uk.ac.ebi.intact.application.dataConversion.psiUpload.util.report.Message java code examples

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

public void addCheckerMessage( Message message ) {
  System.err.println( message.getText() );
  checkerMessages.add( message );
}

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

public void addPersisterMessage( Message message ) {
  System.err.println( message.getText() );
  persisterMessages.add( message );
}

  private static XrefTag createXref( final Element xrefNode, final short type ) {

    XrefTag xref = null;
    try {
      String db = xrefNode.getAttribute( "db" );
      if ( db != null ) {
        db = db.toLowerCase();
      }

      xref = new XrefTag( type,
                xrefNode.getAttribute( "id" ),
                db,
                xrefNode.getAttribute( "secondary" ),
                xrefNode.getAttribute( "version" ) );

    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( xrefNode, e.getMessage() ) );
    }

    return xref;
  }
}

public void addCheckerMessage( Message message ) {
  System.err.println( message.getText() );
  checkerMessages.add( message );
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

public void addCheckerMessage( Message message ) {
  System.err.println( message.getText() );
  checkerMessages.add( message );
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

public void addPersisterMessage( Message message ) {
  System.err.println( message.getText() );
  persisterMessages.add( message );
}

  /**
   * Take &lt;featureList&gt; in parameter.
   *
   * @param element
   */
  public static Collection process( final Element element ) {

    Collection features = new ArrayList( 2 );

    final String name = element.getNodeName();
    if ( false == "featureList".equals( name ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in a " +
                                        "featureList tag." ) );
      // TODO should we carry on here ? If the tag is not right ... the parsing can only fail !
    }

    final NodeList someFeatures = element.getElementsByTagName( "feature" );
    final int count = someFeatures.getLength();

    for ( int i = 0; i < count; i++ ) {
      final Node featureNode = someFeatures.item( i );

      final FeatureTag feature = FeatureParser.process( (Element) featureNode );

      features.add( feature );
    } // features

    return features;
  }
}

public void addPersisterMessage( Message message ) {
  System.err.println( message.getText() );
  persisterMessages.add( message );
}

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

MessageHolder.getInstance().addParserMessage( new Message( entrySet, "ERROR - We should be in entrySet tag." ) );

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

  /**
   * Process a &lt;cellType&gt; in an organism. <br> In order to map it to the IntAct data, we look for the psi-mi
   * <code>primaryRef</code>, and look-up in intact using its <code>id</code>.
   *
   * @param element &lt;cellType&gt;.
   *
   * @return a <code>CellTypeTag</code> if the XML contains a walid psi-mi descriptor.
   *
   * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.model.CellTypeTag
   */
  public static ConfidenceTag process( final Element element ) {

    if ( false == "confidence".equals( element.getNodeName() ) ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, "ERROR - We should be in confidence tag." ) );
    }

    String unit = element.getAttribute( "unit" );
    String value = element.getAttribute( "value" );

    ConfidenceTag confidenceTag = null;
    try {
      confidenceTag = new ConfidenceTag( unit, value );
    } catch ( IllegalArgumentException e ) {
      MessageHolder.getInstance().addParserMessage( new Message( element, e.getMessage() ) );
    }

    return confidenceTag;
  }
}

MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in xref tag." ) );
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );

MessageHolder.getInstance().addParserMessage( new Message( root, "ERROR - We should be in xref tag." ) );
  MessageHolder.getInstance().addParserMessage( new Message( root, e.getMessage() ) );

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