Source of file PsiXmlTrait.php

<?php

/**

 * Copyright 2017 University of Liverpool

 *

 * Licensed under the Apache License, Version 2.0 (the "License");

 * you may not use this file except in compliance with the License.

 * You may obtain a copy of the License at

 *

 * http://www.apache.org/licenses/LICENSE-2.0

 *

 * Unless required by applicable law or agreed to in writing, software

 * distributed under the License is distributed on an "AS IS" BASIS,

 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

 * See the License for the specific language governing permissions and

 * limitations under the License.

 */

namespace pgb_liv\php_ms\Core;

/**

 * Trait for generic methods that are consistent across all HUPO-PSI standards (e.g.

 * CvParam)

 *

 * @author Andrew Collins

 */

trait PsiXmlTrait

{

    const CV_ACCESSION = 'accession';

    const CV_VALUE = 'value';

    const CV_NAME = 'name';

    const CV_UNITACCESSION = 'unitAccession';

    /**

     * Builds an index of seen CvParams of Accession -> Name

     *

     * @var string[]

     */

    private $cvParamIndex = array();

    /**

     *

     * {@inheritdoc}

     *

     * @see \pgb_liv\php_ms\Reader\MzIdentMlReader1Interface::getCvParamName()

     */

    public function getCvParamName($accession)

    {

        $name = $this->cvParamIndex[$accession];

        if (is_null($name)) {

            throw new \OutOfRangeException($accession . ' not seen in data source');

        }

        return $name;

    }

    /**

     * Creates an array object from a CvParam object

     *

     * @param \SimpleXMLElement $xml

     */

    protected function getCvParam($xml)

    {

        $cvParam = array();

        // Required fields

        $cvParam['cvRef'] = (string) $xml->attributes()->cvRef;

        $cvParam[self::CV_ACCESSION] = (string) $xml->attributes()->accession;

        $cvParam['name'] = (string) $xml->attributes()->name;

        if (! isset($this->cvParamIndex[$cvParam[self::CV_ACCESSION]])) {

            $this->cvParamIndex[$cvParam[self::CV_ACCESSION]] = $cvParam['name'];

        }

        // Optional fields

        if (isset($xml->attributes()->value)) {

            $cvParam[self::CV_VALUE] = (string) $xml->attributes()->value;

        }

        if (isset($xml->attributes()->unitAccession)) {

            $cvParam[self::CV_UNITACCESSION] = (string) $xml->attributes()->unitAccession;

        }

        if (isset($xml->attributes()->unitName)) {

            $cvParam['unitName'] = (string) $xml->attributes()->unitName;

        }

        if (isset($xml->attributes()->unitCvRef)) {

            $cvParam['unitCvRef'] = (string) $xml->attributes()->unitCvRef;

        }

        return $cvParam;

    }

    protected function getUserParam()

    {}

    protected function getAttributeId(\SimpleXMLElement $xml)

    {

        return (string) $xml->attributes()->id;

    }

}