BI-2848 - New Genotyping Page Backend: linkage to sample submission

src/main/java/org/breedinginsight/api/model/v1/request/query/GenotypeImportQuery.java

@@ -0,0 +1,69 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.api.model.v1.request.query;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import org.apache.commons.lang3.StringUtils;
+
+import java.util.ArrayList;
+import java.util.List;
+
+@Getter
+@Introspected
+public class GenotypeImportQuery extends QueryParams {
+
+    private String sampleSubmissionId;
+    private String projectNameForSampleSubmission;
+    private String sampleSubmissionCreatedBy;
+    private String genotypingFileName;
+    private String genotypingImportDate;
+    private String genotypingImportBy;
+
+    public SearchRequest constructSearchRequest() {
+        List<FilterRequest> filters = new ArrayList<>();
+
+        if (!StringUtils.isBlank(getSampleSubmissionId())) {
+            filters.add(constructFilterRequest("sampleSubmissionId", getSampleSubmissionId()));
+        }
+        if (!StringUtils.isBlank(getProjectNameForSampleSubmission())) {
+            filters.add(constructFilterRequest("projectNameForSampleSubmission", getProjectNameForSampleSubmission()));
+        }
+        if (!StringUtils.isBlank(getSampleSubmissionCreatedBy())) {
+            filters.add(constructFilterRequest("sampleSubmissionCreatedBy", getSampleSubmissionCreatedBy()));
+        }
+        if (!StringUtils.isBlank(getGenotypingFileName())) {
+            filters.add(constructFilterRequest("genotypingFileName", getGenotypingFileName()));
+        }
+        if (!StringUtils.isBlank(getGenotypingImportDate())) {
+            filters.add(constructFilterRequest("genotypingImportDate", getGenotypingImportDate()));
+        }
+        if (!StringUtils.isBlank(getGenotypingImportBy())) {
+            filters.add(constructFilterRequest("genotypingImportBy", getGenotypingImportBy()));
+        }
+
+        return new SearchRequest(filters);
+    }
+
+    private FilterRequest constructFilterRequest(String field, String value) {
+        return FilterRequest.builder()
+                .field(field)
+                .value(value)
+                .build();
+    }
+}

src/main/java/org/breedinginsight/api/v1/controller/geno/GenotypeDataUploadController.java

@@ -1,3 +1,19 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.breedinginsight.api.v1.controller.geno;
 
 import io.micronaut.http.HttpResponse;
@@ -6,30 +22,65 @@
 import io.micronaut.http.multipart.CompletedFileUpload;
 import lombok.extern.slf4j.Slf4j;
 import org.brapi.client.v2.model.exceptions.ApiException;
-import org.breedinginsight.api.auth.AuthenticatedUser;
-import org.breedinginsight.api.auth.ProgramSecured;
-import org.breedinginsight.api.auth.ProgramSecuredRole;
-import org.breedinginsight.api.auth.SecurityService;
+import org.breedinginsight.api.auth.*;
+import org.breedinginsight.api.model.v1.request.query.GenotypeImportQuery;
+import org.breedinginsight.api.model.v1.request.query.SearchRequest;
+import org.breedinginsight.api.model.v1.response.DataResponse;
 import org.breedinginsight.api.model.v1.response.Response;
+import org.breedinginsight.api.model.v1.validators.QueryValid;
 import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
 import org.breedinginsight.brapps.importer.model.response.ImportResponse;
+import org.breedinginsight.model.GenotypeImportDetails;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.services.ProgramService;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 import org.breedinginsight.services.geno.GenotypeService;
+import org.breedinginsight.utilities.response.ResponseUtils;
+import org.breedinginsight.utilities.response.mappers.GenotypeImportQueryMapper;
 
 import javax.inject.Inject;
+import javax.validation.Valid;
+import java.util.Optional;
 import java.util.UUID;
 
 @Slf4j
 @Controller("/${micronaut.bi.api.version}")
 public class GenotypeDataUploadController {
     private final GenotypeService genoService;
     private final SecurityService securityService;
+    private final ProgramService programService;
+    private final GenotypeImportQueryMapper genotypeImportQueryMapper;
 
