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Merge 23.11 to develop
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@labkey-teamcity
labkey-teamcity committed Jan 30, 2024
2 parents a3efe26 + ca1e956 commit ac1a5f3
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Showing 4 changed files with 125 additions and 17 deletions.
1 change: 1 addition & 0 deletions panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicModule.java
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Expand Up @@ -45,6 +45,7 @@
import org.labkey.panoramapublic.catalog.CatalogImageAttachmentType;
import org.labkey.panoramapublic.model.Journal;
import org.labkey.panoramapublic.model.speclib.SpecLibKey;
import org.labkey.panoramapublic.pipeline.CopyExperimentFinalTask;
import org.labkey.panoramapublic.pipeline.CopyExperimentPipelineProvider;
import org.labkey.panoramapublic.pipeline.PxValidationPipelineProvider;
import org.labkey.panoramapublic.proteomexchange.ExperimentModificationGetter;
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8 changes: 4 additions & 4 deletions panoramapublic/src/org/labkey/panoramapublic/PanoramaPublicNotification.java
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Expand Up @@ -321,12 +321,12 @@ private static void appendUserDetails(User user, String userType, StringBuilder

public static String getUserName(User user)
{
return !StringUtils.isBlank(user.getFullName()) ? user.getFullName() : user.getFriendlyName();
return escape(!StringUtils.isBlank(user.getFullName()) ? user.getFullName() : user.getFriendlyName());
}

private static String getUserDetails(User user)
{
return escape(getUserName(user)) + " (" + escape(user.getEmail()) + ")";
return getUserName(user) + escape(" (" + user.getEmail() + ")");
}

private static String getContainerLink(Container container)
Expand Down Expand Up @@ -385,7 +385,7 @@ public static String getExperimentCopiedMessageBody(ExperimentAnnotations source
User fromUser,
boolean recopy)
{
String journalName = journal.getName();
String journalName = escape(journal.getName());

String accessUrlLink = link(targetExperiment.getShortUrl().renderShortURL());

Expand All @@ -405,7 +405,7 @@ public static String getExperimentCopiedMessageBody(ExperimentAnnotations source
message.append(NL2)
.append("As requested, your data on ").append(journalName).append(" is private. Here are the reviewer account details:")
.append(NL).append("Email: ").append(reviewer.getEmail())
.append(NL).append("Password: ").append(reviewerPassword);
.append(NL).append("Password: ").append(escape(reviewerPassword));
}
else
{
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112 changes: 99 additions & 13 deletions panoramapublic/src/org/labkey/panoramapublic/pipeline/CopyExperimentFinalTask.java
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Expand Up @@ -15,7 +15,6 @@
*/
package org.labkey.panoramapublic.pipeline;

import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.jetbrains.annotations.NotNull;
Expand All @@ -38,6 +37,7 @@
import org.labkey.api.security.InvalidGroupMembershipException;
import org.labkey.api.security.MemberType;
import org.labkey.api.security.MutableSecurityPolicy;
import org.labkey.api.security.PasswordRule;
import org.labkey.api.security.SecurityManager;
import org.labkey.api.security.SecurityPolicy;
import org.labkey.api.security.SecurityPolicyManager;
Expand Down Expand Up @@ -81,6 +81,8 @@
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.security.SecureRandom;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
Expand Down Expand Up @@ -145,7 +147,7 @@ private void finishUp(PipelineJob job, CopyExperimentJobSupport jobSupport) thro
ExperimentAnnotations previousCopy = getPreviousCopyRemoveShortUrl(latestCopiedSubmission, user);

// Update the row in panoramapublic.ExperimentAnnotations - set the shortURL and version
ExperimentAnnotations targetExperiment = updateExperimentAnnotations(container, sourceExperiment, js, previousCopy, jobSupport, user, log);
ExperimentAnnotations targetExperiment = updateExperimentAnnotations(container, sourceExperiment, js, user, log);

