#6038

Committed 09 Jun 2025 03:55PM UTC coverage: 78.96% (+0.01%) from 78.949%

Build # #6038

Build Type

push

Committed by

Commit Message

DT-1792: Restrict researcher actions on summaries with closeouts (#2555)

Run Details

9 of 9 new or added lines in 3 files covered. (100.0%)

1 existing line in 1 file now uncovered.

10144 of 12847 relevant lines covered (78.96%)

0.79 hits per line

Source File
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92.11

/src/main/java/org/broadinstitute/consent/http/db/mapper/DarCollectionSummaryReducer.java

package org.broadinstitute.consent.http.db.mapper;

import java.util.Map;
import java.util.Objects;
import org.broadinstitute.consent.http.models.CloseoutSupplement;
import org.broadinstitute.consent.http.models.DarCollectionSummary;
import org.broadinstitute.consent.http.models.Election;
import org.broadinstitute.consent.http.models.Vote;
import org.broadinstitute.consent.http.util.gson.GsonUtil;
import org.jdbi.v3.core.mapper.MappingException;
import org.jdbi.v3.core.mapper.NoSuchMapperException;
import org.jdbi.v3.core.result.LinkedHashMapRowReducer;
import org.jdbi.v3.core.result.RowView;

public class DarCollectionSummaryReducer implements
    LinkedHashMapRowReducer<Integer, DarCollectionSummary>, RowMapperHelper {

  @Override
  public void accumulate(Map<Integer, DarCollectionSummary> map, RowView rowView) {

    DarCollectionSummary summary = map.computeIfAbsent(
        rowView.getColumn("dar_collection_id", Integer.class),
        id -> rowView.getRow(DarCollectionSummary.class)
    );
    Election election;
    Vote vote;
    Integer datasetId;
    String darStatus;
    String darReferenceId;

    try {
      if (hasColumn(rowView, "closeout", String.class)) {
        String string = rowView.getColumn("closeout", String.class);
        CloseoutSupplement closeout = GsonUtil.getInstance().fromJson(string, CloseoutSupplement.class);
        summary.setCloseoutSupplement(closeout);
      }

      datasetId = rowView.getColumn("dd_datasetid", Integer.class);
      if (Objects.nonNull(datasetId)) {
        summary.addDatasetId(datasetId);
      }

      if (hasColumn(rowView, "dac_name", String.class)) {
        if (Objects.nonNull(rowView.getColumn("dac_name", String.class))) {
          summary.addDacName(rowView.getColumn("dac_name", String.class));
        }
      }

      try {
        darReferenceId = rowView.getColumn("latest_dar_reference_id", String.class);
        if (Objects.nonNull(darReferenceId)) {
          summary.setLatestReferenceId(darReferenceId);
        }
        hasOptionalColumn(rowView, "latest_dar_parent_id", Integer.class)
            .ifPresent(darParentId -> summary.addParentChildRelationship(darParentId, darReferenceId));
        darStatus = rowView.getColumn("dar_status", String.class);
        if (Objects.nonNull(darStatus)) {
          summary.addStatus(darStatus, darReferenceId);
        }
      } catch (MappingException e) {
        //ignore exception, it means dar_status and dar_reference_id wasn't included for this query
      }

      try {
        election = rowView.getRow(Election.class);
        if (Objects.nonNull(election.getElectionId())) {
          summary.addElection(election);
          summary.addDatasetId(election.getDatasetId());
        }
      } catch (MappingException e) {
        // Indicates that we do not have an election for this summary
      }

      try {
        vote = rowView.getRow(Vote.class);
        if (Objects.nonNull(vote.getVoteId())) {
          summary.addVote(vote);
        }
      } catch (MappingException e) {
        // Indicates that we do not have an election for this summary
      }

    } catch (NoSuchMapperException e) {
      //ignore these exceptions, just means there's no elections and votes on the collection for this query
    }
  }
}

