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Merge pull request #529 from ebi-uniprot/TRM-32146-populate-history
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Trm 32146 populate history
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@supun-ebi
supun-ebi authored Jan 10, 2025
2 parents b114116 + 4aaaced commit 196c542
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Showing 15 changed files with 190 additions and 146 deletions.
4 changes: 3 additions & 1 deletion ...ata-rest/src/main/java/org/uniprot/api/support/data/statistics/entity/AttributeQuery.java
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Expand Up @@ -6,7 +6,9 @@

@Data
@Entity
@Table(indexes = @Index(columnList = "attributeName, statistics_category_id", unique = true))
@Table(
name = "attribute_query",
indexes = @Index(columnList = "attributeName, statistics_category_id", unique = true))
public class AttributeQuery {
@Id private Long id;

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4 changes: 2 additions & 2 deletions ...rc/main/java/org/uniprot/api/support/data/statistics/entity/UniProtKBStatisticsEntry.java
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Expand Up @@ -6,7 +6,7 @@

@Data
@Entity
@Table(name = "uniprotkb_statistics_entry")
@Table(name = "uniprotkb_statistics_entry", indexes = @Index(columnList = "release_name"))
public class UniProtKBStatisticsEntry {
@Id private Long id;
private String attributeName;
Expand All @@ -21,7 +21,7 @@ public class UniProtKBStatisticsEntry {

@ManyToOne
@JoinColumn(name = "release_name")
private UniProtRelease releaseName;
private UniProtRelease uniProtRelease;

@Enumerated(EnumType.STRING)
private EntryType entryType;
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13 changes: 9 additions & 4 deletions ...ata-rest/src/main/java/org/uniprot/api/support/data/statistics/entity/UniProtRelease.java
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Expand Up @@ -2,16 +2,21 @@

import java.util.Date;

import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.Table;
import javax.persistence.*;

import lombok.Data;

@Data
@Entity
@Table(name = "uniprot_release")
public class UniProtRelease {
@Id private String id;
@Id private int id;

@Temporal(TemporalType.DATE)
private Date date;

@Enumerated(EnumType.STRING)
private EntryType entryType;

private String name;
}
4 changes: 2 additions & 2 deletions ...a-rest/src/main/java/org/uniprot/api/support/data/statistics/mapper/StatisticsMapper.java
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Expand Up @@ -54,8 +54,8 @@ public StatisticsModuleStatisticsAttribute map(
public StatisticsModuleStatisticsHistory mapHistory(UniProtKBStatisticsEntry entry) {
return StatisticsModuleStatisticsHistoryImpl.builder()
.statisticsType(map(entry.getEntryType()))
.releaseName(entry.getReleaseName().getId())
.releaseDate(entry.getReleaseName().getDate())
.releaseName(entry.getUniProtRelease().getName())
.releaseDate(entry.getUniProtRelease().getDate())
.valueCount(entry.getValueCount())
.entryCount(entry.getEntryCount())
.build();
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3 changes: 2 additions & 1 deletion ...ain/java/org/uniprot/api/support/data/statistics/repository/AttributeQueryRepository.java
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Expand Up @@ -11,5 +11,6 @@
@Repository
@Primary
public interface AttributeQueryRepository extends JpaRepository<AttributeQuery, Long> {
Optional<AttributeQuery> findByStatisticsCategoryAndAttributeNameIgnoreCase(StatisticsCategory statisticsCategory, String attributeName);
Optional<AttributeQuery> findByStatisticsCategoryAndAttributeNameIgnoreCase(
StatisticsCategory statisticsCategory, String attributeName);
}
12 changes: 2 additions & 10 deletions ...rg/uniprot/api/support/data/statistics/repository/UniProtKBStatisticsEntryRepository.java
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Expand Up @@ -15,21 +15,13 @@
@Primary
public interface UniProtKBStatisticsEntryRepository
extends JpaRepository<UniProtKBStatisticsEntry, Long> {
List<UniProtKBStatisticsEntry> findAllByReleaseNameAndEntryType(
UniProtRelease releaseName, EntryType entryType);

