checkpoint commit

Model/lib/conifer/roles/conifer/templates/WDK/model-config.xml.j2

@@ -29,9 +29,6 @@ site_vars file: {{ site_vars }}
              {% if modelconfig_useWeights is defined -%}
              assetsUrl="{{ modelconfig_useWeights }}"
              {% endif -%}
-             {% if modelconfig_secretKeyFile is defined -%}
-             secretKeyFile="{{ modelconfig_secretKeyFile }}"
-             {% endif -%}
              {% if modelconfig_blockedThreshold is defined -%}
              monitorBlockedThreads="{{ modelconfig_monitorBlockedThreads }}"
              {% endif -%}
@@ -145,40 +142,6 @@ site_vars file: {{ site_vars }}
             {% endif -%}
     />
 
-    <accountDb login="{{ modelconfig_accountDb_login }}"
-            password="{{ modelconfig_accountDb_password }}"
-            connectionUrl="{{ modelconfig_accountDb_connectionUrl }}"
-            platform="{{ modelconfig_accountDb_platform }}"
-            accountSchema="{{ modelconfig_accountDb_accountSchema }}"
-            {% if modelconfig_accountDb_maxActive is defined -%}
-            maxActive="{{ modelconfig_accountDb_maxActive }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_maxIdle is defined -%}
-            maxIdle="{{ modelconfig_accountDb_maxIdle }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_minIdle is defined -%}
-            minIdle="{{ modelconfig_accountDb_minIdle }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_maxWait is defined -%}
-            maxWait="{{ modelconfig_accountDb_maxWait }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_defaultFetchSize is defined -%}
-            defaultFetchSize="{{ modelconfig_accountDb_defaultFetchSize }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_showConnections is defined -%}
-            showConnections="{{ modelconfig_accountDb_showConnections }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_showConnectionsInterval is defined -%}
-            showConnectionsInterval="{{ modelconfig_accountDb_showConnectionsInterval }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_showConnectionsDuration is defined -%}
-            showConnectionsDuration="{{ modelconfig_accountDb_showConnectionsDuration }}"
-            {% endif -%}
-            {% if modelconfig_accountDb_driverInitClass is defined -%}
-            driverInitClass="{{ modelconfig_accountDb_driverInitClass }}"
-            {% endif %}
-    />
-
     {% if modelconfig_userDatasetStoreConfig is defined -%}
     {{ modelconfig_userDatasetStoreConfig|indent }}
     {% endif -%}

Model/src/main/java/org/gusdb/wdk/jmx/mbeans/ModelConfig.java

@@ -24,15 +24,13 @@ protected void init() {
     org.gusdb.wdk.model.config.QueryMonitor         queryMonitor         = modelConfig.getQueryMonitor();
     org.gusdb.wdk.model.config.ModelConfigUserDB    modelConfigUserDB    = modelConfig.getUserDB();
     org.gusdb.wdk.model.config.ModelConfigAppDB     modelConfigAppDB     = modelConfig.getAppDB();
-    org.gusdb.wdk.model.config.ModelConfigAccountDB modelConfigAccountDB = modelConfig.getAccountDB();
     org.gusdb.wdk.model.config.ModelConfigUserDatasetStore
       modelConfigUserDatasetStore  = modelConfig.getUserDatasetStoreConfig();
 
     setValuesFromGetters("global", modelConfig);
     setValuesFromGetters("queryMonitor", queryMonitor);
     setValuesFromGetters("userDb", modelConfigUserDB);
     setValuesFromGetters("appDb",  modelConfigAppDB);
-    setValuesFromGetters("accountDb", modelConfigAccountDB);
     setValuesFromGetters("userDatasetStore",  modelConfigUserDatasetStore);
   }
 

Model/src/main/java/org/gusdb/wdk/model/ModelXmlParser.java

@@ -436,9 +436,6 @@ private Map<String, String> loadProperties(String projectId, URL modelPropURL, M
     if (!propMap.containsKey("USER_SCHEMA")) {
       propMap.put("USER_SCHEMA", config.getUserDB().getUserSchema());
     }
-    if (!propMap.containsKey("ACCT_SCHEMA")) {
-      propMap.put("ACCT_SCHEMA", config.getAccountDB().getAccountSchema());
-    }
 
     return propMap;
   }

Model/src/main/java/org/gusdb/wdk/model/Utilities.java

@@ -1,17 +1,11 @@
 package org.gusdb.wdk.model;
 
