From 4b32fa216caede8b0ac4922bbfc3d7fd0d006750 Mon Sep 17 00:00:00 2001 From: Yury Bondarenko Date: Tue, 6 Aug 2024 15:38:55 +0200 Subject: [PATCH 01/18] Make submissiondefinition pagination test more flexible --- .../SubmissionDefinitionsControllerIT.java | 45 +++++++++++-------- .../matcher/SubmissionDefinitionsMatcher.java | 15 +++++-- 2 files changed, 39 insertions(+), 21 deletions(-) diff --git a/dspace-server-webapp/src/test/java/org/dspace/app/rest/SubmissionDefinitionsControllerIT.java b/dspace-server-webapp/src/test/java/org/dspace/app/rest/SubmissionDefinitionsControllerIT.java index babb1fac2326..6ad6aff7e9b0 100644 --- a/dspace-server-webapp/src/test/java/org/dspace/app/rest/SubmissionDefinitionsControllerIT.java +++ b/dspace-server-webapp/src/test/java/org/dspace/app/rest/SubmissionDefinitionsControllerIT.java @@ -8,6 +8,7 @@ package org.dspace.app.rest; import static com.jayway.jsonpath.matchers.JsonPathMatchers.hasJsonPath; +import static org.dspace.app.rest.matcher.SubmissionDefinitionsMatcher.matchSubmissionConfig; import static org.hamcrest.Matchers.allOf; import static org.hamcrest.Matchers.greaterThanOrEqualTo; import static org.hamcrest.Matchers.hasSize; @@ -17,8 +18,12 @@ import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status; +import java.util.List; + import org.dspace.app.rest.matcher.SubmissionDefinitionsMatcher; import org.dspace.app.rest.test.AbstractControllerIntegrationTest; +import org.dspace.app.util.SubmissionConfig; +import org.dspace.app.util.SubmissionConfigReader; import org.dspace.builder.CollectionBuilder; import org.dspace.builder.CommunityBuilder; import org.dspace.content.Collection; @@ -239,13 +244,17 @@ public void findSections() throws Exception { @Test public void findAllPaginationTest() throws Exception { + List definitions = new SubmissionConfigReader().getAllSubmissionConfigs(100, 0); + int totalCount = definitions.size(); + String tokenAdmin = getAuthToken(admin.getEmail(), password); + getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") .param("size", "1") .param("page", "0")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("traditional"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(0)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -259,8 +268,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=6"), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(0))); getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") @@ -268,7 +277,7 @@ public void findAllPaginationTest() throws Exception { .param("page", "1")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("test-hidden"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(1)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -285,8 +294,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page="), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(1))); getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") @@ -294,7 +303,7 @@ public void findAllPaginationTest() throws Exception { .param("page", "2")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("accessConditionNotDiscoverable"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(2)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -311,8 +320,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=6"), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(2))); getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") @@ -320,7 +329,7 @@ public void findAllPaginationTest() throws Exception { .param("page", "3")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("languagetestprocess"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(3)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -337,8 +346,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=6"), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(3))); getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") @@ -346,7 +355,7 @@ public void findAllPaginationTest() throws Exception { .param("page", "4")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("qualdroptest"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(4)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -363,8 +372,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=6"), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(4))); getClient(tokenAdmin).perform(get("/api/config/submissiondefinitions") @@ -372,7 +381,7 @@ public void findAllPaginationTest() throws Exception { .param("page", "5")) .andExpect(status().isOk()) .andExpect(content().contentType(contentType)) - .andExpect(jsonPath("$._embedded.submissiondefinitions[0].id", is("extractiontestprocess"))) + .andExpect(jsonPath("$._embedded.submissiondefinitions[0]", matchSubmissionConfig(definitions.get(5)))) .andExpect(jsonPath("$._links.first.href", Matchers.allOf( Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=0"), Matchers.containsString("size=1")))) @@ -389,8 +398,8 @@ public void findAllPaginationTest() throws Exception { Matchers.containsString("/api/config/submissiondefinitions?"), Matchers.containsString("page=6"), Matchers.containsString("size=1")))) .andExpect(jsonPath("$.page.size", is(1))) - .andExpect(jsonPath("$.page.totalElements", is(7))) - .andExpect(jsonPath("$.page.totalPages", is(7))) + .andExpect(jsonPath("$.page.totalElements", is(totalCount))) + .andExpect(jsonPath("$.page.totalPages", is(totalCount))) .andExpect(jsonPath("$.page.number", is(5))); } diff --git a/dspace-server-webapp/src/test/java/org/dspace/app/rest/matcher/SubmissionDefinitionsMatcher.java b/dspace-server-webapp/src/test/java/org/dspace/app/rest/matcher/SubmissionDefinitionsMatcher.java index 398097db6fba..86f1c7830a0a 100644 --- a/dspace-server-webapp/src/test/java/org/dspace/app/rest/matcher/SubmissionDefinitionsMatcher.java +++ b/dspace-server-webapp/src/test/java/org/dspace/app/rest/matcher/SubmissionDefinitionsMatcher.java @@ -13,6 +13,7 @@ import static org.hamcrest.Matchers.allOf; import static org.hamcrest.Matchers.is; +import org.dspace.app.util.SubmissionConfig; import org.hamcrest.Matcher; /** @@ -25,7 +26,7 @@ private SubmissionDefinitionsMatcher() { } public static Matcher matchSubmissionDefinition(boolean isDefault, String name, String id) { return allOf( matchProperties(isDefault, name, id), - matchLinks() + matchLinks(id) ); } @@ -42,8 +43,8 @@ public static Matcher matchFullEmbeds() { /** * Gets a matcher for all expected links. */ - public static Matcher matchLinks() { - return HalMatcher.matchLinks(REST_SERVER_URL + "config/submissiondefinitions/traditional", + public static Matcher matchLinks(String id) { + return HalMatcher.matchLinks(REST_SERVER_URL + "config/submissiondefinitions/" + id, "collections", "sections", "self" @@ -61,4 +62,12 @@ public static Matcher matchProperties(boolean isDefault, String is(REST_SERVER_URL + "config/submissiondefinitions/" + id + "/sections")) ); } + + public static Matcher matchSubmissionConfig(SubmissionConfig config) { + return matchSubmissionDefinition( + config.isDefaultConf(), + config.getSubmissionName(), + config.getSubmissionName() + ); + } } From 2bcea0f860db9a3dc915119a5e111d057d2b2936 Mon Sep 17 00:00:00 2001 From: autavares-dev Date: Wed, 7 Aug 2024 16:34:38 -0300 Subject: [PATCH 02/18] Changes Group2GroupCache computation --- .../org/dspace/eperson/Group2GroupCache.java | 3 +- .../org/dspace/eperson/GroupServiceImpl.java | 72 +++++++++--------- .../eperson/dao/Group2GroupCacheDAO.java | 74 +++++++++++++++++-- .../dao/impl/Group2GroupCacheDAOImpl.java | 34 +++++++++ 4 files changed, 143 insertions(+), 40 deletions(-) diff --git a/dspace-api/src/main/java/org/dspace/eperson/Group2GroupCache.java b/dspace-api/src/main/java/org/dspace/eperson/Group2GroupCache.java index a1c12371f5ff..0c6ea58b1977 100644 --- a/dspace-api/src/main/java/org/dspace/eperson/Group2GroupCache.java +++ b/dspace-api/src/main/java/org/dspace/eperson/Group2GroupCache.java @@ -15,6 +15,7 @@ import jakarta.persistence.JoinColumn; import jakarta.persistence.ManyToOne; import jakarta.persistence.Table; +import jakarta.persistence.UniqueConstraint; import org.dspace.core.HibernateProxyHelper; /** @@ -23,7 +24,7 @@ * @author kevinvandevelde at atmire.com */ @Entity -@Table(name = "group2groupcache") +@Table(name = "group2groupcache", uniqueConstraints = { @UniqueConstraint(columnNames = {"parent_id", "child_id"}) }) public class Group2GroupCache implements Serializable { @Id diff --git a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java index 3fb20e2f1e6f..b52f17a5c692 100644 --- a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java @@ -20,6 +20,7 @@ import java.util.UUID; import org.apache.commons.collections4.CollectionUtils; +import org.apache.commons.collections4.SetUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; @@ -673,15 +674,14 @@ protected boolean isEPersonInGroup(Context context, Group group, EPerson ePerson /** - * Regenerate the group cache AKA the group2groupcache table in the database - - * meant to be called when a group is added or removed from another group + * Returns a set with pairs of parent and child group UUIDs, representing the new cache table rows. * - * @param context The relevant DSpace Context. - * @param flushQueries flushQueries Flush all pending queries + * @param context The relevant DSpace Context. + * @param flushQueries flushQueries Flush all pending queries + * @return Pairs of parent and child group UUID of the new cache. * @throws SQLException An exception that provides information on a database access error or other errors. */ - protected void rethinkGroupCache(Context context, boolean flushQueries) throws SQLException { - + private Set> computeNewCache(Context context, boolean flushQueries) throws SQLException { Map> parents = new HashMap<>(); List> group2groupResults = groupDAO.getGroup2GroupResults(context, flushQueries); @@ -689,19 +689,8 @@ protected void rethinkGroupCache(Context context, boolean flushQueries) throws S UUID parent = group2groupResult.getLeft(); UUID child = group2groupResult.getRight(); - // if parent doesn't have an entry, create one - if (!parents.containsKey(parent)) { - Set children = new HashSet<>(); - - // add child id to the list - children.add(child); - parents.put(parent, children); - } else { - // parent has an entry, now add the child to the parent's record - // of children - Set children = parents.get(parent); - children.add(child); - } + parents.putIfAbsent(parent, new HashSet<>()); + parents.get(parent).add(child); } // now parents is a hash of all of the IDs of groups that are parents @@ -714,27 +703,42 @@ protected void rethinkGroupCache(Context context, boolean flushQueries) throws S parent.getValue().addAll(myChildren); } - // empty out group2groupcache table - group2GroupCacheDAO.deleteAll(context); - - // write out new one + // write out new cache IN MEMORY ONLY and returns it + Set> newCache = new HashSet<>(); for (Map.Entry> parent : parents.entrySet()) { UUID key = parent.getKey(); - for (UUID child : parent.getValue()) { + newCache.add(Pair.of(key, child)); + } + } + return newCache; + } - Group parentGroup = find(context, key); - Group childGroup = find(context, child); + /** + * Regenerate the group cache AKA the group2groupcache table in the database - + * meant to be called when a group is added or removed from another group + * + * @param context The relevant DSpace Context. + * @param flushQueries flushQueries Flush all pending queries + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + protected void rethinkGroupCache(Context context, boolean flushQueries) throws SQLException { + // current cache in the database + var oldCache = group2GroupCacheDAO.getCache(context); - if (parentGroup != null && childGroup != null && group2GroupCacheDAO - .find(context, parentGroup, childGroup) == null) { - Group2GroupCache group2GroupCache = group2GroupCacheDAO.create(context, new Group2GroupCache()); - group2GroupCache.setParent(parentGroup); - group2GroupCache.setChild(childGroup); - group2GroupCacheDAO.save(context, group2GroupCache); - } - } + // correct cache, computed from the Group table + var newCache = computeNewCache(context, flushQueries); + + var toDelete = SetUtils.difference(oldCache, newCache); + var toCreate = SetUtils.difference(newCache, oldCache); + + for (var pair : toDelete ) { + group2GroupCacheDAO.deleteFromCache(context, pair.getLeft(), pair.getRight()); + } + + for (var pair : toCreate ) { + group2GroupCacheDAO.addToCache(context, pair.getLeft(), pair.getRight()); } } diff --git a/dspace-api/src/main/java/org/dspace/eperson/dao/Group2GroupCacheDAO.java b/dspace-api/src/main/java/org/dspace/eperson/dao/Group2GroupCacheDAO.java index 7db569a59e2b..d41d52c7e618 100644 --- a/dspace-api/src/main/java/org/dspace/eperson/dao/Group2GroupCacheDAO.java +++ b/dspace-api/src/main/java/org/dspace/eperson/dao/Group2GroupCacheDAO.java @@ -9,7 +9,10 @@ import java.sql.SQLException; import java.util.List; +import java.util.Set; +import java.util.UUID; +import org.apache.commons.lang3.tuple.Pair; import org.dspace.core.Context; import org.dspace.core.GenericDAO; import org.dspace.eperson.Group; @@ -25,13 +28,74 @@ */ public interface Group2GroupCacheDAO extends GenericDAO { - public List findByParent(Context context, Group group) throws SQLException; + /** + * Returns the current cache table as a set of UUID pairs. + * @param context The relevant DSpace Context. + * @return Set of UUID pairs, where the first element is the parent UUID and the second one is the child UUID. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + Set> getCache(Context context) throws SQLException; - public List findByChildren(Context context, Iterable groups) throws SQLException; + /** + * Returns all cache entities that are children of a given parent Group entity. + * @param context The relevant DSpace Context. + * @param group Parent group to perform the search. + * @return List of cached groups that are children of the parent group. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + List findByParent(Context context, Group group) throws SQLException; - public Group2GroupCache findByParentAndChild(Context context, Group parent, Group child) throws SQLException; + /** + * Returns all cache entities that are parents of at least one group from a children groups list. + * @param context The relevant DSpace Context. + * @param groups Children groups to perform the search. + * @return List of cached groups that are parents of at least one group from the children groups list. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + List findByChildren(Context context, Iterable groups) throws SQLException; - public Group2GroupCache find(Context context, Group parent, Group child) throws SQLException; + /** + * Returns the cache entity given specific parent and child groups. + * @param context The relevant DSpace Context. + * @param parent Parent group. + * @param child Child gruoup. + * @return Cached group. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + Group2GroupCache findByParentAndChild(Context context, Group parent, Group child) throws SQLException; - public void deleteAll(Context context) throws SQLException; + /** + * Returns the cache entity given specific parent and child groups. + * @param context The relevant DSpace Context. + * @param parent Parent group. + * @param child Child gruoup. + * @return Cached group. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + Group2GroupCache find(Context context, Group parent, Group child) throws SQLException; + + /** + * Completely deletes the current cache table. + * @param context The relevant DSpace Context. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + void deleteAll(Context context) throws SQLException; + + /** + * Deletes a specific cache row given parent and child groups UUIDs. + * @param context The relevant DSpace Context. + * @param parent Parent group UUID. + * @param child Child group UUID. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + void deleteFromCache(Context context, UUID parent, UUID child) throws SQLException; + + /** + * Adds a single row to the cache table given parent and child groups UUIDs. + * @param context The relevant DSpace Context. + * @param parent Parent group UUID. + * @param child Child group UUID. + * @throws SQLException An exception that provides information on a database access error or other errors. + */ + void addToCache(Context context, UUID parent, UUID child) throws SQLException; } diff --git a/dspace-api/src/main/java/org/dspace/eperson/dao/impl/Group2GroupCacheDAOImpl.java b/dspace-api/src/main/java/org/dspace/eperson/dao/impl/Group2GroupCacheDAOImpl.java index 1cd359188ca3..adbd776ffab6 100644 --- a/dspace-api/src/main/java/org/dspace/eperson/dao/impl/Group2GroupCacheDAOImpl.java +++ b/dspace-api/src/main/java/org/dspace/eperson/dao/impl/Group2GroupCacheDAOImpl.java @@ -8,14 +8,18 @@ package org.dspace.eperson.dao.impl; import java.sql.SQLException; +import java.util.HashSet; import java.util.LinkedList; import java.util.List; +import java.util.Set; +import java.util.UUID; import jakarta.persistence.Query; import jakarta.persistence.criteria.CriteriaBuilder; import jakarta.persistence.criteria.CriteriaQuery; import jakarta.persistence.criteria.Predicate; import jakarta.persistence.criteria.Root; +import org.apache.commons.lang3.tuple.Pair; import org.dspace.core.AbstractHibernateDAO; import org.dspace.core.Context; import