List<UniProtKBStatisticsEntry> findAllByReleaseNameAndEntryTypeAndStatisticsCategoryIn(
UniProtRelease uniProtRelease,
EntryType entryType,
Collection<StatisticsCategory> statisticsCategory);

List<UniProtKBStatisticsEntry> findAllByAttributeNameIgnoreCaseAndEntryType(
String attributeName, EntryType entryType);

List<UniProtKBStatisticsEntry> findAllByAttributeNameIgnoreCase(String attributeName);

List<UniProtKBStatisticsEntry> findAllByReleaseName(UniProtRelease releaseName);
List<UniProtKBStatisticsEntry> findAllByUniProtRelease(UniProtRelease uniProtRelease);

List<UniProtKBStatisticsEntry> findAllByReleaseNameAndStatisticsCategoryIn(
List<UniProtKBStatisticsEntry> findAllByUniProtReleaseAndStatisticsCategoryIn(
UniProtRelease releaseName, Collection<StatisticsCategory> statisticsCategory);
}
7 changes: 5 additions & 2 deletions ...ain/java/org/uniprot/api/support/data/statistics/repository/UniProtReleaseRepository.java
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Expand Up @@ -7,11 +7,14 @@
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.stereotype.Repository;
import org.uniprot.api.support.data.statistics.entity.EntryType;
import org.uniprot.api.support.data.statistics.entity.UniProtRelease;

@Repository
@Primary
public interface UniProtReleaseRepository extends JpaRepository<UniProtRelease, String> {
@Query("SELECT MAX (ur.date) from UniProtRelease ur where ur.id<?1")
public interface UniProtReleaseRepository extends JpaRepository<UniProtRelease, Integer> {
@Query("SELECT MAX (ur.date) from UniProtRelease ur where ur.name<?1")
Optional<Date> findPreviousReleaseDate(String currentRelease);

Optional<UniProtRelease> findByNameAndEntryType(String name, EntryType entryType);
}
76 changes: 43 additions & 33 deletions .../src/main/java/org/uniprot/api/support/data/statistics/service/StatisticsServiceImpl.java
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Expand Up @@ -46,20 +46,9 @@ public StatisticsServiceImpl(
@Override
public List<StatisticsModuleStatisticsCategory> findAllByVersionAndStatisticTypeAndCategoryIn(
String version, String statisticType, Set<String> categories) {
List<UniProtKBStatisticsEntry> entries;
if (categories.isEmpty()) {
entries =
statisticsEntryRepository.findAllByReleaseNameAndEntryType(
getRelease(version),
statisticsMapper.map(getStatisticType(statisticType)));
} else {
entries =
statisticsEntryRepository
.findAllByReleaseNameAndEntryTypeAndStatisticsCategoryIn(
getRelease(version),
statisticsMapper.map(getStatisticType(statisticType)),
getCategories(categories));
}
List<UniProtKBStatisticsEntry> entries =
getAllEntriesByVersionAndStatisticTypeAndCategoryIn(
version, statisticType, categories);
return entries.stream()
.collect(Collectors.groupingBy(UniProtKBStatisticsEntry::getStatisticsCategory))
.entrySet()
Expand All @@ -68,15 +57,6 @@ public List<StatisticsModuleStatisticsCategory> findAllByVersionAndStatisticType
.collect(Collectors.toList());
}

private UniProtRelease getRelease(String version) {
return releaseRepository
.findById(version)
.orElseThrow(
() ->
new IllegalArgumentException(
String.format("Invalid Release Version: %s", version)));
}

