#6333

Committed 15 Aug 2025 12:17PM UTC coverage: 83.37% (+0.03%) from 83.338%

Build # #6333

Build Type

push

Committed by

Commit Message

DT-2091: Update DAC Approve Dataset performance (#2636)

Co-authored-by: otchet-broad <111771148+otchet-broad@users.noreply.github.com>

Run Details

83 of 105 new or added lines in 5 files covered. (79.05%)

4 existing lines in 1 file now uncovered.

10949 of 13133 relevant lines covered (83.37%)

0.83 hits per line

Source File
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77.19

/src/main/java/org/broadinstitute/consent/http/db/SamDAO.java

package org.broadinstitute.consent.http.db;

import com.google.api.client.http.EmptyContent;
import com.google.api.client.http.GenericUrl;
import com.google.api.client.http.HttpRequest;
import com.google.api.client.http.HttpResponse;
import com.google.common.util.concurrent.FutureCallback;
import com.google.common.util.concurrent.Futures;
import com.google.common.util.concurrent.ListenableFuture;
import com.google.common.util.concurrent.ListeningExecutorService;
import com.google.common.util.concurrent.MoreExecutors;
import com.google.gson.Gson;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
import com.google.gson.JsonSyntaxException;
import com.google.gson.reflect.TypeToken;
import jakarta.ws.rs.ServerErrorException;
import jakarta.ws.rs.WebApplicationException;
import jakarta.ws.rs.core.MediaType;
import java.lang.reflect.Type;
import java.util.ArrayList;
import java.util.List;
import java.util.concurrent.ExecutorService;
import org.broadinstitute.consent.http.configurations.ServicesConfiguration;
import org.broadinstitute.consent.http.models.AuthUser;
import org.broadinstitute.consent.http.models.sam.EmailResponse;
import org.broadinstitute.consent.http.models.sam.ResourceType;
import org.broadinstitute.consent.http.models.sam.TosResponse;
import org.broadinstitute.consent.http.models.sam.UserStatus;
import org.broadinstitute.consent.http.models.sam.UserStatusDiagnostics;
import org.broadinstitute.consent.http.models.sam.UserStatusInfo;
import org.broadinstitute.consent.http.util.ConsentLogger;
import org.broadinstitute.consent.http.util.HttpClientUtil;
import org.broadinstitute.consent.http.util.ThreadUtils;
import org.checkerframework.checker.nullness.qual.NonNull;
import org.checkerframework.checker.nullness.qual.Nullable;

public class SamDAO implements ConsentLogger {

  private final ExecutorService executorService = new ThreadUtils().getExecutorService(
      SamDAO.class);
  private final HttpClientUtil clientUtil;
  private final ServicesConfiguration configuration;
  private final Integer connectTimeoutMilliseconds;
  public final Integer readTimeoutMilliseconds;

  public SamDAO(HttpClientUtil clientUtil, ServicesConfiguration configuration) {
    this.clientUtil = clientUtil;
    this.configuration = configuration;
    // Defaults to 10 seconds
    this.connectTimeoutMilliseconds = configuration.getTimeoutSeconds() * 1000;
    // Defaults to 60 seconds
    this.readTimeoutMilliseconds = configuration.getTimeoutSeconds() * 6000;
  }

  public List<ResourceType> getResourceTypes(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getV1ResourceTypesUrl());
    HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException("Error getting resource types from Sam: " + response.getStatusMessage(),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    String body = response.parseAsString();
    Type resourceTypesListType = new TypeToken<ArrayList<ResourceType>>() {
    }.getType();
    return new Gson().fromJson(body, resourceTypesListType);
  }

  public UserStatusInfo getRegistrationInfo(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getRegisterUserV2SelfInfoUrl());
    HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(
          "Error getting user registration information from Sam: " + response.getStatusMessage(),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    String body = response.parseAsString();
    return new Gson().fromJson(body, UserStatusInfo.class);
  }

  public UserStatusDiagnostics getSelfDiagnostics(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getV2SelfDiagnosticsUrl());
    HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(
          "Error getting enabled statuses of user from Sam: " + response.getStatusMessage(),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    String body = response.parseAsString();
    return new Gson().fromJson(body, UserStatusDiagnostics.class);
  }

