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Merged
patrick-austin merged 2 commits into from
Apr 1, 2025
Merged

Limit number of files that can be submitted, other bugfixes #73

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3cd7ed5
Limit number of files that can be submitted, other bugfixes
patrick-austin Mar 26, 2025
ed57b56
Javadocs, refactors, anonUserName NullPointer fix
patrick-austin Apr 1, 2025
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6 changes: 5 additions & 1 deletion src/main/config/run.properties.example
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,11 @@ queue.maxActiveDownloads = 10
# Limit the number files per queued Download part. Multiple Datasets will be combined into part
# Downloads based on their fileCount up to this limit. If a single Dataset has a fileCount
# greater than this limit, it will still be submitted in a part by itself.
queue.maxFileCount = 10000
queue.visit.maxPartFileCount = 10000

# Requests to the /queue/files endpoint will be rejected if they exceed this number of files
# Any chunking should be done clientside
queue.files.maxFileCount = 10000

# When queueing Downloads a positive priority will allow a User to proceed.
# Non-positive values will block that User from submitting a request to the queue.
Expand Down
90 changes: 68 additions & 22 deletions src/main/java/org/icatproject/topcat/IcatClient.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
package org.icatproject.topcat;

import java.util.Map;
import java.util.Set;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.ListIterator;
import java.util.ArrayList;
Expand All @@ -21,6 +23,30 @@

public class IcatClient {

public class DatafilesResponse {
public final List<Long> ids = new ArrayList<>();
public final Set<String> missing = new HashSet<>();
public long totalSize = 0L;

/**
* Submit a query for Datafiles, then appends the ids, increments the size, and
* records any missing file locations.
*
* @param query Query to submit
* @throws TopcatException If the query returns not authorized, or not found.
*/
public void submitDatafilesQuery(String query)
throws TopcatException {
JsonArray jsonArray = submitQuery(query);
for (JsonObject jsonObject : jsonArray.getValuesAs(JsonObject.class)) {
JsonObject datafile = jsonObject.getJsonObject("Datafile");
ids.add(datafile.getJsonNumber("id").longValueExact());
missing.remove(datafile.getString("location"));
totalSize += datafile.getJsonNumber("fileSize").longValueExact();
}
}
}

private Logger logger = LoggerFactory.getLogger(IcatClient.class);

private HttpClient httpClient;
Expand Down Expand Up @@ -139,7 +165,7 @@ public String getFullName() throws TopcatException {
* @throws TopcatException
*/
public JsonArray getDatasets(String visitId) throws TopcatException {
String query = "SELECT dataset.id, dataset.fileCount from Dataset dataset";
String query = "SELECT dataset.id, dataset.fileCount, dataset.fileSize from Dataset dataset";
query += " WHERE dataset.investigation.visitId = '" + visitId + "' ORDER BY dataset.id";
return submitQuery(query);
}
Expand All @@ -153,45 +179,44 @@ public JsonArray getDatasets(String visitId) throws TopcatException {
* @throws TopcatException
* @throws UnsupportedEncodingException
*/
public List<Long> getDatafiles(List<String> files) throws TopcatException, UnsupportedEncodingException {
List<Long> datafileIds = new ArrayList<>();
public DatafilesResponse getDatafiles(List<String> files) throws TopcatException, UnsupportedEncodingException {
DatafilesResponse response = new DatafilesResponse();
if (files.size() == 0) {
// Ensure that we don't error when calling .next() below by returning early
return datafileIds;
return response;
}

// Total limit - "entityManager?sessionId=" - `sessionId` - "?query=" - `queryPrefix` - `querySuffix
// Limit is 1024 - 24 - 36 - 7 - 51 - 17
// Limit is 1024 - 24 - 36 - 7 - 48 - 17
int getUrlLimit = Integer.parseInt(Properties.getInstance().getProperty("getUrlLimit", "1024"));
int chunkLimit = getUrlLimit - 135;
String queryPrefix = "SELECT d.id from Datafile d WHERE d.location in (";
int chunkLimit = getUrlLimit - 132;
String queryPrefix = "SELECT d from Datafile d WHERE d.location in (";
String querySuffix = ") ORDER BY d.id";
ListIterator<String> iterator = files.listIterator();

