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jakenoblejakenoble
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Merge pull request #5 from stjudecloud/specimen-molecular
feat(specimenmolecular): add specimen molecular analyte type
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‎src/CDE/V1/Data/SpecimenMolecular.php

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<?php
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namespace CCDI\CDE\V1\Data;
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use ArrayAccess;
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use CCDI\CDE\Validator\ValidatorTrait;
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enum SpecimenMolecular implements ArrayAccess
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{
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use ValidatorTrait;
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case CFDNA;
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case CTDNA;
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case DNA;
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case MIRNA;
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case MESSENGER_RNA;
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case NOT_REPORTED;
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case NUCLEIC_RNA;
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case PROTEIN;
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case RNA;
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case TOTAL_RNA;
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case UNKNOWN;
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/**
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* @var int
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*/
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const CDE_ID = 15063661;
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const URL = 'https://cadsr.cancer.gov/onedata/dmdirect/NIH/NCI/CO/CDEDD?filter=CDEDD.ITEM_ID=15063661%20and%20ver_nr=1';
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const DESCRIPTION = 'The sample or material being subjected to analysis.';
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const CDE_VERSION = 1;
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private const DATA = [
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[
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'value' => self::CFDNA,
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'permissible_value' => 'cfDNA',
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'long_name' => 'Circulating cell-free DNA',
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'public_id' => 2578098,
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'concept_code' => ['C128274'],
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'description' => 'DNA found in blood plasma and other bodily fluids that is not associated with cells.',
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],
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[
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'value' => self::CTDNA,
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'permissible_value' => 'ctDNA',
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'long_name' => 'Circulating Tumor-Derived DNA',
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'public_id' => 4061103,
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'concept_code' => ['C113243'],
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'description' => 'Neoplasm-derived DNA found in blood plasma and other bodily fluids that is not associated with cells.',
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],
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[
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'value' => self::DNA,
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'permissible_value' => 'DNA',
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'long_name' => 'DNA',
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'public_id' => 2581946,
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'concept_code' => ['C449'],
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'description' => 'A long linear double-stranded polymer formed from nucleotides attached to a deoxyribose backbone and found in the nucleus of a cell; associated with the transmission of genetic information.',
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],
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[
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'value' => self::MIRNA,
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'permissible_value' => 'miRNA',
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'long_name' => 'MicroRNA',
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'public_id' => 2938123,
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'concept_code' => ['C25966'],
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'description' => 'A sequence of single-stranded RNA, that is 20-25 nucleotides in length, which is transcribed from DNA but is not translated into a protein. This nucleic acid may regulate the transcription or translation of other genes.',
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],
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[
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'value' => self::MESSENGER_RNA,
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'permissible_value' => 'mRNA',
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'long_name' => 'Messenger RNA',
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'public_id' => 2756502,
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'concept_code' => ['C813'],
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'description' => 'A class of RNA molecule containing protein-coding information in its nucleotide sequence that can be translated into the amino acid sequence of a protein.',
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],
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[
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'value' => self::NOT_REPORTED,
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'permissible_value' => 'Not Reported',
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'long_name' => 'Not Reported',
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'public_id' => 2572578,
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'concept_code' => ['C43234'],
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'description' => 'Not provided or available.',
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],
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[
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'value' => self::NUCLEIC_RNA,
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'permissible_value' => 'Nucleic RNA',
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'long_name' => 'Nucleic RNA Sample',
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'public_id' => 15063892,
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'concept_code' => ['C174108'],
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'description' => 'A biological specimen comprised of the RNA isolated from the nuclei of cells.',
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],
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[
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'value' => self::PROTEIN,
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'permissible_value' => 'Protein',
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'long_name' => 'Protein',
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'public_id' => 2581951,
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'concept_code' => ['C17021'],
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'description' => 'Any of a group of complex organic macromolecules that contain carbon, hydrogen, oxygen, nitrogen, and usually sulfur and are composed of one or more chains of amino acids. Proteins are fundamental components of all living cells and include many substances, such as enzymes, hormones, and antibodies, that are necessary for the proper functioning of an organism.',
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],
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[
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'value' => self::RNA,
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'permissible_value' => 'RNA',
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'long_name' => 'RNA Specimen',
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'public_id' => 14239169,
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'concept_code' => ['C198568'],
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'description' => 'A biospecimen created to contain an isolated or enriched RNA sample.',
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],
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[
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'value' => self::TOTAL_RNA,
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'permissible_value' => 'Total RNA',
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'long_name' => 'Total RNA',
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'public_id' => 10811966,
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'concept_code' => ['C163995'],
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'description' => 'A biological sample comprised of all of the RNA collected from an experimental subject.',
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],
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[
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'value' => self::UNKNOWN,
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'permissible_value' => 'Unknown',
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'long_name' => 'Unknown',
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'public_id' => 5682944,
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'concept_code' => ['C17998'],
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'description' => 'Not known, not observed, not recorded, or refused.',
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],
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];
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}