@Override
public List<StatisticsModuleStatisticsHistory> findAllByAttributeAndStatisticType(
String attribute, String statisticType) {
Expand All @@ -98,14 +78,15 @@ public List<StatisticsModuleStatisticsHistory> findAllByAttributeAndStatisticTyp
@Override
public Collection<StatisticsModuleStatisticsCategory> findAllByVersionAndCategoryIn(
String version, Set<String> categories) {
List<UniProtKBStatisticsEntry> entries;
if (categories.isEmpty()) {
entries = statisticsEntryRepository.findAllByReleaseName(getRelease(version));
} else {
entries =
statisticsEntryRepository.findAllByReleaseNameAndStatisticsCategoryIn(
getRelease(version), getCategories(categories));
List<UniProtKBStatisticsEntry> entries = new LinkedList<>();

for (StatisticsModuleStatisticsType statisticsType :
StatisticsModuleStatisticsType.values()) {
entries.addAll(
getAllEntriesByVersionAndStatisticTypeAndCategoryIn(
version, statisticsType.name(), categories));
}

return entries.stream()
.collect(Collectors.groupingBy(UniProtKBStatisticsEntry::getStatisticsCategory))
.entrySet()
Expand All @@ -115,6 +96,34 @@ public Collection<StatisticsModuleStatisticsCategory> findAllByVersionAndCategor
.collect(Collectors.toList());
}

private List<UniProtKBStatisticsEntry> getAllEntriesByVersionAndStatisticTypeAndCategoryIn(
String version, String statisticType, Set<String> categories) {
List<UniProtKBStatisticsEntry> entries;
StatisticsModuleStatisticsType statisticsModuleStatisticsType =
getStatisticType(statisticType);
EntryType entryType = statisticsMapper.map(statisticsModuleStatisticsType);
UniProtRelease release = getRelease(version, entryType);
if (categories.isEmpty()) {
entries = statisticsEntryRepository.findAllByUniProtRelease(release);
} else {
entries =
statisticsEntryRepository.findAllByUniProtReleaseAndStatisticsCategoryIn(
release, getCategories(categories));
}
return entries;
}

private UniProtRelease getRelease(String version, EntryType entryType) {
return releaseRepository
.findByNameAndEntryType(version, entryType)
.orElseThrow(
() ->
new IllegalArgumentException(
String.format(
"Invalid Release Version: %s or entry type: %s",
version, entryType)));
}

private Map.Entry<StatisticsCategory, List<UniProtKBStatisticsEntry>> groupEntries(
Map.Entry<StatisticsCategory, List<UniProtKBStatisticsEntry>> entry) {
List<UniProtKBStatisticsEntry> groupedEntries =
Expand Down Expand Up @@ -143,7 +152,7 @@ private UniProtKBStatisticsEntry mapToSingleEntry(
.mapToLong(UniProtKBStatisticsEntry::getEntryCount)
.sum());
uniProtKBStatisticsEntry.setDescription(firstEntry.getDescription());
uniProtKBStatisticsEntry.setReleaseName(firstEntry.getReleaseName());
uniProtKBStatisticsEntry.setUniProtRelease(firstEntry.getUniProtRelease());
return uniProtKBStatisticsEntry;
}

Expand Down Expand Up @@ -187,15 +196,16 @@ private Set<StatisticsCategory> getCategories(Set<String> categories) {

private String getAttributeQuery(UniProtKBStatisticsEntry entry) {
Optional<AttributeQuery> attributeQuery =
attributeQueryRepository.findByStatisticsCategoryAndAttributeNameIgnoreCase(entry.getStatisticsCategory(),entry.getAttributeName());
attributeQueryRepository.findByStatisticsCategoryAndAttributeNameIgnoreCase(
entry.getStatisticsCategory(), entry.getAttributeName());
return attributeQuery.map(query -> prepareQuery(query, entry)).orElse("");
}

