Bearer tokens

Model/src/main/java/org/apidb/apicommon/controller/ApiSiteSetup.java

@@ -1,12 +1,11 @@
 package org.apidb.apicommon.controller;
 
-import java.util.Map;
-
 import org.apidb.apicommon.model.comment.CommentFactory;
 import org.apidb.apicommon.model.comment.pojo.Author;
-import org.gusdb.fgputil.accountdb.UserProfile;
 import org.gusdb.fgputil.events.Event;
 import org.gusdb.fgputil.events.Events;
+import org.gusdb.oauth2.client.veupathdb.User;
+import org.gusdb.oauth2.client.veupathdb.UserProperty;
 import org.gusdb.wdk.events.UserProfileUpdateEvent;
 import org.gusdb.wdk.model.WdkModel;
 import org.gusdb.wdk.model.WdkModelException;
@@ -36,13 +35,11 @@ private static void userProfileUpdateListener(Event event)
     UserProfileUpdateEvent updateEvent = (UserProfileUpdateEvent) event;
 
     // check to see if any of the property text fields changed
-    Map<String, String> userProps = updateEvent.getNewProfile().getProperties();
-    Map<String, String> oldProfileProps = updateEvent.getOldProfile()
-        .getProperties();
     boolean commentSearchTextUpdateRequired = false;
-
-    for (String key : oldProfileProps.keySet()) {
-      if (!oldProfileProps.get(key).equals(userProps.get(key))) {
+    String[] commentProps = new String[] { "firstName", "lastName", "organization" };
+    for (String key : commentProps) {
+      UserProperty prop = User.USER_PROPERTIES.get(key);
+      if (!prop.getValue(updateEvent.getOldUser()).equals(prop.getValue(updateEvent.getNewUser()))) {
         commentSearchTextUpdateRequired = true;
       }
     }
@@ -54,12 +51,12 @@ private static void userProfileUpdateListener(Event event)
     // need to write updated text to comment search field
     CommentFactory commentFactory = CommentFactoryManager.getCommentFactory(
         updateEvent.getWdkModel().getProjectId());
-    UserProfile profile = updateEvent.getNewProfile();
+    User user = updateEvent.getNewUser();
 
     commentFactory.updateAuthor(new Author()
-        .setFirstName(profile.getProperties().get("firstName"))
-        .setLastName(profile.getProperties().get("lastName"))
-        .setOrganization(profile.getProperties().get("organization"))
-        .setUserId(profile.getUserId()));
+        .setFirstName(user.getFirstName())
+        .setLastName(user.getLastName())
+        .setOrganization(user.getOrganization())
+        .setUserId(user.getUserId()));
   }
 }

Model/src/main/java/org/apidb/apicommon/model/comment/CommentAlertEmailFormatter.java

@@ -1,14 +1,14 @@
 package org.apidb.apicommon.model.comment;
 
+import java.util.Collection;
+import java.util.stream.Collectors;
+
 import org.apidb.apicommon.model.comment.pojo.CommentRequest;
 import org.apidb.apicommon.model.comment.pojo.ExternalDatabase;
 import org.gusdb.fgputil.FormatUtil;
 import org.gusdb.wdk.model.WdkModel;
 import org.gusdb.wdk.model.user.User;
 
-import java.util.Collection;
-import java.util.stream.Collectors;
-
 public class CommentAlertEmailFormatter {
   private static final String
     FIELD_COMMENT_ID          = "Comment Id",

Model/src/main/java/org/apidb/apicommon/model/comment/CommentFactory.java

@@ -1,28 +1,66 @@
 package org.apidb.apicommon.model.comment;
 
