{"action":"created","comment":{"url":"https://api.github.com/repos/EBIvariation/eva-pipeline/pulls/comments/91689918","pull_request_review_id":12200204,"id":91689918,"diff_hunk":"@@ -0,0 +1,115 @@\n+/*\n+ * Copyright 2014-2016 EMBL - European Bioinformatics Institute\n+ * Copyright 2015 OpenCB\n+ *\n+ * Licensed under the Apache License, Version 2.0 (the \"License\");\n+ * you may not use this file except in compliance with the License.\n+ * You may obtain a copy of the License at\n+ *\n+ *      http://www.apache.org/licenses/LICENSE-2.0\n+ *\n+ * Unless required by applicable law or agreed to in writing, software\n+ * distributed under the License is distributed on an \"AS IS\" BASIS,\n+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n+ * See the License for the specific language governing permissions and\n+ * limitations under the License.\n+ */\n+package uk.ac.ebi.eva.commons.models.converters.data;\n+\n+import com.mongodb.BasicDBObject;\n+import com.mongodb.DBObject;\n+import org.opencb.biodata.models.feature.Genotype;\n+import org.slf4j.Logger;\n+import org.slf4j.LoggerFactory;\n+import org.springframework.core.convert.converter.Converter;\n+\n+import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry;\n+import uk.ac.ebi.eva.commons.models.data.VariantStats;\n+\n+import java.util.LinkedList;\n+import java.util.List;\n+import java.util.Map;\n+\n+/**\n+ * Converts VariantStats into MongoDb objects. Implements spring's interface of converter.\n+ * <p>\n+ * This class is based on OpenCGA MongoDB converters.\n+ */\n+public class VariantStatsToDBObjectConverter implements Converter<VariantSourceEntry, List<DBObject>> {","path":"src/main/java/uk/ac/ebi/eva/commons/models/converters/data/VariantStatsToDBObjectConverter.java","position":38,"original_position":38,"commit_id":"7d7b173ac430f1e98a91bf72e3cfa7207f3af477","original_commit_id":"555712ad996f913c3cda3c64176d4055c75b5d8c","user":{"login":"cyenyxe","id":1433407,"avatar_url":"https://avatars.githubusercontent.com/u/1433407?v=3","gravatar_id":"","url":"https://api.github.com/users/cyenyxe","html_url":"https://github.com/cyenyxe","followers_url":"https://api.github.com/users/cyenyxe/followers","following_url":"https://api.github.com/users/cyenyxe/following{/other_user}","gists_url":"https://api.github.com/users/cyenyxe/gists{/gist_id}","starred_url":"https://api.github.com/users/cyenyxe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cyenyxe/subscriptions","organizations_url":"https://api.github.com/users/cyenyxe/orgs","repos_url":"https://api.github.com/users/cyenyxe/repos","events_url":"https://api.github.com/users/cyenyxe/events{/privacy}","received_events_url":"https://api.github.com/users/cyenyxe/received_events","type":"User","site_admin":false},"body":"I was thinking more on the concept than the object, but given your answer it may be more confusing than anything else.","created_at":"2016-12-09T10:14:35Z","updated_at":"2016-12-09T10:14:35Z","html_url":"https://github.com/EBIvariation/eva-pipeline/pull/49#discussion_r91689918","pull_request_url":"https://api.github.com/repos/EBIvariation/eva-pipeline/pulls/49","_links":{"self":{"href":"https://api.github.com/repos/EBIvariation/eva-pipeline/pulls/comments/91689918"},"html":{"href":"https://github.com/EBIvariation/eva-pipeline/pull/49#discussion_r91689918"},"pull_request":{"href":"https://api.github.com/repos/EBIvariation/eva-pipeline/pulls/49"}}},"pull_request":{"url":"https://api.github.com/repos/EBIvariation/eva-pipeline/pulls/49","id":96710186,"html_url":"https://github.com/EBIvariation/eva-pipeline/pull/49","diff_url":"https://github.com/EBIvariation/eva-pipeline/pull/49.diff","patch_url":"https://github.com/EBIvariation/eva-pipeline/pull/49.patch","issue_url":"https://api.github.com/repos/EBIvariation/eva-pipeline/issues/49","number":49,"state":"open","locked":false,"title":"EVA-22 Unify normalization and load","user":{"login":"jmmut","id":4750555,"avatar_url":"https://avatars.githubusercontent.com/u/4750555?v=3","gravatar_id":"","url":"https://api.github.com/users/jmmut","html_url":"https://github.com/jmmut","followers_url":"https://api.github.com/users/jmmut/followers","following_url":"https://api.github.com/users/jmmut/following{/other_user}","gists_url":"https://api.github.com/users/jmmut/gists{/gist_id}","starred_url":"https://api.github.com/users/jmmut/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmmut/subscriptions","organizations_url":"https://api.github.com/users/jmmut/orgs","repos_url":"https://api.github.com/users/jmmut/repos","events_url":"https://api.github.com/users/jmmut/events{/privacy}","received_events_url":"https://api.github.com/users/jmmut/received_events","type":"User","site_admin":false},"body":"this PR stops using opencga for the normalization and load and uses a spring `VariantLoadStep` used by the `AggregatedVcfJob` and the `GenotypedVcfJob`.\r\n\r\nAs there is quite a lot of code added, here are the main things to note:\r\n\r\n- The step of transform was removed (there's no json anymore)\r\n- VariantLoaderStep now includes the reading, using VcfReader.\r\n  - the bean that instantiates the reader takes as argument the aggregation type. this was the only way I could reuse this step from the genotyped and the aggregated jobs.\r\n- Several classes are copied almost as-is, with these changes:\r\n  - biodata beans (Variant, VariantStats, VariantSourceEntry): removed sample names. Now the variant has a list of sample data (genotypes and other fields).\r\n  - biodata VcfFactories (VariantVcfFactory, VariantAggregatedVcfFactory, VariantVcfEVSFactory, VariantVcfExacFactory): removed code that added sample names to the Variants.\r\n  - opencga converters: removed requirement for sample names inside a Variant (only for writing).\r\n- There is a new test (ApplicationTest) for those cases where all the automated tests work, but not the manual 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