#5348

Committed 04 Sep 2024 02:03PM UTC coverage: 78.316% (+0.007%) from 78.309%

Build # #5348

Build Type

push

Committed by

Commit Message

DCJ-570: Add Associated DAA and DAA File info to Get All DACs  (#2397)

Run Details

7 of 8 new or added lines in 2 files covered. (87.5%)

2 existing lines in 2 files now uncovered.

9885 of 12622 relevant lines covered (78.32%)

0.78 hits per line

Source File
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93.18

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

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


import com.google.cloud.storage.BlobId;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Timestamp;
import java.util.Objects;
import org.broadinstitute.consent.http.enumeration.FileCategory;
import org.broadinstitute.consent.http.models.FileStorageObject;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.jdbi.v3.core.mapper.RowMapper;
import org.jdbi.v3.core.statement.StatementContext;

public class FileStorageObjectMapper implements RowMapper<FileStorageObject>, RowMapperHelper,
    ConsentLogger {

  @Override
  public FileStorageObject map(ResultSet r, StatementContext statementContext) throws SQLException {
    FileStorageObject file = new FileStorageObject();

    if (hasColumn(r, addPrefix("file_name"))) {
      file.setFileName(r.getString(addPrefix("file_name")));
    }

    if (hasColumn(r, addPrefix("file_storage_object_id"))) {
      file.setFileStorageObjectId(r.getInt(addPrefix("file_storage_object_id")));
    }

    if (hasColumn(r, addPrefix("entity_id"))) {
      file.setEntityId(r.getString(addPrefix("entity_id")));
    }

    if (hasColumn(r, addPrefix("gcs_file_uri"))) {
      String value = r.getString(addPrefix("gcs_file_uri"));
      try {
        file.setBlobId(BlobId.fromGsUtilUri(value));
      } catch (Exception e) {
        logException("Error parsing blob id: %s for fso id: %s".formatted(value, file.getFileStorageObjectId()), e);
        file.setBlobId(null);
      }
    }

    if (hasColumn(r, addPrefix("category"))) {
      String value = r.getString(addPrefix("category"));
      try {
        file.setCategory(FileCategory.findValue(value));
      } catch (Exception e) {
        logException("Error parsing file category: %s for fso id: %s".formatted(value, file.getFileStorageObjectId()), e);
        file.setCategory(null);
      }
    }

    if (hasColumn(r, addPrefix("media_type"))) {
      file.setMediaType(r.getString(addPrefix("media_type")));
    }

    if (hasNonZeroColumn(r, addPrefix("create_user_id"))) {
      file.setCreateUserId(r.getInt(addPrefix("create_user_id")));
    }

    if (hasColumn(r, addPrefix("create_date"))) {
      Timestamp createDate = r.getTimestamp(addPrefix("create_date"));
      file.setCreateDate((Objects.nonNull(createDate) ? createDate.toInstant() : null));
    }

    if (hasColumn(r, addPrefix("deleted"))) {
      file.setDeleted(r.getBoolean(addPrefix("deleted")));
    }

    if (hasNonZeroColumn(r, addPrefix("delete_user_id"))) {
      file.setDeleteUserId(r.getInt(addPrefix("delete_user_id")));
    }

    if (hasColumn(r, addPrefix("delete_date"))) {
      Timestamp deleteDate = r.getTimestamp(addPrefix("delete_date"));
      file.setDeleteDate((Objects.nonNull(deleteDate) ? deleteDate.toInstant() : null));
    }

    if (hasNonZeroColumn(r, addPrefix("update_user_id"))) {
      file.setUpdateUserId(r.getInt(addPrefix("update_user_id")));
    }

    if (hasColumn(r, addPrefix("update_date"))) {
      Timestamp updateDate = r.getTimestamp(addPrefix("update_date"));
      file.setUpdateDate((Objects.nonNull(updateDate) ? updateDate.toInstant() : null));
    }

    return file;
  }

  public String getPrefix() {
    return "";
  }

  private String addPrefix(String columnName) {
    return getPrefix() + columnName;
  }
}