String chunkedFiles = "'" + iterator.next() + "'";
String file = iterator.next();
String chunkedFiles = "'" + file + "'";
response.missing.add(file);
int chunkSize = URLEncoder.encode(chunkedFiles, "UTF8").length();
while (iterator.hasNext()) {
String file = "'" + iterator.next() + "'";
int encodedFileLength = URLEncoder.encode(file, "UTF8").length();
file = iterator.next();
String quotedFile = "'" + file + "'";
int encodedFileLength = URLEncoder.encode(quotedFile, "UTF8").length();
if (chunkSize + 3 + encodedFileLength > chunkLimit) {
JsonArray jsonArray = submitQuery(queryPrefix + chunkedFiles + querySuffix);
for (JsonNumber datafileIdJsonNumber : jsonArray.getValuesAs(JsonNumber.class)) {
datafileIds.add(datafileIdJsonNumber.longValueExact());
}
response.submitDatafilesQuery(queryPrefix + chunkedFiles + querySuffix);

chunkedFiles = file;
chunkedFiles = quotedFile;
chunkSize = encodedFileLength;
response.missing.add(file);
} else {
chunkedFiles += "," + file;
chunkedFiles += "," + quotedFile;
chunkSize += 3 + encodedFileLength; // 3 is size of , when encoded as %2C
response.missing.add(file);
}
}
JsonArray jsonArray = submitQuery(queryPrefix + chunkedFiles + querySuffix);
for (JsonNumber datafileIdJsonNumber : jsonArray.getValuesAs(JsonNumber.class)) {
datafileIds.add(datafileIdJsonNumber.longValueExact());
}
response.submitDatafilesQuery(queryPrefix + chunkedFiles + querySuffix);

return datafileIds;
return response;
}

/**
Expand All @@ -209,6 +234,21 @@ public long getDatasetFileCount(long datasetId) throws TopcatException {
return jsonArray.getJsonNumber(0).longValueExact();
}

/**
* Utility method to get the fileSize (not size) of a Dataset by SELECTing its
* child Datafiles. Ideally the fileSize field should be used, this is a
* fallback option if that field is not set.
*
* @param datasetId ICAT Dataset.id
* @return The total size of Datafiles in the specified Dataset
* @throws TopcatException
*/
public long getDatasetFileSize(long datasetId) throws TopcatException {
String query = "SELECT SUM(datafile.fileSize) FROM Datafile datafile WHERE datafile.dataset.id = " + datasetId;
JsonArray jsonArray = submitQuery(query);
return jsonArray.getJsonNumber(0).longValueExact();
}

/**
* Utility method for submitting an unencoded query to the entityManager
* endpoint, and returning the resultant JsonArray.
Expand Down Expand Up @@ -238,6 +278,11 @@ private JsonArray submitQuery(String query) throws TopcatException {
/**
* Gets a single Entity of the specified type, without any other conditions.
*
* NOTE: This function is written and intended for getting Investigation,
* Dataset or Datafile entities as part of the tests. It does not handle casing of
* entities containing multiple words, or querying for a specific instance of an
* entity.
*
* @param entityType Type of ICAT Entity to get
* @return A single ICAT Entity of the specified type as a JsonObject
* @throws TopcatException
Expand Down Expand Up @@ -391,7 +436,8 @@ public int getQueuePriority(String userName) throws TopcatException {
}
}

