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Bug/cite 221 #276

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Bug/cite 221 #276

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1ae05d4
[CITE-221] Added config for creating mongo DB index
PradnyaC11 Jul 3, 2024
4b4e181
[CITE-221] Added config to create mongo index
PradnyaC11 Jul 5, 2024
a8fbf93
[CITE-221] Added index config for key and groupId for citation, colle…
PradnyaC11 Jul 8, 2024
c7a356b
[CITE-221] Added duplicate key exception to methods
PradnyaC11 Jul 9, 2024
7121561
[CITE-221] Added duplicate key exception for group
PradnyaC11 Jul 12, 2024
fec500a
[CITE-221] Added duplicate key exception for group
PradnyaC11 Jul 15, 2024
2ac9b55
[CITE-221] Added few for Duplicate key exceptions and updated logic
PradnyaC11 Jul 16, 2024
73c3aaf
[CITE-221] Reverted duplicate key exceptions changes
PradnyaC11 Jul 17, 2024
0b2624a
[CITE-221] Updated logic so as to not throw duplicate key exception
PradnyaC11 Jul 18, 2024
a87f135
[CITE-221] Updated logic to avoid getting duplicate key exception
PradnyaC11 Jul 19, 2024
12f6aa3
[CITE-221] Addressing PR comment
PradnyaC11 Jul 19, 2024
42d1c8e
[CITE-221] Updated citesphere model version in pom.xml
PradnyaC11 Sep 24, 2024
d7a4219
Merge branch 'develop' into bug/CITE-221
PradnyaC11 Oct 28, 2024
a8a977c
[CITE-221] Addressed PR comments
PradnyaC11 Oct 29, 2024
b039e95
[CITE-221] Addressed PR comments
PradnyaC11 Oct 31, 2024
928ea95
[CITE-221] Resolved code factor dependency issue
PradnyaC11 Oct 31, 2024
1bea700
[CITE-221] Fixed test cases
PradnyaC11 Dec 3, 2024
87abbe4
Merge branch 'develop' into bug/CITE-221
PradnyaC11 Dec 3, 2024
ac2599b
[CITE-221] Fixed code factor issues
PradnyaC11 Dec 3, 2024
426cfbc
Merge branch 'bug/CITE-221' of https://github.com/diging/citesphere i…
PradnyaC11 Dec 5, 2024
d707d59
[CITE-221] Changed java version back to 1.8 because of error in test
PradnyaC11 Feb 21, 2025
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2 changes: 1 addition & 1 deletion citesphere/pom.xml
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Expand Up @@ -25,7 +25,7 @@
<spring.kafka.version>2.2.6.RELEASE</spring.kafka.version>
<spring-social-zotero.version>0.12</spring-social-zotero.version>
<citesphere.messages.version>0.4</citesphere.messages.version>
<citesphere.model.version>1.19</citesphere.model.version>
<citesphere.model.version>1.23-SNAPSHOT</citesphere.model.version>
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this needs to be a proper version


<admin.password>$2a$04$oQo44vqcDIFRoYKiAXoNheurzkwX9dcNmowvTX/hsWuBMwijqn44i</admin.password>

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3 changes: 0 additions & 3 deletions citesphere/src/main/java/edu/asu/diging/citesphere/api/v1/user/GroupApiController.java
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Expand Up @@ -11,14 +11,11 @@
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestHeader;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;

import edu.asu.diging.citesphere.api.v1.V1Controller;
import edu.asu.diging.citesphere.api.v1.model.impl.Collections;
import edu.asu.diging.citesphere.api.v1.model.impl.Group;
import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
import edu.asu.diging.citesphere.core.service.IGroupManager;
import edu.asu.diging.citesphere.core.service.jobs.ISyncJobManager;
import edu.asu.diging.citesphere.core.user.IUserManager;
import edu.asu.diging.citesphere.model.bib.ICitationGroup;
import edu.asu.diging.citesphere.user.IUser;
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1 change: 0 additions & 1 deletion citesphere/src/main/java/edu/asu/diging/citesphere/api/v1/user/ItemApiController.java
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Expand Up @@ -2,7 +2,6 @@

import java.io.IOException;
import java.security.Principal;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;

