DDP-6034-SMIDS

src/main/java/org/broadinstitute/dsm/db/OncHistoryDetail.java

@@ -19,7 +19,10 @@
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import static org.broadinstitute.ddp.db.TransactionWrapper.inTransaction;
 
@@ -39,7 +42,7 @@ public class OncHistoryDetail {
             "oD.fax_sent_3_by, oD.fax_confirmed_3, oD.tissue_received, oD.tissue_problem_option, oD.gender, oD.destruction_policy, oD.unable_obtain_tissue, " +
             "tissue_id, t.notes, count_received, tissue_type, tissue_site, tumor_type, h_e, pathology_report, collaborator_sample_id, block_sent, scrolls_received, sk_id, sm_id, " +
             "sent_gp, first_sm_id, additional_tissue_value_json, expected_return, return_date, return_fedex_id, shl_work_number, tumor_percentage, tissue_sequence, " +
-            " scrolls_count, uss_count, h_e_count, blocks_count " +
+            " scrolls_count, uss_count, h_e_count, blocks_count, t.uss_sm_ids, t.scrolls_sm_ids, t.he_sm_ids " +
             "FROM ddp_onc_history_detail oD " +
             "LEFT JOIN ddp_medical_record m on (oD.medical_record_id = m.medical_record_id AND NOT oD.deleted <=> 1 AND NOT m.deleted <=> 1) " +
             "LEFT JOIN ddp_institution inst on (inst.institution_id = m.institution_id) " +

src/main/java/org/broadinstitute/dsm/db/Tissue.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.dsm.db;
 
+import com.google.gson.Gson;
 import lombok.Data;
 import lombok.NonNull;
 import org.broadinstitute.ddp.db.SimpleResult;
@@ -30,7 +31,7 @@ public class Tissue {
     private static final String SQL_SELECT_TISSUE = "SELECT tissue_id, onc_history_detail_id, notes, count_received, tissue_type, tissue_site, tumor_type, h_e, " +
             "pathology_report, collaborator_sample_id, block_sent, expected_return, return_date, return_fedex_id, scrolls_received, sk_id, sm_id, " +
             "scrolls_count, uss_count, blocks_count, h_e_count, first_sm_id, sent_gp, last_changed, changed_by, additional_tissue_value_json, shl_work_number, " +
-            "tumor_percentage, tissue_sequence FROM ddp_tissue t WHERE NOT (deleted <=> 1) AND onc_history_detail_id = ?";
+            "tumor_percentage, tissue_sequence, uss_sm_ids, scrolls_sm_ids, he_sm_ids FROM ddp_tissue t WHERE NOT (deleted <=> 1) AND onc_history_detail_id = ?";
     private static final String SQL_INSERT_TISSUE = "INSERT INTO ddp_tissue SET onc_history_detail_id = ?, last_changed = ?, changed_by = ?";
     public static final String SQL_SELECT_TISSUE_LAST_CHANGED = "SELECT t.last_changed FROM ddp_institution inst " +
             "LEFT JOIN ddp_participant as p on (p.participant_id = inst.participant_id) LEFT JOIN ddp_instance as ddp on (ddp.ddp_instance_id = p.ddp_instance_id) " +
@@ -123,14 +124,23 @@ public class Tissue {
     @ColumnName (DBConstants.H_E_COUNT)
     private Integer hECount;
 
+    @ColumnName(DBConstants.USS_SMIDS)
+    private TissueSmId[] ussSMID;
+
+    @ColumnName(DBConstants.SCROLL_SMIDS)
+    private TissueSmId[] scrollSMID;
+
+    @ColumnName(DBConstants.HE_SMIDS)
+    private TissueSmId[] heSMID;
+
 
 
     public Tissue(String tissueId, String oncHistoryDetailId, String tNotes, Integer countReceived, String tissueType,
                   String tissueSite, String tumorType, String hE, String pathologyReport, String collaboratorSampleId,
                   String blockSent, String scrollsReceived, String skId, String smId, String sentGp, String firstSmId,
                   String additionalValues, String expectedReturn, String tissueReturnDate,
                   String returnFedexId, String shlWorkNumber, String tumorPercentage, String sequenceResults, Integer scrollsCount,
-                  Integer ussCount, Integer blocksCount, Integer hECount) {
+                  Integer ussCount, Integer blocksCount, Integer hECount, TissueSmId[] ussSMIDs, TissueSmId[] scrollSMIDs, TissueSmId[] heSMID) {
         this.tissueId = tissueId;
         this.oncHistoryDetailId = oncHistoryDetailId;
         this.tNotes = tNotes;
@@ -158,9 +168,13 @@ public Tissue(String tissueId, String oncHistoryDetailId, String tNotes, Integer
         this.hECount = hECount;
         this.blocksCount = blocksCount;
         this.ussCount = ussCount;
+        this.scrollSMID = scrollSMIDs;
+        this.ussSMID = ussSMIDs;
+        this.heSMID = heSMID;
     }
 