     @Inject
-    public GenotypeDataUploadController(GenotypeService genoService, SecurityService securityService) {
+    public GenotypeDataUploadController(GenotypeService genoService, SecurityService securityService,
+                                        ProgramService programService, GenotypeImportQueryMapper genotypeImportQueryMapper) {
         this.genoService = genoService;
         this.securityService = securityService;
+        this.programService = programService;
+        this.genotypeImportQueryMapper = genotypeImportQueryMapper;
+    }
+
+    @Get("programs/{programId}/geno/imports{?genotypeImportQuery*}")
+    @Produces(MediaType.APPLICATION_JSON)
+    @ProgramSecured(roleGroups = ProgramSecuredRoleGroup.PROGRAM_SCOPED_ROLES)
+    public HttpResponse<Response<DataResponse<GenotypeImportDetails>>> getGenotypeImports(
+            @PathVariable UUID programId,
+            @QueryValue @QueryValid(using = GenotypeImportQueryMapper.class) @Valid GenotypeImportQuery genotypeImportQuery) {
+        Optional<Program> program = programService.getById(programId);
+        if (program.isEmpty()) {
+            log.info("programId not found: {}", programId.toString());
+            return HttpResponse.notFound();
+        }
+
+        SearchRequest searchRequest = genotypeImportQuery.constructSearchRequest();
+
+        return ResponseUtils.getQueryResponse(
+                genoService.getGenotypeImports(programId),
+                genotypeImportQueryMapper,
+                searchRequest,
+                genotypeImportQuery
+        );
     }
 
     @Post("programs/{programId}/submissions/{submissionId}/geno/import")

src/main/java/org/breedinginsight/daos/GenotypeImportDAO.java

@@ -0,0 +1,85 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.breedinginsight.daos;
+
+import io.micronaut.http.HttpStatus;
+import org.breedinginsight.dao.db.tables.BiUserTable;
+import org.breedinginsight.dao.db.tables.daos.GenotypeImportDao;
+import org.breedinginsight.dao.db.tables.pojos.GenotypeImportEntity;
+import org.breedinginsight.model.GenotypeImportDetails;
+import org.jooq.Configuration;
+import org.jooq.DSLContext;
+
+import javax.inject.Inject;
+import javax.inject.Singleton;
+import java.time.OffsetDateTime;
+import java.util.List;
+import java.util.UUID;
+
+import static org.breedinginsight.dao.db.Tables.*;
+
+@Singleton
+public class GenotypeImportDAO extends GenotypeImportDao {
+
+    private final DSLContext dsl;
+
+    @Inject
+    public GenotypeImportDAO(Configuration config, DSLContext dsl) {
+        super(config);
+        this.dsl = dsl;
+    }
+
+    public void createGenotypeImportLink(UUID submissionId, UUID importerImportId, UUID userId) {
+        OffsetDateTime now = OffsetDateTime.now();
+
+        insert(GenotypeImportEntity.builder()
+                .id(UUID.randomUUID())
+                .sampleSubmissionId(submissionId)
+                .importerImportId(importerImportId)
+                .createdAt(now)
+                .updatedAt(now)
+                .createdBy(userId)
+                .updatedBy(userId)
+                .build());
+    }
+
+    public List<GenotypeImportDetails> getGenotypeImportsByProgramId(UUID programId) {
+        BiUserTable sampleSubmissionCreatedByUser = BI_USER.as("sampleSubmissionCreatedByUser");
+        BiUserTable genotypingImportByUser = BI_USER.as("genotypingImportByUser");
+
+        return dsl.select(
+                        SAMPLE_SUBMISSION.ID,
+                        SAMPLE_SUBMISSION.NAME,
+                        sampleSubmissionCreatedByUser.NAME,
+                        IMPORTER_IMPORT.UPLOAD_FILE_NAME,
+                        IMPORTER_IMPORT.CREATED_AT,
+                        genotypingImportByUser.NAME)
+                .from(GENOTYPE_IMPORT)
+                .join(SAMPLE_SUBMISSION).on(GENOTYPE_IMPORT.SAMPLE_SUBMISSION_ID.eq(SAMPLE_SUBMISSION.ID))
+                .join(sampleSubmissionCreatedByUser).on(SAMPLE_SUBMISSION.CREATED_BY.eq(sampleSubmissionCreatedByUser.ID))
+                .join(IMPORTER_IMPORT).on(GENOTYPE_IMPORT.IMPORTER_IMPORT_ID.eq(IMPORTER_IMPORT.ID))
+                .join(IMPORTER_PROGRESS).on(IMPORTER_IMPORT.IMPORTER_PROGRESS_ID.eq(IMPORTER_PROGRESS.ID))
+                .join(genotypingImportByUser).on(IMPORTER_IMPORT.USER_ID.eq(genotypingImportByUser.ID))
+                .where(SAMPLE_SUBMISSION.PROGRAM_ID.eq(programId))
+                .and(IMPORTER_IMPORT.PROGRAM_ID.eq(programId))
+                .and(IMPORTER_PROGRESS.STATUSCODE.eq((short) HttpStatus.OK.getCode()))
+                .orderBy(IMPORTER_IMPORT.CREATED_AT.desc())
+                .fetch(record -> GenotypeImportDetails
+                        .parseSqlRecord(record, sampleSubmissionCreatedByUser, genotypingImportByUser));
+    }
+
+}