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26 changes: 26 additions & 0 deletions citesphere/src/main/java/edu/asu/diging/citesphere/config/core/MongoConfig.java
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Expand Up @@ -5,18 +5,23 @@
import java.time.ZoneOffset;
import java.util.Arrays;

import org.springframework.beans.factory.InitializingBean;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.PropertySource;
import org.springframework.core.convert.converter.Converter;
import org.springframework.data.convert.ReadingConverter;
import org.springframework.data.convert.WritingConverter;
import org.springframework.data.domain.Sort;
import org.springframework.data.mongodb.MongoDatabaseFactory;
import org.springframework.data.mongodb.core.MongoTemplate;
import org.springframework.data.mongodb.core.SimpleMongoClientDatabaseFactory;
import org.springframework.data.mongodb.core.convert.DefaultDbRefResolver;
import org.springframework.data.mongodb.core.convert.MappingMongoConverter;
import org.springframework.data.mongodb.core.index.Index;
import org.springframework.data.mongodb.core.index.IndexOperations;
import org.springframework.data.mongodb.core.mapping.MongoMappingContext;
import org.springframework.data.mongodb.repository.config.EnableMongoRepositories;
import org.springframework.stereotype.Component;
Expand All @@ -28,6 +33,10 @@
import com.mongodb.client.MongoClient;
import com.mongodb.client.MongoClients;

import edu.asu.diging.citesphere.model.bib.impl.Citation;
import edu.asu.diging.citesphere.model.bib.impl.CitationCollection;
import edu.asu.diging.citesphere.model.bib.impl.CitationGroup;

@Configuration
@PropertySource({ "classpath:config.properties", "${appConfigFile:classpath:}/app.properties" })
@EnableMongoRepositories({ "edu.asu.diging.citesphere.core.mongo", "edu.asu.diging.citesphere.data.bib" })
Expand Down Expand Up @@ -98,4 +107,21 @@ public OffsetDateTime convert(String source) {
return OffsetDateTime.parse(source);
}
}

@Configuration
public static class MongoIndex implements InitializingBean {

@Autowired
private MongoTemplate mongoTemplate;

@Override
public void afterPropertiesSet() throws Exception {
IndexOperations citationIndexOps = mongoTemplate.indexOps(Citation.class);
citationIndexOps.ensureIndex(new Index().on("key", Sort.Direction.ASC).unique());
IndexOperations citationCollectionIndexOps = mongoTemplate.indexOps(CitationCollection.class);
citationCollectionIndexOps.ensureIndex(new Index().on("key", Sort.Direction.ASC).unique());
IndexOperations citationGorupIndexOps = mongoTemplate.indexOps(CitationGroup.class);
citationGorupIndexOps.ensureIndex(new Index().on("groupId", Sort.Direction.ASC).unique());
}
}
}
28 changes: 18 additions & 10 deletions citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
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Expand Up @@ -14,6 +14,9 @@
import javax.annotation.PostConstruct;
import javax.transaction.Transactional;

import org.bson.types.ObjectId;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.PropertySource;
Expand Down Expand Up @@ -181,15 +184,15 @@ public void updateCitation(IUser user, String groupId, ICitation citation)
throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException {
long citationVersion = zoteroManager.getGroupItemVersion(user, groupId, citation.getKey());
Optional<ICitation> storedCitationOptional = citationStore.findById(citation.getKey());
ICitation updatedCitation = zoteroManager.updateCitation(user, groupId, citation);
if (storedCitationOptional.isPresent()) {
ICitation storedCitation = storedCitationOptional.get();
if (storedCitation.getVersion() != citationVersion) {
throw new CitationIsOutdatedException();
}
citationStore.delete(storedCitation);
updatedCitation.setId(storedCitation.getId());
}

ICitation updatedCitation = zoteroManager.updateCitation(user, groupId, citation);
citationStore.save(updatedCitation);
}

Expand Down Expand Up @@ -251,7 +254,7 @@ public ICitation updateCitationFromZotero(IUser user, String groupId, String ite

Optional<ICitation> oldCitation = citationStore.findById(itemKey);
if (oldCitation.isPresent()) {
citationStore.delete(oldCitation.get());
citation.setId(oldCitation.get().getId());
}
citationStore.save(citation);
return citation;
Expand Down Expand Up @@ -326,8 +329,9 @@ public List<ICitationGroup> getGroups(IUser user) {
if (groupOptional.isPresent()) {
ICitationGroup group = groupOptional.get();
if (group.getMetadataVersion() != groupVersions.get(id)) {
groupRepository.delete((CitationGroup) group);
ObjectId groupID = group.getId();
group = zoteroManager.getGroup(user, id + "", true);
group.setId(groupID);
group.setUpdatedOn(OffsetDateTime.now().toString());
}
addUserToGroup(group, user);
Expand Down Expand Up @@ -379,14 +383,17 @@ public CitationResults getGroupItems(IUser user, String groupId, String collecti