     public static Tissue getTissue(@NonNull ResultSet rs) throws SQLException {
+        Gson gson = new Gson();
         Tissue tissue = new Tissue(
                 rs.getString(DBConstants.TISSUE_ID),
                 rs.getString(DBConstants.ONC_HISTORY_DETAIL_ID),
@@ -188,10 +202,35 @@ public static Tissue getTissue(@NonNull ResultSet rs) throws SQLException {
                 rs.getInt(DBConstants.SCROLLS_COUNT),
                 rs.getInt(DBConstants.USS_COUNT),
                 rs.getInt(DBConstants.BLOCKS_COUNT),
-                rs.getInt(DBConstants.H_E_COUNT));
+                rs.getInt(DBConstants.H_E_COUNT),
+                null,
+                null,
+                null);
+        tissue.setSMIds();
         return tissue;
     }
 
+    private void setSMIds() {
+        if (this.hECount>0){
+           this.heSMID = TissueSmId.getSMIdsForTissueId(this.tissueId, TissueSmId.HE);
+        } else{
+            this.heSMID = new TissueSmId[0];
+        }
+        if (this.ussCount>0){
+            this.ussSMID = TissueSmId.getSMIdsForTissueId(this.tissueId, TissueSmId.USS);
+        }
+        else{
+            this.ussSMID = new TissueSmId[0];
+        }
+        if (this.scrollsCount>0){
+            this.scrollSMID = TissueSmId.getSMIdsForTissueId(this.tissueId, TissueSmId.SCROLLS);
+        }
+        else{
+            this.scrollSMID = new TissueSmId[0];
+        }
+
+    }
+
     public static List<Tissue> getTissue(@NonNull Connection conn, @NonNull String oncHistoryDetailId) {
 
         List<Tissue> tissue = new ArrayList<>();

src/main/java/org/broadinstitute/dsm/db/TissueSmId.java

@@ -0,0 +1,57 @@
+package org.broadinstitute.dsm.db;
+
+import lombok.Data;
+import org.broadinstitute.dsm.db.dao.ddp.tissue.TissueSMIDDao;
+import org.broadinstitute.dsm.db.structure.ColumnName;
+import org.broadinstitute.dsm.db.structure.TableName;
+import org.broadinstitute.dsm.statics.DBConstants;
+
+import java.util.List;
+
+@Data
+@TableName (
+        name = DBConstants.SM_ID_TABLE,
+        alias = DBConstants.SM_ID_TABLE_ALIAS,
+        primaryKey = DBConstants.SM_ID_PK,
+        columnPrefix = "")
+public class TissueSmId {
+
+    @ColumnName(DBConstants.SM_ID_VALUE)
+    private String smIdValue;
+
+    @ColumnName(DBConstants.SM_ID_TYPE_ID)
+    private String smIdType;
+
+    @ColumnName(DBConstants.SM_ID_TISSUE_ID)
+    private String tissueId;
+
+    @ColumnName(DBConstants.SM_ID_PK)
+    private String smIdPk;
+
+    @ColumnName(DBConstants.DELETED)
+    private boolean deleted;
+
+    public static String HE = "he";
+    public static String USS = "uss";
+    public static String SCROLLS = "scrolls";
+    public TissueSmId(){}
+
+    public TissueSmId(String smIdPk, String smIdType, String smIdValue, String tissueId){
+        this.smIdPk = smIdPk;
+        this.smIdType = smIdType;
+        this.smIdValue = smIdValue;
+        this.tissueId = tissueId;
+    }
+
+
+    public static TissueSmId[] getSMIdsForTissueId(String tissueId, String type) {
+        TissueSMIDDao tissueSMIDDao = new TissueSMIDDao();
+        List<TissueSmId> list = tissueSMIDDao.getSMIdsForTissueId(tissueId, type);
+        return list.toArray(new TissueSmId[list.size()]);
+    }
+
+    public String createNewSmId(String tissueId, String userId, String smIdType){
+        String smIdId = new TissueSMIDDao().createNewSMIDForTissue(tissueId, userId, smIdType);
+        return smIdId;
+    }
+}