-import org.apache.log4j.Logger;
-import org.json.JSONArray;
-import org.json.JSONException;
-import org.json.JSONObject;
-
-import javax.activation.DataHandler;
-import javax.mail.*;
-import javax.mail.internet.InternetAddress;
-import javax.mail.internet.MimeBodyPart;
-import javax.mail.internet.MimeMessage;
-import javax.mail.internet.MimeMultipart;
-import java.io.*;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
 import java.sql.Clob;
 import java.sql.SQLException;
 import java.util.Date;
@@ -22,6 +16,20 @@
 import java.util.regex.Pattern;
 import java.util.stream.Stream;
 
+import javax.activation.DataHandler;
+import javax.mail.Address;
+import javax.mail.Message;
+import javax.mail.MessagingException;
+import javax.mail.Multipart;
+import javax.mail.Session;
+import javax.mail.Transport;
+import javax.mail.internet.InternetAddress;
+import javax.mail.internet.MimeBodyPart;
+import javax.mail.internet.MimeMessage;
+import javax.mail.internet.MimeMultipart;
+
+import org.apache.log4j.Logger;
+
 /**
  * This class provided constants that are shared among different WDK model
  * classes. Furthermore, it also provides utility functions to send
@@ -31,16 +39,10 @@
  */
 public class Utilities {
 
-  private static final Logger logger = Logger.getLogger(Utilities.class);
+  private static final Logger LOG = Logger.getLogger(Utilities.class);
 
   public static final int TRUNCATE_DEFAULT = 100;
 
-  /**
-   * The maximum size for parameter values that will be displayed in thr URL as
-   * plain values
-   */
-  public static final int MAX_PARAM_VALUE_SIZE = 100;
-
   /**
    * The maximum number of attributes used in sorting an answer
    */
@@ -56,10 +58,6 @@ public class Utilities {
    */
   public static final String SYSTEM_PROPERTY_GUS_HOME = "GUS_HOME";
 
-  public static final int MAXIMUM_RECORD_INSTANCES = 10000;
-
-  public static final int DEFAULT_PAGE_SIZE = 20;
-
   public static final int DEFAULT_SUMMARY_ATTRIBUTE_SIZE = 6;
 
   public static final int DEFAULT_WEIGHT = 10;
@@ -71,8 +69,6 @@ public class Utilities {
    */
   public static final int MAX_PK_COLUMN_COUNT = 4;
 
-  public static final int MAX_PK_COLUMN_VALUE_SIZE = 1999;
-
   public static final String INTERNAL_PARAM_SET = "InternalParams";
   public static final String INTERNAL_QUERY_SET = "InternalQueries";
   public static final String INTERNAL_QUESTION_SET = "InternalQuestions";
@@ -99,12 +95,12 @@ public class Utilities {
   public static final String COLUMN_DIVIDER = ",";
 
   public static final String WDK_MODEL_KEY = "wdk_model";
-  public static final String WDK_MODEL_BEAN_KEY = "wdkModel"; // cannot change this because of JSPs
   public static final String WDK_USER_KEY = "wdk_user";
-  public static final String WDK_USER_BEAN_KEY = "wdkUser";
+  public static final String BEARER_TOKEN_KEY = "bearer-token";
 
   public static final String WDK_SERVICE_ENDPOINT_KEY = "wdkServiceEndpoint";
 
+
   /*
    * Inner class to act as a JAF DataSource to send HTML e-mail content
    */
@@ -164,22 +160,6 @@ public static String[] toArray(String data) {
     return data.trim().split("\\s+");
   }
 
-  public static String fromArray(String[] data) {
-    return fromArray(data, ",");
-  }
-
-  public static String fromArray(String[] data, String delimiter) {
-    if (data == null)
-      return null;
-    StringBuffer sb = new StringBuffer();
-    for (String value : data) {
-      if (sb.length() > 0)
-        sb.append(delimiter);
-      sb.append(value);
-    }
-    return sb.toString();
-  }
-
   public static String parseValue(Object objValue) {
     if (objValue == null)
       return null;
@@ -197,21 +177,6 @@ private static String parseClob(Clob clobValue) {
     }
   }
 
