Example usage for org.apache.commons.logging Log warn

List of usage examples for org.apache.commons.logging Log warn

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Introduction

In this page you can find the example usage for org.apache.commons.logging Log warn.

Prototype

void warn(Object message);

Source Link

Document

Logs a message with warn log level.

Usage

From source file:de.tudarmstadt.ukp.clarin.webanno.crowdflower.NamedEntityTaskManager.java

/**
 * Aggregates and sets final judgments in the JCases provided by documentsJCas.
 *
 * @param jobID2 the job ID.//from  w  w w  .j  a va  2 s.  com
 * @param documentsJCas the documents.
 * @throws IOException hum?
 * @throws UnsupportedEncodingException hum?
 * @throws CrowdException hum?
 */

public void setCrowdJobAnnotationsInDocs(String jobID2, List<JCas> documentsJCas)
        throws UnsupportedEncodingException, IOException, CrowdException {
    omittedEntities = 0;

    Log LOG = LogFactory.getLog(getClass());

    BufferedReader br = getReaderForRawJudgments(jobID2);
    String line;

    // Jackson JSON object mapper
    ObjectMapper mapper = new ObjectMapper();

    // Maps our own token offsets (needed by JS in the crowdflower task) to Jcas offsets
    // One map for start and end offset conversion each and new mappings for each document (to be able to use multiple documents)
    // Array position is token number
    List<List<Integer>> charStartMappings = new ArrayList<List<Integer>>();
    List<List<Integer>> charEndMappings = new ArrayList<List<Integer>>();

    for (JCas cas : documentsJCas) {
        List<Integer> charStartMapping = new ArrayList<Integer>();
        List<Integer> charEndMapping = new ArrayList<Integer>();
        for (Sentence sentence : select(cas, Sentence.class)) {
            for (Token token : selectCovered(Token.class, sentence)) {
                charStartMapping.add(token.getBegin());
                charEndMapping.add(token.getEnd());
            }
        }
        charStartMappings.add(charStartMapping);
        charEndMappings.add(charEndMapping);
    }

    while ((line = br.readLine()) != null) {
        // Try to process each line, omit data if an error occurs
        try {
            JsonNode elem = mapper.readTree(line);

            // Document string contains one char to specify type (golden vs. not golden)
            // and a new number starting at 0 for each new document
            int documentNo = Integer
                    .valueOf(elem.path(JSON_FIELD_DATA).path(JSON_FIELD_DOCUMENT).getTextValue().substring(1));
            if (documentNo >= documentsJCas.size()) {
                throw new CrowdException(
                        "Error, number of documents changed from first upload! Tried to access document: "
                                + documentNo);
            }

            //Only process elements that are finalized, i.e. elements that don't have missing judgments
            String state = elem.path(JSON_FIELD_STATE).getTextValue();
            if (state.equals(JSON_FIELD_FINALIZED)) {

                JCas cas = documentsJCas.get(documentNo);

                String typeExplicit = elem.path(JSON_FIELD_RESULTS)
                        .path(NamedEntityTask2Data.FIELD_TODECIDE_RESULT).path(JSON_FIELD_AGGREGATED)
                        .getTextValue();
                String type = ne2TaskMap.get(typeExplicit);

                //Type is null when it is not in ne2TaskMap.
                //These are usually difficult cases where workers are unsure or where a wrong word has been marked in task1
                if (type == null) {
                    //We can simply skip any such cases
                    continue;
                }

                String posText = elem.path(JSON_FIELD_DATA).path(NamedEntityTask2Data.FIELD_POSTEXT)
                        .getTextValue();
                int offset = 0;

                // Element numbering in Crowdflower judgments can be different than token numbering in the Cas,
                // to support an always incrementing numbering in a multi-document setting for displayed spans (task1)
                // docOffset is the diff of the marker (saved from task1 and also present in task2 data)
                // to token numbering of the Cas for the current document

                if (!elem.path(JSON_FIELD_DATA).path(NamedEntityTask2Data.FIELD_DOCOFFSET).isMissingNode()) {
                    offset = elem.path(JSON_FIELD_DATA).path(NamedEntityTask2Data.FIELD_DOCOFFSET)
                            .getIntValue();
                }

                JsonNode marker = mapper.readTree(posText);
                int start = marker.path(JSON_FIELD_START_MARKER).getIntValue();
                int end = marker.path(JSON_FIELD_END_MARKER).getIntValue();

                //Map named entity to character offsets and add it to the Cas
                NamedEntity newEntity = new NamedEntity(cas,
                        charStartMappings.get(documentNo).get(start - offset),
                        charEndMappings.get(documentNo).get(end - offset));
                newEntity.setValue(type);
                newEntity.addToIndexes();
            }