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.apidb.apicommon.model.comment.pojo.*;
-import org.apidb.apicommon.model.comment.repo.*;
-import org.gusdb.fgputil.db.pool.DatabaseInstance;
-import org.gusdb.fgputil.runtime.InstanceManager;
-import org.gusdb.fgputil.runtime.Manageable;
-import org.gusdb.wdk.model.WdkModel;
-import org.gusdb.wdk.model.WdkModelException;
-import org.gusdb.wdk.model.config.ModelConfigUserDB;
-import org.gusdb.wdk.model.user.User;
+import static org.apidb.apicommon.model.comment.ReferenceType.ACCESSION;
+import static org.apidb.apicommon.model.comment.ReferenceType.AUTHOR;
+import static org.apidb.apicommon.model.comment.ReferenceType.DIGITAL_OBJECT_ID;
+import static org.apidb.apicommon.model.comment.ReferenceType.PUB_MED;
 
-import javax.sql.DataSource;
 import java.io.IOException;
 import java.net.URL;
 import java.sql.Connection;
 import java.sql.PreparedStatement;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.Set;
+
+import javax.sql.DataSource;
+
+import org.apidb.apicommon.model.comment.pojo.Attachment;
+import org.apidb.apicommon.model.comment.pojo.Author;
+import org.apidb.apicommon.model.comment.pojo.Category;
+import org.apidb.apicommon.model.comment.pojo.Comment;
+import org.apidb.apicommon.model.comment.pojo.CommentRequest;
+import org.apidb.apicommon.model.comment.pojo.ExternalDatabase;
+import org.apidb.apicommon.model.comment.pojo.Project;
+import org.apidb.apicommon.model.comment.pojo.PubMedReference;
+import org.apidb.apicommon.model.comment.repo.DeleteAttachmentQuery;
+import org.apidb.apicommon.model.comment.repo.FindCommentQuery;
+import org.apidb.apicommon.model.comment.repo.GetAllAttachmentsQuery;
+import org.apidb.apicommon.model.comment.repo.GetAttachmentQuery;
+import org.apidb.apicommon.model.comment.repo.GetAuthorQuery;
+import org.apidb.apicommon.model.comment.repo.GetCategoriesQuery;
+import org.apidb.apicommon.model.comment.repo.GetCommentExistsQuery;
+import org.apidb.apicommon.model.comment.repo.GetCommentQuery;
+import org.apidb.apicommon.model.comment.repo.GetExternalDatabaseQuery;
+import org.apidb.apicommon.model.comment.repo.HideCommentQuery;
+import org.apidb.apicommon.model.comment.repo.InsertAttachmentQuery;
+import org.apidb.apicommon.model.comment.repo.InsertAuthorQuery;
+import org.apidb.apicommon.model.comment.repo.InsertCategoryQuery;
+import org.apidb.apicommon.model.comment.repo.InsertCommentQuery;
+import org.apidb.apicommon.model.comment.repo.InsertExternalDatabaseLinkQuery;
+import org.apidb.apicommon.model.comment.repo.InsertExternalDatabaseQuery;
+import org.apidb.apicommon.model.comment.repo.InsertLocationQuery;
+import org.apidb.apicommon.model.comment.repo.InsertReferencesQuery;
+import org.apidb.apicommon.model.comment.repo.InsertSequenceQuery;
+import org.apidb.apicommon.model.comment.repo.InsertStableIdQuery;
+import org.apidb.apicommon.model.comment.repo.Table;
+import org.apidb.apicommon.model.comment.repo.UpdateAttachmentQuery;
+import org.apidb.apicommon.model.comment.repo.UpdateAuthorQuery;
 import org.eupathdb.sitesearch.data.comments.UserCommentUpdater;
+import org.gusdb.fgputil.db.pool.DatabaseInstance;
+import org.gusdb.fgputil.runtime.InstanceManager;
+import org.gusdb.fgputil.runtime.Manageable;
+import org.gusdb.wdk.model.WdkModel;
+import org.gusdb.wdk.model.WdkModelException;
+import org.gusdb.wdk.model.config.ModelConfigUserDB;
+import org.gusdb.wdk.model.user.User;
 
-import static org.apidb.apicommon.model.comment.ReferenceType.*;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 /**
  * Manages user comments on WDK records

Model/src/main/java/org/apidb/apicommon/model/comment/pojo/Author.java

@@ -2,9 +2,8 @@
 
 import org.gusdb.wdk.model.user.User;
 