1	package org.broadinstitute.consent.http.db.mapper;
2
3
4	import com.google.cloud.storage.BlobId;
5	import java.sql.ResultSet;
6	import java.sql.SQLException;
7	import java.sql.Timestamp;
8	import java.util.Objects;
9	import org.broadinstitute.consent.http.enumeration.FileCategory;
10	import org.broadinstitute.consent.http.models.FileStorageObject;
11	import org.broadinstitute.consent.http.util.ConsentLogger;
12	import org.jdbi.v3.core.mapper.RowMapper;
13	import org.jdbi.v3.core.statement.StatementContext;
14
15	public class FileStorageObjectMapper implements RowMapper<FileStorageObject>, RowMapperHelper,	1✔
16	ConsentLogger {
17
18	@Override
19	public FileStorageObject map(ResultSet r, StatementContext statementContext) throws SQLException {
20	FileStorageObject file = new FileStorageObject();	1✔
21
22	if (hasColumn(r, addPrefix("file_name"))) {	1✔
23	file.setFileName(r.getString(addPrefix("file_name")));	1✔
24	}
25
26	if (hasColumn(r, addPrefix("file_storage_object_id"))) {	1✔
27	file.setFileStorageObjectId(r.getInt(addPrefix("file_storage_object_id")));	1✔
28	}
29
30	if (hasColumn(r, addPrefix("entity_id"))) {	1✔
31	file.setEntityId(r.getString(addPrefix("entity_id")));	1✔
32	}
33
34	if (hasColumn(r, addPrefix("gcs_file_uri"))) {	1✔
35	String value = r.getString(addPrefix("gcs_file_uri"));	1✔
36	try {
37	file.setBlobId(BlobId.fromGsUtilUri(value));	1✔
38	} catch (Exception e) {	1✔
39	logException("Error parsing blob id: %s for fso id: %s".formatted(value, file.getFileStorageObjectId()), e);	1✔
40	file.setBlobId(null);	1✔
41	}	1✔
42	}
43
44	if (hasColumn(r, addPrefix("category"))) {	1✔
45	String value = r.getString(addPrefix("category"));	1✔
46	try {
47	file.setCategory(FileCategory.findValue(value));	1✔
48	} catch (Exception e) {	×
NEW 49	logException("Error parsing file category: %s for fso id: %s".formatted(value, file.getFileStorageObjectId()), e);	×
UNCOV 50	file.setCategory(null);	×
51	}	1✔
52	}
53
54	if (hasColumn(r, addPrefix("media_type"))) {	1✔
55	file.setMediaType(r.getString(addPrefix("media_type")));	1✔
56	}
57
58	if (hasNonZeroColumn(r, addPrefix("create_user_id"))) {	1✔
59	file.setCreateUserId(r.getInt(addPrefix("create_user_id")));	1✔
60	}
61
62	if (hasColumn(r, addPrefix("create_date"))) {	1✔
63	Timestamp createDate = r.getTimestamp(addPrefix("create_date"));	1✔
64	file.setCreateDate((Objects.nonNull(createDate) ? createDate.toInstant() : null));	1✔
65	}
66
67	if (hasColumn(r, addPrefix("deleted"))) {	1✔
68	file.setDeleted(r.getBoolean(addPrefix("deleted")));	1✔
69	}
70
71	if (hasNonZeroColumn(r, addPrefix("delete_user_id"))) {	1✔
72	file.setDeleteUserId(r.getInt(addPrefix("delete_user_id")));	1✔
73	}
74
75	if (hasColumn(r, addPrefix("delete_date"))) {	1✔
76	Timestamp deleteDate = r.getTimestamp(addPrefix("delete_date"));	1✔
77	file.setDeleteDate((Objects.nonNull(deleteDate) ? deleteDate.toInstant() : null));	1✔
78	}
79
80	if (hasNonZeroColumn(r, addPrefix("update_user_id"))) {	1✔
81	file.setUpdateUserId(r.getInt(addPrefix("update_user_id")));	1✔
82	}
83
84	if (hasColumn(r, addPrefix("update_date"))) {	1✔
85	Timestamp updateDate = r.getTimestamp(addPrefix("update_date"));	1✔
86	file.setUpdateDate((Objects.nonNull(updateDate) ? updateDate.toInstant() : null));	1✔
87	}
88
89	return file;	1✔
90	}
91
92	public String getPrefix() {
93	return "";	1✔
94	}
95
96	private String addPrefix(String columnName) {
97	return getPrefix() + columnName;	1✔
98	}
99	}

DataBiosphere / consent / #5348

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