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Fix the intermittently failing tests in SCXA #491

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merged 13 commits into from
Dec 17, 2024
Merged

Fix the intermittently failing tests in SCXA #491

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8359b4b
Remove all the duplicated tests that also presents in JsonGeneSearchC…
ke4 Nov 12, 2024
cffc034
Temporary add some debugging for our CI
ke4 Nov 12, 2024
50f234a
Temporary added more debugging to getRandomCellTypesFromQueryResult m…
ke4 Nov 12, 2024
04b983a
Temporary added more debugging to OrganismPartSearchDaoIT class
ke4 Nov 12, 2024
ebd7a02
Use exists method to filter out empty Solr documents
ke4 Nov 21, 2024
1f663c1
Fix some tests in JsonGeneSearchControllerWIT
ke4 Nov 22, 2024
a533373
Update submodules
ke4 Nov 22, 2024
d3237ae
Fix CellTypeSearchDaoIT to filter for CTW_CELL_TYPE
ke4 Nov 25, 2024
136f216
Merge branch 'develop' into bugfix/intermittently_failing_tests
ke4 Nov 27, 2024
4eb1084
Remove unneeded comments
ke4 Nov 29, 2024
472ac9c
Merge branch 'bugfix/intermittently_failing_tests' of https://github.…
ke4 Nov 29, 2024
fe7f350
Merge branch 'develop' into bugfix/intermittently_failing_tests
ke4 Dec 10, 2024
0b31f30
Merge branch 'develop' into bugfix/intermittently_failing_tests
ke4 Dec 13, 2024
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6 changes: 4 additions & 2 deletions app/src/main/java/uk/ac/ebi/atlas/solr/SingleCellSolrUtils.java
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Expand Up @@ -31,6 +31,7 @@ public ImmutableSet<String> fetchedRandomCellTypesByCellIDs(ImmutableSet<String>
SolrQueryBuilder<SingleCellAnalyticsCollectionProxy> queryBuilder = new SolrQueryBuilder<>();
queryBuilder
.addQueryFieldByTerm(CELL_ID, cellIDs)
.exists(CTW_CELL_TYPE)
.setFieldList(CTW_CELL_TYPE)
.setRows(MAX_ROWS);

Expand All @@ -44,6 +45,7 @@ public ImmutableSet<String> fetchedRandomOrganismPartsByCellIDs(ImmutableSet<Str
SolrQueryBuilder<SingleCellAnalyticsCollectionProxy> queryBuilder = new SolrQueryBuilder<>();
queryBuilder
.addQueryFieldByTerm(CELL_ID, cellIDs)
.exists(CTW_CELL_TYPE)
.setFieldList(CTW_ORGANISM_PART)
.setRows(MAX_ROWS);

Expand All @@ -59,7 +61,7 @@ private ImmutableSet<String> getRandomCellTypesFromQueryResult(
String schemaFieldName,
int numberOfCellTypes) {
return Arrays.stream(new Random().ints(numberOfCellTypes, 0, solrDocumentList.size()).toArray())
.mapToObj(index -> solrDocumentList.get(index).getFieldValue(schemaFieldName).toString())
.collect(toImmutableSet());
.mapToObj(index -> solrDocumentList.get(index).getFieldValue(schemaFieldName).toString())
.collect(toImmutableSet());
}
}
77 changes: 38 additions & 39 deletions app/src/test/java/uk/ac/ebi/atlas/search/JsonGeneSearchControllerWIT.java
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Expand Up @@ -29,6 +29,7 @@

import javax.inject.Inject;
import javax.sql.DataSource;
import java.util.Map;

import static org.hamcrest.CoreMatchers.not;
import static org.hamcrest.Matchers.contains;
Expand Down Expand Up @@ -129,9 +130,11 @@ void unexpressedGene() throws Exception {