-import java.util.Map;
-
 public class Author {
+
   private String _firstName;
 
   private String _lastName;
@@ -50,11 +49,10 @@ public Author setUserId(long userId) {
   }
 
   public static Author fromUser(final User user) {
-    final Map<String, String> props = user.getProfileProperties();
     return new Author()
         .setUserId(user.getUserId())
-        .setFirstName(props.get("firstName"))
-        .setLastName(props.get("lastName"))
-        .setOrganization(props.get("organization"));
+        .setFirstName(user.getFirstName())
+        .setLastName(user.getLastName())
+        .setOrganization(user.getOrganization());
   }
 }

Model/src/main/java/org/apidb/apicommon/model/comment/repo/InsertCommentQuery.java

@@ -1,16 +1,18 @@
 package org.apidb.apicommon.model.comment.repo;
 
+import static java.sql.Types.BIGINT;
+import static java.sql.Types.CLOB;
+import static java.sql.Types.VARCHAR;
+
+import java.io.StringReader;
+
 import org.apidb.apicommon.model.comment.ReviewStatus;
 import org.apidb.apicommon.model.comment.pojo.CommentRequest;
 import org.apidb.apicommon.model.comment.pojo.Project;
 import org.gusdb.fgputil.db.runner.BasicArgumentBatch;
 import org.gusdb.fgputil.db.runner.SQLRunner;
 import org.gusdb.wdk.model.user.User;
 
-import java.io.StringReader;
-
-import static java.sql.Types.*;
-
 /**
  * Insert a new comment record.
  */

Model/src/main/java/org/apidb/apicommon/test/SingleTableRecordStreamTest.java

@@ -30,7 +30,6 @@
 import org.gusdb.wdk.model.record.attribute.AttributeField;
 import org.gusdb.wdk.model.record.attribute.AttributeValue;
 import org.gusdb.wdk.model.user.Step;
-import org.gusdb.wdk.model.user.UnregisteredUser.UnregisteredUserType;
 import org.gusdb.wdk.model.user.User;
 import org.gusdb.wdk.model.user.UserCache;
 import org.json.JSONObject;
@@ -105,7 +104,7 @@ public static void main(String[] args) throws Exception {
   /*%%%%%%%%%%%%%%%%%%%%%%%%%%% helper functions %%%%%%%%%%%%%%%%%%%%%%%%%%%*/
 
   private static RunnableObj<Step> createStep(WdkModel model) throws WdkModelException {
-    User user = model.getUserFactory().createUnregistedUser(UnregisteredUserType.GUEST);
+    User user = model.getSystemUser();
     return Step.builder(model, user.getUserId(), model.getStepFactory().getNewStepId())
         .setAnswerSpec(AnswerSpec.builder(model)
             .setQuestionFullName(QUESTION_NAME)

Service/src/main/java/org/apidb/apicommon/service/services/ApiBasketService.java

@@ -86,7 +86,7 @@ protected RevisedRequest<BasketActions> translatePatchRequest(
       return new RevisedRequest<>(
           getTranscriptRecordClass(getWdkModel()),
           new BasketActions(actions.getAction(), Collections.emptyList())
-            .setRunnableAnswerSpec(newSpec.buildRunnable(getSessionUser(), step.get().getContainer())));
+            .setRunnableAnswerSpec(newSpec.buildRunnable(getRequestingUser(), step.get().getContainer())));
     }
 
     // translate IDs to gene PKs if necessary

Service/src/main/java/org/apidb/apicommon/service/services/ApiProjectService.java

@@ -41,7 +41,7 @@ protected JSONObject addSupplementalProjectInfo(JSONObject projectJson) throws W
       // get all organisms in vocabulary of org param of taxon question
       Question taxonQuestion = model.getQuestionByName(TAXON_QUESTION_NAME).get();
       DisplayablyValid<AnswerSpec> spec = QuestionService.getDisplayableAnswerSpec(
-          TAXON_QUESTION_NAME, model, getSessionUser(), name -> taxonQuestion);
+          TAXON_QUESTION_NAME, model, getRequestingUser(), name -> taxonQuestion);
       AbstractEnumParam orgParam = (AbstractEnumParam)taxonQuestion.getParamMap().get(ORGANISM_PARAM_NAME);
       List<String> organisms = orgParam.getVocabInstance(AnswerSpec.getValidQueryInstanceSpec(spec)).getVocabTreeLeafTerms();
 

