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DDP-6034: adding create clinical kits (#351)
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* DDP-6034: adding create clinical kits

* DDP-6034: refactoring

* DDP-6034: fixed NPE
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@SimoneMaiwald
SimoneMaiwald authored Feb 11, 2022
1 parent 4d6846d commit ebc3cc8
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Showing 23 changed files with 1,035 additions and 489 deletions.
8 changes: 1 addition & 7 deletions src/main/java/org/broadinstitute/dsm/DSMServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -192,13 +192,7 @@ protected void setupCustomRouting(@NonNull Config cfg) {
before("*", new LoggingFilter());
afterAfter((req, res) -> MDC.clear());

before(API_ROOT + RoutePath.BSP_KIT_QUERY_PATH, (req, res) -> {
if (!new JWTRouteFilter(bspSecret, null).isAccessAllowed(req)) {
halt(404);
}
res.header(HttpHeaders.CONTENT_TYPE, MediaType.JSON_UTF_8.toString());
});
before(API_ROOT + RoutePath.CLINICAL_KIT_ENDPOINT, (req, res) -> {
before(API_ROOT + "*", (req, res) -> {
if (!new JWTRouteFilter(bspSecret, null).isAccessAllowed(req)) {
halt(404);
}
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213 changes: 111 additions & 102 deletions src/main/java/org/broadinstitute/dsm/db/OncHistoryDetail.java
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149 changes: 100 additions & 49 deletions src/main/java/org/broadinstitute/dsm/db/Tissue.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,14 @@
import java.io.IOException;
import java.sql.*;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import static org.broadinstitute.ddp.db.TransactionWrapper.inTransaction;

@Data
@TableName (
@TableName(
name = DBConstants.DDP_TISSUE,
alias = DBConstants.DDP_TISSUE_ALIAS,
primaryKey = DBConstants.TISSUE_ID,
Expand All @@ -38,17 +39,19 @@ public class Tissue {

private static final Logger logger = LoggerFactory.getLogger(Tissue.class);

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 = ?";
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, sm.sm_id_value, sm.sm_id_type_id, sm.sm_id_pk, sm.deleted, sm.tissue_id FROM ddp_tissue t "
+ "LEFT JOIN sm_id sm on (sm.tissue_id = t.tissue_id AND NOT sm.deleted <=> 1 AND NOT t.deleted <=> 1) "
+ "WHERE NOT (t.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) " +
"LEFT JOIN ddp_medical_record as m on (m.institution_id = inst.institution_id AND NOT m.deleted <=> 1) LEFT JOIN ddp_onc_history_detail as oD on (m.medical_record_id = oD.medical_record_id) " +
"LEFT JOIN ddp_tissue as t on (t.onc_history_detail_id = oD.onc_history_detail_id) WHERE p.participant_id = ?";

@TableName (
@TableName(
name = DBConstants.DDP_TISSUE,
alias = DBConstants.DDP_TISSUE_ALIAS,
primaryKey = DBConstants.TISSUE_ID,
Expand All @@ -59,115 +62,123 @@ public class Tissue {
@ColumnName(DBConstants.ONC_HISTORY_DETAIL_ID)
private long oncHistoryDetailId;

@ColumnName (DBConstants.NOTES)
@ColumnName(DBConstants.NOTES)
private String notes;

@ColumnName (DBConstants.COUNT_RECEIVED)
@ColumnName(DBConstants.COUNT_RECEIVED)
private long countReceived;

@ColumnName (DBConstants.TISSUE_TYPE)
@ColumnName(DBConstants.TISSUE_TYPE)
private String tissueType;

@ColumnName (DBConstants.TISSUE_SITE)
@ColumnName(DBConstants.TISSUE_SITE)
private String tissueSite;

@ColumnName (DBConstants.TUMOR_TYPE)
@ColumnName(DBConstants.TUMOR_TYPE)
private String tumorType;

@ColumnName (DBConstants.H_E)
@ColumnName(DBConstants.H_E)
private String hE;

@ColumnName (DBConstants.PATHOLOGY_REPORT)
@ColumnName(DBConstants.PATHOLOGY_REPORT)
private String pathologyReport;

@ColumnName (DBConstants.COLLABORATOR_SAMPLE_ID)
@ColumnName(DBConstants.COLLABORATOR_SAMPLE_ID)
private String collaboratorSampleId;