if (!userName.startsWith(Properties.getInstance().getProperty("anonUserName"))) {
String anonUserName = Properties.getInstance().getProperty("anonUserName");
if (anonUserName == null || !userName.startsWith(anonUserName)) {
// The anonymous cart username will end with the user's sessionId so cannot do .equals
return priorityMap.getAuthenticatedPriority();
} else {
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/org/icatproject/topcat/PriorityMap.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,10 @@ public PriorityMap() {
Properties properties = Properties.getInstance();

anonUserName = properties.getProperty("anonUserName", "");
if (anonUserName.equals("")) {
logger.warn("anonUserName not defined, cannot distinguish anonymous and authenticated users so "
+ "authenticated priority will be used as default level");
}
anonDownloadEnabled = Boolean.parseBoolean(properties.getProperty("anonDownloadEnabled", "true"));
String defaultString;
if (anonDownloadEnabled) {
Expand Down
66 changes: 35 additions & 31 deletions src/main/java/org/icatproject/topcat/StatusCheck.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import jakarta.ejb.EJB;
import jakarta.ejb.Schedule;
import jakarta.ejb.Singleton;
import jakarta.json.JsonObject;
import jakarta.persistence.EntityManager;
import jakarta.persistence.PersistenceContext;
import jakarta.persistence.TypedQuery;
Expand Down Expand Up @@ -114,35 +115,35 @@ public void updateStatuses(int pollDelay, int pollIntervalWait, IdsClient inject
String queryString = selectString + " and " + notExpiredCondition + " and (" + isActiveCondition + ")";

TypedQuery<Download> query = em.createQuery(queryString, Download.class);
List<Download> downloads = query.getResultList();
List<Download> downloads = query.getResultList();

for (Download download : downloads) {
Date lastCheck = lastChecks.get(download.getId());
Date now = new Date();
long createdSecondsAgo = (now.getTime() - download.getCreatedAt().getTime()) / 1000;
Date lastCheck = lastChecks.get(download.getId());
Date now = new Date();
long createdSecondsAgo = (now.getTime() - download.getCreatedAt().getTime()) / 1000;
if (download.getStatus() == DownloadStatus.PREPARING) {
// If prepareDownload was called previously but caught an exception (other than
// TopcatException), we should not call it again immediately, but should impose
// a delay. See issue #462.
if (lastCheck == null) {
prepareDownload(download, injectedIdsClient);
} else {
long lastCheckSecondsAgo = (now.getTime() - lastCheck.getTime()) / 1000;
prepareDownload(download, injectedIdsClient);
} else {
long lastCheckSecondsAgo = (now.getTime() - lastCheck.getTime()) / 1000;
if (lastCheckSecondsAgo >= pollIntervalWait) {
prepareDownload(download, injectedIdsClient);
}
}
} else if (createdSecondsAgo >= pollDelay) {
prepareDownload(download, injectedIdsClient);
}
}
} else if (download.getPreparedId() != null && createdSecondsAgo >= pollDelay) {
if (lastCheck == null) {
performCheck(download, injectedIdsClient);
} else {
long lastCheckSecondsAgo = (now.getTime() - lastCheck.getTime()) / 1000;
performCheck(download, injectedIdsClient);
} else {
long lastCheckSecondsAgo = (now.getTime() - lastCheck.getTime()) / 1000;
if (lastCheckSecondsAgo >= pollIntervalWait) {
performCheck(download, injectedIdsClient);
}
performCheck(download, injectedIdsClient);
}
}
}
}
}
}

private void performCheck(Download download, IdsClient injectedIdsClient) {
Expand Down Expand Up @@ -250,12 +251,14 @@ private void prepareDownload(Download download, IdsClient injectedIdsClient, Str
String preparedId = idsClient.prepareData(sessionId, download.getInvestigationIds(), download.getDatasetIds(), download.getDatafileIds());
download.setPreparedId(preparedId);

