Example #1
0
 /**
  * Returns true if the given field is a member of any primary key on the given class, for the
  * given source.
  *
  * @param model the Model in which to find ClassDescriptors
  * @param clazz the Class in which to look
  * @param fieldName the name of the field to check
  * @param source the Source that the keys belong to
  * @return true if the field is a primary key
  */
 public static boolean fieldIsPrimaryKey(
     Model model, Class<?> clazz, String fieldName, Source source) {
   Map<PrimaryKeyCacheKey, Set<String>> cache = primaryKeyCache.get();
   PrimaryKeyCacheKey key = new PrimaryKeyCacheKey(model, clazz, source);
   Set<String> fields = cache.get(key);
   if (fields == null) {
     fields = new HashSet<String>();
     for (ClassDescriptor cld : model.getClassDescriptorsForClass(clazz)) {
       for (PrimaryKey pk : getPrimaryKeys(cld, source, null)) {
         fields.addAll(pk.getFieldNames());
       }
     }
     cache.put(key, fields);
   }
   return fields.contains(fieldName);
 }
Example #2
0
 /**
  * Returns whether this primary key can be fetched now.
  *
  * @param pk the PrimaryKey
  * @param cld the ClassDescriptor that the PrimaryKey is in
  * @param pksNotDone a Map of pks not yet fetched
  * @return a boolean
  */
 protected boolean canDoPkNow(
     PrimaryKey pk, ClassDescriptor cld, Map<PrimaryKey, ClassDescriptor> pksNotDone) {
   boolean canDoPkNow = true;
   Iterator<String> fieldNameIter = pk.getFieldNames().iterator();
   while (fieldNameIter.hasNext() && canDoPkNow) {
     String fieldName = fieldNameIter.next();
     FieldDescriptor fd = cld.getFieldDescriptorByName(fieldName);
     if (fd.isReference()) {
       Iterator<ClassDescriptor> otherCldIter = pksNotDone.values().iterator();
       while (otherCldIter.hasNext() && canDoPkNow) {
         ClassDescriptor otherCld = otherCldIter.next();
         Class<? extends FastPathObject> fieldClass =
             ((ReferenceDescriptor) fd).getReferencedClassDescriptor().getType();
         if (otherCld.getType().isAssignableFrom(fieldClass)
             || fieldClass.isAssignableFrom(otherCld.getType())) {
           canDoPkNow = false;
         }
       }
     }
   }
   return canDoPkNow;
 }
Example #3
0
 /**
  * Fetches equivalent objects for a particular primary key.
  *
  * @param pk the PrimaryKey
  * @param cld the ClassDescriptor of the PrimaryKey
  * @param results a Map to hold results that are to be added to the cache
  * @param objectsForCld a List of objects relevant to this PrimaryKey
  * @param fetchedObjectIds a Set to hold ids of objects that are fetched, to prefetch from the
  *     data tracker later
  * @throws ObjectStoreException if something goes wrong
  */
 protected void doPk(
     PrimaryKey pk,
     ClassDescriptor cld,
     Map<InterMineObject, Set<InterMineObject>> results,
     List<InterMineObject> objectsForCld,
     Set<Integer> fetchedObjectIds)
     throws ObjectStoreException {
   Iterator<InterMineObject> objectsForCldIter = objectsForCld.iterator();
   while (objectsForCldIter.hasNext()) {
     int objCount = 0;
     int origObjCount = 0;
     Query q = new Query();
     QueryClass qc = new QueryClass(cld.getType());
     q.addFrom(qc);
     q.addToSelect(qc);
     ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
     q.setConstraint(cs);
     Map<String, Set<Object>> fieldNameToValues = new HashMap<String, Set<Object>>();
     for (String fieldName : pk.getFieldNames()) {
       try {
         QueryField qf = new QueryField(qc, fieldName);
         q.addToSelect(qf);
         Set<Object> values = new HashSet<Object>();
         fieldNameToValues.put(fieldName, values);
         cs.addConstraint(new BagConstraint(qf, ConstraintOp.IN, values));
       } catch (IllegalArgumentException e) {
         QueryForeignKey qf = new QueryForeignKey(qc, fieldName);
         q.addToSelect(qf);
         Set<Object> values = new HashSet<Object>();
         fieldNameToValues.put(fieldName, values);
         cs.addConstraint(new BagConstraint(qf, ConstraintOp.IN, values));
       }
     }
     // Now make a map from the primary key values to source objects
     Map<List<Object>, InterMineObject> keysToSourceObjects =
         new HashMap<List<Object>, InterMineObject>();
     while (objectsForCldIter.hasNext() && (objCount < 500)) {
       InterMineObject object = objectsForCldIter.next();
       origObjCount++;
       try {
         if (DataLoaderHelper.objectPrimaryKeyNotNull(model, object, cld, pk, source, idMap)) {
           List<Collection<Object>> values = new ArrayList<Collection<Object>>();
           boolean skipObject = false;
           Map<String, Set<Object>> fieldsValues = new HashMap<String, Set<Object>>();
           for (String fieldName : pk.getFieldNames()) {
             try {
               Object value = object.getFieldProxy(fieldName);
               Set<Object> fieldValues;
               if (value instanceof InterMineObject) {
                 Integer id = idMap.get(((InterMineObject) value).getId());
                 if (id == null) {
                   Set<InterMineObject> eqs = results.get(value);
                   if (eqs == null) {
                     value = object.getFieldValue(fieldName);
                     eqs = queryEquivalentObjects((InterMineObject) value, source);
                   }
                   fieldValues = new HashSet<Object>();
                   for (InterMineObject obj : eqs) {
                     fieldValues.add(obj.getId());
                   }
                 } else {
                   fieldValues = Collections.singleton((Object) id);
                 }
               } else {
                 fieldValues = Collections.singleton(value);
               }
               values.add(fieldValues);
