{"action":"created","comment":{"url":"https://api.github.com/repos/molgenis/molgenis/pulls/comments/33024399","id":33024399,"diff_hunk":"@@ -0,0 +1,143 @@\n+package org.molgenis.data.annotation.entity.impl;\n+\n+import static org.molgenis.MolgenisFieldTypes.FieldTypeEnum.DECIMAL;\n+import static org.molgenis.data.vcf.VcfRepository.ALT_META;\n+import static org.molgenis.data.vcf.VcfRepository.CHROM_META;\n+import static org.molgenis.data.vcf.VcfRepository.POS_META;\n+import static org.molgenis.data.vcf.VcfRepository.REF_META;\n+\n+import java.util.ArrayList;\n+import java.util.List;\n+\n+import org.molgenis.MolgenisFieldTypes.FieldTypeEnum;\n+import org.molgenis.data.AttributeMetaData;\n+import org.molgenis.data.DataService;\n+import org.molgenis.data.annotation.RepositoryAnnotator;\n+import org.molgenis.data.annotation.entity.AnnotatorInfo;\n+import org.molgenis.data.annotation.entity.EntityAnnotator;\n+import org.molgenis.data.annotation.entity.AnnotatorInfo.Status;\n+import org.molgenis.data.annotation.resources.Resource;\n+import org.molgenis.data.annotation.resources.Resources;\n+import org.molgenis.data.annotation.resources.impl.ResourceImpl;\n+import org.molgenis.data.annotation.resources.impl.SingleResourceConfig;\n+import org.molgenis.data.annotation.resources.impl.TabixRepositoryFactory;\n+import org.molgenis.data.support.DefaultAttributeMetaData;\n+import org.molgenis.data.support.DefaultEntityMetaData;\n+import org.molgenis.framework.server.MolgenisSettings;\n+import org.slf4j.Logger;\n+import org.slf4j.LoggerFactory;\n+import org.springframework.beans.factory.annotation.Autowired;\n+import org.springframework.context.annotation.Bean;\n+\n+public class ExacAnnotator\n+{\n+\n+\t// GMAF|AFR_MAF|AMR_MAF|ASN_MAF|EUR_MAF|AA_MAF|EA_MAF|\n+\tpublic static final String EXAC_AC = \"EXAC_ALLELE_COUNT\";\n+\tpublic static final String EXAC_AC_LABEL = \"EXACALLELECOUNT\";\n+\tpublic static final String EXAC_GMAF = \"EXAC_GMAF\";\n+\tpublic static final String EXAC_GMAF_LABEL = \"EXACGMAF\";\n+\tpublic static final String EXAC_AFR_MAF = \"EXAC_AFR_MAF\";\n+\tpublic static final String EXAC_AFR_MAF_LABEL = \"EXACAFRMAF\";\n+\tpublic static final String EXAC_AMR_MAF = \"EXAC_AMR_MAF\";\n+\tpublic static final String EXAC_AMR_MAF_LABEL = \"EXACAMRMAF\";\n+\tpublic static final String EXAC_ASN_MAF = \"EXAC_ASN_MAF\";\n+\tpublic static final String EXAC_ASN_MAF_LABEL = \"EXACASNMAF\";\n+\tpublic static final String EXAC_EUR_MAF = \"EXAC_EUR_MAF\";\n+\tpublic static final String EXAC_EUR_MAF_LABEL = \"EXACEURMAF\";\n+\tpublic static final String EXAC_AA_MAF = \"EXAC_AA_MAF\";\n+\tpublic static final String EXAC_AA_MAF_LABEL = \"EXACAAMAF\";\n+\tpublic static final String EXAC_EA_MAF = \"EXAC_EA_MAF\";\n+\tpublic static final String EXAC_EA_MAF_LABEL = \"EXACEAMAF\";\n+\n+\tpublic static final String EXAC_FILE_LOCATION_PROPERTY = \"exac_location\";\n+\tpublic static final String EXAC_TABIX_RESOURCE = \"EXACTabixResource\";\n+\tprivate static final Logger LOG = LoggerFactory.getLogger(CaddAnnotator.class);\n+\n+\t@Autowired\n+\tprivate MolgenisSettings molgenisSettings;\n+\t@Autowired\n+\tprivate DataService dataService;\n+\t@Autowired\n+\tprivate Resources resources;\n+\n+\t@Bean\n+\tpublic RepositoryAnnotator exac()\n+\t{\n+\t\tList<AttributeMetaData> attributes = new ArrayList<>();\n+\n+\t\tDefaultAttributeMetaData exac_ac = new DefaultAttributeMetaData(EXAC_AC, FieldTypeEnum.DECIMAL)\n+\t\t.setDescription(\"Allele count in genotypes derived straight from the ExAC AC field\").setLabel(EXAC_AC_LABEL);\n+\t\t\n+\t\tDefaultAttributeMetaData