-  public static String[][] convertContent(String content) throws JSONException {
-    JSONArray jsResult = new JSONArray(content);
-    JSONArray jsRow = (JSONArray) jsResult.get(0);
-    String[][] result = new String[jsResult.length()][jsRow.length()];
-    for (int row = 0; row < result.length; row++) {
-      jsRow = (JSONArray) jsResult.get(row);
-      for (int col = 0; col < result[row].length; col++) {
-        Object cell = jsRow.get(col);
-        result[row][col] = (cell == null || cell == JSONObject.NULL) ? null
-            : cell.toString();
-      }
-    }
-    return result;
-  }
-
   // sendEmail() method overloading: different number of parameters (max 8), different type for attachments
 
   // 7 parameters (missing bcc, datahandlers instead of attachments)
@@ -258,7 +223,7 @@ public static void sendEmail(String smtpServer, String sendTos, String reply,
     String subject, String content, String ccAddresses, String bccAddresses,
     Attachment[] attachments) throws WdkModelException {
 
-    logger.debug("Sending message to: " + sendTos + ", bcc to: " + bccAddresses +
+    LOG.debug("Sending message to: " + sendTos + ", bcc to: " + bccAddresses +
       ",reply: " + reply + ", using SMPT: " + smtpServer);
 
     // create properties and get the session
@@ -317,7 +282,6 @@ public static void sendEmail(String smtpServer, String sendTos, String reply,
     }
   }
 
-
   public static byte[] readFile(File file) throws IOException {
     byte[] buffer = new byte[(int) file.length()];
     InputStream stream = new FileInputStream(file);
@@ -326,18 +290,6 @@ public static byte[] readFile(File file) throws IOException {
     return buffer;
   }
 
-  public static <S,T> int createHashFromValueMap(Map<S,T> map) {
-    StringBuilder buffer = new StringBuilder("{");
-    for (S key : map.keySet()) {
-      if (buffer.length() > 1) {
-        buffer.append(";");
-      }
-      buffer.append(key).append(":").append(map.get(key));
-    }
-    buffer.append("}");
-    return buffer.toString().hashCode();
-  }
-
   public static Map<String, Boolean> parseSortList(String sortList) throws WdkModelException {
     Map<String, Boolean> sortingMap = new LinkedHashMap<String, Boolean>();
     String[] attrCombines = sortList.split(",");

Model/src/main/java/org/gusdb/wdk/model/WdkModel.java

@@ -23,7 +23,6 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
-import java.util.concurrent.locks.ReentrantLock;
 import java.util.stream.Collectors;
 
 import org.apache.log4j.Logger;
@@ -38,13 +37,13 @@
 import org.gusdb.fgputil.functional.FunctionalInterfaces.SupplierWithException;
 import org.gusdb.fgputil.runtime.InstanceManager;
 import org.gusdb.fgputil.runtime.Manageable;
+import org.gusdb.wdk.model.user.User;
 import org.gusdb.wdk.model.analysis.StepAnalysis;
 import org.gusdb.wdk.model.analysis.StepAnalysisPlugins;
 import org.gusdb.wdk.model.answer.single.SingleRecordQuestion;
 import org.gusdb.wdk.model.columntool.ColumnToolBundleMap;
 import org.gusdb.wdk.model.columntool.DefaultColumnToolBundleRef;
 import org.gusdb.wdk.model.config.ModelConfig;
-import org.gusdb.wdk.model.config.ModelConfigAccountDB;
 import org.gusdb.wdk.model.config.ModelConfigAppDB;
 import org.gusdb.wdk.model.config.ModelConfigUserDB;
 import org.gusdb.wdk.model.config.ModelConfigUserDatasetStore;
@@ -69,7 +68,6 @@
 import org.gusdb.wdk.model.user.BasketFactory;
 import org.gusdb.wdk.model.user.FavoriteFactory;
 import org.gusdb.wdk.model.user.StepFactory;
-import org.gusdb.wdk.model.user.User;
 import org.gusdb.wdk.model.user.UserFactory;
 import org.gusdb.wdk.model.user.analysis.StepAnalysisFactory;
 import org.gusdb.wdk.model.user.analysis.StepAnalysisFactoryImpl;
@@ -203,7 +201,6 @@ public static WdkModel construct(String projectId, String gusHome) throws WdkMod
   private ColumnToolBundleMap columnToolBundleMap = new ColumnToolBundleMap();
   private String defaultColumnToolBundleRef;
 
-  private ReentrantLock systemUserLock = new ReentrantLock();
   private User systemUser;
 
   private String buildNumber;
@@ -551,14 +548,12 @@ public void configure(ModelConfig modelConfig) throws WdkModelException {
 
