSON.put("issue_code", cardInfo.getIssueCode());
cardInfoJSON.put("card_type", cardInfo.getCardType());
cardInfoJSON.put("container", container.getId());

cardInfos.put(cardNumber, cardInfoJSON);

JSONObject accessInfoJSON = new JSONObject();
accessInfoJSON.put("report_id", reportid);
accessInfoJSON.put("access_level", accessLevel);
accessInfoJSON.put("card_id", cardNumber);
accessInfoJSON.put("container", container.getId());

accessData.add(accessInfoJSON.toMap());
}

try (DbScope.Transaction transaction = DbSchema.get(WNPRC_ComplianceSchema.NAME, DbSchemaType.Module).getScope().ensureTransaction()) {
Expand All @@ -204,9 +148,6 @@ public void importReport(InputStream stream) throws IOException, AccessReportRow
}
cardsUpdater.upsert(cardsList);

SimpleQueryUpdater dataUpdater = new SimpleQueryUpdater(user, container, WNPRC_ComplianceSchema.NAME, "access_report_data");
dataUpdater.upsert(accessData);

List<Map<String, Object>> cardInfoList = new ArrayList<>(cardInfos.values().stream().map(JSONObject::toMap).toList());
SimpleQueryUpdater cardInfoUpdater = new SimpleQueryUpdater(user, container, WNPRC_ComplianceSchema.NAME, "card_info");
cardInfoUpdater.upsert(cardInfoList);
Expand Down
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