org.dspace.eperson.Group; @@ -35,6 +39,16 @@ protected Group2GroupCacheDAOImpl() { super(); } + @Override + public Set> getCache(Context context) throws SQLException { + Query query = createQuery( + context, + "SELECT new org.apache.commons.lang3.tuple.ImmutablePair(g.parent.id, g.child.id) FROM Group2GroupCache g" + ); + List> results = query.getResultList(); + return new HashSet>(results); + } + @Override public List findByParent(Context context, Group group) throws SQLException { CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context); @@ -90,4 +104,24 @@ public Group2GroupCache find(Context context, Group parent, Group child) throws public void deleteAll(Context context) throws SQLException { createQuery(context, "delete from Group2GroupCache").executeUpdate(); } + + @Override + public void deleteFromCache(Context context, UUID parent, UUID child) throws SQLException { + Query query = getHibernateSession(context).createNativeQuery( + "delete from group2groupcache g WHERE g.parent_id = :parent AND g.child_id = :child" + ); + query.setParameter("parent", parent); + query.setParameter("child", child); + query.executeUpdate(); + } + + @Override + public void addToCache(Context context, UUID parent, UUID child) throws SQLException { + Query query = getHibernateSession(context).createNativeQuery( + "insert into group2groupcache (parent_id, child_id) VALUES (:parent, :child)" + ); + query.setParameter("parent", parent); + query.setParameter("child", child); + query.executeUpdate(); + } } From 743b7049cfeeabfd414c38526bcdbf2e52426739 Mon Sep 17 00:00:00 2001 From: autavares-dev Date: Thu, 8 Aug 2024 15:52:03 -0300 Subject: [PATCH 03/18] Refactor 'var' variables to explicit types --- .../java/org/dspace/eperson/GroupServiceImpl.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java index b52f17a5c692..4cec4c9c0d93 100644 --- a/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java +++ b/dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java @@ -725,19 +725,19 @@ private Set> computeNewCache(Context context, boolean flushQuer */ protected void rethinkGroupCache(Context context, boolean flushQueries) throws SQLException { // current cache in the database - var oldCache = group2GroupCacheDAO.getCache(context); + Set> oldCache = group2GroupCacheDAO.getCache(context); // correct cache, computed from the Group table - var newCache = computeNewCache(context, flushQueries); + Set> newCache = computeNewCache(context, flushQueries); - var toDelete = SetUtils.difference(oldCache, newCache); - var toCreate = SetUtils.difference(newCache, oldCache); + SetUtils.SetView> toDelete = SetUtils.difference(oldCache, newCache); + SetUtils.SetView> toCreate = SetUtils.difference(newCache, oldCache); - for (var pair : toDelete ) { + for (Pair pair : toDelete ) { group2GroupCacheDAO.deleteFromCache(context, pair.getLeft(), pair.getRight()); } - for (var pair : toCreate ) { + for (Pair pair : toCreate ) { group2GroupCacheDAO.addToCache(context, pair.getLeft(), pair.getRight()); } } From b8f4ab0eb3e90b080eaae057fb5ee673d3477dc2 Mon Sep 17 00:00:00 2001 From: "Mark H. Wood" Date: Tue, 17 Sep 2024 08:47:54 -0400 Subject: [PATCH 04/18] More information about failed DOI registrations. --- .../dspace/identifier/doi/DOIOrganiser.java | 3 ++- .../identifier/doi/DataCiteConnector.java | 22 ++++++++++++++++++- 2 files changed, 23 insertions(+), 2 deletions(-) diff --git a/dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java b/dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java index b03af68b42ab..0ee64f94b799 100644 --- a/dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java +++ b/dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java @@ -577,7 +577,8 @@ public void update(DOI doiRow) { } } catch (IdentifierException ex) { if (!