               fieldsValues.put(fieldName, fieldValues);
               for (Object fieldValue : fieldValues) {
                 long time = System.currentTimeMillis();
                 boolean pkQueryFruitless =
                     hints.pkQueryFruitless(cld.getType(), fieldName, fieldValue);
                 String summaryName = Util.getFriendlyName(cld.getType()) + "." + fieldName;
                 if (!savedTimes.containsKey(summaryName)) {
                   savedTimes.put(summaryName, new Long(System.currentTimeMillis() - time));
                   savedCounts.put(summaryName, new Integer(0));
                 }
                 if (pkQueryFruitless) {
                   skipObject = true;
                 }
               }
             } catch (IllegalAccessException e) {
               throw new RuntimeException(e);
             }
           }
           if (!skipObject) {
             objCount++;
             for (String fieldName : pk.getFieldNames()) {
               fieldNameToValues.get(fieldName).addAll(fieldsValues.get(fieldName));
             }
             for (List<Object> valueSet : CollectionUtil.fanOutCombinations(values)) {
               if (keysToSourceObjects.containsKey(valueSet)) {
                 throw new ObjectStoreException(
                     "Duplicate objects found for pk "
                         + cld.getName()
                         + "."
                         + pk.getName()
                         + ": "
                         + object);
               }
               keysToSourceObjects.put(valueSet, object);
             }
           }
         }
       } catch (MetaDataException e) {
         throw new ObjectStoreException(e);
       }
     }
     // Prune BagConstraints using the hints system.
     // boolean emptyQuery = false;
     // Iterator<String> fieldNameIter = pk.getFieldNames().iterator();
     // while (fieldNameIter.hasNext() && (!emptyQuery)) {
     //    String fieldName = fieldNameIter.next();
     //    Set values = fieldNameToValues.get(fieldName);
     // Iterator valueIter = values.iterator();
     // while (valueIter.hasNext()) {
     //    if (hints.pkQueryFruitless(cld.getType(), fieldName, valueIter.next())) {
     //        valueIter.remove();
     //    }
     // }
     //    if (values.isEmpty()) {
     //        emptyQuery = true;
     //    }
     // }
     if (objCount > 0) {
       // Iterate through query, and add objects to results
       // long time = System.currentTimeMillis();
       int matches = 0;
       Results res = lookupOs.execute(q, 2000, false, false, false);
       @SuppressWarnings("unchecked")
       List<ResultsRow<Object>> tmpRes = (List) res;
       for (ResultsRow<Object> row : tmpRes) {
         List<Object> values = new ArrayList<Object>();
         for (int i = 1; i <= pk.getFieldNames().size(); i++) {
           values.add(row.get(i));
         }
         Set<InterMineObject> set = results.get(keysToSourceObjects.get(values));
         if (set != null) {
           set.add((InterMineObject) row.get(0));
           matches++;
         }
         fetchedObjectIds.add(((InterMineObject) row.get(0)).getId());
       }
       // LOG.info("Fetched " + res.size() + " equivalent objects for " + objCount
       //        + " objects in " + (System.currentTimeMillis() - time) + " ms for "
       //        + cld.getName() + "." + pk.getName());
     }
   }
 }
Example #4
0
  /**
   * Look a the values of the given primary key in the object and return true if and only if some
   * part of the primary key is null. If the primary key contains a reference it is sufficient for
   * any of the primary keys of the referenced object to be non-null (ie objectPrimaryKeyIsNull()
   * returning true).
   *
   * @param model the Model in which to find ClassDescriptors
   * @param obj the Object to check
   * @param cld one of the classes that obj is. Only primary keys for this classes will be checked
   * @param pk the primary key to check
   * @param source the Source database
   * @param idMap an IntToIntMap from source IDs to destination IDs
   * @return true if the the given primary key is non-null for the given object
   * @throws MetaDataException if anything goes wrong
   */
  public static boolean objectPrimaryKeyNotNull(
      Model model,
      InterMineObject obj,
      ClassDescriptor cld,
      PrimaryKey pk,
      Source source,
      IntToIntMap idMap)
      throws MetaDataException {
    for (String fieldName : pk.getFieldNames()) {
      FieldDescriptor fd = cld.getFieldDescriptorByName(fieldName);
      if (fd instanceof AttributeDescriptor) {
        Object value;
        try {
          value = obj.getFieldValue(fieldName);
        } catch (IllegalAccessException e) {
          throw new MetaDataException(
              "Failed to get field " + fieldName + " for key " + pk + " from " + obj, e);
        }
        if (value == null) {
          return false;
        }
      } else if (fd instanceof CollectionDescriptor) {
        throw new MetaDataException(
            "Primary key "
                + pk.getName()
                + " for class "
                + cld.getName()
                + " cannot contain collection "
                + fd.getName()
                + ": collections cannot be part of a primary key. Please edit"
                + model.getName()
                + "_keyDefs.properties");
      } else if (fd instanceof ReferenceDescriptor) {
        InterMineObject refObj;
        try {
          refObj = (InterMineObject) obj.getFieldProxy(fieldName);
        } catch (IllegalAccessException e) {
          throw new MetaDataException(
              "Failed to get field " + fieldName + " for key " + pk + " from " + obj, e);
        }
        if (refObj == null) {
          return false;
        }