src/main/java/org/broadinstitute/dsm/db/dao/ddp/tissue/TissueSMIDDao.java

@@ -0,0 +1,122 @@
+package org.broadinstitute.dsm.db.dao.ddp.tissue;
+
+import org.broadinstitute.ddp.db.SimpleResult;
+import org.broadinstitute.dsm.db.TissueSmId;
+import org.broadinstitute.dsm.statics.DBConstants;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Statement;
+import java.util.ArrayList;
+import java.util.List;
+
+import static org.broadinstitute.ddp.db.TransactionWrapper.inTransaction;
+
+public class TissueSMIDDao {
+    private static final Logger logger = LoggerFactory.getLogger(TissueSMIDDao.class);
+
+    public static final String SQL_GET_SM_ID_BASED_ON_TISSUE_ID=" SELECT * from sm_id where tissue_id= ? and sm_id_type_id  = ? and NOT deleted <=> 1";
+    public static final String SQL_TYPE_ID_FOR_TYPE="SELECT sm_id_type_id from sm_id_type where `sm_id_type` = ?";
+    public static final String SQL_INSERT_SM_ID = "INSERT INTO sm_id SET tissue_id = ?, sm_id_type_id = ?, last_changed = ?, changed_by = ?";
+
+    public List<TissueSmId> getSMIdsForTissueId(String tissueId, String type) {
+        String typeId = getTypeForName(type);
+        List<TissueSmId> list = new ArrayList();
+        SimpleResult results = inTransaction((conn) -> {
+            SimpleResult dbVals = new SimpleResult();
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_GET_SM_ID_BASED_ON_TISSUE_ID)) {
+                stmt.setString(1, tissueId);
+                stmt.setString(2, typeId);
+                try (ResultSet rs = stmt.executeQuery()) {
+                    while (rs.next()) {
+                        TissueSmId tissueSmId = new TissueSmId(
+                                rs.getString(DBConstants.SM_ID_PK),
+                                rs.getString(DBConstants.SM_ID_TYPE_ID),
+                                rs.getString(DBConstants.SM_ID_VALUE),
+                                rs.getString(DBConstants.TISSUE_ID)
+                        );
+                        list.add(tissueSmId);
+                    }
+                }
+            }
+            catch (SQLException ex) {
+                dbVals.resultException = ex;
+            }
+            return dbVals;
+        });
+
+        if (results.resultException != null) {
+            throw new RuntimeException("Error getting sm ids for tissue w/ id " + tissueId +" for type "+type, results.resultException);
+        }
+
+        return list;
+    }
+
+
+
+    private static String getTypeForName(String type) {
+        SimpleResult results = inTransaction((conn) -> {
+            SimpleResult dbVals = new SimpleResult();
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_TYPE_ID_FOR_TYPE)) {
+                stmt.setString(1, type);
+                try (ResultSet rs = stmt.executeQuery()) {
+                    if (rs.next()) {
+                        dbVals.resultValue = rs.getString(DBConstants.SM_ID_TYPE_ID);
+                    }
+                }
+            }
+            catch (SQLException ex) {
+                dbVals.resultException = ex;
+            }
+            return dbVals;
+        });
+
+        if (results.resultException != null) {
+            throw new RuntimeException("Error getting type ids for sm id " + type, results.resultException);
+        }
+
+        return (String) results.resultValue;
+    }
+
+    public String createNewSMIDForTissue(String tissueId, String userId, String smIdType) {
+        String smIdtypeId = getTypeForName(smIdType);
+        SimpleResult results = inTransaction((conn) -> {
+            SimpleResult dbVals = new SimpleResult();
+            try (PreparedStatement stmt = conn.prepareStatement(SQL_INSERT_SM_ID, Statement.RETURN_GENERATED_KEYS)) {
+                stmt.setString(1, tissueId);
+                stmt.setString(2, smIdtypeId);
+                stmt.setLong(3, System.currentTimeMillis());
+                stmt.setString(4, userId);
+                int result = stmt.executeUpdate();
+                if (result == 1) {
+                    try (ResultSet rs = stmt.getGeneratedKeys()) {
+                        if (rs.next()) {
+                            logger.info("Created new sm id for tissue w/ id " + tissueId);
+                            dbVals.resultValue = rs.getString(1);
+                        }
+                    }
+                    catch (Exception e) {
+                        throw new RuntimeException("Error getting id of new sm id ", e);
+                    }
+                }
+                else {
+                    throw new RuntimeException("Error adding new sm id for tissue w/ id " + tissueId + " it was updating " + result + " rows");
+                }
+            }
+            catch (SQLException ex) {
+                dbVals.resultException = ex;
+            }
+            return dbVals;
+        });
+
+        if (results.resultException != null) {
+            throw new RuntimeException("Error adding new sm id for tissue w/ id " + tissueId, results.resultException);
+        }
+        else {
+            return (String) results.resultValue;
+        }
+    }
+}