  public UserStatus postRegistrationInfo(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.postRegisterUserV2SelfUrl());
    HttpRequest request = clientUtil.buildPostRequest(genericUrl, new EmptyContent(), authUser);
    HttpResponse response = executeRequest(request);
    String body = response.parseAsString();
    if (!response.isSuccessStatusCode()) {
      var errorMsg = getErrorMessage(authUser, body);
      Exception e = new WebApplicationException(errorMsg, response.getStatusCode());
      logException(errorMsg, new Exception(body));
      throw e;
    }
    return new Gson().fromJson(body, UserStatus.class);
  }

  public static String getErrorMessage(AuthUser authUser, String body) {
    var errorMsg = String.format("Error posting user registration information. Email: %s.",
        authUser.getEmail());
    if (body == null || body.isEmpty()) {
      return errorMsg;
    }
    try {
      JsonElement messageElement = JsonParser.parseString(body).getAsJsonObject().get("message");
      String message = messageElement != null ? messageElement.getAsString() : body;
      if (message.contains("Cannot update azureB2cId")) {
        return String.format(
            "Email: %s. You may have previously signed in with a different authentication provider (Google or Microsoft). Please sign in with that provider. For more information visit: https://support.terra.bio/hc/en-us/community/posts/24089648317467-Cannot-update-azureB2cId-for-user",
            authUser.getEmail());
      }
      return String.format(errorMsg + " %s.", message);
    } catch (JsonSyntaxException e) {  // If the body is not a valid JSON
      return String.format(errorMsg + " %s.", body);
    }
  }

  public void asyncPostRegistrationInfo(AuthUser authUser) {
    ListeningExecutorService listeningExecutorService = MoreExecutors.listeningDecorator(
        executorService);
    ListenableFuture<UserStatus> userStatusFuture =
        listeningExecutorService.submit(() -> postRegistrationInfo(authUser));
    Futures.addCallback(
        userStatusFuture,
        new FutureCallback<>() {
          @Override
          public void onSuccess(@Nullable UserStatus userStatus) {
            logInfo("Successfully registered user in Sam: " + authUser.getEmail());
          }

          @Override
          public void onFailure(@NonNull Throwable throwable) {
            logWarn("Async Post Registration Failure for user: " + authUser.getEmail() + "; "
                + throwable.getMessage());
          }
        },
        listeningExecutorService);
  }

  public String getToSText() throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getToSTextUrl());
    HttpRequest request = clientUtil.buildUnAuthedGetRequest(genericUrl);
    request.getHeaders().setAccept(MediaType.TEXT_PLAIN);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException("Error getting Terms of Service text from Sam: " + response.getStatusMessage(),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    return response.parseAsString();
  }

  public TosResponse getTosResponse(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getSelfTosUrl());
    HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(String.format("Error getting Terms of Service: %s for user %s",
              response.getStatusMessage(), authUser.getEmail()),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    String body = response.parseAsString();
    return new Gson().fromJson(body, TosResponse.class);
  }

  public int acceptTosStatus(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.acceptTosUrl());
    HttpRequest request = clientUtil.buildPutRequest(genericUrl, new EmptyContent(), authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(String.format("Error accepting Terms of Service: %s for user %s",
              response.getStatusMessage(), authUser.getEmail()),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    return response.getStatusCode();
  }

  public int rejectTosStatus(AuthUser authUser) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.rejectTosUrl());
    HttpRequest request = clientUtil.buildPutRequest(genericUrl, new EmptyContent(), authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(
          String.format("Error removing Terms of Service: %s for user %s",
              response.getStatusMessage(), authUser.getEmail()),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    return response.getStatusCode();
  }

  public EmailResponse getV1UserByEmail(AuthUser authUser, String email) throws Exception {
    GenericUrl genericUrl = new GenericUrl(configuration.getV1UserUrl(email));
    HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);
    HttpResponse response = executeRequest(request);
    if (!response.isSuccessStatusCode()) {
      logException(
          "Error getting user by email from Sam: " + response.getStatusMessage(),
          new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));
    }
    String body = response.parseAsString();
    return new Gson().fromJson(body, EmailResponse.class);
  }