(ex instanceof DOIIdentifierException)) { - LOG.error("It wasn't possible to register the identifier online. ", ex); + LOG.error("Registering DOI {} for object {}: the registrar returned an error.", + doiRow.getDoi(), dso.getID(), ex); } DOIIdentifierException doiIdentifierException = (DOIIdentifierException) ex; diff --git a/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java b/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java index 23af904f2c71..e56a82942369 100644 --- a/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java +++ b/dspace-api/src/main/java/org/dspace/identifier/doi/DataCiteConnector.java @@ -461,6 +461,10 @@ public void reserveDOI(Context context, DSpaceObject dso, String doi) log.warn("While reserving the DOI {}, we got a http status code " + "{} and the message \"{}\".", doi, Integer.toString(resp.statusCode), resp.getContent()); + Format format = Format.getCompactFormat(); + format.setEncoding("UTF-8"); + XMLOutputter xout = new XMLOutputter(format); + log.info("We send the following XML:\n{}", xout.outputString(root)); throw new DOIIdentifierException("Unable to parse an answer from " + "DataCite API. Please have a look into DSpace logs.", DOIIdentifierException.BAD_ANSWER); @@ -632,6 +636,14 @@ protected DataCiteResponse sendGetRequest(String doi, String path) return sendHttpRequest(httpget, doi); } + /** + * Send a DataCite metadata document to the registrar. + * + * @param doi identify the object. + * @param metadataRoot describe the object. The root element of the document. + * @return the registrar's response. + * @throws DOIIdentifierException passed through. + */ protected DataCiteResponse sendMetadataPostRequest(String doi, Element metadataRoot) throws DOIIdentifierException { Format format = Format.getCompactFormat(); @@ -640,6 +652,14 @@ protected DataCiteResponse sendMetadataPostRequest(String doi, Element metadataR return sendMetadataPostRequest(doi, xout.outputString(new Document(metadataRoot))); } + /** + * Send a DataCite metadata document to the registrar. + * + * @param doi identify the object. + * @param metadata describe the object. + * @return the registrar's response. + * @throws DOIIdentifierException passed through. + */ protected DataCiteResponse sendMetadataPostRequest(String doi, String metadata) throws DOIIdentifierException { // post mds/metadata/ @@ -687,7 +707,7 @@ protected DataCiteResponse sendMetadataPostRequest(String doi, String metadata) * properties such as request URI and method type. * @param doi DOI string to operate on * @return response from DataCite - * @throws DOIIdentifierException if DOI error + * @throws DOIIdentifierException if registrar returns an error. */ protected DataCiteResponse sendHttpRequest(HttpUriRequest req, String doi) throws DOIIdentifierException { From 532b77c5e9a7fe49c600f3195aa781f9687199ea Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 22:59:16 +0000 Subject: [PATCH 05/18] Bump flyway.version from 10.20.1 to 10.22.0 Bumps `flyway.version` from 10.20.1 to 10.22.0. Updates `org.flywaydb:flyway-core` from 10.20.1 to 10.22.0 - [Release notes](https://github.com/flyway/flyway/releases) - [Commits](https://github.com/flyway/flyway/compare/flyway-10.20.1...flyway-10.22.0) Updates `org.flywaydb:flyway-database-postgresql` from 10.20.1 to 10.22.0 --- updated-dependencies: - dependency-name: org.flywaydb:flyway-core dependency-type: direct:production update-type: version-update:semver-minor - dependency-name: org.flywaydb:flyway-database-postgresql dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d2c75fc60032..a6ac273cae3e 100644 --- a/pom.xml +++ b/pom.xml @@ -25,7 +25,7 @@ 6.4.8.Final 8.0.1.Final 42.7.4 - 10.20.1 + 10.22.0 8.11.4 3.10.8 From 811a4beb345baba0347d0e9068d4712644f2bc98 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 23:02:27 +0000 Subject: [PATCH 06/18] Bump org.apache.james:apache-mime4j-core from 0.8.10 to 0.8.11 Bumps org.apache.james:apache-mime4j-core from 0.8.10 to 0.8.11. --- updated-dependencies: - dependency-name: org.apache.james:apache-mime4j-core dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d2c75fc60032..01db01b9fc99 100644 --- a/pom.xml +++ b/pom.xml @@ -1317,7 +1317,7 @@ org.apache.james apache-mime4j-core - 0.8.10 + 0.8.11 From 5e0b22c115293be1d4584fd41e0576c558f4aca9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 23:03:31 +0000 Subject: [PATCH 07/18] Bump org.apache.velocity:velocity-engine-core from 2.3 to 2.4.1 Bumps org.apache.velocity:velocity-engine-core from 2.3 to 2.4.1. --- updated-dependencies: - dependency-name: org.apache.velocity:velocity-engine-core dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- dspace-api/pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dspace-api/pom.xml b/dspace-api/pom.xml index 9b48128fcb89..599303275f9f 100644 --- a/dspace-api/pom.xml +++ b/dspace-api/pom.xml @@ -784,7 +784,7 @@ org.apache.velocity velocity-engine-core - 2.3 + 2.4.1 From b7f2f1004a9130db1163503d120e84a63d145adc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 9 Dec 2024 23:03:35 +0000 Subject: [PATCH 08/18] Bump com.google.code.gson:gson from 2.10.1 to 2.11.0 Bumps [com.google.code.gson:gson](https://github.com/google/gson) from 2.10.1 to 2.11.0. - [Release notes](https://github.com/google/gson/releases) - [Changelog](https://github.com/google/gson/blob/main/CHANGELOG.md) - [Commits](https://github.com/google/gson/compare/gson-parent-2.10.1...gson-parent-2.11.0) --- updated-dependencies: - dependency-name: com.google.code.gson:gson dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d2c75fc60032..e24f11631db2 100644 --- a/pom.xml +++ b/pom.xml @@ -1353,7 +1353,7 @@ com.google.code.gson gson - 2.10.1 + 2.11.0 false From ede9f54d36d57f802f0cbb915f4c2c59ac791682 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Dec 2024 22:02:04 +0000 Subject: [PATCH 16/18] Bump log4j.version from 2.24.2 to 2.24.3 Bumps `log4j.version` from 2.24.2 to 2.24.3. Updates `org.apache.logging.log4j:log4j-api` from 2.24.2 to 2.24.3 Updates `org.apache.logging.log4j:log4j-core` from 2.24.2 to 2.24.3 Updates `org.apache.logging.log4j:log4j-slf4j2-impl` from 2.24.2 to 2.24.3 --- updated-dependencies: - dependency-name: org.apache.logging.log4j:log4j-api dependency-type: direct:production update-type: version-update:semver-patch - dependency-name: org.apache.logging.log4j:log4j-core dependency-type: direct:production update-type: version-update:semver-patch - dependency-name: org.apache.logging.log4j:log4j-slf4j2-impl dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index d2c75fc60032..ba9f735aa621 100644 --- a/pom.xml +++ b/pom.xml @@ -39,7 +39,7 @@ 1.1.1 9.4.56.v20240826 - 2.24.2 + 2.24.3 2.0.32 1.19.0 From e236634a4c758a6c0d81e929b2f36d49e81b0835 Mon Sep 17 00:00:00 2001 From: Tim Donohue Date: Tue, 17 Dec 2024 13:11:43 -0600 Subject: [PATCH 17/18] Improve Apache Ant download process. Switch to using curl so that we can retry the request if it initially fails. --- Dockerfile | 10 ++++------ Dockerfile.cli | 10 ++++------ Dockerfile.test | 10 ++++------ 3 files changed, 12 insertions(+), 18 deletions(-) diff --git a/Dockerfile b/Dockerfile index fe84d015b548..5aece8b7d37e 100644 --- a/Dockerfile +++ b/Dockerfile @@ -44,14 +44,12 @@ WORKDIR /dspace-src ENV ANT_VERSION=1.10.13 ENV ANT_HOME=/tmp/ant-$ANT_VERSION ENV PATH=$ANT_HOME/bin:$PATH -# Need wget to install ant -RUN apt-get update \ - && apt-get install -y --no-install-recommends wget \ - && apt-get purge -y --auto-remove \ - && rm -rf /var/lib/apt/lists/* # Download and install 'ant' RUN mkdir $ANT_HOME && \ - wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME + curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \ + https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \ + tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \ + rm /tmp/apache-ant.tar.gz # Run necessary 'ant' deploy scripts RUN ant init_installation update_configs update_code update_webapps diff --git a/Dockerfile.cli b/Dockerfile.cli index f13b05fc1308..e43c8eb95dd6 100644 --- a/Dockerfile.cli +++ b/Dockerfile.cli @@ -38,14 +38,12 @@ WORKDIR /dspace-src ENV ANT_VERSION=1.10.13 ENV ANT_HOME=/tmp/ant-$ANT_VERSION ENV PATH=$ANT_HOME/bin:$PATH -# Need wget to install ant -RUN apt-get update \ - && apt-get install -y --no-install-recommends wget \ - && apt-get purge -y --auto-remove \ - && rm -rf /var/lib/apt/lists/* # Download and install 'ant' RUN mkdir $ANT_HOME && \ - wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME + curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \ + https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \ + tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \ + rm /tmp/apache-ant.tar.gz # Run necessary 'ant' deploy scripts RUN ant init_installation update_configs update_code diff --git a/Dockerfile.test b/Dockerfile.test index 2205c1d5605f..90266101dbf0 100644 --- a/Dockerfile.test +++ b/Dockerfile.test @@ -43,14 +43,12 @@ WORKDIR /dspace-src ENV ANT_VERSION=1.10.12 ENV ANT_HOME=/tmp/ant-$ANT_VERSION ENV PATH=$ANT_HOME/bin:$PATH -# Need wget to install ant -RUN apt-get update \ - && apt-get install -y --no-install-recommends wget \ - && apt-get purge -y --auto-remove \ - && rm -rf /var/lib/apt/lists/* # Download and