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Filter expired permissions from RAS Ga4gh Passports #240

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merged 6 commits into from
Feb 11, 2025
Merged

Filter expired permissions from RAS Ga4gh Passports #240

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c34a81f
Filter expired permissions from RAS Ga4gh Passports
Gcolon021 Feb 7, 2025
347a5a5
Refactor date initialization and add test for permission filtering
Gcolon021 Feb 10, 2025
b8088ad
Use `Instant.now()` instead of `new Date().toInstant()`.
Gcolon021 Feb 10, 2025
6ad5215
Use `Instant.now()` instead of `new Date().toInstant()`.
Gcolon021 Feb 10, 2025
0d713ea
Normalize timestamp to seconds in RASPassPortService.
Gcolon021 Feb 10, 2025
68d956a
Update pic-sure-auth-services/src/main/java/edu/harvard/hms/dbmi/avil…
Gcolon021 Feb 10, 2025
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20 changes: 8 additions & 12 deletions ...ces/src/main/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@
import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission;
import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil;
import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil;
import jakarta.annotation.PostConstruct;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand All @@ -21,10 +20,9 @@
import org.springframework.util.LinkedMultiValueMap;
import org.springframework.util.MultiValueMap;

import java.util.HashSet;
import java.util.List;
import java.util.Optional;
import java.util.Set;
import java.time.Instant;
import java.util.*;
import java.util.stream.Collectors;

@Service
public class RASPassPortService {
Expand Down Expand Up @@ -161,20 +159,18 @@ public Optional<String> validateVisa(String visa) {
return Optional.ofNullable(responseVal);
}

public Set<RasDbgapPermission> ga4gpPassportToRasDbgapPermissions(List<String> ga4ghPassports) {
public Set<RasDbgapPermission> ga4gpPassportToRasDbgapPermissions(Set<Optional<Ga4ghPassportV1>> ga4ghPassports) {
if (ga4ghPassports == null) {
return null;
}

logger.debug("Converting ga4ghPassports to RasDbgapPermissions");
HashSet<RasDbgapPermission> rasDbgapPermissions = new HashSet<>();
long date = Instant.now().toEpochMilli() / 1000;
ga4ghPassports.forEach(ga4ghPassport -> {
Optional<Ga4ghPassportV1> parsedGa4ghPassportV1 = JWTUtil.parseGa4ghPassportV1(ga4ghPassport);
if (parsedGa4ghPassportV1.isPresent()) {
Ga4ghPassportV1 ga4ghPassportV1 = parsedGa4ghPassportV1.get();
logger.info("ga4gh_passport_v1: {}", ga4ghPassportV1);

rasDbgapPermissions.addAll(ga4ghPassportV1.getRasDbgagPermissions());
if (ga4ghPassport.isPresent()) {
Ga4ghPassportV1 ga4ghPassportV1 = ga4ghPassport.get();
rasDbgapPermissions.addAll(ga4ghPassportV1.getRasDbgagPermissions().stream().filter(rasDbgapPermission -> date <= rasDbgapPermission.getExpiration()).collect(Collectors.toSet()));
}
});

Expand Down
5 changes: 4 additions & 1 deletion .../harvard/hms/dbmi/avillach/auth/service/impl/authentication/RASAuthenticationService.java
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Expand Up @@ -5,10 +5,12 @@
import com.fasterxml.jackson.databind.node.ObjectNode;
import edu.harvard.hms.dbmi.avillach.auth.entity.Connection;
import edu.harvard.hms.dbmi.avillach.auth.entity.User;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission;
import edu.harvard.hms.dbmi.avillach.auth.service.AuthenticationService;
import edu.harvard.hms.dbmi.avillach.auth.service.impl.*;
import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil;
import edu.harvard.hms.dbmi.avillach.auth.utils.RestClientUtil;
import org.apache.commons.lang3.StringUtils;
import org.slf4j.Logger;
Expand Down Expand Up @@ -142,7 +144,8 @@ private Optional<Passport> extractAndVerifyPassport(Map<String, String> authRequ

protected User updateRasUserRoles(String code, User user, Passport rasPassport) {
logger.info("RAS PASSPORT FOUND ___ USER: {} ___ PASSPORT: {} ___ CODE {}", user.getSubject(), rasPassport, code);
Set<RasDbgapPermission> dbgapPermissions = this.rasPassPortService.ga4gpPassportToRasDbgapPermissions(rasPassport.getGa4ghPassportV1());
Set<Optional<Ga4ghPassportV1>> ga4ghPassports = rasPassport.getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1).filter(Optional::isPresent).collect(Collectors.toSet());
Set<RasDbgapPermission> dbgapPermissions = this.rasPassPortService.ga4gpPassportToRasDbgapPermissions(ga4ghPassports);
Set<String> dbgapRoleNames = this.roleService.getRoleNamesForDbgapPermissions(dbgapPermissions);
user = userService.updateUserRoles(user, dbgapRoleNames);
logger.debug("USER {} ROLES UPDATED {} ___ CODE {}",
Expand Down
89 changes: 80 additions & 9 deletions ...src/test/java/edu/harvard/hms/dbmi/avillach/auth/service/impl/RASPassPortServiceTest.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package edu.harvard.hms.dbmi.avillach.auth.service.impl;

import edu.harvard.hms.dbmi.avillach.auth.enums.PassportValidationResponse;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.Ga4ghPassportV1;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.Passport;
import edu.harvard.hms.dbmi.avillach.auth.model.ras.RasDbgapPermission;
import edu.harvard.hms.dbmi.avillach.auth.utils.JWTUtil;
Expand All @@ -13,13 +14,12 @@
import org.springframework.http.ResponseEntity;
import org.springframework.test.context.ContextConfiguration;

import java.util.Optional;
import java.util.Set;
import java.time.Instant;
import java.util.*;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.stream.Collectors;

import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.Mockito.when;