  /**
   * Private method to handle the general case of sending requests to Sam. We inject timeouts here
   * to prevent Sam from impacting API performance. The default is 10 seconds which should be more
   * than enough for Sam calls.
   *
   * @param request The HttpRequest
   * @return The HttpResponse
   */
  private HttpResponse executeRequest(HttpRequest request) {
    request.setConnectTimeout(connectTimeoutMilliseconds);
    request.setReadTimeout(readTimeoutMilliseconds);
    return clientUtil.handleHttpRequest(request);
  }

}

1	package org.broadinstitute.consent.http.db;
2
3	import com.google.api.client.http.EmptyContent;
4	import com.google.api.client.http.GenericUrl;
5	import com.google.api.client.http.HttpRequest;
6	import com.google.api.client.http.HttpResponse;
7	import com.google.common.util.concurrent.FutureCallback;
8	import com.google.common.util.concurrent.Futures;
9	import com.google.common.util.concurrent.ListenableFuture;
10	import com.google.common.util.concurrent.ListeningExecutorService;
11	import com.google.common.util.concurrent.MoreExecutors;
12	import com.google.gson.Gson;
13	import com.google.gson.JsonElement;
14	import com.google.gson.JsonParser;
15	import com.google.gson.JsonSyntaxException;
16	import com.google.gson.reflect.TypeToken;
17	import jakarta.ws.rs.ServerErrorException;
18	import jakarta.ws.rs.WebApplicationException;
19	import jakarta.ws.rs.core.MediaType;
20	import java.lang.reflect.Type;
21	import java.util.ArrayList;
22	import java.util.List;
23	import java.util.concurrent.ExecutorService;
24	import org.broadinstitute.consent.http.configurations.ServicesConfiguration;
25	import org.broadinstitute.consent.http.models.AuthUser;
26	import org.broadinstitute.consent.http.models.sam.EmailResponse;
27	import org.broadinstitute.consent.http.models.sam.ResourceType;
28	import org.broadinstitute.consent.http.models.sam.TosResponse;
29	import org.broadinstitute.consent.http.models.sam.UserStatus;
30	import org.broadinstitute.consent.http.models.sam.UserStatusDiagnostics;
31	import org.broadinstitute.consent.http.models.sam.UserStatusInfo;
32	import org.broadinstitute.consent.http.util.ConsentLogger;
33	import org.broadinstitute.consent.http.util.HttpClientUtil;
34	import org.broadinstitute.consent.http.util.ThreadUtils;
35	import org.checkerframework.checker.nullness.qual.NonNull;
36	import org.checkerframework.checker.nullness.qual.Nullable;
37
38	public class SamDAO implements ConsentLogger {
39
40	private final ExecutorService executorService = new ThreadUtils().getExecutorService(	1✔
41	SamDAO.class);
42	private final HttpClientUtil clientUtil;
43	private final ServicesConfiguration configuration;
44	private final Integer connectTimeoutMilliseconds;
45	public final Integer readTimeoutMilliseconds;
46
47	public SamDAO(HttpClientUtil clientUtil, ServicesConfiguration configuration) {	1✔
48	this.clientUtil = clientUtil;	1✔
49	this.configuration = configuration;	1✔
50	// Defaults to 10 seconds
51	this.connectTimeoutMilliseconds = configuration.getTimeoutSeconds() * 1000;	1✔
52	// Defaults to 60 seconds
53	this.readTimeoutMilliseconds = configuration.getTimeoutSeconds() * 6000;	1✔
54	}	1✔
55
56	public List<ResourceType> getResourceTypes(AuthUser authUser) throws Exception {
57	GenericUrl genericUrl = new GenericUrl(configuration.getV1ResourceTypesUrl());	1✔
58	HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);	1✔
59	HttpResponse response = executeRequest(request);	1✔
60	if (!response.isSuccessStatusCode()) {	1✔
61	logException("Error getting resource types from Sam: " + response.getStatusMessage(),	×
62	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
63	}
64	String body = response.parseAsString();	1✔
65	Type resourceTypesListType = new TypeToken<ArrayList<ResourceType>>() {	1✔
66	}.getType();	1✔
