<commit_before>/*
 * Copyright 2015 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package embl.ebi.variation.eva.pipeline.jobs;


import embl.ebi.variation.eva.pipeline.listeners.AggregatedJobParametersListener;
import embl.ebi.variation.eva.pipeline.listeners.JobParametersListener;
import org.opencb.biodata.models.variant.VariantSource;
import org.opencb.datastore.core.ObjectMap;
import org.opencb.opencga.storage.core.StorageManagerFactory;
import org.opencb.opencga.storage.core.variant.VariantStorageManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.*;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.job.builder.JobBuilder;
import org.springframework.batch.core.job.builder.JobFlowBuilder;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.RunIdIncrementer;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.builder.StepBuilder;
import org.springframework.batch.core.step.builder.TaskletStepBuilder;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;

import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;

@Configuration
@EnableBatchProcessing
public class VariantAggregatedConfiguration {

    private static final Logger logger = LoggerFactory.getLogger(VariantAggregatedConfiguration.class);
    public static final String jobName = "aggregatedVariantJob";

    @Autowired
    private JobBuilderFactory jobBuilderFactory;
    @Autowired
    private StepBuilderFactory stepBuilderFactory;
    @Autowired
    private AggregatedJobParametersListener listener;
    @Autowired
    JobLauncher jobLauncher;
    @Autowired
    Environment environment;

    @Bean
    public AggregatedJobParametersListener aggregatedJobParametersListener() {
        return new AggregatedJobParametersListener();
    }

    @Bean
    public Job variantJob() {<commit_msg>pipeline:aggregated: rename aggregated job<commit_after>/*
 * Copyright 2015 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package embl.ebi.variation.eva.pipeline.jobs;


import embl.ebi.variation.eva.pipeline.listeners.AggregatedJobParametersListener;
import embl.ebi.variation.eva.pipeline.listeners.JobParametersListener;
import org.opencb.biodata.models.variant.VariantSource;
import org.opencb.datastore.core.ObjectMap;
import org.opencb.opencga.storage.core.StorageManagerFactory;
import org.opencb.opencga.storage.core.variant.VariantStorageManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.*;
import org.springframework.batch.core.configuration.JobRegistry;
import org.springframework.batch.core.configuration.annotation.EnableBatchProcessing;
import org.springframework.batch.core.configuration.annotation.JobBuilderFactory;
import org.springframework.batch.core.configuration.annotation.StepBuilderFactory;
import org.springframework.batch.core.explore.JobExplorer;
import org.springframework.batch.core.job.builder.JobBuilder;
import org.springframework.batch.core.job.builder.JobFlowBuilder;
import org.springframework.batch.core.launch.JobLauncher;
import org.springframework.batch.core.launch.support.RunIdIncrementer;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.builder.StepBuilder;
import org.springframework.batch.core.step.builder.TaskletStepBuilder;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;

import java.net.URI;
import java.net.URISyntaxException;
import java.nio.file.Path;
import java.nio.file.Paths;

@Configuration
@EnableBatchProcessing
public class VariantAggregatedConfiguration {

    private static final Logger logger = LoggerFactory.getLogger(VariantAggregatedConfiguration.class);
    public static final String jobName = "aggregatedVariantJob";

    @Autowired
    private JobBuilderFactory jobBuilderFactory;
    @Autowired
    private StepBuilderFactory stepBuilderFactory;
    @Autowired
    private AggregatedJobParametersListener listener;
    @Autowired
    JobLauncher jobLauncher;
    @Autowired
    Environment environment;

    @Bean
    public AggregatedJobParametersListener aggregatedJobParametersListener() {
        return new AggregatedJobParametersListener();
    }

    @Bean
    public Job aggregatedVariantJob() {
{'fraction_non_alphanumeric': 0.08282254447600539, 'fraction_numerical': 0.002989983555090447, 'mean_word_length': 5.663346613545817, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '2376309', 'n_tokens_mistral': 1759, 'n_tokens_neox': 1753, 'n_words': 401}