Expand Down Expand Up @@ -57,22 +57,93 @@ public void testGa4ghPassPortStudies_IsNull() {
}

@Test
public void testGa4gpPassportStudies_IsNotNull() {
public void testGa4gpPassportStudies_IsNotNull_And_ExpiredPermissionsExcluded() {
Optional<Passport> passport = JWTUtil.parsePassportJWTV11(exampleRasPassport);
Set<RasDbgapPermission> permissions = rasPassPortService.ga4gpPassportToRasDbgapPermissions(passport.get().getGa4ghPassportV1());
Set<Optional<Ga4ghPassportV1>> ga4ghPassports = passport.get().getGa4ghPassportV1().stream().map(JWTUtil::parseGa4ghPassportV1).filter(Optional::isPresent).collect(Collectors.toSet());
Set<RasDbgapPermission> permissions = rasPassPortService.ga4gpPassportToRasDbgapPermissions(ga4ghPassports);
assertNotNull(permissions);
assertTrue(permissions.isEmpty());
}

@Test
public void testGa4gpPassportStudies_HasCorrectStudies() {
Optional<Passport> passport = JWTUtil.parsePassportJWTV11(exampleRasPassport);
Set<RasDbgapPermission> permissions = rasPassPortService.ga4gpPassportToRasDbgapPermissions(passport.get().getGa4ghPassportV1());
long futureDate = (Instant.now().toEpochMilli() / 1000) + 100000;

// Update the expiry date of each permission in our test passport. All permissions in the example passport
// expired in 2022.
Set<Optional<Ga4ghPassportV1>> ga4ghPassports = passport.get().getGa4ghPassportV1().stream()
.map(JWTUtil::parseGa4ghPassportV1)
.filter(Optional::isPresent)
.map(optionalPassport -> {
Ga4ghPassportV1 ga4ghPassportV1 = optionalPassport.get();
List<RasDbgapPermission> rasDbgagPermissions = ga4ghPassportV1.getRasDbgagPermissions();
List<RasDbgapPermission> newExpires = rasDbgagPermissions.stream().peek(rasDbgapPermission -> rasDbgapPermission.setExpiration(futureDate)).toList();
ga4ghPassportV1.setRasDbgagPermissions(newExpires);
return Optional.of(ga4ghPassportV1);
})
.collect(Collectors.toSet());

Set<RasDbgapPermission> permissions = rasPassPortService.ga4gpPassportToRasDbgapPermissions(ga4ghPassports);

assertEquals(2, permissions.size());
assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000300")));
assertTrue(permissions.stream().anyMatch(p -> p.getPhsId().equals("phs000006")));
}

@Test
public void testGa4gpPassportStudies_HalfAreExpired() {
Optional<Passport> passport = JWTUtil.parsePassportJWTV11(exampleRasPassport);
long futureDate = (Instant.now().toEpochMilli() / 1000) + 100000;
long pastDate = (Instant.now().toEpochMilli() / 1000) - 100000;

List<String> expiredPHS = new ArrayList<>();
List<String> validPHS = new ArrayList<>();
// Update the expiry date of each permission in our test passport.
// We alternate: even-indexed permissions become valid, odd-indexed ones remain (or become) invalid.
Set<Optional<Ga4ghPassportV1>> ga4ghPassports = passport.get().getGa4ghPassportV1().stream()
.map(JWTUtil::parseGa4ghPassportV1)
.filter(Optional::isPresent)
.map(optionalPassport -> {
Ga4ghPassportV1 ga4ghPassportV1 = optionalPassport.get();
List<RasDbgapPermission> rasDbgagPermissions = ga4ghPassportV1.getRasDbgagPermissions();

AtomicInteger index = new AtomicInteger();
List<RasDbgapPermission> updatedPermissions = rasDbgagPermissions.stream()
.peek(permission -> {
if (index.getAndIncrement() % 2 == 0) {
// For even indices, use a valid future expiration.
permission.setExpiration(futureDate);
validPHS.add(permission.getPhsId());
} else {
// For odd indices, use an expired (invalid) timestamp.
permission.setExpiration(pastDate);
expiredPHS.add(permission.getPhsId());
}
})
.collect(Collectors.toList());

ga4ghPassportV1.setRasDbgagPermissions(updatedPermissions);
return Optional.of(ga4ghPassportV1);
})
.collect(Collectors.toSet());

// Convert the GA4GH passports to RAS DbGaP permissions. The underlying conversion
// should filter out the ones with invalid expiration dates.
Set<RasDbgapPermission> permissions = rasPassPortService.ga4gpPassportToRasDbgapPermissions(ga4ghPassports);

// We expect only the valid (future-dated) permissions to be returned.
assertEquals(validPHS.size(), permissions.size());

// verify only expected values are in permissions set
List<String> finalPHS = permissions.stream().map(RasDbgapPermission::getPhsId).toList();
assertEquals(finalPHS, validPHS, "The valid phs ids do not match the expected values.");

// verify no expired permissions are in the passport.
expiredPHS.forEach(phs -> assertFalse(finalPHS.contains(phs), "Expired phs id " + phs + " should not appear in the valid permissions."));
}


@Test
public void testValidateVisa_Valid() {
when(restClientUtil.retrievePostResponse(any(String.class), any()))
Expand Down