67	return new Gson().fromJson(body, resourceTypesListType);	1✔
68	}
69
70	public UserStatusInfo getRegistrationInfo(AuthUser authUser) throws Exception {
71	GenericUrl genericUrl = new GenericUrl(configuration.getRegisterUserV2SelfInfoUrl());	1✔
72	HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);	1✔
73	HttpResponse response = executeRequest(request);	1✔
74	if (!response.isSuccessStatusCode()) {	1✔
75	logException(	×
76	"Error getting user registration information from Sam: " + response.getStatusMessage(),	×
77	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
78	}
79	String body = response.parseAsString();	1✔
80	return new Gson().fromJson(body, UserStatusInfo.class);	1✔
81	}
82
83	public UserStatusDiagnostics getSelfDiagnostics(AuthUser authUser) throws Exception {
84	GenericUrl genericUrl = new GenericUrl(configuration.getV2SelfDiagnosticsUrl());	1✔
85	HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);	1✔
86	HttpResponse response = executeRequest(request);	1✔
87	if (!response.isSuccessStatusCode()) {	1✔
88	logException(	×
89	"Error getting enabled statuses of user from Sam: " + response.getStatusMessage(),	×
90	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
91	}
92	String body = response.parseAsString();	1✔
93	return new Gson().fromJson(body, UserStatusDiagnostics.class);	1✔
94	}
95
96	public UserStatus postRegistrationInfo(AuthUser authUser) throws Exception {
97	GenericUrl genericUrl = new GenericUrl(configuration.postRegisterUserV2SelfUrl());	1✔
98	HttpRequest request = clientUtil.buildPostRequest(genericUrl, new EmptyContent(), authUser);	1✔
99	HttpResponse response = executeRequest(request);	1✔
100	String body = response.parseAsString();	1✔
101	if (!response.isSuccessStatusCode()) {	1✔
102	var errorMsg = getErrorMessage(authUser, body);	1✔
103	Exception e = new WebApplicationException(errorMsg, response.getStatusCode());	1✔
104	logException(errorMsg, new Exception(body));	1✔
105	throw e;	1✔
106	}
107	return new Gson().fromJson(body, UserStatus.class);	1✔
108	}
109
110	public static String getErrorMessage(AuthUser authUser, String body) {
111	var errorMsg = String.format("Error posting user registration information. Email: %s.",	1✔
112	authUser.getEmail());	1✔
113	if (body == null \|\| body.isEmpty()) {	1✔
114	return errorMsg;	1✔
115	}
116	try {
117	JsonElement messageElement = JsonParser.parseString(body).getAsJsonObject().get("message");	1✔
118	String message = messageElement != null ? messageElement.getAsString() : body;	1✔
119	if (message.contains("Cannot update azureB2cId")) {	1✔
120	return String.format(	1✔
121	"Email: %s. You may have previously signed in with a different authentication provider (Google or Microsoft). Please sign in with that provider. For more information visit: https://support.terra.bio/hc/en-us/community/posts/24089648317467-Cannot-update-azureB2cId-for-user",
122	authUser.getEmail());	1✔
123	}
124	return String.format(errorMsg + " %s.", message);	1✔
125	} catch (JsonSyntaxException e) { // If the body is not a valid JSON	1✔
126	return String.format(errorMsg + " %s.", body);	1✔
127	}
128	}
129
130	public void asyncPostRegistrationInfo(AuthUser authUser) {
131	ListeningExecutorService listeningExecutorService = MoreExecutors.listeningDecorator(	1✔
132	executorService);
133	ListenableFuture<UserStatus> userStatusFuture =	1✔
134	listeningExecutorService.submit(() -> postRegistrationInfo(authUser));	1✔
135	Futures.addCallback(	1✔
136	userStatusFuture,
137	new FutureCallback<>() {	1✔
138	@Override
139	public void onSuccess(@Nullable UserStatus userStatus) {
140	logInfo("Successfully registered user in Sam: " + authUser.getEmail());	1✔
141	}	1✔
142
143	@Override
144	public void onFailure(@NonNull Throwable throwable) {
NEW 145	logWarn("Async Post Registration Failure for user: " + authUser.getEmail() + "; "	×
NEW 146	+ throwable.getMessage());	×