        if ((refObj.getId() != null) && (idMap.get(refObj.getId()) != null)) {
          // We have previously loaded the object in this reference.
          continue;
        }

        if (refObj instanceof ProxyReference) {
          refObj = ((ProxyReference) refObj).getObject();
        }

        boolean foundNonNullKey = false;
        boolean foundKey = false;
        Set<ClassDescriptor> classDescriptors =
            model.getClassDescriptorsForClass(refObj.getClass());

        CLDS:
        for (ClassDescriptor refCld : classDescriptors) {
          Set<PrimaryKey> primaryKeys;

          if (source == null) {
            primaryKeys =
                new LinkedHashSet<PrimaryKey>(PrimaryKeyUtil.getPrimaryKeys(refCld).values());
          } else {
            primaryKeys = DataLoaderHelper.getPrimaryKeys(refCld, source, null);
          }

          for (PrimaryKey refPK : primaryKeys) {
            foundKey = true;

            if (objectPrimaryKeyNotNull(model, refObj, refCld, refPK, source, idMap)) {
              foundNonNullKey = true;
              break CLDS;
            }
          }
        }

        if (foundKey && (!foundNonNullKey)) {
          return false;
        }
      }
    }

    return true;
  }
Example #5
0
  /**
   * Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor. The Set contains
   * all the primary keys that exist on a particular class that are used by the source, without
   * performing any recursion. The Model.getClassDescriptorsForClass() method is recommended if you
   * wish for all the primary keys of the class' parents as well.
   *
   * @param cld the ClassDescriptor
   * @param source the Source
   * @param os the ObjectStore that these PrimaryKeys are used in, for creating indexes
   * @return a Set of PrimaryKeys
   */
  public static Set<PrimaryKey> getPrimaryKeys(ClassDescriptor cld, Source source, ObjectStore os) {
    GetPrimaryKeyCacheKey key = new GetPrimaryKeyCacheKey(cld, source);
    synchronized (getPrimaryKeyCache) {
      Set<PrimaryKey> keySet = getPrimaryKeyCache.get(key);
      if (keySet == null) {
        keySet = new LinkedHashSet<PrimaryKey>();
        Properties keys = getKeyProperties(source);
        if (keys != null) {
          if (!verifiedSources.contains(source)) {
            String packageNameWithDot =
                cld.getName().substring(0, cld.getName().lastIndexOf('.') + 1);
            LOG.info(
                "Verifying primary key config for source "
                    + source
                    + ", packageName = "
                    + packageNameWithDot);
            for (Map.Entry<Object, Object> entry : keys.entrySet()) {
              String cldName = (String) entry.getKey();
              String keyList = (String) entry.getValue();
              if (!cldName.contains(".")) {
                ClassDescriptor iCld =
                    cld.getModel().getClassDescriptorByName(packageNameWithDot + cldName);
                if (iCld != null) {
                  Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(iCld);