@ColumnName (DBConstants.BLOCK_SENT)
@ColumnName(DBConstants.BLOCK_SENT)
@DbDateConversion(SqlDateConverter.STRING_DAY)
private String blockSent;

@ColumnName (DBConstants.SHL_WORK_NUMBER)
@ColumnName(DBConstants.SHL_WORK_NUMBER)
private String shlWorkNumber;

@ColumnName (DBConstants.SCROLLS_RECEIVED)
@ColumnName(DBConstants.SCROLLS_RECEIVED)
@DbDateConversion(SqlDateConverter.STRING_DAY)
private String scrollsReceived;

@ColumnName (DBConstants.SK_ID)
@ColumnName(DBConstants.SK_ID)
private String skId;

@ColumnName (DBConstants.SM_ID)
@ColumnName(DBConstants.SM_ID)
private String smId;

@ColumnName (DBConstants.SENT_GP)
@ColumnName(DBConstants.SENT_GP)
@DbDateConversion(SqlDateConverter.STRING_DAY)
private String sentGp;

private String changedBy;

@ColumnName (DBConstants.DELETED)
@ColumnName(DBConstants.DELETED)
private boolean deleted;

@ColumnName (DBConstants.FIRST_SM_ID)
@ColumnName(DBConstants.FIRST_SM_ID)
private String firstSmId;

@ColumnName (DBConstants.ADDITIONAL_TISSUE_VALUES)
@ColumnName(DBConstants.ADDITIONAL_TISSUE_VALUES)
@JsonProperty("dynamicFields")
@SerializedName("dynamicFields")
private String additionalValuesJson;

@JsonProperty("dynamicFields")
public Map<String, Object> getDynamicFields() {
try {
return ObjectMapperSingleton.instance().readValue(additionalValuesJson, new TypeReference<Map<String, Object>>() {});
return ObjectMapperSingleton.instance().readValue(additionalValuesJson, new TypeReference<Map<String, Object>>() {
});
} catch (IOException | NullPointerException e) {
return Map.of();
}
}

@ColumnName (DBConstants.TISSUE_RETURN_DATE)
@ColumnName(DBConstants.TISSUE_RETURN_DATE)
@DbDateConversion(SqlDateConverter.STRING_DAY)
private String returnDate;

@ColumnName (DBConstants.RETURN_FEDEX_ID)
@ColumnName(DBConstants.RETURN_FEDEX_ID)
private String returnFedexId;

@ColumnName (DBConstants.EXPECTED_RETURN)
@ColumnName(DBConstants.EXPECTED_RETURN)
@DbDateConversion(SqlDateConverter.STRING_DAY)
private String expectedReturn;

@ColumnName (DBConstants.TUMOR_PERCENTAGE)
@ColumnName(DBConstants.TUMOR_PERCENTAGE)
private String tumorPercentage;

@ColumnName (DBConstants.TISSUE_SEQUENCE)
@ColumnName(DBConstants.TISSUE_SEQUENCE)
private String tissueSequence;

@ColumnName (DBConstants.SCROLLS_COUNT)
@ColumnName(DBConstants.SCROLLS_COUNT)
private long scrollsCount;

@ColumnName (DBConstants.USS_COUNT)
@ColumnName(DBConstants.USS_COUNT)
private long ussCount;

@ColumnName (DBConstants.BLOCKS_COUNT)
@ColumnName(DBConstants.BLOCKS_COUNT)
private long blocksCount;

@ColumnName (DBConstants.H_E_COUNT)
@ColumnName(DBConstants.H_E_COUNT)
private long hECount;

@JsonProperty("hECount")
public long gethECount() {
return hECount;
}

public Tissue() {}
private List<TissueSmId> ussSMID;

private List<TissueSmId> scrollSMID;

private List<TissueSmId> heSMID;

