-
Notifications
You must be signed in to change notification settings - Fork 53
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'TASK-5564' of https://github.com/opencb/cellbase into T…
…ASK-5564
- Loading branch information
Showing
5 changed files
with
109 additions
and
28 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
78 changes: 78 additions & 0 deletions
78
cellbase-lib/src/main/java/org/opencb/cellbase/lib/download/VariationDownloadManager.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * 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 org.opencb.cellbase.lib.download; | ||
|
|
||
| import org.opencb.cellbase.core.config.CellBaseConfiguration; | ||
| import org.opencb.cellbase.core.exception.CellBaseException; | ||
| import org.opencb.cellbase.core.utils.SpeciesUtils; | ||
|
|
||
| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.ArrayList; | ||
| import java.util.Collections; | ||
| import java.util.List; | ||
|
|
||
| import static org.opencb.cellbase.lib.EtlCommons.*; | ||
|
|
||
| public class VariationDownloadManager extends AbstractDownloadManager { | ||
|
|
||
| public VariationDownloadManager(String species, String assembly, Path targetDirectory, CellBaseConfiguration configuration) | ||
| throws IOException, CellBaseException { | ||
| super(species, assembly, targetDirectory, configuration); | ||
| } | ||
|
|
||
| @Override | ||
| public List<DownloadFile> download() throws IOException, InterruptedException, CellBaseException { | ||
| return downloadVariation(); | ||
| } | ||
|
|
||
| public List<DownloadFile> downloadVariation() throws IOException, InterruptedException, CellBaseException { | ||
| List<DownloadFile> downloadFiles = new ArrayList<>(); | ||
|
|
||
| // Check if species is supported | ||
| if (SpeciesUtils.hasData(configuration, speciesConfiguration.getScientificName(), VARIATION_DATA)) { | ||
| logger.info(DOWNLOADING_LOG_MESSAGE, getDataName(VARIATION_DATA)); | ||
|
|
||
| Path variationFolder = downloadFolder.resolve(VARIATION_DATA); | ||
| Files.createDirectories(variationFolder); | ||
|
|
||
| // We do not need to download human variation data from Ensembl. It is already included in the CellBase. | ||
| if (!speciesConfiguration.getScientificName().equals(HOMO_SAPIENS_NAME)) { | ||
| logger.info(DOWNLOADING_FROM_TO_LOG_MESSAGE, speciesShortName + ".vcf.gz"); | ||
| String fileName = variationFolder.resolve(speciesShortName + ".gtf.gz").toString(); | ||
| String url = ensemblHostUrl + "/" + ensemblRelease + "/variation/vcf/" + speciesShortName + "/" | ||
| + speciesShortName + ".vcf.gz"; | ||
| downloadFiles.add(downloadFile(url, fileName)); | ||
| logger.info(OK_LOG_MESSAGE); | ||
| saveDataSource(VARIATION_DATA, ensemblVersion, getTimeStamp(), Collections.singletonList(url), | ||
| variationFolder.resolve(getDataVersionFilename(VARIATION_DATA))); | ||
|
|
||
| fileName = variationFolder.resolve(speciesShortName + "_structural_variations.gtf.gz").toString(); | ||
| url = ensemblHostUrl + "/" + ensemblRelease + "/variation/vcf/" + speciesShortName + "/" | ||
| + speciesShortName + "_structural_variations.vcf.gz"; | ||
| downloadFiles.add(downloadFile(url, fileName)); | ||
| logger.info(OK_LOG_MESSAGE); | ||
| saveDataSource(VARIATION_DATA, ensemblVersion, getTimeStamp(), Collections.singletonList(url), | ||
| variationFolder.resolve(getDataVersionFilename(VARIATION_DATA))); | ||
| } | ||
| logger.info(DOWNLOADING_DONE_LOG_MESSAGE, getDataName(VARIATION_DATA)); | ||
| } | ||
|
|
||
| return downloadFiles; | ||
| } | ||
| } |