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Remove FileTypes Enum and Update References #867

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merged 2 commits into from
Oct 15, 2024
Merged

Remove FileTypes Enum and Update References #867

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a2b1f68
Eliminating enum FileTypes from the code base
Azher2Ali Oct 3, 2024
40fbe84
Removing FileTypes and it's following reference
Azher2Ali Oct 3, 2024
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56 changes: 0 additions & 56 deletions song-core/src/main/java/bio/overture/song/core/model/enums/FileTypes.java
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5 changes: 0 additions & 5 deletions song-server/src/main/java/bio/overture/song/server/model/entity/FileEntity.java
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Expand Up @@ -21,7 +21,6 @@
import bio.overture.song.core.model.FileData;
import bio.overture.song.core.model.Metadata;
import bio.overture.song.core.model.enums.AccessTypes;
import bio.overture.song.core.model.enums.FileTypes;
import bio.overture.song.server.model.enums.TableAttributeNames;
import bio.overture.song.server.model.enums.TableNames;
import com.fasterxml.jackson.annotation.JsonInclude;
Expand Down Expand Up @@ -81,10 +80,6 @@ public void setFileType(@NonNull String fileType) {
this.fileType = fileType;
}

public void setFileType(@NonNull FileTypes type) {
this.fileType = type.toString();
}

public void setFileAccess(@NonNull String fileAccess) {
this.fileAccess = fileAccess;
}
Expand Down
13 changes: 1 addition & 12 deletions song-server/src/main/resources/schemas/fileUpdateRequest.json
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Expand Up @@ -52,18 +52,7 @@
"pattern": "^[A-Za-z0-9_\\.\\-\\[\\]\\(\\)]+$"
},
"fileType": {
"type": "string",
"enum": [
"FASTA",
"FAI",
"FASTQ",
"BAM",
"BAI",
"VCF",
"TBI",
"IDX",
"XML"
]
"type": "string"
}
}
}
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53 changes: 0 additions & 53 deletions song-server/src/test/java/bio/overture/song/server/constants/ConstantsTest.java
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Expand Up @@ -23,18 +23,6 @@
import static bio.overture.song.core.model.enums.AnalysisStates.PUBLISHED;
import static bio.overture.song.core.model.enums.AnalysisStates.SUPPRESSED;
import static bio.overture.song.core.model.enums.AnalysisStates.UNPUBLISHED;
import static bio.overture.song.core.model.enums.FileTypes.BAI;
import static bio.overture.song.core.model.enums.FileTypes.BAM;
import static bio.overture.song.core.model.enums.FileTypes.FAI;
import static bio.overture.song.core.model.enums.FileTypes.FASTA;
import static bio.overture.song.core.model.enums.FileTypes.FASTQ;
import static bio.overture.song.core.model.enums.FileTypes.IDX;
import static bio.overture.song.core.model.enums.FileTypes.TBI;
import static bio.overture.song.core.model.enums.FileTypes.TGZ;
import static bio.overture.song.core.model.enums.FileTypes.VCF;
import static bio.overture.song.core.model.enums.FileTypes.XML;
import static bio.overture.song.core.model.enums.FileTypes.resolveFileType;
import static bio.overture.song.core.model.enums.FileTypes.values;
import static bio.overture.song.core.testing.SongErrorAssertions.assertExceptionThrownBy;
import static bio.overture.song.server.model.enums.InfoSearchResponseColumns.ANALYSIS_ID;
import static bio.overture.song.server.model.enums.InfoSearchResponseColumns.INFO;
Expand Down Expand Up @@ -91,47 +79,6 @@ public void testAccessTypes() {
IllegalStateException.class, () -> resolveAccessType("somethingNotAccessType"));
}