private String prepareQuery(AttributeQuery query, UniProtKBStatisticsEntry entry) {
String result = query.getQuery();
if (result.contains(PREVIOUS_RELEASE_DATE)) {
SimpleDateFormat simpleDateFormat = new SimpleDateFormat("yyyy-MM-dd");
String currentRelease = entry.getReleaseName().getId();
String currentRelease = entry.getUniProtRelease().getName();
Date previousReleaseDate =
releaseRepository
.findPreviousReleaseDate(currentRelease)
Expand Down
13 changes: 7 additions & 6 deletions ...a-rest/src/test/java/org/uniprot/api/support/data/statistics/TestEntityGeneratorUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,14 +63,15 @@ public class TestEntityGeneratorUtil {
};
public static final UniProtRelease[] RELEASES =
new UniProtRelease[] {
createRelease(REL_0, DATES[0]),
createRelease(REL_1, DATES[1]),
createRelease(REL_2, DATES[2])
createRelease(0, REL_0, DATES[0]),
createRelease(1, REL_1, DATES[1]),
createRelease(2, REL_2, DATES[2])
};

private static UniProtRelease createRelease(String name, Date date) {
private static UniProtRelease createRelease(int id, String name, Date date) {
UniProtRelease release = new UniProtRelease();
release.setId(name);
release.setId(id);
release.setName(name);
release.setDate(date);
return release;
}
Expand Down Expand Up @@ -110,7 +111,7 @@ private static UniProtKBStatisticsEntry createStatisticsEntry(int index) {
uniprotkbStatisticsEntry.setValueCount(VALUE_COUNTS[index]);
uniprotkbStatisticsEntry.setEntryCount(ENTRY_COUNTS[index]);
uniprotkbStatisticsEntry.setDescription(DESCRIPTIONS[index]);
uniprotkbStatisticsEntry.setReleaseName(
uniprotkbStatisticsEntry.setUniProtRelease(
Set.of(0, 1, 3, 4, 5).contains(index) ? RELEASES[0] : RELEASES[1]);
uniprotkbStatisticsEntry.setEntryType(ENTRY_TYPES[index]);
return uniprotkbStatisticsEntry;
Expand Down
28 changes: 14 additions & 14 deletions .../test/java/org/uniprot/api/support/data/statistics/controller/StatisticsControllerIT.java
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Expand Up @@ -39,7 +39,7 @@ static void postgreSQLProperties(DynamicPropertyRegistry registry) {
@Test
void getByReleaseAndType() throws Exception {
this.mockMvc
.perform(get("/statistics/releases/2021_03/reviewed"))
.perform(get("/statistics/releases/2021_02/reviewed"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(3)))
Expand All @@ -52,7 +52,7 @@ void getByReleaseAndType() throws Exception {
.andExpect(
jsonPath(
"$.results[0].items[0].query",
is("(reviewed:true) AND (previous_release_date:2021-03-25)")))
is("(reviewed:true) AND (previous_release_date:2021-01-25)")))
.andExpect(jsonPath("$.results[0].items[0].count", is(329)))
.andExpect(jsonPath("$.results[0].items[0].entryCount", is(254)))
.andExpect(jsonPath("$.results[1].categoryName", is("TOP_ORGANISM")))
Expand Down Expand Up @@ -91,7 +91,7 @@ void getByReleaseAndType() throws Exception {
@Test
void getByRelease() throws Exception {
this.mockMvc
.perform(get("/statistics/releases/2021_03"))
.perform(get("/statistics/releases/2021_02"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(3)))
Expand All @@ -104,7 +104,7 @@ void getByRelease() throws Exception {
.andExpect(
jsonPath(
"$.results[0].items[0].query",
is("(previous_release_date:2021-03-25)")))
is("(previous_release_date:2021-01-25)")))
.andExpect(jsonPath("$.results[0].items[0].count", is(329)))
.andExpect(jsonPath("$.results[0].items[0].entryCount", is(254)))