install 'ant' RUN mkdir $ANT_HOME && \ - wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME + curl --silent --show-error --location --fail --retry 5 --output /tmp/apache-ant.tar.gz \ + https://archive.apache.org/dist/ant/binaries/apache-ant-${ANT_VERSION}-bin.tar.gz && \ + tar -zx --strip-components=1 -f /tmp/apache-ant.tar.gz -C $ANT_HOME && \ + rm /tmp/apache-ant.tar.gz # Run necessary 'ant' deploy scripts RUN ant init_installation update_configs update_code update_webapps From 6d7a3fcb725bbb5e42790ba5c57292477f2f3f01 Mon Sep 17 00:00:00 2001 From: Tim Donohue Date: Tue, 17 Dec 2024 14:13:21 -0600 Subject: [PATCH 18/18] Significantly speed up build of dspace-dependencies by only copying over POM files --- Dockerfile.dependencies | 58 ++++++++++++++++++++++++++++++++++++----- 1 file changed, 51 insertions(+), 7 deletions(-) diff --git a/Dockerfile.dependencies b/Dockerfile.dependencies index 34bfbc3b8c78..04233cd415fa 100644 --- a/Dockerfile.dependencies +++ b/Dockerfile.dependencies @@ -6,7 +6,7 @@ # To build with other versions, use "--build-arg JDK_VERSION=[value]" ARG JDK_VERSION=17 -# Step 1 - Run Maven Build +# Step 1 - Download all Dependencies FROM docker.io/maven:3-eclipse-temurin-${JDK_VERSION} AS build ARG TARGET_DIR=dspace-installer WORKDIR /app @@ -19,16 +19,60 @@ RUN chown -Rv dspace: /app # Switch to dspace user & run below commands as that user USER dspace -# Copy the DSpace source code (from local machine) into the workdir (excluding .dockerignore contents) -ADD --chown=dspace . /app/ +# This next part may look odd, but it speeds up the build of this image *significantly*. +# Copy ONLY the POMs to this image (from local machine). This will allow us to download all dependencies *without* +# performing any code compilation steps. + +# Parent POM +ADD --chown=dspace pom.xml /app/ +RUN mkdir -p /app/dspace + +# 'dspace' module POM. Includes 'additions' ONLY, as it's the only submodule that is required to exist. +ADD --chown=dspace dspace/pom.xml /app/dspace/ +RUN mkdir -p /app/dspace/modules/ +ADD --chown=dspace dspace/modules/pom.xml /app/dspace/modules/ +RUN mkdir -p /app/dspace/modules/additions +ADD --chown=dspace dspace/modules/additions/pom.xml /app/dspace/modules/additions/ + +# 'dspace-api' module POM +RUN mkdir -p /app/dspace-api +ADD --chown=dspace dspace-api/pom.xml /app/dspace-api/ + +# 'dspace-iiif' module POM +RUN mkdir -p /app/dspace-iiif +ADD --chown=dspace dspace-iiif/pom.xml /app/dspace-iiif/ + +# 'dspace-oai' module POM +RUN mkdir -p /app/dspace-oai +ADD --chown=dspace dspace-oai/pom.xml /app/dspace-oai/ + +# 'dspace-rdf' module POM +RUN mkdir -p /app/dspace-rdf +ADD --chown=dspace dspace-rdf/pom.xml /app/dspace-rdf/ + +# 'dspace-server-webapp' module POM +RUN mkdir -p /app/dspace-server-webapp +ADD --chown=dspace dspace-server-webapp/pom.xml /app/dspace-server-webapp/ + +# 'dspace-services' module POM +RUN mkdir -p /app/dspace-services +ADD --chown=dspace dspace-services/pom.xml /app/dspace-services/ + +# 'dspace-sword' module POM +RUN mkdir -p /app/dspace-sword +ADD --chown=dspace dspace-sword/pom.xml /app/dspace-sword/ + +# 'dspace-swordv2' module POM +RUN mkdir -p /app/dspace-swordv2 +ADD --chown=dspace dspace-swordv2/pom.xml /app/dspace-swordv2/ # Trigger the installation of all maven dependencies (hide download progress messages) # Maven flags here ensure that we skip final assembly, skip building test environment and skip all code verification checks. -# These flags speed up this installation as much as reasonably possible. -ENV MAVEN_FLAGS="-P-assembly -P-test-environment -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxml.skip=true" -RUN mvn --no-transfer-progress install ${MAVEN_FLAGS} +# These flags speed up this installation and skip tasks we cannot perform as we don't have the full source code. +ENV MAVEN_FLAGS="-P-assembly -P-test-environment -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxjc.skip=true -Dxml.skip=true" +RUN mvn --no-transfer-progress verify ${MAVEN_FLAGS} -# Clear the contents of the /app directory (including all maven builds), so no artifacts remain. +# Clear the contents of the /app directory (including all maven target folders), so no artifacts remain. # This ensures when dspace:dspace is built, it will use the Maven local cache (~/.m2) for dependencies USER root RUN rm -rf /app/*