        }
        //We catch all exceptions here, in order to guarantee best effort in processing the data.
        //That is, we try to assign to every sentence and don't stop if there is a problem and inform the user afterwards.
        catch (Exception e) {
            omittedEntities++;
            LOG.warn("Warning, omitted a sentence from task2 import because of an error in processing it: "
                    + e.getMessage());
            e.printStackTrace();
        }
    }
}

From source file:org.acmsl.queryj.api.AbstractTemplateGeneratorThread.java

/**
 * Runs the template generation process.
 * @param templateGenerator the template generator.
 * @param template the template.// w  w w  .  j av a2s. c o m
 * @param outputDir the output folder.
 * @param rootFolder the root folder.
 * @param charset the {@link Charset} to use.
 * @param threadIndex the thread index.
 * @param barrier the cyclic barrier.
 * @param log the {@link Log} instance.
 */
@ThreadSafe
protected void runGenerator(@NotNull final TG templateGenerator, @NotNull final T template,
        @NotNull final File outputDir, @NotNull final File rootFolder, @NotNull final Charset charset,
        final int threadIndex, @Nullable final CyclicBarrier barrier, @Nullable final Log log) {
    boolean generated = false;

    try {
        generated = templateGenerator.write(template, outputDir, rootFolder, charset);
    } catch (@NotNull final QueryJBuildException unknownException) {
        if (log != null) {
            log.warn(unknownException);
        }
    } catch (@NotNull final IOException ioException) {
        if (log != null) {
            log.warn(ioException);
        }
    }

    if (generated) {
        if (log != null) {
            log.debug(buildSuccessLogMessage(template, threadIndex));
        }
    }

    if (barrier != null) {
        try {
            barrier.await();
        } catch (@NotNull final InterruptedException interrupted) {
            if (log != null) {
                log.debug("Interrupted thread", interrupted);
            }

            Thread.currentThread().interrupt();
        } catch (@NotNull final BrokenBarrierException brokenBarrier) {
            if (log != null) {
                log.warn(AbstractTemplateWritingHandler.BROKEN_BARRIER_LITERAL, brokenBarrier);
            }
        }
    }
}

From source file:org.acmsl.queryj.customsql.handlers.customsqlvalidation.ReportMissingPropertiesHandler.java

/**
 * Reports any undeclared property./*from   w  ww.j a  v a  2 s .  c o  m*/
 * @param properties the declared properties.
 * @param columns the properties from the result set.
 * @param sql the query itself.
 * @param log the log.
 */
protected void diagnoseMissingProperties(@NotNull final List<Property<String>> properties,
        @NotNull final List<Property<String>> columns, @NotNull final Sql<String> sql,
        @Nullable final Log log) {
    if (log != null) {
        @NotNull
        final List<Property<String>> t_lMissingProperties = detectMissingProperties(properties, columns);

        int t_iIndex = 1;

        for (@Nullable
        final Property<String> t_MissingProperty : t_lMissingProperties) {
            if (t_MissingProperty != null) {
                log.warn("Column not declared (" + t_iIndex + ", " + t_MissingProperty.getColumnName() + ", "
                        + t_MissingProperty.getType() + "), in sql " + sql.getId());
            }

            t_iIndex++;
        }
    }
}

From source file:org.acmsl.queryj.customsql.handlers.customsqlvalidation.ReportMissingPropertiesHandlerTest.java

/**
 * Checks whether it detects missing properties.
 * Throws QueryJBuildException/*from  w w w  . j av  a 2  s .c  o m*/
 */
@Test
public void detects_missing_properties() throws QueryJBuildException {
    @NotNull
    final Log t_Log = EasyMock.createNiceMock(Log.class);

    @NotNull
    final ReportMissingPropertiesHandler instance = new ReportMissingPropertiesHandler() {
        /**
         * {@inheritDoc}
         */
        @Nullable
        @Override
        protected Log retrieveLog() {
            return t_Log;
        }
    };

    @NotNull
    final QueryJCommand t_Parameters = new ConfigurationQueryJCommandImpl(
            new SerializablePropertiesConfiguration());

    @NotNull
    final List<Property<String>> t_lProperties = new ArrayList<>(2);
    t_lProperties.add(new PropertyElement<>("name", "name", 1, String.class.getSimpleName(), false));
    t_lProperties.add(new PropertyElement<>("tmst", "tmst", 2, "Date", false));

    @NotNull
    final List<Property<String>> t_lColumns = new ArrayList<>(3);
    t_lColumns.add(new PropertyElement<>("name", "name", 1, String.class.getSimpleName(), false));
    t_lColumns.add(new PropertyElement<>("tmst", "tmst", 2, "Date", false));
    t_lColumns.add(new PropertyElement<>("flag", "flg", 3, int.class.getSimpleName(), false));

