#5612

Committed 25 Mar 2025 08:50PM UTC coverage: 79.273% (-0.06%) from 79.335%

Build # #5612

Build Type

push

Committed by

Commit Message

[DT-643][risk=no] Optimize tests so they can run locally. (#2471)

Co-authored-by: fboulnois <fboulnois@users.noreply.github.com>

Run Details

10273 of 12959 relevant lines covered (79.27%)

0.79 hits per line

Source File
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71.43

/src/main/java/org/broadinstitute/consent/http/service/dao/DraftFileStorageServiceDAO.java

package org.broadinstitute.consent.http.service.dao;

import com.google.cloud.storage.BlobId;
import com.google.inject.Inject;
import jakarta.ws.rs.NotFoundException;
import java.io.InputStream;
import java.sql.SQLException;
import java.time.Instant;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.Map;
import java.util.UUID;
import org.broadinstitute.consent.http.cloudstore.GCSService;
import org.broadinstitute.consent.http.db.FileStorageObjectDAO;
import org.broadinstitute.consent.http.enumeration.FileCategory;
import org.broadinstitute.consent.http.models.FileStorageObject;
import org.broadinstitute.consent.http.models.User;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.glassfish.jersey.media.multipart.FormDataBodyPart;
import org.jdbi.v3.core.Jdbi;

public class DraftFileStorageServiceDAO implements ConsentLogger {

  Jdbi jdbi;
  GCSService gcsService;
  FileStorageObjectDAO fileStorageObjectDAO;

  @Inject
  public DraftFileStorageServiceDAO(Jdbi jdbi, GCSService gcsService,
      FileStorageObjectDAO fileStorageObjectDAO) {
    this.jdbi = jdbi;
    this.gcsService = gcsService;
    this.fileStorageObjectDAO = fileStorageObjectDAO;
  }

  public List<FileStorageObject> storeDraftFiles(UUID associatedId, User user,
      Map<String, FormDataBodyPart> files) throws SQLException {
    List<FileStorageObject> fileStorageObjects = new ArrayList<>();
    jdbi.useHandle(handle -> {
      handle.getConnection().setAutoCommit(false);
      try {
        files.forEach((String key, FormDataBodyPart file) -> {
          fileStorageObjects.add(store(file, user, associatedId));
        });
      } catch (Exception e) {
        fileStorageObjects.forEach(file -> {
          try {
            deleteStoredFile(file, user);
          } catch (SQLException ex) {
            logWarn(String.format("Error rolling back files in GCS for draft: %s, gcsuri: %s",
                associatedId.toString(), file.getBlobId().toGsUtilUri()));
            throw new RuntimeException(ex);
          }
        });
        handle.getConnection().rollback();
      }
      handle.commit();
    });
    return fileStorageObjects;
  }

  public void deleteStoredFile(FileStorageObject fileStorageObject, User user) throws SQLException, NotFoundException {
    jdbi.useHandle(handle -> {
      handle.getConnection().setAutoCommit(false);
      try {
        gcsService.deleteDocument(fileStorageObject.getBlobId().getName());
        fileStorageObjectDAO.deleteFileById(fileStorageObject.getFileStorageObjectId(),
            user.getUserId(), new Date().toInstant());
      } catch (Exception e) {
        logWarn(String.format("Error deleting stored file for user: %s, file obj id: %d, error: %s",
            user.getEmail(), fileStorageObject.getFileStorageObjectId(), e));
        handle.rollback();
        throw new NotFoundException("Error deleting stored file for user: " + user.getEmail(), e);
      }
      handle.commit();
    });
  }

  private FileStorageObject store(FormDataBodyPart file, User user, UUID draftId)
      throws RuntimeException {
    BlobId blobId;
    try {
      // upload to GCS
      blobId = gcsService.storeDocument(file.getValueAs(InputStream.class),
          file.getMediaType().toString(), UUID.randomUUID());
      Integer fileStorageObjectId = fileStorageObjectDAO.insertNewFile(file.getName(),
          FileCategory.DRAFT_UPLOADED_FILE.getValue(), blobId.toGsUtilUri(),
          file.getMediaType().toString(), draftId.toString(), user.getUserId(), Instant.now());
      return fileStorageObjectDAO.findFileById(fileStorageObjectId);
    } catch (Exception e) {
      logWarn(String.format("Error storing file for user: %s, draft id : %s, error: %s",
          user.getEmail(), draftId.toString(), e));
      throw new RuntimeException(e);
    }
  }
}