try {
Long size = idsClient.getSize(sessionId, download.getInvestigationIds(), download.getDatasetIds(), download.getDatafileIds());
download.setSize(size);
} catch(Exception e) {
logger.error("prepareDownload: setting size to -1 as getSize threw exception: " + e.getMessage());
download.setSize(-1);
if (download.getSize() <= 0) {
try {
Long size = idsClient.getSize(sessionId, download.getInvestigationIds(), download.getDatasetIds(), download.getDatafileIds());
download.setSize(size);
} catch(Exception e) {
logger.error("prepareDownload: setting size to -1 as getSize threw exception: " + e.getMessage());
download.setSize(-1);
}
}

if (download.getIsTwoLevel() || !download.getTransport().matches("https|http")) {
Expand Down Expand Up @@ -285,19 +288,20 @@ private void prepareDownload(Download download, IdsClient injectedIdsClient, Str
* @param sessionIds Map from Facility to functional sessionId
* @param facilityName Name of ICAT Facility to get the sessionId for
* @return Functional ICAT sessionId
* @throws InternalException If the facilityName cannot be mapped to an ICAT url
* @throws BadRequestException If the login fails
* @throws Exception If the login fails
*/
private String getQueueSessionId(Map<String, String> sessionIds, String facilityName)
throws InternalException, BadRequestException {
throws Exception {
String sessionId = sessionIds.get(facilityName);
if (sessionId == null) {
IcatClient icatClient = new IcatClient(FacilityMap.getInstance().getIcatUrl(facilityName));
Properties properties = Properties.getInstance();
String plugin = properties.getProperty("queue.account." + facilityName + ".plugin");
String username = properties.getProperty("queue.account." + facilityName + ".username");
String password = properties.getProperty("queue.account." + facilityName + ".password");
sessionId = icatClient.login(plugin, username, password);
String jsonString = icatClient.login(plugin, username, password);
JsonObject jsonObject = Utils.parseJsonObject(jsonString);
sessionId = jsonObject.getString("sessionId");
sessionIds.put(facilityName, sessionId);
}
return sessionId;
Expand All @@ -315,7 +319,7 @@ private String getQueueSessionId(Map<String, String> sessionIds, String facility
*/
public void startQueuedDownloads(int maxActiveDownloads) throws Exception {
if (maxActiveDownloads == 0) {
logger.debug("Preparing of queued jobs disabled by config, skipping");
logger.trace("Preparing of queued jobs disabled by config, skipping");
return;
}

Expand All @@ -332,7 +336,7 @@ public void startQueuedDownloads(int maxActiveDownloads) throws Exception {
int activeDownloadsSize = activeDownloads.size();
if (activeDownloadsSize >= maxActiveDownloads) {
String format = "More downloads currently RESTORING {} than maxActiveDownloads {}, cannot prepare queued jobs";
logger.info(format, activeDownloadsSize, maxActiveDownloads);
logger.trace(format, activeDownloadsSize, maxActiveDownloads);
return;
}
availableDownloads -= activeDownloadsSize;
Expand All @@ -346,13 +350,13 @@ public void startQueuedDownloads(int maxActiveDownloads) throws Exception {
Map<String, String> sessionIds = new HashMap<>();
if (maxActiveDownloads <= 0) {
// No limits on how many to submit
logger.info("Preparing {} queued downloads", queuedDownloads.size());
logger.trace("Preparing {} queued downloads", queuedDownloads.size());
for (Download queuedDownload : queuedDownloads) {
queuedDownload.setStatus(DownloadStatus.PREPARING);
prepareDownload(queuedDownload, null, getQueueSessionId(sessionIds, queuedDownload.getFacilityName()));
}
} else {
logger.info("Preparing up to {} queued downloads", availableDownloads);
logger.trace("Preparing up to {} queued downloads", availableDownloads);
HashMap<Integer, List<Download>> mapping = new HashMap<>();
for (Download queuedDownload : queuedDownloads) {
String sessionId = getQueueSessionId(sessionIds, queuedDownload.getFacilityName());
Expand Down
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