// If there is a Panorama Public data catalog entry associated with the previous copy of the experiment, move it to the
// new container.
Expand Down Expand Up @@ -340,11 +342,10 @@ private Pair<User, String> assignReviewer(JournalSubmission js, ExperimentAnnota
{
if (previousCopy == null || previousCopy.isPublic())
{
String reviewerPassword = createPassword();
User reviewer;
ReviewerAndPassword reviewerAndPassword;
try
{
reviewer = createReviewerAccount(jobSupport.getReviewerEmailPrefix(), reviewerPassword, user, log);
reviewerAndPassword = createReviewerAccount(jobSupport.getReviewerEmailPrefix(), user, log);
}
catch (ValidEmail.InvalidEmailException e)
{
Expand All @@ -354,6 +355,7 @@ private Pair<User, String> assignReviewer(JournalSubmission js, ExperimentAnnota
{
throw new PipelineJobException("Error creating a new account for reviewer", e);
}
User reviewer = reviewerAndPassword.getReviewer();
assignReader(reviewer, targetExperiment.getContainer(), user);
js.getJournalExperiment().setReviewer(reviewer.getUserId());
SubmissionManager.updateJournalExperiment(js.getJournalExperiment(), user);
Expand All @@ -363,7 +365,7 @@ private Pair<User, String> assignReviewer(JournalSubmission js, ExperimentAnnota
// CONSIDER: Make this configurable through the Panorama Public admin console.
addToGroup(reviewer, "Reviewers", targetExperiment.getContainer().getProject(), log);

return new Pair<>(reviewer, reviewerPassword);
return new Pair<>(reviewer, reviewerAndPassword.getPassword());
}
}
else
Expand Down Expand Up @@ -463,10 +465,8 @@ private ExperimentAnnotations getPreviousCopyRemoveShortUrl(Submission latestCop

@NotNull
private ExperimentAnnotations updateExperimentAnnotations(Container targetContainer, ExperimentAnnotations sourceExperiment, JournalSubmission js,
ExperimentAnnotations previousCopy, CopyExperimentJobSupport jobSupport,
User user, Logger log) throws PipelineJobException
{

log.info("Updating TargetedMS experiment entry in target folder " + targetContainer.getPath());
ExperimentAnnotations targetExperiment = ExperimentAnnotationsManager.getExperimentInContainer(targetContainer);
if (targetExperiment == null)
Expand Down Expand Up @@ -625,7 +625,7 @@ private Set<User> getUsersWithRole(Container container, Role role)

}

private User createReviewerAccount(String reviewerEmailPrefix, String password, User user, Logger log) throws ValidEmail.InvalidEmailException, SecurityManager.UserManagementException
private ReviewerAndPassword createReviewerAccount(String reviewerEmailPrefix, User user, Logger log) throws ValidEmail.InvalidEmailException, SecurityManager.UserManagementException
{
if(StringUtils.isBlank(reviewerEmailPrefix))
{
Expand All @@ -644,10 +644,14 @@ private User createReviewerAccount(String reviewerEmailPrefix, String password,

log.info("Creating a reviewer account.");
SecurityManager.NewUserStatus newUser = SecurityManager.addUser(email, user, true);
log.info("Created reviewer with email: " + newUser.getUser().getEmail());

log.info("Generating password.");
String password = createPassword(newUser.getUser());
SecurityManager.setPassword(email, password);
log.info("Set reviewer password successfully.");

log.info("Created reviewer with email: User " + newUser.getUser().getEmail());
return newUser.getUser();
return new ReviewerAndPassword(newUser.getUser(), password);
}

private void assignReader(UserPrincipal reader, Container target, User pipelineJobUser)
Expand All @@ -657,9 +661,91 @@ private void assignReader(UserPrincipal reader, Container target, User pipelineJ
SecurityPolicyManager.savePolicy(newPolicy, pipelineJobUser);
}

public static String createPassword()
private static class ReviewerAndPassword
{
private final User _reviewer;
private final String _password;

public ReviewerAndPassword(@NotNull User reviewer, @NotNull String password)
{
_reviewer = reviewer;
_password = password;
}

public User getReviewer()
{
return _reviewer;
}

public String getPassword()
{
return _password;
}
}

private static String createPassword(User user)
{
String password;
do {
password = PasswordGenerator.generate();
} while (!PasswordRule.Strong.isValidForLogin(password, user, null));

return password;
}

private static class PasswordGenerator
{
return RandomStringUtils.randomAlphabetic(8);
private static final List<Character> LOWERCASE = "abcdefghijklmnopqrstuvwxyz".chars().mapToObj(c -> (char)c).collect(Collectors.toList());
private static final List<Character> UPPERCASE = "ABCDEFGHIJKLMNOPQRSTUVWXYZ".chars().mapToObj(c -> (char)c).collect(Collectors.toList());
private static final List<Character> DIGITS = "0123456789".chars().mapToObj(c -> (char)c).collect(Collectors.toList());
private static final List<Character> SYMBOLS = "!@#$%^&*+=?".chars().mapToObj(c -> (char)c).collect(Collectors.toList());

private static final int PASSWORD_LEN = 14;

public static String generate()
{
SecureRandom random = new SecureRandom();