     ModelConfigAppDB appDbConfig = modelConfig.getAppDB();
     ModelConfigUserDB userDbConfig = modelConfig.getUserDB();
-    ModelConfigAccountDB accountDbConfig = modelConfig.getAccountDB();
     ModelConfigUserDatasetStore udsConfig = modelConfig.getUserDatasetStoreConfig();
 
     QueryLogger.initialize(modelConfig.getQueryMonitor());
 
     appDb = new DatabaseInstance(appDbConfig, DB_INSTANCE_APP, true);
     userDb = new DatabaseInstance(userDbConfig, DB_INSTANCE_USER, true);
-    accountDb = new DatabaseInstance(accountDbConfig, DB_INSTANCE_ACCOUNT, true);
 
     // set true to avoid a broken dev irods at build time
     if ( udsConfig == null ) {
@@ -599,6 +594,8 @@ public void configure(ModelConfig modelConfig) throws WdkModelException {
         new UnconfiguredStepAnalysisFactory(this) :
         new StepAnalysisFactoryImpl(this));
 
+    systemUser = userFactory.createUnregisteredUser().getSecond();
+
     LOG.info("WDK Model configured.");
   }
 
@@ -1360,17 +1357,6 @@ public String queryParamDisplayName(String paramName) {
   }
 
   public User getSystemUser() {
-    if (systemUser == null) {
-      try {
-        systemUserLock.lock();
-        if (systemUser == null) {
-          systemUser = userFactory.createUnregistedUser();
-        }
-      }
-      finally {
-        systemUserLock.unlock();
-      }
-    }
     return systemUser;
   }
 

Model/src/main/java/org/gusdb/wdk/model/WdkSqlScriptRunner.java

@@ -22,11 +22,11 @@
  */
 public class WdkSqlScriptRunner {
 
-  private static enum DbType { APP, USER, ACCT }
+  private static enum DbType { APP, USER }
 
   public static void main(String[] args) {
     if (args.length != 3 && args.length != 5) {
-      System.err.println("USAGE: fgpJava " + WdkSqlScriptRunner.class.getName() + " <project_id> [APP|USER|ACCT] <sql_file> [<auto_commit> <stopOnError>]");
+      System.err.println("USAGE: fgpJava " + WdkSqlScriptRunner.class.getName() + " <project_id> [APP|USER] <sql_file> [<auto_commit> <stopOnError>]");
       System.exit(1);
     }
     BufferedReader sqlReader = null;
@@ -46,7 +46,6 @@ public static void main(String[] args) {
       ModelConfigDB dbConfig = (
           whichDb.equals(DbType.APP) ? modelConf.getAppDB() :
           whichDb.equals(DbType.USER) ? modelConf.getUserDB() :
-          whichDb.equals(DbType.ACCT) ? modelConf.getAccountDB() :
           null ); // should never happen; value already validated
 
       db = new DatabaseInstance(dbConfig);

Model/src/main/java/org/gusdb/wdk/model/answer/AnswerValue.java

@@ -53,9 +53,9 @@
 import org.gusdb.wdk.model.record.Field;
 import org.gusdb.wdk.model.record.PrimaryKeyDefinition;
 import org.gusdb.wdk.model.record.PrimaryKeyIterator;
-import org.gusdb.wdk.model.record.ResultSetPrimaryKeyIterator;
 import org.gusdb.wdk.model.record.RecordClass;
 import org.gusdb.wdk.model.record.RecordInstance;
+import org.gusdb.wdk.model.record.ResultSetPrimaryKeyIterator;
 import org.gusdb.wdk.model.record.TableField;
 import org.gusdb.wdk.model.record.attribute.AttributeField;
 import org.gusdb.wdk.model.record.attribute.ColumnAttributeField;

Model/src/main/java/org/gusdb/wdk/model/answer/TransformUtil.java

@@ -12,10 +12,10 @@
 import org.gusdb.wdk.model.query.spec.QueryInstanceSpec;
 import org.gusdb.wdk.model.question.Question;
 import org.gusdb.wdk.model.user.Step;
+import org.gusdb.wdk.model.user.StepContainer.ListStepContainer;
 import org.gusdb.wdk.model.user.Strategy;
 import org.gusdb.wdk.model.user.User;
 import org.gusdb.wdk.model.user.UserCache;
-import org.gusdb.wdk.model.user.StepContainer.ListStepContainer;
 
 /**
  * Provides a utility to use transform questions to convert an answer value of