src/main/java/org/broadinstitute/dsm/db/dao/kit/BSPDummyKitDao.java

@@ -2,11 +2,13 @@
 
 import org.broadinstitute.ddp.db.SimpleResult;
 import org.broadinstitute.dsm.db.DDPInstance;
+import org.broadinstitute.dsm.db.OncHistoryDetail;
 import org.broadinstitute.dsm.db.dao.Dao;
 import org.broadinstitute.dsm.db.dto.kit.ClinicalKitDto;
 import org.broadinstitute.dsm.model.elasticsearch.ESProfile;
 import org.broadinstitute.dsm.model.elasticsearch.ElasticSearchParticipantDto;
 import org.broadinstitute.dsm.statics.DBConstants;
+import org.broadinstitute.dsm.util.DBUtil;
 import org.broadinstitute.dsm.util.ElasticSearchUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -22,6 +24,7 @@ public class BSPDummyKitDao implements Dao<ClinicalKitDto> {
 
     private static final String SQL_UPDATE_DUMMY_KIT = "UPDATE ddp_kit SET kit_label = ? where dsm_kit_request_id = ?";
     private static final String SQL_SELECT_RANDOM_PT = "SELECT ddp_participant_id FROM ddp_kit_request req, ddp_kit kit where req.dsm_kit_request_id = kit.dsm_kit_request_id and deactivated_date is null and ddp_instance_id = ? group by ddp_participant_id ORDER BY RAND() LIMIT 1";
+        private static final String SQL_SELECT_RANDOM_SUFFIX = " ORDER BY RAND() LIMIT 1";
     private static final Logger logger = LoggerFactory.getLogger(BSPDummyKitDao.class);
 
     public void updateKitLabel(String kitLabel, String dsmKitRequestId) {
@@ -83,6 +86,29 @@ public Optional<String> getRandomParticipantIdForStudy(String ddpInstanceId) {
         return Optional.ofNullable((String) results.resultValue);
     }
 
+    public Optional<String> getRandomOncHistoryForStudy(String ddpInstanceName) {
+        SimpleResult results = inTransaction((conn) -> {
+            SimpleResult dbVals = new SimpleResult();
+            try (PreparedStatement stmt = conn.prepareStatement(DBUtil.getFinalQuery(OncHistoryDetail.SQL_SELECT_ONC_HISTORY_DETAIL , SQL_SELECT_RANDOM_SUFFIX))) {
+                stmt.setString(1, ddpInstanceName);
+                ResultSet rs = stmt.executeQuery();
+                if (rs.next()) {
+                    dbVals.resultValue =  Optional.of(rs.getString(DBConstants.DDP_PARTICIPANT_ID));
+                }else{
+
+                }
+            }
+            catch (SQLException e) {
+                dbVals.resultException = e;
+            }
+            return dbVals;
+        });
+        if (results.resultException != null) {
+            throw new RuntimeException("Problem getting a random participant id for instance " + ddpInstanceName, results.resultException);
+        }
+        return (Optional<String>) results.resultValue;
+    }
+
     @Override
     public int create(ClinicalKitDto clinicalKitDto) {
         return 0;
@@ -97,4 +123,6 @@ public int delete(int id) {
     public Optional<ClinicalKitDto> get(long id) {
         return Optional.empty();
     }
+
+
 }

src/main/java/org/broadinstitute/dsm/model/Patch.java

@@ -31,6 +31,7 @@ public class Patch {
     public static final String ONC_HISTORY_ID = "oncHistoryDetailId";
     public static final String PARTICIPANT_DATA_ID = "participantDataId";
     public static final String DDP_PARTICIPANT_ID = "ddpParticipantId";
+    public static final String TISSUEID = "tissueId";
 
     private String id;
     private String parent; //for new added rows at oncHistoryDetails/tissue