Service/src/main/java/org/apidb/apicommon/service/services/OrganismMetricsService.java

@@ -110,7 +110,7 @@ private String resolveOrganism(String recordClassUrlSegment, String primaryKeyVa
       throw new BadRequestException("Record type with url segment '" + recordClassUrlSegment + "' does not contain an '" + ORGANISM_ATTRIBUTE + "' attribute.");
     }
     PrimaryKeyValue pkValue = getPkValue(recordClass, primaryKeyValues);
-    List<RecordInstance> records = RecordClass.getRecordInstances(getSessionUser(), pkValue);
+    List<RecordInstance> records = RecordClass.getRecordInstances(getRequestingUser(), pkValue);
     if (records.isEmpty()) {
       throw new BadRequestException("Primary Key '" + primaryKeyValues + "' does not map to any records of type '" + recordClassUrlSegment + "'.");
     }

Service/src/main/java/org/apidb/apicommon/service/services/TranscriptToggleService.java

@@ -36,7 +36,7 @@ public void setTranscriptFlag(@PathParam("stepId") Integer stepId, String body)
     LOG.info("Action is to turn filter: " + filterTurnedOn);
 
     Step step = getWdkModel().getStepFactory().getStepByIdAndUserId(
-        stepId, getSessionUser().getUserId(), ValidationLevel.SYNTACTIC)
+        stepId, getRequestingUser().getUserId(), ValidationLevel.SYNTACTIC)
         .orElseThrow(() -> new NotFoundException("No step exists with ID " + stepId));
 
     AnswerSpecBuilder newSpec = AnswerSpec.builder(step.getAnswerSpec());

Service/src/main/java/org/apidb/apicommon/service/services/comments/AbstractUserCommentService.java

@@ -1,23 +1,24 @@
 package org.apidb.apicommon.service.services.comments;
 
+import java.util.function.Supplier;
+
+import javax.ws.rs.NotAuthorizedException;
+import javax.ws.rs.NotFoundException;
+
 import org.apidb.apicommon.controller.CommentFactoryManager;
 import org.apidb.apicommon.model.comment.CommentFactory;
 import org.apidb.apicommon.model.comment.pojo.Comment;
 import org.gusdb.wdk.model.WdkModelException;
 import org.gusdb.wdk.model.user.User;
 import org.gusdb.wdk.service.service.AbstractWdkService;
 
-import javax.ws.rs.NotAuthorizedException;
-import javax.ws.rs.NotFoundException;
-import java.util.function.Supplier;
-
 public abstract class AbstractUserCommentService extends AbstractWdkService {
   protected CommentFactory getCommentFactory() {
     return CommentFactoryManager.getCommentFactory(getWdkModel().getProjectId());
   }
 
   protected User fetchUser() {
-    final User out = getSessionUser();
+    final User out = getRequestingUser();
     if (out.isGuest())
       throw new NotAuthorizedException("you must login before performing this action");
     return out;

Service/src/main/java/org/apidb/apicommon/service/services/jbrowse/JBrowseUserDatasetsService.java

@@ -55,7 +55,7 @@ public JSONObject getAllUserDatasetsJBrowse(@PathParam("organism") String public
     catch (Exception e) {
         tracks = new JSONArray();
         Exception e2 = new WdkModelException("Unable to load JBrowse user datasets for user with ID " +
-            getSessionUser().getUserId() + ", organism " + publicOrganismAbbrev, e);
+            getRequestingUser().getUserId() + ", organism " + publicOrganismAbbrev, e);
         LOG.error("Could not load JBrowse user datasets", e2);
         Events.trigger(new ErrorEvent(new ServerErrorBundle(e2), getErrorContext(ErrorLocation.WDK_SERVICE)));
     }