<commit_before>package org.ensembl.healthcheck.configuration;

import uk.co.flamingpenguin.jewel.cli.Option;

/**
 * These are configuration parameters that I found by grepping through the
 * healthchecks for System.getProperty. They are here so they can be set on on
 * the command line or property files.
 * 
 */
public interface ConfigureMiscProperties {

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.Biotypes
	//
	@Option(longName = "biotypes.file", description = "Parameter used only in the test org.ensembl.healthcheck.testcase.generic.Biotypes")
	String getBiotypesFile();

	boolean isBiotypesFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionExonCoords
	// org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionBase
	// org.ensembl.healthcheck.testcase.generic.GeneStatus
	//
	@Option(longName = "ignore.previous.checks", description = "Parameter used only in "
			+ "org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionExonCoords, "
			+ "org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionBase "
			+ "and org.ensembl.healthcheck.testcase.generic.GeneStatus")
	String getIgnorePreviousChecks();

	boolean isIgnorePreviousChecks();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.CompareSchema
	//
	@Option(longName = "schema.file", description = "Parameter used only in "
			+ "org.ensembl.healthcheck.testcase.generic.CompareSchema, "
	)
	String getSchemaFile();
	boolean isSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.funcgen.CompareFuncgenSchema
	//
	@Option(longName = "funcgen_schema.file", description = "Parameter used only in "
		+ "and org.ensembl.healthcheck.testcase.funcgen.CompareFuncgenSchema"
	)
	String getFuncgenSchemaFile();
	boolean isFuncgenSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.variation.CompareVariationSchema
	//
	@Option(longName = "variation_schema.file", description = "Parameter used only in "
		+ "org.ensembl.healthcheck.testcase.variation.CompareVariationSchema "
	)
	String getVariationSchemaFile();
	boolean isVariationSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.LogicNamesDisplayable
	//
	@Option(longName = "logicnames.file", description = "Parameter used only in "
			+ "org.ensembl.healthcheck.testcase.generic.LogicNamesDisplayable")
	String getLogicnamesFile();

	boolean isLogicnamesFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.AbstractPerlBasedTestCase
	//<commit_msg>removed LogicNamesDisplayable methods as not used any more<commit_after>package org.ensembl.healthcheck.configuration;

import uk.co.flamingpenguin.jewel.cli.Option;

/**
 * These are configuration parameters that I found by grepping through the
 * healthchecks for System.getProperty. They are here so they can be set on on
 * the command line or property files.
 * 
 */
public interface ConfigureMiscProperties {

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.Biotypes
	//
	@Option(longName = "biotypes.file", description = "Parameter used only in the test org.ensembl.healthcheck.testcase.generic.Biotypes")
	String getBiotypesFile();

	boolean isBiotypesFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionExonCoords
	// org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionBase
	// org.ensembl.healthcheck.testcase.generic.GeneStatus
	//
	@Option(longName = "ignore.previous.checks", description = "Parameter used only in "
			+ "org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionExonCoords, "
			+ "org.ensembl.healthcheck.testcase.generic.ComparePreviousVersionBase "
			+ "and org.ensembl.healthcheck.testcase.generic.GeneStatus")
	String getIgnorePreviousChecks();

	boolean isIgnorePreviousChecks();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.generic.CompareSchema
	//
	@Option(longName = "schema.file", description = "Parameter used only in "
			+ "org.ensembl.healthcheck.testcase.generic.CompareSchema, "
	)
	String getSchemaFile();
	boolean isSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.funcgen.CompareFuncgenSchema
	//
	@Option(longName = "funcgen_schema.file", description = "Parameter used only in "
		+ "and org.ensembl.healthcheck.testcase.funcgen.CompareFuncgenSchema"
	)
	String getFuncgenSchemaFile();
	boolean isFuncgenSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.variation.CompareVariationSchema
	//
	@Option(longName = "variation_schema.file", description = "Parameter used only in "
		+ "org.ensembl.healthcheck.testcase.variation.CompareVariationSchema "
	)
	String getVariationSchemaFile();
	boolean isVariationSchemaFile();

	// Used in:
	//
	// org.ensembl.healthcheck.testcase.AbstractPerlBasedTestCase
	//
{'fraction_non_alphanumeric': 0.11790393013100436, 'fraction_numerical': 0.0, 'mean_word_length': 4.54147465437788, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5013501', 'n_tokens_mistral': 1581, 'n_tokens_neox': 1521, 'n_words': 268}