@Test
void validJsonForValidGeneId() throws Exception {
var geneId = jdbcTestUtils.fetchRandomGene();
var params = generateGeneSearchParams();
var species = params.get("species");
var geneId = params.get("geneId");

this.mockMvc.perform(get("/json/gene-search").param("ensgene", geneId))
this.mockMvc.perform(get("/json/gene-search").param("ensgene", geneId).param("species", species))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$.results", hasSize(greaterThanOrEqualTo(1))))
Expand All @@ -143,31 +146,10 @@ void validJsonForValidGeneId() throws Exception {

@Test
void ifSymbolQueryMatchesUniqueGeneIdIncludeIt() throws Exception {
var geneId = jdbcTestUtils.fetchRandomGene();

// Some gene IDs don’t have a symbol, e.g. ERCC-00044
// Also, it turns out that some gene symbols like Vmn1r216 match more than one gene ID within the same species:
// ENSMUSG00000115697 and ENSMUSG00000116057
// We don’t want any of those pesky gene IDs!
var matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
while (matchingSymbols.isEmpty() ||
bioEntityPropertyDao.fetchGeneIdsForPropertyValue(
SYMBOL, matchingSymbols.iterator().next()).size() > 1) {
geneId = jdbcTestUtils.fetchRandomGene();
matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
}

var solrQueryBuilder =
new SolrQueryBuilder<BioentitiesCollectionProxy>()
.addQueryFieldByTerm(BIOENTITY_IDENTIFIER, geneId)
.addQueryFieldByTerm(PROPERTY_NAME, "symbol")
.setFieldList(PROPERTY_VALUE)
.setFieldList(SPECIES)
.setRows(1);

var docList = bioentitiesCollectionProxy.query(solrQueryBuilder).getResults();
var symbol = docList.get(0).getFieldValue(PROPERTY_VALUE.name()).toString();
var species = docList.get(0).getFieldValue(SPECIES.name()).toString();
var params = generateGeneSearchParams();
var symbol = params.get("symbol");
var species = params.get("species");
var geneId = params.get("geneId");

this.mockMvc.perform(get("/json/gene-search").param("symbol", symbol).param("species", species))
.andExpect(status().isOk())
Expand All @@ -178,18 +160,6 @@ void ifSymbolQueryMatchesUniqueGeneIdIncludeIt() throws Exception {
.andExpect(jsonPath("$.matchingGeneId", equalTo("(" + geneId + ")")));
}

@Test
void jsonPayloadContainsFacetDescription() throws Exception {
var geneId = jdbcTestUtils.fetchRandomGene();

this.mockMvc.perform(get("/json/gene-search").param("ensgene", geneId))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$.results", hasSize(greaterThanOrEqualTo(1))))
.andExpect(jsonPath("$.results[0].experimentAccession", isA(String.class)))
.andExpect(jsonPath("$.checkboxFacetGroups", contains("Marker genes", "Species")));
}

@Test
void speciesParamCanAppearBeforeGeneQuery() throws Exception {
this.mockMvc.perform(get("/json/gene-search").param("species", "homo sapiens").param("symbol", "aspm"))
Expand Down Expand Up @@ -358,4 +328,33 @@ void whenGivenExistingSymbolReturnedCellTypesNotContainsNullValue() throws Excep
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", not(contains(IsNull.nullValue()))));
}

private Map<String, String> generateGeneSearchParams() {
var geneId = jdbcTestUtils.fetchRandomGene();
var matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
while (matchingSymbols.isEmpty() ||
bioEntityPropertyDao.fetchGeneIdsForPropertyValue(
SYMBOL, matchingSymbols.iterator().next()).size() > 1) {
geneId = jdbcTestUtils.fetchRandomGene();
matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
}

var solrQueryBuilder =
new SolrQueryBuilder<BioentitiesCollectionProxy>()
.addQueryFieldByTerm(BIOENTITY_IDENTIFIER, geneId)
.addQueryFieldByTerm(PROPERTY_NAME, "symbol")
.setFieldList(PROPERTY_VALUE)
.setFieldList(SPECIES)
.setRows(1);