@Test
public void testFileTypes() {
assertEquals(FASTA.toString(), "FASTA");
assertEquals(FAI.toString(), "FAI");
assertEquals(FASTQ.toString(), "FASTQ");
assertEquals(BAM.toString(), "BAM");
assertEquals(BAI.toString(), "BAI");
assertEquals(VCF.toString(), "VCF");
assertEquals(TBI.toString(), "TBI");
assertEquals(IDX.toString(), "IDX");
assertEquals(XML.toString(), "XML");
assertEquals(TGZ.toString(), "TGZ");

assertEquals(FASTA.getExtension(), "fasta");
assertEquals(FAI.getExtension(), "fai");
assertEquals(FASTQ.getExtension(), "fastq");
assertEquals(BAM.getExtension(), "bam");
assertEquals(BAI.getExtension(), "bai");
assertEquals(VCF.getExtension(), "vcf");
assertEquals(TBI.getExtension(), "tbi");
assertEquals(IDX.getExtension(), "idx");
assertEquals(XML.getExtension(), "xml");
assertEquals(TGZ.getExtension(), "tgz");

assertEquals(values().length, 10);

assertEquals(resolveFileType("FASTA"), FASTA);
assertEquals(resolveFileType("FAI"), FAI);
assertEquals(resolveFileType("FASTQ"), FASTQ);
assertEquals(resolveFileType("BAM"), BAM);
assertEquals(resolveFileType("BAI"), BAI);
assertEquals(resolveFileType("VCF"), VCF);
assertEquals(resolveFileType("TBI"), TBI);
assertEquals(resolveFileType("IDX"), IDX);
assertEquals(resolveFileType("XML"), XML);
assertEquals(resolveFileType("TGZ"), TGZ);

assertExceptionThrownBy(
IllegalStateException.class, () -> resolveFileType("somethingThatsNotAFileType"));
}

@Test
public void testInfoTypes() {
assertEquals(STUDY.toString(), "Study");
Expand Down
3 changes: 1 addition & 2 deletions song-server/src/test/java/bio/overture/song/server/service/DeserializationTest.java
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Expand Up @@ -18,7 +18,6 @@
package bio.overture.song.server.service;

import static bio.overture.song.core.model.enums.AnalysisStates.UNPUBLISHED;
import static bio.overture.song.core.model.enums.FileTypes.BAM;
import static bio.overture.song.core.utils.JsonUtils.fromJson;
import static bio.overture.song.core.utils.JsonUtils.objectToTree;
import static bio.overture.song.core.utils.JsonUtils.readTree;
Expand Down Expand Up @@ -123,7 +122,7 @@ public void nonEmptyInfoFields_allEmpty_success() {
.objectId("sfdsdfsdf")
.studyId("ABC123")
.fileName("something.bam")
.fileType(BAM.toString())
.fileType("BAM")
.build();
val fileList = List.of(f1);
val fff = new ObjectMapper().valueToTree(f1);
Expand Down
9 changes: 3 additions & 6 deletions song-server/src/test/java/bio/overture/song/server/service/EntityTest.java
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Expand Up @@ -29,16 +29,13 @@
import static bio.overture.song.server.utils.TestConstants.TUMOUR_NORMAL_DESIGNATION;
import static bio.overture.song.server.utils.TestFiles.assertInfoKVPair;
import static com.google.common.collect.Lists.newArrayList;
import static java.util.Arrays.stream;
import static java.util.stream.Collectors.toList;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;

import bio.overture.song.core.model.Metadata;
import bio.overture.song.core.model.enums.FileTypes;
import bio.overture.song.server.model.Upload;
import bio.overture.song.server.model.entity.Donor;
import bio.overture.song.server.model.entity.FileEntity;
Expand All @@ -53,15 +50,15 @@
import bio.overture.song.server.model.legacy.LegacyEntity;
import com.fasterxml.jackson.databind.JsonNode;
import java.time.LocalDateTime;
import java.util.Arrays;
import java.util.List;
import lombok.val;
import org.junit.Test;

public class EntityTest {
private static final String DEFAULT_STUDY_ID = "ABC123";
private static final List<String> SAMPLE_TYPES = newArrayList(SAMPLE_TYPE);
private static final List<String> FILE_TYPES =
stream(FileTypes.values()).map(FileTypes::toString).collect(toList());
private static final List<String> FILE_TYPES = Arrays.asList("mp3", "mp4", "BAM");