List<Character> passwordChars = new ArrayList<>(PASSWORD_LEN);
List<Character> allChars = new ArrayList<>();

// Initialize the list with all possible characters
allChars.addAll(LOWERCASE);
allChars.addAll(UPPERCASE);
allChars.addAll(DIGITS);
allChars.addAll(SYMBOLS);

// Ensure that there is at least one character from each character category.
addChar(LOWERCASE, passwordChars, allChars, random);
addChar(UPPERCASE, passwordChars, allChars, random);
addChar(DIGITS, passwordChars, allChars, random);
addChar(SYMBOLS, passwordChars, allChars, random);

// Shuffle the list of remaining characters
Collections.shuffle(allChars);

// Add more characters until we are at the desired password length
while (passwordChars.size() < PASSWORD_LEN)
{
addChar(allChars, passwordChars, allChars, random);
}

Collections.shuffle(passwordChars);

return passwordChars.stream().map(String::valueOf).collect(Collectors.joining());
}

/**
* Pick a random character from the given character category, add it to the list of password characters, and
* remove it from the list of all available characters to ensure character uniqueness in the password.
*/
private static void addChar(List<Character> categoryChars, List<Character> passwordChars, List<Character> allChars, SecureRandom random)
{
int randomIdx = random.nextInt(0, categoryChars.size());
Character selected = categoryChars.get(randomIdx);
passwordChars.add(selected);
allChars.remove(selected); // Remove from the list of all available chars so that we have unique characters in the password
}
}

private void assignPxId(ExperimentAnnotations targetExpt, boolean useTestDb) throws ProteomeXchangeServiceException
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21 changes: 21 additions & 0 deletions panoramapublic/test/src/org/labkey/test/tests/panoramapublic/PanoramaPublicBaseTest.java
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Expand Up @@ -37,9 +37,12 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;

public class PanoramaPublicBaseTest extends TargetedMSTest implements PostgresOnlyTest
{
Expand Down Expand Up @@ -75,6 +78,10 @@ public class PanoramaPublicBaseTest extends TargetedMSTest implements PostgresOn

static final String SAMPLEDATA_FOLDER = "panoramapublic/";

private static final Pattern REVIEWER_PASSWORD_LINE = Pattern.compile("Password:\s(\\S+)");
private static final String PASSWORD_SPECIAL_CHARS = "!@#$%^&*+=?";
private static final int REVIEWER_PASSWORD_LEN = 14;

PortalHelper portalHelper = new PortalHelper(this);

@Override
Expand Down Expand Up @@ -439,6 +446,20 @@ private void verifyCopy(String shortAccessUrl, String experimentTitle, @Nullable
String messageText = new BodyWebPart(getDriver(), "View Message").getComponentElement().getText();
var srcFolderTxt = "Source folder: " + "/" + projectName + "/" + folderName;
assertTextPresent(new TextSearcher(messageText), text, srcFolderTxt);

// Unescaped special Markdown characters in the message may cause the password to render incorrectly.
// Extract the reviewer password and check that it has the correct length and expected characters.
Matcher match = REVIEWER_PASSWORD_LINE.matcher(messageText);
assertTrue("Could not find reviewer password in the message", match.find());
String password = match.group(1);
assertEquals("Unexpected length of reviewer password", REVIEWER_PASSWORD_LEN, password.length());
for (int i = 0; i < password.length(); i++)
{
char c = password.charAt(i);
assertTrue("Unexpected character '"+ c + "' in reviewer password " + password,
Character.isUpperCase(c) || Character.isLowerCase(c)
|| Character.isDigit(c) || PASSWORD_SPECIAL_CHARS.contains(String.valueOf(c)));
}
}

@Override
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