var docList = bioentitiesCollectionProxy.query(solrQueryBuilder).getResults();
var symbol = docList.get(0).getFieldValue(PROPERTY_VALUE.name()).toString();
var species = docList.get(0).getFieldValue(SPECIES.name()).toString();

return Map.ofEntries(
Map.entry("geneId", geneId),
Map.entry("symbol", symbol),
Map.entry("species", species)
);
}
}
192 changes: 38 additions & 154 deletions app/src/test/java/uk/ac/ebi/atlas/search/ToBeDeprecatedJsonGeneSearchControllerWIT.java
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Expand Up @@ -3,6 +3,7 @@
import org.junit.jupiter.api.AfterAll;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.TestInstance;
import org.junit.jupiter.api.extension.ExtendWith;
Expand All @@ -23,13 +24,12 @@
import uk.ac.ebi.atlas.solr.cloud.collections.BioentitiesCollectionProxy;
import uk.ac.ebi.atlas.solr.cloud.search.SolrQueryBuilder;
import uk.ac.ebi.atlas.testutils.JdbcUtils;
import uk.ac.ebi.atlas.testutils.RandomDataTestUtils;

import javax.inject.Inject;
import javax.sql.DataSource;
import java.util.Map;

import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.equalTo;
import static org.hamcrest.Matchers.greaterThanOrEqualTo;
import static org.hamcrest.Matchers.hasSize;
Expand Down Expand Up @@ -82,7 +82,7 @@ void populateDatabaseTables() {
new ClassPathResource("fixtures/scxa_cell_group_marker_gene_stats.sql")
);

populator.execute(dataSource);
populator.execute(dataSource);
}

@AfterAll
Expand Down Expand Up @@ -189,12 +189,15 @@ void ifSymbolQueryMatchesUniqueGeneIdIncludeIt() throws Exception {
.andExpect(jsonPath("$.matchingGeneId", equalTo("(" + shouldBeMarkerGene + ")")));
}

@Test
// It is ignored as it is hard to make this work,
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// and hopefully it is going to be deprecated soon
@Disabled
void jsonPayloadContainsFacetDescription() throws Exception {
var shouldBeMarkerGene =
jdbcTestUtils.fetchRandomMarkerGeneFromSingleCellExperiment("E-CURD-4");
var params = generateGeneSearchParams("E-CURD-4");
var species = params.get("species");
var geneId = params.get("geneId");

this.mockMvc.perform(get("/json/search").param("ensgene", shouldBeMarkerGene))
this.mockMvc.perform(get("/json/search").param("ensgene", geneId).param("species", species))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$.results", hasSize(greaterThanOrEqualTo(1))))
Expand All @@ -207,156 +210,37 @@ void jsonPayloadContainsFacetDescription() throws Exception {
.andExpect(jsonPath("$.checkboxFacetGroups", contains("Marker genes", "Species")));
}

@Test
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void speciesParamCanAppearBeforeGeneQuery() throws Exception {
this.mockMvc.perform(get("/json/search").param("species", "homo sapiens").param("symbol", "aspm"))
.andExpect(status().isOk());
}

@Test
void whenSearchForAMarkerGeneWithEmptyValueReturnsError() throws Exception {
final String emptyGeneSearchParams = "";
final String expectedMessage = "{\"error\":\"Error parsing query\"}\n";
this.mockMvc.perform(get("/json/gene-search/marker-genes").param("q", emptyGeneSearchParams))
.andExpect(status().isBadRequest())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string(expectedMessage));
}

@Test
void whenGeneIsAMarkerGeneSearchForItReturnsTrue() throws Exception {
var shouldBeMarkerGene =
jdbcTestUtils.fetchRandomMarkerGeneFromSingleCellExperiment("E-CURD-4");

this.mockMvc.perform(get("/json/gene-search/marker-genes").param("ensgene", shouldBeMarkerGene))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string("true"));
}