ICitationGroup group = null;
Optional<ICitationGroup> groupOptional = groupRepository.findFirstByGroupId(new Long(groupId));
if (!groupOptional.isPresent() || !groupOptional.get().getUsers().contains(user.getUsername())) {
if (!groupOptional.isPresent()) {
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hm, I'm fairly certain this create a security issue here. Basically, doesn't this say "if the group does not yet locally exist, get it from zotero" (that's fine zotero will complain if the user does not have access), however, "if the group does exist, let's just add the user to the group" (this seems wrong, where is the check if the user has access?).

group = zoteroManager.getGroup(user, groupId, false);
if (group != null) {
group.getUsers().add(user.getUsername());
groupRepository.save((CitationGroup) group);
}
} else {
group = groupOptional.get();
if (!group.getUsers().contains(user.getUsername())){
group.getUsers().add(user.getUsername());
}
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this should not be needed, should it? this else should only be called if the group is present and the user has access to it?

}

if (group == null) {
Expand All @@ -399,13 +406,14 @@ public CitationResults getGroupItems(IUser user, String groupId, String collecti
long previousVersion = group.getContentVersion();
// first update the group info
// if we are using a previously stored group, delete it
ICitationGroup zeteroGroup = null;
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spelling mistake

if (group.getId() != null) {
groupRepository.delete((CitationGroup) group);
group = zoteroManager.getGroup(user, groupId + "", true);
zeteroGroup = zoteroManager.getGroup(user, groupId + "", true);
zeteroGroup.setId(group.getId());
}
group.setUpdatedOn(OffsetDateTime.now().toString());
addUserToGroup(group, user);
group = groupRepository.save((CitationGroup) group);
zeteroGroup.setUpdatedOn(OffsetDateTime.now().toString());
addUserToGroup(zeteroGroup, user);
group = groupRepository.save((CitationGroup) zeteroGroup);

// then update content
results.setNotModified(false);
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2 changes: 0 additions & 2 deletions citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/GroupManager.java
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Expand Up @@ -6,7 +6,6 @@
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;

import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
import edu.asu.diging.citesphere.core.service.ICitationCollectionManager;
import edu.asu.diging.citesphere.core.service.ICitationManager;
import edu.asu.diging.citesphere.core.service.IGroupManager;
Expand Down Expand Up @@ -43,7 +42,6 @@ public ICitationGroup getGroup(IUser user, String groupId) {
Optional<ICitationGroup> groupOptional = groupRepository.findFirstByGroupId(new Long(groupId));
if (groupOptional.isPresent() && groupOptional.get().getUsers().contains(user.getUsername())) {
return (ICitationGroup) groupOptional.get();
}

ICitationGroup group = zoteroManager.getGroup(user, groupId, false);
if (group != null) {
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4 changes: 0 additions & 4 deletions .../src/main/java/edu/asu/diging/citesphere/core/service/jobs/impl/UploadFileJobManager.java
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Expand Up @@ -18,15 +18,11 @@
import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
import edu.asu.diging.citesphere.core.kafka.IKafkaRequestProducer;
import edu.asu.diging.citesphere.core.repository.jobs.UploadFileJobRepository;
import edu.asu.diging.citesphere.core.service.ICitationManager;
import edu.asu.diging.citesphere.core.service.IGroupManager;
import edu.asu.diging.citesphere.core.service.giles.GilesUploadChecker;
import edu.asu.diging.citesphere.core.service.giles.GilesUploadService;
import edu.asu.diging.citesphere.core.service.jobs.IUploadFileJobManager;
import edu.asu.diging.citesphere.core.service.jwt.IJwtTokenService;
import edu.asu.diging.citesphere.core.service.upload.IFileStorageManager;
import edu.asu.diging.citesphere.model.bib.ICitation;
import edu.asu.diging.citesphere.model.bib.ICitationGroup;
import edu.asu.diging.citesphere.model.bib.IGilesUpload;
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2 changes: 0 additions & 2 deletions citesphere/src/main/java/edu/asu/diging/citesphere/web/user/DownloadGilesFileController.java
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Expand Up @@ -12,15 +12,13 @@
import org.springframework.ui.Model;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;

import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
import edu.asu.diging.citesphere.core.service.ICitationManager;
import edu.asu.diging.citesphere.model.bib.ICitation;
import edu.asu.diging.citesphere.model.bib.IGilesUpload;
import edu.asu.diging.citesphere.model.bib.impl.IGilesFile;
import edu.asu.diging.citesphere.user.IUser;

@Controller
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1 change: 0 additions & 1 deletion citesphere/src/main/java/edu/asu/diging/citesphere/web/user/SyncItemController.java
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Expand Up @@ -7,7 +7,6 @@
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.servlet.mvc.support.RedirectAttributes;

import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
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