exac_gmaf = new DefaultAttributeMetaData(EXAC_GMAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"Global minor allele frequency derived straight from the ExAC GMAF field\").setLabel(EXAC_GMAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_aa_maf = new DefaultAttributeMetaData(EXAC_AA_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"African/African latino minor allele frequency derived straight from the ExAC AMR_MAF field\").setLabel(EXAC_AA_MAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_amr_maf = new DefaultAttributeMetaData(EXAC_AMR_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"American latino minor allele frequency derived straight from the ExAC AMR_MAF field\").setLabel(EXAC_AMR_MAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_afr_maf = new DefaultAttributeMetaData(EXAC_AFR_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"African minor allele frequency derived straight from the ExAC AFR_MAF field\").setLabel(EXAC_AFR_MAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_asn_maf = new DefaultAttributeMetaData(EXAC_ASN_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"Asia minor allele frequency derived straight from the ExAC ASN_MAF field\").setLabel(EXAC_ASN_MAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_eur_maf = new DefaultAttributeMetaData(EXAC_EUR_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"European minor allele frequency derived straight from the ExAC EUR_MAF field\").setLabel(EXAC_EUR_MAF_LABEL);\n+\n+\t\tDefaultAttributeMetaData exac_ea_maf = new DefaultAttributeMetaData(EXAC_EA_MAF, FieldTypeEnum.DECIMAL)\n+\t\t\t\t.setDescription(\"European American minor allele frequency derived straight from the ExAC AE_MAF field\").setLabel(EXAC_EA_MAF_LABEL);\n+\n+\t\tattributes.add(exac_gmaf);\n+\t\tattributes.add(exac_afr_maf);\n+\t\tattributes.add(exac_amr_maf);\n+\t\tattributes.add(exac_asn_maf);\n+\t\tattributes.add(exac_ea_maf);\n+\t\tattributes.add(exac_eur_maf);\n+\t\tattributes.add(exac_aa_maf);\n+\n+\t\tAnnotatorInfo exacInfo = AnnotatorInfo\n+\t\t\t\t.create(Status.BETA,\n+\t\t\t\t\t\tAnnotatorInfo.Type.POPULATION_REFERENCE,\n+\t\t\t\t\t\t\"exac\",\n+\t\t\t\t\t\t\" The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate\"\n+\t\t\t\t\t\t+ \" and harmonize exome sequencing data from a wide variety of large-scale sequencing projects\"\n+\t\t\t\t\t\t+ \", and to make summary data available for the wider scientific community.The data set provided\"\n+\t\t\t\t\t\t+ \" on this website spans 60,706 unrelated individuals sequenced as part of various \"\n+\t\t\t\t\t\t+ \"disease-specific and population genetic studies. \",\n+\t\t\t\t\t\tattributes);\n+\t\tEntityAnnotator entityAnnotator = new AnnotatorImpl(EXAC_TABIX_RESOURCE, exacInfo, new LocusQueryCreator(),\n+\t\t\t\tnew VariantResultFilter(), dataService, resources);\n+\n+\t\treturn new RepositoryAnnotatorImpl(entityAnnotator);\n+\t}\n+\n+\t@Bean\n+\tResource exacResource()\n+\t{\n+\t\tResource exacTabixResource = null;\n+\n+\t\tDefaultEntityMetaData repoMetaData = new DefaultEntityMetaData(EXAC_TABIX_RESOURCE);\n+\t\trepoMetaData.addAttributeMetaData(CHROM_META);\n+\t\trepoMetaData.addAttributeMetaData(POS_META);\n+\t\trepoMetaData.addAttributeMetaData(REF_META);\n+\t\trepoMetaData.addAttributeMetaData(ALT_META);\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"AC\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"GMAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"AFR_MAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"AMR_MAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"ASN_MAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"EUR_MAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"AA_MAF\", DECIMAL));\n+\t\trepoMetaData.addAttributeMetaData(new