                  String[] tokens = keyList.split(",");
                  for (int i = 0; i < tokens.length; i++) {
                    String token = tokens[i].trim();
                    if (map.get(token) == null) {
                      throw new IllegalArgumentException(
                          "Primary key "
                              + token
                              + " for class "
                              + cldName
                              + " required by datasource "
                              + source.getName()
                              + " in "
                              + source.getName()
                              + "_keys.properties is not defined in "
                              + cld.getModel().getName()
                              + "_keyDefs.properties");
                    }
                  }
                } else {
                  LOG.warn(
                      "Ignoring entry for "
                          + cldName
                          + " in file "
                          + cld.getModel().getName()
                          + "_keyDefs.properties - not in model!");
                }
              }
            }
            verifiedSources.add(source);
          }
          Map<String, PrimaryKey> map = PrimaryKeyUtil.getPrimaryKeys(cld);
          String cldName = TypeUtil.unqualifiedName(cld.getName());
          String keyList = (String) keys.get(cldName);
          if (keyList != null) {
            String[] tokens = keyList.split(",");
            for (int i = 0; i < tokens.length; i++) {
              String token = tokens[i].trim();
              if (map.get(token) == null) {
                throw new IllegalArgumentException(
                    "Primary key "
                        + token
                        + " for class "
                        + cld.getName()
                        + " required by data source "
                        + source.getName()
                        + " in "
                        + source.getName()
                        + "_keys.properties is not defined in "
                        + cld.getModel().getName()
                        + "_keyDefs.properties");
              } else {
                keySet.add(map.get(token));
              }
            }
          }
          for (Map.Entry<Object, Object> entry : keys.entrySet()) {
            String propKey = (String) entry.getKey();
            String fieldList = (String) entry.getValue();
            int posOfDot = propKey.indexOf('.');
            if (posOfDot > 0) {
              String propCldName = propKey.substring(0, posOfDot);
              if (cldName.equals(propCldName)) {
                String keyName = propKey.substring(posOfDot + 1);
                PrimaryKey pk = new PrimaryKey(keyName, fieldList, cld);
                if (!keySet.contains(pk)) {
                  keySet.add(pk);
                  if (os instanceof ObjectStoreInterMineImpl) {
                    ObjectStoreInterMineImpl osimi = (ObjectStoreInterMineImpl) os;
                    DatabaseSchema schema = osimi.getSchema();
                    ClassDescriptor tableMaster = schema.getTableMaster(cld);
                    String tableName = DatabaseUtil.getTableName(tableMaster);
                    List<String> fields = new ArrayList<String>();

                    for (String field : pk.getFieldNames()) {
                      String colName = DatabaseUtil.generateSqlCompatibleName(field);
                      if (tableMaster.getReferenceDescriptorByName(field, true) != null) {
                        colName += "id";
                      }
                      fields.add(colName);
                    }
                    String sql =
                        "CREATE INDEX "
                            + tableName
                            + "__"
                            + keyName
                            + " ON "
                            + tableName
                            + " ("
                            + StringUtil.join(fields, ", ")
                            + ")";
                    System.out.println("Creating index: " + sql);
                    LOG.info("Creating index: " + sql);
                    Connection conn = null;
                    try {
                      conn = osimi.getConnection();
                      conn.createStatement().execute(sql);
                    } catch (SQLException e) {
                      LOG.warn("Index creation failed", e);
                    } finally {
                      if (conn != null) {
                        osimi.releaseConnection(conn);
                      }
                    }
                  }
                }
              }
            }
          }
        } else {
          throw new IllegalArgumentException(
              "Unable to find keys for source "
                  + source.getName()
                  + " in file "
                  + source.getName()
                  + "_keys.properties");
        }
        getPrimaryKeyCache.put(key, keySet);
      }
      return keySet;
    }
  }