@Test
public void testNullMetadata() {
Expand Down Expand Up @@ -634,7 +631,7 @@ public void testFile() {
file1.setFileMd5sum("b1");
file1.setFileName("c1");
file1.setFileSize(13L);
file1.setFileType(FILE_TYPES.get(0));
file1.setFileType("mp4");
file1.setObjectId("d1");
file1.setStudyId("e1");

Expand Down
3 changes: 1 addition & 2 deletions song-server/src/test/java/bio/overture/song/server/service/FileServiceTest.java
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Expand Up @@ -20,7 +20,6 @@
import static bio.overture.song.core.exceptions.ServerErrors.STUDY_ID_DOES_NOT_EXIST;
import static bio.overture.song.core.model.enums.AccessTypes.CONTROLLED;
import static bio.overture.song.core.model.enums.AccessTypes.OPEN;
import static bio.overture.song.core.model.enums.FileTypes.FAI;
import static bio.overture.song.core.testing.SongErrorAssertions.assertSongError;
import static bio.overture.song.core.utils.RandomGenerator.createRandomGenerator;
import static bio.overture.song.server.utils.TestConstants.DEFAULT_ANALYSIS_ID;
Expand Down Expand Up @@ -109,7 +108,7 @@ public void testCreateAndDeleteFile() {

f.setFileSize(0L);
f.setDataType(randomGenerator.generateRandomAsciiString(10));
f.setFileType(FAI);
f.setFileType("FAI");
f.setFileMd5sum("6bb8ee7218e96a59e0ad898b4f5360f1");
f.setInfo(metadata);
f.setFileAccess(OPEN);
Expand Down
10 changes: 4 additions & 6 deletions song-server/src/test/java/bio/overture/song/server/service/PublishAnalysisTest.java
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Expand Up @@ -22,8 +22,6 @@
import static bio.overture.song.core.exceptions.ServerErrors.MISSING_STORAGE_OBJECTS;
import static bio.overture.song.core.model.enums.AnalysisStates.PUBLISHED;
import static bio.overture.song.core.model.enums.AnalysisStates.UNPUBLISHED;
import static bio.overture.song.core.model.enums.FileTypes.BAM;
import static bio.overture.song.core.model.enums.FileTypes.VCF;
import static bio.overture.song.core.utils.RandomGenerator.createRandomGenerator;
import static bio.overture.song.core.utils.RandomGenerator.randomList;
import static bio.overture.song.server.service.PublishAnalysisTest.RangeType.ALL;
Expand Down Expand Up @@ -356,11 +354,11 @@ public FileEntity generateFile(Analysis a) {
String fileName = randomGenerator.generateRandomUUIDAsString() + ".";

if (legacyAnalysisTypeName == LegacyAnalysisTypeName.SEQUENCING_READ) {
fileType = BAM.toString();
fileName += BAM.getExtension();
fileType = "BAM";
fileName += "BAM";
} else if (legacyAnalysisTypeName == LegacyAnalysisTypeName.VARIANT_CALL) {
fileType = VCF.toString();
fileName += VCF.getExtension() + ".gz";
fileType = "VCF";
fileName += "VCF" + ".gz";
}
val file =
FileEntity.builder()
Expand Down
3 changes: 1 addition & 2 deletions ...erver/src/test/java/bio/overture/song/server/utils/securestudy/impl/SecureFileTester.java
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Expand Up @@ -21,7 +21,6 @@
import static java.lang.String.format;

import bio.overture.song.core.model.enums.AccessTypes;
import bio.overture.song.core.model.enums.FileTypes;
import bio.overture.song.core.utils.RandomGenerator;
import bio.overture.song.server.model.entity.FileEntity;
import bio.overture.song.server.service.FileService;
Expand Down Expand Up @@ -64,7 +63,7 @@ protected String createId(String existingStudyId, Object context) {
analysisService.checkAnalysisExists(analysisData.getExistingId());
val existingAnalysisId = analysisData.getExistingId();

val type = getRandomGenerator().randomEnum(FileTypes.class).toString();
val type = "mp4";
val file =
FileEntity.builder()
.fileAccess(getRandomGenerator().randomEnum(AccessTypes.class).toString())
Expand Down