DefaultAttributeMetaData(\"EA_MAF\", DECIMAL));\n+\n+\t\trepoMetaData.addAttribute(\"id\").setIdAttribute(true).setVisible(false);\n+\n+\t\texacTabixResource = new ResourceImpl(EXAC_TABIX_RESOURCE, new SingleResourceConfig(EXAC_FILE_LOCATION_PROPERTY,\n+\t\t\t\tmolgenisSettings), new TabixRepositoryFactory(repoMetaData));\n+\n+\t\treturn exacTabixResource;\n+\t}\n+}","path":"molgenis-data-annotators/src/main/java/org/molgenis/data/annotation/entity/impl/ExacAnnotator.java","position":143,"original_position":143,"commit_id":"70d8152a76121342a27a5c7e1a2bcfc856e2e09b","original_commit_id":"70d8152a76121342a27a5c7e1a2bcfc856e2e09b","user":{"login":"fdlk","id":1523838,"avatar_url":"https://avatars.githubusercontent.com/u/1523838?v=3","gravatar_id":"","url":"https://api.github.com/users/fdlk","html_url":"https://github.com/fdlk","followers_url":"https://api.github.com/users/fdlk/followers","following_url":"https://api.github.com/users/fdlk/following{/other_user}","gists_url":"https://api.github.com/users/fdlk/gists{/gist_id}","starred_url":"https://api.github.com/users/fdlk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fdlk/subscriptions","organizations_url":"https://api.github.com/users/fdlk/orgs","repos_url":"https://api.github.com/users/fdlk/repos","events_url":"https://api.github.com/users/fdlk/events{/privacy}","received_events_url":"https://api.github.com/users/fdlk/received_events","type":"User","site_admin":false},"body":"WHOO!!","created_at":"2015-06-23T09:33:42Z","updated_at":"2015-06-23T09:33:42Z","html_url":"https://github.com/molgenis/molgenis/pull/3199#discussion_r33024399","pull_request_url":"https://api.github.com/repos/molgenis/molgenis/pulls/3199","_links":{"self":{"href":"https://api.github.com/repos/molgenis/molgenis/pulls/comments/33024399"},"html":{"href":"https://github.com/molgenis/molgenis/pull/3199#discussion_r33024399"},"pull_request":{"href":"https://api.github.com/repos/molgenis/molgenis/pulls/3199"}}},"pull_request":{"url":"https://api.github.com/repos/molgenis/molgenis/pulls/3199","id":38316816,"html_url":"https://github.com/molgenis/molgenis/pull/3199","diff_url":"https://github.com/molgenis/molgenis/pull/3199.diff","patch_url":"https://github.com/molgenis/molgenis/pull/3199.patch","issue_url":"https://api.github.com/repos/molgenis/molgenis/issues/3199","number":3199,"state":"open","locked":false,"title":"Feature/3495","user":{"login":"brammiedema","id":8615347,"avatar_url":"https://avatars.githubusercontent.com/u/8615347?v=3","gravatar_id":"","url":"https://api.github.com/users/brammiedema","html_url":"https://github.com/brammiedema","followers_url":"https://api.github.com/users/brammiedema/followers","following_url":"https://api.github.com/users/brammiedema/following{/other_user}","gists_url":"https://api.github.com/users/brammiedema/gists{/gist_id}","starred_url":"https://api.github.com/users/brammiedema/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brammiedema/subscriptions","organizations_url":"https://api.github.com/users/brammiedema/orgs","repos_url":"https://api.github.com/users/brammiedema/repos","events_url":"https://api.github.com/users/brammiedema/events{/privacy}","received_events_url":"https://api.github.com/users/brammiedema/received_events","type":"User","site_admin":false},"body":"Added 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