1	package org.broadinstitute.consent.http.db.mapper;
2
3	import java.util.Map;
4	import java.util.Objects;
5	import org.broadinstitute.consent.http.models.CloseoutSupplement;
6	import org.broadinstitute.consent.http.models.DarCollectionSummary;
7	import org.broadinstitute.consent.http.models.Election;
8	import org.broadinstitute.consent.http.models.Vote;
9	import org.broadinstitute.consent.http.util.gson.GsonUtil;
10	import org.jdbi.v3.core.mapper.MappingException;
11	import org.jdbi.v3.core.mapper.NoSuchMapperException;
12	import org.jdbi.v3.core.result.LinkedHashMapRowReducer;
13	import org.jdbi.v3.core.result.RowView;
14
15	public class DarCollectionSummaryReducer implements	1✔
16	LinkedHashMapRowReducer<Integer, DarCollectionSummary>, RowMapperHelper {
17
18	@Override
19	public void accumulate(Map<Integer, DarCollectionSummary> map, RowView rowView) {
20
21	DarCollectionSummary summary = map.computeIfAbsent(	1✔
22	rowView.getColumn("dar_collection_id", Integer.class),	1✔
23	id -> rowView.getRow(DarCollectionSummary.class)	1✔
24	);
25	Election election;
26	Vote vote;
27	Integer datasetId;
28	String darStatus;
29	String darReferenceId;
30
31	try {
32	if (hasColumn(rowView, "closeout", String.class)) {	1✔
33	String string = rowView.getColumn("closeout", String.class);	1✔
34	CloseoutSupplement closeout = GsonUtil.getInstance().fromJson(string, CloseoutSupplement.class);	1✔
35	summary.setCloseoutSupplement(closeout);	1✔
36	}
37
38	datasetId = rowView.getColumn("dd_datasetid", Integer.class);	1✔
39	if (Objects.nonNull(datasetId)) {	1✔
40	summary.addDatasetId(datasetId);	1✔
41	}
42
43	if (hasColumn(rowView, "dac_name", String.class)) {	1✔
44	if (Objects.nonNull(rowView.getColumn("dac_name", String.class))) {	1✔
45	summary.addDacName(rowView.getColumn("dac_name", String.class));	1✔
46	}
47	}
48
49	try {
50	darReferenceId = rowView.getColumn("latest_dar_reference_id", String.class);	1✔
51	if (Objects.nonNull(darReferenceId)) {	1✔
52	summary.setLatestReferenceId(darReferenceId);	1✔
53	}
54	hasOptionalColumn(rowView, "latest_dar_parent_id", Integer.class)	1✔
55	.ifPresent(darParentId -> summary.addParentChildRelationship(darParentId, darReferenceId));	1✔
56	darStatus = rowView.getColumn("dar_status", String.class);	1✔
57	if (Objects.nonNull(darStatus)) {	1✔
58	summary.addStatus(darStatus, darReferenceId);	1✔
59	}
UNCOV 60	} catch (MappingException e) {	×
61	//ignore exception, it means dar_status and dar_reference_id wasn't included for this query
62	}	1✔
63
64	try {
65	election = rowView.getRow(Election.class);	1✔
66	if (Objects.nonNull(election.getElectionId())) {	1✔
67	summary.addElection(election);	1✔
68	summary.addDatasetId(election.getDatasetId());	1✔
69	}
70	} catch (MappingException e) {	×
71	// Indicates that we do not have an election for this summary
72	}	1✔
73
74	try {
75	vote = rowView.getRow(Vote.class);	1✔
76	if (Objects.nonNull(vote.getVoteId())) {	1✔
77	summary.addVote(vote);	1✔
78	}
79	} catch (MappingException e) {	×
80	// Indicates that we do not have an election for this summary
81	}	1✔
82
83	} catch (NoSuchMapperException e) {	1✔
84	//ignore these exceptions, just means there's no elections and votes on the collection for this query
85	}	1✔
86	}	1✔
87	}

DataBiosphere / consent / #6038

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