‎src/Transformer/V0/SpecimenMolecularTransformer.php

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<?php
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namespace CCDI\Transformer\V0;
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use CCDI\CDE\V1\Data\SpecimenMolecular;
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/**
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* @method static string|null|SpecimenMolecular transform($permissibleValue, $key = null)
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*/
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class SpecimenMolecularTransformer extends AbstractTransformer
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{
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protected static array $MAPPINGS = [
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[
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'value' => SpecimenMolecular::CFDNA,
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'regex' => '/^(cfdna)$/i',
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],
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[
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'value' => SpecimenMolecular::CTDNA,
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'regex' => '/^(ctdna)$/i',
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],
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[
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'value' => SpecimenMolecular::DNA,
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'regex' => '/^(dna)$/i',
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],
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[
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'value' => SpecimenMolecular::MIRNA,
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'regex' => '/^(mirna)$/i',
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],
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[
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'value' => SpecimenMolecular::MESSENGER_RNA,
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'regex' => '/^(mrna)$/i',
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],
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[
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'value' => SpecimenMolecular::NOT_REPORTED,
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'regex' => '/^(not reported)$/i',
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],
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[
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'value' => SpecimenMolecular::NUCLEIC_RNA,
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'regex' => '/^(nucleic rna)$/i',
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],
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[
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'value' => SpecimenMolecular::PROTEIN,
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'regex' => '/^(protein)$/i',
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],
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[
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'value' => SpecimenMolecular::RNA,
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'regex' => '/^(rna)$/i',
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],
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[
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'value' => SpecimenMolecular::TOTAL_RNA,
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'regex' => '/^(total rna)$/i',
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],
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[
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'value' => SpecimenMolecular::UNKNOWN,
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'regex' => '/^(unknown)$/i',
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],
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];
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}

‎tests/SpecimenMolecularTransformerTest.php

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<?php
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use CCDI\CDE\V1\Data\SpecimenMolecular;
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use CCDI\Transformer\V0\SpecimenMolecularTransformer;
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use PHPUnit\Framework\TestCase;
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class SpecimenMolecularTransformerTest extends TestCase
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{
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public function testCFDNAInput()
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{
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$string = 'cfDNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testCTDNAInput()
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{
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$string = 'ctDNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testDNAInput()
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{
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$string = 'DNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testMIRNAInput()
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{
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$string = 'miRNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testMRNAInput()
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{
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$string = 'mRNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testNotreportedInput()
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{
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$string = 'Not Reported';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testNuclericRNAInput()
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{
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$string = 'Nucleic RNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testProtetinInput()
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{
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$string = 'Protein';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testRNAInput()
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{
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$string = 'RNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testTotalRNAInput()
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{
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$string = 'Total RNA';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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public function testUnknownInput()
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{
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$string = 'Unknown';
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$this->assertTrue(SpecimenMolecular::validate($string));
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtolower($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform(strtoupper($string), 'permissible_value'))
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);
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$this->assertTrue(
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SpecimenMolecular::validate(SpecimenMolecularTransformer::transform($string, 'permissible_value'))
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);
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}
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}

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