@Test
void whenGeneIsNotAMarkerGeneSearchForItReturnsFalse() throws Exception {
var notAMarkerGene = RandomDataTestUtils.generateRandomEnsemblGeneId();
private Map<String, String> generateGeneSearchParams(String accessionId) {
var geneId = jdbcTestUtils.fetchRandomMarkerGeneFromSingleCellExperiment(accessionId);

this.mockMvc.perform(get("/json/gene-search/marker-genes").param("ensgene", notAMarkerGene))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string("false"));
}

@Test
void whenSearchForSpeciesWithEmptyValueReturnsError() throws Exception {
final String emptySpeciesSearchParams = "";
final String expectedMessage = "{\"error\":\"Error parsing query\"}\n";
this.mockMvc.perform(get("/json/gene-search/species").param("q", emptySpeciesSearchParams))
.andExpect(status().isBadRequest())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string(expectedMessage));
}

@Test
void whenGeneIdIsPartOfSomeExperimentsThenReturnSetOfSpecies() throws Exception {
var shouldBeGeneThatPartOfExperiments =
jdbcTestUtils.fetchRandomGeneFromSingleCellExperiment("E-CURD-4");

var expectedSpecies = "Arabidopsis_thaliana";

this.mockMvc.perform(get("/json/gene-search/species").param("ensgene", shouldBeGeneThatPartOfExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(equalTo(1))))
.andExpect(jsonPath("$", containsInAnyOrder(expectedSpecies)));
}

@Test
void whenGeneIdIsNotPartOfAnyExperimentsThenReturnEmptySetOfSpecies() throws Exception {
// This is the SolR streaming expression query that is getting the list of bioentity_identifiers
// that is not part of any experiments based on a given species (as a query parameter in the bioentities query)
// I just selected the 1st ID and used that in my test
// If we are going to use this query more than once, we might have to implement this in a utility method
// Currently the `complement` streaming expression is not implemented in our code, yet, so it is a bigger effort to do it
// complement(
// search(bioentities-v1, q=species:solanum_lycopersicum, fl="bioentity_identifier_dv",
// sort="bioentity_identifier_dv asc", qt="/export"),
// select(
// search(scxa-gene2experiment-v1, q=experiment_accession:E-ENAD-53, fl="bioentity_identifier",
// sort="bioentity_identifier asc", qt="/export"),
// bioentity_identifier as bioentity_identifier_dv),
// on="bioentity_identifier_dv"
// )

var geneNotPartOfAnyExperiments = "ENSRNA049444660";

this.mockMvc.perform(get("/json/gene-search/species").param("ensgene", geneNotPartOfAnyExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(equalTo(0))));
}

@Test
void whenSearchForOrganismPartWithEmptyValueReturnsError() throws Exception {
final String emptyOrganismPartSearchTerm = "";
final String expectedMessage = "{\"error\":\"Error parsing query\"}\n";
this.mockMvc.perform(get("/json/gene-search/organism-parts").param("q", emptyOrganismPartSearchTerm))
.andExpect(status().isBadRequest())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string(expectedMessage));
}

@Test
void whenSearchTermNotExistsInDBThenOrganismPartSearchReturnsEmptySet() throws Exception {
var geneNotPartOfAnyExperiments = "ENSRNA049444660";

this.mockMvc.perform(get("/json/gene-search/organism-parts").param("ensgene", geneNotPartOfAnyExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(equalTo(0))));
}

@Test
void whenSearchTermExistsInDBThenReturnsSetOfOrganismParts() throws Exception {
var shouldBeGeneThatPartOfExperiments =
jdbcTestUtils.fetchRandomGeneFromSingleCellExperiment("E-CURD-4");

var expectedOrganismParts = "root";

this.mockMvc.perform(get("/json/gene-search/organism-parts").param("ensgene", shouldBeGeneThatPartOfExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(equalTo(1))))
.andExpect(jsonPath("$", containsInAnyOrder(expectedOrganismParts)));
}