UNCOV 147	}	×
148	},
149	listeningExecutorService);
150	}	1✔
151
152	public String getToSText() throws Exception {
153	GenericUrl genericUrl = new GenericUrl(configuration.getToSTextUrl());	1✔
154	HttpRequest request = clientUtil.buildUnAuthedGetRequest(genericUrl);	1✔
155	request.getHeaders().setAccept(MediaType.TEXT_PLAIN);	1✔
156	HttpResponse response = executeRequest(request);	1✔
157	if (!response.isSuccessStatusCode()) {	1✔
158	logException("Error getting Terms of Service text from Sam: " + response.getStatusMessage(),	×
159	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
160	}
161	return response.parseAsString();	1✔
162	}
163
164	public TosResponse getTosResponse(AuthUser authUser) throws Exception {
165	GenericUrl genericUrl = new GenericUrl(configuration.getSelfTosUrl());	1✔
166	HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);	1✔
167	HttpResponse response = executeRequest(request);	1✔
168	if (!response.isSuccessStatusCode()) {	1✔
NEW 169	logException(String.format("Error getting Terms of Service: %s for user %s",	×
NEW 170	response.getStatusMessage(), authUser.getEmail()),	×
UNCOV 171	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
172	}
173	String body = response.parseAsString();	1✔
174	return new Gson().fromJson(body, TosResponse.class);	1✔
175	}
176
177	public int acceptTosStatus(AuthUser authUser) throws Exception {
178	GenericUrl genericUrl = new GenericUrl(configuration.acceptTosUrl());	1✔
179	HttpRequest request = clientUtil.buildPutRequest(genericUrl, new EmptyContent(), authUser);	1✔
180	HttpResponse response = executeRequest(request);	1✔
181	if (!response.isSuccessStatusCode()) {	1✔
NEW 182	logException(String.format("Error accepting Terms of Service: %s for user %s",	×
NEW 183	response.getStatusMessage(), authUser.getEmail()),	×
UNCOV 184	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
185	}
186	return response.getStatusCode();	1✔
187	}
188
189	public int rejectTosStatus(AuthUser authUser) throws Exception {
190	GenericUrl genericUrl = new GenericUrl(configuration.rejectTosUrl());	1✔
191	HttpRequest request = clientUtil.buildPutRequest(genericUrl, new EmptyContent(), authUser);	1✔
192	HttpResponse response = executeRequest(request);	1✔
193	if (!response.isSuccessStatusCode()) {	1✔
194	logException(	×
NEW 195	String.format("Error removing Terms of Service: %s for user %s",	×
NEW 196	response.getStatusMessage(), authUser.getEmail()),	×
UNCOV 197	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
198	}
199	return response.getStatusCode();	1✔
200	}
201
202	public EmailResponse getV1UserByEmail(AuthUser authUser, String email) throws Exception {
203	GenericUrl genericUrl = new GenericUrl(configuration.getV1UserUrl(email));	1✔
204	HttpRequest request = clientUtil.buildGetRequest(genericUrl, authUser);	1✔
205	HttpResponse response = executeRequest(request);	1✔
206	if (!response.isSuccessStatusCode()) {	1✔
207	logException(	×
208	"Error getting user by email from Sam: " + response.getStatusMessage(),	×
209	new ServerErrorException(response.getStatusMessage(), response.getStatusCode()));	×
210	}
211	String body = response.parseAsString();	1✔
212	return new Gson().fromJson(body, EmailResponse.class);	1✔
213	}
214
215	/**
216	* Private method to handle the general case of sending requests to Sam. We inject timeouts here
217	* to prevent Sam from impacting API performance. The default is 10 seconds which should be more
218	* than enough for Sam calls.
219	*
220	* @param request The HttpRequest
221	* @return The HttpResponse
222	*/
223	private HttpResponse executeRequest(HttpRequest request) {
224	request.setConnectTimeout(connectTimeoutMilliseconds);	1✔
225	request.setReadTimeout(readTimeoutMilliseconds);	1✔
226	return clientUtil.handleHttpRequest(request);	1✔
227	}
228
229	}

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