src/main/java/org/breedinginsight/model/GenotypeImportDetails.java

@@ -0,0 +1,65 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.model;
+
+import io.micronaut.core.annotation.Introspected;
+import lombok.Getter;
+import lombok.NoArgsConstructor;
+import lombok.Setter;
+import lombok.ToString;
+import lombok.experimental.Accessors;
+import lombok.experimental.SuperBuilder;
+import lombok.extern.jackson.Jacksonized;
+import org.breedinginsight.dao.db.tables.BiUserTable;
+import org.jooq.Record;
+
+import java.time.OffsetDateTime;
+import java.util.UUID;
+
+import static org.breedinginsight.dao.db.Tables.IMPORTER_IMPORT;
+import static org.breedinginsight.dao.db.Tables.SAMPLE_SUBMISSION;
+
+@Getter
+@Setter
+@Accessors(chain = true)
+@ToString
+@SuperBuilder
+@NoArgsConstructor
+@Introspected
+@Jacksonized
+public class GenotypeImportDetails {
+    private UUID sampleSubmissionId;
+    private String projectNameForSampleSubmission;
+    private String sampleSubmissionCreatedBy;
+    private String genotypingFileName;
+    private OffsetDateTime genotypingImportDate;
+    private String genotypingImportBy;
+
+    public static GenotypeImportDetails parseSqlRecord(Record record,
+                                                       BiUserTable sampleSubmissionCreatedByUser,
+                                                       BiUserTable genotypingImportByUser) {
+        return GenotypeImportDetails.builder()
+                .sampleSubmissionId(record.get(SAMPLE_SUBMISSION.ID))
+                .projectNameForSampleSubmission(record.get(SAMPLE_SUBMISSION.NAME))
+                .sampleSubmissionCreatedBy(record.get(sampleSubmissionCreatedByUser.NAME))
+                .genotypingFileName(record.get(IMPORTER_IMPORT.UPLOAD_FILE_NAME))
+                .genotypingImportDate(record.get(IMPORTER_IMPORT.CREATED_AT))
+                .genotypingImportBy(record.get(genotypingImportByUser.NAME))
+                .build();
+    }
+}

src/main/java/org/breedinginsight/services/geno/GenotypeService.java

@@ -1,3 +1,19 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.breedinginsight.services.geno;
 
 import io.micronaut.http.multipart.CompletedFileUpload;
@@ -6,11 +22,15 @@
 import org.breedinginsight.model.GermplasmGenotype;
 import org.breedinginsight.services.exceptions.AuthorizationException;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
+import org.breedinginsight.model.GenotypeImportDetails;
 
+import java.util.List;
 import java.util.UUID;
 
 public interface GenotypeService {
     ImportResponse submitGenotypeData(UUID userId, UUID programId, UUID submissionId, CompletedFileUpload uploadedFile) throws DoesNotExistException, AuthorizationException, ApiException;
 
     GermplasmGenotype retrieveGenotypeData(UUID programId, UUID germplasmId) throws DoesNotExistException, AuthorizationException, ApiException;
+
+    List<GenotypeImportDetails> getGenotypeImports(UUID programId);
 }