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

import org.ensembl.healthcheck.GroupOfTests;
import org.ensembl.healthcheck.testcase.eg_core.CircularAwareFeatureCoords;
import org.ensembl.healthcheck.testcase.eg_core.DuplicateTopLevel;
import org.ensembl.healthcheck.testcase.eg_core.EGCompareCoreSchema;
import org.ensembl.healthcheck.testcase.eg_core.EnaSeqRegionName;
import org.ensembl.healthcheck.testcase.eg_core.PeptideTranslationAttribs;
import org.ensembl.healthcheck.testcase.eg_core.ProteinCodingGene;
import org.ensembl.healthcheck.testcase.eg_core.ProteinTranslation;
import org.ensembl.healthcheck.testcase.eg_core.SimpleFeatureAnalysisTypes;
import org.ensembl.healthcheck.testcase.generic.AssemblyExceptions;
import org.ensembl.healthcheck.testcase.generic.AssemblyMapping;
import org.ensembl.healthcheck.testcase.generic.AssemblyMultipleOverlap;
import org.ensembl.healthcheck.testcase.generic.AssemblySeqregion;
import org.ensembl.healthcheck.testcase.generic.CanonicalTranscriptCoding;
import org.ensembl.healthcheck.testcase.generic.CompareSchema;
import org.ensembl.healthcheck.testcase.generic.CoreForeignKeys;
import org.ensembl.healthcheck.testcase.generic.DuplicateAssembly;
import org.ensembl.healthcheck.testcase.generic.ExonRank;
import org.ensembl.healthcheck.testcase.generic.ExonStrandOrder;
import org.ensembl.healthcheck.testcase.generic.ExonTranscriptStartEnd;
import org.ensembl.healthcheck.testcase.generic.GeneCoordSystem;
import org.ensembl.healthcheck.testcase.generic.Karyotype;
import org.ensembl.healthcheck.testcase.generic.NullTranscripts;
import org.ensembl.healthcheck.testcase.generic.SeqRegionAttribsPresent;
import org.ensembl.healthcheck.testcase.generic.SeqRegionCoordSystem;
import org.ensembl.healthcheck.testcase.generic.SeqRegionsTopLevel;
import org.ensembl.healthcheck.testcase.generic.StableID;
import org.ensembl.healthcheck.testcase.generic.Strand;
import org.ensembl.healthcheck.testcase.generic.TranscriptsTranslate;
import org.ensembl.healthcheck.testcase.generic.TranslationStartEnd;
import org.ensembl.healthcheck.testcase.generic.TranslationStartEndExon;

/**
 * Group of tests that should be run to assess gene models for Ensembl Genomes.
 * Failures/warnings are not acceptable.
 * 
 * @author dstaines
 * 
 */
public class EGCoreGeneModelCritical extends GroupOfTests {

	public EGCoreGeneModelCritical() {
		addTest(
			AssemblyExceptions.class, 
			AssemblyMultipleOverlap.class,
			AssemblySeqregion.class, 
			CanonicalTranscriptCoding.class,
			CircularAwareFeatureCoords.class, 
			CompareSchema.class, 
			EGCompareCoreSchema.class,
			CoreForeignKeys.class,
			DuplicateAssembly.class, 
			DuplicateTopLevel.class,
			ExonRank.class, 
			ExonStrandOrder.class,
			ExonTranscriptStartEnd.class, 
			GeneCoordSystem.class,
			Karyotype.class, 
			NullTranscripts.class,
			PeptideTranslationAttribs.class, 
			ProteinCodingGene.class,<commit_msg>Removed CompareSchema, because it is redundant and creates confusing messages belonging to 'no_database'<commit_after>package org.ensembl.healthcheck.testgroup;

import org.ensembl.healthcheck.GroupOfTests;
import org.ensembl.healthcheck.testcase.eg_core.CircularAwareFeatureCoords;
import org.ensembl.healthcheck.testcase.eg_core.DuplicateTopLevel;
import org.ensembl.healthcheck.testcase.eg_core.EGCompareCoreSchema;
import org.ensembl.healthcheck.testcase.eg_core.EnaSeqRegionName;
import org.ensembl.healthcheck.testcase.eg_core.PeptideTranslationAttribs;
import org.ensembl.healthcheck.testcase.eg_core.ProteinCodingGene;
import org.ensembl.healthcheck.testcase.eg_core.ProteinTranslation;
import org.ensembl.healthcheck.testcase.eg_core.SimpleFeatureAnalysisTypes;
import org.ensembl.healthcheck.testcase.generic.AssemblyExceptions;
import org.ensembl.healthcheck.testcase.generic.AssemblyMapping;
import org.ensembl.healthcheck.testcase.generic.AssemblyMultipleOverlap;
import org.ensembl.healthcheck.testcase.generic.AssemblySeqregion;
import org.ensembl.healthcheck.testcase.generic.CanonicalTranscriptCoding;
import org.ensembl.healthcheck.testcase.generic.CompareSchema;
import org.ensembl.healthcheck.testcase.generic.CoreForeignKeys;
import org.ensembl.healthcheck.testcase.generic.DuplicateAssembly;
import org.ensembl.healthcheck.testcase.generic.ExonRank;
import org.ensembl.healthcheck.testcase.generic.ExonStrandOrder;
import org.ensembl.healthcheck.testcase.generic.ExonTranscriptStartEnd;
import org.ensembl.healthcheck.testcase.generic.GeneCoordSystem;
import org.ensembl.healthcheck.testcase.generic.Karyotype;
import org.ensembl.healthcheck.testcase.generic.NullTranscripts;
import org.ensembl.healthcheck.testcase.generic.SeqRegionAttribsPresent;
import org.ensembl.healthcheck.testcase.generic.SeqRegionCoordSystem;
import org.ensembl.healthcheck.testcase.generic.SeqRegionsTopLevel;
import org.ensembl.healthcheck.testcase.generic.StableID;
import org.ensembl.healthcheck.testcase.generic.Strand;
import org.ensembl.healthcheck.testcase.generic.TranscriptsTranslate;
import org.ensembl.healthcheck.testcase.generic.TranslationStartEnd;
import org.ensembl.healthcheck.testcase.generic.TranslationStartEndExon;

/**
 * Group of tests that should be run to assess gene models for Ensembl Genomes.
 * Failures/warnings are not acceptable.
 * 
 * @author dstaines
 * 
 */
public class EGCoreGeneModelCritical extends GroupOfTests {

	public EGCoreGeneModelCritical() {
		addTest(
			AssemblyExceptions.class, 
			AssemblyMultipleOverlap.class,
			AssemblySeqregion.class, 
			CanonicalTranscriptCoding.class,
			CircularAwareFeatureCoords.class, 
			EGCompareCoreSchema.class,
			CoreForeignKeys.class,
			DuplicateAssembly.class, 
			DuplicateTopLevel.class,
			ExonRank.class, 
			ExonStrandOrder.class,
			ExonTranscriptStartEnd.class, 
			GeneCoordSystem.class,
			Karyotype.class, 
			NullTranscripts.class,
			PeptideTranslationAttribs.class, 
			ProteinCodingGene.class,
{'fraction_non_alphanumeric': 0.08313659359190556, 'fraction_numerical': 0.0, 'mean_word_length': 6.855629139072848, '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': '938100', 'n_tokens_mistral': 1979, 'n_tokens_neox': 1871, 'n_words': 230}