    @NotNull
    final Sql<String> t_Sql = new SqlElement<>("id", "dao", "name", "String", SqlCardinality.SINGLE, "all",
            true, false, "description");

    new QueryJCommandWrapper<List<Property<String>>>(t_Parameters)
            .setSetting(RetrieveResultPropertiesHandler.CURRENT_PROPERTIES, t_lProperties);
    new QueryJCommandWrapper<List<Property<String>>>(t_Parameters)
            .setSetting(RetrieveResultSetColumnsHandler.CURRENT_COLUMNS, t_lColumns);
    new QueryJCommandWrapper<Sql<String>>(t_Parameters).setSetting(RetrieveQueryHandler.CURRENT_SQL, t_Sql);

    t_Log.warn(EasyMock.anyObject());
    EasyMock.expectLastCall();

    EasyMock.replay(t_Log);

    Assert.assertFalse(instance.handle(t_Parameters));

    EasyMock.verify(t_Log);
}

From source file:org.acmsl.queryj.customsql.handlers.customsqlvalidation.ReportUnusedPropertiesHandler.java

/**
 * Reports any unused property./* w  w w  .  j ava 2 s .  c  o m*/
 * @param properties the declared properties.
 * @param columns the properties from the result set.
 * @param sql the query itself.
 * @param log the {@link Log}.
 */
protected void diagnoseUnusedProperties(@NotNull final List<Property<String>> properties,
        @NotNull final List<Property<String>> columns, @NotNull final Sql<String> sql,
        @Nullable final Log log) {
    if (log != null) {
        @NotNull
        final List<Property<String>> t_lExtraProperties = detectExtraProperties(properties, columns);

        int t_iIndex = 1;

        for (@Nullable
        final Property<String> t_ExtraProperty : t_lExtraProperties) {
            if (t_ExtraProperty != null) {
                log.warn("Column declared but not used (" + t_iIndex + ", " + t_ExtraProperty.getColumnName()
                        + ", " + t_ExtraProperty.getType() + "), in sql " + sql.getId());
            }

            t_iIndex++;
        }
    }
}

From source file:org.acmsl.queryj.customsql.handlers.customsqlvalidation.ReportUnusedPropertiesHandlerTest.java

/**
 * Checks whether it detects unused properties.
 * Throws QueryJBuildException//from   www  .j  a  v  a2 s.c  o  m
 */
@Test
public void detects_unused_properties() throws QueryJBuildException {
    @NotNull
    final Log t_Log = EasyMock.createNiceMock(Log.class);

    @NotNull
    final ReportUnusedPropertiesHandler instance = new ReportUnusedPropertiesHandler() {
        /**
         * {@inheritDoc}
         */
        @Nullable
        @Override
        protected Log retrieveLog() {
            return t_Log;
        }
    };

    @NotNull
    final QueryJCommand t_Parameters = new ConfigurationQueryJCommandImpl(
            new SerializablePropertiesConfiguration());

    @NotNull
    final List<Property<String>> t_lProperties = new ArrayList<>(3);
    t_lProperties.add(new PropertyElement<>("name", "name", 1, String.class.getSimpleName(), false));
    t_lProperties.add(new PropertyElement<>("tmst", "tmst", 2, "Date", false));
    t_lProperties.add(new PropertyElement<>("flag", "flg", 3, int.class.getSimpleName(), false));

    @NotNull
    final List<Property<String>> t_lColumns = new ArrayList<>(2);
    t_lColumns.add(new PropertyElement<>("name", "name", 1, String.class.getSimpleName(), false));
    t_lColumns.add(new PropertyElement<>("tmst", "tmst", 2, "Date", false));

    @NotNull
    final Sql<String> t_Sql = new SqlElement<>("id", "dao", "name", String.class.getSimpleName(),
            SqlCardinality.SINGLE, "all", true, false, "description");

    new QueryJCommandWrapper<List<Property<String>>>(t_Parameters)
            .setSetting(RetrieveResultPropertiesHandler.CURRENT_PROPERTIES, t_lProperties);
    new QueryJCommandWrapper<List<Property<String>>>(t_Parameters)
            .setSetting(RetrieveResultSetColumnsHandler.CURRENT_COLUMNS, t_lColumns);
    new QueryJCommandWrapper<Sql<String>>(t_Parameters).setSetting(RetrieveQueryHandler.CURRENT_SQL, t_Sql);

    t_Log.warn(EasyMock.anyObject());
    EasyMock.expectLastCall();

    EasyMock.replay(t_Log);

    Assert.assertFalse(instance.handle(t_Parameters));