public Tissue() {
}

public Tissue(long tissueId, long oncHistoryDetailId, String notes, long 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 additionalValuesJson, String expectedReturn, String returnDate,
String returnFedexId, String shlWorkNumber, String tumorPercentage, String tissueSequence, long scrollsCount,
long ussCount, long blocksCount, long hECount) {
long ussCount, long blocksCount, long hECount, List<TissueSmId> ussSMIDs, List<TissueSmId> scrollSMIDs, List<TissueSmId> heSMID) {
this.tissueId = tissueId;
this.oncHistoryDetailId = oncHistoryDetailId;
this.notes = notes;
Expand Down Expand Up @@ -195,6 +206,9 @@ public Tissue(long tissueId, long oncHistoryDetailId, String notes, long countRe
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 {
Expand Down Expand Up @@ -228,32 +242,72 @@ public static Tissue getTissue(@NonNull ResultSet rs) throws SQLException {
rs.getLong(DBConstants.SCROLLS_COUNT),
rs.getLong(DBConstants.USS_COUNT),
rs.getLong(DBConstants.BLOCKS_COUNT),
rs.getLong(DBConstants.H_E_COUNT));
rs.getLong(DBConstants.H_E_COUNT),
new ArrayList<>(), new ArrayList<>(), new ArrayList<>());
return tissue;
}

public static List<Tissue> getTissue(@NonNull Connection conn, @NonNull String oncHistoryDetailId) {
public static TissueSmId getSMIds(ResultSet rs) {
return TissueSmId.getSMIdsForTissueId(rs);
}

List<Tissue> tissue = new ArrayList<>();
public static List<Tissue> getTissue(@NonNull Connection conn, @NonNull String oncHistoryDetailId) {
List<Tissue> tissueList = new ArrayList<>();
SimpleResult dbVals = new SimpleResult();
Map<Long, Tissue> tissues = new HashMap<>();
try (PreparedStatement stmt = conn.prepareStatement(SQL_SELECT_TISSUE)) {
stmt.setString(1, oncHistoryDetailId);
try (ResultSet rs = stmt.executeQuery()) {
while (rs.next()) {
tissue.add(getTissue(rs));
TissueSmId tissueSmId = getSMIds(rs);
Tissue tissue;
if (tissueSmId != null && tissues.containsKey(tissueSmId.getTissueId())) {
tissue = tissues.get(tissueSmId.getTissueId());
} else {
tissue = getTissue(rs);
}
if (tissueSmId != null) {
tissue.setSmIdBasedOnType(tissueSmId, rs);
}
tissues.put(tissue.tissueId, tissue);
}
}
}
catch (SQLException ex) {
} catch (SQLException ex) {
dbVals.resultException = ex;
}

if (dbVals.resultException != null) {
throw new RuntimeException("Error getting tissue for oncHistoryDetails w/ id " + oncHistoryDetailId, dbVals.resultException);
}
tissueList.addAll(tissues.values());
logger.info("Found " + tissueList.size() + " tissue for oncHistoryDetails w/ id " + oncHistoryDetailId);
return tissueList;
}

logger.info("Found " + tissue.size() + " tissue for oncHistoryDetails w/ id " + oncHistoryDetailId);
return tissue;
public void setSmIdBasedOnType(TissueSmId tissueSmId, ResultSet rs) {
if (tissueSmId == null || tissueSmId.getSmIdType() == null) {
return;
}
try {
String type = rs.getString(DBConstants.SM_ID_TYPE_TABLE_ALIAS + "." + DBConstants.SM_ID_TYPE);
switch (type.toLowerCase()) {
case "he": {
this.heSMID.add(tissueSmId);
break;

}
case "uss": {
this.ussSMID.add(tissueSmId);
break;
}
case "scrolls": {
this.scrollSMID.add(tissueSmId);
break;
}
}
} catch (SQLException throwables) {
throwables.printStackTrace();
}
}

public static String createNewTissue(@NonNull String oncHistoryId, @NonNull String user) {
Expand All @@ -270,16 +324,13 @@ public static String createNewTissue(@NonNull String oncHistoryId, @NonNull Stri
logger.info("Created new tissue for oncHistoryDetail w/ id " + oncHistoryId);
dbVals.resultValue = rs.getString(1);
}
}
catch (Exception e) {
} catch (Exception e) {
throw new RuntimeException("Error getting id of new institution ", e);
}
}
else {
} else {
throw new RuntimeException("Error adding new tissue for oncHistoryDetail w/ id " + oncHistoryId + " it was updating " + result + " rows");
}
}
catch (SQLException ex) {
} catch (SQLException ex) {
dbVals.resultException = ex;
}
return dbVals;
Expand Down
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