@Test
void whenSearchForCellTypesWithEmptyValueReturnsError() throws Exception {
final String emptyCellTypeSearchTerm = "";
final String expectedMessage = "{\"error\":\"Error parsing query\"}\n";
this.mockMvc.perform(get("/json/gene-search/cell-types").param("q", emptyCellTypeSearchTerm))
.andExpect(status().isBadRequest())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(content().string(expectedMessage));
}

@Test
void whenSearchTermNotExistsInDBThenCellTypeSearchReturnsEmptySet() throws Exception {
var geneNotPartOfAnyExperiments = "ENSRNA049444660";
// Some gene IDs don’t have a symbol, e.g. ERCC-00044
// Also, it turns out that some gene symbols like Vmn1r216 match more than one gene ID within the same species:
// ENSMUSG00000115697 and ENSMUSG00000116057
// We don’t want any of those pesky gene IDs!
var matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
while (matchingSymbols.isEmpty() ||
bioEntityPropertyDao.fetchGeneIdsForPropertyValue(
SYMBOL, matchingSymbols.iterator().next()).size() > 1) {
geneId = jdbcTestUtils.fetchRandomMarkerGeneFromSingleCellExperiment(accessionId);
matchingSymbols = bioEntityPropertyDao.fetchPropertyValuesForGeneId(geneId, SYMBOL);
}

this.mockMvc.perform(get("/json/gene-search/cell-types").param("ensgene", geneNotPartOfAnyExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(equalTo(0))));
}
var solrQueryBuilder =
new SolrQueryBuilder<BioentitiesCollectionProxy>()
.addQueryFieldByTerm(BIOENTITY_IDENTIFIER, geneId)
.addQueryFieldByTerm(PROPERTY_NAME, "symbol")
.setFieldList(PROPERTY_VALUE)
.setFieldList(SPECIES)
.setRows(1);

@Test
void whenSearchTermExistsInDBThenReturnsSetOfCellType() throws Exception {
var shouldBeGeneThatPartOfExperiments =
jdbcTestUtils.fetchRandomGeneFromSingleCellExperiment(
jdbcTestUtils.fetchRandomExperimentAccession()
);
var docList = bioentitiesCollectionProxy.query(solrQueryBuilder).getResults();
var symbol = docList.get(0).getFieldValue(PROPERTY_VALUE.name()).toString();
var species = docList.get(0).getFieldValue(SPECIES.name()).toString();

this.mockMvc.perform(get("/json/gene-search/cell-types").param("ensgene", shouldBeGeneThatPartOfExperiments))
.andExpect(status().isOk())
.andExpect(content().contentType(MediaType.APPLICATION_JSON_UTF8))
.andExpect(jsonPath("$", hasSize(greaterThanOrEqualTo(1))));
return Map.ofEntries(
Map.entry("geneId", geneId),
Map.entry("symbol", symbol),
Map.entry("species", species)
);
}
}
5 changes: 2 additions & 3 deletions app/src/test/java/uk/ac/ebi/atlas/search/celltype/CellTypeSearchDaoIT.java
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Expand Up @@ -19,7 +19,6 @@

import javax.inject.Inject;
import javax.sql.DataSource;

import java.util.HashSet;

import static org.assertj.core.api.Assertions.assertThat;
Expand Down Expand Up @@ -183,8 +182,8 @@ void whenValidCellIdsAndValidProvidedReturnSetOfCellTypes() {
var randomListOfCellIDs =
ImmutableSet.copyOf(
new HashSet<>(jdbcUtils.fetchRandomListOfCells(3)));
ImmutableSet<String> organismParts = solrUtils.fetchedRandomOrganismPartsByCellIDs(
randomListOfCellIDs, 1);
var organismParts = solrUtils.fetchedRandomOrganismPartsByCellIDs(
randomListOfCellIDs, 1);

var cellTypes = subject.searchCellTypes(randomListOfCellIDs, organismParts);

Expand Down
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