    EasyMock.verify(t_Log);
}

From source file:org.acmsl.queryj.metadata.AbstractSqlDecorator.java

/**
 * Retrieves the parameters./*  w  ww  .  j av  a2 s .  co m*/
 * @param parameterRefs the parameter references.
 * @param sqlParameterDAO the {@link SqlParameterDAO} instance.
 * @param metadataTypeManager the metadata type manager.
 * @return such information.
 */
@NotNull
protected List<Parameter<DecoratedString, ?>> getParameters(@NotNull final List<ParameterRef> parameterRefs,
        @NotNull final SqlParameterDAO sqlParameterDAO, final MetadataTypeManager metadataTypeManager) {
    @NotNull
    final List<Parameter<DecoratedString, ?>> result = new ArrayList<>();

    for (@Nullable
    final ParameterRef t_ParameterRef : parameterRefs) {
        @Nullable
        final Parameter<String, ?> t_Parameter;

        if (t_ParameterRef != null) {
            t_Parameter = sqlParameterDAO.findByPrimaryKey(t_ParameterRef.getId());

            if (t_Parameter != null) {
                result.add(new CachingParameterDecorator<>(t_Parameter, metadataTypeManager));
            } else {
                try {
                    final Log t_Log = UniqueLogFactory.getLog(SqlDecorator.class);

                    if (t_Log != null) {
                        t_Log.warn("Referenced parameter not found:" + t_ParameterRef.getId());
                    }
                } catch (@NotNull final Throwable throwable) {
                    // class-loading problem.
                }
            }
        }
    }

    return result;
}

From source file:org.acmsl.queryj.metadata.AbstractSqlDecorator.java

/**
 * Retrieves the result class./*from  w ww  . j av  a  2  s  . c o  m*/
 * @param dao the DAO name.
 * @param repository the repository.
 * @param cardinality the cardinality.
 * @param resultRef the result ref.
 * @param resultDAO the {@link SqlResultDAO} instance.
 * @return such information.
 */
@NotNull
protected String getResultClass(@Nullable final DecoratedString dao, @Nullable final DecoratedString repository,
        @NotNull final SqlCardinality cardinality, @Nullable final ResultRef resultRef,
        @NotNull final SqlResultDAO resultDAO) {
    @NotNull
    final StringBuilder result = new StringBuilder();

    final boolean multiple = cardinality.equals(SqlCardinality.MULTIPLE);

    if (multiple) {
        result.append(MULTIPLE_RESULT_CLASS);
    }

    if (resultRef == null) {
        if (multiple) {
            result.append('<');
        }
        if (dao != null) {
            result.append(dao.getVoName());
        } else if (repository != null) {
            result.append(repository.getVoName());
        }
        if (multiple) {
            result.append('>');
        }
    } else {
        @Nullable
        final Result<String> t_Result = resultDAO.findByPrimaryKey(resultRef.getId());

        if (t_Result != null) {
            if (multiple) {
                result.append('<');
            }
            result.append(t_Result.getClassValue());
            if (multiple) {
                result.append('>');
            }
        } else {
            try {
                final Log t_Log = UniqueLogFactory.getLog(Literals.CUSTOM_SQL);

                if (t_Log != null) {
                    t_Log.warn(Literals.REFERENCED_RESULT_NOT_FOUND + resultRef.getId());
                }
            } catch (@NotNull final Throwable throwable) {
                // class-loading problem.
            }
        }
    }

    return result.toString();
}

From source file:org.acmsl.queryj.metadata.AbstractSqlDecorator.java

/**
 * Retrieves the result./*from  w w  w.  ja v a  2  s .  co m*/
 * @param resultRef the {@link ResultRef} instance.
 * @param sqlResultDAO the {@link SqlResultDAO} instance.
 * @return such information.
 */
@Nullable
protected Result<DecoratedString> getResult(@Nullable final ResultRef resultRef,
        @NotNull final SqlResultDAO sqlResultDAO) {
    @Nullable
    Result<DecoratedString> result = null;

    if (resultRef != null) {
        @Nullable
        final Result<String> t_Result = sqlResultDAO.findByPrimaryKey(resultRef.getId());

        if (t_Result != null) {
            result = decorate(t_Result);
        } else {
            try {
                final Log t_Log = UniqueLogFactory.getLog(Literals.CUSTOM_SQL);

                if (t_Log != null) {
                    t_Log.warn(Literals.REFERENCED_RESULT_NOT_FOUND + resultRef.getId());
                }
            } catch (@NotNull final Throwable throwable) {
                // class-loading problem.
            }
        }
    }

    return result;
}

From source file:org.adeptnet.atlassian.common.AuthenticatorInterface.java

default public Principal getUserFromUserName(final HttpServletRequest request,
        final HttpServletResponse response, final String userName, final String method) {
    final Log log = getLog();
    final Principal user = getUser(userName);
    if (user == null) {
        log.warn(String.format("User not found: %s", userName));
        return null;
    }//from ww w  .  j  av  a  2  s  . c o  m
    log.info(String.format("Logged in %s via %s", user, method));
    if (!authoriseUserAndEstablishSession(request, response, user)) {
        log.warn(String.format("User not authorised: %s", userName));
        return null;
    }
    return user;
}