.andExpect(jsonPath("$.results[1].categoryName", is("TOP_ORGANISM")))
Expand Down Expand Up @@ -137,7 +137,7 @@ void getByRelease() throws Exception {
@Test
void getByReleaseAndTypeAndSingleCategory() throws Exception {
this.mockMvc
.perform(get("/statistics/releases/2021_03/reviewed?categories=EUKARYOTA"))
.perform(get("/statistics/releases/2021_02/reviewed?categories=EUKARYOTA"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(1)))
Expand Down Expand Up @@ -165,7 +165,7 @@ void getByReleaseAndTypeAndSingleCategory() throws Exception {
@Test
void getByReleaseAndSingleCategory() throws Exception {
this.mockMvc
.perform(get("/statistics/releases/2021_03?categories=EUKARYOTA"))
.perform(get("/statistics/releases/2021_02?categories=EUKARYOTA"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(1)))
Expand All @@ -189,7 +189,7 @@ void getByReleaseAndTypeAndMultipleCategories() throws Exception {
this.mockMvc
.perform(
get(
"/statistics/releases/2021_03/reviewed?categories=EUKARYOTA,TOP_ORGANISM"))
"/statistics/releases/2021_02/reviewed?categories=EUKARYOTA,TOP_ORGANISM"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(2)))
Expand Down Expand Up @@ -229,7 +229,7 @@ void getByReleaseAndTypeAndMultipleCategories() throws Exception {
@Test
void getByReleaseAndMultipleCategories() throws Exception {
this.mockMvc
.perform(get("/statistics/releases/2021_03?categories=EUKARYOTA,TOP_ORGANISM"))
.perform(get("/statistics/releases/2021_02?categories=EUKARYOTA,TOP_ORGANISM"))
.andDo(log())
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(2)))
Expand Down Expand Up @@ -268,8 +268,8 @@ void getAllByAttributeAndStatisticsType() throws Exception {
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(1)))
.andExpect(jsonPath("$.results[0].statisticsType", is("REVIEWED")))
.andExpect(jsonPath("$.results[0].releaseName", is("2021_03")))
.andExpect(jsonPath("$.results[0].releaseDate", is("2021-05-25")))
.andExpect(jsonPath("$.results[0].releaseName", is("2021_02")))
.andExpect(jsonPath("$.results[0].releaseDate", is("2021-03-25")))
.andExpect(jsonPath("$.results[0].valueCount", is(35360)))
.andExpect(jsonPath("$.results[0].entryCount", is(35360)));
}
Expand Down Expand Up @@ -311,13 +311,13 @@ void getAllByAttributeAndAttributeType_withoutAttributeType() throws Exception {
.andExpect(status().isOk())
.andExpect(jsonPath("$.results.size()", is(2)))
.andExpect(jsonPath("$.results[0].statisticsType", is("REVIEWED")))
.andExpect(jsonPath("$.results[0].releaseName", is("2021_03")))
.andExpect(jsonPath("$.results[0].releaseDate", is("2021-05-25")))
.andExpect(jsonPath("$.results[0].releaseName", is("2021_02")))
.andExpect(jsonPath("$.results[0].releaseDate", is("2021-03-25")))
.andExpect(jsonPath("$.results[0].valueCount", is(35360)))
.andExpect(jsonPath("$.results[0].entryCount", is(35360)))
.andExpect(jsonPath("$.results[1].statisticsType", is("UNREVIEWED")))
.andExpect(jsonPath("$.results[1].releaseName", is("2021_03")))
.andExpect(jsonPath("$.results[1].releaseDate", is("2021-05-25")))
.andExpect(jsonPath("$.results[1].releaseName", is("2021_02")))
.andExpect(jsonPath("$.results[1].releaseDate", is("2021-03-25")))
.andExpect(jsonPath("$.results[1].valueCount", is(12793422)))
.andExpect(jsonPath("$.results[1].entryCount", is(12793422)));
}
Expand Down
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