1	package org.broadinstitute.consent.http.service.dao;
2
3	import com.google.cloud.storage.BlobId;
4	import com.google.inject.Inject;
5	import jakarta.ws.rs.NotFoundException;
6	import java.io.InputStream;
7	import java.sql.SQLException;
8	import java.time.Instant;
9	import java.util.ArrayList;
10	import java.util.Date;
11	import java.util.List;
12	import java.util.Map;
13	import java.util.UUID;
14	import org.broadinstitute.consent.http.cloudstore.GCSService;
15	import org.broadinstitute.consent.http.db.FileStorageObjectDAO;
16	import org.broadinstitute.consent.http.enumeration.FileCategory;
17	import org.broadinstitute.consent.http.models.FileStorageObject;
18	import org.broadinstitute.consent.http.models.User;
19	import org.broadinstitute.consent.http.util.ConsentLogger;
20	import org.glassfish.jersey.media.multipart.FormDataBodyPart;
21	import org.jdbi.v3.core.Jdbi;
22
23	public class DraftFileStorageServiceDAO implements ConsentLogger {
24
25	Jdbi jdbi;
26	GCSService gcsService;
27	FileStorageObjectDAO fileStorageObjectDAO;
28
29	@Inject
30	public DraftFileStorageServiceDAO(Jdbi jdbi, GCSService gcsService,
31	FileStorageObjectDAO fileStorageObjectDAO) {	1✔
32	this.jdbi = jdbi;	1✔
33	this.gcsService = gcsService;	1✔
34	this.fileStorageObjectDAO = fileStorageObjectDAO;	1✔
35	}	1✔
36
37	public List<FileStorageObject> storeDraftFiles(UUID associatedId, User user,
38	Map<String, FormDataBodyPart> files) throws SQLException {
39	List<FileStorageObject> fileStorageObjects = new ArrayList<>();	1✔
40	jdbi.useHandle(handle -> {	1✔
41	handle.getConnection().setAutoCommit(false);	1✔
42	try {
43	files.forEach((String key, FormDataBodyPart file) -> {	1✔
44	fileStorageObjects.add(store(file, user, associatedId));	1✔
45	});	1✔
46	} catch (Exception e) {	×
47	fileStorageObjects.forEach(file -> {	×
48	try {
49	deleteStoredFile(file, user);	×
50	} catch (SQLException ex) {	×
51	logWarn(String.format("Error rolling back files in GCS for draft: %s, gcsuri: %s",	×
52	associatedId.toString(), file.getBlobId().toGsUtilUri()));	×
53	throw new RuntimeException(ex);	×
54	}	×
55	});	×
56	handle.getConnection().rollback();	×
57	}	1✔
58	handle.commit();	1✔
59	});	1✔
60	return fileStorageObjects;	1✔
61	}
62
63	public void deleteStoredFile(FileStorageObject fileStorageObject, User user) throws SQLException, NotFoundException {
64	jdbi.useHandle(handle -> {	1✔
65	handle.getConnection().setAutoCommit(false);	1✔
66	try {
67	gcsService.deleteDocument(fileStorageObject.getBlobId().getName());	1✔
68	fileStorageObjectDAO.deleteFileById(fileStorageObject.getFileStorageObjectId(),	1✔
69	user.getUserId(), new Date().toInstant());	1✔
70	} catch (Exception e) {	1✔
71	logWarn(String.format("Error deleting stored file for user: %s, file obj id: %d, error: %s",	1✔
72	user.getEmail(), fileStorageObject.getFileStorageObjectId(), e));	1✔
73	handle.rollback();	1✔
74	throw new NotFoundException("Error deleting stored file for user: " + user.getEmail(), e);	1✔
75	}	1✔
76	handle.commit();	1✔
77	});	1✔
78	}	1✔
79
80	private FileStorageObject store(FormDataBodyPart file, User user, UUID draftId)
81	throws RuntimeException {
82	BlobId blobId;
83	try {
84	// upload to GCS
85	blobId = gcsService.storeDocument(file.getValueAs(InputStream.class),	1✔
86	file.getMediaType().toString(), UUID.randomUUID());	1✔
87	Integer fileStorageObjectId = fileStorageObjectDAO.insertNewFile(file.getName(),	1✔
88	FileCategory.DRAFT_UPLOADED_FILE.getValue(), blobId.toGsUtilUri(),	1✔
89	file.getMediaType().toString(), draftId.toString(), user.getUserId(), Instant.now());	1✔
90	return fileStorageObjectDAO.findFileById(fileStorageObjectId);	1✔
91	} catch (Exception e) {	×
92	logWarn(String.format("Error storing file for user: %s, draft id : %s, error: %s",	×
93	user.getEmail(), draftId.toString(), e));	×
94	throw new RuntimeException(e);	×
95	}
96	}
97	}

DataBiosphere / consent / #5612

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